Publications
Publications de l'Unité
19 publications
Manirakiza, Eric; Chaumier, Timothée; Tirichine, Leïla
Genomic sequences and annotations of two Pseudomonas species isolated from marine and terrestrial habitats Article de journal
Dans: Microbiol Resour Announc ., vol. -, iss. -, no. -, p. e0037324, 2024.
@article{nokey,
title = {Genomic sequences and annotations of two Pseudomonas species isolated from marine and terrestrial habitats},
author = {Eric Manirakiza and Timothée Chaumier and Leïla Tirichine},
editor = {ASM Journals},
doi = { https://doi.org/10.1128/mra.00373-24},
year = {2024},
date = {2024-08-27},
journal = {Microbiol Resour Announc .},
volume = {-},
number = {-},
issue = {-},
pages = {e0037324},
abstract = {Here, we present the complete genome sequences and annotations of two species of the Pseudomonas genus isolated from marine and terrestrial environments. Both genomes and their annotations are available on BacBrowse (https://BacBrowse.univ-nantes.fr). This study will contribute to a better understanding of the diversity present within the Pseudomonas genus.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Zarif, Mhammad; Rousselot, Ellyn; Jesus, Bruno; Tirichine, Leïla; Duc, Céline
H3K27me3 and EZH Are Involved in the Control of the Heat-Stress-Elicited Morphological Changes in Diatoms Article de journal
Dans: Int. J. Mol. Sci., vol. 25, iss. 15, p. 8373, 2024.
@article{nokey,
title = {H3K27me3 and EZH Are Involved in the Control of the Heat-Stress-Elicited Morphological Changes in Diatoms},
author = {Mhammad Zarif and Ellyn Rousselot and Bruno Jesus and Leïla Tirichine and Céline Duc},
editor = {MDPI},
url = {https://www.mdpi.com/1422-0067/25/15/8373},
doi = {doi.org/10.3390/ijms25158373},
year = {2024},
date = {2024-07-31},
journal = {Int. J. Mol. Sci.},
volume = {25},
issue = {15},
pages = {8373},
abstract = {Marine water temperatures are increasing due to anthropogenic climate change, constituting a major threat to marine ecosystems. Diatoms are major marine primary producers, and as such, they are subjected to marine heat waves and rising ocean temperatures. Additionally, under low tide, diatoms are regularly exposed to high temperatures. However, physiological and epigenetic responses to long-term exposure to heat stress remain largely unknown in the diatom Phaeodactylum tricornutum. In this study, we investigated changes in cell morphology, photosynthesis, and H3K27me3 abundance (an epigenetic mark consisting of the tri-methylation of lysine 27 on histone H3) after moderate and elevated heat stresses. Mutants impaired in PtEZH—the enzyme depositing H3K27me3—presented reduced growth and moderate changes in their PSII quantum capacities. We observed shape changes for the three morphotypes of P. tricornutum (fusiform, oval, and triradiate) in response to heat stress. These changes were found to be under the control of PtEZH. Additionally, both moderate and elevated heat stresses modulated the expression of genes encoding proteins involved in photosynthesis. Finally, heat stress elicited a reduction of genome-wide H3K27me3 levels in the various morphotypes. Hence, we provided direct evidence of epigenetic control of the H3K27me3 mark in the responses of Phaeodactylum tricornutum to heat stress.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Scalabrini, Mathieu; Loquet, Denis; Rochard, Camille; Marie, Mélyne Baudin; Assailly, Coralie; Brissonnet, Yoan; Daligault, Franck; Saumonneau, Amélie; Lambert, Annie; Grandjean, Cyrille; Deniaud, David; Lottin, Paul; Pascual, Sagrario; Fontaine, Laurent; Balloy, Viviane; Gouin, Sébastien G
Multivalent inhibition of the fumigatus KDNase Article de journal
Dans: Org Biomol Chem, vol. 22, no. 28, p. 5783–5789, 2024, ISSN: 1477-0539.
@article{pmid38938184,
title = {Multivalent inhibition of the fumigatus KDNase},
author = {Mathieu Scalabrini and Denis Loquet and Camille Rochard and Mélyne Baudin Marie and Coralie Assailly and Yoan Brissonnet and Franck Daligault and Amélie Saumonneau and Annie Lambert and Cyrille Grandjean and David Deniaud and Paul Lottin and Sagrario Pascual and Laurent Fontaine and Viviane Balloy and Sébastien G Gouin},
doi = {10.1039/d4ob00601a},
issn = {1477-0539},
year = {2024},
date = {2024-07-01},
urldate = {2024-07-01},
journal = {Org Biomol Chem},
volume = {22},
number = {28},
pages = {5783--5789},
abstract = { is a saprophytic fungus and opportunistic pathogen often causing fatal infections in immunocompromised patients. Recently KDNAse, an exoglycosidase hydrolyzing 3-deoxy-D-galacto-D--nonulosonic acid (KDN), a rare sugar from the sialic acid family, was identified and characterized. The principal function of KDNAse is still unclear, but a study suggests a critical role in fungal cell wall morphology and virulence. Potent KDNAse inhibitors are required to better probe the enzyme's biological role and as potential antivirulence factors. In this work, we developed a set of KDNAse inhibitors based on enzymatically stable thio-KDN motifs. C2, C9-linked heterodi-KDN were designed to fit into unusually close KDN sugar binding pockets in the protein. A polymeric compound with an average of 54 KDN motifs was also designed by click chemistry. Inhibitory assays performed on recombinant KDNAse showed a moderate and strong enzymatic inhibition for the two classes of compounds, respectively. The poly-KDN showed more than a nine hundred fold improved inhibitory activity (IC = 1.52 ± 0.37 μM, 17-fold in a KDN molar basis) compared to a monovalent KDN reference, and is to our knowledge, the best synthetic inhibitor described for a KDNase. Multivalency appears to be a relevant strategy for the design of potent KDNase inhibitors. Importantly, poly-KDN was shown to strongly decrease filamentation when co-cultured with at micromolar concentrations, opening interesting perspectives in the development of antivirulence factors.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Roman, Dávid; Meisinger, Philippe; Guillonneau, Richard; Peng, Chia-Chi; Peltner, Lukas K; Jordan, Paul M; Haensch, Veit; Götze, Sebastian; Werz, Oliver; Hertweck, Christian; Chen, Yin; Beemelmanns, Christine
Structure Revision of a Widespread Marine Sulfonolipid Class Based on Isolation and Total Synthesis Article de journal
Dans: Angew Chem Int Ed Engl, vol. 63, no. 23, p. e202401195, 2024, ISSN: 1521-3773.
@article{pmid38529534,
title = {Structure Revision of a Widespread Marine Sulfonolipid Class Based on Isolation and Total Synthesis},
author = {Dávid Roman and Philippe Meisinger and Richard Guillonneau and Chia-Chi Peng and Lukas K Peltner and Paul M Jordan and Veit Haensch and Sebastian Götze and Oliver Werz and Christian Hertweck and Yin Chen and Christine Beemelmanns},
url = { hal-04587238v1 },
doi = {10.1002/anie.202401195},
issn = {1521-3773},
year = {2024},
date = {2024-06-01},
urldate = {2024-06-01},
journal = {Angew Chem Int Ed Engl},
volume = {63},
number = {23},
pages = {e202401195},
abstract = {The cosmopolitan marine Roseobacter clade is of global biogeochemical importance. Members of this clade produce sulfur-containing amino lipids (SALs) involved in biofilm formation and marine surface colonization processes. Despite their physiological relevance and abundance, SALs have only been explored through genomic mining approaches and lipidomic studies based on mass spectrometry, which left the relative and absolute structures of SALs unresolved, hindering progress in biochemical and functional investigations. Herein, we report the structural revision of a new group of SALs, which we named cysteinolides, using a combination of analytical techniques, isolation and degradation experiments and total synthetic efforts. Contrary to the previously proposed homotaurine-based structures, cysteinolides are composed of an N,O-acylated cysteinolic acid-containing head group carrying various different (α-hydroxy)carboxylic acids. We also performed the first validated targeted-network based analysis, which allowed us to map the distribution and structural diversity of cysteinolides across bacterial lineages. Beyond offering structural insight, our research provides SAL standards and validated analytical data. This information holds significance for forthcoming investigations into bacterial sulfonolipid metabolism and biogeochemical nutrient cycling within marine environments.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Cordova, Luis A.; González-Quintanilla, David; Heymann, Dominique
Why are osteoporosis patients treated with antiresorptive therapies considered like oncology patients regarding their oral health care? Article de journal
Dans: Osteoporosis International, 2024, ISSN: 1433-2965.
@article{cordova_why_2024,
title = {Why are osteoporosis patients treated with antiresorptive therapies considered like oncology patients regarding their oral health care?},
author = {Luis A. Cordova and David González-Quintanilla and Dominique Heymann},
url = {https://doi.org/10.1007/s00198-024-07173-7},
doi = {10.1007/s00198-024-07173-7},
issn = {1433-2965},
year = {2024},
date = {2024-06-01},
urldate = {2024-06-01},
journal = {Osteoporosis International},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Rey, Verónica; Tornín, Juan; Alba-Linares, Juan Jose; Robledo, Cristina; Murillo, Dzohara; Rodríguez, Aida; Gallego, Borja; Huergo, Carmen; Viera, Cristina; Braña, Alejandro; Astudillo, Aurora; Heymann, Dominique; Szuhai, Karoly; Bovée, Judith V M G; Fernández, Agustín F; Fraga, Mario F; Alonso, Javier; Rodríguez, René
A personalized medicine approach identifies enasidenib as an efficient treatment for IDH2 mutant chondrosarcoma Article de journal
Dans: EBioMedicine, vol. 102, p. 105090, 2024, ISSN: 2352-3964.
@article{pmid38547578b,
title = {A personalized medicine approach identifies enasidenib as an efficient treatment for IDH2 mutant chondrosarcoma},
author = {Verónica Rey and Juan Tornín and Juan Jose Alba-Linares and Cristina Robledo and Dzohara Murillo and Aida Rodríguez and Borja Gallego and Carmen Huergo and Cristina Viera and Alejandro Braña and Aurora Astudillo and Dominique Heymann and Karoly Szuhai and Judith V M G Bovée and Agustín F Fernández and Mario F Fraga and Javier Alonso and René Rodríguez},
url = {inserm-04524777v1 },
doi = {10.1016/j.ebiom.2024.105090},
issn = {2352-3964},
year = {2024},
date = {2024-04-01},
urldate = {2024-04-01},
journal = {EBioMedicine},
volume = {102},
pages = {105090},
abstract = {BACKGROUND: Sarcomas represent an extensive group of malignant diseases affecting mesodermal tissues. Among sarcomas, the clinical management of chondrosarcomas remains a complex challenge, as high-grade tumours do not respond to current therapies. Mutations in the isocitrate dehydrogenase (IDH) 1 and 2 genes are among the most common mutations detected in chondrosarcomas and may represent a therapeutic opportunity. The presence of mutated IDH (mIDH) enzymes results in the accumulation of the oncometabolite 2-HG leading to molecular alterations that contribute to drive tumour growth.
METHODS: We developed a personalized medicine strategy based on the targeted NGS/Sanger sequencing of sarcoma samples (n = 6) and the use of matched patient-derived cell lines as a drug-testing platform. The anti-tumour potential of IDH mutations found in two chondrosarcoma cases was analysed in vitro, in vivo and molecularly (transcriptomic and DNA methylation analyses).
FINDINGS: We treated several chondrosarcoma models with specific mIDH1/2 inhibitors. Among these treatments, only the mIDH2 inhibitor enasidenib was able to decrease 2-HG levels and efficiently reduce the viability of mIDH2 chondrosarcoma cells. Importantly, oral administration of enasidenib in xenografted mice resulted in a complete abrogation of tumour growth. Enasidenib induced a profound remodelling of the transcriptomic landscape not associated to changes in the 5 mC methylation levels and its anti-tumour effects were associated with the repression of proliferative pathways such as those controlled by E2F factors.
INTERPRETATION: Overall, this work provides preclinical evidence for the use of enasidenib to treat mIDH2 chondrosarcomas.
FUNDING: Supported by the Spanish Research Agency/FEDER (grants PID2022-142020OB-I00; PID2019-106666RB-I00), the ISC III/FEDER (PI20CIII/00020; DTS18CIII/00005; CB16/12/00390; CB06/07/1009; CB19/07/00057); the GEIS group (GEIS-62); and the PCTI (Asturias)/FEDER (IDI/2021/000027).},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
METHODS: We developed a personalized medicine strategy based on the targeted NGS/Sanger sequencing of sarcoma samples (n = 6) and the use of matched patient-derived cell lines as a drug-testing platform. The anti-tumour potential of IDH mutations found in two chondrosarcoma cases was analysed in vitro, in vivo and molecularly (transcriptomic and DNA methylation analyses).
FINDINGS: We treated several chondrosarcoma models with specific mIDH1/2 inhibitors. Among these treatments, only the mIDH2 inhibitor enasidenib was able to decrease 2-HG levels and efficiently reduce the viability of mIDH2 chondrosarcoma cells. Importantly, oral administration of enasidenib in xenografted mice resulted in a complete abrogation of tumour growth. Enasidenib induced a profound remodelling of the transcriptomic landscape not associated to changes in the 5 mC methylation levels and its anti-tumour effects were associated with the repression of proliferative pathways such as those controlled by E2F factors.
INTERPRETATION: Overall, this work provides preclinical evidence for the use of enasidenib to treat mIDH2 chondrosarcomas.
FUNDING: Supported by the Spanish Research Agency/FEDER (grants PID2022-142020OB-I00; PID2019-106666RB-I00), the ISC III/FEDER (PI20CIII/00020; DTS18CIII/00005; CB16/12/00390; CB06/07/1009; CB19/07/00057); the GEIS group (GEIS-62); and the PCTI (Asturias)/FEDER (IDI/2021/000027).
Evin, Manon; Koumeir, Charbel; Bongrand, Arthur; Delpon, Gregory; Haddad, Ferid; Mouchard, Quentin; Potiron, Vincent; Saade, Gaëlle; Servagent, Noël; Villoing, Daphnée; Métivier, Vincent; Chiavassa, Sophie
Methodology for small animals targeted irradiations at conventional and ultra-high dose rates 65 MeV proton beam Article de journal
Dans: Phys Med, vol. 120, p. 103332, 2024, ISSN: 1724-191X.
@article{pmid38518627,
title = {Methodology for small animals targeted irradiations at conventional and ultra-high dose rates 65 MeV proton beam},
author = {Manon Evin and Charbel Koumeir and Arthur Bongrand and Gregory Delpon and Ferid Haddad and Quentin Mouchard and Vincent Potiron and Gaëlle Saade and Noël Servagent and Daphnée Villoing and Vincent Métivier and Sophie Chiavassa},
url = { hal-04556782v1 },
doi = {10.1016/j.ejmp.2024.103332},
issn = {1724-191X},
year = {2024},
date = {2024-04-01},
urldate = {2024-04-01},
journal = {Phys Med},
volume = {120},
pages = {103332},
abstract = {As part of translational research projects, mice may be irradiated on radiobiology platforms such as the one at the ARRONAX cyclotron. Generally, these platforms do not feature an integrated imaging system. Moreover, in the context of ultra-high dose-rate radiotherapy (FLASH-RT), treatment planning should consider potential changes in the beam characteristics and internal movements in the animal. A patient-like set-up and methodology has been implemented to ensure target coverage during conformal irradiations of the brain, lungs and intestines. In addition, respiratory cycle amplitudes were quantified by fluoroscopic acquisitions on a mouse, to ensure organ coverage and to assess the impact of respiration during FLASH-RT using the 4D digital phantom MOBY. Furthermore, beam incidence direction was studied from mice µCBCT and Monte Carlo simulations. Finally,in vivodosimetry with dose-rate independent radiochromic films (OC-1) and their LET dependency were investigated. The immobilization system ensures that the animal is held in a safe and suitable position. The geometrical evaluation of organ coverage, after the addition of the margins around the organs, was satisfactory. Moreover, no measured differences were found between CONV and FLASH beams enabling a single model of the beamline for all planning studies. Finally, the LET-dependency of the OC-1 film was determined and experimentally verified with phantoms, as well as the feasibility of using these filmsin vivoto validate the targeting. The methodology developed ensures accurate and reproducible preclinical irradiations in CONV and FLASH-RT without in-room image guidance in terms of positioning, dose calculation andin vivodosimetry.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Agranier, Eva; Crétin, Pauline; Joublin-Delavat, Aurélie; Veillard, Léa; Touahri, Katia; Delavat, François
Development and utilization of new O<sub>2</sub>-independent bioreporters Article de journal
Dans: Microbiology Spectrum, vol. 0, no. 0, p. e04091-23, 2024.
@article{doi:10.1128/spectrum.04091-23,
title = {Development and utilization of new O_{2}-independent bioreporters},
author = {Eva Agranier and Pauline Crétin and Aurélie Joublin-Delavat and Léa Veillard and Katia Touahri and François Delavat},
url = {https://journals.asm.org/doi/abs/10.1128/spectrum.04091-23
hal-04505221v1 },
doi = {10.1128/spectrum.04091-23},
year = {2024},
date = {2024-03-05},
urldate = {2024-03-05},
journal = {Microbiology Spectrum},
volume = {0},
number = {0},
pages = {e04091-23},
abstract = {Fluorescent proteins are used for decades, and have allowed major discoveries in biology in a wide variety of fields, and are used in environmental as well as clinical contexts. Green fluorescent protein (GFP) and all its derivatives share a common feature: they rely on the presence of dioxygen (O2) for protein maturation and fluorescence. This dependency precludes their use in anoxic environments. Here, we constructed a series of genetic circuits allowing production of KOFP-7, an O2-independant flavin-binding fluorescent protein. We demonstrated that Escherichia coli cells producing KOFP-7 are fluorescent, both at the population and single-cell levels. Importantly, we showed that, unlike cells producing GFP, cells producing KOFP-7 are fluorescent in anoxia. Finally, we demonstrated that Vibrio diazotrophicus NS1, a facultative anaerobe, is fluorescent in the absence of O2 when KOFP-7 is produced. Altogether, the development of new genetic circuits allowing O2-independent fluorescence will open new perspective to study anaerobic processes.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Jean-Philippe Combier Sabine Tourneur, Serge Plaza
microRNA-encoded peptides inhibit seed germination of the root parasitic plant Orobanche cumana Article de journal
Dans: New Phytologist, 2024.
@article{nokey,
title = {microRNA-encoded peptides inhibit seed germination of the root parasitic plant Orobanche cumana},
author = {Sabine Tourneur, Jean-Philippe Combier, Serge Plaza, Stéphane Muños, Philippe Delavault},
url = {hal-04578646v1 },
doi = { https://doi.org/10.1002/ppp3.10501},
year = {2024},
date = {2024-02-19},
urldate = {2024-02-19},
journal = {New Phytologist},
abstract = {Societal Impact Statement
The root parasitic plant Orobanche cumana (sunflower broomrape) is one of the major pests of sunflower crops. Despite intense efforts to develop effective agricultural practices and breeding programs, selective control of broomrapes is still rare and ineffective in terms of sustainability. It is thus essential to develop new specific control methods against those pests. miRNA-encoded peptides (miPEPs) are a new class of peptides regulating the expression of miRNAs and their corresponding target genes. This study demonstrates that certain miPEPs strongly inhibit the germination of broomrape seeds by regulating their miR gene, making them good candidates for use as biocontrol agents against this pathogen.
Summary
Root parasitic plants of the Orobanchaceae family are a constant and growing threat to agriculture worldwide. Among them, the parasitic weed Orobanche cumana, the sunflower broomrape, causes significant losses to sunflower production in European-Asian and North African countries. Despite the use of several conventional control methods against this pathogen, none has proved effective or durable, underlining the need to develop innovative strategies. miRNA-encoded peptides (miPEPs) are regulatory peptides stimulating the expression of their own primary transcript of miRNA, and plant watering with those molecules leads to down-regulating specifically miRNA target genes and altering plant physiology.
Through seed germination assays and qRT-PCR analysis, we investigated the impact of exogenous treatments of synthetic miPEPs on broomrape seed germination.
First, we report that the conserved miRNA repertoire of O. cumana consists of 39 members. Thirty-nine miPEPs were designed, synthetized, and assayed, 11 of which strongly inhibited O. cumana seed germination. Interestingly, miPEP319a showed the strongest inhibiting effect while miPEP319b did not. Three out of the four corresponding miR319 target genes showed upregulation after treatment with a germination stimulant, which was impaired by treatment with miPEP319a. This downregulation of expression is associated with an increase in the expression of the corresponding pri-miR319a.
We reveal thus that the use of miPEPs can increase our knowledge of key molecular mechanisms underlying a complex parasite interaction and should provide a new phytosanitary method to control broomrape parasitism with highly specific and biodegradable natural substances.
},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The root parasitic plant Orobanche cumana (sunflower broomrape) is one of the major pests of sunflower crops. Despite intense efforts to develop effective agricultural practices and breeding programs, selective control of broomrapes is still rare and ineffective in terms of sustainability. It is thus essential to develop new specific control methods against those pests. miRNA-encoded peptides (miPEPs) are a new class of peptides regulating the expression of miRNAs and their corresponding target genes. This study demonstrates that certain miPEPs strongly inhibit the germination of broomrape seeds by regulating their miR gene, making them good candidates for use as biocontrol agents against this pathogen.
Summary
Root parasitic plants of the Orobanchaceae family are a constant and growing threat to agriculture worldwide. Among them, the parasitic weed Orobanche cumana, the sunflower broomrape, causes significant losses to sunflower production in European-Asian and North African countries. Despite the use of several conventional control methods against this pathogen, none has proved effective or durable, underlining the need to develop innovative strategies. miRNA-encoded peptides (miPEPs) are regulatory peptides stimulating the expression of their own primary transcript of miRNA, and plant watering with those molecules leads to down-regulating specifically miRNA target genes and altering plant physiology.
Through seed germination assays and qRT-PCR analysis, we investigated the impact of exogenous treatments of synthetic miPEPs on broomrape seed germination.
First, we report that the conserved miRNA repertoire of O. cumana consists of 39 members. Thirty-nine miPEPs were designed, synthetized, and assayed, 11 of which strongly inhibited O. cumana seed germination. Interestingly, miPEP319a showed the strongest inhibiting effect while miPEP319b did not. Three out of the four corresponding miR319 target genes showed upregulation after treatment with a germination stimulant, which was impaired by treatment with miPEP319a. This downregulation of expression is associated with an increase in the expression of the corresponding pri-miR319a.
We reveal thus that the use of miPEPs can increase our knowledge of key molecular mechanisms underlying a complex parasite interaction and should provide a new phytosanitary method to control broomrape parasitism with highly specific and biodegradable natural substances.
Schimith, Lucia Emanueli; da Silva, Vitória Machado; da Costa-Silva, Dennis Guilherme; Monteiro, Linda Karolynne Seregni; Muccillo-Baisch, Ana Luiza; André-Miral, Corinne; Hort, Mariana Appel
Preclinical toxicological assessment of polydatin in zebrafish model Article de journal
Dans: Drug Chem Toxicol, p. 1–10, 2024, ISSN: 1525-6014.
@article{pmid38311823,
title = {Preclinical toxicological assessment of polydatin in zebrafish model},
author = {Lucia Emanueli Schimith and Vitória Machado da Silva and Dennis Guilherme da Costa-Silva and Linda Karolynne Seregni Monteiro and Ana Luiza Muccillo-Baisch and Corinne André-Miral and Mariana Appel Hort},
url = {https://hal.science/hal-04610793v1},
doi = {10.1080/01480545.2024.2311287},
issn = {1525-6014},
year = {2024},
date = {2024-02-01},
urldate = {2024-02-01},
journal = {Drug Chem Toxicol},
pages = {1--10},
abstract = {Polydatin (3,4',5-trihydroxystilbene-3-β-D-glucoside, piceid), a natural stilbenoid found in different plant sources, has gained increasing attention for its potential health benefits. However, prior to its widespread adoption in human therapeutics and consumer products, a comprehensive investigation of its toxicological effects is crucial. In this study, the toxicity of polydatin was investigated in a developmental toxicity test using zebrafish () as a valuable model for preclinical assessments. We employed the Fish Embryo Test (FET test - OECD n°236) to investigate the effects of polydatin on survival, hatchability, development, and behavior of zebrafish embryo-larval stage. Remarkably, the results demonstrated that polydatin up to 435 μM showed no toxicity. Throughout the exposure period, zebrafish embryos exposed to polydatin exhibited normal development, with no significant mortality observed. Furthermore, hatching success and heartbeat rate were unaffected, and no morphological abnormalities were identified, signifying a lack of teratogenic effects and cardiotoxicity. Locomotion activity assessment revealed normal swimming patterns and response to stimuli, indicating no neurotoxic effects. Our study provides valuable insights into the toxicological profile of polydatin, suggesting that it may offer potential therapeutic benefits under a considerable concentration range. In addition, zebrafish model proves to be an efficient system for early-stage toxicological screening, guiding further investigations into the secure utilization of polydatin for human health and wellness.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Timothée, Chaumier; Yang, Feng; Manirakiza, Eric; Ait-Mohamed, Ouardia; Wu, Yue; Chandola, Udita; Jesus, Bruno; Piganeau, Gwenael; Groisillier, Agnès; Tirichine, Leila
Genome-wide assessment of genetic diversity and transcript variations in 17 accessions of the model diatom Phaeodactylum tricornutum Article de journal
Dans: ISME Communications, vol. 4, iss. 1, p. ycad008, 2024.
@article{Timothée2024,
title = {Genome-wide assessment of genetic diversity and transcript variations in 17 accessions of the model diatom Phaeodactylum tricornutum},
author = {Chaumier Timothée and Feng Yang and Eric Manirakiza and Ouardia Ait-Mohamed and Yue Wu and Udita Chandola and Bruno Jesus and Gwenael Piganeau and Agnès Groisillier and Leila Tirichine},
url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10833087/},
doi = {10.1093/ismeco/ycad008},
year = {2024},
date = {2024-01-10},
urldate = {2024-01-10},
journal = {ISME Communications},
volume = {4},
issue = {1},
pages = {ycad008},
abstract = {Diatoms, a prominent group of phytoplankton, have a significant impact on both the oceanic food chain and carbon sequestration, thereby playing a crucial role in regulating the climate. These highly diverse organisms show a wide geographic distribution across various latitudes. In addition to their ecological significance, diatoms represent a vital source of bioactive compounds that are widely used in biotechnology applications. In the present study, we investigated the genetic and transcriptomic diversity of 17 accessions of the model diatom Phaeodactylum tricornutum including those sampled a century ago as well as more recently collected accessions. The analysis of the data reveals a higher genetic diversity and the emergence of novel clades, indicating an increasing diversity within the P. tricornutum population structure, compared to the previous study and a persistent long-term balancing selection of genes in old and newly sampled accessions. However, the study did not establish a clear link between the year of sampling and genetic diversity, thereby, rejecting the hypothesis of loss of heterozygoty in cultured strains. Transcript analysis identified novel transcript including noncoding RNA and other categories of small RNA such as PiwiRNAs. Additionally, transcripts analysis using differential expression as well as Weighted Gene Correlation Network Analysis has provided evidence that the suppression or downregulation of genes cannot be solely attributed to loss-of-function mutations. This implies that other contributing factors, such as epigenetic modifications, may play a crucial role in regulating gene expression. Our study provides novel genetic resources, which are now accessible through the platform PhaeoEpiview (https://PhaeoEpiView.univ-nantes.fr), that offer both ease of use and advanced tools to further investigate microalgae biology and ecology, consequently enriching our current understanding of these organisms.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Goux, Marine; Demonceaux, Marie; Hendrickx, Johann; Solleux, Claude; Lormeau, Emilie; Fredslund, Folmer; Tezé, David; Offmann, Bernard; André-Miral, Corinne
Sucrose phosphorylase from Alteromonas mediterranea: structural insight into the regioselective α-glucosylation of (+)-catechin Article de journal
Dans: Biochimie, 2024.
@article{Goux2023.04.11.536264,
title = {Sucrose phosphorylase from Alteromonas mediterranea: structural insight into the regioselective α-glucosylation of (+)-catechin},
author = {Marine Goux and Marie Demonceaux and Johann Hendrickx and Claude Solleux and Emilie Lormeau and Folmer Fredslund and David Tezé and Bernard Offmann and Corinne André-Miral},
url = {https://www.biorxiv.org/content/10.1101/2023.04.11.536264v2
hal-04095395v2 },
doi = {10.1016/j.biochi.2024.01.004},
year = {2024},
date = {2024-01-09},
urldate = {2024-01-09},
journal = {Biochimie},
publisher = {Cold Spring Harbor Laboratory},
abstract = {Sucrose phosphorylases, through transglycosylation reactions, are interesting enzymes that can transfer regioselectively glucose from sucrose, the donor substrate, onto acceptors like flavonoids to form glycoconjugates and hence modulate their solubility and bioactivity. Here, we report for the first time the structure of sucrose phosphorylase from the marine bacteria Alteromonas mediterranea (AmSP) and its enzymatic properties. Kinetics of sucrose hydrolysis and transglucosylation capacities on (+)-catechin were investigated. Wild-type enzyme (AmSP-WT) displayed high hydrolytic activity on sucrose and was devoid of transglucosylation activity on (+)-catechin. Two variants, AmSP-Q353F and AmSP-P140D catalysed the regiospecific transglucosylation of (+)-catechin: 89 % of a novel compound (+)-catechin-4′-O-α-d-glucopyranoside (CAT-4′) for AmSP-P140D and 92 % of (+)-catechin-3′-O-α-d-glucopyranoside (CAT-3′) for AmSP-Q353F. The compound CAT-4′ was fully characterized by NMR and mass spectrometry. An explanation for this difference in regiospecificity was provided at atomic level by molecular docking simulations: AmSP-P140D was found to preferentially bind (+)-catechin in a mode that favours glucosylation on its hydroxyl group in position 4′ while the binding mode in AmSP-Q353F favoured glucosylation on its hydroxyl group in position 3’.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Nifontova, Galina; Charlier, Cathy; Ayadi, Nizar; Fleury, Fabrice; Karaulov, Alexander; Sukhanova, Alyona; Nabiev, Igor
Photonic Crystal Surface Mode Real-Time Imaging of RAD51 DNA Repair Protein Interaction with the ssDNA Substrate Article de journal
Dans: Biosensors, vol. 14, no. 1, 2024, ISSN: 2079-6374.
@article{bios14010043,
title = {Photonic Crystal Surface Mode Real-Time Imaging of RAD51 DNA Repair Protein Interaction with the ssDNA Substrate},
author = {Galina Nifontova and Cathy Charlier and Nizar Ayadi and Fabrice Fleury and Alexander Karaulov and Alyona Sukhanova and Igor Nabiev},
url = {https://www.mdpi.com/2079-6374/14/1/43
hal-04449485v1 },
doi = {10.3390/bios14010043},
issn = {2079-6374},
year = {2024},
date = {2024-01-01},
urldate = {2024-01-01},
journal = {Biosensors},
volume = {14},
number = {1},
abstract = {Photonic crystals (PCs) are promising tools for label-free sensing in drug discovery screening, diagnostics, and analysis of ligand-receptor interactions. Imaging of PC surface modes has emerged as a novel approach to the detection of multiple binding events at the sensor surface. PC surface modification and decoration with recognition units yield an interface providing the highly sensitive detection of cancer biomarkers, antibodies, and oligonucleotides. The RAD51 protein plays a central role in DNA repair via the homologous recombination pathway. This recombinase is essential for the genome stability and its overexpression is often correlated with aggressive cancer. RAD51 is therefore a potential target in the therapeutic strategy for cancer. Here, we report the designing of a PC-based array sensor for real-time monitoring of oligonucleotide-RAD51 recruitment by means of surface mode imaging and validation of the concept of this approach. Our data demonstrate that the designed biosensor ensures the highly sensitive multiplexed analysis of association-dissociation events and detection of the biomarker of DNA damage using a microfluidic PC array. The obtained results highlight the potential of the developed technique for testing the functionality of candidate drugs, discovering new molecular targets and drug entities. This paves the way to further adaption and bioanalytical use of the biosensor for high-content screening to identify new DNA repair inhibitor drugs targeting the RAD51 nucleoprotein filament or to discover new molecular targets.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Jubelin, Camille; Muñoz-Garcia, Javier; Ollivier, Emilie; Cochonneau, Denis; Vallette, François; Heymann, Marie-Françoise; Oliver, Lisa; Heymann, Dominique
Identification of MCM4 and PRKDC as new regulators of osteosarcoma cell dormancy based on 3D cell cultures Article de journal
Dans: Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, p. 119660, 2024, ISSN: 0167-4889.
@article{JUBELIN2024119660,
title = {Identification of MCM4 and PRKDC as new regulators of osteosarcoma cell dormancy based on 3D cell cultures},
author = {Camille Jubelin and Javier Muñoz-Garcia and Emilie Ollivier and Denis Cochonneau and François Vallette and Marie-Françoise Heymann and Lisa Oliver and Dominique Heymann},
url = {https://www.sciencedirect.com/science/article/pii/S016748892400003X
inserm-04501791v1 },
doi = {https://doi.org/10.1016/j.bbamcr.2024.119660},
issn = {0167-4889},
year = {2024},
date = {2024-01-01},
urldate = {2024-01-01},
journal = {Biochimica et Biophysica Acta (BBA) - Molecular Cell Research},
pages = {119660},
abstract = {Dormancy is a potential way for tumors to develop drug resistance and escape treatment. However, the mechanisms involved in cancer dormancy remain poorly understood. This is mainly because there is no in vitro culture model making it possible to spontaneously induce dormancy. In this context, the present work proposes the use of three-dimensional (3D) spheroids developed from osteosarcoma cell lines as a relevant model for studying cancer dormancy. MNNG-HOS, SaOS-2, 143B, MG-63, U2OS and SJSA-1 cell lines were cultured in 3D using the Liquid Overlay Technique (LOT). Dormancy was studied by staining cancer cells with a lipophilic dye (DiD), and long-term DiD+ cells were considered as dormant cancer cells. The role of the extracellular matrix in inducing dormancy was investigated by embedding cells into methylcellulose or Geltrex™. Gene expression of DiD+ cells was assessed with a Nanostring™ approach and the role of the genes detected in dormancy was validated by a transient down-expression model using siRNA treatment. Proliferation was measured using fluorescence microscopy and the xCELLigence technology. We observed that MNNG-HOS, 143B and MG-G3 cell lines had a reduced proliferation rate in 3D compared to 2D. U2OS cells had an increased proliferation rate when they were cultured in Geltrex™ compared to other 3D culture methods. Using 3D cultures, a transcriptomic signature of dormancy was obtained and showed a decreased expression of 18 genes including ETV4, HELLS, ITGA6, MCM4, PRKDC, RAD21 and UBE2T. The treatment with siRNA targeting these genes showed that cancer cell proliferation was reduced when the expression of ETV4 and MCM4 were decreased, whereas proliferation was increased when the expression of RAD21 was decreased. 3D culture facilitates the maintenance of dormant cancer cells characterized by a reduced proliferation and less differential gene expression as compared to proliferative cells. Further studies of the genes involved has enabled us to envisage their role in regulating cell proliferation.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Morot, Amandine; Delavat, François; Bazire, Alexis; Paillard, Christine; Dufour, Alain; Rodrigues, Sophie
Genetic Insights into Biofilm Formation by a Pathogenic Strain of Vibrio harveyi Article de journal
Dans: Microorganisms, vol. 12, no. 1, 2024, ISSN: 2076-2607.
@article{microorganisms12010186,
title = {Genetic Insights into Biofilm Formation by a Pathogenic Strain of Vibrio harveyi},
author = {Amandine Morot and François Delavat and Alexis Bazire and Christine Paillard and Alain Dufour and Sophie Rodrigues},
url = {https://www.mdpi.com/2076-2607/12/1/186
hal-04406039v1 },
doi = {10.3390/microorganisms12010186},
issn = {2076-2607},
year = {2024},
date = {2024-01-01},
urldate = {2024-01-01},
journal = {Microorganisms},
volume = {12},
number = {1},
abstract = {The Vibrio genus includes bacteria widely distributed in aquatic habitats and the infections caused by these bacteria can affect a wide range of hosts. They are able to adhere to numerous surfaces, which can result in biofilm formation that helps maintain them in the environment. The involvement of the biofilm lifestyle in the virulence of Vibrio pathogens of aquatic organisms remains to be investigated. Vibrio harveyi ORM4 is a pathogen responsible for an outbreak in European abalone Haliotis tuberculata populations. In the present study, we used a dynamic biofilm culture technique coupled with laser scanning microscopy to characterize the biofilm formed by V. harveyi ORM4. We furthermore used RNA-seq analysis to examine the global changes in gene expression in biofilm cells compared to planktonic bacteria, and to identify biofilm- and virulence-related genes showing altered expression. A total of 1565 genes were differentially expressed, including genes associated with motility, polysaccharide synthesis, and quorum sensing. The up-regulation of 18 genes associated with the synthesis of the type III secretion system suggests that this virulence factor is induced in V. harveyi ORM4 biofilms, providing indirect evidence of a relationship between biofilm and virulence.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Renodon-Corniere, Axelle; Mikawa, Tsutomu; Kuwabara, Naoyuki; Ito, Kentaro; Levitsky, Dmitri; Iwasaki, Hiroshi; Takahashi, Masayuki
Human Rad51 Protein Requires Higher Concentrations of Calcium Ions for D-Loop Formation than for Oligonucleotide Strand Exchange Article de journal
Dans: International Journal of Molecular Sciences, vol. 25, no. 7, 2024, ISSN: 1422-0067.
@article{ijms25073633,
title = {Human Rad51 Protein Requires Higher Concentrations of Calcium Ions for D-Loop Formation than for Oligonucleotide Strand Exchange},
author = {Axelle Renodon-Corniere and Tsutomu Mikawa and Naoyuki Kuwabara and Kentaro Ito and Dmitri Levitsky and Hiroshi Iwasaki and Masayuki Takahashi},
url = {https://www.mdpi.com/1422-0067/25/7/3633},
doi = {10.3390/ijms25073633},
issn = {1422-0067},
year = {2024},
date = {2024-01-01},
urldate = {2024-01-01},
journal = {International Journal of Molecular Sciences},
volume = {25},
number = {7},
abstract = {Human Rad51 protein (HsRad51)-promoted DNA strand exchange, a crucial step in homologous recombination, is regulated by proteins and calcium ions. Both the activator protein Swi5/Sfr1 and Ca2+ ions stimulate different reaction steps and induce perpendicular DNA base alignment in the presynaptic complex. To investigate the role of base orientation in the strand exchange reaction, we examined the Ca2+ concentration dependence of strand exchange activities and structural changes in the presynaptic complex. Our results show that optimal D-loop formation (strand exchange with closed circular DNA) required Ca2+ concentrations greater than 5 mM, whereas 1 mM Ca2+ was sufficient for strand exchange between two oligonucleotides. Structural changes indicated by increased fluorescence intensity of poly(dεA) (a poly(dA) analog) reached a plateau at 1 mM Ca2+. Ca2+ > 2 mM was required for saturation of linear dichroism signal intensity at 260 nm, associated with rigid perpendicular DNA base orientation, suggesting a correlation with the stimulation of D-loop formation. Therefore, Ca2+ exerts two different effects. Thermal stability measurements suggest that HsRad51 binds two Ca2+ ions with KD values of 0.2 and 2.5 mM, implying that one step is stimulated by one Ca2+ bond and the other by two Ca2+ bonds. Our results indicate parallels between the Mg2+ activation of RecA and the Ca2+ activation of HsRad51.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Childs, Alexa; Gerrand, Craig; Brennan, Bernadette; Young, Robin; Rankin, Kenneth S.; Parry, Michael; Stevenson, Jonathan; Flanagan, Adrienne M.; Taylor, Rachel M.; Fern, Lorna; Heymann, Dominique; Vance, Filipa; Sherriff, Jenny; Singh, Saurabh; Begum, Rubina; Forsyth, Sharon L.; Reczko, Krystyna; Sparksman, Kate; Wilson, William; Strauss, Sandra J.
A Prospective Observational Cohort Study for Newly Diagnosed Osteosarcoma Patients in the UK: ICONIC Study Initial Results Article de journal
Dans: Cancers, vol. 16, no. 13, 2024, ISSN: 2072-6694.
@article{cancers16132351,
title = {A Prospective Observational Cohort Study for Newly Diagnosed Osteosarcoma Patients in the UK: ICONIC Study Initial Results},
author = {Alexa Childs and Craig Gerrand and Bernadette Brennan and Robin Young and Kenneth S. Rankin and Michael Parry and Jonathan Stevenson and Adrienne M. Flanagan and Rachel M. Taylor and Lorna Fern and Dominique Heymann and Filipa Vance and Jenny Sherriff and Saurabh Singh and Rubina Begum and Sharon L. Forsyth and Krystyna Reczko and Kate Sparksman and William Wilson and Sandra J. Strauss},
url = {https://www.mdpi.com/2072-6694/16/13/2351},
doi = {10.3390/cancers16132351},
issn = {2072-6694},
year = {2024},
date = {2024-01-01},
urldate = {2024-01-01},
journal = {Cancers},
volume = {16},
number = {13},
abstract = {There has been little change to the standard treatment for osteosarcoma (OS) over the last 25 years and there is an unmet need to identify new biomarkers and novel therapeutic approaches if outcomes are to improve. Furthermore, there is limited evidence on the impact of OS treatment on patient-reported outcomes (PROs). ICONIC (Improving Outcomes through Collaboration in Osteosarcoma; NCT04132895) is a prospective observational cohort study recruiting newly diagnosed OS patients across the United Kingdom (UK) with matched longitudinal collection of clinical, biological, and PRO data. During Stage 1, which assessed the feasibility of recruitment and data collection, 102 patients were recruited at 22 sites with representation from patient groups frequently excluded in OS studies, including patients over 50 years and those with less common primary sites. The feasibility of collecting clinical and biological samples, in addition to PRO data, has been established and there is ongoing analysis of these data as part of Stage 2. ICONIC will provide a unique, prospective cohort of newly diagnosed OS patients representative of the UK patient population, with fully annotated clinical outcomes linked to molecularly characterised biospecimens, allowing for comprehensive analyses to better understand biology and develop new biomarkers and novel therapeutic approaches.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Ghergus, Dana; Martin, Mickaël; Knapp, Anne-Marie; Delmotte, Fabien; Joublin-Delavat, Aurélie; Jung, Sophie; Schickel, Jean-Nicolas; Mendel, Isabelle; Dupuis, Arnaud; Drénou, Bernard; Ghesquières, Hervé; Salles, Gilles; Baseggio, Lucile; Herbrecht, Raoul; Korganow, Anne-Sophie; Vallat, Laurent; Soulas-Sprauel, Pauline; Meffre, Eric; Martin, Thierry
Normal B cells express ZAP70 in chronic lymphocytic leukemia: A link between autoimmunity and lymphoproliferation? Article de journal
Dans: Am J Hematol, vol. 99, no. 1, p. 48–56, 2024, ISSN: 1096-8652.
@article{pmid37853951,
title = {Normal B cells express ZAP70 in chronic lymphocytic leukemia: A link between autoimmunity and lymphoproliferation?},
author = {Dana Ghergus and Mickaël Martin and Anne-Marie Knapp and Fabien Delmotte and Aurélie Joublin-Delavat and Sophie Jung and Jean-Nicolas Schickel and Isabelle Mendel and Arnaud Dupuis and Bernard Drénou and Hervé Ghesquières and Gilles Salles and Lucile Baseggio and Raoul Herbrecht and Anne-Sophie Korganow and Laurent Vallat and Pauline Soulas-Sprauel and Eric Meffre and Thierry Martin},
url = {https://hal.science/hal-04343628v1},
doi = {10.1002/ajh.27137},
issn = {1096-8652},
year = {2024},
date = {2024-01-01},
urldate = {2024-01-01},
journal = {Am J Hematol},
volume = {99},
number = {1},
pages = {48--56},
abstract = {ZAP70 has a prognostic value in chronic lymphocytic leukemia (CLL), through altered B-cell receptor signaling, which is important in CLL pathogenesis. A good correlation between ZAP70 expression in CLL cells and the occurrence of autoimmune phenomena has been reported. Yet, the great majority of CLL-associated autoimmune cytopenia is due to polyclonal immunoglobulin (Ig) G synthesized by nonmalignant B cells, and this phenomenon is poorly understood. Here, we show, using flow cytometry, that a substantial percentage of CD5- nonmalignant B cells from CLL patients expresses ZAP70 compared with CD5- B cells from healthy subjects. This ZAP70 expression in normal B cells from CLL patients was also evidenced by the detection of ZAP70 mRNA at single-cell level with polyclonal Ig heavy- and light-chain gene transcripts. ZAP70+ normal B cells belong to various B-cell subsets and their presence in the naïve B-cell subset suggests that ZAP70 expression may occur during early B-cell development in CLL patients and potentially before malignant transformation. The presence of ZAP70+ normal B cells is associated with autoimmune cytopenia in CLL patients in our cohort of patients, and recombinant antibodies produced from these ZAP70+ nonmalignant B cells were frequently autoreactive including anti-platelet reactivity. These results provide a better understanding of the implication of ZAP70 in CLL leukemogenesis and the mechanisms of autoimmune complications of CLL.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Graton, Jérôme; Goupille, Anaïs; Ferré, Tanguy; Offmann, Bernard; André-Miral, Corinne; Questel, Jean-Yves Le
Antioxidant properties of catechin and its 3′O-α-glucoside: Insights from computational chemistry calculations Article de journal
Dans: Computational and Theoretical Chemistry, vol. 1236, p. 114608, 2024, ISSN: 2210-271X.
@article{GRATON2024114608,
title = {Antioxidant properties of catechin and its 3′O-α-glucoside: Insights from computational chemistry calculations},
author = {Jérôme Graton and Anaïs Goupille and Tanguy Ferré and Bernard Offmann and Corinne André-Miral and Jean-Yves Le Questel},
url = {https://www.sciencedirect.com/science/article/pii/S2210271X24001476
https://hal.science/hal-04610796v1},
doi = {https://doi.org/10.1016/j.comptc.2024.114608},
issn = {2210-271X},
year = {2024},
date = {2024-01-01},
urldate = {2024-01-01},
journal = {Computational and Theoretical Chemistry},
volume = {1236},
pages = {114608},
abstract = {Density functional theory (DFT) calculations were used to investigate the conformational landscape of catechin and one of its main glucoside derivative (catechin-3′ O- α −glucopyranoside), and to determine the corresponding antioxidant properties. These investigations were carried out in benzene and water using the SMD universal continuum solvation model. Both properties were found to be significantly affected. The structures are characterized in both solvents by strong intramolecular hydrogen bonds (IMHB). In an apolar environment, Hydrogen Atom Transfer (HAT) is by far favored whereas in water the Sequential Proton Loss Electron Transfer (SPLET) mechanism is strongly preferred. In benzene, the catechin fragment has the best antioxidant character (from 27 kJ/mole) whereas in polar surroundings, the glucoside derivative has a slightly better antiradical activity (from 5 kJ/mole). Our results confirm the key role of the 3′-OH and 4′-OH groups of the catechole ring in these properties.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
42 publications
Panez-Toro, Isidora; Heymann, Dominique; Gouin, François; Amiaud, Jérôme; Heymann, Marie-Françoise; Córdova, Luis A.
Roles of inflammatory cell infiltrate in periprosthetic osteolysis Article de journal
Dans: Frontiers in Immunology, vol. 14, p. 1310262, 2023, ISSN: 1664-3224.
@article{panez-toro_roles_2023,
title = {Roles of inflammatory cell infiltrate in periprosthetic osteolysis},
author = {Isidora Panez-Toro and Dominique Heymann and François Gouin and Jérôme Amiaud and Marie-Françoise Heymann and Luis A. Córdova},
url = {https://www.frontiersin.org/articles/10.3389/fimmu.2023.1310262/full
inserm-04501796v1 },
doi = {10.3389/fimmu.2023.1310262},
issn = {1664-3224},
year = {2023},
date = {2023-12-01},
urldate = {2023-12-01},
journal = {Frontiers in Immunology},
volume = {14},
pages = {1310262},
abstract = {Classically, particle-induced periprosthetic osteolysis at the implant–bone interface has explained the aseptic loosening of joint replacement. This response is preceded by triggering both the innate and acquired immune response with subsequent activation of osteoclasts, the bone-resorbing cells. Although particle-induced periprosthetic osteolysis has been considered a foreign body chronic inflammation mediated by myelomonocytic-derived cells, current reports describe wide heterogeneous inflammatory cells infiltrating the periprosthetic tissues. This review aims to discuss the role of those non-myelomonocytic cells in periprosthetic tissues exposed to wear particles by showing original data. Specifically, we discuss the role of T cells (CD3+
, CD4+, and CD8+) and B cells (CD20+) coexisting with CD68+/TRAP−multinucleated giant cells associated with both polyethylene and metallic particles infiltrating retrieved periprosthetic membranes. This review contributes valuable insight to support the complex cell and molecular mechanisms behind the aseptic loosening theories of orthopedic implants.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
, CD4+, and CD8+) and B cells (CD20+) coexisting with CD68+/TRAP−multinucleated giant cells associated with both polyethylene and metallic particles infiltrating retrieved periprosthetic membranes. This review contributes valuable insight to support the complex cell and molecular mechanisms behind the aseptic loosening theories of orthopedic implants.
Evgeniia Gerasimovich Galina Nifontova, Fabrice Fleury
Photonic Crystal Surface Mode Imaging for Multiplexed Real-Time Detection of Antibodies, Oligonucleotides, and DNA Repair Proteins Article de journal
Dans: EPJ Web of Conferences, vol. 287, 2023.
@article{nokey,
title = {Photonic Crystal Surface Mode Imaging for Multiplexed Real-Time Detection of Antibodies, Oligonucleotides, and DNA Repair Proteins},
author = { Galina Nifontova, Evgeniia Gerasimovich, Fabrice Fleury, Alyona Sukhanova, Igor Nabiev },
url = {hal-04363661v1 },
doi = {https://doi.org/10.1051/epjconf/202328703007 },
year = {2023},
date = {2023-10-13},
journal = {EPJ Web of Conferences},
volume = {287},
abstract = {Abstract. Sensors based on photonic crystal (PC) surface mode imaging are promising tools for
label-free drug screening and discovery, diagnostics, and analysis of ligand–receptor interactions.
Imaging of PC surface modes has been demonstrated to allow simultaneous real-time detection of
multiple events at the sensor surface. Here, we report the engineering of a lateral-flow microfluidic
assay where PC surface mode imaging is used for multiplexed detection of biomolecular targets
(antibodies, oligonucleotides, and a DNA repair protein), as well as kinetic data on their interactions
obtained without additional labelling or signal amplification. Our data demonstrate the suitability of
the biosensing platform designed for ultrasensitive, quick, and low-cost detection and monitoring of
interactions between different biomolecules},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
label-free drug screening and discovery, diagnostics, and analysis of ligand–receptor interactions.
Imaging of PC surface modes has been demonstrated to allow simultaneous real-time detection of
multiple events at the sensor surface. Here, we report the engineering of a lateral-flow microfluidic
assay where PC surface mode imaging is used for multiplexed detection of biomolecular targets
(antibodies, oligonucleotides, and a DNA repair protein), as well as kinetic data on their interactions
obtained without additional labelling or signal amplification. Our data demonstrate the suitability of
the biosensing platform designed for ultrasensitive, quick, and low-cost detection and monitoring of
interactions between different biomolecules
Charbel Koumeir Manon Evin, Quentin Mouchard
Dosimetric environment of preclinical FLASH hadrontherapy studies at the ARRONAX cyclotron Conférence
2023.
@conference{nokey,
title = {Dosimetric environment of preclinical FLASH hadrontherapy studies at the ARRONAX cyclotron},
author = { Manon Evin , Charbel Koumeir , Quentin Mouchard , Grégory Delpon , Ferid Haddad , Vincent Potiron , Gaëlle Saade , Mathieu Chocry , Noël Servagent , Stéphane Supiot , Vincent Métivier , Sophie Chiavassa },
url = {hal-04245917v1 },
year = {2023},
date = {2023-10-10},
urldate = {2023-10-10},
keywords = {},
pubstate = {published},
tppubtype = {conference}
}
Charbel Koumeir Manon Evin, Quentin Mouchard
2023.
@conference{nokey,
title = {Dosimetric environment and first results of the studies on the physicochemical and biological mechanisms of FLASH hadrontherapy at the ARRONAX cyclotron},
author = {Manon Evin, Charbel Koumeir , Quentin Mouchard , Guillaume Blain , Craff Emeline , Grégory Delpon , Vincent Fiegel , Giovanna Rosa Fois, Youssef Ghannam , Ferid Haddad , Lydia Maigne , Vincent Potiron, Gaëlle Saade , Noël Servagent , Stéphane Supiot (3) , Sarra Terfas , Johan Vandenborre , Vincent Métivier , Sophie Chiavassa },
url = { hal-04249398v1 },
year = {2023},
date = {2023-10-04},
urldate = {2023-10-04},
keywords = {},
pubstate = {published},
tppubtype = {conference}
}
Dubois, Nolwenn; Muñoz-Garcia, Javier; Heymann, Dominique; Renodon-Cornière, Axelle
High glucose exposure drives intestinal barrier dysfunction by altering its morphological, structural and functional properties. Article de journal
Dans: Biochemical pharmacology, vol. 216, p. 115765, 2023, ISSN: 1873-2968 0006-2952, (Place: England).
@article{dubois_high_2023,
title = {High glucose exposure drives intestinal barrier dysfunction by altering its morphological, structural and functional properties.},
author = {Nolwenn Dubois and Javier Muñoz-Garcia and Dominique Heymann and Axelle Renodon-Cornière},
url = {hal-04210189v1 },
doi = {10.1016/j.bcp.2023.115765},
issn = {1873-2968 0006-2952},
year = {2023},
date = {2023-10-01},
urldate = {2023-10-01},
journal = {Biochemical pharmacology},
volume = {216},
pages = {115765},
abstract = {High dietary glucose consumption and hyperglycemia can result in chronic complications. Several studies suggest that high glucose (HG) induces dysfunction of the intestinal barrier. However, the precise changes remain unclear. In our study, we used in vitro models composed of Caco-2 and/or HT29-MTX cells in both monoculture and co-culture to assess the effects of long-term HG exposure on the morphological, structural, and functional properties of the intestinal barrier. Cells were grown in medium containing normal physiologic glucose (NG, 5.5 mM) or a clinically relevant HG (25 mM) concentration until 21 days. Results demonstrated that HG induced morphological changes, with the layers appearing denser and less organized than under physiological conditions, which is in accordance with the increased migration capacity of Caco-2 cells and proliferation properties of HT29-MTX cells. Although we mostly observed a small decrease in mRNA and protein expressions of three junction proteins (ZO-1, OCLN and E-cad) in both Caco-2 and HT29-MTX cells cultured in HG medium, confocal microscopy showed that HG induced a remarkable reduction in their immunofluorescence intensity, triggering disruption of their associated structural network. In addition, we highlighted that HG affected different functionalities (permeability, mucus production and alkaline phosphatase activity) of monolayers with Caco-2 and HT29-MTX cells. Interestingly, these alterations were stronger in co-culture than in monoculture, suggesting a cross-relationship between enterocytes and goblet cells. Controlling hyperglycemia remains a major therapeutical method for reducing damage to the intestinal barrier and improving therapies.},
note = {Place: England},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Ghannam, Youssef; Chiavassa, Sophie; Saade, Gaëlle; Koumeir, Charbel; Blain, Guillaume; Delpon, Grégory; Evin, Manon; Haddad, Ferid; Maigne, Lydia; Mouchard, Quentin; Servagent, Noël; Potiron, Vincent; Supiot, Stéphane
First evidence of in vivo effect of FLASH radiotherapy with helium ions in zebrafish embryos Article de journal
Dans: Radiother Oncol, vol. 187, p. 109820, 2023, ISSN: 1879-0887.
@article{pmid37516363,
title = {First evidence of in vivo effect of FLASH radiotherapy with helium ions in zebrafish embryos},
author = {Youssef Ghannam and Sophie Chiavassa and Gaëlle Saade and Charbel Koumeir and Guillaume Blain and Grégory Delpon and Manon Evin and Ferid Haddad and Lydia Maigne and Quentin Mouchard and Noël Servagent and Vincent Potiron and Stéphane Supiot},
url = {hal-04201747v1 },
doi = {10.1016/j.radonc.2023.109820},
issn = {1879-0887},
year = {2023},
date = {2023-10-01},
urldate = {2023-10-01},
journal = {Radiother Oncol},
volume = {187},
pages = {109820},
abstract = {The ability to reduce toxicity of ultra-high dose rate (UHDR) helium ion irradiation has not been reported in vivo. Here, we tested UHDR helium ion irradiation in an embryonic zebrafish model. Our results show that UHDR helium ions spare body development and reduce spine curvature, compared to conventional dose rate.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Pu, Yi; Li, Lu; Peng, Haoning; Liu, Lunxu; Heymann, Dominique; Robert, Caroline; Vallette, François; Shen, Shensi
Drug-tolerant persister cells in cancer: the cutting edges and future directions Article de journal
Dans: Nature Reviews Clinical Oncology, 2023, ISSN: 1759-4782.
@article{pu_drug-tolerant_2023,
title = {Drug-tolerant persister cells in cancer: the cutting edges and future directions},
author = {Yi Pu and Lu Li and Haoning Peng and Lunxu Liu and Dominique Heymann and Caroline Robert and François Vallette and Shensi Shen},
url = {https://doi.org/10.1038/s41571-023-00815-5
inserm-04501799v1 },
doi = {10.1038/s41571-023-00815-5},
issn = {1759-4782},
year = {2023},
date = {2023-09-01},
urldate = {2023-09-01},
journal = {Nature Reviews Clinical Oncology},
abstract = {Drug-tolerant persister (DTP) cell populations were originally discovered in antibiotic-resistant bacterial biofilms. Similar populations with comparable features have since been identified among cancer cells and have been linked with treatment resistance that lacks an underlying genomic alteration. Research over the past decade has improved our understanding of the biological roles of DTP cells in cancer, although clinical knowledge of the role of these cells in treatment resistance remains limited. Nonetheless, targeting this population is anticipated to provide new treatment opportunities. In this Perspective, we aim to provide a clear definition of the DTP phenotype, discuss the underlying characteristics of these cells, their biomarkers and vulnerabilities, and encourage further research on DTP cells that might improve our understanding and enable the development of more effective anticancer therapies.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Prasanna, Maruthi; Calvino, Rubén Varela; Lambert, Annie; Romero, Maria Arista; Pujals, Sylvia; Trottein, François; Camberlein, Emilie; Grandjean, Cyrille; Csaba, Noemi
Semisynthetic Pneumococcal Glycoconjugate Nanovaccine Article de journal
Dans: Bioconjugate Chemistry, vol. 34, no. 9, p. 1563–1575, 2023, ISSN: 1043-1802, (Publisher: American Chemical Society).
@article{prasanna_semisynthetic_2023,
title = {Semisynthetic Pneumococcal Glycoconjugate Nanovaccine},
author = {Maruthi Prasanna and Rubén Varela Calvino and Annie Lambert and Maria Arista Romero and Sylvia Pujals and François Trottein and Emilie Camberlein and Cyrille Grandjean and Noemi Csaba},
url = {https://doi.org/10.1021/acs.bioconjchem.3c00252
hal-04209406v1 },
doi = {10.1021/acs.bioconjchem.3c00252},
issn = {1043-1802},
year = {2023},
date = {2023-09-01},
urldate = {2023-09-01},
journal = {Bioconjugate Chemistry},
volume = {34},
number = {9},
pages = {1563--1575},
abstract = {Pneumococcal conjugate vaccines offer an excellent safety profile and high protection against the serotypes comprised in the vaccine. However, inclusion of protein antigens fromStreptococcus pneumoniaecombined with potent adjuvants and a suitable delivery system are expected to both extend protection to serotype strains not represented in the formulation and stimulate a broader immune response, thus more effective in young children, elderly, and immunocompromised populations. Along this line, nanoparticle (NP) delivery systems can enhance the immunogenicity of antigens by protecting them from degradation and increasing their uptake by antigen-presenting cells, as well as offering co-delivery with adjuvants. We report herein the encapsulation of a semisynthetic glycoconjugate (GC) composed of a synthetic tetrasaccharide mimicking theS. pneumoniae serotype 14 capsular polysaccharide (CP14) linked to the Pneumococcal surface protein A (PsaA) using chitosan NPs (CNPs). These GC-loaded chitosan nanoparticles (GC-CNPs) were not toxic to human monocyte-derived dendritic cells (MoDCs), showed enhanced uptake, and displayed better immunostimulatory properties in comparison to the naked GC. A comparative study was carried out in mice to evaluate the immune response elicited by the glycoconjugate-administered subcutaneously (SC), where the GC-CNPs displayed 100-fold higher IgG response as compared with the group treated with nonencapsulated GC. Overall, the study demonstrates the potential of this chitosan-based nanovaccine for efficient delivery of glycoconjugate antigens.},
note = {Publisher: American Chemical Society},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Lin, Xin; Tirichine, Leïla; Zhang, Xu
The dynamic duo: how DNA methylation and gene transcription help diatoms thrive in modern oceans Article de journal
Dans: Journal of Experimental Botany, vol. 74, iss. 14, p. 3879–3882, 2023, ISSN: 00220957.
@article{Lin2023,
title = {The dynamic duo: how DNA methylation and gene transcription help diatoms thrive in modern oceans},
author = {Xin Lin and Leïla Tirichine and Xu Zhang},
url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10400112/
hal-04284583v1 },
doi = {10.1093/jxb/erad205},
issn = {00220957},
year = {2023},
date = {2023-08-03},
urldate = {2023-08-03},
journal = {Journal of Experimental Botany},
volume = {74},
issue = {14},
pages = {3879–3882},
abstract = {DNA methylation is essential for maintaining genome stability, mediating gene expression, and aiding species in adapting to their environment. Wan et al. (2023) measured the changes in phenotypic traits of the model diatom Phaeodactylum tricornutum in response to a 2-year exposure to ocean acidification, warming, or both, and analysed the concomitant changes in DNA methylation and transcriptomic patterns. Their study revealed that DNA methylation and gene transcription work in concert to enable unicellular phytoplankton to adapt to dynamic environmental changes.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Hisanaga, Tetsuya; Romani, Facundo; Wu, Shuangyang; Kowar, Teresa; Wu, Yue; Lintermann, Ruth; Fridrich, Arie; Cho, Chung Hyun; Chaumier, Timothée; Jamge, Bhagyshree; Montgomery, Sean A; Axelsson, Elin; Akimcheva, Svetlana; Dierschke, Tom; Bowman, John L; Fujiwara, Takayuki; Hirooka, Shunsuke; Miyagishima, Shin-Ya; Dolan, Liam; Tirichine, Leila; Schubert, Daniel; Berger, Frédéric
The Polycomb repressive complex 2 deposits H3K27me3 and represses transposable elements in a broad range of eukaryotes Article de journal
Dans: Current Biology, vol. 33, iss. 20, p. 4367-4380.e9, 2023.
@article{Hisanaga2023,
title = {The Polycomb repressive complex 2 deposits H3K27me3 and represses transposable elements in a broad range of eukaryotes},
author = {Tetsuya Hisanaga and Facundo Romani and Shuangyang Wu and Teresa Kowar and Yue Wu and Ruth Lintermann and Arie Fridrich and Chung Hyun Cho and Timothée Chaumier and Bhagyshree Jamge and Sean A Montgomery and Elin Axelsson and Svetlana Akimcheva and Tom Dierschke and John L Bowman and Takayuki Fujiwara and Shunsuke Hirooka and Shin-Ya Miyagishima and Liam Dolan and Leila Tirichine and Daniel Schubert and Frédéric Berger},
url = {https://www.sciencedirect.com/science/article/pii/S0960982223011533?via%3Dihub
hal-04284522v1},
doi = {10.1016/j.cub.2023.08.073},
year = {2023},
date = {2023-08-02},
urldate = {2023-08-02},
journal = {Current Biology},
volume = {33},
issue = {20},
pages = {4367-4380.e9},
abstract = {The mobility of transposable elements (TEs) contributes to evolution of genomes. Their uncontrolled activity causes genomic instability; therefore, expression of TEs is silenced by host genomes. TEs are marked with DNA and H3K9 methylation, which are associated with silencing in flowering plants, animals, and fungi. However, in distantly related groups of eukaryotes, TEs are marked by H3K27me3 deposited by the Polycomb repressive complex 2 (PRC2), an epigenetic mark associated with gene silencing in flowering plants and animals. The direct silencing of TEs by PRC2 has so far only been shown in one species of ciliates. To test if PRC2 silences TEs in a broader range of eukaryotes, we generated mutants with reduced PRC2 activity and analyzed the role of PRC2 in extant species along the lineage of Archaeplastida and in the diatom P. tricornutum. In this diatom and the red alga C. merolae, a greater proportion of TEs than genes were repressed by PRC2, whereas a greater proportion of genes than TEs were repressed by PRC2 in bryophytes. In flowering plants, TEs contained potential cis-elements recognized by transcription factors and associated with neighbor genes as transcriptional units repressed by PRC2. Thus, silencing of TEs by PRC2 is observed not only in Archaeplastida but also in diatoms and ciliates, suggesting that PRC2 deposited H3K27me3 to silence TEs in the last common ancestor of eukaryotes. We hypothesize that during the evolution of Archaeplastida, TE fragments marked with H3K27me3 were selected to shape transcriptional regulation, controlling networks of genes regulated by PRC2.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Wu, Yue; Tirichine, Leila
Chromosome-Wide Distribution and Characterization of H3K36me3 and H3K27Ac in the Marine Model Diatom Phaeodactylum tricornutum Article de journal
Dans: Plants (Basel), vol. 12, iss. 15, p. 2852, 2023.
@article{Wu2023b,
title = {Chromosome-Wide Distribution and Characterization of H3K36me3 and H3K27Ac in the Marine Model Diatom Phaeodactylum tricornutum},
author = {Yue Wu and Leila Tirichine },
url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10421102/
hal-04284555v1 },
doi = { 10.3390/plants12152852},
year = {2023},
date = {2023-08-02},
urldate = {2023-08-02},
journal = {Plants (Basel)},
volume = {12},
issue = {15},
pages = {2852},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Lailheugue, Vincent; Merlin, Isabelle; Boutet, Stéphanie; Perreau, François; Pouvreau, Jean-Bernard; Delgrange, Sabine; Ducrot, Paul-Henri; Cottyn-Boitte, Betty; Mouille, Gregory; Lauvergeat, Virginie
Vitislactone, a non-canonical strigolactone exudated by grapevine rootstocks in response to nitrogen starvation Article de journal
Dans: Phytochemistry, vol. 215, p. 113837, 2023, ISSN: 1873-3700.
@article{pmid37640279,
title = {Vitislactone, a non-canonical strigolactone exudated by grapevine rootstocks in response to nitrogen starvation},
author = {Vincent Lailheugue and Isabelle Merlin and Stéphanie Boutet and François Perreau and Jean-Bernard Pouvreau and Sabine Delgrange and Paul-Henri Ducrot and Betty Cottyn-Boitte and Gregory Mouille and Virginie Lauvergeat},
url = { hal-04247159v1 },
doi = {10.1016/j.phytochem.2023.113837},
issn = {1873-3700},
year = {2023},
date = {2023-08-01},
urldate = {2023-08-01},
journal = {Phytochemistry},
volume = {215},
pages = {113837},
abstract = {Strigolactones are compounds produced by plant roots in response to nutrient deficiency, acting both as local and systemic signals to control development and nutrition. Strigolactones are exuded in the rhizosphere to positively influence interactions with beneficial microbes. LC-MS/MS analysis shows that two genetically distinct grapevine rootstocks exudate one or two non-canonical strigolactones when subjected to low nitrogen conditions. Gene expression profiles and orobanche seed germination assays confirm that the biosynthesis and exudation of non-canonical compounds is the preferred pathway. The first compound, corresponding to heliolactone or 6-epi-heliolactone, is only exuded by the rootstock showing lower shoot branching and a higher level of mycorrhization with arbuscular mycorrhizal fungi. The structure of the second compound exuded by both rootstocks was identified by NMR and LC-MS/MS analysis. It is a non-canonical strigolactone, which has never been identified in another species. This first identification of a natural compound with the potential to stimulate beneficial root-microbe interactions in grapevines opens new perspectives in viticulture.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Depienne, Sébastien; Bouzelha, Mohammed; Courtois, Emmanuelle; Pavageau, Karine; Lalys, Pierre-Alban; Marchand, Maia; Alvarez-Dorta, Dimitri; Nedellec, Steven; Marín-Fernández, Laura; Grandjean, Cyrille; Boujtita, Mohammed; Deniaud, David; Mével, Mathieu; Gouin, Sébastien G.
Click-electrochemistry for the rapid labeling of virus, bacteria and cell surfaces Article de journal
Dans: Nature Communications, vol. 14, no. 1, p. 5122, 2023, ISSN: 2041-1723.
@article{depienne_click-electrochemistry_2023,
title = {Click-electrochemistry for the rapid labeling of virus, bacteria and cell surfaces},
author = {Sébastien Depienne and Mohammed Bouzelha and Emmanuelle Courtois and Karine Pavageau and Pierre-Alban Lalys and Maia Marchand and Dimitri Alvarez-Dorta and Steven Nedellec and Laura Marín-Fernández and Cyrille Grandjean and Mohammed Boujtita and David Deniaud and Mathieu Mével and Sébastien G. Gouin},
url = {https://doi.org/10.1038/s41467-023-40534-0
https://dx.doi.org/10.26434/chemrxiv-2023-q3sd8
hal-04246348v1 },
doi = {10.1038/s41467-023-40534-0},
issn = {2041-1723},
year = {2023},
date = {2023-08-01},
urldate = {2023-08-01},
journal = {Nature Communications},
volume = {14},
number = {1},
pages = {5122},
abstract = {Methods for direct covalent ligation of microorganism surfaces remain poorly reported, and mostly based on metabolic engineering for bacteria and cells functionalization. While effective, a faster method avoiding the bio-incorporation step would be highly complementary. Here, we used N-methylluminol (NML), a fully tyrosine-selective protein anchoring group after one-electron oxidation, to label the surface of viruses, living bacteria and cells. The functionalization was performed electrochemically and in situ by applying an electric potential to aqueous buffered solutions of tagged NML containing the viruses, bacteria or cells. The broad applicability of the click-electrochemistry method was explored on recombinant adeno-associated viruses (rAAV2), Escherichia coli (Gram-) and Staphyloccocus epidermidis (Gram + ) bacterial strains, and HEK293 and HeLa eukaryotic cell lines. Surface electro-conjugation was achieved in minutes to yield functionalized rAAV2 that conserved both structural integrity and infectivity properties, and living bacteria and cell lines that were still alive and able to divide.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Antoine, Babuty; Boisseau, Pierre; Drillaud, Nicolas; Eveillard, Marion; Fouassier, Marc
MYH9-related disease: Assessment of the pathogenicity of a new mutation Article de journal
Dans: EJHaem, vol. 4, no. 3, p. 869–871, 2023, ISSN: 2688-6146.
@article{pmid37601883,
title = {MYH9-related disease: Assessment of the pathogenicity of a new mutation},
author = {Babuty Antoine and Pierre Boisseau and Nicolas Drillaud and Marion Eveillard and Marc Fouassier},
doi = {10.1002/jha2.715},
issn = {2688-6146},
year = {2023},
date = {2023-08-01},
urldate = {2023-08-01},
journal = {EJHaem},
volume = {4},
number = {3},
pages = {869--871},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Venturell, Paul; Teletchea, Stéphane; Bartolozzi P. Bales A.M., Bird A. T.; Teletchea, Fabrice
Dans: Cybium, vol. 47, iss. 3, p. 315-323, 2023, ISBN: 0399-0974.
@article{nokey,
title = {A student-based expansion of the strategies of reproduction in fish (STOREFISH) database to 288 North American freshwater and anadromous species for 14 egg and larval traits},
author = {Paul Venturell and Stéphane Teletchea and Bales A.M., Bartolozzi P., Bird A.T., Blevins T.K., Campaniello S.J., Caizergue M., Carlu L., Chancerelle G., Colletta B., Dauphin L., Doche B., Derolf P.M., De Wever T., Dewig E.M., Dixon L.M., Durand C., Eck M., Faatauira T., Fisher S.M., Fix G., Fournier S., Gauthy A., Golitin C., Guyader S., Hachet F., Harnay P., Hawkins S.G., Kaufling A., Khan M., Kesterson W.J., Klein M.K., Lejeune C., Loiseau J., Loyau R., Luginbuhl S.B., Maeso J., Marc T., Martineau L., Meurillon T., Mesnieres E., Mohra R., Mccord A.O., Mcdonald Z.N., Mckay A.B., Miller T., Minhinnett S.R., Poujoulat R., Profit V., Psurny G.Q., Raymond G., Redinger R.R., Rech G., Rider A.L., Rodriguez L., Sanders S.S., Salou G., Saucier T.E., Schwer J.D., Seymour R.D., Seznec C., Shook B.L., Soler J., Tettling L., Thornburg G.E., Tottoli T., Veber E., Verdier L., Verin R., Vigot M., Vigouroux E., Voss K.N., Weir J.L. and Fabrice Teletchea},
editor = {Société Française d'Ichtyologie},
url = {https://sfi-cybium.fr/fr/student-based-expansion-strategies-reproduction-fish-storefish-database-288-north-american},
doi = {10.26028/cybium/2023-006},
isbn = {0399-0974},
year = {2023},
date = {2023-07-01},
urldate = {2023-07-01},
journal = {Cybium},
volume = {47},
issue = {3},
pages = {315-323},
abstract = {Teleosts exhibit the highest reproductive diversity of all vertebrates, but this diversity has not been extensively analyzed, in part due to a lack of synthesis of life history information. The original STOREFISH (STrategies Of REproduction in FISH) database was published in 2007, and then released online in 2020 to facilitate data visualization and utilization (www.storefish.org). The original database contains information on 50 life history traits from ~1,200 references for 80 freshwater and anadromous species, mostly from Europe. Here, we describe the process and results of an international effort to update and extend the database for 14 egg and larval traits from North American freshwater and anadromous species, and then reassess previous bivari- ate relationships. Students in the United States and France used data from nearly 800 references to increase the STOREFISH database to 8,081 records (70% increase) for 368 species (360% increase) and 41 families (116% increase). We extracted fewer records per species than the original database because we included many species for which relatively little information was known. However, the distribution of records among trait values was similar to the original database. Updating and expanding the database improved the accuracy of the incuba- tion time-temperature relationship below 10°C, and challenged a previous assumption regarding the larval size- egg diameter relationship. Our expansion effort progressed smoothly and quickly via an educational model that emphasized supervised research and collaboration. We are extending this approach to include validators for data curation, and both pure and applied research that demonstrates the utility of the STOREFISH database to biodi- versity research, conservation, assessment, management, and aquaculture.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Muñoz-Garcia, Javier; Heymann, Dominique; Giurgea, Irina; Legendre, Marie; Amselem, Serge; Castañeda, Beatriz; Lézot, Frédéric; Vargas-Franco, Jorge William
Pharmacological options in the treatment of osteogenesis imperfecta: A comprehensive review of clinical and potential alternatives Article de journal
Dans: Biochem Pharmacol, vol. 213, p. 115584, 2023, ISSN: 1873-2968.
@article{pmid37148979,
title = {Pharmacological options in the treatment of osteogenesis imperfecta: A comprehensive review of clinical and potential alternatives},
author = {Javier Muñoz-Garcia and Dominique Heymann and Irina Giurgea and Marie Legendre and Serge Amselem and Beatriz Castañeda and Frédéric Lézot and Jorge William Vargas-Franco},
url = { inserm-04100355v1 },
doi = {10.1016/j.bcp.2023.115584},
issn = {1873-2968},
year = {2023},
date = {2023-07-01},
urldate = {2023-07-01},
journal = {Biochem Pharmacol},
volume = {213},
pages = {115584},
abstract = {Osteogenesis imperfecta (OI) is a genetically heterogeneous connective tissue disorder characterized by bone fragility and different extra-skeletal manifestations. The severity of these manifestations makes it possible to classify OI into different subtypes based on the main clinical features. This review aims to outline and describe the current pharmacological alternatives for treating OI, grounded on clinical and preclinical reports, such as antiresorptive agents, anabolic agents, growth hormone, and anti-TGFβ antibody, among other less used agents. The different options and their pharmacokinetic and pharmacodynamic properties will be reviewed and discussed, focusing on the variability of their response and the molecular mechanisms involved to attain the main clinical goals, which include decreasing fracture incidence, improving pain, and promoting growth, mobility, and functional independence.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Panez-Toro, Isidora; Muñoz-García, Javier; Vargas-Franco, Jorge W.; Renodon-Cornière, Axelle; Heymann, Marie-Françoise; Lézot, Frédéric; Heymann, Dominique
Advances in Osteosarcoma Article de journal
Dans: Current Osteoporosis Reports, 2023, ISSN: 1544-1873, 1544-2241.
@article{panez-toro_advances_2023,
title = {Advances in Osteosarcoma},
author = {Isidora Panez-Toro and Javier Muñoz-García and Jorge W. Vargas-Franco and Axelle Renodon-Cornière and Marie-Françoise Heymann and Frédéric Lézot and Dominique Heymann},
url = {https://link.springer.com/10.1007/s11914-023-00803-9
inserm-04119793v1 },
doi = {10.1007/s11914-023-00803-9},
issn = {1544-1873, 1544-2241},
year = {2023},
date = {2023-06-01},
urldate = {2023-06-01},
journal = {Current Osteoporosis Reports},
abstract = {Purpose of Review
This article gives a brief overview of the most recent developments in osteosarcoma treatment, including targeting of signaling pathways, immune checkpoint inhibitors, drug delivery strategies as single or combined approaches, and the identification of new therapeutic targets to face this highly heterogeneous disease.
Recent Findings
Osteosarcoma is one of the most common primary malignant bone tumors in children and young adults, with a high risk of bone and lung metastases and a 5-year survival rate around 70% in the absence of metastases and 30% if metastases are detected at the time of diagnosis. Despite the novel advances in neoadjuvant chemotherapy, the effective treatment for osteosarcoma has not improved in the last 4 decades. The emergence of immunotherapy has transformed the paradigm of treatment, focusing therapeutic strategies on the potential of immune checkpoint inhibitors. However, the most recent clinical trials show a slight improvement over the conventional polychemotherapy scheme.
Summary
The tumor microenvironment plays a crucial role in the pathogenesis of osteosarcoma by controlling the tumor growth, the metastatic process and the drug resistance and paved the way of new therapeutic options that must be validated by accurate pre-clinical studies and clinical trials.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
This article gives a brief overview of the most recent developments in osteosarcoma treatment, including targeting of signaling pathways, immune checkpoint inhibitors, drug delivery strategies as single or combined approaches, and the identification of new therapeutic targets to face this highly heterogeneous disease.
Recent Findings
Osteosarcoma is one of the most common primary malignant bone tumors in children and young adults, with a high risk of bone and lung metastases and a 5-year survival rate around 70% in the absence of metastases and 30% if metastases are detected at the time of diagnosis. Despite the novel advances in neoadjuvant chemotherapy, the effective treatment for osteosarcoma has not improved in the last 4 decades. The emergence of immunotherapy has transformed the paradigm of treatment, focusing therapeutic strategies on the potential of immune checkpoint inhibitors. However, the most recent clinical trials show a slight improvement over the conventional polychemotherapy scheme.
Summary
The tumor microenvironment plays a crucial role in the pathogenesis of osteosarcoma by controlling the tumor growth, the metastatic process and the drug resistance and paved the way of new therapeutic options that must be validated by accurate pre-clinical studies and clinical trials.
Loussouarn, Delphine; Oliver, Lisa; Salaud, Celine; Samarut, Edouard; Bourgade, Raphaël; Béroud, Christophe; Morenton, Emilie; Heymann, Dominique; Vallette, Francois M.
Spatial Distribution of Immune Cells in Primary and Recurrent Glioblastoma: A Small Case Study Article de journal
Dans: Cancers, vol. 15, no. 12, p. 3256, 2023, ISSN: 2072-6694.
@article{loussouarn_spatial_2023,
title = {Spatial Distribution of Immune Cells in Primary and Recurrent Glioblastoma: A Small Case Study},
author = {Delphine Loussouarn and Lisa Oliver and Celine Salaud and Edouard Samarut and Raphaël Bourgade and Christophe Béroud and Emilie Morenton and Dominique Heymann and Francois M. Vallette},
url = {https://www.mdpi.com/2072-6694/15/12/3256
hal-04254114v1 },
doi = {10.3390/cancers15123256},
issn = {2072-6694},
year = {2023},
date = {2023-06-01},
urldate = {2023-06-01},
journal = {Cancers},
volume = {15},
number = {12},
pages = {3256},
abstract = {Only a minority of patients with glioblastoma (GBM) respond to immunotherapy, and always only partially. There is a lack of knowledge on immune distribution in GBM and in its tumor microenvironment (TME). To address the question, we used paired primary and recurrent tumors from GBM patients to study the composition and the evolution of the immune landscape upon treatment. We studied the expression of a handful of immune markers (CD3, CD8, CD68, PD-L1 and PD-1) in GBM tissues in 15 paired primary and recurrent GBM. In five selected patients, we used Nanostring Digital Spatial Profiling (DSP) to obtain simultaneous assessments of multiple biomarkers both within the tumor and the microenvironment in paired primary and recurrent GBM. Our results suggest that the evolution of the immune landscape between paired primary and recurrent GBM tumors is highly heterogeneous. However, our study identifies B3-H7 and HLA-DR as potential targets in primary and recurrent GBM. Spatial profiling of immune markers from matched primary and recurrent GBM shows a nonlinear complex evolution during the progression of cancer. Nonetheless, our study demonstrated a global increase in macrophages, and revealed differential localization of some markers, such as B7-H3 and HLA-DR, between GBM and its TME.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Mauro, E; Lapaillerie, D; Tumiotto, C; Charlier, Cathy; Martins, F; Sousa, S F; Métifiot, M; Weigel, Pierre; Yamatsugu, K; Kanai, M; Munier-Lehmann, H; Richetta, C; Maisch, M; Dutrieux, J; Batisse, J; Ruff, M; Delelis, O; Lesbats, P; Parissi, V
Modulation of the functional interfaces between retroviral intasomes and the human nucleosome Article de journal
Dans: mBio, p. e0108323, 2023, ISSN: 2150-7511.
@article{pmid37382440,
title = {Modulation of the functional interfaces between retroviral intasomes and the human nucleosome},
author = {E Mauro and D Lapaillerie and C Tumiotto and Cathy Charlier and F Martins and S F Sousa and M Métifiot and Pierre Weigel and K Yamatsugu and M Kanai and H Munier-Lehmann and C Richetta and M Maisch and J Dutrieux and J Batisse and M Ruff and O Delelis and P Lesbats and V Parissi},
doi = {10.1128/mbio.01083-23},
issn = {2150-7511},
year = {2023},
date = {2023-06-01},
urldate = {2023-06-01},
journal = {mBio},
pages = {e0108323},
abstract = {Infection by retroviruses as HIV-1 requires the stable integration of their genome into the host cells. This process needs the formation of integrase (IN)-viral DNA complexes, called intasomes, and their interaction with the target DNA wrapped around nucleosomes within cell chromatin. To provide new tools to analyze this association and select drugs, we applied the AlphaLISA technology to the complex formed between the prototype foamy virus (PFV) intasome and nucleosome reconstituted on 601 Widom sequence. This system allowed us to monitor the association between both partners and select small molecules that could modulate the intasome/nucleosome association. Using this approach, drugs acting either on the DNA topology within the nucleosome or on the IN/histone tail interactions have been selected. Within these compounds, doxorubicin and histone binders calixarenes were characterized using biochemical, molecular simulations and cellular approaches. These drugs were shown to inhibit both PFV and HIV-1 integration . Treatment of HIV-1-infected PBMCs with the selected molecules induces a decrease in viral infectivity and blocks the integration process. Thus, in addition to providing new information about intasome-nucleosome interaction determinants, our work also paves the way for further unedited antiviral strategies that target the final step of intasome/chromatin anchoring. IMPORTANCE In this work, we report the first monitoring of retroviral intasome/nucleosome interaction by AlphaLISA. This is the first description of the AlphaLISA application for large nucleoprotein complexes (>200 kDa) proving that this technology is suitable for molecular characterization and bimolecular inhibitor screening assays using such large complexes. Using this system, we have identified new drugs disrupting or preventing the intasome/nucleosome complex and inhibiting HIV-1 integration both and in infected cells. This first monitoring of the retroviral/intasome complex should allow the development of multiple applications including the analyses of the influence of cellular partners, the study of additional retroviral intasomes, and the determination of specific interfaces. Our work also provides the technical bases for the screening of larger libraries of drugs targeting specifically these functional nucleoprotein complexes, or additional nucleosome-partner complexes, as well as for their characterization.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Charbel Koumeir Manon Evin, Quentin Mouchard
2023.
@conference{nokey,
title = {Environnement dosimétrique et premiers résultats des études sur les mécanismes physico-chimiques et biologiques de l'hadronthérapie FLASH au cyclotron ARRONAX},
author = { Manon Evin , Charbel Koumeir , Quentin Mouchard , Guillaume Blain , Craff Emeline , Grégory Delpon , Vincent Fiegel , Giovanna Rosa Fois, Youssef Ghannam , Ferid Haddad , Lydia Maigne, Vincent Potiron , Gaëlle Saade, Noël Servagent , Stéphane Supiot , Johan Vandenborre , Sarra Terfas , Vincent Métivier , Sophie Chiavassa},
url = { hal-04246385v1 },
year = {2023},
date = {2023-06-01},
urldate = {2023-06-01},
keywords = {},
pubstate = {published},
tppubtype = {conference}
}
Sanejouand, Yves-Henri
On the unknown proteins of eukaryotic proteomes Article de journal
Dans: Journal of Molecular Evolution, vol. 91, p. 492-501, 2023.
@article{sanejouand2023unknown,
title = {On the unknown proteins of eukaryotic proteomes},
author = {Yves-Henri Sanejouand},
url = {https://doi.org/10.1007/s00239-023-10116-1
hal-03863835},
doi = {10.1007/s00239-023-10116-1},
year = {2023},
date = {2023-05-23},
urldate = {2023-05-23},
journal = {Journal of Molecular Evolution},
volume = {91},
pages = {492-501},
abstract = {In order to study unknown proteins on a large scale, a reference system has been set up for the three major eukaryotic lineages, built with 36 proteomes as taxonomically diverse as possible. Proteins from 362 eukaryotic proteomes with no known homologue in this set were then analyzed, focusing noteworthy on singletons, that is, on unknown proteins with no known homologue in their own proteome. Consistently, according to Uniprot, for a given species, no more than 12% of the singletons thus found are known at the protein level. Also, since they rely on the information found in the alignment of homologous sequences, predictions of AlphaFold2 for their tridimensional structure are usually poor. In the case of metazoan species, the number of singletons seems to increase as a function of the evolutionary distance from the reference system. Interestingly, no such trend is found in the cases of viridiplantae and fungi, as if the timescale on which singletons are added to proteomes were different in metazoa and in other eukaryotic kingdoms. In order to confirm this phenomenon, further studies of proteomes closer to those of the reference system are however needed.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Wu, Yue; Chaumier, Timothée; Manirakiza, Eric; Veluchamy, Alaguraj; Tirichine, Leila
PhaeoEpiView: an epigenome browser of the newly assembled genome of the model diatom Phaeodactylum tricornutum Article de journal
Dans: Scientific Reports , vol. 13, p. 8320, 2023, ISSN: 2045-2322.
@article{Wu2023,
title = {PhaeoEpiView: an epigenome browser of the newly assembled genome of the model diatom Phaeodactylum tricornutum},
author = {Yue Wu and Timothée Chaumier and Eric Manirakiza and Alaguraj Veluchamy and Leila Tirichine},
url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10206091/
hal-04284562v1 },
doi = { 10.1038/s41598-023-35403-1},
issn = {2045-2322},
year = {2023},
date = {2023-05-23},
urldate = {2023-05-23},
journal = {Scientific Reports },
volume = {13},
pages = {8320},
abstract = {Recent advances in DNA sequencing technologies particularly long-read sequencing, greatly improved genomes assembly. However, this has created discrepancies between published annotations and epigenome tracks, which have not been updated to keep pace with the new assemblies. Here, we used the latest improved telomere-to-telomere assembly of the model pennate diatom Phaeodactylum tricornutum to lift over the gene models from Phatr3, a previously annotated reference genome. We used the lifted genes annotation and newly published transposable elements to map the epigenome landscape, namely DNA methylation and post-translational modifications of histones. This provides the community with PhaeoEpiView, a browser that allows the visualization of epigenome data and transcripts on an updated and contiguous reference genome, to better understand the biological significance of the mapped data. We updated previously published histone marks with a more accurate peak calling using mono instead of poly(clonal) antibodies and deeper sequencing. PhaeoEpiView (https://PhaeoEpiView.univ-nantes.fr) will be continuously updated with the newly published epigenomic data, making it the largest and richest epigenome browser of any stramenopile. In the upcoming era of molecular environmental studies, where epigenetics plays a significant role, we anticipate that PhaeoEpiView will become a widely used tool.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Demonceaux, Marie; Goux, Marine; Schimith, Lucia Emanueli; Santos, Michele Goulart Dos; Hendrickx, Johann; Offmann, Bernard; André-Miral, Corinne
Enzymatic synthesis, characterization and molecular docking of a new functionalized polyphenol: Resveratrol-3, 4’-⍺-diglucoside Article de journal
Dans: Results in Chemistry, p. 100956, 2023.
@article{demonceaux2023enzymatic,
title = {Enzymatic synthesis, characterization and molecular docking of a new functionalized polyphenol: Resveratrol-3, 4’-⍺-diglucoside},
author = {Marie Demonceaux and Marine Goux and Lucia Emanueli Schimith and Michele Goulart Dos Santos and Johann Hendrickx and Bernard Offmann and Corinne André-Miral},
url = {https://www.sciencedirect.com/science/article/pii/S2211715623001959},
doi = {10.1016/j.rechem.2023.100956},
year = {2023},
date = {2023-05-16},
urldate = {2023-05-16},
journal = {Results in Chemistry},
pages = {100956},
publisher = {Elsevier},
abstract = {Transglucosylation of resveratrol by the Q345F variant of sucrose phosphorylase from Bifidobacterium adolescentis (BaSP) was extensively studied during the last decade. Indeed, Q345F is able to catalyze the synthesis of resveratrol-3-O-⍺-D-glucoside (RES-3) with yield up to 97% using a cost-effective glucosyl donor, sucrose (Kraus et al., Chemical Communications, 53(90), 12182–12184 (2017)). Despite the fact that two further products were detectable in low amounts after glucoside synthesis, they were never identified. Here, we isolated and fully characterized one of those two minor products: resveratrol-3,4′-O-⍺-D-diglucoside (RES-3,4′). This original compound had never been described before. Using bioinformatics models, we successfully explained the formation of this diglucosylated product. Indeed, with RES-3 as acceptor substrate, Q345F is able to transfer a glucosyl moiety in position 4′-OH, what had been reported as impossible in the literature. The low yield observed is due to the steric hindrance into the catalytic site between RES-3 and residues Tyr132 and Tyr344. Nevertheless, the substrate orientation in the active site is favored by stabilizing interactions. Ring A of RES-3 bearing the diol moiety is stabilized by hydrogen bonds with residues Asp50, Arg135, Asn347 and Arg399. Hydroxyl group OH-4′ shares hydrogen bonds with the catalytic residues Asp192 and Glu232. Multiple hydrophobic contacts complete the stabilization of the substrate to favor the glucosylation at position 4′. Understanding of the mechanisms allowing the glucosylation at position 4′ of resveratrol will help the development of enzymatic tools to target and control the enzymatic synthesis of original ⍺-glucosylated polyphenols with high added value and better biodisponibility.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Téletchéa, Stéphane; Esque, Jérémy; Urbain, Aurélie; Etchebest, Catherine; de Brevern, Alexandre G.
Evaluation of Transmembrane Protein Structural Models Using HPMScore Article de journal
Dans: BioMedInformatics, vol. 3, no. 2, p. 306–326, 2023, ISSN: 2673-7426.
@article{biomedinformatics3020021,
title = {Evaluation of Transmembrane Protein Structural Models Using HPMScore},
author = {Stéphane Téletchéa and Jérémy Esque and Aurélie Urbain and Catherine Etchebest and Alexandre G. de Brevern},
url = {https://www.mdpi.com/2673-7426/3/2/21
https://hal.science/hal-03251546v1, HAL},
doi = {10.3390/biomedinformatics3020021},
issn = {2673-7426},
year = {2023},
date = {2023-05-02},
urldate = {2023-05-02},
journal = {BioMedInformatics},
volume = {3},
number = {2},
pages = {306--326},
abstract = {Transmembrane proteins (TMPs) are a class of essential proteins for biological and therapeutic purposes. Despite an increasing number of structures, the gap with the number of available sequences remains impressive. The choice of a dedicated function to select the most probable/relevant model among hundreds is a specific problem of TMPs. Indeed, the majority of approaches are mostly focused on globular proteins. We developed an alternative methodology to evaluate the quality of TMP structural models. HPMScore took into account sequence and local structural information using the unsupervised learning approach called hybrid protein model. The methodology was extensively evaluated on very different TMP all-α proteins. Structural models with different qualities were generated, from good to bad quality. HPMScore performed better than DOPE in recognizing good comparative models over more degenerated models, with a Top 1 of 46.9% against DOPE 40.1%, both giving the same result in 13.0%. When the alignments used are higher than 35%, HPM is the best for 52%, against 36% for DOPE (12% for both). These encouraging results need further improvement particularly when the sequence identity falls below 35%. An area of enhancement would be to train on a larger training set. A dedicated web server has been implemented and provided to the scientific community. It can be used with structural models generated from comparative modeling to deep learning approaches.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Metz, Raphaël; Rauscher, Aurore; Vaugier, Loïg; Supiot, Stéphane; Drouet, Franck; Campion, Loic; Rousseau, Caroline
Comparison of Hormone-Sensitive Oligorecurrent Prostate Cancer Patients Based on Routine Use of Choline and/or PSMA PET/CT to Guide Metastasis-Directed Therapy Article de journal
Dans: Cancers, vol. 15, no. 6, 2023, ISSN: 2072-6694.
@article{cancers15061898,
title = {Comparison of Hormone-Sensitive Oligorecurrent Prostate Cancer Patients Based on Routine Use of Choline and/or PSMA PET/CT to Guide Metastasis-Directed Therapy},
author = {Raphaël Metz and Aurore Rauscher and Loïg Vaugier and Stéphane Supiot and Franck Drouet and Loic Campion and Caroline Rousseau},
url = {https://www.mdpi.com/2072-6694/15/6/1898},
doi = {10.3390/cancers15061898},
issn = {2072-6694},
year = {2023},
date = {2023-03-22},
urldate = {2023-01-01},
journal = {Cancers},
volume = {15},
number = {6},
abstract = {Background: In hormone-sensitive oligorecurrent prostate cancer (PC), the literature showed [68Ga]Ga-PSMA (PSMA) and [18F]F-choline (FCH) PET/CT can successfully guide metastasis-directed therapies (MDT). This observational retrospective study aimed to explore, in routine use, the impact of FCH or PSMA PET/CT in guiding MDT for hormone-sensitive oligometastatic PC at different recurrences. Methods: In 2017-2020, patients initially treated with radical prostatectomy but, in biochemical recurrence (with PSA ≤ 2 ng/mL), diagnosed as oligometastatic based on FCH or PSMA PET/CT, were identified. MDT was stereotactic body radiotherapy (SBRT), elective nodal or prostate bed radiotherapy ± boost and ± androgen deprivation therapy (ADT). The primary endpoint was biochemical relapse-free survival (BR-FS), defined as a PSA increase ≥ 0.2 ng/mL above the nadir and increasing over two successive samples and the secondaries were ADT-free survival (ADT-FS). Results: 123 patients (70 PSMA and 53 FCH) were included. The median follow-up was 42.2 months. The median BR-FS was 24.7 months in the PSMA group versus 13.0 months in the FCH group (p = 0.008). Similarly, ADT-FS (p = 0.001) was longer in patients in the PSMA group. In multivariate analysis, a short PSA doubling time before imaging (p = 0.005) and MDT with SBRT (p = 0.001) were poor prognostic factors for BR-FS. Conclusions: Routine use of FCH or PSMA PET/CT in hormone-sensitive PC showed an advantage for using PSMA PET/CT to guide MDT in terms of BR-FS and ADT-FS in patients with low PSA value. Prospective studies are needed to confirm these hypotheses.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Violo, Typhaine; Lambert, Annie; Pillot, Aline; Fanuel, Mathieu; Mac-Béar, Jessica; Broussard, Cédric; Grandjean, Cyrille; Camberlein, Emilie
Site-Selective Unnatural Amino Acid Incorporation at Single or Multiple Positions to Control Sugar-Protein Connectivity in Glycoconjugate Vaccine Candidates Article de journal
Dans: Chemistry--A European Journal, vol. 29, no. 15, p. e202203497, 2023, ISBN: 1521-3765.
@article{violo2023site,
title = {Site-Selective Unnatural Amino Acid Incorporation at Single or Multiple Positions to Control Sugar-Protein Connectivity in Glycoconjugate Vaccine Candidates},
author = {Typhaine Violo and Annie Lambert and Aline Pillot and Mathieu Fanuel and Jessica Mac-Béar and Cédric Broussard and Cyrille Grandjean and Emilie Camberlein},
url = {https://chemistry-europe.onlinelibrary.wiley.com/doi/full/10.1002/chem.202203497
hal-03918892v2
},
doi = {10.1002/chem.202203497},
isbn = {1521-3765},
year = {2023},
date = {2023-03-13},
urldate = {2023-03-13},
journal = {Chemistry--A European Journal},
volume = {29},
number = {15},
pages = {e202203497},
publisher = {Wiley Online Library},
abstract = {In cellulo site-specific unnatural amino acid incorporation based on amber stop codon reassignment is a powerful tool to modify proteins at defined positions. This technique is herein applied to the selective functionalization of the Pneumococcal surface adhesin A protein at three distinct positions. Nϵ-propargyloxycarbonyl-l-lysine residues were incorporated and their alkyne groups reacted using click-chemistry with a synthetic azido-functionalized tetrasaccharide representative of one repeat unit of the Streptococcus pneumoniae serotype 14 capsular polysaccharide. Anti-PsaA antibody response induced in mice by the trivalent glycoconjugate was determined in comparison with corresponding monovalent and randomly functionalized conjugates. Our results suggest that controlled was superior to random conjugation for preserving antigenicity. In definitive, the reported strategy offers a unique opportunity to study the impact of carbohydrate antigen-carrier protein connectivity on immunogenicity.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Hoguin, Antoine; Yang, Feng; Groisillier, Agnès; Bowler, Chris; Genovesio, Auguste; Ait-Mohamed, Ouardia; Vieira, Fabio Rocha Jimenez; Tirichine, Leila
The model diatom Phaeodactylum tricornutum provides insights into the diversity and function of microeukaryotic DNA methyltransferases Article de journal
Dans: Communications Biology, vol. 6, iss. 1, no. 1, p. 253, 2023, ISSN: 23993642.
@article{Hoguin2023,
title = {The model diatom Phaeodactylum tricornutum provides insights into the diversity and function of microeukaryotic DNA methyltransferases},
author = {Antoine Hoguin and Feng Yang and Agnès Groisillier and Chris Bowler and Auguste Genovesio and Ouardia Ait-Mohamed and Fabio Rocha Jimenez Vieira and Leila Tirichine},
editor = {Nature},
url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9998398/
hal-04024906v1 },
doi = {10.1038/s42003-023-04629-0 },
issn = {23993642},
year = {2023},
date = {2023-03-09},
urldate = {2023-03-09},
journal = {Communications Biology},
volume = {6},
number = {1},
issue = {1},
pages = {253},
abstract = {Cytosine methylation is an important epigenetic mark involved in the transcriptional control of transposable elements in mammals, plants and fungi. The Stramenopiles-Alveolate-Rhizaria (SAR) lineages are a major group of ecologically important marine microeukaryotes, including the phytoplankton groups diatoms and dinoflagellates. However, little is known about their DNA methyltransferase diversity. Here, we performed an in-silico analysis of DNA methyltransferases found in marine microeukaryotes and showed that they encode divergent DNMT3, DNMT4, DNMT5 and DNMT6 enzymes. Furthermore, we found three classes of enzymes within the DNMT5 family. Using a CRISPR/Cas9 strategy we demonstrated that the loss of the DNMT5a gene correlates with a global depletion of DNA methylation and overexpression of young transposable elements in the model diatom Phaeodactylum tricornutum. The study provides a view of the structure and function of a DNMT family in the SAR supergroup using an attractive model species.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Demeyer, Alexandre; Fonteneau, Lucie; Liennard, Marion; Foyer, Claire; Weigel, Pierre; Laurent, Adèle; Lebreton, Jacques; Fleury, Fabrice; Mathé-Allainmat, Monique
Synthesis and Biological Evaluation of DIDS Analogues as Efficient Inhibitors of RAD51 Involved in Homologous Recombination Article de journal
Dans: Bioorg Med Chem Lett, p. 129261, 2023, ISSN: 1464-3405.
@article{pmid36990245,
title = {Synthesis and Biological Evaluation of DIDS Analogues as Efficient Inhibitors of RAD51 Involved in Homologous Recombination},
author = {Alexandre Demeyer and Lucie Fonteneau and Marion Liennard and Claire Foyer and Pierre Weigel and Adèle Laurent and Jacques Lebreton and Fabrice Fleury and Monique Mathé-Allainmat},
url = {hal-04234850v1 },
doi = {10.1016/j.bmcl.2023.129261},
issn = {1464-3405},
year = {2023},
date = {2023-03-01},
urldate = {2023-03-01},
journal = {Bioorg Med Chem Lett},
pages = {129261},
abstract = {RAD51 is a pivotal protein of the homologous recombination DNA repair pathway, and is overexpressed in some cancer cells, disrupting then the efficiency of cancer-treatments. The development of RAD51 inhibitors appears as a promising solution to restore these cancer cells sensitization to radio- or chemotherapy. From a small molecule identified as a modulator of RAD51, the 4,4'-diisothiocyanostilbene-2,2'-disulfonic acid (DIDS), two series of analogues with small or bulky substituents on the aromatic parts of the stilbene moiety were prepared for a structure-activity relationship study. Three compounds, the cyano analogue (12), and benzamide (23) or phenylcarbamate (29) analogues of DIDS were characterized as novel potent RAD51 inhibitors with HR inhibition in the micromolar range.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Saade, Gaëlle; Bogaerts, Eva; Chiavassa, Sophie; Blain, Guillaume; Delpon, Grégory; Evin, Manon; Ghannam, Youssef; Haddad, Ferid; Haustermans, Karin; Koumeir, Charbel; others,
Ultrahigh-Dose-Rate Proton Irradiation Elicits Reduced Toxicity in Zebrafish Embryos Article de journal
Dans: Advances in Radiation Oncology, vol. 8, no. 2, p. 101124, 2023.
@article{saade2023ultrahigh,
title = {Ultrahigh-Dose-Rate Proton Irradiation Elicits Reduced Toxicity in Zebrafish Embryos},
author = {Gaëlle Saade and Eva Bogaerts and Sophie Chiavassa and Guillaume Blain and Grégory Delpon and Manon Evin and Youssef Ghannam and Ferid Haddad and Karin Haustermans and Charbel Koumeir and others},
url = {https://www.sciencedirect.com/science/article/pii/S2452109422002305
hal-03940364v1 },
doi = {10.1016/j.adro.2022.101124},
year = {2023},
date = {2023-03-01},
urldate = {2023-03-01},
journal = {Advances in Radiation Oncology},
volume = {8},
number = {2},
pages = {101124},
publisher = {Elsevier},
abstract = {Purpose
Recently, ultrahigh-dose-rate radiation therapy (UHDR-RT) has emerged as a promising strategy to increase the benefit/risk ratio of external RT. Extensive work is on the way to characterize the physical and biological parameters that control the so-called “Flash” effect. However, this healthy/tumor differential effect is observable in in vivo models, which thereby drastically limits the amount of work that is achievable in a timely manner.
Methods and Materials
In this study, zebrafish embryos were used to compare the effect of UHDR irradiation (8-9 kGy/s) to conventional RT dose rate (0.2 Gy/s) with a 68 MeV proton beam. Viability, body length, spine curvature, and pericardial edema were measured 4 days postirradiation.
Results
We show that body length is significantly greater after UHDR-RT compared with conventional RT by 180 µm at 30 Gy and 90 µm at 40 Gy, while pericardial edema is only reduced at 30 Gy. No differences were obtained in terms of survival or spine curvature.
Conclusions
Zebrafish embryo length appears as a robust endpoint, and we anticipate that this model will substantially fasten the study of UHDR proton-beam parameters necessary for “Flash.”},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Recently, ultrahigh-dose-rate radiation therapy (UHDR-RT) has emerged as a promising strategy to increase the benefit/risk ratio of external RT. Extensive work is on the way to characterize the physical and biological parameters that control the so-called “Flash” effect. However, this healthy/tumor differential effect is observable in in vivo models, which thereby drastically limits the amount of work that is achievable in a timely manner.
Methods and Materials
In this study, zebrafish embryos were used to compare the effect of UHDR irradiation (8-9 kGy/s) to conventional RT dose rate (0.2 Gy/s) with a 68 MeV proton beam. Viability, body length, spine curvature, and pericardial edema were measured 4 days postirradiation.
Results
We show that body length is significantly greater after UHDR-RT compared with conventional RT by 180 µm at 30 Gy and 90 µm at 40 Gy, while pericardial edema is only reduced at 30 Gy. No differences were obtained in terms of survival or spine curvature.
Conclusions
Zebrafish embryo length appears as a robust endpoint, and we anticipate that this model will substantially fasten the study of UHDR proton-beam parameters necessary for “Flash.”
Demonceaux, Marie; Goux, Marine; Hendrickx, Johann; Solleux, Claude; Cadet, Frédéric; Lormeau, Émilie; Offmann, Bernard; André-Miral, Corinne
Regioselective glucosylation of (+)-catechin using a new variant of sucrose phosphorylase from Bifidobacterium adolescentis Article de journal
Dans: Organic & Biomolecular Chemistry, vol. 21, no. 11, p. 2307–2311, 2023.
@article{demonceaux2023regioselective,
title = {Regioselective glucosylation of (+)-catechin using a new variant of sucrose phosphorylase from Bifidobacterium adolescentis},
author = {Marie Demonceaux and Marine Goux and Johann Hendrickx and Claude Solleux and Frédéric Cadet and Émilie Lormeau and Bernard Offmann and Corinne André-Miral},
doi = {10.1039/D3OB00191A},
year = {2023},
date = {2023-02-22},
urldate = {2023-02-22},
journal = {Organic & Biomolecular Chemistry},
volume = {21},
number = {11},
pages = {2307--2311},
publisher = {Royal Society of Chemistry},
abstract = {Mutation Q345F in sucrose phosphorylase from Bifidobacterium adolescentis (BaSP) has shown to allow efficient (+)-catechin glucosylation yielding a regioisomeric mixture: (+)-catechin-3′-O-α-D-glucopyranoside, (+)-catechin-5-O-α-D-glucopyranoside and (+)-catechin-3′,5-O-α-D-diglucopyranoside with a ratio of 51 : 25 : 24. Here, we efficiently increased the control of (+)-catechin glucosylation regioselectivity with a new variant Q345F/P134D. The same products were obtained with a ratio of 82 : 9 : 9. Thanks to bioinformatics models, we successfully explained the glucosylation favoured at the OH-3′ position due to the mutation P134D.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Nifontova, Galina; Petrova, Irina; Gerasimovich, Evgeniia; Konopsky, Valery N.; Ayadi, Nizar; Charlier, Cathy; Fleury, Fabrice; Karaulov, Alexander; Sukhanova, Alyona; Nabiev, Igor
Label-Free Multiplexed Microfluidic Analysis of Protein Interactions Based on Photonic Crystal Surface Mode Imaging Article de journal
Dans: International Journal of Molecular Sciences, vol. 24, no. 5, 2023, ISSN: 1422-0067.
@article{ijms24054347b,
title = {Label-Free Multiplexed Microfluidic Analysis of Protein Interactions Based on Photonic Crystal Surface Mode Imaging},
author = {Galina Nifontova and Irina Petrova and Evgeniia Gerasimovich and Valery N. Konopsky and Nizar Ayadi and Cathy Charlier and Fabrice Fleury and Alexander Karaulov and Alyona Sukhanova and Igor Nabiev},
url = {https://www.mdpi.com/1422-0067/24/5/4347},
doi = {10.3390/ijms24054347},
issn = {1422-0067},
year = {2023},
date = {2023-02-22},
urldate = {2023-02-22},
journal = {International Journal of Molecular Sciences},
volume = {24},
number = {5},
abstract = {High-throughput protein assays are crucial for modern diagnostics, drug discovery, proteomics, and other fields of biology and medicine. It allows simultaneous detection of hundreds of analytes and miniaturization of both fabrication and analytical procedures. Photonic crystal surface mode (PC SM) imaging is an effective alternative to surface plasmon resonance (SPR) imaging used in conventional gold-coated, label-free biosensors. PC SM imaging is advantageous as a quick, label-free, and reproducible technique for multiplexed analysis of biomolecular interactions. PC SM sensors are characterized by a longer signal propagation at the cost of a lower spatial resolution, which makes them more sensitive than classical SPR imaging sensors. We describe an approach for designing label-free protein biosensing assays employing PC SM imaging in the microfluidic mode. Label-free, real-time detection of PC SM imaging biosensors using two-dimensional imaging of binding events has been designed to study arrays of model proteins (antibodies, immunoglobulin G-binding proteins, serum proteins, and DNA repair proteins) at 96 points prepared by automated spotting. The data prove feasibility of simultaneous PC SM imaging of multiple protein interactions. The results pave the way to further develop PC SM imaging as an advanced label-free microfluidic assay for the multiplexed detection of protein interactions.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Tirichine, Leila; Piganeau, Gwenael
Editorial: Algal symbiotic relationships in freshwater and marine environments Article de journal
Dans: Front. Plant Sci., 2023.
@article{nokey,
title = {Editorial: Algal symbiotic relationships in freshwater and marine environments},
author = {Leila Tirichine and Gwenael Piganeau},
url = {https://www.frontiersin.org/articles/10.3389/fpls.2023.1155759/full
hal-04284580v1 },
doi = {doi: 10.3389/fpls.2023.1155759},
year = {2023},
date = {2023-02-20},
urldate = {2023-02-20},
journal = {Front. Plant Sci.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Shao, Zhanru; andFabio Vieira, Osei Ampomah; Dorrell, Richard; Li, Shaoxuan; Tirichine, Leila; Bulone, Vincent; Duan, Delin; Bowler, Chris
Characterization of a Marine Diatom Chitin Synthase Using a Combination of Meta-Omics, Genomics, and Heterologous Expression Approaches. Article de journal
Dans: mSystems, 2023.
@article{nokey,
title = {Characterization of a Marine Diatom Chitin Synthase Using a Combination of Meta-Omics, Genomics, and Heterologous Expression Approaches. },
author = {Zhanru Shao and Osei Ampomah andFabio Vieira and Richard Dorrell and Shaoxuan Li and Leila Tirichine and Vincent Bulone and Delin Duan and Chris Bowler},
doi = {doi: 10.1128/msystems.01131-22},
year = {2023},
date = {2023-02-15},
urldate = {2023-02-15},
journal = {mSystems},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Madel, Maria-Bernadette; Halper, Julia; Ibáñez, Lidia; Claire, Lozano; Rouleau, Matthieu; Boutin, Antoine; Mahler, Adrien; Pontier-Bres, Rodolphe; Ciucci, Thomas; Topi, Majlinda; Hue, Christophe; Amiaud, Jerome; Iborra, Salvador; Sancho, David; Heymann, Dominique; Garchon, Henri-Jean; Czerucka, Dorota; Apparailly, Florence; Duroux-Richard, Isabelle; Wakkach, Abdelilah; Blin-Wakkach, Claudine
Specific targeting of inflammatory osteoclastogenesis by the probiotic yeast S. boulardii CNCM I-745 reduces bone loss in osteoporosis Article de journal
Dans: eLife, vol. 12, p. e82037, 2023, ISSN: 2050-084X.
@article{10.7554/eLife.82037,
title = {Specific targeting of inflammatory osteoclastogenesis by the probiotic yeast S. boulardii CNCM I-745 reduces bone loss in osteoporosis},
author = {Maria-Bernadette Madel and Julia Halper and Lidia Ibáñez and Lozano Claire and Matthieu Rouleau and Antoine Boutin and Adrien Mahler and Rodolphe Pontier-Bres and Thomas Ciucci and Majlinda Topi and Christophe Hue and Jerome Amiaud and Salvador Iborra and David Sancho and Dominique Heymann and Henri-Jean Garchon and Dorota Czerucka and Florence Apparailly and Isabelle Duroux-Richard and Abdelilah Wakkach and Claudine Blin-Wakkach},
editor = {Yi-Ping Li and Mone Zaidi and Marco Ponzetti},
url = {https://doi.org/10.7554/eLife.82037},
doi = {10.7554/eLife.82037},
issn = {2050-084X},
year = {2023},
date = {2023-02-01},
urldate = {2023-02-01},
journal = {eLife},
volume = {12},
pages = {e82037},
publisher = {eLife Sciences Publications, Ltd},
abstract = {Bone destruction is a hallmark of chronic inflammation, and bone-resorbing osteoclasts arising under such a condition differ from steady-state ones. However, osteoclast diversity remains poorly explored. Here, we combined transcriptomic profiling, differentiation assays and in vivo analysis in mouse to decipher specific traits for inflammatory and steady-state osteoclasts. We identified and validated the pattern-recognition receptors (PRR) Tlr2, Dectin-1, and Mincle, all involved in yeast recognition as major regulators of inflammatory osteoclasts. We showed that administration of the yeast probiotic textitSaccharomyces boulardii CNCM I-745 (textitSb) in vivo reduced bone loss in ovariectomized but not sham mice by reducing inflammatory osteoclastogenesis. This beneficial impact of textitSb is mediated by the regulation of the inflammatory environment required for the generation of inflammatory osteoclasts. We also showed that textitSb derivatives as well as agonists of Tlr2, Dectin-1, and Mincle specifically inhibited directly the differentiation of inflammatory but not steady-state osteoclasts in vitro. These findings demonstrate a preferential use of the PRR-associated costimulatory differentiation pathway by inflammatory osteoclasts, thus enabling their specific inhibition, which opens new therapeutic perspectives for inflammatory bone loss.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Saumonneau, Amélie; Lagneau, Nathan; Ogonda, Lydia Awuor; Dupré, Catherine; Dutertre, Stéphanie; Grizeau, Dominique; Tellier, Charles; Grandjean, Cyrille; Daligault, Franck
Disruption of Botryococcus braunii colonies by glycoside hydrolases Article de journal
Dans: Bioresource Technology Reports, vol. 21, p. 101335, 2023, ISSN: 2589-014X.
@article{SAUMONNEAU2023101335,
title = {Disruption of Botryococcus braunii colonies by glycoside hydrolases},
author = {Amélie Saumonneau and Nathan Lagneau and Lydia Awuor Ogonda and Catherine Dupré and Stéphanie Dutertre and Dominique Grizeau and Charles Tellier and Cyrille Grandjean and Franck Daligault},
url = {https://www.sciencedirect.com/science/article/pii/S2589014X23000063
hal-03973352v1 },
doi = {10.1016/j.biteb.2023.101335},
issn = {2589-014X},
year = {2023},
date = {2023-01-13},
urldate = {2023-01-13},
journal = {Bioresource Technology Reports},
volume = {21},
pages = {101335},
abstract = {Microalgae are a promising alternative resource to fossil-based products. Botryococcus braunii is a colonial green microalga having the ability to convert CO2 by photosynthesis into long chain hydrocarbons. These are excreted and trapped in an extracellular matrix (ECM). A panel of glycosidases ranging from arabinanase, galactananase to endoglucanase was tested for their ability to lyse the polysaccharides maintaining the B. braunii colony integrity in order to release the hydrocarbons present in the extracellular matrix without harming the cells. The BpGH9 endoglucanase from Bacillus pumilus was fused with CtCBM3a from Clostridium thermocellum and yellow fluorescent protein to probe the presence of microcrystalline cellulose in the cell wall of B. braunii and to increase the efficacy of the endoglucanase. All the tested enzymes were able to some extent to dissociate the cells from the extracellular matrix while keeping them alive, suggesting the feasibility of a semi-continuous in situ recovery of hydrocarbons.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Poulet, Axel; Rousselot, Ellyn; Téletchéa, Stéphane; Noirot, Céline; Jacob, Yannick; Wolfswinkel, Josien; Thiriet, Christophe; Duc, Céline
The Histone Chaperone Network Is Highly Conserved in Physarum polycephalum Article de journal
Dans: International Journal of Molecular Sciences, vol. 24, no. 2, 2023, ISSN: 1422-0067.
@article{ijms24021051,
title = {The Histone Chaperone Network Is Highly Conserved in Physarum polycephalum},
author = {Axel Poulet and Ellyn Rousselot and Stéphane Téletchéa and Céline Noirot and Yannick Jacob and Josien Wolfswinkel and Christophe Thiriet and Céline Duc},
url = {https://www.mdpi.com/1422-0067/24/2/1051
hal-03978828v1 },
doi = {10.3390/ijms24021051},
issn = {1422-0067},
year = {2023},
date = {2023-01-01},
urldate = {2023-01-01},
journal = {International Journal of Molecular Sciences},
volume = {24},
number = {2},
abstract = {The nucleosome is composed of histones and DNA. Prior to their deposition on chromatin, histones are shielded by specialized and diverse proteins known as histone chaperones. They escort histones during their entire cellular life and ensure their proper incorporation in chromatin. Physarum polycephalum is a Mycetozoan, a clade located at the crown of the eukaryotic tree. We previously found that histones, which are highly conserved between plants and animals, are also highly conserved in Physarum. However, histone chaperones differ significantly between animal and plant kingdoms, and this thus probed us to further study the conservation of histone chaperones in Physarum and their evolution relative to animal and plants. Most of the known histone chaperones and their functional domains are conserved as well as key residues required for histone and chaperone interactions. Physarum is divergent from yeast, plants and animals, but PpHIRA, PpCABIN1 and PpSPT6 are similar in structure to plant orthologues. PpFACT is closely related to the yeast complex, and the Physarum genome encodes the animal-specific APFL chaperone. Furthermore, we performed RNA sequencing to monitor chaperone expression during the cell cycle and uncovered two distinct patterns during S-phase. In summary, our study demonstrates the conserved role of histone chaperones in handling histones in an early-branching eukaryote.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Oliver, Lisa; Álvarez-Arenas, Arturo; Salaud, Céline; Jiménez-Sanchez, Juan; Calvo, Gabriel F.; Belmonte-Beitia, Juan; Blandin, Stephanie; Vidal, Luciano; Pérez, Victor; Heymann, Dominique; Vallette, François M.
A Simple 3D Cell Culture Method for Studying the Interactions between Human Mesenchymal Stromal/Stem Cells and Patients Derived Glioblastoma Article de journal
Dans: Cancers, vol. 15, no. 4, 2023, ISSN: 2072-6694.
@article{cancers15041304,
title = {A Simple 3D Cell Culture Method for Studying the Interactions between Human Mesenchymal Stromal/Stem Cells and Patients Derived Glioblastoma},
author = {Lisa Oliver and Arturo Álvarez-Arenas and Céline Salaud and Juan Jiménez-Sanchez and Gabriel F. Calvo and Juan Belmonte-Beitia and Stephanie Blandin and Luciano Vidal and Victor Pérez and Dominique Heymann and François M. Vallette},
url = {https://www.mdpi.com/2072-6694/15/4/1304
inserm-04001934v1 },
doi = {10.3390/cancers15041304},
issn = {2072-6694},
year = {2023},
date = {2023-01-01},
urldate = {2023-01-01},
journal = {Cancers},
volume = {15},
number = {4},
abstract = {We have developed a 3D biosphere model using patient-derived cells (PDCs) from glioblastoma (GBM), the major form of primary brain tumors in adult, plus cancer-activated fibroblasts (CAFs), obtained by culturing mesenchymal stem cells with GBM conditioned media. The effect of MSC/CAFs on the proliferation, cell-cell interactions, and response to treatment of PDCs was evaluated. Proliferation in the presence of CAFs was statistically lower but the spheroids formed within the 3D-biosphere were larger. A treatment for 5 days with Temozolomide (TMZ) and irradiation, the standard therapy for GBM, had a marked effect on cell number in monocultures compared to co-cultures and influenced cancer stem cells composition, similar to that observed in GBM patients. Mathematical analyses of spheroids growth and morphology confirm the similarity with GBM patients. We, thus, provide a simple and reproducible method to obtain 3D cultures from patient-derived biopsies and co-cultures with MSC with a near 100% success. This method provides the basis for relevant in vitro functional models for a better comprehension of the role of tumor microenvironment and, for precision and/or personalized medicine, potentially to predict the response to treatments for each GBM patient.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Jacquot, Perrine; Muñoz-Garcia, Javier; Fleury, Maurine; Cochonneau, Denis; Gaussin, Rémi; Enouf, Elise; Roze, Caroline; Ollivier, Emilie; Cinier, Mathieu; Heymann, Dominique
Engineering of a Bispecific Nanofitin with Immune Checkpoint Inhibitory Activity Conditioned by the Cross-Arm Binding to EGFR and PDL1 Article de journal
Dans: Biomolecules, vol. 13, no. 4, 2023, ISSN: 2218-273X.
@article{biom13040636,
title = {Engineering of a Bispecific Nanofitin with Immune Checkpoint Inhibitory Activity Conditioned by the Cross-Arm Binding to EGFR and PDL1},
author = {Perrine Jacquot and Javier Muñoz-Garcia and Maurine Fleury and Denis Cochonneau and Rémi Gaussin and Elise Enouf and Caroline Roze and Emilie Ollivier and Mathieu Cinier and Dominique Heymann},
url = {https://www.mdpi.com/2218-273X/13/4/636
inserm-04056943v1 },
doi = {10.3390/biom13040636},
issn = {2218-273X},
year = {2023},
date = {2023-01-01},
urldate = {2023-01-01},
journal = {Biomolecules},
volume = {13},
number = {4},
abstract = {Re-education of the tumor microenvironment with immune checkpoint inhibitors (ICI) has provided the most significant advancement in cancer management, with impressive efficacy and durable response reported. However, low response rates and a high frequency of immune-related adverse events (irAEs) remain associated with ICI therapies. The latter can be linked to their high affinity and avidity for their target that fosters on-target/off-tumor binding and subsequent breaking of immune self-tolerance in normal tissues. Many multispecific protein formats have been proposed to increase the tumor cell's selectivity of ICI therapies. In this study, we explored the engineering of a bispecific Nanofitin by the fusion of an anti-epidermal growth factor receptor (EGFR) and anti-programmed cell death ligand 1 (PDL1) Nanofitin modules. While lowering the affinity of the Nanofitin modules for their respective target, the fusion enables the simultaneous engagement of EGFR and PDL1, which translates into a selective binding to tumor cells co-expressing EGFR and PDL1 only. We demonstrated that affinity-attenuated bispecific Nanofitin could elicit PDL1 blockade exclusively in an EGFR-directed manner. Overall, the data collected highlight the potential of this approach to enhance the selectivity and safety of PDL1 checkpoint inhibition.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Mam, Bhavika; Tsitsanou, Katerina E.; Liggri, Panagiota G. V.; Saitta, Francesca; Stamati, Evgenia C. V.; Mahita, Jarjapu; Leonis, Georgios; Drakou, Christina E.; Papadopoulos, Manthos; Arnaud, Philippe; Offmann, Bernard; Fessas, Dimitrios; Sowdhamini, Ramanathan; Zographos, Spyros E.
Influence of pH on indole-dependent heterodimeric interactions between Anopheles gambiae odorant-binding proteins OBP1 and OBP4 Article de journal
Dans: International Journal of Biological Macromolecules, vol. 245, p. 125422, 2023, ISSN: 0141-8130.
@article{MAM2023125422,
title = {Influence of pH on indole-dependent heterodimeric interactions between Anopheles gambiae odorant-binding proteins OBP1 and OBP4},
author = {Bhavika Mam and Katerina E. Tsitsanou and Panagiota G. V. Liggri and Francesca Saitta and Evgenia C. V. Stamati and Jarjapu Mahita and Georgios Leonis and Christina E. Drakou and Manthos Papadopoulos and Philippe Arnaud and Bernard Offmann and Dimitrios Fessas and Ramanathan Sowdhamini and Spyros E. Zographos},
url = {https://www.sciencedirect.com/science/article/pii/S0141813023023164},
doi = {https://doi.org/10.1016/j.ijbiomac.2023.125422},
issn = {0141-8130},
year = {2023},
date = {2023-01-01},
urldate = {2023-01-01},
journal = {International Journal of Biological Macromolecules},
volume = {245},
pages = {125422},
abstract = {Insect Odorant Binding Proteins (OBPs) constitute important components of their olfactory apparatus, as they are essential for odor recognition. OBPs undergo conformational changes upon pH change, altering their interactions with odorants. Moreover, they can form heterodimers with novel binding characteristics. Anopheles gambiae OBP1 and OBP4 were found capable of forming heterodimers possibly involved in the specific perception of the attractant indole. In order to understand how these OBPs interact in the presence of indole and to investigate the likelihood of a pH-dependent heterodimerization mechanism, the crystal structures of OBP4 at pH 4.6 and 8.5 were determined. Structural comparison to each other and with the OBP4-indole complex (3Q8I, pH 6.85) revealed a flexible N-terminus and conformational changes in the α4-loop-α5 region at acidic pH. Fluorescence competition assays showed a weak binding of indole to OBP4 that becomes further impaired at acidic pH. Additional Molecular Dynamic and Differential Scanning Calorimetry studies displayed that the influence of pH on OBP4 stability is significant compared to the modest effect of indole. Furthermore, OBP1-OBP4 heterodimeric models were generated at pH 4.5, 6.5, and 8.5, and compared concerning their interface energy and cross-correlated motions in the absence and presence of indole. The results indicate that the increase in pH may induce the stabilization of OBP4 by increasing its helicity, thereby enabling indole binding at neutral pH that further stabilizes the protein and possibly promotes the creation of a binding site for OBP1. A decrease in interface stability and loss of correlated motions upon transition to acidic pH may provoke the heterodimeric dissociation allowing indole release. Finally, we propose a potential OBP1-OBP4 heterodimer formation/disruption mechanism induced by pH change and indole binding.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Oyanedel, Daniel; Lagorce, Arnaud; Bruto, Maxime; Haffner, Philippe; Morot, Amandine; Labreuche, Yannick; Dorant, Yann; Divonne, Sébastien La Forest; Delavat, François; Inguimbert, Nicolas; Montagnani, Caroline; Morga, Benjamin; Toulza, Eve; Chaparro, Cristian; Escoubas, Jean-Michel; Gueguen, Yannick; Vidal-Dupiol, Jeremie; Lorgeril, Julien; Petton, Bruno; Degremont, Lionel; Tourbiez, Delphine; Pimparé, Léa-Lou; Leroy, Marc; Romatif, Océane; Pouzadoux, Juliette; Mitta, Guillaume; Roux, Frédérique Le; Charrière, Guillaume M.; Travers, Marie-Agnès; Destoumieux-Garzón, Delphine
Cooperation and cheating orchestrate Vibrio assemblages and polymicrobial synergy in oysters infected with OsHV-1 virus Article de journal
Dans: Proceedings of the National Academy of Sciences, vol. 120, no. 40, p. e2305195120, 2023.
@article{<LineBreak>doi:10.1073/pnas.2305195120,
title = {Cooperation and cheating orchestrate Vibrio assemblages and polymicrobial synergy in oysters infected with OsHV-1 virus},
author = {Daniel Oyanedel and Arnaud Lagorce and Maxime Bruto and Philippe Haffner and Amandine Morot and Yannick Labreuche and Yann Dorant and Sébastien La Forest Divonne and François Delavat and Nicolas Inguimbert and Caroline Montagnani and Benjamin Morga and Eve Toulza and Cristian Chaparro and Jean-Michel Escoubas and Yannick Gueguen and Jeremie Vidal-Dupiol and Julien Lorgeril and Bruno Petton and Lionel Degremont and Delphine Tourbiez and Léa-Lou Pimparé and Marc Leroy and Océane Romatif and Juliette Pouzadoux and Guillaume Mitta and Frédérique Le Roux and Guillaume M. Charrière and Marie-Agnès Travers and Delphine Destoumieux-Garzón},
url = {https://www.pnas.org/doi/abs/10.1073/pnas.2305195120
https://www.biorxiv.org/content/early/2023/02/11/2023.02.11.528104},
doi = {10.1073/pnas.2305195120},
year = {2023},
date = {2023-01-01},
urldate = {2023-01-01},
journal = {Proceedings of the National Academy of Sciences},
volume = {120},
number = {40},
pages = {e2305195120},
abstract = {Polymicrobial infections threaten the health of humans and animals but remain understudied in natural systems. We recently described the Pacific Oyster Mortality Syndrome (POMS), a polymicrobial disease affecting oyster production worldwide. In the French Atlantic coast, the disease involves coinfection with ostreid herpesvirus 1 (OsHV-1) and virulent Vibrio. However, it is unknown whether consistent Vibrio populations are associated with POMS in different regions, how Vibrio contribute to POMS, and how they interact with OsHV-1 during pathogenesis. By connecting field-based approaches in a Mediterranean ecosystem, laboratory infection assays and functional genomics, we uncovered a web of interdependencies that shape the structure and function of the POMS pathobiota. We show that Vibrio harveyi and Vibrio rotiferianus are predominant in OsHV-1-diseased oysters and that OsHV-1 drives the partition of the Vibrio community observed in the field. However only V. harveyi synergizes with OsHV-1 by promoting mutual growth and accelerating oyster death. V. harveyi shows high-virulence potential and dampens oyster cellular defenses through a type 3 secretion system, making oysters a more favorable niche for microbe colonization. In addition, V. harveyi produces a key siderophore called vibrioferrin. This important resource promotes the growth of V. rotiferianus, which cooccurs with V. harveyi in diseased oysters, and behaves as a cheater by benefiting from V. harveyi metabolite sharing. Our data show that cooperative behaviors contribute to synergy between bacterial and viral coinfecting partners. Additional cheating behaviors further shape the polymicrobial consortium. Controlling cooperative behaviors or countering their effects opens avenues for mitigating polymicrobial diseases.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Jubelin, Camille; Muñoz-Garcia, Javier; Cochonneau, Denis; Ollivier, Emilie; Vallette, François; Heymann, Marie-Françoise; Oliver, Lisa; Heymann, Dominique
Dans: Front Bioeng Biotechnol, vol. 11, p. 1260049, 2023, ISSN: 2296-4185.
@article{pmid37869710,
title = {Technical report: liquid overlay technique allows the generation of homogeneous osteosarcoma, glioblastoma, lung and prostate adenocarcinoma spheroids that can be used for drug cytotoxicity measurements},
author = {Camille Jubelin and Javier Muñoz-Garcia and Denis Cochonneau and Emilie Ollivier and François Vallette and Marie-Françoise Heymann and Lisa Oliver and Dominique Heymann},
url = { inserm-04501811v1 },
doi = {10.3389/fbioe.2023.1260049},
issn = {2296-4185},
year = {2023},
date = {2023-01-01},
urldate = {2023-01-01},
journal = {Front Bioeng Biotechnol},
volume = {11},
pages = {1260049},
abstract = { The mechanisms involved in cancer initiation, progression, drug resistance, and disease recurrence are traditionally investigated through adherent monolayer (2D) cell models. However, solid malignant tumor growth is characterized by progression in three dimensions (3D), and an increasing amount of evidence suggests that 3D culture models, such as spheroids, are suitable for mimicking cancer development. The aim of this report was to reaffirm the relevance of simpler 3D culture methods to produce highly reproducible spheroids, especially in the context of drug cytotoxicity measurements. Human A549 lung adenocarcinoma, LnCaP prostate adenocarcinoma, MNNG/HOS osteosarcoma and U251 glioblastoma cell lines were grown into spheroids for 20 days using either Liquid Overlay Technique (LOT) or Hanging Drop (HD) in various culture plates. Their morphology was examined by microscopy. Sensitivity to doxorubicin was compared between MNNG/HOS cells grown in 2D and 3D. For all cell lines studied, the morphology of spheroids generated in round-bottom multiwell plates was more repeatable than that of those generated in flat-bottom multiwell plates. HD had no significant advantage over LOT when the spheroids were cultured in round-bottom plates. Finally, the IC of doxorubicin on MNNG/HOS cultured in 3D was 18.8 times higher than in 2D cultures (3D IC = 15.07 ± 0.3 µM; 2D IC = 0.8 ± 0.4 µM; * < 0.05). In conclusion, we propose that the LOT method, despite and because of its simplicity, is a relevant 3D model for drug response measurements that could be scaled up for high throughput screening.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
and Claude Becker,; Berthomé, Richard; Delavault, Philippe; Flutre, Timothée; Fréville, Hélène; Gibot-Leclerc, Stéphanie; Corre, Valérie Le; Morel, Jean-Benoit; Moutier, Nathalie; Muños, Stéphane; Richard-Molard, Céline; Westwood, James; Courty, Pierre-Emmanuel; de Saint Germain, Alexandre; Louarn, Gaëtan; Roux, Fabrice
The ecologically relevant genetics of plant-plant interactions Article de journal
Dans: Trends Plant Sci, vol. 28, no. 1, p. 31–42, 2023, ISSN: 1878-4372.
@article{pmid36114125,
title = {The ecologically relevant genetics of plant-plant interactions},
author = { and Claude Becker and Richard Berthomé and Philippe Delavault and Timothée Flutre and Hélène Fréville and Stéphanie Gibot-Leclerc and Valérie Le Corre and Jean-Benoit Morel and Nathalie Moutier and Stéphane Muños and Céline Richard-Molard and James Westwood and Pierre-Emmanuel Courty and Alexandre de Saint Germain and Gaëtan Louarn and Fabrice Roux},
url = {hal-03800896v1 },
doi = {10.1016/j.tplants.2022.08.014},
issn = {1878-4372},
year = {2023},
date = {2023-01-01},
urldate = {2023-01-01},
journal = {Trends Plant Sci},
volume = {28},
number = {1},
pages = {31--42},
abstract = {Interactions among plants have been long recognized as a major force driving plant community dynamics and crop yield. Surprisingly, our knowledge of the ecological genetics associated with variation of plant-plant interactions remains limited. In this opinion article by scientists from complementary disciplines, the international PLANTCOM network identified four timely questions to foster a better understanding of the mechanisms mediating plant assemblages. We propose that by identifying the key relationships among phenotypic traits involved in plant-plant interactions and the underlying adaptive genetic and molecular pathways, while considering environmental fluctuations at diverse spatial and time scales, we can improve predictions of genotype-by-genotype-by-environment interactions and modeling of productive and stable plant assemblages in wild habitats and crop fields.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
35 publications
CHALOPIN, Antoine
2022.
@mastersthesis{chalopin2022,
title = {Caractérisation des cellules tumorales circulantes de sarcomes osseux : identification de nouveaux marqueurs de la pathologie recidivante},
author = {Antoine CHALOPIN},
url = {https://theses.hal.science/tel-03937416},
year = {2022},
date = {2022-12-20},
urldate = {2022-12-20},
keywords = {},
pubstate = {published},
tppubtype = {mastersthesis}
}
Martinez, Lisa; Pouvreau, Jean-Bernard; Montiel, Gregory; Jestin, Christophe; Delavault, Philippe; Simier, Philippe; Poulin, Lucie
Soil microbiota promotes early developmental stages of Phelipanche ramosa L. Pomel during plant parasitism on Brassica napus L. Article de journal
Dans: Plant and Soil, vol. 483, p. 667–691 , 2022.
@article{martinez2022soil,
title = {Soil microbiota promotes early developmental stages of Phelipanche ramosa L. Pomel during plant parasitism on Brassica napus L.},
author = {Lisa Martinez and Jean-Bernard Pouvreau and Gregory Montiel and Christophe Jestin and Philippe Delavault and Philippe Simier and Lucie Poulin},
url = {hal-04370677v1 },
doi = {https://doi.org/10.1007/s11104-022-05822-6},
year = {2022},
date = {2022-12-08},
urldate = {2022-12-08},
journal = {Plant and Soil},
volume = {483},
pages = {667–691 },
publisher = {Springer},
abstract = {Purpose
The root holoparasitic plant Phelipanche ramosa has become a major constraint for rapeseed cultivation in western France for the last decades and its control remains challenging. To date, few studies have considered soil microbiota as a third partner of the parasitic plant-plant interaction. Therefore, we here addressed the question of how soil microbiota interferes with host-derived signal metabolites required for host plant recognition by the parasitic plant.
Methods
Using a branched broomrape infested soil (genetic group 1) from a rapeseed field, we first provided soil physicochemical and microbiological descriptions by metabarcoding, followed by P. ramosa seed germination and prehaustorium formation bioassays, and by in vitro co-cultivation with Brassica napus.
Results
Co-cultivation in presence of soil microorganisms promoted parasitic plant seed germination and attachments to host’s roots. Seed germination assays showed that only the combination of gluconasturtiin (main rapeseed glucosinolate) with soil extracts stimulated broomrape germination. This suggests a microbial conversion of gluconasturtiin into germination stimulants via soil microbial myrosinase enzymes. Furthermore, soil bacteria Arthrobacter, Ralstonia, Actinobacterium, Proteobacterium spp. and fungus Penicillium spp. were isolated and screened for myrosinase activity. Pre-germinated seeds treated with soil extracts or differentially filtrated soil extracts also promoted the formation of P. ramosa prehaustorium and led to more parasitic attachments on rapeseed roots in co-cultivation assays. This thus suggests that this enhancement of parasitic attachments could also be partly attributed to soil microbial production of haustorium inducing factors.
Conclusion
Soil microbiota influences B. napus - P. ramosa interaction by altering direct and indirect recognition signals.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The root holoparasitic plant Phelipanche ramosa has become a major constraint for rapeseed cultivation in western France for the last decades and its control remains challenging. To date, few studies have considered soil microbiota as a third partner of the parasitic plant-plant interaction. Therefore, we here addressed the question of how soil microbiota interferes with host-derived signal metabolites required for host plant recognition by the parasitic plant.
Methods
Using a branched broomrape infested soil (genetic group 1) from a rapeseed field, we first provided soil physicochemical and microbiological descriptions by metabarcoding, followed by P. ramosa seed germination and prehaustorium formation bioassays, and by in vitro co-cultivation with Brassica napus.
Results
Co-cultivation in presence of soil microorganisms promoted parasitic plant seed germination and attachments to host’s roots. Seed germination assays showed that only the combination of gluconasturtiin (main rapeseed glucosinolate) with soil extracts stimulated broomrape germination. This suggests a microbial conversion of gluconasturtiin into germination stimulants via soil microbial myrosinase enzymes. Furthermore, soil bacteria Arthrobacter, Ralstonia, Actinobacterium, Proteobacterium spp. and fungus Penicillium spp. were isolated and screened for myrosinase activity. Pre-germinated seeds treated with soil extracts or differentially filtrated soil extracts also promoted the formation of P. ramosa prehaustorium and led to more parasitic attachments on rapeseed roots in co-cultivation assays. This thus suggests that this enhancement of parasitic attachments could also be partly attributed to soil microbial production of haustorium inducing factors.
Conclusion
Soil microbiota influences B. napus - P. ramosa interaction by altering direct and indirect recognition signals.
Joublin-Delavat, Aurélie; Touahri, Katia; Crétin, Pauline; Morot, Amandine; Rodrigues, Sophie; Jesus, Bruno; Trigodet, Florian; Delavat, François
Genetic and physiological insights into the diazotrophic activity of a non-cyanobacterial marine diazotroph Article de journal
Dans: Environmental Microbiology, vol. 24, no. 12, p. 6510–6523, 2022, ISSN: 1462-2912, 1462-2920.
@article{joublindelavat_genetic_2022,
title = {Genetic and physiological insights into the diazotrophic activity of a non-cyanobacterial marine diazotroph},
author = {Aurélie Joublin-Delavat and Katia Touahri and Pauline Crétin and Amandine Morot and Sophie Rodrigues and Bruno Jesus and Florian Trigodet and François Delavat},
url = {https://onlinelibrary.wiley.com/doi/10.1111/1462-2920.16261
hal-03993957v1 },
doi = {10.1111/1462-2920.16261},
issn = {1462-2912, 1462-2920},
year = {2022},
date = {2022-12-01},
urldate = {2022-12-01},
journal = {Environmental Microbiology},
volume = {24},
number = {12},
pages = {6510--6523},
abstract = {Nitrogen (N2) fixation, or diazotrophy, supports a large part of primary production in oceans. Culture-independent approaches highlighted the presence in abundance of marine non-cyanobacterial diazotrophs (NCD), but their ecophysiology remains elusive, mostly because of the low number of isolated NCD and because of the lack of available genetic tools for these isolates. Here, a dual genetic and functional approach allowed unveiling the ecophysiology of a marine NCD affiliated to the species Vibrio diazotrophicus. Physiological characterization of the first marine NCD mutant obtained so far was performed using a soft-gellan assay, demonstrating that a ΔnifH mutant is not able to grow in nitrogen-free media. Furthermore, we demonstrated that V. diazotrophicus produces a thick biofilm under diazotrophic conditions, suggesting biofilm production as an adaptive response of this NCD to cope with the inhibition of nitrogen fixation by molecular oxygen. Finally, the genomic signature of V. diazotrophicus is essentially absent from metagenomic data of Tara Ocean expeditions, despite having been isolated from various marine environments. We think that the genetically tractable V. diazotrophicus strain used in this study may serve as an ideal model to study the ecophysiology of these overlooked procaryotic group.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Beird, Hannah C; Bielack, Stefan S; Flanagan, Adrienne M; Gill, Jonathan; Heymann, Dominique; Janeway, Katherine A; Livingston, J Andrew; Roberts, Ryan D; Strauss, Sandra J; Gorlick, Richard
Osteosarcoma Article de journal
Dans: Nat Rev Dis Primers, vol. 8, no. 1, p. 77, 2022, ISSN: 2056-676X.
@article{pmid36481668,
title = {Osteosarcoma},
author = {Hannah C Beird and Stefan S Bielack and Adrienne M Flanagan and Jonathan Gill and Dominique Heymann and Katherine A Janeway and J Andrew Livingston and Ryan D Roberts and Sandra J Strauss and Richard Gorlick},
url = {inserm-04502548v1 },
doi = {10.1038/s41572-022-00409-y},
issn = {2056-676X},
year = {2022},
date = {2022-12-01},
urldate = {2022-12-01},
journal = {Nat Rev Dis Primers},
volume = {8},
number = {1},
pages = {77},
abstract = {Osteosarcoma is the most common primary malignant tumour of the bone. Osteosarcoma incidence is bimodal, peaking at 18 and 60 years of age, and is slightly more common in males. The key pathophysiological mechanism involves several possible genetic drivers of disease linked to bone formation, causing malignant progression and metastasis. While there have been significant improvements in the outcome of patients with localized disease, with event-free survival outcomes exceeding 60%, in patients with metastatic disease, event-free survival outcomes remain poor at less than 30%. The suspicion of osteosarcoma based on radiographs still requires pathological evaluation of a bone biopsy specimen for definitive diagnosis and CT imaging of the chest should be performed to identify lung nodules. So far, population-based screening and surveillance strategies have not been implemented due to the rarity of osteosarcoma and the lack of reliable markers. Current screening focuses only on groups at high risk such as patients with genetic cancer predisposition syndromes. Management of osteosarcoma requires a multidisciplinary team of paediatric and medical oncologists, orthopaedic and general surgeons, pathologists, radiologists and specialist nurses. Survivors of osteosarcoma require specialized medical follow-up, as curative treatment consisting of chemotherapy and surgery has long-term adverse effects, which also affect the quality of life of patients. The development of osteosarcoma model systems and related research as well as the evaluation of new treatment approaches are ongoing to improve disease outcomes, especially for patients with metastases.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Vincent Potiron Gaëlle Saade, Stéphane Supiot
Reduction of radiotoxicity by ultra-high dose rate protontherapy in zebrafish embryos Conférence
2022.
@conference{nokey,
title = {Reduction of radiotoxicity by ultra-high dose rate protontherapy in zebrafish embryos},
author = { Gaëlle Saade, Vincent Potiron, Stéphane Supiot },
url = {hal-03886413v1 },
year = {2022},
date = {2022-10-05},
urldate = {2022-10-05},
keywords = {},
pubstate = {published},
tppubtype = {conference}
}
Potiron, V; Delpon, G; Ollivier, L; Vaugier, L; Doré, M; Guimas, V; Rio, E; Thillays, F; Llagostera, C; Moignier, A; Josset, S; Chiavassa, S; Perennec, T; Supiot, S
[Clinical research in radiation oncology: how to move from the laboratory to the patient?] Article de journal
Dans: Cancer Radiother, vol. 26, no. 6-7, p. 808–813, 2022, ISSN: 1769-6658.
@article{pmid35999162b,
title = {[Clinical research in radiation oncology: how to move from the laboratory to the patient?]},
author = {V Potiron and G Delpon and L Ollivier and L Vaugier and M Doré and V Guimas and E Rio and F Thillays and C Llagostera and A Moignier and S Josset and S Chiavassa and T Perennec and S Supiot},
url = {hal-03777900v1 },
doi = {10.1016/j.canrad.2022.07.009},
issn = {1769-6658},
year = {2022},
date = {2022-10-01},
urldate = {2022-10-01},
journal = {Cancer Radiother},
volume = {26},
number = {6-7},
pages = {808--813},
abstract = {Translational research in radiation oncology is undergoing intense development. An increasingly rapid transfer is taking place from the laboratory to the patients, both in the selection of patients who can benefit from radiotherapy and in the development of innovative irradiation strategies or the development of combinations with drugs. Accelerating the passage of discoveries from the laboratory to the clinic represents the ideal of any translational research program but requires taking into account the multiple obstacles that can slow this progress. The ambition of the RadioTransNet network, a project to structure preclinical research in radiation oncology in France, is precisely to promote scientific and clinical interactions at the interface of radiotherapy and radiobiology, in its preclinical positioning, in order to identify priorities for strategic research dedicated to innovation in radiotherapy. The multidisciplinary radiotherapy teams with experts in biology, medicine, medical physics, mathematics and engineering sciences are able to meet these new challenges which will allow these advances to be made available to patients as quickly as possible.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Heymann, Clément J F; Bobin-Dubigeon, Christine; Muñoz-Garcia, Javier; Cochonneau, Denis; Ollivier, Emilie; Heymann, Marie-Françoise; Heymann, Dominique
Lipopolysaccharide-binding protein expression is associated to the metastatic status of osteosarcoma patients Article de journal
Dans: J Bone Oncol, vol. 36, p. 100451, 2022, ISSN: 2212-1366.
@article{pmid35990515,
title = {Lipopolysaccharide-binding protein expression is associated to the metastatic status of osteosarcoma patients},
author = {Clément J F Heymann and Christine Bobin-Dubigeon and Javier Muñoz-Garcia and Denis Cochonneau and Emilie Ollivier and Marie-Françoise Heymann and Dominique Heymann},
url = {inserm-03746641v1 },
doi = {10.1016/j.jbo.2022.100451},
issn = {2212-1366},
year = {2022},
date = {2022-10-01},
urldate = {2022-10-01},
journal = {J Bone Oncol},
volume = {36},
pages = {100451},
abstract = {Osteosarcoma (OS) is a rare malignant primary bone tumours characterized by a high genetic and cell composition heterogeneity. Unfortunately, despite the use of drug combinations and the recent development of immunotherapies, the overall survival has not improved in the last four decades. Due to the key role of the tumour microenvironment in the pathogenesis of OS, a better understanding of its microenvironment is mandatory to develop new therapeutic approaches. From retrospective biological cohorts of OS, we analysed by immunohistochemistry the presence of lipopolysaccharide (LPS)-binding protein (LBP) in diagnostic biopsies with local disease and compared their level of infiltration to patients suffering from metastatic status. LBP is considered as a marker of LPS exposure and can indirectly reflect the presence of Gram-negative microbiota. LBP were detected in the cytoplasm of OS cells as well as in tumour-associated macrophage. Tumour samples of patients with local disease were significantly enriched in LBP compared to tumour tissues of patients with metastatic status. Lung metastatic tissues showed similar level of LBP compared to paired primary tumours. Overall, this study strongly suggests the presence of Gram-negative bacteria in OS tissues and demonstrated their significant differential level according the metastatic status. This tumour-associated microbiome may help in the conceptualisation of new therapeutic approach to trigger efficient therapeutic responses against cancer.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Léost, Françoise; Delpon, Grégory; Garcion, Emmanuel; Gestin, Jean-François; Hatt, Mathieu; Potiron, Vincent; Rbah-Vidal, Latifa; Supiot, Stéphane
vol. 109, no. 10, 2022, ISSN: 1769-6917.
@proceedings{pmid35908990,
title = {Adaptation of the tumour and its ecosystem to radiotherapies: Mechanisms, imaging and therapeutic approaches » XIVe édition du workshop organisé par le réseau « Vectorisation, Imagerie, Radiothérapies » du Cancéropôle Grand-Ouest, 22–25 septembre 2021, Le Bono, France},
author = {Françoise Léost and Grégory Delpon and Emmanuel Garcion and Jean-François Gestin and Mathieu Hatt and Vincent Potiron and Latifa Rbah-Vidal and Stéphane Supiot},
url = {hal-04511672v1 },
doi = {10.1016/j.bulcan.2022.06.005},
issn = {1769-6917},
year = {2022},
date = {2022-10-01},
urldate = {2022-10-01},
journal = {Bull Cancer},
volume = {109},
number = {10},
pages = {1088--1093},
abstract = {The fourteenth edition of the workshop covered the latest advances in internal and external radiotherapy obtained through a better understanding of the adaptive capacity of the tumor and its microenvironment, from different disciplinary angles, chemistry, biology, physics, and medicine, paving the way for numerous technological innovations. The biological aspects and the contribution of imaging in monitoring and understanding the adaptation of tumors to radiotherapy were presented, before focusing on innovative radiotherapy strategies and machine learning and data-driven techniques. Finally, the challenges were explored in the radiobiology of targeted radionuclide therapy as well as data science and machine learning in radiomics.},
keywords = {},
pubstate = {published},
tppubtype = {proceedings}
}
Guillaume Blain Giovanna Rosa Fois, Sophie Chiavassa
Microdosimetry and radiolytic species production in UHDR proton beam using GATE and Geant4-DNA Conférence
2022.
@conference{nokey,
title = {Microdosimetry and radiolytic species production in UHDR proton beam using GATE and Geant4-DNA},
author = {Giovanna Rosa Fois, Guillaume Blain, Sophie Chiavassa, Grégory Delpon, Manon Evin, Vincent Fiegel , Mohammad Ghalei , Ferid Haddad , S. Incerti , Charbel Koumeir, Vincent Métivier , Quentin Mouchard , Freddy Poirier , Vincent Potiron , Noël Servagent, Stéphane Supiot, Hoang Ngoc Tran , Johan Vandenborre , Lydia Maigne },
url = {hal-03886937v1 },
year = {2022},
date = {2022-10-01},
urldate = {2022-10-01},
keywords = {},
pubstate = {published},
tppubtype = {conference}
}
Rodríguez-Pena, Alejandro; Armendariz, Estibaliz; Oyarbide, Alvaro; Morales, Xabier; Ortiz-Espinosa, Sergio; de Córdoba, Borja Ruiz-Fernández; Cochonneau, Denis; Cornago, Iñaki; Heymann, Dominique; Argemi, Josepmaría; D'Avola, Delia; Sangro, Bruno; Lecanda, Fernando; Pio, Ruben; Cortés-Domínguez, Iván; Ortiz-de-Solórzano, Carlos
Design and validation of a tunable inertial microfluidic system for the efficient enrichment of circulating tumor cells in blood Article de journal
Dans: Bioeng Transl Med, vol. 7, no. 3, p. e10331, 2022, ISSN: 2380-6761.
@article{pmid36176621,
title = {Design and validation of a tunable inertial microfluidic system for the efficient enrichment of circulating tumor cells in blood},
author = {Alejandro Rodríguez-Pena and Estibaliz Armendariz and Alvaro Oyarbide and Xabier Morales and Sergio Ortiz-Espinosa and Borja Ruiz-Fernández de Córdoba and Denis Cochonneau and Iñaki Cornago and Dominique Heymann and Josepmaría Argemi and Delia D'Avola and Bruno Sangro and Fernando Lecanda and Ruben Pio and Iván Cortés-Domínguez and Carlos Ortiz-de-Solórzano},
url = {inserm-03659450v1 },
doi = {10.1002/btm2.10331},
issn = {2380-6761},
year = {2022},
date = {2022-09-01},
urldate = {2022-09-01},
journal = {Bioeng Transl Med},
volume = {7},
number = {3},
pages = {e10331},
abstract = {The analysis of circulating tumor cells (CTCs) in blood is a powerful noninvasive alternative to conventional tumor biopsy. Inertial-based separation is a promising high-throughput, marker-free sorting strategy for the enrichment and isolation of CTCs. Here, we present and validate a double spiral microfluidic device that efficiently isolates CTCs with a fine-tunable cut-off value of 9 μm and a separation range of 2 μm. We designed the device based on computer simulations that introduce a novel, customized inertial force term, and provide practical fabrication guidelines. We validated the device using calibration beads, which allowed us to refine the simulations and redesign the device. Then we validated the redesigned device using blood samples and a murine model of metastatic breast cancer. Finally, as a proof of principle, we tested the device using peripheral blood from a patient with hepatocellular carcinoma, isolating more than 17 CTCs/ml, with purity/removal values of 96.03% and 99.99% of white blood cell and red blood cells, respectively. These results confirm highly efficient CTC isolation with a stringent cut-off value and better separation results than the state of the art.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Jubelin, Camille; Muñoz-Garcia, Javier; Griscom, Laurent; Cochonneau, Denis; Ollivier, Emilie; Heymann, Marie-Françoise; Vallette, François M; Oliver, Lisa; Heymann, Dominique
Three-dimensional in vitro culture models in oncology research Article de journal
Dans: Cell Biosci, vol. 12, no. 1, p. 155, 2022, ISSN: 2045-3701.
@article{pmid36089610,
title = {Three-dimensional in vitro culture models in oncology research},
author = {Camille Jubelin and Javier Muñoz-Garcia and Laurent Griscom and Denis Cochonneau and Emilie Ollivier and Marie-Françoise Heymann and François M Vallette and Lisa Oliver and Dominique Heymann},
url = { hal-03798394v1 },
doi = {10.1186/s13578-022-00887-3},
issn = {2045-3701},
year = {2022},
date = {2022-09-01},
urldate = {2022-09-01},
journal = {Cell Biosci},
volume = {12},
number = {1},
pages = {155},
abstract = {Cancer is a multifactorial disease that is responsible for 10 million deaths per year. The intra- and inter-heterogeneity of malignant tumors make it difficult to develop single targeted approaches. Similarly, their diversity requires various models to investigate the mechanisms involved in cancer initiation, progression, drug resistance and recurrence. Of the in vitro cell-based models, monolayer adherent (also known as 2D culture) cell cultures have been used for the longest time. However, it appears that they are often less appropriate than the three-dimensional (3D) cell culture approach for mimicking the biological behavior of tumor cells, in particular the mechanisms leading to therapeutic escape and drug resistance. Multicellular tumor spheroids are widely used to study cancers in 3D, and can be generated by a multiplicity of techniques, such as liquid-based and scaffold-based 3D cultures, microfluidics and bioprinting. Organoids are more complex 3D models than multicellular tumor spheroids because they are generated from stem cells isolated from patients and are considered as powerful tools to reproduce the disease development in vitro. The present review provides an overview of the various 3D culture models that have been set up to study cancer development and drug response. The advantages of 3D models compared to 2D cell cultures, the constraint, and the fields of application of these models and their techniques of production are also discussed.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Chandola, Udita; Trottier, Camille; Gaudin, Marinna; Manirakiza, Erik; Menicot, Samuel; Louvet, Isabelle; Lacour, Thomas; Chaumier, Timothée; Tanaka, Atsuko; Chaffron, Samuel; Tirichine, Leila
Combined in vivo and in situ genome-resolved metagenomics reveals novel symbiotic nitrogen fixing interactions between non-cyanobacterial diazotrophs and microalgae Article de journal À paraître
Dans: bioRxiv, À paraître.
@article{Chandola2022.08.25.505241,
title = {Combined in vivo and in situ genome-resolved metagenomics reveals novel symbiotic nitrogen fixing interactions between non-cyanobacterial diazotrophs and microalgae},
author = {Udita Chandola and Camille Trottier and Marinna Gaudin and Erik Manirakiza and Samuel Menicot and Isabelle Louvet and Thomas Lacour and Timothée Chaumier and Atsuko Tanaka and Samuel Chaffron and Leila Tirichine},
url = {https://www.biorxiv.org/content/early/2022/08/25/2022.08.25.505241},
doi = {10.1101/2022.08.25.505241},
year = {2022},
date = {2022-08-25},
urldate = {2022-08-25},
journal = {bioRxiv},
publisher = {Cold Spring Harbor Laboratory},
abstract = {Non-cyanobacteria diazotrophs (NCDs) were shown to dominate in surface waters shifting the long-held paradigm of cyanobacteria dominance and raising fundamental questions on how these putative heterotrophic bacteria thrive in sunlit oceans. Here, we report an unprecedented finding in the widely used model diatom Phaeodactylum triconrnutum (Pt) of NCDs sustaining diatom cells in the absence of bioavailable nitrogen. We identified PtNCDs using metagenomics sequencing and detected nitrogenase gene in silico and/or by PCR. We demonstrated nitrogen fixation in PtNCDs and their close genetic affiliation with NCDs from the environment. We showed the wide occurrence of this type of symbiosis with the isolation of NCDs from other microalgae and their identification in the environment and in co-occurrence with photosynthetic microalgae. Overall, this study provides evidence for a previously overlooked symbiosis using a multidisciplinary model-based approach which will consequently help understand the different players driving global marine nitrogen fixation.Competing Interest StatementThe authors have declared no competing interest.},
keywords = {},
pubstate = {forthcoming},
tppubtype = {article}
}
Wu, Yue; Timothée, Chaumier; Manirakiza, Eric; Veluchamy, Alaguraj; Tirichine, Leila
PhaeoEpiView: An epigenome browser of the newly assembled genome of the model diatom Phaeodactylum tricornutum Article de journal À paraître
Dans: bioRxiv, À paraître.
@article{Wu2022.07.29.502047,
title = {PhaeoEpiView: An epigenome browser of the newly assembled genome of the model diatom Phaeodactylum tricornutum},
author = {Yue Wu and Chaumier Timothée and Eric Manirakiza and Alaguraj Veluchamy and Leila Tirichine},
url = {https://www.biorxiv.org/content/early/2022/08/01/2022.07.29.502047},
doi = {10.1101/2022.07.29.502047},
year = {2022},
date = {2022-08-01},
urldate = {2022-01-01},
journal = {bioRxiv},
publisher = {Cold Spring Harbor Laboratory},
abstract = {Motivation Recent advances in DNA sequencing technologies in particular of long reads type greatly improved genomes assembly leading to discrepancies between both published annotations and epigenome tracks which did not keep pace with new assemblies. This comprises the availability of accurate resources which penalizes the progress in research.Results Here, we used the latest improved telomere to telomere assembly of the model pennate diatom Phaeodactylum tricornutum to lift over the gene models from Phatr3, a previously annotated reference genome. We used the lifted genome annotation including genes and transposable elements to map the epigenome landscape, namely DNA methylation and post translational modifications of histones providing the community with PhaeoEpiView, a browser that allows the visualization of epigenome data as well as transcripts on an updated reference genome to better understand the biological significance of the mapped data on contiguous genome rather than a fragmented one. We updated previously published histone marks with a more accurate mapping using monoclonal antibodies instead of polyclonal and deeper sequencing. PhaeoEpiView will be continuously updated with the newly published epigenomic data making it the largest and richest epigenome browser of any stramenopile. We expect that PhaeoEpiView will be a standard tool for the coming era of molecular environmental studies where epigenetics holds a place of choice.Availability PhaeoEpiView is available at: https://PhaeoEpiView.univ-nantes.frCompeting Interest StatementThe authors have declared no competing interest.},
keywords = {},
pubstate = {forthcoming},
tppubtype = {article}
}
Ollivier, Luc; Orione, Charles; Bore, Paul; Misery, Laurent; Legoupil, Delphine; Leclere, Jean-Christophe; Coste, Anne; Girault, Gilles; Sicard-Cras, Iona; Kacperek, Clemence; Lucia, Francois; Stefan, Dinu; Thillays, François; Rio, Emmanuel; Lesueur, Paul; Berthou, Christian; Heymann, Dominique; Champiat, Stéphane; Supiot, Stéphane; Vaugier, Loig; Kao, William
Abscopal Response in Metastatic Melanoma: Real-World Data of a Retrospective, Multicenter Study Article de journal
Dans: Cancers (Basel), vol. 14, no. 17, 2022, ISSN: 2072-6694.
@article{pmid36077747,
title = {Abscopal Response in Metastatic Melanoma: Real-World Data of a Retrospective, Multicenter Study},
author = {Luc Ollivier and Charles Orione and Paul Bore and Laurent Misery and Delphine Legoupil and Jean-Christophe Leclere and Anne Coste and Gilles Girault and Iona Sicard-Cras and Clemence Kacperek and Francois Lucia and Dinu Stefan and François Thillays and Emmanuel Rio and Paul Lesueur and Christian Berthou and Dominique Heymann and Stéphane Champiat and Stéphane Supiot and Loig Vaugier and William Kao},
url = {inserm-03878079v1 },
doi = {10.3390/cancers14174213},
issn = {2072-6694},
year = {2022},
date = {2022-08-01},
urldate = {2022-08-01},
journal = {Cancers (Basel)},
volume = {14},
number = {17},
abstract = {OBJECTIVE: To evaluate the incidence of the abscopal response (AR) in patients with metastatic melanoma requiring palliative radiotherapy (RT).
PATIENTS AND METHODS: Patients treated for metastatic melanoma between January 1998 and February 2020 in four oncology departments were screened. Patients with progression under immune checkpoint inhibitors or without ongoing systemic treatment, and requiring palliative RT were considered. The AR was defined as an objective response according to RECIST and/or iRECIST for at least one non-irradiated metastasis at distance (≥10 cm) from the irradiated lesion. Primary endpoint was the rate of AR. Secondary endpoints were overall survival (OS), progression-free survival (PFS), local control (LC) of the irradiated lesion, and toxicity as assessed by CTCAE v5.
RESULTS: Over the period considered, 118 patients were included and analyzed. Fifteen patients (12.7%) had an AR. With a median follow-up of 7.7 months (range, 0.2-242.2), median OS and PFS after RT were significantly longer in patients with an AR compared to those without: 28 vs. 6.6 months ( < 0.01) and not reached vs. .2 months, respectively. No grade ≥2 toxicity was reported. Patients who developed an AR were more likely to be treated with immunotherapy (93.3% vs. 55.9%, 0.02). In multivariate analysis, they had a higher number of irradiated metastases treated concomitantly (HR = 16.9, < 0.01) and a higher rate of mild infections during RT (HR = 403.5, < 0.01).
CONCLUSIONS: AR in metastatic melanoma seems to be highly prognostic of overall survival, although it is a rare phenomenon. It may be promoted by multiple concomitant treatments with RT and immunotherapy and by acute inflammatory events such as infection.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
PATIENTS AND METHODS: Patients treated for metastatic melanoma between January 1998 and February 2020 in four oncology departments were screened. Patients with progression under immune checkpoint inhibitors or without ongoing systemic treatment, and requiring palliative RT were considered. The AR was defined as an objective response according to RECIST and/or iRECIST for at least one non-irradiated metastasis at distance (≥10 cm) from the irradiated lesion. Primary endpoint was the rate of AR. Secondary endpoints were overall survival (OS), progression-free survival (PFS), local control (LC) of the irradiated lesion, and toxicity as assessed by CTCAE v5.
RESULTS: Over the period considered, 118 patients were included and analyzed. Fifteen patients (12.7%) had an AR. With a median follow-up of 7.7 months (range, 0.2-242.2), median OS and PFS after RT were significantly longer in patients with an AR compared to those without: 28 vs. 6.6 months ( < 0.01) and not reached vs. .2 months, respectively. No grade ≥2 toxicity was reported. Patients who developed an AR were more likely to be treated with immunotherapy (93.3% vs. 55.9%, 0.02). In multivariate analysis, they had a higher number of irradiated metastases treated concomitantly (HR = 16.9, < 0.01) and a higher rate of mild infections during RT (HR = 403.5, < 0.01).
CONCLUSIONS: AR in metastatic melanoma seems to be highly prognostic of overall survival, although it is a rare phenomenon. It may be promoted by multiple concomitant treatments with RT and immunotherapy and by acute inflammatory events such as infection.
Fornier, Suzanne Daignan; de Saint Germain, Alexandre; Retailleau, Pascal; Pillot, Jean-Paul; Taulera, Quentin; Andna, Lucile; Miesch, Laurence; Rochange, Soizic; Pouvreau, Jean-Bernard; Boyer, François-Didier
Noncanonical Strigolactone Analogues Highlight Selectivity for Stimulating Germination in Two Populations Article de journal
Dans: J Nat Prod, vol. 85, no. 8, p. 1976–1992, 2022, ISSN: 1520-6025.
@article{pmid35776904,
title = {Noncanonical Strigolactone Analogues Highlight Selectivity for Stimulating Germination in Two Populations},
author = {Suzanne Daignan Fornier and Alexandre de Saint Germain and Pascal Retailleau and Jean-Paul Pillot and Quentin Taulera and Lucile Andna and Laurence Miesch and Soizic Rochange and Jean-Bernard Pouvreau and François-Didier Boyer},
url = {hal-03712428v1 },
doi = {10.1021/acs.jnatprod.2c00282},
issn = {1520-6025},
year = {2022},
date = {2022-08-01},
urldate = {2022-08-01},
journal = {J Nat Prod},
volume = {85},
number = {8},
pages = {1976--1992},
abstract = {Strigolactones (SLs) are plant hormones exuded in the rhizosphere with a signaling role for the development of arbuscular mycorrhizal (AM) fungi and as stimulants of seed germination of the parasitic weeds , , and , the most threatening weeds of major crops worldwide. is present mainly on rape, hemp, and tobacco in France. 2a preferentially attacks hemp, while 1 attacks rapeseed. The recently isolated cannalactone () from hemp root exudates has been characterized as a noncanonical SL that selectively stimulates the germination of 2a seeds in comparison with 1. In the present work, (-)-solanacol (), a canonical orobanchol-type SL exuded by tobacco and tomato, was established to possess a remarkable selective germination stimulant activity for 2a seeds. Two cannalactone analogues, named (±)-SdL19 and (±)-SdL118, have been synthesized. They have an unsaturated acyclic carbon chain with a tertiary hydroxy group and a methyl or a cyclopropyl group instead of a cyclohexane A-ring, respectively. (±)-SdL analogues are able to selectively stimulate 2a, revealing that these minimal structural elements are key for this selective bioactivity. In addition, (±)-SdL19 is able to inhibit shoot branching in and and induces hyphal branching in the AM fungus , like SLs.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Lapaillerie, Delphine; Charlier, Cathy; Guyonnet-Dupérat, Véronique; Murigneux, Emilie; Fernandes, Henrique S.; Martins, Fábio G.; Magalhães, Rita P.; Vieira, Tatiana F.; Richetta, Clémence; Subra, Frédéric; Lebourgeois, Samuel; Charpentier, Charlotte; Descamps, Diane; Visseaux, Benoît; Weigel, Pierre; Favereaux, Alexandre; Beauvineau, Claire; Buron, Frédéric; Teulade-Fichou, Marie-Paule; Routier, Sylvain; Gallois-Montbrun, Sarah; Meertens, Laurent; Delelis, Olivier; Sousa, Sérgio F.; Parissi, Vincent
Selection of Bis-Indolyl Pyridines and Triphenylamines as New Inhibitors of SARS-CoV-2 Cellular Entry by Modulating the Spike Protein/ACE2 Interfaces Article de journal
Dans: Antimicrobial Agents and Chemotherapy, vol. 0, no. 0, p. e00083-22, 2022.
@article{doi:10.1128/aac.00083-22,
title = {Selection of Bis-Indolyl Pyridines and Triphenylamines as New Inhibitors of SARS-CoV-2 Cellular Entry by Modulating the Spike Protein/ACE2 Interfaces},
author = {Delphine Lapaillerie and Cathy Charlier and Véronique Guyonnet-Dupérat and Emilie Murigneux and Henrique S. Fernandes and Fábio G. Martins and Rita P. Magalhães and Tatiana F. Vieira and Clémence Richetta and Frédéric Subra and Samuel Lebourgeois and Charlotte Charpentier and Diane Descamps and Benoît Visseaux and Pierre Weigel and Alexandre Favereaux and Claire Beauvineau and Frédéric Buron and Marie-Paule Teulade-Fichou and Sylvain Routier and Sarah Gallois-Montbrun and Laurent Meertens and Olivier Delelis and Sérgio F. Sousa and Vincent Parissi},
url = {https://journals.asm.org/doi/abs/10.1128/aac.00083-22
hal-03826873v1 },
doi = {10.1128/aac.00083-22},
year = {2022},
date = {2022-07-05},
urldate = {2022-07-05},
journal = {Antimicrobial Agents and Chemotherapy},
volume = {0},
number = {0},
pages = {e00083-22},
abstract = {Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the infectious agent that has caused the current coronavirus disease (COVID) pandemic. Viral infection relies on the viral S (spike) protein/cellular receptor ACE2 interaction. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the infectious agent that has caused the current coronavirus disease (COVID) pandemic. Viral infection relies on the viral S (spike) protein/cellular receptor ACE2 interaction. Disrupting this interaction would lead to early blockage of viral replication. To identify chemical tools to further study these functional interfaces, 139,146 compounds from different chemical libraries were screened through an S/ACE2 in silico virtual molecular model. The best compounds were selected for further characterization using both cellular and biochemical approaches, reiterating SARS-CoV-2 entry and the S/ACE2 interaction. We report here two selected hits, bis-indolyl pyridine AB-00011778 and triphenylamine AB-00047476. Both of these compounds can block the infectivity of lentiviral vectors pseudotyped with the SARS-CoV-2 S protein as well as wild-type and circulating variant SARS-CoV-2 strains in various human cell lines, including pulmonary cells naturally susceptible to infection. AlphaLISA and biolayer interferometry confirmed a direct inhibitory effect of these drugs on the S/ACE2 association. A specific study of the AB-00011778 inhibitory properties showed that this drug inhibits viral replication with a 50% effective concentration (EC50) between 0.1 and 0.5 μM depending on the cell lines. Molecular docking calculations of the interaction parameters of the molecules within the S/ACE2 complex from both wild-type and circulating variants of the virus showed that the molecules may target multiple sites within the S/ACE2 interface. Our work indicates that AB-00011778 constitutes a good tool for modulating this interface and a strong lead compound for further therapeutic purposes.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Bertorelle, Franck; Wegner, K David; Bakulić, Martina Perić; Fakhouri, Hussein; Comby-Zerbino, Clothilde; Sagar, Amin; Bernadó, Pau; Resch-Genger, Ute; Bonačić-Koutecký, Vlasta; Guével, Xavier Le; Antoine, Rodolphe
Tailoring the NIR-II Photoluminescence of Single Thiolated Au Nanoclusters by Selective Binding to Proteins Article de journal
Dans: Chemistry, vol. 28, no. 39, p. e202200570, 2022, ISSN: 1521-3765.
@article{pmid35703399,
title = {Tailoring the NIR-II Photoluminescence of Single Thiolated Au Nanoclusters by Selective Binding to Proteins},
author = {Franck Bertorelle and K David Wegner and Martina Perić Bakulić and Hussein Fakhouri and Clothilde Comby-Zerbino and Amin Sagar and Pau Bernadó and Ute Resch-Genger and Vlasta Bonačić-Koutecký and Xavier Le Guével and Rodolphe Antoine},
url = {hal-03740182v1 },
doi = {10.1002/chem.202200570},
issn = {1521-3765},
year = {2022},
date = {2022-07-01},
urldate = {2022-07-01},
journal = {Chemistry},
volume = {28},
number = {39},
pages = {e202200570},
abstract = {Atomically precise gold nanoclusters are a fascinating class of nanomaterials that exhibit molecule-like properties and have outstanding photoluminescence (PL). Their ultrasmall size, molecular chemistry, and biocompatibility make them extremely appealing for selective biomolecule labeling in investigations of biological mechanisms at the cellular and anatomical levels. In this work, we report a simple route to incorporate a preformed Au nanocluster into a model bovine serum albumin (BSA) protein. A new approach combining small-angle X-ray scattering and molecular modeling provides a clear localization of a single Au within the protein to a cysteine residue on the gold nanocluster surface. Attaching Au to BSA strikingly modifies the PL properties with enhancement and a redshift in the second near-infrared (NIR-II) window. This study paves the way to conrol the design of selective sensitive probes in biomolecules through a ligand-based strategy to enable the optical detection of biomolecules in a cellular environment by live imaging.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Sulser, Sandra; Vucicevic, Andrea; Bellini, Veronica; Moritz, Roxane; Delavat, François; Sentchilo, Vladimir; Carraro, Nicolas; van der Meer, Jan Roelof
A bistable prokaryotic differentiation system underlying development of conjugative transfer competence Article de journal
Dans: Plos Genetics, vol. 18, iss. 6, p. e1010286, 2022.
@article{doi.org/10.1371/journal.pgen.1010286,
title = {A bistable prokaryotic differentiation system underlying development of conjugative transfer competence},
author = {Sandra Sulser and Andrea Vucicevic and Veronica Bellini and Roxane Moritz and François Delavat and Vladimir Sentchilo and Nicolas Carraro and Jan Roelof van der Meer},
url = {hal-04202182v1 },
doi = {10.1371/journal.pgen.1010286},
year = {2022},
date = {2022-06-28},
urldate = {2022-06-28},
journal = {Plos Genetics},
volume = {18},
issue = {6},
pages = {e1010286},
abstract = {The mechanisms and impact of horizontal gene transfer processes to distribute gene functions with potential adaptive benefit among prokaryotes have been well documented. In contrast, little is known about the life-style of mobile elements mediating horizontal gene transfer, whereas this is the ultimate determinant for their transfer fitness. Here, we investigate the life-style of an integrative and conjugative element (ICE) within the genus Pseudomonas that is a model for a widespread family transmitting genes for xenobiotic compound metabolism and antibiotic resistances. Previous work showed bimodal ICE activation, but by using single cell time-lapse microscopy coupled to combinations of chromosomally integrated single copy ICE promoter-driven fluorescence reporters, RNA sequencing and mutant analysis, we now describe the complete regulon leading to the arisal of differentiated dedicated transfer competent cells. The regulon encompasses at least three regulatory nodes and five (possibly six) further conserved gene clusters on the ICE that all become expressed under stationary phase conditions. Time-lapse microscopy indicated expression of two regulatory nodes (i.e., bisR and alpA-bisDC) to precede that of the other clusters. Notably, expression of all clusters except of bisR was confined to the same cell subpopulation, and was dependent on the same key ICE regulatory factors. The ICE thus only transfers from a small fraction of cells in a population, with an estimated proportion of between 1.7-4%, which express various components of a dedicated transfer competence program imposed by the ICE, and form the centerpiece of ICE conjugation. The components mediating transfer competence are widely conserved, underscoring their selected fitness for efficient transfer of this class of mobile elements.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Jubelin, Camille; Cochonneau, Denis; Moranton, Emilie; Munoz-Garcia, Javier; Heymann, Dominique
Circulating Tumor Cells and ctDNA in Sarcomas Chapitre d'ouvrage
Dans: Leong, Stanley P.; Nathanson, S. David; Zager, Jonathan S. (Ed.): Cancer Metastasis Through the Lymphovascular System, p. 121–128, Springer, 2022.
@inbook{jubelin2022circulating,
title = {Circulating Tumor Cells and ctDNA in Sarcomas},
author = {Camille Jubelin and Denis Cochonneau and Emilie Moranton and Javier Munoz-Garcia and Dominique Heymann},
editor = {Stanley P. Leong and S. David Nathanson and Jonathan S. Zager},
doi = {10.1007/978-3-030-93084-4_12},
year = {2022},
date = {2022-06-25},
urldate = {2022-06-25},
booktitle = {Cancer Metastasis Through the Lymphovascular System},
pages = {121--128},
publisher = {Springer},
abstract = {Sarcomas are clustered in two oncological entities named bone and soft tissue sarcomas. Both are rare cancers originating from the mesenchyme, characterized by their propensity to induce the development of lung metastases. Sarcoma cells escaping from the primary tumor site spread to the pulmonary tissue through the bloodstream where they found a favorable microenvironment to establish metastatic foci. The low number of patients, the high histological, genetic, and molecular heterogeneity of sarcomas combined with the absence of specific markers expressed by cancer cells make the detection and follow-up of the minimal residual disease challenging. Over the last decade, tremendous technological progress has been made towards the detection of recurrent diseases. The literature is now enriched of information describing the use of liquid biopsies in clinical care of sarcoma patients. This chapter aims to give a brief overview of the most recent data available on the detection of circulating tumor cells and circulating tumor DNA in sarcomas.},
keywords = {},
pubstate = {published},
tppubtype = {inbook}
}
Guillaume Blain Vincent Fiegel, Manon Evin
2022.
@conference{nokey,
title = {Hydrogen peroxide formation to investigate the radiolytic ROS production mechanism under proton FLASH conditions},
author = { Vincent Fiegel , Guillaume Blain , Manon Evin , Quentin Mouchard , Charbel Koumeir, Noël Servagent , Mohammad Ghalei , Giovanna Rosa Fois , Vincent Métivier, Freddy Poirier , Vincent Potiron , Stéphane Supiot , Ferid Haddad , Grégory Delpon , Sophie Chiavassa , Johan Vandenborre , Lydia Maigne },
url = { hal-03963165v1 },
year = {2022},
date = {2022-06-15},
urldate = {2022-06-15},
keywords = {},
pubstate = {published},
tppubtype = {conference}
}
Schimith, Lucia E; Santos, Michele G Dos; Arbo, Bruno D; André-Miral, Corinne; Muccillo-Baisch, Ana L; Hort, Mariana A
Polydatin as a therapeutic alternative for central nervous system disorders: A systematic review of animal studies Article de journal
Dans: Phytotherapy Research, vol. 36, no. 7, p. 2852–2877, 2022.
@article{schimith2022polydatin,
title = {Polydatin as a therapeutic alternative for central nervous system disorders: A systematic review of animal studies},
author = {Lucia E Schimith and Michele G Dos Santos and Bruno D Arbo and Corinne André-Miral and Ana L Muccillo-Baisch and Mariana A Hort},
url = {https://onlinelibrary.wiley.com/doi/10.1002/ptr.7497},
doi = {10.1002/ptr.7497},
year = {2022},
date = {2022-05-25},
urldate = {2022-05-25},
journal = {Phytotherapy Research},
volume = {36},
number = {7},
pages = {2852--2877},
publisher = {Wiley Online Library},
abstract = {Polydatin, or piceid, is a natural stilbene found in grapes, peanuts, and wines. Polydatin presents pharmacological activities, including neuroprotective properties, exerting preventive and/or therapeutic effects in central nervous system (CNS) disorders. In the present study, we summarize and discuss the neuroprotective effects of polydatin in CNS disorders and related pathological conditions in preclinical animal studies. A systematic review was performed by searching online databases, returning a total of 110 records, where 27 articles were selected and discussed here. The included studies showed neuroprotective effects of polydatin in experimental models of neurological disorders, including cerebrovascular disorders, Parkinson's disease, traumatic brain injuries, diabetic neuropathy, glioblastoma, and neurotoxicity induced by chemical agents. Most studies were focused on stroke (22.2%) and conducted in male rodents. The intervention protocol with polydatin was mainly acute (66.7%), with postdamage induction treatment being the most commonly used regimen (55.2%). Overall, polydatin ameliorated behavioral dysfunctions and/or promoted neurological function by virtue of its antioxidant and antiinflammatory properties. In summary, this review offers important scientific evidence for the neuroprotective effects and distinct pharmacological mechanisms of polydatin that not only enhances the present understanding but is also useful for the development of future preclinical and clinical investigations.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Zhao, Xue; Hoguin, Antoine; Chaumier, Timothée; Tirichine, Leila
Epigenetic Control of Diatom Genomes: An Overview from In Silico Characterization to Functional Studies Chapitre d'ouvrage
Dans: Falciatore, Angela; Mock, Thomas (Ed.): The Molecular Life of Diatoms, p. 179–202, Springer International Publishing, Cham, 2022, ISBN: 978-3-030-92499-7.
@inbook{Zhao2022,
title = {Epigenetic Control of Diatom Genomes: An Overview from In Silico Characterization to Functional Studies},
author = {Xue Zhao and Antoine Hoguin and Timothée Chaumier and Leila Tirichine},
editor = {Angela Falciatore and Thomas Mock},
url = {https://doi.org/10.1007/978-3-030-92499-7_7},
doi = {10.1007/978-3-030-92499-7_7},
isbn = {978-3-030-92499-7},
year = {2022},
date = {2022-05-12},
urldate = {2022-01-01},
booktitle = {The Molecular Life of Diatoms},
pages = {179--202},
publisher = {Springer International Publishing},
address = {Cham},
abstract = {Epigenetics and its role in genome regulation is one of the most exciting areas of modern science. After a brief history of epigenetics and an introduction to the molecular basics of this discipline of science, this chapter describes the current knowledge of epigenetic components in diatoms, namely writers and erasers of DNA methylation and histone modifications. With a particular focus on the model pennate diatom Phaeodactylum tricornutum, we describe our current understanding of the contribution of few epigenetic factors to diatoms biology. Further, short regulatory non-coding RNAs (ncRNAs) as well as long ncRNAs are described in light of recent research. We highlight future studies and directions with a focus on epigenomic editing and environmental epigenetics.},
keywords = {},
pubstate = {published},
tppubtype = {inbook}
}
de Cordoba, Borja Ruiz-Fernandez; Moreno, Haritz; Valencia, Karmele; Perurena, Naiara; Ruedas, Pablo; Walle, Thomas; Pezonaga-Torres, Alberto; Hinojosa, Juan; Guruceaga, Elisabet; Pineda-Lucena, Antonio; Abengozar-Muela, Marta; Cochonneau, Denis; Zandueta, Carolina; Martinez-Canarias, Susana; Teijeira, Alvaro; Ajona, Daniel; Ortiz-Espinosa, Sergio; Morales, Xabier; de Solorzano, Carlos Ortiz; Santisteban, Marta; Ramos-Garcia, Luis I; Guembe, Laura; Strnad, Vratislav; Heymann, Dominique; Hervas-Stubbs, Sandra; Pio, Ruben; Rodriguez-Ruiz, Maria E; de Andrea, Carlos E; Vicent, Silvestre; Melero, Ignacio; Lecanda, Fernando; Martinez-Monge, Rafael
Tumor ENPP1(CD203a)/Haptoglobin Axis Exploits Myeloid-Derived Suppressor Cells to Promote Post-Radiotherapy Local Recurrence in Breast Cancer Article de journal
Dans: Cancer Discov, vol. 12, no. 5, p. 1356-1377, 2022, ISSN: 2159-8290.
@article{pmid35086922,
title = {Tumor ENPP1(CD203a)/Haptoglobin Axis Exploits Myeloid-Derived Suppressor Cells to Promote Post-Radiotherapy Local Recurrence in Breast Cancer},
author = {Borja Ruiz-Fernandez de Cordoba and Haritz Moreno and Karmele Valencia and Naiara Perurena and Pablo Ruedas and Thomas Walle and Alberto Pezonaga-Torres and Juan Hinojosa and Elisabet Guruceaga and Antonio Pineda-Lucena and Marta Abengozar-Muela and Denis Cochonneau and Carolina Zandueta and Susana Martinez-Canarias and Alvaro Teijeira and Daniel Ajona and Sergio Ortiz-Espinosa and Xabier Morales and Carlos Ortiz de Solorzano and Marta Santisteban and Luis I Ramos-Garcia and Laura Guembe and Vratislav Strnad and Dominique Heymann and Sandra Hervas-Stubbs and Ruben Pio and Maria E Rodriguez-Ruiz and Carlos E de Andrea and Silvestre Vicent and Ignacio Melero and Fernando Lecanda and Rafael Martinez-Monge},
url = {https://pubmed.ncbi.nlm.nih.gov/35086922/
hal-03550024v1 },
doi = {10.1158/2159-8290.CD-21-0932},
issn = {2159-8290},
year = {2022},
date = {2022-05-01},
urldate = {2022-05-01},
journal = {Cancer Discov},
volume = {12},
number = {5},
pages = {1356-1377},
abstract = {Locoregional failure (LRF) in breast cancer patients post-surgery and post-irradiation (IR) is linked to a dismal prognosis. In a refined new model, we identified Enpp1 (Ectonucleotide pyrophosphatase /phosphodiesterase 1/CD203a) to be closely associated with LRF. Enpp1high circulating tumor cells (CTC) contribute to relapse by a self-seeding mechanism. This process requires the infiltration of PMN-MDSC and neutrophil extracellular traps (NET) formation. Genetic and pharmacological Enpp1 inhibition or NET blockade extend relapse-free survival. Furthermore, in combination with fractionated irradiation (FD), Enpp1 abrogation obliterates LRF. Mechanistically, Enpp1-generated adenosinergic metabolites enhance Haptoglobin (Hp) expression. This inflammatory mediator elicits myeloid invasiveness and promotes NET formation. Accordingly, a significant increase in ENPP1 and NET formation is detected in relapsed human breast cancer tumors. Moreover, high ENPP1 or HP levels are associated with poor prognosis. These findings unveil the ENPP1/HP axis as an unanticipated mechanism exploited by tumor cells linking inflammation to immune remodeling favoring local relapse.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Sorée, Marion; Delavat, François; Lambert, Christophe; Lozach, Solen; Papin, Mathias; Petton, Bruno; Passerini, Delphine; Dégremont, Lionel; Heath, Dominique Hervio
Life history of oysters influences Vibrio parahaemolyticus accumulation in Pacific oysters (Crassostrea gigas ) Article de journal
Dans: Environmental Microbiology, p. 1462–2920.15996, 2022, ISSN: 1462-2912, 1462-2920.
@article{soree_life_2022,
title = {Life history of oysters influences Vibrio parahaemolyticus accumulation in Pacific oysters (Crassostrea gigas )},
author = {Marion Sorée and François Delavat and Christophe Lambert and Solen Lozach and Mathias Papin and Bruno Petton and Delphine Passerini and Lionel Dégremont and Dominique Hervio Heath},
url = {https://onlinelibrary.wiley.com/doi/10.1111/1462-2920.15996
hal-04202208v1 },
doi = {10.1111/1462-2920.15996},
issn = {1462-2912, 1462-2920},
year = {2022},
date = {2022-05-01},
urldate = {2022-05-01},
journal = {Environmental Microbiology},
pages = {1462--2920.15996},
abstract = {Vibrio parahaemolyticus infection in humans is asso- ciated with raw oyster consumption. Evaluation of V. parahaemolyticus presence in oysters is of most interest because of the economic and public health issues that it represents. To explore V. para- haemolyticus accumulation and depuration in adult Crassostrea gigas, we developed a GFP-tagged V. parahaemolyticus strain (IFVp201-gfp+), as well as a rapid and efficient quantification method in C. gigas oysters haemolymph by flow cytometry. Impact of the life history of C. gigas on accumulation and depuration of V. parahaemolyticus IFVp201 was sub- sequently investigated. We found that naive oysters, i.e. grown in controlled facilities with UV treated sea- water, accumulated significantly more IFVp201 than environmental oysters, i.e. grown in intertidal envi- ronment. We hypothesized that environmental oys- ters could have been immune primed, thus could limit V. parahaemolyticus accumulation. Meanwhile, both naive and environmental oysters had similardepuration rates.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Bourdareau, Simon; Godfroy, Olivier; Gueno, Josselin; Scornet, Delphine; Coelho, Susana M.; Tirichine, Leila; Cock, Jean Mark
An Efficient Chromatin Immunoprecipitation Protocol for the Analysis of Histone Modification Distributions in the Brown Alga Ectocarpus Article de journal
Dans: Methods Protoc. , vol. 36, iss. 3, p. 36, 2022.
@article{nokey,
title = {An Efficient Chromatin Immunoprecipitation Protocol for the Analysis of Histone Modification Distributions in the Brown Alga Ectocarpus},
author = {Simon Bourdareau and Olivier Godfroy and Josselin Gueno and Delphine Scornet and Susana M. Coelho and Leila Tirichine and Jean Mark Cock},
url = {hal-03658367v1 },
doi = {doi: 10.3390/mps5030036},
year = {2022},
date = {2022-04-25},
urldate = {2022-04-25},
journal = {Methods Protoc. },
volume = {36},
issue = {3},
pages = {36},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Villoing, Daphnée; Koumeir, Charbel; Bongrand, Arthur; Guertin, Arnaud; Haddad, Ferid; Métivier, Vincent; Poirier, Freddy; Potiron, Vincent; Servagent, Noël; Supiot, Stéphane; Delpon, Grégory; Chiavassa, Sophie
Technical note: Proton beam dosimetry at ultra-high dose rates (FLASH): Evaluation of GAFchromic™ (EBT3, EBT-XD) and OrthoChromic (OC-1) film performances Article de journal
Dans: Med Phys, vol. 49, no. 4, p. 2732–2745, 2022, ISSN: 2473-4209.
@article{pmid35179234,
title = {Technical note: Proton beam dosimetry at ultra-high dose rates (FLASH): Evaluation of GAFchromic™ (EBT3, EBT-XD) and OrthoChromic (OC-1) film performances},
author = {Daphnée Villoing and Charbel Koumeir and Arthur Bongrand and Arnaud Guertin and Ferid Haddad and Vincent Métivier and Freddy Poirier and Vincent Potiron and Noël Servagent and Stéphane Supiot and Grégory Delpon and Sophie Chiavassa},
url = {hal-03609664v1 },
doi = {10.1002/mp.15526},
issn = {2473-4209},
year = {2022},
date = {2022-04-01},
urldate = {2022-04-01},
journal = {Med Phys},
volume = {49},
number = {4},
pages = {2732--2745},
abstract = {PURPOSE: The ARRONAX cyclotron facility offers the possibility to deliver proton beams from low to ultra-high dose rates (UHDR). As a good control of the dosimetry is a prerequisite of UHDR experimentations, we evaluated in different conditions the usability and the dose rate dependency of several radiochromic films commonly used for dosimetry in radiotherapy.
METHODS: We compared the dose rate dependency of three types of radiochromic films: GAFchromic™ EBT3 and GAFchromic™ EBT-XD (Ashland Inc., Wayne, NJ, USA), and OrthoChromic OC-1 (OrthoChrome Inc., Hillsborough, NJ, USA), after proton irradiations at various mean dose rates (0.25, 40, 1500, and 7500 Gy/s) and for 10 doses (2-130 Gy). We also evaluated the dose rate dependency of each film considering beam structures, from single pulse to multiple pulses with various frequencies.
RESULTS: EBT3 and EBT-XD films showed differences of response between conventional (0.25 Gy/s) and UHDR (7500 Gy/s) conditions, above 10 Gy. On the contrary, OC-1 films did not present overall difference of response for doses except below 3 Gy. We observed an increase of the netOD with the mean dose rate for EBT3 and EBT-XD films. OC-1 films did not show any impact of the mean dose rate up to 7500 Gy/s, above 3 Gy. No difference was found based on the beam structure, for all three types of films.
CONCLUSIONS: EBT3 and EBT-XD radiochromic films should be used with caution for the dosimetry of UHDR proton beams over 10 Gy. Their overresponse, which increases with mean dose rate and dose, could lead to non-negligible overestimations of the absolute dose. OC-1 films are dose rate independent up to 7500 Gy/s in proton beams. Films response is not impacted by the beam structure. A broader investigation of the usability of OC-1 films in UHDR conditions should be conducted at intermediate and higher mean dose rates and other beam energies.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
METHODS: We compared the dose rate dependency of three types of radiochromic films: GAFchromic™ EBT3 and GAFchromic™ EBT-XD (Ashland Inc., Wayne, NJ, USA), and OrthoChromic OC-1 (OrthoChrome Inc., Hillsborough, NJ, USA), after proton irradiations at various mean dose rates (0.25, 40, 1500, and 7500 Gy/s) and for 10 doses (2-130 Gy). We also evaluated the dose rate dependency of each film considering beam structures, from single pulse to multiple pulses with various frequencies.
RESULTS: EBT3 and EBT-XD films showed differences of response between conventional (0.25 Gy/s) and UHDR (7500 Gy/s) conditions, above 10 Gy. On the contrary, OC-1 films did not present overall difference of response for doses except below 3 Gy. We observed an increase of the netOD with the mean dose rate for EBT3 and EBT-XD films. OC-1 films did not show any impact of the mean dose rate up to 7500 Gy/s, above 3 Gy. No difference was found based on the beam structure, for all three types of films.
CONCLUSIONS: EBT3 and EBT-XD radiochromic films should be used with caution for the dosimetry of UHDR proton beams over 10 Gy. Their overresponse, which increases with mean dose rate and dose, could lead to non-negligible overestimations of the absolute dose. OC-1 films are dose rate independent up to 7500 Gy/s in proton beams. Films response is not impacted by the beam structure. A broader investigation of the usability of OC-1 films in UHDR conditions should be conducted at intermediate and higher mean dose rates and other beam energies.
Muñoz-Garcia, Javier; Vargas-Franco, Jorge William; Royer, Bénédicte Brounais-Le; Cochonneau, Denis; Amiaud, Jérôme; Heymann, Marie-Françoise; Heymann, Dominique; Lézot, Frédéric
Inhibiting Endothelin Receptors with Macitentan Strengthens the Bone Protective Action of RANKL Inhibition and Reduces Metastatic Dissemination in Osteosarcoma Article de journal
Dans: Cancers, vol. 14, no. 7, p. 1765, 2022, ISSN: 2072-6694.
@article{cancers14071765,
title = {Inhibiting Endothelin Receptors with Macitentan Strengthens the Bone Protective Action of RANKL Inhibition and Reduces Metastatic Dissemination in Osteosarcoma},
author = {Javier Muñoz-Garcia and Jorge William Vargas-Franco and Bénédicte Brounais-Le Royer and Denis Cochonneau and Jérôme Amiaud and Marie-Françoise Heymann and Dominique Heymann and Frédéric Lézot},
url = {https://www.mdpi.com/2072-6694/14/7/1765
inserm-03625367v1 },
doi = {10.3390/cancers14071765},
issn = {2072-6694},
year = {2022},
date = {2022-03-30},
urldate = {2022-03-30},
journal = {Cancers},
volume = {14},
number = {7},
pages = {1765},
abstract = {Current treatments for osteosarcoma, combining conventional polychemotherapy and surgery, make it possible to attain a five-year survival rate of 70% in affected individuals. The presence of chemoresistance and metastases significantly shorten the patient’s lifespan, making identification of new therapeutic tools essential. Inhibiting bone resorption has been shown to be an efficient adjuvant strategy impacting the metastatic dissemination of osteosarcoma, tumor growth, and associated bone destruction. Unfortunately, over-apposition of mineralized matrix by normal and tumoral osteoblasts was associated with this inhibition. Endothelin signaling is implicated in the functional differentiation of osteoblasts, raising the question of the potential value of inhibiting it alone, or in combination with bone resorption repression. Using mouse models of osteosarcoma, the impact of macitentan, an endothelin receptor inhibitor, was evaluated regarding tumor growth, metastatic dissemination, matrix over-apposition secondary to RANKL blockade, and safety when combined with chemotherapy. The results showed that macitentan has no impact on tumor growth or sensitivity to ifosfamide, but significantly reduces tumoral osteoid tissue formation and the metastatic capacity of the osteosarcoma. To conclude, macitentan appears to be a promising therapeutic adjuvant for osteosarcoma alone or associated with bone resorption inhibitors.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Sanejouand, Yves-Henri
At least three xenon binding sites in the glycine binding domain of the N-methyl D-aspartate receptor Article de journal
Dans: Archives of biochemistry and biophysics, vol. 724, p. 109265, 2022, (arXiv: 2203.02219).
@article{sanejouand_at_2022,
title = {At least three xenon binding sites in the glycine binding domain of the N-methyl D-aspartate receptor},
author = {Yves-Henri Sanejouand},
url = {http://arxiv.org/abs/2203.02219
hal-03863820v1 },
doi = {https://doi.org/10.1016/j.abb.2022.109265},
year = {2022},
date = {2022-03-01},
urldate = {2022-03-01},
journal = {Archives of biochemistry and biophysics},
volume = {724},
pages = {109265},
abstract = {Xenon can produce general anesthesia. Its main protein target is the N-methyl-D-aspartate receptor, a ionotropic channel playing a pivotal role in the function of the central nervous system. The molecular mechanisms allowing this noble gas to have such a specific effect remain obscure, probably as a consequence of the lack of structural data at the atomic level of detail. Herein, as a result of five independent molecular dynamics simulations, three different binding sites were found for xenon in the glycine binding domain of the Nmethyl-D-aspartate receptor. The absolute binding free energy of xenon in these sites ranges between -8 and -14 kJ·mole−1. However, it depends significantly upon the protein conformer chosen for performing the calculation, suggesting that larger values could probably be obtained, if other conformers were considered. These three sites are next to each other, one of them being next to the glycine site. This could explain why the F758W and F758Y mutations can prevent competitive inhibition by xenon without affecting glycine binding.},
note = {arXiv: 2203.02219},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Gueno, Josselin; Borg, Michael; Bourdareau, Simon; Cossard, Guillaume; Godfroy, Olivier; Lipinska, Agnieszka; Tirichine, Leila; Cock, J Mark; Coelho, Susana M
Chromatin landscape associated with sexual differentiation in a UV sex determination system Article de journal
Dans: Nucleic Acids Res, vol. 50, iss. 6, p. 3307-3322, 2022, ISSN: 1362-4962.
@article{pmid35253891,
title = {Chromatin landscape associated with sexual differentiation in a UV sex determination system},
author = {Josselin Gueno and Michael Borg and Simon Bourdareau and Guillaume Cossard and Olivier Godfroy and Agnieszka Lipinska and Leila Tirichine and J Mark Cock and Susana M Coelho},
doi = {doi: 10.1093/nar/gkac145},
issn = {1362-4962},
year = {2022},
date = {2022-03-01},
urldate = {2022-03-01},
journal = {Nucleic Acids Res},
volume = {50},
issue = {6},
pages = {3307-3322},
abstract = {In many eukaryotes, such as dioicous mosses and many algae, sex is determined by UV sex chromosomes and is expressed during the haploid phase of the life cycle. In these species, the male and female developmental programs are initiated by the presence of the U- or V-specific regions of the sex chromosomes but, as in XY and ZW systems, sexual differentiation is largely driven by autosomal sex-biased gene expression. The mechanisms underlying the regulation of sex-biased expression of genes during sexual differentiation remain elusive. Here, we investigated the extent and nature of epigenomic changes associated with UV sexual differentiation in the brown alga Ectocarpus, a model UV system. Six histone modifications were quantified in near-isogenic lines, leading to the identification of 16 chromatin signatures across the genome. Chromatin signatures correlated with levels of gene expression and histone PTMs changes in males versus females occurred preferentially at genes involved in sex-specific pathways. Despite the absence of chromosome scale dosage compensation and the fact that UV sex chromosomes recombine across most of their length, the chromatin landscape of these chromosomes was remarkably different to that of autosomes. Hotspots of evolutionary young genes in the pseudoautosomal regions appear to drive the exceptional chromatin features of UV sex chromosomes.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Jubelin, Camille; Munoz-Garcia, Javier; Cochonneau, Denis; Moranton, Emilie; Heymann, Marie Françoise; Heymann, Dominique
Biological evidence of cancer stem-like cells and recurrent disease in osteosarcoma Article de journal
Dans: Cancer Drug Resistance, vol. 5, iss. 5, p. 184-198, 2022.
@article{jubelin2022biological,
title = {Biological evidence of cancer stem-like cells and recurrent disease in osteosarcoma},
author = {Camille Jubelin and Javier Munoz-Garcia and Denis Cochonneau and Emilie Moranton and Marie Françoise Heymann and Dominique Heymann},
url = { inserm-03550410v1 },
doi = {10.20517/cdr.2021.130},
year = {2022},
date = {2022-02-16},
urldate = {2022-02-16},
journal = {Cancer Drug Resistance},
volume = {5},
issue = {5},
pages = {184-198},
abstract = {Sarcomas are a large family of cancers originating in the mesenchyme. Composed of more than 100 histological subtypes, soft tissue and bone sarcomas remain clinically challenging, particularly in children and adolescents in whom sarcomas are the second most common malignant entities. Osteosarcoma is the main primary bone tumor in adolescents and young adults and is characterized by a high propensity to induce distant metastatic foci and become multi-drug resistant. The innate and acquired resistance of osteosarcoma can be explained by high histological heterogeneity and genetic/molecular diversity. In the last decade, the notion of cancer stem-like cells (CSCs) has emerged. This subset of cancer cells has been linked to drug resistance properties, recurrence of the disease, and therapeutic failure. Although CSCs remain controversial, many elements are in favor of them playing a role in the development of the drug resistance profile. The present review gives a brief overview of the most recent biological evidence of the presence of CSCs in osteosarcomas and their role in the drug resistance profile of these rare oncological entities. Their use as promising therapeutic targets is discussed.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Cadé, Marie; Muñoz-Garcia, Javier; Babuty, Antoine; Paré, Louis; Cochonneau, Denis; Fekir, Karim; Chatelais, Mathias; Heymann, Marie-Françoise; Lokajczyk, Anna; Boisson-Vidal, Catherine; Heymann, Dominique
FVIII regulates the molecular profile of endothelial cells: functional impact on the blood barrier and macrophage behavior Article de journal
Dans: Cell Mol Life Sci, vol. 79, no. 3, p. 145, 2022, ISSN: 1420-9071.
@article{pmid35190870,
title = {FVIII regulates the molecular profile of endothelial cells: functional impact on the blood barrier and macrophage behavior},
author = {Marie Cadé and Javier Muñoz-Garcia and Antoine Babuty and Louis Paré and Denis Cochonneau and Karim Fekir and Mathias Chatelais and Marie-Françoise Heymann and Anna Lokajczyk and Catherine Boisson-Vidal and Dominique Heymann},
url = {hal-03600694v1 },
doi = {10.1007/s00018-022-04178-5},
issn = {1420-9071},
year = {2022},
date = {2022-02-01},
urldate = {2022-02-01},
journal = {Cell Mol Life Sci},
volume = {79},
number = {3},
pages = {145},
abstract = {Hemophilia A is an inherited X-linked recessive bleeding disorder caused by deficient activity of blood coagulation factor VIII (FVIII). In addition, hemophilia patients show associated diseases including osteopenia, altered inflammation and vascular fragility which may represent the consequence of recurrent bleeding or may be related to the direct FVIII deficiency. Nowadays, recombinant FVIII is proposed to treat hemophilia patients with no circulating FVIII inhibitor. Initially described as a coenzyme to factor IXa for initiating thrombin generation, there is emerging evidence that FVIII is involved in multiple biological systems, including bone, vascular and immune systems. The present study investigated: (i) the functional activities of recombinant human FVIII (rFVIII) on endothelial cells, and (ii) the impact of rFVIII activities on the functional interactions of human monocytes and endothelial cells. We then investigated whether rFVIII had a direct effect on the adhesion of monocytes to the endothelium under physiological flow conditions. We observed that direct biological activities for rFVIII in endothelial cells were characterized by: (i) a decrease in endothelial cell adhesion to the underlying extracellular matrix; (ii) regulation of the transcriptomic and protein profiles of endothelial cells; (iii) an increase in the vascular tubes formed and vascular permeability in vitro; and (iv) an increase in monocyte adhesion activated endothelium and transendothelial migration. By regulating vascular permeability plus leukocyte adhesion and transendothelial migration, the present work highlights new biological functions for FVIII.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Santos, Michele Goulart Dos; Schimith, Lucia Emanueli; André-Miral, Corinne; Muccillo-Baisch, Ana Luiza; Arbo, Bruno Dutra; Hort, Mariana Appel
Neuroprotective effects of resveratrol in in vivo and in vitro experimental models of Parkinson’s disease: A systematic review Article de journal
Dans: Neurotoxicity Research, p. 1–27, 2022.
@article{dos2022neuroprotective,
title = {Neuroprotective effects of resveratrol in in vivo and in vitro experimental models of Parkinson’s disease: A systematic review},
author = {Michele Goulart Dos Santos and Lucia Emanueli Schimith and Corinne André-Miral and Ana Luiza Muccillo-Baisch and Bruno Dutra Arbo and Mariana Appel Hort},
editor = {Springer},
doi = {10.1007/s12640-021-00450-x},
year = {2022},
date = {2022-01-12},
urldate = {2022-01-12},
journal = {Neurotoxicity Research},
pages = {1--27},
publisher = {Springer},
abstract = {Parkinson’s disease (PD) is currently the second most common neurodegenerative disease, being characterized by motor and non-motor symptoms. The therapeutic options available for its treatment are limited, do not slow the progression of the disease, and have serious side effects. For this reason, many studies have sought to find compounds with neuroprotective properties that bring additional benefits to current therapy. In this context, resveratrol is a phenolic compound, found in many plant species, capable of crossing the blood–brain barrier and having multiple biological properties. Experimental studies in vitro and in vivo have shown that it can prevent or slow the progression of a variety of diseases, including PD. In this systematic review, we summarize the effects of resveratrol in experimental in vivo and in vitro models of PD and discuss the molecular mechanisms involved in its action. The bibliographic search was performed in the databases of PubMed, Web of Science, SciELO, and Google Scholar, and based on the inclusion criteria, 41 articles were selected and discussed. Most of the included studies have demonstrated neuroprotective effects of resveratrol. In general, resveratrol prevented behavioral and/or neurological disorders, improved antioxidant defenses, reduced neuroinflammatory processes, and inhibited apoptosis. In summary, this systematic review offers important scientific evidence of neuroprotective effects of resveratrol in PD and also provide valuable information about its mechanism of action that can support future clinical studies.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Colliec-Jouault, Sylvia; Sinquin, Corinne; Ratiskol, Jacqueline; Heymann, Dominique; Ruiz-Velasco, Carmen; Chesneau, Julie
Anti-metastatic marine bacterial exopolysaccharide derivative and uses thereof Patent
2022, (US Patent 11,219,638).
@patent{colliec2022anti,
title = {Anti-metastatic marine bacterial exopolysaccharide derivative and uses thereof},
author = {Sylvia Colliec-Jouault and Corinne Sinquin and Jacqueline Ratiskol and Dominique Heymann and Carmen Ruiz-Velasco and Julie Chesneau},
url = {https://patents.google.com/patent/US11219638B2/en},
year = {2022},
date = {2022-01-11},
urldate = {2022-01-11},
publisher = {Google Patents},
abstract = {The invention provides a low-molecular-weight (15 kDa) over-sulfated exopolysaccharide (GYS15) prepared from a marine native exopolysaccharide excreted by a mesophilic marine bacterium from a deep-sea hydrothermal environment, and relates to the use of this low-molecular-weight over-sulfated exopolysaccharide for the prevention or inhibition of metastases formation.},
note = {US Patent 11,219,638},
keywords = {},
pubstate = {published},
tppubtype = {patent}
}
Chabaud, Mireille; Auriac, Marie-Christine; Boniface, Marie-Claude; Delgrange, Sabine; Folletti, Tifaine; Jardinaud, Marie-Françoise; Legendre, Alexandra; Pérez-Vich, Begoña; Pouvreau, Jean-Bernard; Velasco, Leonardo; Delavault, Philippe; Muños, Stéphane
Wild species: A reservoir of resistance genes for sustainable pyramidal resistance to broomrape in sunflower Article de journal
Dans: Front Plant Sci, vol. 13, p. 1038684, 2022, ISSN: 1664-462X.
@article{pmid36340383,
title = {Wild species: A reservoir of resistance genes for sustainable pyramidal resistance to broomrape in sunflower},
author = {Mireille Chabaud and Marie-Christine Auriac and Marie-Claude Boniface and Sabine Delgrange and Tifaine Folletti and Marie-Françoise Jardinaud and Alexandra Legendre and Begoña Pérez-Vich and Jean-Bernard Pouvreau and Leonardo Velasco and Philippe Delavault and Stéphane Muños},
url = {hal-03877893v1 },
doi = {10.3389/fpls.2022.1038684},
issn = {1664-462X},
year = {2022},
date = {2022-01-01},
urldate = {2022-01-01},
journal = {Front Plant Sci},
volume = {13},
pages = {1038684},
abstract = { Wall., sunflower broomrape, is one of the major pests for the sunflower crop. Breeding for resistant varieties in sunflower has been the most efficient method to control this parasitic weed. However, more virulent broomrape populations continuously emerge by overcoming genetic resistance. It is thus essential to identify new broomrape resistances acting at various stages of the interaction and combine them to improve resistance durability. In this study, 71 wild sunflowers and wild relatives accessions from 16 species were screened in pots for their resistance to broomrape at the late emergence stage. From this initial screen, 18 accessions from 9 species showing resistance, were phenotyped at early stages of the interaction: the induction of broomrape seed germination by sunflower root exudates, the attachment to the host root and the development of tubercles in rhizotron assays. We showed that wild accessions are an important source of resistance to the most virulent broomrape races, affecting various stages of the interaction: the inability to induce broomrape seed germination, the development of incompatible attachments or necrotic tubercles, and the arrest of emerged structure growth. Cytological studies of incompatible attachments showed that several cellular mechanisms were shared among resistant species.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Strat, Yoran Le; Tonon, Thierry; Leblanc, Catherine; Groisillier, Agnès
Characterization of Redox Sensitive Brown Algal Mannitol-1-Phosphatases Article de journal
Dans: 2022.
@article{nokey,
title = {Characterization of Redox Sensitive Brown Algal Mannitol-1-Phosphatases},
author = {Yoran Le Strat and Thierry Tonon and Catherine Leblanc and Agnès Groisillier},
url = {https://doi.org/10.3390/phycology3010001
https://hal.science/hal-04256946v1
hal-04256946v1},
doi = {10.3390/phycology3010001},
year = {2022},
date = {2022-01-01},
urldate = {2022-01-01},
abstract = {Citation: Le Strat, Y.; Tonon, T.; Leblanc, C.; Groisillier, A. Characterization of Redox Sensitive Brown Algal Mannitol-1-Phosphatases. Phycology 2023, 3, 1-12. https:// Abstract: Macroalgae (seaweeds) are key primary producers in marine coastal habitats and largely contribute to global ocean carbon fluxes. They also represent attractive renewable feedstock for the production of biofuels, food, feed, and bioactive. Brown algae are seaweeds that produce alginates and fucose containing sulfated polysaccharides in their cell wall and laminarin and mannitol for carbon storage. The availability of genomes of the kelp Saccharina japonica and of the filamentous Ectocarpus sp. paved the way for the biochemical characterization of recombinant enzymes involved in their polysaccharide and carbohydrates synthesis, including, notably, mannitol. Brown algal mannitol biosynthesis starts with the conversion of fructose-6-phospate into mannitol-1-phosphate (mannitol-1P), and this intermediate is hydrolysed by a haloacid dehalogenase phosphatase (M1Pase) to produce mannitol. We report here the biochemical characterization of a second M1Pase in Ectocarpus sp. (EsM1Pase1). Both Ectocarpus M1Pases were redox-sensitive enzymes, with EsM1Pase1 active only in presence of the reducing agent. Such catalytic properties have not been observed for any M1Pases yet. EsM1Pases were specific to mannitol-1-P, in contrast to S. japonica M1Pases that could act on other phosphorylated sugars. Finally, brown algal M1Pases formed two well-supported clades, with possible distinct subcellular localization and physiological role(s) under diverse environmental conditions and/or life cycle stages.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
34 publications
Bourdareau, Simon; Tirichine, Leila; Lombard, Bérangère; Loew, Damarys; Scornet, Delphine; Wu, Yue; Coelho, Susana M; Cock, Mark J
Histone modifications during the life cycle of the brown alga Ectocarpus Article de journal
Dans: Genome Biology, vol. 22, no. 1, 2021, ISSN: 1474760X.
@article{Bourdareau2021,
title = {Histone modifications during the life cycle of the brown alga Ectocarpus},
author = {Simon Bourdareau and Leila Tirichine and Bérangère Lombard and Damarys Loew and Delphine Scornet and Yue Wu and Susana M Coelho and Mark J Cock},
url = {https://pubmed.ncbi.nlm.nih.gov/33397407/},
doi = {10.1186/s13059-020-02216-8},
issn = {1474760X},
year = {2021},
date = {2021-12-01},
journal = {Genome Biology},
volume = {22},
number = {1},
publisher = {BioMed Central Ltd},
abstract = {Background: Brown algae evolved complex multicellularity independently of the animal and land plant lineages and are the third most developmentally complex phylogenetic group on the planet. An understanding of developmental processes in this group is expected to provide important insights into the evolutionary events necessary for the emergence of complex multicellularity. Here, we focus on mechanisms of epigenetic regulation involving post-translational modifications of histone proteins. Results: A total of 47 histone post-translational modifications are identified, including a novel mark H2AZR38me1, but Ectocarpus lacks both H3K27me3 and the major polycomb complexes. ChIP-seq identifies modifications associated with transcription start sites and gene bodies of active genes and with transposons. H3K79me2 exhibits an unusual pattern, often marking large genomic regions spanning several genes. Transcription start sites of closely spaced, divergently transcribed gene pairs share a common nucleosome-depleted region and exhibit shared histone modification peaks. Overall, patterns of histone modifications are stable through the life cycle. Analysis of histone modifications at generation-biased genes identifies a correlation between the presence of specific chromatin marks and the level of gene expression. Conclusions: The overview of histone post-translational modifications in the brown alga presented here will provide a foundation for future studies aimed at understanding the role of chromatin modifications in the regulation of brown algal genomes.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Depienne, Sébastien; Alvarez-Dorta, Dimitri; Croyal, Mikael; Temgoua, Ranil C T; Charlier, Cathy; Deniaud, David; Mével, Mathieu; Boujtita, Mohammed; Gouin, Sébastien G
Luminol anchors improve the electrochemical-tyrosine-click labelling of proteins Article de journal
Dans: Chem Sci, vol. 12, no. 46, p. 15374–15381, 2021, ISSN: 2041-6520.
@article{pmid34976358,
title = {Luminol anchors improve the electrochemical-tyrosine-click labelling of proteins},
author = {Sébastien Depienne and Dimitri Alvarez-Dorta and Mikael Croyal and Ranil C T Temgoua and Cathy Charlier and David Deniaud and Mathieu Mével and Mohammed Boujtita and Sébastien G Gouin},
url = {hal-03429234v2 },
doi = {10.1039/d1sc04809k},
issn = {2041-6520},
year = {2021},
date = {2021-12-01},
urldate = {2021-12-01},
journal = {Chem Sci},
volume = {12},
number = {46},
pages = {15374--15381},
abstract = {New methods for chemo-selective modifications of peptides and native proteins are important in chemical biology and for the development of therapeutic conjugates. Less abundant and uncharged amino-acid residues are interesting targets to form less heterogeneous conjugates and preserve biological functions. Phenylurazole (PhUr), -methylphenylurazole (NMePhUr) and -methylluminol (NMeLum) derivatives were described as tyrosine (Y) anchors after chemical or enzymatic oxidations. Recently, we developed the first electrochemical Y-bioconjugation method coined eY-click to activate PhUr in biocompatible media. In this work, we assessed the limitations, benefits and relative efficiencies of eY-click conjugations performed with a set of PhUr, NMePhUr and NMeLum derivatives. Results evidenced a high efficiency of NMeLum that showed a complete Y-chemoselectivity on polypeptides and biologically relevant proteins after soft electrochemical activation. Side reactions on nucleophilic or heteroaromatic amino-acids such as lysine or tryptophan were never observed during mass spectrometry analysis. Myoglobine, bovine serum albumin, a plant mannosidase, glucose oxidase and the therapeutically relevant antibody trastuzumab were efficiently labelled with a fluorescent probe in a two-step approach combining eY-click and strain-promoted azide-alkyne cyclization (SPAAC). The proteins conserved their structural integrity as observed by circular dichroism and the trastuzumab conjugate showed a similar binding affinity for the natural HER2 ligand as shown by bio-layer interferometry. Compared to our previously described protocol with PhUr, eY-click with NMeLum species showed faster reaction kinetics, higher (complete) Y-chemoselectivity and reactivity, and offers the interesting possibility of the double tagging of solvent-exposed Y.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Cornet, Florent; Pillot, Jean-Paul; Bris, Philippe Le; Pouvreau, Jean-Bernard; Arnaud, Nicolas; de Saint Germain, Alexandre; Rameau, Catherine
Strigolactones (SLs) modulate the plastochron by regulating KLUH (KLU) transcript abundance in Arabidopsis Article de journal
Dans: New Phytol, vol. 232, no. 5, p. 1909–1916, 2021, ISSN: 1469-8137.
@article{pmid34498760,
title = {Strigolactones (SLs) modulate the plastochron by regulating KLUH (KLU) transcript abundance in Arabidopsis},
author = {Florent Cornet and Jean-Paul Pillot and Philippe Le Bris and Jean-Bernard Pouvreau and Nicolas Arnaud and Alexandre de Saint Germain and Catherine Rameau},
doi = {10.1111/nph.17725},
issn = {1469-8137},
year = {2021},
date = {2021-12-01},
urldate = {2021-12-01},
journal = {New Phytol},
volume = {232},
number = {5},
pages = {1909--1916},
abstract = {The timing of leaf emergence at the shoot apical meristem, or plastochron, is highly regulated in plants. Among the genes known to regulate the plastochron in Arabidopsis (Arabidopsis thaliana), KLUH (KLU), orthologous to the rice (Oryza sativa) PLASTOCHRON1, encodes the cytochrome P450 CYP78A5, and is thought to act through generation of a still unknown mobile signal. As klu mutants display not only a short plastochron but also a branching phenotype reminiscent of strigolactone (SL) mutants, we investigated whether KLU/CYP78A5 is involved in SL biosynthesis. We combined a genetic approach, a parasitic plant seed germination bioassay to test klu root exudates, and analysis of transcript abundances of SL-biosynthesis genes in the Arabidopsis klu mutants. We demonstrate that KLU is not involved in the SL-biosynthesis pathway. Moreover, this work allowed us to uncover a new role for SL during Arabidopsis development in modulating plastochron via a KLU-dependent pathway. Globally our data reveal that KLU is required for plastochron-specific SL responses, a first indication of crosstalk between SL and the KLU-derived signal.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Charbel Koumeir Noël Servagent, Guillaume Blain
Proton beam FLASH online monitoring at ARRONAX cyclotron Conférence
2021.
@conference{nokey,
title = {Proton beam FLASH online monitoring at ARRONAX cyclotron},
author = { Noël Servagent, Charbel Koumeir, Guillaume Blain, A. Bongrand, Sophie Chiavassa, Sylvain Deffe, Grégory Delpon, Arnaud Guertin, Stéphane Lucas, Vincent Métivier, Quentin Mouchard, Freddy Poirier, Vincent Potiron, Lucas Schoenauen, Edmond Sterpin, Daphnée Villoing, Rudi Labarbe, Severine Rossomme, Ferid Haddad },
url = { hal-03934393v1 },
year = {2021},
date = {2021-12-01},
urldate = {2021-12-01},
keywords = {},
pubstate = {published},
tppubtype = {conference}
}
UHDR proton beam vs conventional: hydrogen peroxide as FLASH effect sensor Conférence
2021.
@conference{nokey,
title = {UHDR proton beam vs conventional: hydrogen peroxide as FLASH effect sensor},
url = {hal-03957666v1 },
year = {2021},
date = {2021-12-01},
urldate = {2021-12-01},
keywords = {},
pubstate = {published},
tppubtype = {conference}
}
Eisenhofer R Armbrecht L, Utge J
Paleo-diatom composition from Santa Barbara Basin deep-sea sediments: a comparison of 18S-V9 and diat-rbcL metabarcoding vs shotgun metagenomics. Article de journal
Dans: ISME Commun, 2021.
@article{nokey,
title = {Paleo-diatom composition from Santa Barbara Basin deep-sea sediments: a comparison of 18S-V9 and diat-rbcL metabarcoding vs shotgun metagenomics. },
author = {Armbrecht L, Eisenhofer R, Utge J, Sibert EC, Rocha F, Ward R, Pierella Karlusich JJ, Tirichine L, Norris R, Summers M, Bowler C},
doi = {doi: 10.1038/s43705-021-00070-8.},
year = {2021},
date = {2021-11-09},
urldate = {2021-11-09},
journal = {ISME Commun},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Guo, Xia; Xuan, Ning; Liu, Guoxia; Xie, Hongyan; Lou, Qinian; Arnaud, Philippe; Offmann, Bernard; Picimbon, Jean-François
An Expanded Survey of the Moth PBP/GOBP Clade in Bombyx mori: New Insight into Expression and Functional Roles Article de journal
Dans: Frontiers in Physiology, vol. 12, p. 1701, 2021, ISSN: 1664-042X.
@article{10.3389/fphys.2021.712593,
title = {An Expanded Survey of the Moth PBP/GOBP Clade in Bombyx mori: New Insight into Expression and Functional Roles},
author = {Xia Guo and Ning Xuan and Guoxia Liu and Hongyan Xie and Qinian Lou and Philippe Arnaud and Bernard Offmann and Jean-François Picimbon},
url = {https://www.frontiersin.org/article/10.3389/fphys.2021.712593},
doi = {10.3389/fphys.2021.712593},
issn = {1664-042X},
year = {2021},
date = {2021-10-28},
urldate = {2021-01-01},
journal = {Frontiers in Physiology},
volume = {12},
pages = {1701},
abstract = {We studied the expression profile and ontogeny (from the egg stage through the larval stages and pupal stages, to the elderly adult age) of four OBPs from the silkworm moth Bombyx mori. We first showed that male responsiveness to female sex pheromone in the silkworm moth B. mori does not depend on age variation; whereas the expression of BmorPBP1, BmorPBP2, BmorGOBP1, and BmorGOBP2 varies with age. The expression profile analysis revealed that the studied OBPs are expressed in non-olfactory tissues at different developmental stages. In addition, we tested the effect of insecticide exposure on the expression of the four OBPs studied. Exposure to a toxic macrolide insecticide endectocide molecule (abamectin) led to the modulated expression of all four genes in different tissues. The higher expression of OBPs was detected in metabolic tissues, such as the thorax, gut, and fat body. All these data strongly suggest some alternative functions for these proteins other than olfaction. Finally, we carried out ligand docking studies and reported that PBP1 and GOBP2 have the capacity of binding vitamin K1 and multiple different vitamins.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Velic, Denis; Demeyer, Alexandre; Peterlini, Thibaut; Benhelli-Mokrani, Houda; Mathé-Allainmat, Monique; Masson, Jean-Yves; Fleury, Fabrice
Molecular Determinant of DIDS Analogs Targeting RAD51 Activity Article de journal
Dans: Molecules, vol. 26, no. 18, p. 5460, 2021, ISSN: 1420-3049.
@article{velic_molecular_2021,
title = {Molecular Determinant of DIDS Analogs Targeting RAD51 Activity},
author = {Denis Velic and Alexandre Demeyer and Thibaut Peterlini and Houda Benhelli-Mokrani and Monique Mathé-Allainmat and Jean-Yves Masson and Fabrice Fleury},
url = {https://www.mdpi.com/1420-3049/26/18/5460},
doi = {10.3390/molecules26185460},
issn = {1420-3049},
year = {2021},
date = {2021-09-15},
urldate = {2021-09-15},
journal = {Molecules},
volume = {26},
number = {18},
pages = {5460},
abstract = {RAD51 is the central protein in DNA repair by homologous recombination (HR), involved in several steps of this process. It is shown that overexpression of the RAD51 protein is correlated with increased survival of cancer cells to cancer treatments. For the past decade, RAD51 overexpression-mediated resistance has justified the development of targeted inhibitors. One of the first molecules described to inhibit RAD51 was the 4,4 -diisothiocyanato-stilbene-2,2 -disulfonic acid (DIDS) molecule. This small molecule is effective in inhibiting different functions of RAD51, however its mode of action and the chemical functions involved in this inhibition have not been identified. In this work, we used several commercial molecules derived from DIDS to characterize the structural determinants involved in modulating the activity of RAD51. By combining biochemical and biophysical approaches, we have shown that DIDS and two analogs were able to inhibit the binding of RAD51 to ssDNA and prevent the formation of D-loop by RAD51. Both isothiocyanate substituents of DIDS appear to be essential in the inhibition of RAD51. These results open the way to the synthesis of new molecules derived from DIDS that should be greater modulators of RAD51 and more efficient for HR inhibition.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Demeyer, Alexandre; Benhelli-Mokrani, Houda; Chénais, B.; Weigel, Pierre; Fleury, Fabrice
Inhibiting homologous recombination by targeting RAD51 protein Article de journal
Dans: Biochimica et Biophysica Acta (BBA) - Reviews on Cancer, vol. 1876, no. 2, p. 188597, 2021, ISSN: 0304419X.
@article{demeyer_inhibiting_2021,
title = {Inhibiting homologous recombination by targeting RAD51 protein},
author = {Alexandre Demeyer and Houda Benhelli-Mokrani and B. Chénais and Pierre Weigel and Fabrice Fleury},
url = {https://linkinghub.elsevier.com/retrieve/pii/S0304419X21000949},
doi = {10.1016/j.bbcan.2021.188597},
issn = {0304419X},
year = {2021},
date = {2021-09-15},
urldate = {2021-09-15},
journal = {Biochimica et Biophysica Acta (BBA) - Reviews on Cancer},
volume = {1876},
number = {2},
pages = {188597},
abstract = {Homologous recombination (HR) is involved in repairing DNA double-strand breaks (DSB), the most harmful for the cell. Regulating HR is essential for maintaining genomic stability. In many forms of cancer, overactivation of HR increases tumor resistance to DNA-damaging treatments. RAD51, HR's core protein, is very often overexpressed in these cancers and plays a critical role in cancer cell development and survival. Targeting RAD51 directly to reduce its activity and its expression is therefore one strategy to sensitize and overcome resistance cancer cells to existing DNA-damaging therapies which remains the limiting factor for the success of targeted therapy.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Le, Van-Tuyen; Bertrand, Samuel; du Pont, Thibaut Robiou; Fleury, Fabrice; Caroff, Nathalie; Bourgeade-Delmas, Sandra; Gentil, Emmanuel; Logé, Cedric; Genta-Jouve, Gregory; Grovel, Olivier
Untargeted Metabolomics Approach for the Discovery of Environment-Related Pyran-2-Ones Chemodiversity in a Marine-Sourced Penicillium restrictum Article de journal
Dans: Marine Drugs, vol. 19, no. 7, p. 378, 2021, ISSN: 1660-3397.
@article{le_untargeted_2021,
title = {Untargeted Metabolomics Approach for the Discovery of Environment-Related Pyran-2-Ones Chemodiversity in a Marine-Sourced Penicillium restrictum},
author = {Van-Tuyen Le and Samuel Bertrand and Thibaut Robiou du Pont and Fabrice Fleury and Nathalie Caroff and Sandra Bourgeade-Delmas and Emmanuel Gentil and Cedric Logé and Gregory Genta-Jouve and Olivier Grovel},
url = {https://www.mdpi.com/1660-3397/19/7/378},
doi = {10.3390/md19070378},
issn = {1660-3397},
year = {2021},
date = {2021-09-15},
journal = {Marine Drugs},
volume = {19},
number = {7},
pages = {378},
abstract = {Very little is known about chemical interactions between fungi and their mollusc host within marine environments. Here, we investigated the metabolome of a Penicillium restrictum MMS417 strain isolated from the blue mussel Mytilus edulis collected on the Loire estuary, France. Following the OSMAC approach with the use of 14 culture media, the effect of salinity and of a musselderived medium on the metabolic expression were analysed using HPLC-UV/DAD-HRMS/MS. An untargeted metabolomics study was performed using principal component analysis (PCA), orthogonal projection to latent structure discriminant analysis (O-PLSDA) and molecular networking (MN). It highlighted some compounds belonging to sterols, macrolides and pyran-2-ones, which were specifically induced in marine conditions. In particular, a high chemical diversity of pyran-2-ones was found to be related to the presence of mussel extract in the culture medium. Mass spectrometry (MS)- and UV-guided purification resulted in the isolation of five new natural fungal pyran-2-one derivatives—5,6-dihydro-6S-hydroxymethyl-4-methoxy-2H-pyran-2-one (1), (6S, 1’R, 2’S)-LL-P880β (3), 5,6-dihydro-4-methoxy-6S-(1’S, 2’S-dihydroxy pent-3’(E)-enyl)-2H-pyran-2-one (4), 4-methoxy-6(1’R, 2’S-dihydroxy pent-3’(E)-enyl)-2H-pyran-2-one (6) and 4-methoxy-2H-pyran-2-one (7)—together with the known (6S, 1’S, 2’S)-LL-P880β (2), (1’R, 2’S)-LL-P880γ (5), 5,6-dihydro-4-methoxy-2H-pyran2-one (8), (6S, 1’S, 2’R)-LL-P880β (9), (6S, 1’S)-pestalotin (10), 1’R-dehydropestalotin (11) and 6-pentyl4-methoxy-2H-pyran-2-one (12) from the mussel-derived culture medium extract. The structures of 1-12 were determined by 1D- and 2D-MMR experiments as well as high-resolution tandem MS, ECD and DP4 calculations. Some of these compounds were evaluated for their cytotoxic, antibacterial, antileishmanial and in-silico PTP1B inhibitory activities. These results illustrate the utility in using host-derived media for the discovery of new natural products.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Cabezas-Pérusse, Yari; Daligault, Franck; Ferrières, Vincent; Tasseau, Olivier; Tranchimand, Sylvain
Modulation of the Activity and Regioselectivity of a Glycosidase: Development of a Convenient Tool for the Synthesis of Specific Disaccharides Article de journal
Dans: Molecules, vol. 26, no. 18, p. 5445, 2021.
@article{cabezas2021modulation,
title = {Modulation of the Activity and Regioselectivity of a Glycosidase: Development of a Convenient Tool for the Synthesis of Specific Disaccharides},
author = {Yari Cabezas-Pérusse and Franck Daligault and Vincent Ferrières and Olivier Tasseau and Sylvain Tranchimand},
url = {https://www.mdpi.com/1420-3049/26/18/5445},
doi = {10.3390/molecules26185445},
year = {2021},
date = {2021-09-07},
urldate = {2021-09-07},
journal = {Molecules},
volume = {26},
number = {18},
pages = {5445},
publisher = {MDPI},
abstract = {The synthesis of disaccharides, particularly those containing hexofuranoside rings, requires a large number of steps by classical chemical means. The use of glycosidases can be an alternative to limit the number of steps, as they catalyze the formation of controlled glycosidic bonds starting from simple and easy to access building blocks; the main drawbacks are the yields, due to the balance between the hydrolysis and transglycosylation of these enzymes, and the enzyme-dependent regioselectivity. To improve the yield of the synthesis of β-d-galactofuranosyl-(1→X)-d-mannopyranosides catalyzed by an arabinofuranosidase, in this study we developed a strategy to mutate, then screen the catalyst, followed by a tailored molecular modeling methodology to rationalize the effects of the identified mutations. Two mutants with a 2.3 to 3.8-fold increase in transglycosylation yield were obtained, and in addition their accumulated regioisomer kinetic profiles were very different from the wild-type enzyme. Those differences were studied in silico by docking and molecular dynamics, and the methodology revealed a good predictive quality in regards with the regioisomer profiles, which is in good agreement with the experimental transglycosylation kinetics. So, by engineering CtAraf51, new biocatalysts were enabled to obtain the attractive central motif from the Leishmania lipophosphoglycan core with a higher yield and regioselectivity.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Morot, Amandine; Fekih, Sahar El; Bidault, Adeline; Ferrand, Alizée Le; Jouault, Albane; Kavousi, Javid; Bazire, Alexis; Pichereau, Vianney; Dufour, Alain; Paillard, Christine; Delavat, François
Virulence of Vibrio harveyi ORM4 toward the European abalone Haliotis tuberculata involves both quorum sensing and a type III secretion system Article de journal
Dans: Environmental Microbiology, vol. 23, no. 9, p. 5273-5288, 2021.
@article{https://doi.org/10.1111/1462-2920.15592,
title = {Virulence of Vibrio harveyi ORM4 toward the European abalone Haliotis tuberculata involves both quorum sensing and a type III secretion system},
author = {Amandine Morot and Sahar El Fekih and Adeline Bidault and Alizée Le Ferrand and Albane Jouault and Javid Kavousi and Alexis Bazire and Vianney Pichereau and Alain Dufour and Christine Paillard and François Delavat},
url = {https://sfamjournals.onlinelibrary.wiley.com/doi/abs/10.1111/1462-2920.15592
hal-04209594v1 },
doi = {https://doi.org/10.1111/1462-2920.15592},
year = {2021},
date = {2021-05-14},
urldate = {2021-05-14},
journal = {Environmental Microbiology},
volume = {23},
number = {9},
pages = {5273-5288},
abstract = {Abstract Environmental Vibrio strains represent a major threat in aquaculture, but the understanding of their virulence mechanisms heavily relies on the transposition of knowledge from human-pathogen vibrios. Here, the genetic bases of the virulence of Vibrio harveyi ORM4 toward the European abalone Haliotis tuberculata were characterized. We demonstrated that luxO, encoding a major regulator of the quorum sensing system, is crucial for the virulence of this strain, and that its deletion leads to a decrease in swimming motility, biofilm formation, and exopolysaccharide production. Furthermore, the biofilm formation by V. harveyi ORM4 was increased by abalone serum, which required LuxO. The absence of LuxO in V. harveyi ORM4 yielded opposite phenotypes compared with other Vibrio species including V. campbellii (still frequently named V. harveyi). In addition, we report a full Type III Secretion System (T3SS) gene cluster in the V. harveyi ORM4 genome. LuxO was shown to negatively regulate the promoter activity of exsA, encoding the major regulator of the T3SS genes, and the deletion of exsA abolished the virulence of V. harveyi ORM4. These results unveil virulence mechanisms set up by this environmentally important bacterial pathogen, and pave the way for a better molecular understanding of the regulation of its pathogenicity. This article is protected by copyright. All rights reserved.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Teze, David; Zhao, Jiao; Wiemann, Mathias; Ara, Kazi Z G; Lupo, Rossana; Zeuner, Birgitte; Vuillemin, Marlène; Rønne, Mette E; Carlström, Göran; Duus, Jens Ø; Sanejouand, Yves-Henri; O'Donohue, Michael J; Karlsson, Eva Nordberg; Fauré, Régis; Stålbrand, Henrik; Svensson, Birte
Rational Enzyme Design without Structural Knowledge: A Sequence-Based Approach for Efficient Generation of Transglycosylases Article de journal
Dans: Chemistry – A European Journal, vol. 27, no. 40, p. 10323–10334, 2021, ISSN: 0947-6539, 1521-3765.
@article{https://doi.org/10.1002/chem.202100110,
title = {Rational Enzyme Design without Structural Knowledge: A Sequence-Based Approach for Efficient Generation of Transglycosylases},
author = {David Teze and Jiao Zhao and Mathias Wiemann and Kazi Z G Ara and Rossana Lupo and Birgitte Zeuner and Marlène Vuillemin and Mette E Rønne and Göran Carlström and Jens Ø Duus and Yves-Henri Sanejouand and Michael J O'Donohue and Eva Nordberg Karlsson and Régis Fauré and Henrik Stålbrand and Birte Svensson},
url = {https://chemistry-europe.onlinelibrary.wiley.com/doi/abs/10.1002/chem.202100110},
doi = {https://doi.org/10.1002/chem.202100110},
issn = {0947-6539, 1521-3765},
year = {2021},
date = {2021-04-29},
urldate = {2021-04-29},
journal = {Chemistry – A European Journal},
volume = {27},
number = {40},
pages = {10323--10334},
abstract = {Glycobiology is dogged by the relative scarcity of synthetic, defined oligosaccharides. Enzyme-catalysed glycosylation using glycoside hydrolases is feasible but is hampered by the innate hydrolytic activity of these enzymes. Protein engineering is useful to remedy this, but it usually requires prior structural knowledge of the target enzyme, and/or relies on extensive, time-consuming screening and analysis. Here we describe a straightforward strategy that involves rational rapid in silico analysis of protein sequences. The method pinpoints 6‒12 single mutant candidates to improve transglycosylation yields. Requiring very little prior knowledge of the target enzyme other than its sequence, the method is generic and procures catalysts for the formation of glycosidic bonds involving various d / l -, α/β-pyranosides or furanosides, and exo - and endo -action. Moreover, mutations validated in one enzyme can be transposed to others, even distantly related enzymes.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Robla, Sandra; Prasanna, Maruthi; Varela-Calviño, Rubén; Grandjean, Cyrille; Csaba, Noemi
A chitosan-based nanosystem as pneumococcal vaccine delivery platform Article de journal
Dans: Drug Delivery and Translational Research, vol. 11, no. 2, p. 581–597, 2021, ISSN: 2190-3948.
@article{robla_chitosan-based_2021,
title = {A chitosan-based nanosystem as pneumococcal vaccine delivery platform},
author = {Sandra Robla and Maruthi Prasanna and Rubén Varela-Calviño and Cyrille Grandjean and Noemi Csaba},
url = {https://doi.org/10.1007/s13346-021-00928-3},
doi = {10.1007/s13346-021-00928-3},
issn = {2190-3948},
year = {2021},
date = {2021-04-01},
urldate = {2021-06-16},
journal = {Drug Delivery and Translational Research},
volume = {11},
number = {2},
pages = {581--597},
abstract = {Chitosan-based nanosystems have been described as interesting tools for antigen delivery and for enhancing the immunogenicity of nasally administered vaccines. As a possible vaccine delivery method, the chemical conjugation of chitosan nanocapsules with the Streptococcus pneumoniae cell membrane protein PsaA (pneumococcal surface adhesin A) is suggested here. The antigen PsaA, common to all pneumococcus serotypes, is expected to improve its uptake by immune cells and to activate specific T cells, generating an adaptive immune response against pneumococcus. With this aim, chitosan nanocapsules with thiol-maleimide conjugation between the polymer (chitosan) and the antigen (PsaA) were designed to enable the surface presentation of PsaA for immune cell recognition. Spherical-shaped particles, with a size of 266 ± 32 nm, positive charge of +30 ± 1 mV, and good stability profiles in simulated nasal fluids (up to 24 h) were achieved. PsaA association rates were three times higher compared with nanocapsules without covalent polymer-protein conjugation. Cytotoxicity studies in cell culture media showed non-toxic effect under 150 µg/mL concentration of nanocapsules, and subsequent studies on the maturation of immature dendritic cells in the presence of antigen-conjugated nanocapsules displayed peripheral blood mononuclear cell activation and lymphocyte differentiation after their presentation by dendritic cells. Secretion of TNFα following exposure to nanocapsules and the ability of nanocapsules to activate CD4 and CD8 T lymphocytes had also been studied.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Sanejouand, Yves-Henri
Normal-mode driven exploration of protein domain motions Article de journal
Dans: J. Comput. Chem., vol. 42, p. 2250, 2021.
@article{sanejouand2021normalmode,
title = {Normal-mode driven exploration of protein domain motions},
author = {Yves-Henri Sanejouand},
url = {https://arxiv.org/abs/2103.11959},
doi = {10.1002/jcc.26755},
year = {2021},
date = {2021-03-22},
urldate = {2021-03-22},
journal = {J. Comput. Chem.},
volume = {42},
pages = {2250},
abstract = {Domain motions involved in the function of proteins can often be well described as a combination of motions along a handfull of low-frequency modes, that is, with the values of a few normal coordinates. This means that, when the functional motion of a protein is unknown, it should prove possible to predict it, since it amounts to guess a few values. However, without the help of additional experimental data, using normal coordinates for generating accurate conformers far away from the initial one is not so straightforward. To do so, a new approach is proposed: instead of building conformers directly with the values of a subset of normal coordinates, they are built in two steps, the conformer built with normal coordinates being just used for defining a set of distance constraints, the final conformer being built so as to match them. Note that this approach amounts to transform the problem of generating accurate protein conformers using normal coordinates into a better known one: the distance-geometry problem, which is herein solved with the help of the ROSETTA software. In the present study, this approach allowed to rebuild accurately six large amplitude conformational changes, using at most six low-frequency normal coordinates. As a consequence of the low-dimensionality of the corresponding subspace, random exploration also proved enough for generating low-energy conformers close to the known end-point of the conformational change of the LAO binding protein, lysozyme T4 and adenylate kinase.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Sanejouand, Yves-Henri
On the vibrational free energy of hydrated proteins Article de journal
Dans: Physical Biology, vol. 18, no. 3, p. 036003, 2021.
@article{Sanejouand_2021,
title = {On the vibrational free energy of hydrated proteins},
author = {Yves-Henri Sanejouand},
url = {https://doi.org/10.1088/1478-3975/abdc0f},
doi = {10.1088/1478-3975/abdc0f},
year = {2021},
date = {2021-03-01},
urldate = {2021-03-01},
journal = {Physical Biology},
volume = {18},
number = {3},
pages = {036003},
publisher = {IOP Publishing},
abstract = {When the hydration shell of a protein is filled with at least 0.6 gram of water per gram of protein, a significant anti-correlation between the vibrational free energy and the potential energy of energy-minimized conformers is observed. This means that low potential energy, well-hydrated, protein conformers tend to be more rigid than high-energy ones. On the other hand, in the case of CASP target 624, when its hydration shell is filled, a significant energy gap is observed between the crystal structure and the best conformers proposed during the prediction experiment, strongly suggesting that including explicit water molecules may help identifying unlikely conformers among good-looking ones.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Zhao, Xue; Rastogi, Achal; Cabanillas, Anne Flore Deton; Mohamed, Ouardia Ait; Cantrel, Catherine; Lombard, Berangère; Murik, Omer; Genovesio, Auguste; Bowler, Chris; Bouyer, Daniel; Loew, Damarys; Lin, Xin; Veluchamy, Alaguraj; Vieira, Fabio Rocha Jimenez; Tirichine, Leila
Genome wide natural variation of H3K27me3 selectively marks genes predicted to be important for cell differentiation in Phaeodactylum tricornutum Article de journal
Dans: New Phytologist, p. nph.17129, 2021, ISSN: 0028-646X.
@article{Zhao2020b,
title = {Genome wide natural variation of H3K27me3 selectively marks genes predicted to be important for cell differentiation in Phaeodactylum tricornutum},
author = {Xue Zhao and Achal Rastogi and Anne Flore {Deton Cabanillas} and Ouardia {Ait Mohamed} and Catherine Cantrel and Berangère Lombard and Omer Murik and Auguste Genovesio and Chris Bowler and Daniel Bouyer and Damarys Loew and Xin Lin and Alaguraj Veluchamy and Fabio Rocha Jimenez Vieira and Leila Tirichine},
url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.17129},
doi = {10.1111/nph.17129},
issn = {0028-646X},
year = {2021},
date = {2021-01-01},
urldate = {2020-12-01},
journal = {New Phytologist},
pages = {nph.17129},
publisher = {Blackwell Publishing Ltd},
abstract = {In multicellular organisms, Polycomb Repressive Complex2 (PRC2) is known to deposit tri-methylation of lysine 27 of histone H3 (H3K27me3) to establish and maintain gene silencing, critical for developmentally regulated processes. The PRC2 complex is absent in both widely studied model yeasts, which initially suggested that PRC2 arose with the emergence of multicellularity. However, its discovery in several unicellular species including microalgae questions its role in unicellular eukaryotes. Here, we use Phaeodactylum tricornutum enhancer of zeste E(z) knockouts and show that P. tricornutum E(z) is responsible for di- and tri-methylation of lysine 27 of histone H3. H3K27me3 depletion abolishes cell morphology in P. tricornutum providing evidence for its role in cell differentiation. Genome-wide profiling of H3K27me3 in fusiform and triradiate cells further revealed genes that may specify cell identity. These results suggest a role for PRC2 and its associated mark in cell differentiation in unicellular species, and highlight their ancestral function in a broader evolutionary context than currently is appreciated.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Hoguin, Antoine; Rastogi, Achal; Bowler, Chris; Tirichine, Leila
Genome ‑ wide analysis of allele ‑ specific expression of genes in the model diatom Phaeodactylum tricornutum Article de journal
Dans: Scientific Reports, p. 1–10, 2021, ISSN: 2045-2322.
@article{Hoguin2021,
title = {Genome ‑ wide analysis of allele ‑ specific expression of genes in the model diatom Phaeodactylum tricornutum},
author = {Antoine Hoguin and Achal Rastogi and Chris Bowler and Leila Tirichine},
url = {https://doi.org/10.1038/s41598-021-82529-1},
doi = {10.1038/s41598-021-82529-1},
issn = {2045-2322},
year = {2021},
date = {2021-01-01},
journal = {Scientific Reports},
pages = {1--10},
publisher = {Nature Publishing Group UK},
abstract = {Recent advances in next generation sequencing technologies have allowed the discovery of widespread autosomal allele-specific expression (aASE) in mammals and plants with potential phenotypic effects. Extensive numbers of genes with allele-specific expression have been described in the diatom Fragilariopsis cylindrus in association with adaptation to external cues, as well as in Fistulifera solaris in the context of natural hybridization. However, the role of aASE and its extent in diatoms remain elusive. In this study, we investigate allele-specific expression in the model diatom Phaeodactylum tricornutum by the re-analysis of previously published whole genome RNA sequencing data and polymorphism calling. We found that 22% of P. tricornutum genes show moderate bias in allelic expression while 1% show nearly complete monoallelic expression. Biallelic expression associates with genes encoding components of protein metabolism while moderately biased genes associate with functions in catabolism and protein transport. We validated candidate genes by pyrosequencing and found that moderate biases in allelic expression were less stable than monoallelically expressed genes that showed consistent bias upon experimental validations at the population level and in subcloning experiments. Our approach provides the basis for the analysis of aASE in P. tricornutum and could be routinely implemented to test for variations in allele expression under different environmental conditions.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Assailly, Coralie; Bridot, Clarisse; Saumonneau, Amélie; Lottin, Paul; Roubinet, Benoit; Krammer, Eva-Maria; François, Francesca; Vena, Federica; Landemarre, Ludovic; Dorta, Dimitri Alvarez; Deniaud, David; Grandjean, Cyrille; Tellier, Charles; Pascual, Sagrario; Montembault, Véronique; Fontaine, Laurent; Daligault, Franck; Bouckaert, Julie; Gouin, Sébastien G
Polyvalent Transition-State Analogues of Sialyl Substrates Strongly Inhibit Bacterial Sialidases** Article de journal
Dans: Chemistry – A European Journal, vol. 27, no. 9, p. 3142-3150, 2021.
@article{https://doi.org/10.1002/chem.202004672,
title = {Polyvalent Transition-State Analogues of Sialyl Substrates Strongly Inhibit Bacterial Sialidases**},
author = {Coralie Assailly and Clarisse Bridot and Amélie Saumonneau and Paul Lottin and Benoit Roubinet and Eva-Maria Krammer and Francesca François and Federica Vena and Ludovic Landemarre and Dimitri Alvarez Dorta and David Deniaud and Cyrille Grandjean and Charles Tellier and Sagrario Pascual and Véronique Montembault and Laurent Fontaine and Franck Daligault and Julie Bouckaert and Sébastien G Gouin},
url = {https://chemistry-europe.onlinelibrary.wiley.com/doi/abs/10.1002/chem.202004672},
doi = {https://doi.org/10.1002/chem.202004672},
year = {2021},
date = {2021-01-01},
journal = {Chemistry – A European Journal},
volume = {27},
number = {9},
pages = {3142-3150},
abstract = {Abstract Bacterial sialidases (SA) are validated drug targets expressed by common human pathogens such as Streptococcus pneumoniae, Vibrio cholerae, or Clostridium perfringens. Noncovalent inhibitors of bacterial SA capable of reaching the submicromolar level are rarely reported. In this work, multi- and polyvalent compounds are developed, based on the transition-state analogue 2-deoxy-2,3-didehydro-N-acetylneuraminic (DANA). Poly-DANA inhibits the catalytic activity of SA from S. pneumoniae (NanA) and the symbiotic microorganism B. thetaiotaomicron (BtSA) at the picomolar and low nanomolar levels (expressed in moles of molecules and of DANA, respectively). Each DANA grafted to the polymer surpasses the inhibitory potential of the monovalent analogue by more than four orders of magnitude, which represents the highest multivalent effect reported so far for an enzyme inhibition. The synergistic interaction is shown to operate exclusively in the catalytic domain, and not in the flanked carbohydrate-binding module (CBM). These results offer interesting perspectives for the multivalent inhibition of other SA families lacking a CBM, such as viral, parasitic, or human SA.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Ogonda, Lydia A; Saumonneau, Amélie; Dion, Michel; Muge, Edward K; Wamalwa, Benson M; Mulaa, Francis J; Tellier, Charles
Characterization and engineering of two new GH9 and GH48 cellulases from a Bacillus pumilus isolated from Lake Bogoria Article de journal
Dans: Biotechnology Letters, vol. 43, p. 691–700, 2021.
@article{ogondacharacterization,
title = {Characterization and engineering of two new GH9 and GH48 cellulases from a Bacillus pumilus isolated from Lake Bogoria},
author = {Lydia A Ogonda and Amélie Saumonneau and Michel Dion and Edward K Muge and Benson M Wamalwa and Francis J Mulaa and Charles Tellier},
doi = {10.1007/s10529-020-03056-z},
year = {2021},
date = {2021-01-01},
journal = {Biotechnology Letters},
volume = {43},
pages = {691–700},
publisher = {Springer},
abstract = {Objectives. To search for new alkaliphilic cellulases and to improve their efficiency on crystalline cellulose through molecular engineering
Results. Two novel cellulases, BpGH9 and BpGH48, from a Bacillus pumilus strain were identified, cloned and biochemically characterized. BpGH9 is a modular endocellulase belonging to the glycoside hydrolase 9 family (GH9), which contains a catalytic module (GH) and a carbohydrate-binding module belonging to class 3 and subclass c (CBM3c). This enzyme is extremely tolerant to high alkali pH and remains significantly active at pH 10. BpGH48 is an exocellulase, belonging to the glycoside hydrolase 48 family (GH48) and acts on the reducing end of oligo-β1,4 glucanes. A truncated form of BpGH9 and a chimeric fusion with an additional CBM3a module was constructed. The deletion of the CBM3c module results in a significant decline in the catalytic activity. However, fusion of CBM3a, although in a non native position, enhanced the activity of BpGH9 on crystalline cellulose.
Conclusions. A new alkaliphilic endocellulase BpGH9, was cloned and engineered as a fusion protein (CBM3a-BpGH9), which led to an improved activity on crystalline cellulose.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Results. Two novel cellulases, BpGH9 and BpGH48, from a Bacillus pumilus strain were identified, cloned and biochemically characterized. BpGH9 is a modular endocellulase belonging to the glycoside hydrolase 9 family (GH9), which contains a catalytic module (GH) and a carbohydrate-binding module belonging to class 3 and subclass c (CBM3c). This enzyme is extremely tolerant to high alkali pH and remains significantly active at pH 10. BpGH48 is an exocellulase, belonging to the glycoside hydrolase 48 family (GH48) and acts on the reducing end of oligo-β1,4 glucanes. A truncated form of BpGH9 and a chimeric fusion with an additional CBM3a module was constructed. The deletion of the CBM3c module results in a significant decline in the catalytic activity. However, fusion of CBM3a, although in a non native position, enhanced the activity of BpGH9 on crystalline cellulose.
Conclusions. A new alkaliphilic endocellulase BpGH9, was cloned and engineered as a fusion protein (CBM3a-BpGH9), which led to an improved activity on crystalline cellulose.
Duc, Céline; Thiriet, Christophe
Replication-Coupled Chromatin Remodeling: An Overview of Disassembly and Assembly of Chromatin during Replication Article de journal
Dans: International Journal of Molecular Sciences, vol. 22, no. 3, 2021, ISSN: 1422-0067.
@article{ijms22031113,
title = {Replication-Coupled Chromatin Remodeling: An Overview of Disassembly and Assembly of Chromatin during Replication},
author = {Céline Duc and Christophe Thiriet},
url = {https://www.mdpi.com/1422-0067/22/3/1113
hal-04210949v1 },
doi = {10.3390/ijms22031113},
issn = {1422-0067},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {International Journal of Molecular Sciences},
volume = {22},
number = {3},
abstract = {The doubling of genomic DNA during the S-phase of the cell cycle involves the global remodeling of chromatin at replication forks. The present review focuses on the eviction of nucleosomes in front of the replication forks to facilitate the passage of replication machinery and the mechanism of replication-coupled chromatin assembly behind the replication forks. The recycling of parental histones as well as the nuclear import and the assembly of newly synthesized histones are also discussed with regard to the epigenetic inheritance.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Rahmani, Alexandra; Delavat, François; Lambert, Christophe; Goic, Nelly Le; Dabas, Eric; Paillard, Christine; Pichereau, Vianney
Dans: Frontiers in Cellular and Infection Microbiology, vol. 11, p. 634427, 2021, ISSN: 2235-2988.
@article{rahmani_implication_2021,
title = {Implication of the Type IV Secretion System in the Pathogenicity of Vibrio tapetis, the Etiological Agent of Brown Ring Disease Affecting the Manila Clam Ruditapes philippinarum},
author = {Alexandra Rahmani and François Delavat and Christophe Lambert and Nelly Le Goic and Eric Dabas and Christine Paillard and Vianney Pichereau},
url = {https://www.frontiersin.org/articles/10.3389/fcimb.2021.634427/full},
doi = {10.3389/fcimb.2021.634427},
issn = {2235-2988},
year = {2021},
date = {2021-01-01},
urldate = {2021-04-29},
journal = {Frontiers in Cellular and Infection Microbiology},
volume = {11},
pages = {634427},
abstract = {Vibrio tapetis is a Gram-negative bacterium that causes infections of mollusk bivalves and fish. The Brown Ring Disease (BRD) is an infection caused by V. tapetis that primarily affects the Manila clam Ruditapes philippinarum. Recent studies have shown that a type IV secretion system (T4SS) gene cluster is exclusively found in strains of V. tapetis pathogenic to clams. However, whether the T4SS is implicated or not during the infection process remains unknown. The aim of this study was to create and characterize a V. tapetis T4SS null mutant, obtained by a near-complete deletion of the virB4 gene, in order to determine the role of T4SS in the development of BRD. This study demonstrated that the T4SS is neither responsible for the loss of hemocyte adhesion capacities, nor for the decrease of the lysosomal activity during BRD. Nevertheless, we observed a 50% decrease of the BRD prevalence and a decrease of mortality dynamics with the DvirB4 mutant. This work demonstrates that the T4SS of V. tapetis plays an important role in the development of BRD in the Manila clam.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Lapaillerie, Delphine; Charlier, Cathy; Fernandes, Henrique S; Sousa, Sergio F; Lesbats, Paul; Weigel, Pierre; Favereaux, Alexandre; Guyonnet-Duperat, Véronique; Parissi, Vincent
In Silico, In Vitro and In Cellulo Models for Monitoring SARS-CoV-2 Spike/Human ACE2 Complex, Viral Entry and Cell Fusion Article de journal
Dans: Viruses, vol. 13, no. 3, p. 365, 2021, ISSN: 1999-4915.
@article{lapaillerie_silico_2021,
title = {In Silico, In Vitro and In Cellulo Models for Monitoring SARS-CoV-2 Spike/Human ACE2 Complex, Viral Entry and Cell Fusion},
author = {Delphine Lapaillerie and Cathy Charlier and Henrique S Fernandes and Sergio F Sousa and Paul Lesbats and Pierre Weigel and Alexandre Favereaux and Véronique Guyonnet-Duperat and Vincent Parissi},
url = {https://www.mdpi.com/1999-4915/13/3/365},
doi = {10.3390/v13030365},
issn = {1999-4915},
year = {2021},
date = {2021-01-01},
urldate = {2021-04-30},
journal = {Viruses},
volume = {13},
number = {3},
pages = {365},
abstract = {Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiologic agent responsible for the recent coronavirus disease 2019 (COVID-19) pandemic. Productive SARS-CoV-2 infection relies on viral entry into cells expressing angiotensin-converting enzyme 2 (ACE2). Indeed, viral entry into cells is mostly mediated by the early interaction between the viral spike protein S and its ACE2 receptor. The S/ACE2 complex is, thus, the first contact point between the incoming virus and its cellular target; consequently, it has been considered an attractive therapeutic target. To further characterize this interaction and the cellular processes engaged in the entry step of the virus, we set up various in silico, in vitro and in cellulo approaches that allowed us to specifically monitor the S/ACE2 association. We report here a computational model of the SARS-CoV-2 S/ACE2 complex, as well as its biochemical and biophysical monitoring using pulldown, AlphaLISA and biolayer interferometry (BLI) binding assays. This led us to determine the kinetic parameters of the S/ACE2 association and dissociation steps. In parallel to these in vitro approaches, we developed in cellulo transduction assays using SARS-CoV-2 pseudotyped lentiviral vectors and HEK293T-ACE2 cell lines generated in-house. This allowed us to recapitulate the early replication stage of the infection mediated by the S/ACE2 interaction and to detect cell fusion induced by the interaction. Finally, a cell imaging system was set up to directly monitor the S/ACE2 interaction in a cellular context and a flow cytometry assay was developed to quantify this association at the cell surface. Together, these different approaches are available for both basic and clinical research, aiming to characterize the entry step of the original SARS-CoV-2 strain and its variants as well as to investigate the possible chemical modulation of this interaction. All these models will help in identifying new antiviral agents and new chemical tools for dissecting the virus entry step.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Floch, Aline; Téletchéa, Stéphane; Tournamille, Christophe; de Brevern, Alexandre G; Pirenne, France
A Review of the Literature Organized Into a New Database: RHeference Article de journal
Dans: Transfusion Medicine Reviews, 2021, ISSN: 0887-7963.
@article{FLOCH2021,
title = {A Review of the Literature Organized Into a New Database: RHeference},
author = {Aline Floch and Stéphane Téletchéa and Christophe Tournamille and Alexandre G de Brevern and France Pirenne},
url = {https://www.sciencedirect.com/science/article/pii/S0887796321000109},
doi = {https://doi.org/10.1016/j.tmrv.2021.04.002},
issn = {0887-7963},
year = {2021},
date = {2021-01-01},
journal = {Transfusion Medicine Reviews},
abstract = {Hundreds of articles containing heterogeneous data describe D variants or add to the knowledge of known alleles. Data can be difficult to find despite existing online blood group resources and genetic and literature databases. We have developed a modern, elaborate database for D variants, thanks to an extensive literature search with meticulous curation of 387 peer-reviewed articles and 80 abstracts from major conferences and other sources. RHeference contains entries for 710 RHD alleles, 11 RHCE alleles, 30 phenotype descriptions (preventing data loss from historical sources), 35 partly characterized alleles, 3 haplotypes, and 16 miscellaneous entries. The entries include molecular, phenotypic, serological, alloimmunization, haplotype, geographical, and other data, detailed for each source. The main characteristics are summarized for each entry. The sources for all information are included and easily accessible through doi and PMID links. Overall, the database contains more than 10,000 individual pieces of data. We have set up the database architecture based on our previous expertise on database setup and biocuration for other topics, using modern technologies such as the Django framework, BioPython, Bootstrap, and Jquery. This architecture allows an easy access to data and enables simple and complex queries: combining multiple mutations, keywords, or any of the characteristics included in the database. RHeference provides a complement to existing resources and will continue to grow as our knowledge expands and new articles are published. The database url is http://www.rheference.org/.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Prasanna, Maruthi; Podsiadla-Bialoskorska, Malgorzata; Mielecki, Damian; Ruffier, Nicolas; Fateh, Amina; Lambert, Annie; Fanuel, Mathieu; Camberlein, Emilie; Szolajska, Ewa; Grandjean, Cyrille
On the use of adenovirus dodecahedron as a carrier for glycoconjugate vaccines Article de journal
Dans: Glycoconjugate Journal, 2021, ISSN: 1573-4986.
@article{prasanna_use_2021,
title = {On the use of adenovirus dodecahedron as a carrier for glycoconjugate vaccines},
author = {Maruthi Prasanna and Malgorzata Podsiadla-Bialoskorska and Damian Mielecki and Nicolas Ruffier and Amina Fateh and Annie Lambert and Mathieu Fanuel and Emilie Camberlein and Ewa Szolajska and Cyrille Grandjean},
url = {https://doi.org/10.1007/s10719-021-09999-3},
doi = {10.1007/s10719-021-09999-3},
issn = {1573-4986},
year = {2021},
date = {2021-01-01},
urldate = {2021-06-16},
journal = {Glycoconjugate Journal},
abstract = {Virus-Like Particles (VLPs) have been used as immunogenic molecules in numerous recombinant vaccines. VLPs can also serve as vaccine platform to exogenous antigens, usually peptides incorporated within the protein sequences which compose the VLPs or conjugated to them. We herein described the conjugation of a synthetic tetrasaccharide mimicking the Streptococcus pneumoniae serotype 14 capsular polysaccharide to recombinant adenoviral type 3 dodecahedron, formed by the self-assembling of twelve penton bases and investigated the induced immune response when administered subcutaneously (s.c.). Whether formulated in the form of a dodecahedron or disassembled, the glycoconjugate induced an anti-protein response after two and three immunizations equivalent to that observed when the native dodecahedron was administered. On the other hand, the glycoconjugate induced a weak anti-IgM response which diminishes after two doses but no IgM-to-IgG switch was observed in mice against the serotype 14 capsular polysaccharide. In definitive, the whole conjugation process preserved both particulate nature and immunogenicity of the adenoviral dodecahedron. Further studies are needed to fully exploit adenoviral dodecahedron potential in terms of plasticity towards sequence engineering and of its capacity to stimulate the immune system via the intranasal route of administration as well as to shift the response to the carbohydrate antigen by playing both with the carbohydrate to protein ratio and the length of the synthetic carbohydrate antigen.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Gheyouche, Ennys; Bagueneau, Matthias; Loirand, Gervaise; Offmann, Bernard; Téletchéa, Stéphane
Structural Design and Analysis of the RHOA-ARHGEF1 Binding Mode: Challenges and Applications for Protein-Protein Interface Prediction Article de journal
Dans: Frontiers in Molecular Biosciences, vol. 8, p. 643728, 2021, ISSN: 2296-889X.
@article{gheyouche_structural_2021,
title = {Structural Design and Analysis of the RHOA-ARHGEF1 Binding Mode: Challenges and Applications for Protein-Protein Interface Prediction},
author = {Ennys Gheyouche and Matthias Bagueneau and Gervaise Loirand and Bernard Offmann and Stéphane Téletchéa},
doi = {10.3389/fmolb.2021.643728},
issn = {2296-889X},
year = {2021},
date = {2021-01-01},
journal = {Frontiers in Molecular Biosciences},
volume = {8},
pages = {643728},
abstract = {The interaction between two proteins may involve local movements, such as small side-chains re-positioning or more global allosteric movements, such as domain rearrangement. We studied how one can build a precise and detailed protein-protein interface using existing protein-protein docking methods, and how it can be possible to enhance the initial structures using molecular dynamics simulations and data-driven human inspection. We present how this strategy was applied to the modeling of RHOA-ARHGEF1 interaction using similar complexes of RHOA bound to other members of the Rho guanine nucleotide exchange factor family for comparative assessment. In parallel, a more crude approach based on structural superimposition and molecular replacement was also assessed. Both models were then successfully refined using molecular dynamics simulations leading to protein structures where the major data from scientific literature could be recovered. We expect that the detailed strategy used in this work will prove useful for other protein-protein interface design. The RHOA-ARHGEF1 interface modeled here will be extremely useful for the design of inhibitors targeting this protein-protein interaction (PPI).},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Poulet, Axel; Mishra, Laxmi Narayan; Téletchéa, Stéphane; Hayes, Jeffrey J; Jacob, Yannick; Thiriet, Christophe; Duc, Céline
Identification and characterization of histones in Physarum polycephalum evidence a phylogenetic vicinity of Mycetozoans to the animal kingdom Article de journal
Dans: NAR Genomics and Bioinformatics, vol. 3, no. 4, 2021, ISSN: 2631-9268, (lqab107).
@article{10.1093/nargab/lqab107,
title = {Identification and characterization of histones in Physarum polycephalum evidence a phylogenetic vicinity of Mycetozoans to the animal kingdom},
author = {Axel Poulet and Laxmi Narayan Mishra and Stéphane Téletchéa and Jeffrey J Hayes and Yannick Jacob and Christophe Thiriet and Céline Duc},
url = {https://doi.org/10.1093/nargab/lqab107
hal-03595485v1 },
doi = {10.1093/nargab/lqab107},
issn = {2631-9268},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {NAR Genomics and Bioinformatics},
volume = {3},
number = {4},
abstract = {Physarum polycephalum belongs to Mycetozoans, a phylogenetic clade apart from the animal, plant and fungus kingdoms. Histones are nuclear proteins involved in genome organization and regulation and are among the most evolutionary conserved proteins within eukaryotes. Therefore, this raises the question of their conservation in Physarum and the position of this organism within the eukaryotic phylogenic tree based on histone sequences. We carried out a comprehensive study of histones in Physarum polycephalum using genomic, transcriptomic and molecular data. Our results allowed to identify the different isoforms of the core histones H2A, H2B, H3 and H4 which exhibit strong conservation of amino acid residues previously identified as subject to post-translational modifications. Furthermore, we also identified the linker histone H1, the most divergent histone, and characterized a large number of its PTMs by mass spectrometry. We also performed an in-depth investigation of histone genes and transcript structures. Histone proteins are highly conserved in Physarum and their characterization will contribute to a better understanding of the polyphyletic Mycetozoan group. Our data reinforce that P. polycephalum is evolutionary closer to animals than plants and located at the crown of the eukaryotic tree. Our study provides new insights in the evolutionary history of Physarum and eukaryote lineages.},
note = {lqab107},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Brun, Guillaume; Spallek, Thomas; Simier, Philippe; Delavault, Philippe
Molecular actors of seed germination and haustoriogenesis in parasitic weeds Article de journal
Dans: Plant Physiol, vol. 185, no. 4, p. 1270-1281, 2021, ISSN: 0032-0889 (Print) 0032-0889.
@article{RN8,
title = {Molecular actors of seed germination and haustoriogenesis in parasitic weeds},
author = {Guillaume Brun and Thomas Spallek and Philippe Simier and Philippe Delavault},
url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8133557/pdf/kiaa041.pdf},
doi = {10.1093/plphys/kiaa041},
issn = {0032-0889 (Print) 0032-0889},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {Plant Physiol},
volume = {185},
number = {4},
pages = {1270-1281},
abstract = {One-sentence summary Recent advances provide insight into the molecular mechanisms underlying host-dependent seed germination and haustorium formation in parasitic plants.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Germain, Alexandre Saint; Jacobs, Anse; Brun, Guillaume; Pouvreau, Jean-Bernard; Braem, Lukas; Cornu, David; Clavé, Guillaume; Baudu, Emmanuelle; Steinmetz, Vincent; Servajean, Vincent; Wicke, Susann; Gevaert, Kris; Simier, Philippe; Goormachtig, Sophie; Delavault, Philippe; Boyer, François-Didier
A Phelipanche ramosa KAI2 protein perceives strigolactones and isothiocyanates enzymatically Article de journal
Dans: Plant Commun, vol. 2, no. 5, p. 100166, 2021, ISSN: 2590-3462.
@article{RN13,
title = {A Phelipanche ramosa KAI2 protein perceives strigolactones and isothiocyanates enzymatically},
author = {Alexandre Saint Germain and Anse Jacobs and Guillaume Brun and Jean-Bernard Pouvreau and Lukas Braem and David Cornu and Guillaume Clavé and Emmanuelle Baudu and Vincent Steinmetz and Vincent Servajean and Susann Wicke and Kris Gevaert and Philippe Simier and Sophie Goormachtig and Philippe Delavault and François-Didier Boyer},
url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8553955/pdf/main.pdf},
doi = {10.1016/j.xplc.2021.100166},
issn = {2590-3462},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {Plant Commun},
volume = {2},
number = {5},
pages = {100166},
abstract = {Phelipanche ramosa is an obligate root-parasitic weed that threatens major crops in central Europe. In order to germinate, it must perceive various structurally divergent host-exuded signals, including isothiocyanates (ITCs) and strigolactones (SLs). However, the receptors involved are still uncharacterized. Here, we identify five putative SL receptors in P. ramosa and show that PrKAI2d3 is involved in the stimulation of seed germination. We demonstrate the high plasticity of PrKAI2d3, which allows it to interact with different chemicals, including ITCs. The SL perception mechanism of PrKAI2d3 is similar to that of endogenous SLs in non-parasitic plants. We provide evidence that PrKAI2d3 enzymatic activity confers hypersensitivity to SLs. Additionally, we demonstrate that methylbutenolide-OH binds PrKAI2d3 and stimulates P. ramosa germination with bioactivity comparable to that of ITCs. This study demonstrates that P. ramosa has extended its signal perception system during evolution, a fact that should be considered for the development of specific and efficient biocontrol methods.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Lopez-Obando, Mauricio; Guillory, Ambre; Boyer, François-Didier; Cornu, David; Hoffmann, Beate; Bris, Philippe Le; Pouvreau, Jean-Bernard; Delavault, Philippe; Rameau, Catherine; Germain, Alexandre Saint; Bonhomme, Sandrine
The Physcomitrium (Physcomitrella) patens PpKAI2L receptors for strigolactones and related compounds function via MAX2-dependent and -independent pathways Article de journal
Dans: Plant Cell, vol. 33, no. 11, p. 3487-3512, 2021, ISSN: 1040-4651 (Print) 1040-4651.
@article{RN27,
title = {The Physcomitrium (Physcomitrella) patens PpKAI2L receptors for strigolactones and related compounds function via MAX2-dependent and -independent pathways},
author = {Mauricio Lopez-Obando and Ambre Guillory and François-Didier Boyer and David Cornu and Beate Hoffmann and Philippe Le Bris and Jean-Bernard Pouvreau and Philippe Delavault and Catherine Rameau and Alexandre Saint Germain and Sandrine Bonhomme},
url = {https://academic.oup.com/plcell/article-abstract/33/11/3487/6359828?redirectedFrom=fulltext},
doi = {10.1093/plcell/koab217},
issn = {1040-4651 (Print) 1040-4651},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {Plant Cell},
volume = {33},
number = {11},
pages = {3487-3512},
abstract = {In angiosperms, the α/β hydrolase DWARF14 (D14), along with the F-box protein MORE AXILLARY GROWTH2 (MAX2), perceives strigolactones (SL) to regulate developmental processes. The key SL biosynthetic enzyme CAROTENOID CLEAVAGE DIOXYGENASE8 (CCD8) is present in the moss Physcomitrium patens, and PpCCD8-derived compounds regulate moss extension. The PpMAX2 homolog is not involved in the SL response, but 13 PpKAI2LIKE (PpKAI2L) genes homologous to the D14 ancestral paralog KARRIKIN INSENSITIVE2 (KAI2) encode candidate SL receptors. In Arabidopsis thaliana, AtKAI2 perceives karrikins and the elusive endogenous KAI2-Ligand (KL). Here, germination assays of the parasitic plant Phelipanche ramosa suggested that PpCCD8-derived compounds are likely noncanonical SLs. (+)-GR24 SL analog is a good mimic for PpCCD8-derived compounds in P. patens, while the effects of its enantiomer (-)-GR24, a KL mimic in angiosperms, are minimal. Interaction and binding assays of seven PpKAI2L proteins pointed to the stereoselectivity toward (-)-GR24 for a single clade of PpKAI2L (eu-KAI2). Enzyme assays highlighted the peculiar behavior of PpKAI2L-H. Phenotypic characterization of Ppkai2l mutants showed that eu-KAI2 genes are not involved in the perception of PpCCD8-derived compounds but act in a PpMAX2-dependent pathway. In contrast, mutations in PpKAI2L-G, and -J genes abolished the response to the (+)-GR24 enantiomer, suggesting that PpKAI2L-G, and -J proteins are receptors for moss SLs.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Pouvreau, Jean-Bernard; Poulin, Lucie; Huet, Sarah; Delavault, Philippe
Strigolactone-Like Bioactivity via Parasitic Plant Germination Bioassay Article de journal
Dans: Methods Mol Biol, vol. 2309, p. 59–73, 2021, ISSN: 1940-6029.
@article{pmid34028679b,
title = {Strigolactone-Like Bioactivity via Parasitic Plant Germination Bioassay},
author = {Jean-Bernard Pouvreau and Lucie Poulin and Sarah Huet and Philippe Delavault},
doi = {10.1007/978-1-0716-1429-7_6},
issn = {1940-6029},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {Methods Mol Biol},
volume = {2309},
pages = {59--73},
abstract = {Strigolactones are a class of plant hormones involved in shoot branching, growth of symbiotic arbuscular mycorrhizal fungi, and germination of parasitic plant seeds. Assaying new molecules or compound exhibiting strigolactone-like activities is therefore important but unfortunately time-consuming and hard to implement because of the extremely low concentrations at which they are active. Seeds of parasite plants are natural integrator of these hormones since they can perceive molecule concentrations in the picomolar to nanomolar range stimulating their germination. Here we describe a simple and inexpensive method to evaluate the activity of these molecules by scoring the germination of parasitic plant seeds upon treatment with these molecules. Up to four molecules can be assayed from a single 96-well plate by this method. A comparison of SL-like bioactivities between molecules is done by determining the EC50 and the maximum percentage of germination.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Muñoz-Garcia, Javier; Cochonneau, Denis; Télétchéa, Stéphane; Moranton, Emilie; Lanoe, Didier; Brion, Régis; Lézot, Frédéric; Heymann, Marie-Françoise; Heymann, Dominique
The twin cytokines interleukin-34 and CSF-1: masterful conductors of macrophage homeostasis Article de journal
Dans: Theranostics, vol. 11, no. 4, p. 1568–1593, 2021, ISSN: 1838-7640.
@article{pmid33408768,
title = {The twin cytokines interleukin-34 and CSF-1: masterful conductors of macrophage homeostasis},
author = {Javier Muñoz-Garcia and Denis Cochonneau and Stéphane Télétchéa and Emilie Moranton and Didier Lanoe and Régis Brion and Frédéric Lézot and Marie-Françoise Heymann and Dominique Heymann},
doi = {10.7150/thno.50683},
issn = {1838-7640},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {Theranostics},
volume = {11},
number = {4},
pages = {1568--1593},
abstract = {Macrophages are specialized cells that control tissue homeostasis. They include non-resident and tissue-resident macrophage populations which are characterized by the expression of particular cell surface markers and the secretion of molecules with a wide range of biological functions. The differentiation and polarization of macrophages relies on specific growth factors and their receptors. Macrophage-colony stimulating factor (CSF-1) and interleukine-34 (IL-34), also known as "twin" cytokines, are part of this regluatory landscape. CSF-1 and IL-34 share a common receptor, the macrophage-colony stimulating factor receptor (CSF-1R), which is activated in a similar way by both factors and turns on identical signaling pathways. However, there is some discrete differential activation leading to specific activities. In this review, we disscuss recent progress in understanding of the role of the twin cytokines in macrophage differentiation, from their interaction with CSF-1R and the activation of signaling pathways, to their implication in macrophage polarization of non-resident and tissue-resident macrophages. A special focus on IL-34, its involvement in pathophsyiological contexts, and its potential as a theranostic target for macrophage therapy will be proposed.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Hoguin, Antoine; Mohamed, Ouardia Ait; Bowler, Chris; Genovesio, Auguste; Vieira, Fabio Rocha Jimenez; Tirichine, Leila
Evolutionary analysis of DNA methyltransferases in microeukaryotes: Insights from the model diatom Phaeodactylum tricornutum Article de journal
Dans: bioRxiv, 2021.
@article{Hoguin2021.06.11.447926,
title = {Evolutionary analysis of DNA methyltransferases in microeukaryotes: Insights from the model diatom Phaeodactylum tricornutum},
author = {Antoine Hoguin and Ouardia Ait Mohamed and Chris Bowler and Auguste Genovesio and Fabio Rocha Jimenez Vieira and Leila Tirichine},
url = {https://www.biorxiv.org/content/early/2021/06/11/2021.06.11.447926},
doi = {10.1101/2021.06.11.447926},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {bioRxiv},
publisher = {Cold Spring Harbor Laboratory},
abstract = {Cytosine DNA methylation is an important epigenetic mark in eukaryotes that is involved in the transcriptional control of mainly transposable elements in mammals, plants, and fungi. Eukaryotes encode a diverse set of DNA methyltransferases that were iteratively acquired and lost during evolution. The Stramenopiles-Alveolate-Rhizaria (SAR) lineages are a major group of ecologically important marine microeukaryotes that include the main phytoplankton classes such as diatoms and dinoflagellates. However, little is known about the diversity of DNA methyltransferases and their role in the deposition and maintenance of DNA methylation in microalgae. We performed a phylogenetic analysis of DNA methyltransferase families found in marine microeukaryotes and show that they encode divergent DNMT3, DNMT4, DNMT5 and DNMT6 enzymes family revisiting previously established phylogenies. Furthermore, we reveal a novel group of DNMTs with three classes of enzymes within the DNMT5 family. Using a CRISPR/Cas9 strategy we demonstrate that the loss of the DNMT5 gene correlates with a global depletion of DNA methylation and overexpression of transposable elements in the model diatom Phaeodactylum tricornutum. The study provides a pioneering view of the structure and function of a DNMT family in the SAR supergroup.Competing Interest StatementThe authors have declared no competing interest.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Armbrecht, Linda; Eisenhofer, Raphael; Utge, José; Sibert, Elizabeth C; Rocha, Fabio; Ward, Ryan; Karlusich, Juan José Pierella; Tirichine, Leila; Norris, Richard; Summers, Mindi; Bowler, Chris
Paleo-diatom composition from Santa Barbara Basin deep-sea sediments: a comparison of 18S-V9 and diat-rbcL metabarcoding vs shotgun metagenomics Article de journal
Dans: ISME Communications, vol. 1, no. 1, p. 1–10, 2021.
@article{armbrecht2021paleo,
title = {Paleo-diatom composition from Santa Barbara Basin deep-sea sediments: a comparison of 18S-V9 and diat-rbcL metabarcoding vs shotgun metagenomics},
author = {Linda Armbrecht and Raphael Eisenhofer and José Utge and Elizabeth C Sibert and Fabio Rocha and Ryan Ward and Juan José Pierella Karlusich and Leila Tirichine and Richard Norris and Mindi Summers and Chris Bowler},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {ISME Communications},
volume = {1},
number = {1},
pages = {1--10},
publisher = {Nature Publishing Group},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
36 publications
Chabot, Thomas; Cheraud, Yvonnick; Fleury, Fabrice
Relationships between DNA repair and RTK-mediated signaling pathways Article de journal
Dans: Biochimica et Biophysica Acta (BBA) - Reviews on Cancer, p. 188495, 2020, ISSN: 0304419X.
@article{Chabot2020,
title = {Relationships between DNA repair and RTK-mediated signaling pathways},
author = {Thomas Chabot and Yvonnick Cheraud and Fabrice Fleury},
url = {https://linkinghub.elsevier.com/retrieve/pii/S0304419X20302146},
doi = {10.1016/j.bbcan.2020.188495},
issn = {0304419X},
year = {2020},
date = {2020-12-01},
journal = {Biochimica et Biophysica Acta (BBA) - Reviews on Cancer},
pages = {188495},
publisher = {Elsevier},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Méresse, Sarah; Fodil, Mostefa; Fleury, Fabrice; Chénais, Benoît
Fucoxanthin, a Marine-Derived Carotenoid from Brown Seaweeds and Microalgae: A Promising Bioactive Compound for Cancer Therapy Article de journal
Dans: International Journal of Molecular Sciences, vol. 21, no. 23, p. 9273, 2020, ISSN: 1422-0067.
@article{Meresse2020,
title = {Fucoxanthin, a Marine-Derived Carotenoid from Brown Seaweeds and Microalgae: A Promising Bioactive Compound for Cancer Therapy},
author = {Sarah Méresse and Mostefa Fodil and Fabrice Fleury and Benoît Chénais},
url = {https://www.mdpi.com/1422-0067/21/23/9273},
doi = {10.3390/ijms21239273},
issn = {1422-0067},
year = {2020},
date = {2020-12-01},
journal = {International Journal of Molecular Sciences},
volume = {21},
number = {23},
pages = {9273},
publisher = {Multidisciplinary Digital Publishing Institute},
abstract = {Fucoxanthin is a well-known carotenoid of the xanthophyll family, mainly produced by marine organisms such as the macroalgae of the fucus genus or microalgae such as Phaeodactylum tricornutum. Fucoxanthin has antioxidant and anti-inflammatory properties but also several anticancer effects. Fucoxanthin induces cell growth arrest, apoptosis, and/or autophagy in several cancer cell lines as well as in animal models of cancer. Fucoxanthin treatment leads to the inhibition of metastasis-related migration, invasion, epithelial–mesenchymal transition, and angiogenesis. Fucoxanthin also affects the DNA repair pathways, which could be involved in the resistance phenotype of tumor cells. Moreover, combined treatments of fucoxanthin, or its metabolite fucoxanthinol, with usual anticancer treatments can support conventional therapeutic strategies by reducing drug resistance. This review focuses on the current knowledge of fucoxanthin with its potential anticancer properties, showing that fucoxanthin could be a promising compound for cancer therapy by acting on most of the classical hallmarks of tumor cells.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Ait-Mohamed, Ouardia; Vanclová, Anna M G Novák; Joli, Nathalie; Liang, Yue; Zhao, Xue; Genovesio, Auguste; Tirichine, Leila; Bowler, Chris; Dorrell, Richard G
PhaeoNet: A Holistic RNAseq-Based Portrait of Transcriptional Coordination in the Model Diatom Phaeodactylum tricornutum Article de journal
Dans: Frontiers in Plant Science, vol. 11, 2020, ISSN: 1664462X.
@article{Ait-Mohamed2020,
title = {PhaeoNet: A Holistic RNAseq-Based Portrait of Transcriptional Coordination in the Model Diatom Phaeodactylum tricornutum},
author = {Ouardia Ait-Mohamed and Anna M G {Novák Vanclová} and Nathalie Joli and Yue Liang and Xue Zhao and Auguste Genovesio and Leila Tirichine and Chris Bowler and Richard G Dorrell},
url = {https://pubmed.ncbi.nlm.nih.gov/33178253/},
doi = {10.3389/fpls.2020.590949},
issn = {1664462X},
year = {2020},
date = {2020-10-01},
journal = {Frontiers in Plant Science},
volume = {11},
publisher = {Frontiers Media S.A.},
abstract = {Transcriptional coordination is a fundamental component of prokaryotic and eukaryotic cell biology, underpinning the cell cycle, physiological transitions, and facilitating holistic responses to environmental stress, but its overall dynamics in eukaryotic algae remain poorly understood. Better understanding of transcriptional partitioning may provide key insights into the primary metabolism pathways of eukaryotic algae, which frequently depend on intricate metabolic associations between the chloroplasts and mitochondria that are not found in plants. Here, we exploit 187 publically available RNAseq datasets generated under varying nitrogen, iron and phosphate growth conditions to understand the co-regulatory principles underpinning transcription in the model diatom Phaeodactylum tricornutum. Using WGCNA (Weighted Gene Correlation Network Analysis), we identify 28 merged modules of co-expressed genes in the P. tricornutum genome, which show high connectivity and correlate well with previous microarray-based surveys of gene co-regulation in this species. We use combined functional, subcellular localization and evolutionary annotations to reveal the fundamental principles underpinning the transcriptional co-regulation of genes implicated in P. tricornutum chloroplast and mitochondrial metabolism, as well as the functions of diverse transcription factors underpinning this co-regulation. The resource is publically available as PhaeoNet, an advanced tool to understand diatom gene co-regulation.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Chabot, Thomas
Université de Nantes, 2020, (294 pages).
@phdthesis{chabot2020modulation,
title = {Modulation de l'activité du Rad51 par le récepteur tyrosine kinase c-Met dans la réparation des cassures double-brin de l'ADN},
author = {Thomas Chabot},
url = {https://www.theses.fr/2020NANT1013},
year = {2020},
date = {2020-10-01},
school = {Université de Nantes},
abstract = {L'instabilité génomique due à la dérégulation des voies de réparation de l'ADN peut être à l’initiation de cancer et entraîner par la suite une résistance à la chimiothérapie et à la radiothérapie. La compréhension de ces mécanismes biologiques est donc essentielle dans la lutte contre le cancer. RAD51 est la protéine centrale de la voie de réparation des cassures double-brin de l'ADN par recombinaison homologue. Cette réparation conduit à une réparation fidèle de l'ADN. L'activité recombinase de la protéine RAD51 est finement régulée par des modifications post- traductionnelles telles que la phosphorylation. Au cours de la dernière décennie, de plus en plus d’études, suggèrent l'existence d'une relation entre les récepteurs à activité tyrosine kinases, souvent suractivés et impliqués dans l’agressivité et la prolifération cancéreuse, et la réparation de l'ADN. Parmi ces récepteurs à activité tyrosine kinases, le duo c-Met/HGF-SF est souvent muté, sur exprimé ou activé constitutivement dans de nombreux cancers et son inhibition a été montrée comme induisant une diminution de la réparation par recombinaison homologue. Au travers de cette thèse, nous montrons pour la première fois que c-Met est capable de phosphoryler la protéine RAD51 sur quatre résidus tyrosine localisés principalement dans l'interface monomère- monomère du nucléofilament de la recombinase humaine. Nous montrons l’implication de ces phosphorylations sur l’activité de RAD51 dans les différentes étapes de la recombinaison homologue. L'ensemble des résultats obtenus suggère le rôle possible de ces modifications dans la régulation de RAD51 et souligne l'importance de c-Met dans la réponse aux lésions de l'ADN.},
note = {294 pages},
keywords = {},
pubstate = {published},
tppubtype = {phdthesis}
}
Carraro, Nicolas; Richard, Xavier; Sulser, Sandra; Delavat, François; Mazza, Christian; van der Meer, Jan Roelof
An analog to digital converter controls bistable transfer competence development of a widespread bacterial integrative and conjugative element Article de journal
Dans: eLife, vol. 9, p. 1–40, 2020, ISSN: 2050084X.
@article{Carraro2020,
title = {An analog to digital converter controls bistable transfer competence development of a widespread bacterial integrative and conjugative element},
author = {Nicolas Carraro and Xavier Richard and Sandra Sulser and François Delavat and Christian Mazza and Jan Roelof van der Meer},
url = {hal-04202217v1 },
doi = {10.7554/eLife.57915},
issn = {2050084X},
year = {2020},
date = {2020-07-01},
urldate = {2020-07-01},
journal = {eLife},
volume = {9},
pages = {1--40},
publisher = {eLife Sciences Publications Ltd},
abstract = {Conjugative transfer of the integrative and conjugative element ICEclc in Pseudomonas requires development of a transfer competence state in stationary phase, which arises only in 3-5% of individual cells. The mechanisms controlling this bistable switch between non-active and transfer competent cells have long remained enigmatic. Using a variety of genetic tools and epistasis experiments in P. putida, we uncovered an ‘upstream' cascade of three consecutive transcription factor-nodes, which controls transfer competence initiation. One of the uncovered transcription factors (named BisR) is representative for a new regulator family. Initiation activates a feedback loop, controlled by a second hitherto unrecognized heteromeric transcription factor named BisDC. Stochastic modeling and experimental data demonstrated the feedback loop to act as a scalable converter of unimodal (population-wide or ‘analog') input to bistable (subpopulation-specific or ‘digital') output. The feedback loop further enables prolonged production of BisDC, which ensures expression of the ‘downstream' functions mediating ICE transfer competence in activated cells. Phylogenetic analyses showed that the ICEclc regulatory constellation with BisR and BisDC is widespread among Gamma-and Beta-proteobacteria, including various pathogenic strains, highlighting its evolutionary conservation and prime importance to control the behaviour of this wide family of conjugative elements.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Fleury, Fabrice; Demeyer, Alexandre; Weigel, Pierre; Chenais, Benoit; Mathé, Monique; Lebreton, Jacques
Disulfonate stilbenes for use in the treatment of proliferative diseases Patent
WO2020104634A1, 2020.
@patent{demeyer2020,
title = {Disulfonate stilbenes for use in the treatment of proliferative diseases},
author = {Fabrice Fleury and Alexandre Demeyer and Pierre Weigel and Benoit Chenais and Monique Mathé and Jacques Lebreton},
url = {https://worldwide.espacenet.com/patent/search/family/064564793/publication/WO2020104634A1?q=pn%3DWO2020104634A1},
year = {2020},
date = {2020-05-28},
number = {WO2020104634A1},
abstract = {This invention relates to compounds of general formula: wherein R0A and R0B are independently selected from hydrogen and pharmaceutically acceptable cations; and RA and RB are identical and selected from amide, carbamate, sulphonamide, azido, cyano and halide. The invention also relates to a pharmaceutical composition comprising a compound according to the invention. According to an embodiment, the composition further comprises another active ingredient, especially an antineoplastic agent. The invention also relates to a compound or a composition according to the invention for use as a medicament, especially a compound or a composition for use in the treatment of a proliferative disease such as for example cancer.},
keywords = {},
pubstate = {published},
tppubtype = {patent}
}
Dhingra, Surbhi; Sowdhamini, Ramanathan; Sanejouand, Yves-Henri; Cadet, Frédéric; Offmann, Bernard
Customised fragment libraries for ab initio protein structure prediction using a structural alphabet Article de journal
Dans: arXiv:2005.01696, 2020.
@article{Dhingra2020,
title = {Customised fragment libraries for ab initio protein structure prediction using a structural alphabet},
author = {Surbhi Dhingra and Ramanathan Sowdhamini and Yves-Henri Sanejouand and Frédéric Cadet and Bernard Offmann},
url = {https://arxiv.org/pdf/2005.01696.pdf},
year = {2020},
date = {2020-05-01},
journal = {arXiv:2005.01696},
abstract = {Motivation: Computational protein structure prediction has taken over the structural community in past few decades, mostly focusing on the development of Template-Free modelling (TFM) or ab initio modelling protocols. Fragment-based assembly (FBA), falls under this category and is by far the most popular approach to solve the spatial arrangements of proteins. FBA approaches usually rely on sequence based profile comparison to generate fragments from a representative structural database. Here we report the use of Protein Blocks (PBs), a structural alphabet (SA) to perform such sequence comparison and to build customised fragment libraries for TFM. Results: We demonstrate that predicted PB sequences for a query protein can be used to search for high quality fragments that overall cover above 90% of the query. The fragments generated are of minimum length of 11 residues, and fragments that cover more than 30% of the query length were often obtained. Our work shows that PBs can serve as a good way to extract structurally similar fragments from a database of representatives of non-homologous structures and of the proteins that contain less ordered regions.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Ayadi, Nizar; Lafont, Florian; Charlier, Cathy; Benhelli-Mokrani, Houda; Sokolov, Pavel; Sukhanova, Alyona; Fleury, Fabrice; Nabiev, Igor
Comparative Advantages and Limitations of Quantum Dots in Protein Array Applications Chapitre d'ouvrage
Dans: Quantum Dots, vol. 2135, p. 259–273, Springer, New York, NY, Humana, 2020.
@inbook{cEQ3:ayadi_FLEURY:2020,
title = {Comparative Advantages and Limitations of Quantum Dots in Protein Array Applications},
author = {Nizar Ayadi and Florian Lafont and Cathy Charlier and Houda Benhelli-Mokrani and Pavel Sokolov and Alyona Sukhanova and Fabrice Fleury and Igor Nabiev},
year = {2020},
date = {2020-04-01},
booktitle = {Quantum Dots},
volume = {2135},
pages = {259--273},
publisher = {Springer},
address = {New York, NY},
edition = {Humana},
series = {Methods in Molecular Biology},
keywords = {},
pubstate = {published},
tppubtype = {inbook}
}
Zhao, Xue; Hoguin, Antoine; Chaumier, Timothée; Tirichine, Leila
Epigenetic control of diatom genomes: An overview from in Silico characterisation to functional studies Chapitre d'ouvrage
Dans: The molecular life of diatoms, Springer Nature Switzerland AG, 2020.
@inbook{cEQ5:ZHAO_TIRICHINE:2020,
title = {Epigenetic control of diatom genomes: An overview from in Silico characterisation to functional studies},
author = {Xue Zhao and Antoine Hoguin and Timothée Chaumier and Leila Tirichine},
year = {2020},
date = {2020-04-01},
booktitle = {The molecular life of diatoms},
publisher = {Springer Nature Switzerland AG},
keywords = {},
pubstate = {published},
tppubtype = {inbook}
}
Yaremenko, Ivan A; Coghi, Paolo; Prommana, Parichat; Qiu, Congling; Radulov, Peter S; Qu, Yuanqing; Belyakova, Yulia Yu; Zanforlin, Enrico; Kokorekin, Vladimir A; Wu, Yuki Yu Jun; Fleury, Fabrice; Uthaipibull, Chairat; Wong, Vincent Kam Wai; Terent'ev, Alexander O
Synthetic Peroxides Promote Apoptosis of Cancer Cells by Inhibiting P-Glycoprotein ABCB5 Article de journal
Dans: ChemMedChem, vol. 15, no. 13, p. 1118–1127, 2020, ISSN: 18607187.
@article{Yaremenko2020b,
title = {Synthetic Peroxides Promote Apoptosis of Cancer Cells by Inhibiting P-Glycoprotein ABCB5},
author = {Ivan A Yaremenko and Paolo Coghi and Parichat Prommana and Congling Qiu and Peter S Radulov and Yuanqing Qu and Yulia Yu Belyakova and Enrico Zanforlin and Vladimir A Kokorekin and Yuki Yu Jun Wu and Fabrice Fleury and Chairat Uthaipibull and Vincent Kam Wai Wong and Alexander O Terent'ev},
doi = {10.1002/cmdc.202000042},
issn = {18607187},
year = {2020},
date = {2020-03-10},
journal = {ChemMedChem},
volume = {15},
number = {13},
pages = {1118--1127},
abstract = {This article discloses a new horizon for the application of peroxides in medical chemistry. Stable cyclic peroxides are demonstrated to have cytotoxic activity against cancer cells: in addition a mechanism of cytotoxic action is proposed. Synthetic bridged 1,2,4,5‐tetraoxanes and ozonides were effective against HepG2 cancer cells and some ozonides selectively targeted liver cancer cells (the selectivity indexes for compounds 11 b and 12 a are 8 and 5, respectively).
In some instances, tetraoxanes and ozonides were more selective than paclitaxel, artemisinin and artenusic acid.
Annexin V flow‐cytometry analysis revealed that the active ozonides 22 a and 23 a induced cell death of HepG2 by apoptosis. Further study showed that compounds 22 a and 23 a exhibited a strong inhibitory effect on P‐glycoprotein (P‐gp/ABCB5)‐overexpressing HepG2 cancer cells. ABCB5 is a key player in the multidrug‐resistant phenotype of liver cancer. Peroxides failed to demonstrate a direct correlation between oxidative potential and their biological activity. To our knowledge this is the first time that peroxide diastereoisomers have been found to show stereospecific antimalarial action against the chloroquine‐sensitive 3D7 strain of Plasmodium falciparum. Stereoisomeric ozonide 12 b is 11 times more active than stereoisomeric ozonide 12 a (IC50=5.81 vs 65.18 μm). Current findings mean that ozonides merit further investigation as potential therapeutic agents for drug‐resistant hepatocellular carcinoma.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
In some instances, tetraoxanes and ozonides were more selective than paclitaxel, artemisinin and artenusic acid.
Annexin V flow‐cytometry analysis revealed that the active ozonides 22 a and 23 a induced cell death of HepG2 by apoptosis. Further study showed that compounds 22 a and 23 a exhibited a strong inhibitory effect on P‐glycoprotein (P‐gp/ABCB5)‐overexpressing HepG2 cancer cells. ABCB5 is a key player in the multidrug‐resistant phenotype of liver cancer. Peroxides failed to demonstrate a direct correlation between oxidative potential and their biological activity. To our knowledge this is the first time that peroxide diastereoisomers have been found to show stereospecific antimalarial action against the chloroquine‐sensitive 3D7 strain of Plasmodium falciparum. Stereoisomeric ozonide 12 b is 11 times more active than stereoisomeric ozonide 12 a (IC50=5.81 vs 65.18 μm). Current findings mean that ozonides merit further investigation as potential therapeutic agents for drug‐resistant hepatocellular carcinoma.
Dussouy, Christophe; Kishor, Chandan; Lambert, Annie; Lamoureux, Clément; Blanchard, Helen; Grandjean, Cyrille
Linear triazole-linked pseudo oligogalactosides as scaffolds for galectin inhibitor development. Article de journal
Dans: Chemical biology & drug design, 2020, ISSN: 1747-0285 (Electronic).
@article{Dussouy2020,
title = {Linear triazole-linked pseudo oligogalactosides as scaffolds for galectin inhibitor development.},
author = {Christophe Dussouy and Chandan Kishor and Annie Lambert and Clément Lamoureux and Helen Blanchard and Cyrille Grandjean},
doi = {10.1111/cbdd.13683},
issn = {1747-0285 (Electronic)},
year = {2020},
date = {2020-03-01},
journal = {Chemical biology & drug design},
abstract = {Galectins play key roles in numerous biological processes. Their mode of action depends on their localization which can be extracellular, cytoplasmic or nuclear, and is partly mediated through interactions with β-galactose containing glycans. Galectins have emerged as novel therapeutic targets notably for the treatment of inflammatory disorders and cancers. This has stimulated the design of carbohydrate-based inhibitors targeting the carbohydrate recognition domains (CRDs) of the galectins. Pursuing this approach, we reasoned that linear oligo-galactosides obtained by straightforward iterative click-chemistry could mimic poly-lactosamine motifs expressed at eukaryote cell surfaces which the extracellular form of galectin-3, a prominent member of the galectin family, specifically recognizes. Affinities towards galectin-3 consistently increased with the length of the representative oligogalactosides but without reaching that of oligo-lactosamines. Elucidation of the X-ray crystal structures of the galectin-3 CRD in complex with a synthesized di- and tri-galactoside confirmed that the compounds bind within the carbohydrate-binding site. The atomic structures revealed that binding interactions mainly occur with the galactose moiety at the non-reducing end, primarily with subsites C and D of the CRD, differing from oligo-lactosamine which bind more consistently across the whole groove formed by the five subsites (A-E) of the galectin-3 CRD.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Aganyants, Hovsep; Weigel, Pierre; Hovhannisyan, Yeranuhi; Lecocq, Michèle; Koloyan, Haykanush; Hambardzumyan, Artur; Hovsepyan, Anichka; Hallet, Jean Noël; Sakanyan, Vehary
Rational engineering of the substrate specificity of a thermostable d-hydantoinase (Dihydropyrimidinase) Article de journal
Dans: High-Throughput, vol. 9, no. 1, 2020, ISSN: 25715135.
@article{Aganyants2020,
title = {Rational engineering of the substrate specificity of a thermostable d-hydantoinase (Dihydropyrimidinase)},
author = {Hovsep Aganyants and Pierre Weigel and Yeranuhi Hovhannisyan and Michèle Lecocq and Haykanush Koloyan and Artur Hambardzumyan and Anichka Hovsepyan and Jean Noël Hallet and Vehary Sakanyan},
doi = {10.3390/ht9010005},
issn = {25715135},
year = {2020},
date = {2020-03-01},
journal = {High-Throughput},
volume = {9},
number = {1},
publisher = {MDPI AG},
abstract = {D-hydantoinases catalyze an enantioselective opening of 5-and 6-membered cyclic structures and therefore can be used for the production of optically pure precursors for biomedical applications. The thermostable D-hydantoinase from Geobacillus stearothermophilus ATCC 31783 is a manganese-dependent enzyme and exhibits low activity towards bulky hydantoin derivatives. Homology modeling with a known 3D structure (PDB code: 1K1D) allowed us to identify the amino acids to be mutated at the substrate binding site and in its immediate vicinity to modulate the substrate specificity. Both single and double substituted mutants were generated by site-directed mutagenesis at appropriate sites located inside and outside of the stereochemistry gate loops (SGL) involved in the substrate binding. Substrate specificity and kinetic constant data demonstrate that the replacement of Phe159 and Trp287 with alanine leads to an increase in the enzyme activity towards D,L-5-benzyl and D,L-5-indolylmethyl hydantoins. The length of the side chain and the hydrophobicity of substrates are essential parameters to consider when designing the substrate binding pocket for bulky hydantoins. Our data highlight that D-hydantoinase is the authentic dihydropyrimidinase involved in the pyrimidine reductive catabolic pathway in moderate thermophiles.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Storozhylova, Nataliya; Crecente-Campo, José; Cabaleiro, David; Lugo, Luis; Dussouy, Christophe; Simões, Sandra; Monteiro, Madalena; Grandjean, Cyrille; Alonso, María J
An In Situ Hyaluronic Acid-Fibrin Hydrogel Containing Drug-Loaded Nanocapsules for Intra-Articular Treatment of Inflammatory Joint Diseases Article de journal
Dans: Regenerative Engineering and Translational Medicine, vol. 6, no. 2, p. 201–216, 2020, ISSN: 23644141.
@article{Storozhylova2020,
title = {An In Situ Hyaluronic Acid-Fibrin Hydrogel Containing Drug-Loaded Nanocapsules for Intra-Articular Treatment of Inflammatory Joint Diseases},
author = {Nataliya Storozhylova and José Crecente-Campo and David Cabaleiro and Luis Lugo and Christophe Dussouy and Sandra Sim{õ}es and Madalena Monteiro and Cyrille Grandjean and María J Alonso},
doi = {10.1007/s40883-020-00154-2},
issn = {23644141},
year = {2020},
date = {2020-01-01},
journal = {Regenerative Engineering and Translational Medicine},
volume = {6},
number = {2},
pages = {201--216},
publisher = {Regenerative Engineering and Translational Medicine},
abstract = {Abstract: Intra-articular (IA) administration of drugs is an appealing route for the effective treatment of large-joint diseases. However, a key limitation of this route is the premature elimination of the injected drugs from the synovial cavity. The objective of this work was to develop an easily injectable controlled release system intended to prolong the activity of anti-inflammatory drugs in the articular cavity. The system was an in situ forming hydrogel, made of fibrin and hyaluronic acid (HA), loaded with nanocapsules (NCs). The NCs, consisting of an olive oil core surrounded by a HA shell, were loaded with two different drugs, dexamethasone (DMX) and a galectin-3 inhibitor. They presented a particle size in the range of 122–135 nm and a surface charge of − 29/− 31 mV. The gelation time, rheological properties and porosity of the system could be adjusted by different parameters, such as addition of fibrin crosslinkers factor XIII and α2-antiplasmin. The non-crosslinked HA-fibrin hydrogels containing 30% (v/v) NCs showed the capacity to control the release of the encapsulated drug, DMX, for 72 h in simulated synovial fluid. The preliminary in vivo evaluation of the system containing a galectin-3 inhibitor in an acute synovitis rat model showed a suppression of inflammation after IA administration compared with the non-treated control. In brief, this work shows the possibility to combine an in situ forming hydrogel and NCs as a drug delivery strategy for IA administration and suggests its potential for the treatment of arthropathies. Lay Summary: This work describes the development and characterization of a new in situ forming hydrogel adapted for intra-articular administration of anti-inflammatory drugs. The prolonged local delivery of these drugs is expected to improve the treatment of large-joint arthropathies. To achieve this objective, the hydrogel, made of biodegradable materials, was loaded with nanodeposits of drugs, named nanocapsules. The efficacy of the system, containing a new galectin-3 inhibitor as a drug candidate, was tested in a rat model of acute synovial inflammation. These results represent the first insights on the in vivo activity of a new galectin-3 inhibitor on a potential galectin-3 immunotherapeutic target for inflammatory joints diseases. [Figure not available: see fulltext.]},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Sato, Shinya; Nanjappa, Deepak; Dorrell, Richard G; Vieira, Fabio Rocha Jimenez; Kazamia, Elena; Tirichine, Leila; Veluchamy, Alaguraj; Heilig, Roland; Aury, Jean Marc; Jaillon, Olivier; Wincker, Patrick; Fussy, Zoltan; Obornik, Miroslav; Muñoz-Gómez, Sergio A; Mann, David G; Bowler, Chris; Zingone, Adriana
Dans: Scientific Reports, vol. 10, no. 1, p. 1–12, 2020, ISSN: 20452322.
@article{Sato2020,
title = {Genome-enabled phylogenetic and functional reconstruction of an araphid pennate diatom Plagiostriata sp. CCMP470, previously assigned as a radial centric diatom, and its bacterial commensal},
author = {Shinya Sato and Deepak Nanjappa and Richard G Dorrell and Fabio Rocha Jimenez Vieira and Elena Kazamia and Leila Tirichine and Alaguraj Veluchamy and Roland Heilig and Jean Marc Aury and Olivier Jaillon and Patrick Wincker and Zoltan Fussy and Miroslav Obornik and Sergio A Mu{ñ}oz-Gómez and David G Mann and Chris Bowler and Adriana Zingone},
doi = {10.1038/s41598-020-65941-x},
issn = {20452322},
year = {2020},
date = {2020-01-01},
journal = {Scientific Reports},
volume = {10},
number = {1},
pages = {1--12},
abstract = {Diatoms are an ecologically fundamental and highly diverse group of algae, dominating marine primary production in both open-water and coastal communities. The diatoms include both centric species, which may have radial or polar symmetry, and the pennates, which include raphid and araphid species and arose within the centric lineage. Here, we use combined microscopic and molecular information to reclassify a diatom strain CCMP470, previously annotated as a radial centric species related to Leptocylindrus danicus, as an araphid pennate species in the staurosiroid lineage, within the genus Plagiostriata. CCMP470 shares key ultrastructural features with Plagiostriata taxa, such as the presence of a sternum with parallel striae, and the presence of a highly reduced labiate process on its valve; and this evolutionary position is robustly supported by multigene phylogenetic analysis. We additionally present a draft genome of CCMP470, which is the first genome available for a staurosiroid lineage. 270 Pfams (19%) found in the CCMP470 genome are not known in other diatom genomes, which otherwise does not hold big novelties compared to genomes of non-staurosiroid diatoms. Notably, our DNA library contains the genome of a bacterium within the Rhodobacterales, an alpha-proteobacterial lineage known frequently to associate with algae. We demonstrate the presence of commensal alpha-proteobacterial sequences in other published algal genome and transcriptome datasets, which may indicate widespread and persistent co-occurrence.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Rastogi, Achal; Vieira, Fabio Rocha Jimenez; Deton-Cabanillas, Anne-Flore; Veluchamy, Alaguraj; Cantrel, Catherine; Wang, Gaohong; Vanormelingen, Pieter; Bowler, Chris; Piganeau, Gwenael; Hu, Hanhua; Others,
A genomics approach reveals the global genetic polymorphism, structure, and functional diversity of ten accessions of the marine model diatom Phaeodactylum tricornutum Article de journal
Dans: The ISME journal, vol. 14, no. 2, p. 347–363, 2020.
@article{rastogi2020genomics,
title = {A genomics approach reveals the global genetic polymorphism, structure, and functional diversity of ten accessions of the marine model diatom Phaeodactylum tricornutum},
author = {Achal Rastogi and Fabio Rocha Jimenez Vieira and Anne-Flore Deton-Cabanillas and Alaguraj Veluchamy and Catherine Cantrel and Gaohong Wang and Pieter Vanormelingen and Chris Bowler and Gwenael Piganeau and Hanhua Hu and Others},
doi = {https://doi.org/10.1038/s41396-019-0528-3},
year = {2020},
date = {2020-01-01},
journal = {The ISME journal},
volume = {14},
number = {2},
pages = {347--363},
publisher = {Nature Publishing Group},
abstract = {Diatoms emerged in the Mesozoic period and presently constitute one of the main primary producers in the world's ocean and are of a major economic importance. In the current study, using whole genome sequencing of ten accessions of the model diatom Phaeodactylum tricornutum, sampled at broad geospatial and temporal scales, we draw a comprehensive landscape of the genomic diversity within the species. We describe strong genetic subdivisions of the accessions into four genetic clades (A–D) with constituent populations of each clade possessing a conserved genetic and functional makeup, likely a consequence of the limited dispersal of P. tricornutum in the open ocean. We further suggest dominance of asexual reproduction across all the populations, as implied by high linkage disequilibrium. Finally, we show limited yet compelling signatures of genetic and functional convergence inducing changes in the selection pressure on many genes and metabolic pathways. We propose these findings to have significant implications for understanding the genetic structure of diatom populations in nature and provide a framework to assess the genomic underpinnings of their ecological success and impact on aquatic ecosystems where they play a major role. Our work provides valuable resources for functional genomics and for exploiting the biotechnological potential of this model diatom species.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Fan, Xiao; Han, Wentao; Teng, Linhong; Jiang, Peng; Zhang, Xiaowen; Xu, Dong; Li, Chang; Pellegrini, Matteo; Wu, Chunhui; Wang, Yitao; Kaczurowski, Michelle Joyce Slade; Lin, Xin; Tirichine, Leila; Mock, Thomas; Ye, Naihao
Single-base methylome profiling of the giant kelp Saccharina japonica reveals significant differences in DNA methylation to microalgae and plants Article de journal
Dans: New Phytologist, vol. 225, no. 1, p. 234–249, 2020, ISSN: 14698137.
@article{Fan2020,
title = {Single-base methylome profiling of the giant kelp Saccharina japonica reveals significant differences in DNA methylation to microalgae and plants},
author = {Xiao Fan and Wentao Han and Linhong Teng and Peng Jiang and Xiaowen Zhang and Dong Xu and Chang Li and Matteo Pellegrini and Chunhui Wu and Yitao Wang and Michelle Joyce Slade Kaczurowski and Xin Lin and Leila Tirichine and Thomas Mock and Naihao Ye},
doi = {10.1111/nph.16125},
issn = {14698137},
year = {2020},
date = {2020-01-01},
journal = {New Phytologist},
volume = {225},
number = {1},
pages = {234--249},
abstract = {Brown algae have convergently evolved plant-like body plans and reproductive cycles, which in plants are controlled by differential DNA methylation. This contribution provides the first single-base methylome profiles of haploid gametophytes and diploid sporophytes of a multicellular alga. Although only c. 1.4% of cytosines in Saccharina japonica were methylated mainly at CHH sites and characterized by 5-methylcytosine (5mC), there were significant differences between life-cycle stages. DNA methyltransferase 2 (DNMT2), known to efficiently catalyze tRNA methylation, is assumed to methylate the genome of S. japonica in the structural context of tRNAs as the genome does not encode any other DNA methyltransferases. Circular and long noncoding RNA genes were the most strongly methylated regulatory elements in S. japonica. Differential expression of genes was negatively correlated with DNA methylation with the highest methylation levels measured in both haploid gametophytes. Hypomethylated and highly expressed genes in diploid sporophytes included genes involved in morphogenesis and halogen metabolism. The data herein provide evidence that cytosine methylation, although occurring at a low level, is significantly contributing to the formation of different life-cycle stages, tissue differentiation and metabolism in brown algae.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Zhao, Xue; Cabanillas, Anne Flore Deton; Veluchamy, Alaguraj; Bowler, Chris; Vieira, Fabio Rocha Jimenez; Tirichine, Leila
Probing the Diversity of Polycomb and Trithorax Proteins in Cultured and Environmentally Sampled Microalgae Article de journal
Dans: Frontiers in Marine Science, vol. 7, p. 189, 2020, ISSN: 2296-7745.
@article{10.3389/fmars.2020.00189,
title = {Probing the Diversity of Polycomb and Trithorax Proteins in Cultured and Environmentally Sampled Microalgae},
author = {Xue Zhao and Anne Flore {Deton Cabanillas} and Alaguraj Veluchamy and Chris Bowler and Fabio Rocha Jimenez Vieira and Leila Tirichine},
url = {https://www.frontiersin.org/article/10.3389/fmars.2020.00189},
doi = {10.3389/fmars.2020.00189},
issn = {2296-7745},
year = {2020},
date = {2020-01-01},
journal = {Frontiers in Marine Science},
volume = {7},
pages = {189},
abstract = {Polycomb (PcG) and Trithorax (TrxG) complexes are two evolutionarily conserved epigenetic regulatory components that act antagonistically to regulate the expression of genes involved in cell differentiation and development in multicellular organisms. The absence of PcG in both yeast models Saccharomyces cerevisiae and Schizosaccharomyces pombe suggested that polycomb proteins might have evolved together with the emergence of multicellular organisms. However, high throughput sequencing of several microalgal genomes and transcriptomes reveals an unprecedented abundance and diversity of genes encoding the components of these complexes. We report here the diversity of genes encoding PcG and TrxG proteins in microalgae from the Marine Microbial Eukaryote Transcriptome Sequencing Project database (MMETSP) and detected at broad scale in Tara Oceans genomics datasets using a highly sensitive method called eDAF (enhanced Domain Architecture Filtering). Further, we explored the correlation between environmental factors measured during the Tara Oceans expedition and transcript levels of PcG and TrxG components. PcG and TrxG are responsible for the deposition of a number of histone marks among which a TrxG associated mark, H3K4me3 which we profiled genome wide in the model diatom Phaeodactylum tricornutum to understand its role in microalgae and revisited the previously published histone code and co-occurrence with other histone marks including the antagonizing Polycomb deposited mark H3K27me3.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Yaremenko, Ivan A; Radulov, Peter S; Belyakova, Yulia Yu; Demina, Arina A; Fomenkov, Dmitriy I; Barsukov, Denis V; Subbotina, Irina R; Fleury, Fabrice; Terent'ev, Alexander O
Dans: Chemistry - A European Journal, vol. 26, no. 21, p. 4734–4751, 2020, ISSN: 15213765.
@article{Yaremenko2020a,
title = {Catalyst Development for the Synthesis of Ozonides and Tetraoxanes Under Heterogeneous Conditions: Disclosure of an Unprecedented Class of Fungicides for Agricultural Application},
author = {Ivan A Yaremenko and Peter S Radulov and Yulia Yu Belyakova and Arina A Demina and Dmitriy I Fomenkov and Denis V Barsukov and Irina R Subbotina and Fabrice Fleury and Alexander O Terent'ev},
doi = {10.1002/chem.201904555},
issn = {15213765},
year = {2020},
date = {2020-01-01},
journal = {Chemistry - A European Journal},
volume = {26},
number = {21},
pages = {4734--4751},
abstract = {The catalyst H3+xPMo12−x+6Mox+5O40 supported on SiO2 was developed for peroxidation of 1,3- and 1,5-diketones with hydrogen peroxide with the formation of bridged 1,2,4,5-tetraoxanes and bridged 1,2,4-trioxolanes (ozonides) with high yield based on isolated products (up to 86 and 90 %, respectively) under heterogeneous conditions. Synthesis of peroxides under heterogeneous conditions is a rare process and represents a challenge for this field of chemistry, because peroxides tend to decompose on the surface of a catalyst. A new class of antifungal agents for crop protection, that is, cyclic peroxides: bridged 1,2,4,5-tetraoxanes and bridged ozonides, was discovered. Some ozonides and tetraoxanes exhibit a very high antifungal activity and are superior to commercial fungicides, such as Triadimefon and Kresoxim-methyl. It is important to note that none of the fungicides used in agricultural chemistry contains a peroxide fragment.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Lafont, Florian; Fleury, Fabrice; Benhelli-Mokrani, Houda
DNA-PKcs Ser2056 auto-phosphorylation is affected by an O-GlcNAcylation/phosphorylation interplay Article de journal
Dans: Biochimica et Biophysica Acta (BBA) - General Subjects, vol. 1864, no. 12, p. 129705, 2020, ISSN: 0304-4165.
@article{LAFONT2020129705,
title = {DNA-PKcs Ser2056 auto-phosphorylation is affected by an O-GlcNAcylation/phosphorylation interplay},
author = {Florian Lafont and Fabrice Fleury and Houda Benhelli-Mokrani},
url = {http://www.sciencedirect.com/science/article/pii/S0304416520302178},
doi = {https://doi.org/10.1016/j.bbagen.2020.129705},
issn = {0304-4165},
year = {2020},
date = {2020-01-01},
journal = {Biochimica et Biophysica Acta (BBA) - General Subjects},
volume = {1864},
number = {12},
pages = {129705},
abstract = {Background DNA dependent Protein Kinase (DNA-PK) is an heterotrimeric complex regulating the Non Homologous End Joining (NHEJ) double strand break (DSB) repair pathway. The activity of its catalytic subunit (DNA-PKcs) is regulated by multiple phosphorylations, like the Ser2056 one that impacts DSB end processing and telomeres integrity. O-GlcNAcylation is a post translational modification (PTM) closely related to phosphorylation and its implication in the modulation of DNA-PKcs activity during the DNA Damage Response (DDR) is unknown. Methods Using IP techniques, and HeLa cell line, we evaluated the effect of pharmacological or siOGT mediated O-GlcNAc level modulation on DNA-PKcs O-GlcNAcylation. We used the RPA32 phosphorylation as a DNA-PKcs activity reporter substrate to evaluate the effect of O-GlcNAc modulators. Results We show here that human DNA-PKcs is an O-GlcNAc modified protein and that this new PTM is responsive to the cell O-GlcNAcylation level modulation. Our findings reveal that DNA-PKcs hypo O-GlcNAcylation affects its kinase activity and that the bleomycin-induced Ser2056 phosphorylation, is modulated by DNA-PKcs O-GlcNAcylation. Conclusions DNA-PKcs Ser2056 phosphorylation is antagonistically linked to DNA-PKcs O-GlcNAcylation level modulation. General significance Given the essential role of DNA-PKcs Ser2056 phosphorylation in the DDR, this study brings data about the role of cell O-GlcNAc level on genome integrity maintenance.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Vil', Vera A; Yaremenko, Ivan A; Fomenkov, Dmitri I; Levitsky, Dmitri O; Fleury, Fabrice; Terent'ev, Alexander O
Ion exchange resin-catalyzed synthesis of bridged tetraoxanes possessing in vitro cytotoxicity against HeLa cancer cells Article de journal
Dans: Chemistry of Heterocyclic Compounds, vol. 56, no. 6, p. 722–726, 2020, ISSN: 1573-8353.
@article{Vil2020,
title = {Ion exchange resin-catalyzed synthesis of bridged tetraoxanes possessing in vitro cytotoxicity against HeLa cancer cells},
author = {Vera A Vil' and Ivan A Yaremenko and Dmitri I Fomenkov and Dmitri O Levitsky and Fabrice Fleury and Alexander O Terent'ev},
url = {https://doi.org/10.1007/s10593-020-02722-4},
doi = {10.1007/s10593-020-02722-4},
issn = {1573-8353},
year = {2020},
date = {2020-01-01},
journal = {Chemistry of Heterocyclic Compounds},
volume = {56},
number = {6},
pages = {722--726},
abstract = {Bridged 1,2,4,5-tetraoxanes were prepared using available acidic ion exchange resin with high yields despite the possibility of peroxide decomposition under heterogeneous conditions. The bridged tetraoxanes demonstrated high cytotoxicity against HeLa cancer cells in vitro, which in some cases was higher than that of cisplatin, artesunate, and dihydroartemisinin.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Teze, David; Coines, Joan; Raich, Lluís; Kalichuk, Valentina; Solleux, Claude; Tellier, Charles; André-Miral, Corinne; Svensson, Birte; Rovira, Carme
A Single Point Mutation Converts GH84 O-GlcNAc Hydrolases into Phosphorylases: Experimental and Theoretical Evidence Article de journal
Dans: Journal of the American Chemical Society, vol. 142, no. 5, p. 2120–2124, 2020, ISSN: 15205126.
@article{Teze2020,
title = {A Single Point Mutation Converts GH84 O-GlcNAc Hydrolases into Phosphorylases: Experimental and Theoretical Evidence},
author = {David Teze and Joan Coines and Lluís Raich and Valentina Kalichuk and Claude Solleux and Charles Tellier and Corinne André-Miral and Birte Svensson and Carme Rovira},
doi = {10.1021/jacs.9b09655},
issn = {15205126},
year = {2020},
date = {2020-01-01},
journal = {Journal of the American Chemical Society},
volume = {142},
number = {5},
pages = {2120--2124},
abstract = {Glycoside hydrolases and phosphorylases are two major classes of enzymes responsible for the cleavage of glycosidic bonds. Here we show that two GH84 O-GlcNAcase enzymes can be converted to efficient phosphorylases by a single point mutation. Noteworthy, the mutated enzymes are over 10-fold more active than naturally occurring glucosaminide phosphorylases. We rationalize this novel transformation using molecular dynamics and QM/MM metadynamics methods, showing that the mutation changes the electrostatic potential at the active site and reduces the energy barrier for phosphorolysis by 10 kcaltextperiodcenteredmol-1. In addition, the simulations unambiguously reveal the nature of the intermediate as a glucose oxazolinium ion, clarifying the debate on the nature of such a reaction intermediate in glycoside hydrolases operating via substrate-assisted catalysis.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Violo, Typhaine; Dussouy, Christophe; Tellier, Charles; Grandjean, Cyrille; Camberlein, Emilie
Homogenous Glycoconjugate Produced by Combined Unnatural Amino Acid Incorporation and Click-Chemistry for Vaccine Purposes Article de journal
Dans: Journal of visualized experiments : JoVE, 2020.
@article{violo:hal-02990572,
title = {Homogenous Glycoconjugate Produced by Combined Unnatural Amino Acid Incorporation and Click-Chemistry for Vaccine Purposes},
author = {Typhaine Violo and Christophe Dussouy and Charles Tellier and Cyrille Grandjean and Emilie Camberlein},
url = {https://hal.archives-ouvertes.fr/hal-02990572},
doi = {10.3791/60821},
year = {2020},
date = {2020-01-01},
journal = {Journal of visualized experiments : JoVE},
publisher = {JoVE},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Visnapuu, Triinu; Teze, David; Kjeldsen, Christian; Lie, Aleksander; Duus, Jens Øllgaard; André-Miral, Corinne; Pedersen, Lars Haastrup; Stougaard, Peter; Svensson, Birte
Identification and characterization of a β-n-acetylhexosaminidase with a biosynthetic activity from the marine bacterium paraglaciecola hydrolytica S66T Article de journal
Dans: International Journal of Molecular Sciences, vol. 21, no. 2, 2020, ISSN: 14220067.
@article{Visnapuu2020,
title = {Identification and characterization of a β-n-acetylhexosaminidase with a biosynthetic activity from the marine bacterium paraglaciecola hydrolytica S66T},
author = {Triinu Visnapuu and David Teze and Christian Kjeldsen and Aleksander Lie and Jens Øllgaard Duus and Corinne André-Miral and Lars Haastrup Pedersen and Peter Stougaard and Birte Svensson},
doi = {10.3390/ijms21020417},
issn = {14220067},
year = {2020},
date = {2020-01-01},
journal = {International Journal of Molecular Sciences},
volume = {21},
number = {2},
publisher = {MDPI AG},
abstract = {β-N-Acetylhexosaminidases are glycoside hydrolases (GHs) acting on N-acetylated carbohydrates and glycoproteins with the release of N-acetylhexosamines. Members of the family GH20 have been reported to catalyze the transfer of N-acetylglucosamine (GlcNAc) to an acceptor, i.e., the reverse of hydrolysis, thus representing an alternative to chemical oligosaccharide synthesis. Two putative GH20 β-N-acetylhexosaminidases, PhNah20A and PhNah20B, encoded by the marine bacterium Paraglaciecola hydrolytica S66T, are distantly related to previously characterized enzymes. Remarkably, PhNah20A was located by phylogenetic analysis outside clusters of other studied β-N-acetylhexosaminidases, in a unique position between bacterial and eukaryotic enzymes. We successfully produced recombinant PhNah20A showing optimum activity at pH 6.0 and 50◦C, hydrolysis of GlcNAc β-1,4 and β-1,3 linkages in chitobiose (GlcNAc)2 and GlcNAc-1,3-β-Gal-1,4-β-Glc (LNT2), a human milk oligosaccharide core structure. The kinetic parameters of PhNah20A for p-nitrophenyl-GlcNAc and p-nitrophenyl-GalNAc were highly similar: kcat /KM being 341 and 344 mM−1 s−1, respectively. PhNah20A was unstable in dilute solution, but retained full activity in the presence of 0.5% bovine serum albumin (BSA). PhNah20A catalyzed the formation of LNT2, the non-reducing trisaccharide β-Gal-1,4-β-Glc-1,1-β-GlcNAc, and in low amounts the β-1,2-or β-1,3-linked trisaccharide β-Gal-1,4(β-GlcNAc)-1,x-Glc by a transglycosylation of lactose using 2-methyl-(1,2-dideoxy-α-d-glucopyrano)-oxazoline (NAG-oxazoline) as the donor. PhNah20A is the first characterized member of a distinct subgroup within GH20 β-N-acetylhexosaminidases.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Ostafe, Raluca; Fontaine, Nicolas; Frank, David; Chong, Matthieu Ng Fuk; Prodanovic, Radivoje; Pandjaitan, Rudy; Offmann, Bernard; Cadet, Frédéric; Fischer, Rainer
One-shot optimization of multiple enzyme parameters: Tailoring glucose oxidase for pH and electron mediators Article de journal
Dans: Biotechnology and Bioengineering, vol. 117, no. 1, p. 17–29, 2020, ISSN: 10970290.
@article{Ostafe2020,
title = {One-shot optimization of multiple enzyme parameters: Tailoring glucose oxidase for pH and electron mediators},
author = {Raluca Ostafe and Nicolas Fontaine and David Frank and Matthieu {Ng Fuk Chong} and Radivoje Prodanovic and Rudy Pandjaitan and Bernard Offmann and Frédéric Cadet and Rainer Fischer},
doi = {10.1002/bit.27169},
issn = {10970290},
year = {2020},
date = {2020-01-01},
journal = {Biotechnology and Bioengineering},
volume = {117},
number = {1},
pages = {17--29},
abstract = {Enzymes are biological catalysts with many industrial applications, but natural enzymes are usually unsuitable for industrial processes because they are not optimized for the process conditions. The properties of enzymes can be improved by directed evolution, which involves multiple rounds of mutagenesis and screening. By using mathematical models to predict the structure–activity relationship of an enzyme, and by defining the optimal combination of mutations in silico, we can significantly reduce the number of bench experiments needed, and hence the time and investment required to develop an optimized product. Here, we applied our innovative sequence–activity relationship methodology (innov'SAR) to improve glucose oxidase activity in the presence of different mediators across a range of pH values. Using this machine learning approach, a predictive model was developed and the optimal combination of mutations was determined, leading to a glucose oxidase mutant (P1) with greater specificity for the mediators ferrocene–methanol (12-fold) and nitrosoaniline (8-fold), compared to the wild-type enzyme, and better performance in three pH-adjusted buffers. The kcat/KM ratio of P1 increased by up to 121 folds compared to the wild type enzyme at pH 5.5 in the presence of ferrocene methanol.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Hendrickx, Johann; Tran, Vinh; Sanejouand, Yves-Henri
Numerous severely twisted N-acetylglucosamine conformations found in the protein databank Article de journal
Dans: Proteins: Structure, Function and Bioinformatics, vol. 88, no. 10, p. 1376–1383, 2020, ISSN: 10970134.
@article{Hendrickx2020,
title = {Numerous severely twisted N-acetylglucosamine conformations found in the protein databank},
author = {Johann Hendrickx and Vinh Tran and Yves-Henri Sanejouand},
doi = {10.1002/prot.25957},
issn = {10970134},
year = {2020},
date = {2020-01-01},
journal = {Proteins: Structure, Function and Bioinformatics},
volume = {88},
number = {10},
pages = {1376--1383},
abstract = {Taking advantage of the known planarity of the N-acetyl group of N-acetylglucosamine, an analysis of the quality of carbohydrate structures found in the protein databank was performed. Few obvious defects of the local geometry of the carbonyl group were observed. However, the N-acetyl group was often found in the less favorable cis conformation (12% of the cases). It was also found severely twisted in numerous instances, especially in structures with a resolution poorer than 1.9 Å determined between 2000 and 2015. Though the automated PDB-REDO procedure has proved able to improve nearly 85% of the structural models deposited to the PDB, and does prove able to cure most severely twisted conformations of the N-acetyl group, it fails to correct its high rate of cis conformations. More generally, for structures with a resolution poorer than 1.6 Å, it produces N-acetylglucosamine models in slightly poorer agreement with experimental data, as measured using real-space correlation coefficients. Significant improvements are thus still needed, at least as far as this carbohydrate structure is concerned.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Liu, Guoxia; Xuan, Ning; Rajashekar, Balaji; Arnaud, Philippe; Offmann, Bernard; Picimbon, Jean-François
Comprehensive History of CSP Genes: Evolution, Phylogenetic Distribution and Functions Article de journal
Dans: Genes, vol. 11, no. 4, p. 413, 2020.
@article{liu2020comprehensive,
title = {Comprehensive History of CSP Genes: Evolution, Phylogenetic Distribution and Functions},
author = {Guoxia Liu and Ning Xuan and Balaji Rajashekar and Philippe Arnaud and Bernard Offmann and Jean-François Picimbon},
doi = {10.3390/genes11040413},
year = {2020},
date = {2020-01-01},
journal = {Genes},
volume = {11},
number = {4},
pages = {413},
publisher = {Multidisciplinary Digital Publishing Institute},
abstract = {In this review we present the developmental, histological, evolutionary and functional properties of insect chemosensory proteins (CSPs) in insect species. CSPs are small globular proteins folded like a prism and notoriously known for their complex and arguably obscure function(s), particularly in pheromone olfaction. Here, we focus on direct functional consequences on protein function depending on duplication, expression and RNA editing. The result of our analysis is important for understanding the significance of RNA-editing on functionality of CSP genes, particularly in the brain tissue.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Dhingra, Surbhi; Sowdhamini, Ramanathan; Cadet, Frédéric; Offmann, Bernard
A glance into the evolution of template-free protein structure prediction methodologies Article de journal
Dans: Biochimie, vol. 175, p. 85 - 92, 2020, ISSN: 0300-9084.
@article{DHINGRA202085,
title = {A glance into the evolution of template-free protein structure prediction methodologies},
author = {Surbhi Dhingra and Ramanathan Sowdhamini and Frédéric Cadet and Bernard Offmann},
url = {http://www.sciencedirect.com/science/article/pii/S0300908420300961},
doi = {https://doi.org/10.1016/j.biochi.2020.04.026},
issn = {0300-9084},
year = {2020},
date = {2020-01-01},
journal = {Biochimie},
volume = {175},
pages = {85 - 92},
abstract = {Prediction of protein structures using computational approaches has been explored for over two decades, paving a way for more focused research and development of algorithms in comparative modelling, ab intio modelling and structure refinement protocols. A tremendous success has been witnessed in template-based modelling protocols, whereas strategies that involve template-free modelling still lag behind, specifically for larger proteins (>150 a.a.). Various improvements have been observed in ab initio protein structure prediction methodologies overtime, with recent ones attributed to the usage of deep learning approaches to construct protein backbone structure from its amino acid sequence. This review highlights the major strategies undertaken for template-free modelling of protein structures while discussing few tools developed under each strategy. It will also briefly comment on the progress observed in the field of ab initio modelling of proteins over the course of time as seen through the evolution of CASP platform.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Nagaraja, Anamya Ajjolli; Charton, Philippe; Cadet, Xavier F; Fontaine, Nicolas; Delsaut, Mathieu; Wiltschi, Birgit; Voit, Alena; Offmann, Bernard; Damour, Cedric; Grondin-Perez, Brigitte; Cadet, Frederic
A Machine Learning Approach for Efficient Selection of Enzyme Concentrations and Its Application for Flux Optimization Article de journal
Dans: Catalysts, vol. 10, no. 3, 2020, ISSN: 2073-4344.
@article{catal10030291,
title = {A Machine Learning Approach for Efficient Selection of Enzyme Concentrations and Its Application for Flux Optimization},
author = {Anamya Ajjolli Nagaraja and Philippe Charton and Xavier F Cadet and Nicolas Fontaine and Mathieu Delsaut and Birgit Wiltschi and Alena Voit and Bernard Offmann and Cedric Damour and Brigitte Grondin-Perez and Frederic Cadet},
url = {https://www.mdpi.com/2073-4344/10/3/291},
doi = {10.3390/catal10030291},
issn = {2073-4344},
year = {2020},
date = {2020-01-01},
journal = {Catalysts},
volume = {10},
number = {3},
abstract = {The metabolic engineering of pathways has been used extensively to produce molecules of interest on an industrial scale. Methods like gene regulation or substrate channeling helped to improve the desired product yield. Cell-free systems are used to overcome the weaknesses of engineered strains. One of the challenges in a cell-free system is selecting the optimized enzyme concentration for optimal yield. Here, a machine learning approach is used to select the enzyme concentration for the upper part of glycolysis. The artificial neural network approach (ANN) is known to be inefficient in extrapolating predictions outside the box: high predicted values will bump into a sort of “glass ceiling”. In order to explore this “glass ceiling” space, we developed a new methodology named glass ceiling ANN (GC-ANN). Principal component analysis (PCA) and data classification methods are used to derive a rule for a high flux, and ANN to predict the flux through the pathway using the input data of 121 balances of four enzymes in the upper part of glycolysis. The outcomes of this study are i. in silico selection of optimum enzyme concentrations for a maximum flux through the pathway and ii. experimental in vitro validation of the “out-of-the-box” fluxes predicted using this new approach. Surprisingly, flux improvements of up to 63% were obtained. Gratifyingly, these improvements are coupled with a cost decrease of up to 25% for the assay.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Arbo, Bruno Dutra; André-Miral, Corinne; Nasre-Nasser, Raif Gregorio; Schimith, Lúcia Emanueli; Santos, Michele Goulart; Costa-Silva, Dennis; Muccillo-Baisch, Ana Luiza; Hort, Mariana Appel
Resveratrol Derivatives as Potential Treatments for Alzheimer’s and Parkinson’s Disease Article de journal
Dans: Frontiers in Aging Neuroscience, vol. 12, p. 103, 2020, ISSN: 1663-4365.
@article{10.3389/fnagi.2020.00103,
title = {Resveratrol Derivatives as Potential Treatments for Alzheimer’s and Parkinson’s Disease},
author = {Bruno Dutra Arbo and Corinne André-Miral and Raif Gregorio Nasre-Nasser and Lúcia Emanueli Schimith and Michele Goulart Santos and Dennis Costa-Silva and Ana Luiza Muccillo-Baisch and Mariana Appel Hort},
url = {https://www.frontiersin.org/article/10.3389/fnagi.2020.00103},
doi = {10.3389/fnagi.2020.00103},
issn = {1663-4365},
year = {2020},
date = {2020-01-01},
urldate = {2020-01-01},
journal = {Frontiers in Aging Neuroscience},
volume = {12},
pages = {103},
abstract = {Neurodegenerative diseases are characterized by the progressive loss of neurons in different regions of the nervous system. Alzheimer’s disease (AD) and Parkinson’s disease (PD) are the two most prevalent neurodegenerative diseases, and the symptoms associated with these pathologies are closely related to the regions that are most affected by the process of neurodegeneration. Despite their high prevalence, currently, there is no cure or disease-modifying drugs for the treatment of these conditions. In the last decades, due to the need for the development of new treatments for neurodegenerative diseases, several authors have investigated the neuroprotective actions of naturally occurring molecules, such as resveratrol. Resveratrol is a stilbene found in several plants, including grapes, blueberries, raspberries, and peanuts. Studies have shown that resveratrol presents neuroprotective actions in experimental models of AD and PD, however, its clinical application is limited due to its rapid metabolism and low bioavailability. In this context, studies have proposed that structural changes in the resveratrol molecule, including glycosylation, alkylation, halogenation, hydroxylation, methylation, and prenylation could lead to the development of derivatives with enhanced bioavailability and pharmacological activity. Therefore, this review article aims to discuss how resveratrol derivatives could represent viable molecules in the search for new drugs for the treatment of AD and PD.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Téletchéa, Stéphane; Téletchéa, Fabrice
STOREFISH 2.0: a database on the reproductive strategies of teleost fishes Article de journal
Dans: Database, vol. 2020, 2020, ISSN: 1758-0463, (baaa095).
@article{10.1093/database/baaa095,
title = {STOREFISH 2.0: a database on the reproductive strategies of teleost fishes},
author = {Stéphane Téletchéa and Fabrice Téletchéa},
url = {https://doi.org/10.1093/database/baaa095},
doi = {10.1093/database/baaa095},
issn = {1758-0463},
year = {2020},
date = {2020-01-01},
journal = {Database},
volume = {2020},
abstract = {Teleost fishes show the most outstanding reproductive diversity of all vertebrates. Yet to date, no one has been able to decisively explain this striking variability nor to perform large-scale phylogenetic analyses of reproductive modes. Here, we describe STrategies Of REproduction in FISH (STOREFISH) 2.0, an online database easing the sharing of an original data set on reproduction published in 2007, enriched with automated data extraction and presentation to display the knowledge acquired on temperate freshwater fish species. STOREFISH 2.0 contains the information for 80 freshwater fish species and 50 traits from the analysis of 1219 references. It is anticipated that this new database could be useful for freshwater biodiversity research, conservation, assessment and management.Database URL: www.storefish.org},
note = {baaa095},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Dussouy, Christophe; Téletchéa, Stéphane; Lambert, Annie; Charlier, Cathy; Botez, Iuliana; Ceuninck, Frédéric De; Grandjean, Cyrille
Access to Galectin-3 Inhibitors from Chemoenzymatic Synthons Article de journal
Dans: The Journal of Organic Chemistry, vol. 85, no. 24, p. 16099-16114, 2020, (PMID: 33200927).
@article{doi:10.1021/acs.joc.0c01927b,
title = {Access to Galectin-3 Inhibitors from Chemoenzymatic Synthons},
author = {Christophe Dussouy and Stéphane Téletchéa and Annie Lambert and Cathy Charlier and Iuliana Botez and Frédéric De Ceuninck and Cyrille Grandjean},
url = {https://doi.org/10.1021/acs.joc.0c01927},
doi = {10.1021/acs.joc.0c01927},
year = {2020},
date = {2020-01-01},
journal = {The Journal of Organic Chemistry},
volume = {85},
number = {24},
pages = {16099-16114},
abstract = {Chemoenzymatic strategies are useful for providing both regio- and stereoselective access to bioactive oligosaccharides. We show herein that a glycosynthase mutant of a Thermus thermophilus α-glycosidase can react with unnatural glycosides such as 6-azido-6-deoxy-d-glucose/glucosamine to lead to β-d-galactopyranosyl-(1→3)-d-glucopyranoside or β-d-galactopyranosyl-(1→3)-2-acetamido-2-deoxy-d-glucopyranoside derivatives bearing a unique azide function. Taking advantage of the orthogonality between the azide and the hydroxyl functional groups, the former was next selectively reacted to give rise to a library of galectin-3 inhibitors. Combining enzyme substrate promiscuity and bioorthogonality thus appears as a powerful strategy to rapidly access to sugar-based ligands},
note = {PMID: 33200927},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Rathor, Pramod; Borza, Tudor; Liu, Yanhui; Qin, Yuan; Stone, Sophia; Zhang, Junzeng; Hui, Joseph P M; Berrue, Fabrice; Groisillier, Agnès; Tonon, Thierry; Yurgel, Svetlana; Potin, Philippe; Prithiviraj, Balakrishnan
Low Mannitol Concentrations in Arabidopsis thaliana Expressing Ectocarpus Genes Improve Salt Tolerance Article de journal
Dans: Plants, vol. 9, no. 11, 2020, ISSN: 2223-7747.
@article{plants9111508,
title = {Low Mannitol Concentrations in Arabidopsis thaliana Expressing Ectocarpus Genes Improve Salt Tolerance},
author = {Pramod Rathor and Tudor Borza and Yanhui Liu and Yuan Qin and Sophia Stone and Junzeng Zhang and Joseph P M Hui and Fabrice Berrue and Agnès Groisillier and Thierry Tonon and Svetlana Yurgel and Philippe Potin and Balakrishnan Prithiviraj},
url = {https://www.mdpi.com/2223-7747/9/11/1508},
doi = {10.3390/plants9111508},
issn = {2223-7747},
year = {2020},
date = {2020-01-01},
journal = {Plants},
volume = {9},
number = {11},
abstract = {Mannitol is abundant in a wide range of organisms, playing important roles in biotic and abiotic stress responses. Nonetheless, mannitol is not produced by a vast majority of plants, including many important crop plants. Mannitol-producing transgenic plants displayed improved tolerance to salt stresses though mannitol production was rather low, in the µM range, compared to mM range found in plants that innately produce mannitol. Little is known about the molecular mechanisms underlying salt tolerance triggered by low concentrations of mannitol. Reported here is the production of mannitol in Arabidopsis thaliana, by expressing two mannitol biosynthesis genes from the brown alga Ectocarpus sp. strain Ec32. To date, no brown algal genes have been successfully expressed in land plants. Expression of mannitol-1-phosphate dehydrogenase and mannitol-1-phosphatase genes was associated with the production of 42.3-52.7 nmol g−1 fresh weight of mannitol, which was sufficient to impart salinity and temperature stress tolerance. Transcriptomics revealed significant differences in the expression of numerous genes, in standard and salinity stress conditions, including genes involved in K+ homeostasis, ROS signaling, plant development, photosynthesis, ABA signaling and secondary metabolism. These results suggest that the improved tolerance to salinity stress observed in transgenic plants producing mannitol in µM range is achieved by the activation of a significant number of genes, many of which are involved in priming and modulating the expression of genes involved in a variety of functions including hormone signaling, osmotic and oxidative stress, and ion homeostasis.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Billard, Estelle; Goyet, Vincent; Delavault, Philippe; Simier, Philippe; Montiel, Grégory
Correction to: Cytokinin treated microcalli of Phelipanche ramosa: an efficient model for studying haustorium formation in holoparasitic plants Article de journal
Dans: Plant Cell, Tissue and Organ Culture (PCTOC), vol. 141, no. 3, p. 555-555, 2020, ISSN: 1573-5044.
@article{RN31,
title = {Correction to: Cytokinin treated microcalli of Phelipanche ramosa: an efficient model for studying haustorium formation in holoparasitic plants},
author = {Estelle Billard and Vincent Goyet and Philippe Delavault and Philippe Simier and Grégory Montiel},
url = {https://doi.org/10.1007/s11240-020-01832-3
https://link.springer.com/content/pdf/10.1007/s11240-020-01832-3.pdf},
doi = {10.1007/s11240-020-01832-3},
issn = {1573-5044},
year = {2020},
date = {2020-01-01},
urldate = {2020-01-01},
journal = {Plant Cell, Tissue and Organ Culture (PCTOC)},
volume = {141},
number = {3},
pages = {555-555},
abstract = {The caption to Fig. 4 belonged to Fig. 5 and vice versa in the initial online publication. The original article has been corrected.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Delavault, Philippe
Are root parasitic plants like any other plant pathogens? Article de journal
Dans: New Phytol, vol. 226, no. 3, p. 641-643, 2020, ISSN: 0028-646x.
@article{RN2,
title = {Are root parasitic plants like any other plant pathogens?},
author = {Philippe Delavault},
url = {https://nph.onlinelibrary.wiley.com/doi/10.1111/nph.16504},
doi = {10.1111/nph.16504},
issn = {0028-646x},
year = {2020},
date = {2020-01-01},
urldate = {2020-01-01},
journal = {New Phytol},
volume = {226},
number = {3},
pages = {641-643},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Fernández-Aparicio, Monica; Delavault, Philippe; Timko, Michael
Management of Infection by Parasitic Weeds: A Review Article de journal
Dans: Plants (Basel), vol. 9, no. 9, 2020, ISSN: 2223-7747 (Print) 2223-7747.
@article{RN3,
title = {Management of Infection by Parasitic Weeds: A Review},
author = {Monica Fernández-Aparicio and Philippe Delavault and Michael Timko},
url = {https://mdpi-res.com/d_attachment/plants/plants-09-01184/article_deploy/plants-09-01184.pdf},
doi = {10.3390/plants9091184},
issn = {2223-7747 (Print) 2223-7747},
year = {2020},
date = {2020-01-01},
urldate = {2020-01-01},
journal = {Plants (Basel)},
volume = {9},
number = {9},
abstract = {Parasitic plants rely on neighboring host plants to complete their life cycle, forming vascular connections through which they withdraw needed nutritive resources. In natural ecosystems, parasitic plants form one component of the plant community and parasitism contributes to overall community balance. In contrast, when parasitic plants become established in low biodiversified agroecosystems, their persistence causes tremendous yield losses rendering agricultural lands uncultivable. The control of parasitic weeds is challenging because there are few sources of crop resistance and it is difficult to apply controlling methods selective enough to kill the weeds without damaging the crop to which they are physically and biochemically attached. The management of parasitic weeds is also hindered by their high fecundity, dispersal efficiency, persistent seedbank, and rapid responses to changes in agricultural practices, which allow them to adapt to new hosts and manifest increased aggressiveness against new resistant cultivars. New understanding of the physiological and molecular mechanisms behind the processes of germination and haustorium development, and behind the crop resistant response, in addition to the discovery of new targets for herbicides and bioherbicides will guide researchers on the design of modern agricultural strategies for more effective, durable, and health compatible parasitic weed control.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Huet, Sarah; Pouvreau, Jean-Bernard; Delage, Erwan; Delgrange, Sabine; Marais, Coralie; Bahut, Muriel; Delavault, Philippe; Simier, Philippe; Poulin, Lucie
Populations of the Parasitic Plant Influence Their Seed Microbiota Article de journal
Dans: Front Plant Sci, vol. 11, p. 1075, 2020, ISSN: 1664-462X.
@article{pmid32765559,
title = {Populations of the Parasitic Plant Influence Their Seed Microbiota},
author = {Sarah Huet and Jean-Bernard Pouvreau and Erwan Delage and Sabine Delgrange and Coralie Marais and Muriel Bahut and Philippe Delavault and Philippe Simier and Lucie Poulin},
doi = {10.3389/fpls.2020.01075},
issn = {1664-462X},
year = {2020},
date = {2020-01-01},
urldate = {2020-01-01},
journal = {Front Plant Sci},
volume = {11},
pages = {1075},
abstract = {Seeds of the parasitic weed are well adapted to their hosts because they germinate and form haustorial structures to connect to roots in response to diverse host-derived molecular signals. presents different genetic groups that are preferentially adapted to certain hosts. Since there are indications that microbes play a role in the interaction especially in the early stages of the interaction, we studied the microbial diversity harbored by the parasitic seeds with respect to their host and genetic group. Twenty-six seed lots from seven cropping plots of three different hosts-oilseed rape, tobacco, and hemp-in the west of France were characterized for their bacterial and fungal communities using 16S rRNA gene and ITS (Internal transcribed spacer) sequences, respectively. First seeds were characterized genetically using twenty microsatellite markers and phenotyped for their sensibility to various germination stimulants including strigolactones and isothiocyanates. This led to the distinction of three groups that corresponded to their host of origin. The observed seed diversity was correlated to the host specialization and germination stimulant sensitivity within species. Microbial communities were both clustered by host and plot of origin. The seed core microbiota was composed of seventeen species that were also retrieved from soil and was in lower abundances for bacteria and similar abundances for fungi compared to seeds. The host-related core microbiota of parasitic seeds was limited and presumably well adapted to the interaction with its hosts. Two microbial candidates of species and were especially identified in seeds from oilseed rape plots, suggesting their involvement in host recognition and specialization as well as seed fitness for by improving the production of isothiocyanates from glucosinolates in the rhizosphere of oilseed rape.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
29 publications
Bogoeva, Vanya; Rangelov, Miroslav; Todorova, Nadezhda; Lambert, Annie; Bridot, Clarisse; Yordanova, Anna; Roos, Goedele; Grandjean, Cyrille; Bouckaert, Julie
Binding of Gold(III) Porphyrin by the Pro-metastatic Regulatory Protein Human Galectin-3 Article de journal
Dans: Molecules, vol. 24, no. 24, 2019, ISSN: 14203049.
@article{Bogoeva2019,
title = {Binding of Gold(III) Porphyrin by the Pro-metastatic Regulatory Protein Human Galectin-3},
author = {Vanya Bogoeva and Miroslav Rangelov and Nadezhda Todorova and Annie Lambert and Clarisse Bridot and Anna Yordanova and Goedele Roos and Cyrille Grandjean and Julie Bouckaert},
doi = {10.3390/molecules24244561},
issn = {14203049},
year = {2019},
date = {2019-12-01},
journal = {Molecules},
volume = {24},
number = {24},
publisher = {MDPI AG},
abstract = {Gold(III) porphyrin presents an attractive alternative to the use of, for example, cisplatin in chemotherapy. However, approaches that allow to selectively target cancer cells are highly sought. Many plant and mammalian lectins have been shown to bind oligosaccharide sequences of the aberrant glycosylation pattern found on cancerous tumors. For example human galectin-3, of the galectin family specific for ß-galactoside, is overexpressed in the extracellular matrix of tumorigenous and metastatic tissues. We searched for non-carbohydrate ligands for galectin-3 that can guide a cytotoxic drug to the cancer cells by maintaining its affinity for tumor associated carbohydrate antigens. Previous findings showed that zinc tetrasulfonatophenylporphyrin can bind galectin-3 with sub-micromolar affinity without disturbing lactose binding. Gold(III) porphyrin is not only cytotoxic to cancer cells, it knows also a potential application as photosensitiser in photodynamic therapy. We investigated the binding of gold(III) porphyrin to galectin-3 using different biophysical interaction techniques and demonstrated a low micromolar affinity of human galectin-3 for the cytotoxic compound. Co-crystallization attempts in order to understand the binding mode of gold porphyrin to galectin-3 failed, but molecular docking emphasized a highly populated secondary binding site that does not hinder lactose or Thomsen Friendenreich disaccharide binding. This suggests that gold(III) porphyrin might significantly enhance its concentration and delivery to cancer cells by binding to human galectin-3 that keeps its orientation towards tumor associated carbohydrate antigens.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
de Saint Germain, Alexandre; Retailleau, Pascal; Norsikian, Stéphanie; Servajean, Vincent; Pelissier, Franck; Steinmetz, Vincent; Pillot, Jean-Paul; Rochange, Soizic; Pouvreau, Jean-Bernard; Boyer, François-Didier
Contalactone, a contaminant formed during chemical synthesis of the strigolactone reference GR24 is also a strigolactone mimic Article de journal
Dans: Phytochemistry, vol. 168, p. 112112, 2019, ISSN: 1873-3700.
@article{pmid31499274,
title = {Contalactone, a contaminant formed during chemical synthesis of the strigolactone reference GR24 is also a strigolactone mimic},
author = {Alexandre de Saint Germain and Pascal Retailleau and Stéphanie Norsikian and Vincent Servajean and Franck Pelissier and Vincent Steinmetz and Jean-Paul Pillot and Soizic Rochange and Jean-Bernard Pouvreau and François-Didier Boyer},
url = {hal-03010596v1 },
doi = {10.1016/j.phytochem.2019.112112},
issn = {1873-3700},
year = {2019},
date = {2019-12-01},
urldate = {2019-12-01},
journal = {Phytochemistry},
volume = {168},
pages = {112112},
abstract = {Strigolactone (SL) plant hormones control plant architecture and are key players in both symbiotic and parasitic interactions. GR24, a synthetic SL analog, is the worldwide reference compound used in all bioassays for investigating the role of SLs in plant development and in rhizospheric interactions. In 2012, the first characterization of the SL receptor reported the detection of an unknown compound after incubation of GR24 samples with the SL receptor. We reveal here the origin of this compound (P270), which comes from a by-product formed during GR24 chemical synthesis. We present the identification of this by-product, named contalactone. A proposed chemical pathway for its formation is provided as well as an evaluation of its bioactivity on pea, Arabidopsis, root parasitic plant seeds and AM fungi, characterizing it as a SL mimic. Quality of GR24 samples can be easily checked by carrying out microscale hydrolysis in a basic aqueous medium to easily detect P270 as indicator of the presence of the contalactone impurity. In all cases, before being used for bioassays, GR24 must be careful purified by preparative HPLC.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Gheyouche, Ennys; Launay, Romain; Lethiec, Jean; Labeeuw, Antoine; Roze, Caroline; Amossé, Alan; Téletchéa, Stéphane
Docknmine, a web portal to assemble and analyse virtual and experimental interaction data Article de journal
Dans: International Journal of Molecular Sciences, vol. 20, no. 20, 2019, ISSN: 14220067.
@article{Gheyouche2019,
title = {Docknmine, a web portal to assemble and analyse virtual and experimental interaction data},
author = {Ennys Gheyouche and Romain Launay and Jean Lethiec and Antoine Labeeuw and Caroline Roze and Alan Amossé and Stéphane Téletchéa},
doi = {10.3390/ijms20205062},
issn = {14220067},
year = {2019},
date = {2019-10-01},
journal = {International Journal of Molecular Sciences},
volume = {20},
number = {20},
publisher = {MDPI AG},
abstract = {Scientists have to perform multiple experiments producing qualitative and quantitative data to determine if a compound is able to bind to a given target. Due to the large diversity of the potential ligand chemical space, the possibility of experimentally exploring a lot of compounds on a target rapidly becomes out of reach. Scientists therefore need to use virtual screening methods to determine the putative binding mode of ligands on a protein and then post-process the raw docking experiments with a dedicated scoring function in relation with experimental data. Two of the major difficulties for comparing docking predictions with experiments mostly come from the lack of transferability of experimental data and the lack of standardisation in molecule names. Although large portals like PubChem or ChEMBL are available for general purpose, there is no service allowing a formal expert annotation of both experimental data and docking studies. To address these issues, researchers build their own collection of data in flat files, often in spreadsheets, with limited possibilities of extensive annotations or standardisation of ligand descriptions allowing cross-database retrieval. We have conceived the dockNmine platform to provide a service allowing an expert and authenticated annotation of ligands and targets. First, this portal allows a scientist to incorporate controlled information in the database using reference identifiers for the protein (Uniprot ID) and the ligand (SMILES description), the data and the publication associated to it. Second, it allows the incorporation of docking experiments using forms that automatically parse useful parameters and results. Last, the web interface provides a lot of pre-computed outputs to assess the degree of correlations between docking experiments and experimental data.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Tripathi, Neha; Vetrivel, Iyanar; Téletchéa, Stéphane; Jean, Mickaël; Legembre, Patrick; Laurent, Adèle D
Investigation of phospholipase Cγ1 interaction with SLP76 using molecular modeling methods for identifying novel inhibitors Article de journal
Dans: International Journal of Molecular Sciences, vol. 20, no. 19, 2019, ISSN: 14220067.
@article{Tripathi2019,
title = {Investigation of phospholipase Cγ1 interaction with SLP76 using molecular modeling methods for identifying novel inhibitors},
author = {Neha Tripathi and Iyanar Vetrivel and Stéphane Téletchéa and Mickaël Jean and Patrick Legembre and Adèle D Laurent},
doi = {10.3390/ijms20194721},
issn = {14220067},
year = {2019},
date = {2019-10-01},
journal = {International Journal of Molecular Sciences},
volume = {20},
number = {19},
publisher = {MDPI AG},
abstract = {The enzyme phospholipase C gamma 1 (PLCγ1) has been identified as a potential drug target of interest for various pathological conditions such as immune disorders, systemic lupus erythematosus, and cancers. Targeting its SH3 domain has been recognized as an efficient pharmacological approach for drug discovery against PLCγ1. Therefore, for the first time, a combination of various biophysical methods has been employed to shed light on the atomistic interactions between PLCγ1 and its known binding partners. Indeed, molecular modeling of PLCγ1 with SLP76 peptide and with previously reported inhibitors (ritonavir, anethole, daunorubicin, diflunisal, and rosiglitazone) facilitated the identification of the common critical residues (Gln805, Arg806, Asp808, Glu809, Asp825, Gly827, and Trp828) as well as the quantification of their interaction through binding energies calculations. These features are in agreement with previous experimental data. Such an in depth biophysical analysis of each complex provides an opportunity to identify new inhibitors through pharmacophore mapping, molecular docking and MD simulations. From such a systematic procedure, a total of seven compounds emerged as promising inhibitors, all characterized by a strong binding with PLCγ1 and a comparable or higher binding affinity to ritonavir (ΔGbind < -25 kcal/mol), one of the most potent inhibitor reported till now.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Nagaraja, Anamya Ajjolli; Fontaine, Nicolas; Delsaut, Mathieu; Charton, Philippe; Damour, Cedric; Offmann, Bernard; Grondin-Perez, Brigitte; Cadet, Frédéric
Flux prediction using artificial neural network (ANN) for the upper part of glycolysis Article de journal
Dans: PLOS ONE, vol. 14, no. 5, p. e0216178, 2019, ISSN: 1932-6203.
@article{AjjolliNagaraja2019,
title = {Flux prediction using artificial neural network (ANN) for the upper part of glycolysis},
author = {Anamya {Ajjolli Nagaraja} and Nicolas Fontaine and Mathieu Delsaut and Philippe Charton and Cedric Damour and Bernard Offmann and Brigitte Grondin-Perez and Frédéric Cadet},
editor = {Marie-Joelle Virolle},
url = {https://dx.plos.org/10.1371/journal.pone.0216178},
doi = {10.1371/journal.pone.0216178},
issn = {1932-6203},
year = {2019},
date = {2019-05-01},
journal = {PLOS ONE},
volume = {14},
number = {5},
pages = {e0216178},
publisher = {Public Library of Science},
abstract = {The selection of optimal enzyme concentration in multienzyme cascade reactions for the highest product yield in practice is very expensive and time-consuming process. The modelling of biological pathways is a difficult process because of the complexity of the system. The mathematical modelling of the system using an analytical approach depends on the many parameters of enzymes which rely on tedious and expensive experiments. The artificial neural network (ANN) method has been successively applied in different fields of science to perform complex functions. In this study, ANN models were trained to predict the flux for the upper part of glycolysis as inferred by NADH consumption, using four enzyme concentrations i.e., phosphoglucoisomerase, phosphofructokinase, fructose-bisphosphate-aldolase, triose-phosphate-isomerase. Out of three ANN algorithms, the neuralnet package with two activation functions, “logistic” and “tanh” were implemented. The prediction of the flux was very efficient: RMSE and R2 were 0.847, 0.93 and 0.804, 0.94 respectively for logistic and tanh functions using a cross validation procedure. This study showed that a systemic approach such as ANN could be used for accurate prediction of the flux through the metabolic pathway. This could help to save a lot of time and costs, particularly from an industrial perspective. The R-code is available at: https://github.com/DSIMB/ANN-Glycolysis-Flux-Prediction.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Téletchéa, Stéphane; Santuz, H; Léonard, S; Etchebest, Catherine
Repository of enriched structures of proteins involved in the red blood cell environment (RESPIRE) Article de journal
Dans: PLoS ONE, vol. 14, no. 2, 2019, ISSN: 19326203.
@article{Teletchea2019,
title = {Repository of enriched structures of proteins involved in the red blood cell environment (RESPIRE)},
author = {Stéphane Téletchéa and H Santuz and S Léonard and Catherine Etchebest},
doi = {10.1371/journal.pone.0211043},
issn = {19326203},
year = {2019},
date = {2019-02-01},
journal = {PLoS ONE},
volume = {14},
number = {2},
publisher = {Public Library of Science},
abstract = {The Red Blood Cell (RBC) is a metabolically-driven cell vital for processes such a gas transport and homeostasis. RBC possesses at its surface exposing antigens proteins that are critical in blood transfusion. Due to their importance, numerous studies address the cell function as a whole but more and more details of RBC structure and protein content are now studied using massive state-of-the art characterisation techniques. Yet, the resulting information is frequently scattered in many scientific articles, in many databases and specialized web servers. To provide a more compendious view of erythrocytes and of their protein content, we developed a dedicated database called RESPIRE that aims at gathering a comprehensive and coherent ensemble of information and data about proteins in RBC. This cell-driven database lists proteins found in erythrocytes. For a given protein entry, initial data are processed from external portals and enriched by using state-of-the-art bioinformatics methods. As structural information is extremely useful to understand protein function and predict the impact of mutations, a strong effort has been put on the prediction of protein structures with a special treatment for membrane proteins. Browsing the database is available through text search for reference gene names or protein identifiers, through pre-defined queries or via hyperlinks. The RESPIRE database provides valuable information and unique annotations that should be useful to a wide audience of biologists, clinicians and structural biologists.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Brissonnet, Yoan; Compain, Guillaume; Renoux, Brigitte; Krammer, Eva Maria; Daligault, Franck; Deniaud, David; Papot, Sébastien; Gouin, Sébastien G
Monitoring glycosidase activity for clustered sugar substrates, a study on β-glucuronidase Article de journal
Dans: RSC Advances, vol. 9, no. 69, p. 40263–40267, 2019, ISSN: 20462069.
@article{Brissonnet2019a,
title = {Monitoring glycosidase activity for clustered sugar substrates, a study on β-glucuronidase},
author = {Yoan Brissonnet and Guillaume Compain and Brigitte Renoux and Eva Maria Krammer and Franck Daligault and David Deniaud and Sébastien Papot and Sébastien G Gouin},
doi = {10.1039/c9ra08847d},
issn = {20462069},
year = {2019},
date = {2019-01-01},
journal = {RSC Advances},
volume = {9},
number = {69},
pages = {40263--40267},
abstract = {Determination of glycosidase hydrolysis kinetics for a monovalent sugar substrate is relatively straightforward and classically achieved by monitoring the fluorescence signal released from the sugar-conjugated probe after enzymatic hydrolysis. Naturally occuring sugar epitopes are, however, often clustered on biopolymers or at biological surfaces, and previous reports have shown that glycosidase hydrolytic rates can differ greatly with multivalent presentation of the sugar epitopes. New probes are needed to make it easier to interpret the importance of substrate clustering towards a specific enzyme activity. In this work, we developed multivalent glucuronide substrates attached to fluorescent amino-coumarines through self-immolative linkers to enable real time-monitoring of the hydrolysing activity of E.coli β-glucuronidases (GUS) towards clustered substrates. GUS are exoglycosidases of considerable therapeutic interest cleaving β-d-glucuronides and are found in the lysosomes, in the tumoral microenvironment, and are expressed by gut microbiota. GUS showed a much lower catalytic efficiency in hydrolysing clustered glucuronides due to a significantly lower enzymatic velocity and affinity for the substrates. GUS was 52-fold less efficient in hydrolysing GlcA substrates presented on an octameric silsequioxane (COSS) compared with a monovalent GlcA of similar chemical structure. Thus, kinetic and thermodynamic data of GUS hydrolysis towards multivalent glucuronides were easily obtained with these new types of enzymatically-triggered probes. More generally, adapting the substrate nature and valency of these new probes, should improve understanding of the impact of multivalency for a specific enzyme.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Murik, Omer; Tirichine, Leila; Prihoda, Judit; Thomas, Yann; Araújo, Wagner L; Allen, Andrew E; Fernie, Alisdair R; Bowler, Chris
Downregulation of mitochondrial alternative oxidase affects chloroplast function, redox status and stress response in a marine diatom Article de journal
Dans: New Phytologist, vol. 221, no. 3, p. 1303–1316, 2019, ISSN: 14698137.
@article{Murik2019,
title = {Downregulation of mitochondrial alternative oxidase affects chloroplast function, redox status and stress response in a marine diatom},
author = {Omer Murik and Leila Tirichine and Judit Prihoda and Yann Thomas and Wagner L Ara{ú}jo and Andrew E Allen and Alisdair R Fernie and Chris Bowler},
doi = {10.1111/nph.15479},
issn = {14698137},
year = {2019},
date = {2019-01-01},
journal = {New Phytologist},
volume = {221},
number = {3},
pages = {1303--1316},
abstract = {Diatom dominance in contemporary aquatic environments indicates that they have developed unique and effective mechanisms to cope with the rapid and considerable fluctuations that characterize these environments. In view of their evolutionary history from a secondary endosymbiosis, inter-organellar regulation of biochemical activities may be of particular relevance. Diatom mitochondrial alternative oxidase (AOX) is believed to play a significant role in supplying chloroplasts with ATP produced in the mitochondria. Using the model diatom Phaeodactylum tricornutum we generated AOX knockdown lines, and followed sensitivity to stressors, photosynthesis and transcriptome and metabolome profiles of wild-type and knockdown lines. We show here that expression of the AOX gene is upregulated by various stresses including H 2 O 2 , heat, high light illumination, and iron or nitrogen limitation. AOX knockdown results in hypersensitivity to stress. Knockdown lines also show significantly reduced photosynthetic rates and their chloroplasts are more oxidized. Comparisons of transcriptome and metabolome profiles suggest a strong impact of AOX activity on gene expression, which is carried through to the level of the metabolome. Our data provide evidence for the involvement of mitochondrial AOX in processes central to the cell biology of diatoms, revealing that cross-talk between mitochondria and chloroplasts is crucial for maintaining sensitivity to changing environments.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Huang, Ruiping; Ding, Jiancheng; Gao, Kunshan; de Carvalho, Maria Helena; Tirichine, Leila; Bowler, Chris; Lin, Xin
A Potential Role for Epigenetic Processes in the Acclimation Response to Elevated pCO2 in the Model Diatom Phaeodactylum tricornutum Article de journal
Dans: Frontiers in Microbiology, vol. 9, p. 3342, 2019, ISSN: 1664-302X.
@article{10.3389/fmicb.2018.03342,
title = {A Potential Role for Epigenetic Processes in the Acclimation Response to Elevated pCO2 in the Model Diatom Phaeodactylum tricornutum},
author = {Ruiping Huang and Jiancheng Ding and Kunshan Gao and Maria Helena de Carvalho and Leila Tirichine and Chris Bowler and Xin Lin},
url = {https://www.frontiersin.org/article/10.3389/fmicb.2018.03342},
doi = {10.3389/fmicb.2018.03342},
issn = {1664-302X},
year = {2019},
date = {2019-01-01},
journal = {Frontiers in Microbiology},
volume = {9},
pages = {3342},
abstract = {Understanding of the molecular responses underpinning diatom responses to ocean acidification is fundamental for predicting how important primary producers will be shaped by the continuous rise in atmospheric CO2. In this study, we have analyzed global transcriptomic changes of the model diatom Phaeodactylum tricornutum following growth for 15 generations in elevated pCO2 by strand-specific RNA sequencing (ssRNA-seq). Our results indicate that no significant effects of elevated pCO2 and associated carbonate chemistry changes on the physiological performance of the cells were observed after 15 generations whereas the expression of genes encoding histones and other genes involved in chromatin structure were significantly down-regulated, while the expression of transposable elements (TEs) and genes encoding histone acetylation enzymes were significantly up-regulated. Furthermore, we identified a series of long non-protein coding RNAs (lncRNAs) specifically responsive to elevated pCO2, suggesting putative regulatory roles for these largely uncharacterized genome components. Taken together, our integrative analyses reveal that epigenetic elements such as TEs, histone modifications and lncRNAs may have important roles in the acclimation of diatoms to elevated pCO2 over short time scales and thus may influence longer term adaptive processes in response to progressive ocean acidification.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Shao, Zhanru; Thomas, Yann; Hembach, Lea; Xing, Xiaohui; Duan, Delin; Moerschbacher, Bruno M; Bulone, Vincent; Tirichine, Leila; Bowler, Chris
Dans: New Phytologist, vol. 221, no. 4, p. 1890–1905, 2019, ISSN: 14698137.
@article{Shao2019,
title = {Comparative characterization of putative chitin deacetylases from Phaeodactylum tricornutum and Thalassiosira pseudonana highlights the potential for distinct chitin-based metabolic processes in diatoms},
author = {Zhanru Shao and Yann Thomas and Lea Hembach and Xiaohui Xing and Delin Duan and Bruno M Moerschbacher and Vincent Bulone and Leila Tirichine and Chris Bowler},
doi = {10.1111/nph.15510},
issn = {14698137},
year = {2019},
date = {2019-01-01},
journal = {New Phytologist},
volume = {221},
number = {4},
pages = {1890--1905},
abstract = {Chitin is generally considered to be present in centric diatoms but not in pennate species. Many aspects of chitin biosynthetic pathways have not been explored in diatoms. We retrieved chitin metabolic genes from pennate (Phaeodactylum tricornutum) and centric (Thalassiosira pseudonana) diatom genomes. Chitin deacetylase (CDA) genes from each genome (PtCDA and TpCDA) were overexpressed in P. tricornutum. We performed comparative analysis of their sequence structure, phylogeny, transcriptional profiles, localization and enzymatic activities. The chitin relevant proteins show complex subcellular compartmentation. PtCDA was likely acquired by horizontal gene transfer from prokaryotes, whereas TpCDA has closer relationships with sequences in Opisthokonta. Using transgenic P. tricornutum lines expressing CDA-green fluorescent protein (GFP) fusion proteins, PtCDA predominantly localizes to Golgi apparatus whereas TpCDA localizes to endoplasmic reticulum/chloroplast endoplasmic reticulum membrane. CDA-GFP overexpression upregulated the transcription of chitin synthases and potentially enhanced the ability of chitin synthesis. Although both CDAs are active on GlcNAc 5 , TpCDA is more active on the highly acetylated chitin polymer DA60. We have addressed the ambiguous characters of CDAs from P. tricornutum and T. pseudonana. Differences in localization, evolution, expression and activities provide explanations underlying the greater potential of centric diatoms for chitin biosynthesis. This study paves the way for in vitro applications of novel CDAs.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Velic, Denis; Charlier, Cathy; Popova, Milena; Jaunet-Lahary, Titouan; Bouchouireb, Zakaria; Henry, Sébastien; Weigel, Pierre; Masson, Jean-Yves; Laurent, Adèle D; Nabiev, Igor; Fleury, Fabrice
Interactions of the Rad51 inhibitor DIDS with human and bovine serum albumins: Optical spectroscopy and isothermal calorimetry approaches Article de journal
Dans: Biochimie, vol. 167, p. 187–197, 2019, ISSN: 0300-9084.
@article{VELIC2019187,
title = {Interactions of the Rad51 inhibitor DIDS with human and bovine serum albumins: Optical spectroscopy and isothermal calorimetry approaches},
author = {Denis Velic and Cathy Charlier and Milena Popova and Titouan Jaunet-Lahary and Zakaria Bouchouireb and Sébastien Henry and Pierre Weigel and Jean-Yves Masson and Adèle D Laurent and Igor Nabiev and Fabrice Fleury},
url = {http://www.sciencedirect.com/science/article/pii/S0300908419302743},
doi = {https://doi.org/10.1016/j.biochi.2019.09.016},
issn = {0300-9084},
year = {2019},
date = {2019-01-01},
journal = {Biochimie},
volume = {167},
pages = {187--197},
abstract = {Rad51 is a key protein in DNA repair by homologous recombination and an important target for development of drugs in cancer therapy. 4′-diisothiocyanostilbene-2,2′-disulfonic acid (DIDS) has been used in clinic during the past 30 years as an inhibitor of anion transporters and channels. Recently DIDS has been demonstrated to affect Rad51-mediated homologous pairing and strand exchange, key processes in homologous recombination. Consequently, DIDS has been considered as a potential revertant of radio- and chemo-resistance of cancer cells, the major causes of therapy failure. Here, we have investigated the behavior of DIDS towards serum albumins. The effects of environmental factors, primarily, solvent polarity, on DIDS stability were evaluated, and the mechanisms of interaction of DIDS with human or bovine serum albumin were analyzed using isothermal calorimetry, circular dichroism and fluorescence spectroscopies. DIDS interaction with both serum albumins have been demonstrated, and the interaction characteristics have been determined. By comparing these characteristics for several DIDS derivatives, we have identified the DIDS moiety essential for the interaction. Furthermore, site competition data indicate that human albumin has two DIDS-binding sites: a high-affinity site in the IIIA subdomain and a low-affinity one in the IB subdomain. Molecular docking has revealed the key molecular moieties of DIDS responsible for its interactions in each site and shown that the IB site can bind two ligands. These findings show that binding of DIDS to serum albumin may change the balance between the free and bound DIDS forms, thereby affecting its bioavailability and efficacy against Rad51.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Chabot, Thomas; Defontaine, Alain; Marquis, Damien; Renodon-Corniere, Axelle; Courtois, Emmanuelle; Fleury, Fabrice; Cheraud, Yvonnick
New phosphorylation sites of rad51 by c-met modulates presynaptic filament stability Article de journal
Dans: Cancers, vol. 11, no. 3, 2019, ISSN: 20726694.
@article{Chabot2019a,
title = {New phosphorylation sites of rad51 by c-met modulates presynaptic filament stability},
author = {Thomas Chabot and Alain Defontaine and Damien Marquis and Axelle Renodon-Corniere and Emmanuelle Courtois and Fabrice Fleury and Yvonnick Cheraud},
doi = {10.3390/cancers11030413},
issn = {20726694},
year = {2019},
date = {2019-01-01},
journal = {Cancers},
volume = {11},
number = {3},
abstract = {Genomic instability through deregulation of DNA repair pathways can initiate cancer and subsequently result in resistance to chemo and radiotherapy. Understanding these biological mechanisms is therefore essential to overcome cancer. RAD51 is the central protein of the Homologous Recombination (HR) DNA repair pathway, which leads to faithful DNA repair of DSBs. The recombinase activity of RAD51 requires nucleofilament formation and is regulated by post-translational modifications such as phosphorylation. In the last decade, studies have suggested the existence of a relationship between receptor tyrosine kinases (RTK) and Homologous Recombination DNA repair. Among these RTK the c-MET receptor is often overexpressed or constitutively activated in many cancer types and its inhibition induces the decrease of HR. In this study, we show for the first time that c-MET is able to phosphorylate the RAD51 protein. We demonstrate in vitro that c-MET phosphorylates four tyrosine residues localized mainly in the subunit-subunit interface of RAD51. Whereas these post-translational modifications do not affect the presynaptic filament formation, they strengthen its stability against the inhibitor effect of the BRC peptide obtained from BRCA2. Taken together, these results confirm the role of these modifications in the regulation of the BRCA2-RAD51 interaction and underline the importance of c-MET in DNA damage response.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Brinkø, Anne; Risinger, Christian; Lambert, Annie; Blixt, Ola; Grandjean, Cyrille; Jensen, Henrik H
Combining Click Reactions for the One-Pot Synthesis of Modular Biomolecule Mimetics Article de journal
Dans: Organic Letters, vol. 21, no. 18, p. 7544–7548, 2019, ISSN: 15237052.
@article{Brinkø2019,
title = {Combining Click Reactions for the One-Pot Synthesis of Modular Biomolecule Mimetics},
author = {Anne Brinkø and Christian Risinger and Annie Lambert and Ola Blixt and Cyrille Grandjean and Henrik H Jensen},
doi = {10.1021/acs.orglett.9b02811},
issn = {15237052},
year = {2019},
date = {2019-01-01},
journal = {Organic Letters},
volume = {21},
number = {18},
pages = {7544--7548},
abstract = {Here, we report on the first combined one-pot use of the two so-called "click reactions": The thiol-ene coupling and the copper-catalyzed alkyne-azide cycloaddition. These reactions were employed in an alternating and one-pot fashion to combine appropriately functionalized monomeric carbohydrate building blocks to create mimics of trisaccharides and tetrasaccharides as single anomers, with only minimal purification necessary. The deprotected oligosaccharide mimics were found to bind both plant lectins and human galectin-3.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Pillot, Aline; Defontaine, Alain; Fateh, Amina; Lambert, Annie; Prasanna, Maruthi; Fanuel, Mathieu; Pipelier, Muriel; Csaba, Noemi; Violo, Typhaine; Camberlein, Emilie; Grandjean, Cyrille
Site-Specific Conjugation for Fully Controlled Glycoconjugate Vaccine Preparation Article de journal
Dans: Frontiers in Chemistry, vol. 7, no. November, p. 1–9, 2019, ISSN: 22962646.
@article{Pillot2019,
title = {Site-Specific Conjugation for Fully Controlled Glycoconjugate Vaccine Preparation},
author = {Aline Pillot and Alain Defontaine and Amina Fateh and Annie Lambert and Maruthi Prasanna and Mathieu Fanuel and Muriel Pipelier and Noemi Csaba and Typhaine Violo and Emilie Camberlein and Cyrille Grandjean},
doi = {10.3389/fchem.2019.00726},
issn = {22962646},
year = {2019},
date = {2019-01-01},
journal = {Frontiers in Chemistry},
volume = {7},
number = {November},
pages = {1--9},
abstract = {Glycoconjugate vaccines are formed by covalently link a carbohydrate antigen to a carrier protein whose role is to achieve a long lasting immune response directed against the carbohydrate antigen. The nature of the sugar antigen, its length, its ratio per carrier protein and the conjugation chemistry impact on both structure and the immune response of a glycoconjugate vaccine. In addition it has long been assumed that the sites at which the carbohydrate antigen is attached can also have an impact. These important issue can now be addressed owing to the development of novel chemoselective ligation reactions as well as techniques such as site-selective mutagenesis, glycoengineering, or extension of the genetic code. The preparation and characterization of homogeneous bivalent pneumococcal vaccines is reported. The preparation and characterization of homogeneous bivalent pneumococcal vaccines is reported. A synthetic tetrasaccharide representative of the serotype 14 capsular polysaccharide of Streptococcus pneumoniae has been linked using the thiol/maleimide coupling chemistry to four different Pneumococcal surface adhesin A (PsaA) mutants, each harboring a single cysteine mutation at a defined position. Humoral response of these 1 to 1 carbohydrate antigen/PsaA conjugates have been assessed in mice. Our results showed that the carbohydrate antigen-PsaA connectivity impacts the anti-carrier response and raise questions about the design of glycoconjugate vaccine whereby the protein plays the dual role of immunogen and carrier.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Prasanna, Maruthi; Soulard, Daphnée; Camberlein, Emilie; Ruffier, Nicolas; Lambert, Annie; Trottein, François; Csaba, Noemi; Grandjean, Cyrille
Semisynthetic glycoconjugate based on dual role protein/PsaA as a pneumococcal vaccine Article de journal
Dans: European Journal of Pharmaceutical Sciences, vol. 129, p. 31–41, 2019, ISSN: 0928-0987.
@article{PRASANNA201931,
title = {Semisynthetic glycoconjugate based on dual role protein/PsaA as a pneumococcal vaccine},
author = {Maruthi Prasanna and Daphnée Soulard and Emilie Camberlein and Nicolas Ruffier and Annie Lambert and François Trottein and Noemi Csaba and Cyrille Grandjean},
url = {http://www.sciencedirect.com/science/article/pii/S0928098718305487},
doi = {https://doi.org/10.1016/j.ejps.2018.12.013},
issn = {0928-0987},
year = {2019},
date = {2019-01-01},
journal = {European Journal of Pharmaceutical Sciences},
volume = {129},
pages = {31--41},
abstract = {Pneumococcal infections remain a major public health concern worldwide. The currently available vaccines in the market are based on pneumococcal capsular polysaccharides but they still need to be improved to secure an optimal coverage notably in population at risk. To circumvent this, association of virulence pneumococcal proteins to the polysaccharide valencies has been proposed with the hope to observe an additive - if not synergistic - protective effect. Along this line, the use of the highly conserved and ubiquitous pneumococcal surface adhesin A (PsaA) as a protein carrier for a synthetic pneumococcal oligosaccharide is demonstrated herein for the first time. A tetrasaccharide mimicking functional antigenic determinants from the S. pneumoniae serotype 14 capsular polysaccharide (Pn14TS) was chemically synthesised. The mature PsaA (mPsaA) was expressed in E. coli and purified using affinity chromatography. The Pn14PS was conjugated to mPsaA using maleimide-thiol coupling chemistry to obtain mPsaA-Pn14PS conjugate (protein/sugar molar ratio: 1/5.4). The mPsaA retained the structural conformation after the conjugation and lyophilisation. The prepared glycoconjugate adjuvanted with α-galactosylceramide, a potent activator of invariant Natural Killer T cells, was tested in mice for its immunological response upon subcutaneous injection in comparison with mPsaA alone and a model BSA conjugate (BSA-Pn14PS, used here as a control). Mice immunised with the mPsaA-Pn14TS produced a robust IgG response against mPsaA and against the capsular polysaccharide from pneumococcal serotype 14. These data provide the basis for novel pneumococcal vaccine development.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Brissonnet, Yoan; Assailly, Coralie; Saumonneau, Amélie; Bouckaert, Julie; Maillasson, Mike; Petitot, Clémence; Roubinet, Benoit; Didak, Blanka; Landemarre, Ludovic; Bridot, Clarisse; Blossey, Ralf; Deniaud, David; Yan, Xibo; Bernard, Julien; Tellier, Charles; Grandjean, Cyrille; Daligault, Franck; Gouin, Sébastien G
Multivalent Thiosialosides and Their Synergistic Interaction with Pathogenic Sialidases Article de journal
Dans: Chemistry - A European Journal, vol. 25, no. 9, p. 2358–2365, 2019, ISSN: 15213765.
@article{Brissonnet2019b,
title = {Multivalent Thiosialosides and Their Synergistic Interaction with Pathogenic Sialidases},
author = {Yoan Brissonnet and Coralie Assailly and Amélie Saumonneau and Julie Bouckaert and Mike Maillasson and Clémence Petitot and Benoit Roubinet and Blanka Didak and Ludovic Landemarre and Clarisse Bridot and Ralf Blossey and David Deniaud and Xibo Yan and Julien Bernard and Charles Tellier and Cyrille Grandjean and Franck Daligault and Sébastien G Gouin},
doi = {10.1002/chem.201805790},
issn = {15213765},
year = {2019},
date = {2019-01-01},
journal = {Chemistry - A European Journal},
volume = {25},
number = {9},
pages = {2358--2365},
abstract = {Sialidases (SAs) hydrolyze sialyl residues from glycoconjugates of the eukaryotic cell surface and are virulence factors expressed by pathogenic bacteria, viruses, and parasites. The catalytic domains of SAs are often flanked with carbohydrate-binding module(s) previously shown to bind sialosides and to enhance enzymatic catalytic efficiency. Herein, non-hydrolyzable multivalent thiosialosides were designed as probes and inhibitors of V. cholerae, T. cruzi, and S. pneumoniae (NanA) sialidases. NanA was truncated from the catalytic and lectinic domains (NanA-L and NanA-C) to probe their respective roles upon interacting with sialylated surfaces and the synthetically designed di- and polymeric thiosialosides. The NanA-L domain was shown to fully drive NanA binding, improving affinity for the thiosialylated surface and compounds by more than two orders of magnitude. Importantly, each thiosialoside grafted onto the polymer was also shown to reduce NanA and NanA-C catalytic activity with efficiency that was 3000-fold higher than that of the monovalent thiosialoside reference. These results extend the concept of multivalency for designing potent bacterial and parasitic sialidase inhibitors.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Naretto, Anaïs; Fanuel, Mathieu; Ropartz, David; Rogniaux, Hélène; Larocque, Robert; Czjzek, Mirjam; Tellier, Charles; Michel, Gurvan
The agar-specific hydrolase ZgAgaC from the marine bacterium Zobellia galactanivorans defines a new GH16 protein subfamily Article de journal
Dans: Journal of Biological Chemistry, vol. 294, no. 17, p. 6923–6939, 2019, ISSN: 1083351X.
@article{Naretto2019,
title = {The agar-specific hydrolase ZgAgaC from the marine bacterium Zobellia galactanivorans defines a new GH16 protein subfamily},
author = {Anaïs Naretto and Mathieu Fanuel and David Ropartz and Hélène Rogniaux and Robert Larocque and Mirjam Czjzek and Charles Tellier and Gurvan Michel},
doi = {10.1074/jbc.RA118.006609},
issn = {1083351X},
year = {2019},
date = {2019-01-01},
journal = {Journal of Biological Chemistry},
volume = {294},
number = {17},
pages = {6923--6939},
abstract = {Agars are sulfated galactans from red macroalgae and are composed of a D-galactose (G unit) and L-galactose (L unit) alternatively linked by α-1, 3 and β-1, 4 glycosidicbonds. The sepolysaccharides display high complexity, with numerous modifications of their backbone (e.g. presence of a 3, 6-anhydro-bridge (LA unit) and sulfations and methylation). Currently, bacterial polysaccharidases that hydrolyze agars (α-agarases and α-porphyranases) have been characterized on simple agarose and more rarely on porphyran, a polymer containing both agarobiose (G-LA) and porphyranobiose (GL6S) motifs. How bacteria can degrade complex agars remains therefore an open question. Here, we studied an enzyme from the marine bacterium Zobellia galactanivorans (ZgAgaC) that is distantly related to the glycoside hydrolase 16 (GH16) family α-agarases and α-porphyranases. Using a large red algae collection, we demonstrate that ZgAgaC hydrolyzes not only agarose but also complex agars from Ceramiales species. Using tandem MS analysis, we elucidated the structure of a purified hexasaccharide product, L6S-G-LA2Me-G(2Pentose)-LA2S-G, released by the activity of ZgAgaC on agar extracted from Osmundea pinnatifida. By resolving the crystal structure of ZgAgaC at high resolution (1.3 Å) and comparison with the structures of ZgAgaB and ZgPorA in complex with their respective substrates, we determined that ZgAgaC recognizes agarose via a mechanism different from that of classical α-agarases. Moreover, we identified conserved residues involved in the binding of complex oligoagars and demonstrate a probable influence of the acidic polysaccharide's pH microenvironment on hydrolase activity. Finally, a phylogenetic analysis supported the notion that ZgAgaC homologs define a new GH16 subfamily distinct from α-porphyranases and classical α-agarases.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Caignec, Cédric Le; Ory, Benjamin; Lamoureux, François; O'Donohue, Marie Francoise; Orgebin, Emilien; Lindenbaum, Pierre; Téletchéa, Stéphane; Saby, Manon; Hurst, Anna; Nelson, Katherine; Gilbert, Shawn R; Wilnai, Yael; Zeitlin, Leonid; Segev, Eitan; Tesfaye, Robel; Nizon, Mathilde; Cogne, Benjamin; Bezieau, Stéphane; Geoffroy, Loic; Hamel, Antoine; Mayrargue, Emmanuelle; de Courtivron, Benoît; Decock-Giraudaud, Aliette; Charrier, Céline; Pichon, Olivier; Retière, Christelle; Redon, Richard; Pepler, Alexander; McWalter, Kirsty; Costa, Lydie Da; Toutain, Annick; Gleizes, Pierre Emmanuel; Baud'huin, Marc; Isidor, Bertrand
RPL13 Variants Cause Spondyloepimetaphyseal Dysplasia with Severe Short Stature Article de journal
Dans: American Journal of Human Genetics, vol. 105, no. 5, p. 1040–1047, 2019, ISSN: 15376605.
@article{LeCaignec2019,
title = {RPL13 Variants Cause Spondyloepimetaphyseal Dysplasia with Severe Short Stature},
author = {Cédric Le Caignec and Benjamin Ory and François Lamoureux and Marie Francoise O'Donohue and Emilien Orgebin and Pierre Lindenbaum and Stéphane Téletchéa and Manon Saby and Anna Hurst and Katherine Nelson and Shawn R Gilbert and Yael Wilnai and Leonid Zeitlin and Eitan Segev and Robel Tesfaye and Mathilde Nizon and Benjamin Cogne and Stéphane Bezieau and Loic Geoffroy and Antoine Hamel and Emmanuelle Mayrargue and Beno{î}t de Courtivron and Aliette Decock-Giraudaud and Céline Charrier and Olivier Pichon and Christelle Retière and Richard Redon and Alexander Pepler and Kirsty McWalter and Lydie Da Costa and Annick Toutain and Pierre Emmanuel Gleizes and Marc Baud'huin and Bertrand Isidor},
doi = {10.1016/j.ajhg.2019.09.024},
issn = {15376605},
year = {2019},
date = {2019-01-01},
journal = {American Journal of Human Genetics},
volume = {105},
number = {5},
pages = {1040--1047},
abstract = {Variants in genes encoding ribosomal proteins have thus far been associated with Diamond-Blackfan anemia, a rare inherited bone marrow failure, and isolated congenital asplenia. Here, we report one de novo missense variant and three de novo splice variants in RPL13, which encodes ribosomal protein RPL13 (also called eL13), in four unrelated individuals with a rare bone dysplasia causing severe short stature. The three splice variants (c.477+1GtextgreaterT, c.477+1GtextgreaterA, and c.477+2 TtextgreaterC) result in partial intron retention, which leads to an 18-amino acid insertion. In contrast to observations from Diamond-Blackfan anemia, we detected no evidence of significant pre-rRNA processing disturbance in cells derived from two affected individuals. Consistently, we showed that the insertion-containing protein is stably expressed and incorporated into 60S subunits similar to the wild-type protein. Erythroid proliferation in culture and ribosome profile on sucrose gradient are modified, suggesting a change in translation dynamics. We also provide evidence that RPL13 is present at high levels in chondrocytes and osteoblasts in mouse growth plates. Taken together, we show that the identified RPL13 variants cause a human ribosomopathy defined by a rare skeletal dysplasia, and we highlight the role of this ribosomal protein in bone development.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Ghosh, Pritha; Joshi, Adwait; Guita, Niang; Offmann, Bernard; Sowdhamini, Ramanathan
EcRBPome: A comprehensive database of all known E. coli RNA-binding proteins Article de journal
Dans: BMC Genomics, vol. 20, no. 1, p. 1–6, 2019, ISSN: 14712164.
@article{Ghosh2019,
title = {EcRBPome: A comprehensive database of all known E. coli RNA-binding proteins},
author = {Pritha Ghosh and Adwait Joshi and Niang Guita and Bernard Offmann and Ramanathan Sowdhamini},
doi = {10.1186/s12864-019-5755-5},
issn = {14712164},
year = {2019},
date = {2019-01-01},
journal = {BMC Genomics},
volume = {20},
number = {1},
pages = {1--6},
publisher = {BMC Genomics},
abstract = {The repertoire of RNA-binding proteins (RBPs) in bacteria play a crucial role in their survival, and interactions with the host machinery, but there is little information, record or characterisation in bacterial genomes. As a first step towards this, we have chosen the bacterial model system Escherichia coli, and organised all RBPs in this organism into a comprehensive database named EcRBPome. It contains RBPs recorded from 614 complete E. coli proteomes available in the RefSeq database (as of October 2018). The database provides various features related to the E. coli RBPs, like their domain architectures, PDB structures, GO and EC annotations etc. It provides the assembly, bioproject and biosample details of each strain, as well as cross-strain comparison of occurrences of various RNA-binding domains (RBDs). The percentage of RBPs, the abundance of the various RBDs harboured by each strain have been graphically represented in this database and available alongside other files for user download. To the best of our knowledge, this is the first database of its kind and we hope that it will be of great use to the biological community.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
David, Benoit; Arnaud, Philippe; Tellier, Charles; Sanejouand, Yves-Henri
Toward the design of efficient transglycosidases: the case of the GH1 of Thermus thermophilus Article de journal
Dans: Protein Engineering, Design and Selection, vol. 32, no. 7, p. 309–316, 2019, ISSN: 1741-0126.
@article{10.1093/protein/gzz032,
title = {Toward the design of efficient transglycosidases: the case of the GH1 of Thermus thermophilus},
author = {Benoit David and Philippe Arnaud and Charles Tellier and Yves-Henri Sanejouand},
url = {https://doi.org/10.1093/protein/gzz032},
doi = {10.1093/protein/gzz032},
issn = {1741-0126},
year = {2019},
date = {2019-01-01},
journal = {Protein Engineering, Design and Selection},
volume = {32},
number = {7},
pages = {309--316},
abstract = {Using the information available in the sequences of well-characterized transglycosidases found in plants, mutations were introduced in the glycoside hydrolase of the bacterium Thermus thermophilus, with the aim of turning it into an efficient transglycosidase. All mutants happen to have fair catalytic efficiencies, being at worst 25 times less efficient than the wild type. Noteworthy, W120F, one of our high transglycosylation yield (≈ 50%) mutants, is only two times less efficient than the wild type. Interestingly, while in the wild type the sidechain of the acid–base is only found able to sample a pair of equivalent conformations during 0.5-µs-long molecular dynamics simulations, its flexibility is much higher in the case of the high transglycosylation yield mutants. Our results thus suggest that engineering the flexibility of the acid–base of a retaining glycoside hydrolase could be a general way to turn it into an efficient transglycosidase.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Chaaya, Nancy; Shahsavarian, Melody A; Maffucci, Irene; Friboulet, Alain; Offmann, Bernard; Léger, Jean Benoist; Rousseau, Sylvain; Avalle, Bérangère; Padiolleau-Lefèvre, Séverine
Genetic background and immunological status influence B cell repertoire diversity in mice Article de journal
Dans: Scientific Reports, vol. 9, no. 1, p. 1–7, 2019, ISSN: 20452322.
@article{Chaaya2019,
title = {Genetic background and immunological status influence B cell repertoire diversity in mice},
author = {Nancy Chaaya and Melody A Shahsavarian and Irene Maffucci and Alain Friboulet and Bernard Offmann and Jean Benoist Léger and Sylvain Rousseau and Bérang{è}re Avalle and Séverine Padiolleau-Lef{è}vre},
doi = {10.1038/s41598-019-50714-y},
issn = {20452322},
year = {2019},
date = {2019-01-01},
journal = {Scientific Reports},
volume = {9},
number = {1},
pages = {1--7},
abstract = {The relationship between the immune repertoire and the physiopathological status of individuals is essential to apprehend the genesis and the evolution of numerous pathologies. Nevertheless, the methodological approaches to understand these complex interactions are challenging. We performed a study evaluating the diversity harbored by different immune repertoires as a function of their physiopathological status. In this study, we base our analysis on a murine scFv library previously described and representing four different immune repertoires: i) healthy and naïve, ii) healthy and immunized, iii) autoimmune prone and naïve, and iv) autoimmune prone and immunized. This library, 2.6 × 109 in size, is submitted to high throughput sequencing (Next Generation Sequencing, NGS) in order to analyze the gene subgroups encoding for immunoglobulins. A comparative study of the distribution of immunoglobulin gene subgroups present in the four libraries has revealed shifts in the B cell repertoire originating from differences in genetic background and immunological status of mice.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Vetrivel, Iyanar; de Brevern, Alexandre G; Cadet, Frédéric; Srinivasan, Narayanaswamy; Offmann, Bernard
Structural variations within proteins can be as large as variations observed across their homologues Article de journal
Dans: Biochimie, vol. 167, p. 162–170, 2019, ISSN: 61831638.
@article{Vetrivel2019,
title = {Structural variations within proteins can be as large as variations observed across their homologues},
author = {Iyanar Vetrivel and Alexandre G de Brevern and Frédéric Cadet and Narayanaswamy Srinivasan and Bernard Offmann},
doi = {10.1016/j.biochi.2019.09.013},
issn = {61831638},
year = {2019},
date = {2019-01-01},
journal = {Biochimie},
volume = {167},
pages = {162--170},
abstract = {Understanding the structural plasticity of proteins is key to understanding the intricacies of their functions and mechanistic basis. In the current study, we analyzed the available multiple crystal structures of the same protein for the structural differences. For this purpose we used an abstraction of protein structures referred as Protein Blocks (PBs) that was previously established. We also characterized the nature of the structural variations for a few proteins using molecular dynamics simulations. In both the cases, the structural variations were summarized in the form of substitution matrices of PBs. We show that certain conformational states are preferably replaced by other specific conformational states. Interestingly, these structural variations are highly similar to those previously observed across structures of homologous proteins (r2 = 0.923) or across the ensemble of conformations from NMR data (r2 = 0.919). Thus our study quantitatively shows that overall trends of structural changes in a given protein are nearly identical to the trends of structural differences that occur in the topologically equivalent positions in homologous proteins. Specific case studies are used to illustrate the nature of these structural variations.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Richoux, Florian; Servantie, Charlène; Borès, Cynthia; Téletchéa, Stéphane
Comparing two deep learning sequence-based models for protein-protein interaction prediction Article de journal
Dans: arXiv, vol. 1901.06268, 2019.
@article{Richoux2019,
title = {Comparing two deep learning sequence-based models for protein-protein interaction prediction},
author = {Florian Richoux and Charlène Servantie and Cynthia Borès and Stéphane Téletchéa},
url = {http://arxiv.org/abs/1901.06268},
year = {2019},
date = {2019-01-01},
journal = {arXiv},
volume = {1901.06268},
abstract = {Biological data are extremely diverse, complex but also quite sparse. The recent developments in deep learning methods are offering new possibilities for the analysis of complex data. However, it is easy to be get a deep learning model that seems to have good results but is in fact either overfitting the training data or the validation data. In particular, the fact to overfit the validation data, called "information leak", is almost never treated in papers proposing deep learning models to predict protein-protein interactions (PPI). In this work, we compare two carefully designed deep learning models and show pitfalls to avoid while predicting PPIs through machine learning methods. Our best model predicts accurately more than 78% of human PPI, in very strict conditions both for training and testing. The methodology we propose here allow us to have strong confidences about the ability of a model to scale up on larger datasets. This would allow sharper models when larger datasets would be available, rather than current models prone to information leaks. Our solid methodological foundations shall be applicable to more organisms and whole proteome networks predictions.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Vetrivel, Iyanar; Hoffmann, Lionel; Guegan, Sean; Offmann, Bernard; Laurent, Adele D
PBmapclust: Mapping and Clustering the Protein Conformational Space Using a Structural Alphabet Proceedings Article
Dans: Byska, Jan; Krone, Michael; Sommer, Björn (Ed.): Workshop on Molecular Graphics and Visual Analysis of Molecular Data, The Eurographics Association, 2019, ISBN: 978-3-03868-085-7.
@inproceedings{lva.20191097b,
title = {PBmapclust: Mapping and Clustering the Protein Conformational Space Using a Structural Alphabet},
author = {Iyanar Vetrivel and Lionel Hoffmann and Sean Guegan and Bernard Offmann and Adele D Laurent},
editor = {Jan Byska and Michael Krone and Björn Sommer},
doi = {10.2312/molva.20191097},
isbn = {978-3-03868-085-7},
year = {2019},
date = {2019-01-01},
booktitle = {Workshop on Molecular Graphics and Visual Analysis of Molecular Data},
publisher = {The Eurographics Association},
abstract = {Analyzing the data from molecular dynamics simulation of biological macromolecules like proteins is challenging. We propose a simple tool called PBmapclust that is based on a well established structural alphabet called Protein blocks (PB). PBs help in tracing the trajectory of the protein backbone by categorizing it into 16 distinct structural states. PBmapclust provides a time vs. amino acid residue plot that is color coded to match each of the PBs. Color changes correspond to structural changes, giving a visual overview of the simulation. Further, PBmapclust enables the user to "map" the conformational space sampled by the protein during the MD simulation by clustering the conformations. The ability to generate sub-maps for specific residues and specific time intervals allows the user to focus on residues of interest like for active sites or disordered regions. We have included an illustrative case study to demonstrate the utility of the tool. It describes the effect of the disordered domain of a HSP90 co-chaperone on the conformation of its active site residues. The scripts required to perform PBmapclust are made freely available under the GNU general public license.},
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
}
Liu, Guoxia; Arnaud, Philippe; Offmann, Bernard; Picimbon, Jean-François
Pheromone, Natural Odor and Odorant Reception Suppressing Agent (ORSA) for Insect Control Book Section
Dans: Olfactory Concepts of Insect Control-Alternative to Insecticides, p. 311–345, Springer, Cham, 2019.
@incollection{liu2019pheromone,
title = {Pheromone, Natural Odor and Odorant Reception Suppressing Agent (ORSA) for Insect Control},
author = {Guoxia Liu and Philippe Arnaud and Bernard Offmann and Jean-François Picimbon},
doi = {10.1007/978-3-030-05165-5},
year = {2019},
date = {2019-01-01},
booktitle = {Olfactory Concepts of Insect Control-Alternative to Insecticides},
pages = {311--345},
publisher = {Springer, Cham},
abstract = {Odorant-binding proteins (OBPs) are small ``bowl-like'' globular pro- teins, highly abundant in the antennae of most insect species. These proteins are believed to mediate reception of odor molecules at the periphery of sensory receptor neurons. Therefore, they may represent crucial targets for becoming new methods of insect pest control by directly interfering with the olfactory acuity of the insect. The current better understanding of molecular mechanisms underlying odor detec- tion and the knowledge about the functional binding sites of OBPs and many other families of binding proteins in various insect species is elucidated here. Such infor- mation forms the basis for the synthesis of new inhibitor olfactory compounds (Odorant Reception-Suppressing Agents, ORSAs) to interact specifically with the groups of insect pests.},
keywords = {},
pubstate = {published},
tppubtype = {incollection}
}
Caputi, L; Carradec, Q; Eveillard, D; Kirilovsky, A; Pelletier, E; Karlusich, J J Pierella; Vieira, F Rocha Jimenez; Villar, E; Chaffron, S; Malviya, S; Scalco, E; Acinas, S G; Alberti, A; Aury, J -M; Benoiston, A -S; Bertrand, A; Biard, T; Bittner, L; Boccara, M; Brum, J R; Brunet, C; Busseni, G; Carratalà, A; Claustre, H; Coelho, L P; Colin, S; Daniello, S; Silva, C Da; Core, M Del; Doré, H; Gasparini, S; Kokoszka, F; Jamet, J -L; Lejeusne, C; Lepoivre, C; Lescot, M; Lima-Mendez, G; Lombard, F; Lukeš, J; Maillet, N; Madoui, M -A; Martinez, E; Mazzocchi, M G; Néou, M B; Paz-Yepes, J; Poulain, J; Ramondenc, S; Romagnan, J -B; Roux, S; Manta, D Salvagio; Sanges, R; Speich, S; Sprovieri, M; Sunagawa, S; Taillandier, V; Tanaka, A; Tirichine, Leila; Trottier, Camille; Uitz, J; Veluchamy, A; Veselá, J; Vincent, F; Yau, S; Kandels-Lewis, S; Searson, S; Dimier, C; Picheral, M; Bork, P; Boss, E; de Vargas, C; Follows, M J; Grimsley, N; Guidi, L; Hingamp, P; Karsenti, E; Sordino, P; Stemmann, L; Sullivan, M B; Tagliabue, A; Zingone, A; Garczarek, L; DÓrtenzio, F; Testor, P; Not, F; DÁlcalà, M R; Wincker, P; Bowler, C; Iudicone, D
Community-Level Responses to Iron Availability in Open Ocean Plankton Ecosystems Article de journal
Dans: Global Biogeochemical Cycles, vol. 33, no. 3, 2019, ISSN: 19449224.
@article{Caputi2019,
title = {Community-Level Responses to Iron Availability in Open Ocean Plankton Ecosystems},
author = {L Caputi and Q Carradec and D Eveillard and A Kirilovsky and E Pelletier and J J Pierella Karlusich and F Rocha Jimenez Vieira and E Villar and S Chaffron and S Malviya and E Scalco and S G Acinas and A Alberti and J -M Aury and A -S Benoiston and A Bertrand and T Biard and L Bittner and M Boccara and J R Brum and C Brunet and G Busseni and A Carratalà and H Claustre and L P Coelho and S Colin and S Daniello and C Da Silva and M Del Core and H Doré and S Gasparini and F Kokoszka and J -L Jamet and C Lejeusne and C Lepoivre and M Lescot and G Lima-Mendez and F Lombard and J Lukeš and N Maillet and M -A Madoui and E Martinez and M G Mazzocchi and M B Néou and J Paz-Yepes and J Poulain and S Ramondenc and J -B Romagnan and S Roux and D Salvagio Manta and R Sanges and S Speich and M Sprovieri and S Sunagawa and V Taillandier and A Tanaka and Leila Tirichine and Camille Trottier and J Uitz and A Veluchamy and J Veselá and F Vincent and S Yau and S Kandels-Lewis and S Searson and C Dimier and M Picheral and P Bork and E Boss and C de Vargas and M J Follows and N Grimsley and L Guidi and P Hingamp and E Karsenti and P Sordino and L Stemmann and M B Sullivan and A Tagliabue and A Zingone and L Garczarek and F DÓrtenzio and P Testor and F Not and M R DÁlcalà and P Wincker and C Bowler and D Iudicone},
doi = {10.1029/2018GB006022},
issn = {19449224},
year = {2019},
date = {2019-01-01},
journal = {Global Biogeochemical Cycles},
volume = {33},
number = {3},
abstract = {Predicting responses of plankton to variations in essential nutrients is hampered by limited in situ measurements, a poor understanding of community composition, and the lack of reference gene catalogs for key taxa. Iron is a key driver of plankton dynamics and, therefore, of global biogeochemical cycles and climate. To assess the impact of iron availability on plankton communities, we explored the comprehensive bio-oceanographic and bio-omics data sets from Tara Oceans in the context of the iron products from two state-of-the-art global scale biogeochemical models. We obtained novel information about adaptation and acclimation toward iron in a range of phytoplankton, including picocyanobacteria and diatoms, and identified whole subcommunities covarying with iron. Many of the observed global patterns were recapitulated in the Marquesas archipelago, where frequent plankton blooms are believed to be caused by natural iron fertilization, although they are not captured in large-scale biogeochemical models. This work provides a proof of concept that integrative analyses, spanning from genes to ecosystems and viruses to zooplankton, can disentangle the complexity of plankton communities and can lead to more accurate formulations of resource bioavailability in biogeochemical models, thus improving our understanding of plankton resilience in a changing environment.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Duc, Céline; Yoth, Marianne; Jensen, Silke; Mouniée, Nolwenn; Bergman, Casey M; Vaury, Chantal; Brasset, Emilie
Trapping a somatic endogenous retrovirus into a germline piRNA cluster immunizes the germline against further invasion Article de journal
Dans: Genome Biology, vol. 20, no. 1, p. 127, 2019, ISSN: 1474-760X.
@article{duc_trapping_2019,
title = {Trapping a somatic endogenous retrovirus into a germline piRNA cluster immunizes the germline against further invasion},
author = {Céline Duc and Marianne Yoth and Silke Jensen and Nolwenn Mouniée and Casey M Bergman and Chantal Vaury and Emilie Brasset},
url = {https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1736-x},
doi = {10.1186/s13059-019-1736-x},
issn = {1474-760X},
year = {2019},
date = {2019-01-01},
urldate = {2019-01-01},
journal = {Genome Biology},
volume = {20},
number = {1},
pages = {127},
abstract = {Background: For species survival, the germline must faithfully transmit genetic information to the progeny. Transposable elements (TEs) constitute a significant threat to genome stability due to their mobility. In the metazoan germline, their mobilization is limited by a class of small RNAs called PIWI-interacting RNAs (piRNAs) produced by dedicated genomic loci called piRNA clusters. Although the piRNA pathway is an adaptive genomic immunity system, it remains unclear how the germline gains protection from a new transposon invasion.
Results: To address this question, we analyze Drosophila melanogaster lines harboring a deletion within flamenco, a major piRNA cluster specifically expressed in somatic follicular cells. This deletion leads to derepression of the retrotransposon ZAM in the somatic follicular cells and subsequent germline genome invasion. In this mutant line, we identify de novo production of sense and antisense ZAM-derived piRNAs that display a germinal molecular signature. These piRNAs originated from a new ZAM insertion into a germline dual-strand piRNA cluster and silence ZAM expression specifically in germ cells. Finally, we find that ZAM trapping in a germinal piRNA cluster is a frequent event that occurs early during the isolation of the mutant line.
Conclusions: Transposons can hijack the host developmental process to propagate whenever their silencing is lost. Here, we show that the germline can protect itself by trapping invading somatic-specific TEs into germline piRNA clusters. This is the first demonstration of “auto-immunization” of a germline endangered by mobilization of a surrounding somatic TE.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Results: To address this question, we analyze Drosophila melanogaster lines harboring a deletion within flamenco, a major piRNA cluster specifically expressed in somatic follicular cells. This deletion leads to derepression of the retrotransposon ZAM in the somatic follicular cells and subsequent germline genome invasion. In this mutant line, we identify de novo production of sense and antisense ZAM-derived piRNAs that display a germinal molecular signature. These piRNAs originated from a new ZAM insertion into a germline dual-strand piRNA cluster and silence ZAM expression specifically in germ cells. Finally, we find that ZAM trapping in a germinal piRNA cluster is a frequent event that occurs early during the isolation of the mutant line.
Conclusions: Transposons can hijack the host developmental process to propagate whenever their silencing is lost. Here, we show that the germline can protect itself by trapping invading somatic-specific TEs into germline piRNA clusters. This is the first demonstration of “auto-immunization” of a germline endangered by mobilization of a surrounding somatic TE.
Brun, Guillaume; Thoiron, Séverine; Braem, Lukas; Pouvreau, Jean-Bernard; Montiel, Grégory; Lechat, Marc-Marie; Simier, Philippe; Gevaert, Kris; Goormachtig, Sophie; Delavault, Philippe
CYP707As are effectors of karrikin and strigolactone signalling pathways in Arabidopsis thaliana and parasitic plants Article de journal
Dans: Plant Cell Environ, vol. 42, no. 9, p. 2612-2626, 2019, ISSN: 0140-7791.
@article{RN7,
title = {CYP707As are effectors of karrikin and strigolactone signalling pathways in Arabidopsis thaliana and parasitic plants},
author = {Guillaume Brun and Séverine Thoiron and Lukas Braem and Jean-Bernard Pouvreau and Grégory Montiel and Marc-Marie Lechat and Philippe Simier and Kris Gevaert and Sophie Goormachtig and Philippe Delavault},
url = {https://onlinelibrary.wiley.com/doi/10.1111/pce.13594},
doi = {10.1111/pce.13594},
issn = {0140-7791},
year = {2019},
date = {2019-01-01},
urldate = {2019-01-01},
journal = {Plant Cell Environ},
volume = {42},
number = {9},
pages = {2612-2626},
abstract = {Karrikins stimulate Arabidopsis thaliana germination, whereas parasitic weeds of the Orobanchaceae family have evolved to respond to host-exuded compounds such as strigolactones, dehydrocostus lactone, and 2-phenylethyl isothiocyanate. In Phelipanche ramosa, strigolactone-induced germination was shown to require one of the CYP707A proteins involved in abscisic acid catabolism. Here, germination and gene expression were analysed to investigate the role of CYP707As in germination of both parasitic plants and Arabidopsis upon perception of germination stimulants, after using pharmacological inhibitors and Arabidopsis mutants disrupting germination signals. CYP707A genes were up-regulated upon treatment with effective germination stimulants in both parasitic plants and Arabidopsis. Obligate parasitic plants exhibited both intensified up-regulation of CYP707A genes and increased sensitivity to the CYP707A inhibitor abscinazole-E2B, whereas Arabidopsis cyp707a mutants still positively responded to germination stimulation. In Arabidopsis, CYP707A regulation required the canonical karrikin signalling pathway KAI2/MAX2/SMAX1 and the transcription factor WRKY33. Finally, CYP707As and WRKY33 also modulated Arabidopsis root architecture in response to the synthetic strigolactone rac-GR24, and wrky33-1 exhibited a shoot hyperbranched phenotype. This study suggests that the lack of host-independent germination in obligate parasites is associated with an exacerbated CYP707A induction and that CYP707As and WRKY33 are new players involved in a variety of strigolactone/karrikin responses.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Stojanova, Bojana; Delourme, Régine; Duffé, Philippe; Delavault, Philippe; Simier, Philippe
Genetic differentiation and host preference reveal non-exclusive host races in the generalist parasitic weed Phelipanche ramosa Article de journal
Dans: Weed Research, vol. 59, no. 2, p. 107-118, 2019, ISSN: 0043-1737.
@article{RN32,
title = {Genetic differentiation and host preference reveal non-exclusive host races in the generalist parasitic weed Phelipanche ramosa},
author = {Bojana Stojanova and Régine Delourme and Philippe Duffé and Philippe Delavault and Philippe Simier},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/wre.12353
https://onlinelibrary.wiley.com/doi/10.1111/wre.12353},
doi = {https://doi.org/10.1111/wre.12353},
issn = {0043-1737},
year = {2019},
date = {2019-01-01},
urldate = {2019-01-01},
journal = {Weed Research},
volume = {59},
number = {2},
pages = {107-118},
abstract = {Summary We developed 20 microsatellite markers to genotype over 100 populations of the parasitic weed Phelipanche ramosa, which covers a wide host crop and geographic range. A representative core collection of 15 populations was also used in cross-infestation assays to study host preference during germination, attachment and shoot formation. We observed low genetic differentiation within most of the populations, but high genetic differentiation between populations partitioned into 3 genetic groups with different host preferences and geographic distributions. Genetic group 1 is detected exclusively in western France and on various host crops, notably winter oilseed rape (WOSR) and not hemp. Cross-infection assays confirmed its incompatibility with hemp and showed its preference for WOSR and tobacco in terms of germination and attachment success. The group 2 populations share a large geographic distribution in France and Europe, low germination success with WOSR and high germination success, attachment success and shoot formation with hemp, tobacco or tomato. The subclades 2a and 2b include most of the French populations in hemp crops in eastern France and in tobacco fields in several European countries respectively. The genetic analyses revealed the potential of the three groups to increase their geographic range in the future. Intermediate genetic groups showed higher intrapopulation diversity and represent potential stocks for new host race emergence. Those findings argue in favour of the existence of host races in P. ramosa and should be considered for appropriate management strategies, notably in breeding programmes for resistance against this parasitic weed.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
8 publications
Cochetel, Noé; Météier, Eloïse; Merlin, Isabelle; Hévin, Cyril; Pouvreau, Jean-Bernard; Coutos-Thévenot, Pierre; Hernould, Michel; Vivin, Philippe; Cookson, Sarah Jane; Ollat, Nathalie; Lauvergeat, Virginie
Potential contribution of strigolactones in regulating scion growth and branching in grafted grapevine in response to nitrogen availability Article de journal
Dans: J Exp Bot, vol. 69, no. 16, p. 4099–4112, 2018, ISSN: 1460-2431.
@article{pmid29860350,
title = {Potential contribution of strigolactones in regulating scion growth and branching in grafted grapevine in response to nitrogen availability},
author = {Noé Cochetel and Eloïse Météier and Isabelle Merlin and Cyril Hévin and Jean-Bernard Pouvreau and Pierre Coutos-Thévenot and Michel Hernould and Philippe Vivin and Sarah Jane Cookson and Nathalie Ollat and Virginie Lauvergeat},
doi = {10.1093/jxb/ery206},
issn = {1460-2431},
year = {2018},
date = {2018-07-01},
urldate = {2018-07-01},
journal = {J Exp Bot},
volume = {69},
number = {16},
pages = {4099--4112},
abstract = {In grafted plants, rootstocks assure the mineral nutrition of the scion and modify its development. In this study, we show that two grapevine rootstock genotypes have different shoot branching architectures when cultivated as cuttings and that this trait is transmitted to the scion when grafted. Shoot branching plasticity in response to nitrogen supply was also studied. As strigolactones are known to have a role in the regulation of shoot development in response to nutrient availability, their involvement in the control of scion architecture by the rootstock was investigated. Functional characterization of putative grapevine strigolactone biosynthetic genes in Arabidopsis mutants or grapevine cell suspensions showed similar functions to those of Arabidopsis. Both rootstocks produced strigolactone-like compounds; the quantity produced in response to nitrogen treatments differed between the two rootstock genotypes and correlated with the expression of putative strigolactone biosynthetic genes. Exudation of strigolactone-like compounds by both rootstocks was closely related to the developmental pattern of the scion in grafted plants. These results suggest that differential regulation of strigolactone biosynthesis in response to nitrogen availability may contribute to the control of scion development conferred by each rootstock genotype.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Benhelli-Mokrani, Houda; Mansuroglu, Zeyni; Chauderlier, Alban; Albaud, Benoit; Gentien, David; Sommer, Sabrina; Schirmer, Claire; Laqueuvre, Lucie; Josse, Thibaut; Buée, Luc; Lefebvre, Bruno; Galas, Marie Christine; Souès, Sylvie; Bonnefoy, Eliette
Genome-wide identification of genic and intergenic neuronal DNA regions bound by Tau protein under physiological and stress conditions Article de journal
Dans: Nucleic acids research, vol. 46, no. 21, p. 11405–11422, 2018, ISSN: 13624962.
@article{Benhelli-Mokrani2018,
title = {Genome-wide identification of genic and intergenic neuronal DNA regions bound by Tau protein under physiological and stress conditions},
author = {Houda Benhelli-Mokrani and Zeyni Mansuroglu and Alban Chauderlier and Benoit Albaud and David Gentien and Sabrina Sommer and Claire Schirmer and Lucie Laqueuvre and Thibaut Josse and Luc Buée and Bruno Lefebvre and Marie Christine Galas and Sylvie Sou{è}s and Eliette Bonnefoy},
doi = {10.1093/nar/gky929},
issn = {13624962},
year = {2018},
date = {2018-01-01},
journal = {Nucleic acids research},
volume = {46},
number = {21},
pages = {11405--11422},
abstract = {Tauopathies such as Alzheimer's Disease (AD) are neurodegenerative disorders for which there is presently no cure. They are named after the abnormal oligomerization/aggregation of the neuronal microtubule-associated Tau protein. Besides its role as a microtubule-associated protein, a DNA-binding capacity and a nuclear localization for Tau protein has been described in neurons. While questioning the potential role of Tau-DNA binding in the development of tauopathies, we have carried out a large-scale analysis of the interaction of Tau protein with the neuronal genome under physiological and heat stress conditions using the ChIP-on-chip technique that combines Chromatin ImmunoPrecipitation (ChIP) with DNA microarray (chip). Our findings show that Tau protein specifically interacts with genic and intergenic DNA sequences of primary culture of neurons with a preference for DNA regions positioned beyond the ±5000 bp range from transcription start site. An AG-rich DNA motif was found recurrently present within Tau-interacting regions and 30% of Tau-interacting regions overlapped DNA sequences coding for lncRNAs. Neurological processes affected in AD were enriched among Tau-interacting regions with in vivo gene expression assays being indicative of a transcriptional repressor role for Tau protein, which was exacerbated in neurons displaying nuclear pathological oligomerized forms of Tau protein.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Deriabin, Konstantin V; Yaremenko, Ivan A; Chislov, Mikhail V; Fleury, Fabrice; Terent'Ev, Alexander O; Islamova, Regina M
Similar nature leads to improved properties: Cyclic organosilicon triperoxides as promising curing agents for liquid polysiloxanes Article de journal
Dans: New Journal of Chemistry, vol. 42, no. 18, p. 15006–15013, 2018, ISSN: 13699261.
@article{Deriabin2018,
title = {Similar nature leads to improved properties: Cyclic organosilicon triperoxides as promising curing agents for liquid polysiloxanes},
author = {Konstantin V Deriabin and Ivan A Yaremenko and Mikhail V Chislov and Fabrice Fleury and Alexander O Terent'Ev and Regina M Islamova},
doi = {10.1039/c8nj02499e},
issn = {13699261},
year = {2018},
date = {2018-01-01},
journal = {New Journal of Chemistry},
volume = {42},
number = {18},
pages = {15006--15013},
publisher = {Royal Society of Chemistry},
abstract = {Cyclic organosilicon triperoxides were found to be vinyl-selective free-radical initiators for thermal curing at 100-180 °C of vinyl-terminated polydimethylsiloxane and trimethylsilyl-terminated polymethylhydrosiloxane producing homogeneous transparent silicone rubbers with antibacterial properties. The usage of the cyclic organosilicon triperoxides as the curing agents does not require free radical inhibitors in comparison with diacyl- and dialkyl peroxides. Among the tested compounds, the peroxide with the Me-Si-Me fragment and two cyclohexane rings is a much more active curing agent (180 °C},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Lafont, Florian; Ayadi, Nizar; Charlier, Cathy; Weigel, Pierre; Nabiev, Igor; Benhelli-Mokrani, Houda; Fleury, Fabrice
Assessment of DNA-PKcs kinase activity by quantum dot–based microarray Article de journal
Dans: Scientific Reports, vol. 8, no. 1, p. 1–12, 2018, ISSN: 20452322.
@article{Lafont2018,
title = {Assessment of DNA-PKcs kinase activity by quantum dot–based microarray},
author = {Florian Lafont and Nizar Ayadi and Cathy Charlier and Pierre Weigel and Igor Nabiev and Houda Benhelli-Mokrani and Fabrice Fleury},
doi = {10.1038/s41598-018-29256-2},
issn = {20452322},
year = {2018},
date = {2018-01-01},
journal = {Scientific Reports},
volume = {8},
number = {1},
pages = {1--12},
abstract = {Therapeutic efficacy against cancer is often based on a variety of DNA lesions, including DNA double-strand breaks (DSBs) which are repaired by homologous recombination and non-homologous end joining (NHEJ) pathways. In the past decade, the functions of the DNA repair proteins have been described as a potential mechanism of resistance in tumor cells. Therefore, the DNA repair proteins have become targets to improve the efficacy of anticancer therapy. Given the central role of DNA-PKcs in NHEJ, the therapeutic efficacy of targeting DNA-PKcs is frequently described as a strategy to prevent repair of treatment-induced DNA damage in cancer cells. The screening of a new inhibitor acting as a sensitizer requires the development of a high-throughput tool in order to identify and assess the most effective molecule. Here, we describe the elaboration of an antibody microarray dedicated to the NHEJ pathway that we used to evaluate the DNA-PKcs kinase activity in response to DNA damage. By combining a protein microarray with Quantum-Dot detection, we show that it is possible to follow the modification of phosphoproteomic cellular profiles induced by inhibitors during the response to DNA damage. Finally, we discuss the promising tool for screening kinase inhibitors and targeting DSB repair to improve cancer treatment.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Jaunet-Lahary, Titouan; Vercauteren, Daniel P; Fleury, Fabrice; Laurent, Adèle D
Computational simulations determining disulfonic stilbene derivative bioavailability within human serum albumin Article de journal
Dans: Physical Chemistry Chemical Physics, vol. 20, no. 26, p. 18020–18030, 2018, ISSN: 14639076.
@article{Jaunet-Lahary2018,
title = {Computational simulations determining disulfonic stilbene derivative bioavailability within human serum albumin},
author = {Titouan Jaunet-Lahary and Daniel P Vercauteren and Fabrice Fleury and Adèle D Laurent},
doi = {10.1039/c8cp00704g},
issn = {14639076},
year = {2018},
date = {2018-01-01},
journal = {Physical Chemistry Chemical Physics},
volume = {20},
number = {26},
pages = {18020--18030},
publisher = {Royal Society of Chemistry},
abstract = {Disulfonic stilbene (DS) derivatives are a member of the large family of compounds widely employed in medicine and biology as modulators for membrane transporters or inhibitors of a protein involved in DNA repair. They constitute interesting compounds that have not yet been investigated within the bioavailability framework. No crystallographic structures exist involving such compounds embedded in the most common drug carrier, human serum albumin (HSA). The present work studies, for the first time, the physico-chemical features driving the inclusion of three DS derivatives (amino, nitro and acetamido, named DADS, DNDS and DATDS, respectively) within the four common HSA binding sites using combined molecular docking and molecular dynamics simulations. A careful analysis of each ligand within each of the studied binding sites is carried out, highlighting specific interactions and key residues playing a role in stabilizing the ligand within each pocket. The comparison between DADS, DNDS and DATDS reveals that depending on the binding site, the conclusions are rather different. For instance, the IB binding site shows a specificity to DADS compounds while IIIA is the most favorable site for DNDS and DATDS. 2018},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Cadet, Frédéric; Fontaine, Nicolas; Li, Guangyue; Sanchis, Joaquin; Chong, Matthieu Ng Fuk; Pandjaitan, Rudy; Vetrivel, Iyanar; Offmann, Bernard; Reetz, Manfred T
A machine learning approach for reliable prediction of amino acid interactions and its application in the directed evolution of enantioselective enzymes Article de journal
Dans: Scientific Reports, vol. 8, no. 1, p. 1–15, 2018, ISSN: 20452322.
@article{Cadet2018,
title = {A machine learning approach for reliable prediction of amino acid interactions and its application in the directed evolution of enantioselective enzymes},
author = {Frédéric Cadet and Nicolas Fontaine and Guangyue Li and Joaquin Sanchis and Matthieu {Ng Fuk Chong} and Rudy Pandjaitan and Iyanar Vetrivel and Bernard Offmann and Manfred T Reetz},
doi = {10.1038/s41598-018-35033-y},
issn = {20452322},
year = {2018},
date = {2018-01-01},
journal = {Scientific Reports},
volume = {8},
number = {1},
pages = {1--15},
abstract = {Directed evolution is an important research activity in synthetic biology and biotechnology. Numerous reports describe the application of tedious mutation/screening cycles for the improvement of proteins. Recently, knowledge-based approaches have facilitated the prediction of protein properties and the identification of improved mutants. However, epistatic phenomena constitute an obstacle which can impair the predictions in protein engineering. We present an innovative sequence-activity relationship (innov'SAR) methodology based on digital signal processing combining wet-lab experimentation and computational protein design. In our machine learning approach, a predictive model is developed to find the resulting property of the protein when the n single point mutations are permuted (2n combinations). The originality of our approach is that only sequence information and the fitness of mutants measured in the wet-lab are needed to build models. We illustrate the application of the approach in the case of improving the enantioselectivity of an epoxide hydrolase from Aspergillus niger. n = 9 single point mutants of the enzyme were experimentally assessed for their enantioselectivity and used as a learning dataset to build a model. Based on combinations of the 9 single point mutations (29), the enantioselectivity of these 512 variants were predicted, and candidates were experimentally checked: better mutants with higher enantioselectivity were indeed found.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Dion, Johann; Storozhylova, Nataliya; Dahbi, S; Lambert, Annie; Téletchéa, Stéphane; Dussouy, Christophe; Grandjean, Cyrille
Design and screening of sugar-derived small molecule inhibitors of galectins. Proceedings Article
Dans: J. Protein Proteomics, 2018.
@inproceedings{dion2018,
title = {Design and screening of sugar-derived small molecule inhibitors of galectins.},
author = {Johann Dion and Nataliya Storozhylova and S Dahbi and Annie Lambert and Stéphane Téletchéa and Christophe Dussouy and Cyrille Grandjean},
year = {2018},
date = {2018-01-01},
booktitle = {J. Protein Proteomics},
journal = {J. Protein Proteomics},
volume = {9},
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
}
Brun, Guillaume; Braem, Lukas; Thoiron, Séverine; Gevaert, Kris; Goormachtig, Sophie; Delavault, Philippe
Seed germination in parasitic plants: what insights can we expect from strigolactone research? Article de journal
Dans: J Exp Bot, vol. 69, no. 9, p. 2265-2280, 2018, ISSN: 0022-0957.
@article{RN5,
title = {Seed germination in parasitic plants: what insights can we expect from strigolactone research?},
author = {Guillaume Brun and Lukas Braem and Séverine Thoiron and Kris Gevaert and Sophie Goormachtig and Philippe Delavault},
url = {https://watermark.silverchair.com/erx472.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAt4wggLaBgkqhkiG9w0BBwagggLLMIICxwIBADCCAsAGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQM1yniRk8_noMBOyNMAgEQgIICkQSx0NkVWTLILIUWSlmnkftHgPP-m5t-cQPJknvKituLwilM0lvjYzZ8hS9XgfOcZXtWI5s8xbpatlB8cdpZP9UIDbsBGHsUHt7S7HlpuAZMTQ45haVuNqJvyuKge5jMk7hS88X3g81iv7EI3sBpzHd2YIKMfNhaf48kbTwwrzS4DRYGNAvL4WBc-raLQpiuWzkwcigfD-aABZkBD1-gFe8IEUnOb2RkmjlUr_liOJU7PFy_Cx4vIQEP2JYFSTWPLCUjkUom_5WQQc6OEtCE9DM41tXRLSckgbL81--d43m9Fej8gsZ4BfyxtqW2HQeS-iOmIDEWFFSwij_htBntsNJyL2q_vklyiqNPmXnr7aAG5USvV7SKNyBXBLiZMhcK4LNAPAEXOmSdSzYuMfXoO0kbljSM6ht_Z5lxwGuDDEByCqSieqyirwwsSP5G7zjEwBgLyWku3qPSVQlSht3Zw5syxIR8XT1sWmvYDcKEttmpmlsNbJCFK8vfRSi8KeAAbs1zSzg17FzgpZCOkqRY5GKdESZfeVuNdyzEA5rlbuLLEKwV2LRm2RAg8b2ygsderPTNrSDDfwLwbN5VRWZF7lyhSHemRqDOnYU59ezeS882026E4kS2LpG_zwSjma0HyCHEE2GNywtVrwKfa_0_gKE1Q-OQ8INzeshP-lrHHZqa8Q4bZLCQXLfyE1qlJnLTroDX4UIpRRhA1Ildrf_lGv2vFlPxs9DzFqjLPoqsmb5cBVdv819hiJTgqzR4v-Nm2sw1H5Vp2V8l6aPIab9ijg3ZIlpm-B6VUnUsjZA5gxKdSDHHZzIQluh9wxsUc6c_WYBWNA20_EOSP9ALg-sQsplZk3VAb1WhQh7antobYSAx_A},
doi = {10.1093/jxb/erx472},
issn = {0022-0957},
year = {2018},
date = {2018-01-01},
urldate = {2018-01-01},
journal = {J Exp Bot},
volume = {69},
number = {9},
pages = {2265-2280},
abstract = {Obligate root-parasitic plants belonging to the Orobanchaceae family are deadly pests for major crops all over the world. Because these heterotrophic plants severely damage their hosts even before emerging from the soil, there is an unequivocal need to design early and efficient methods for their control. The germination process of these species has probably undergone numerous selective pressure events in the course of evolution, in that the perception of host-derived molecules is a necessary condition for seeds to germinate. Although most of these molecules belong to the strigolactones, structurally different molecules have been identified. Since strigolactones are also classified as novel plant hormones that regulate several physiological processes other than germination, the use of autotrophic model plant species has allowed the identification of many actors involved in the strigolactone biosynthesis, perception, and signal transduction pathways. Nevertheless, many questions remain to be answered regarding the germination process of parasitic plants. For instance, how did parasitic plants evolve to germinate in response to a wide variety of molecules, while autotrophic plants do not? What particular features are associated with their lack of spontaneous germination? In this review, we attempt to illustrate to what extent conclusions from research into strigolactones could be applied to better understand the biology of parasitic plants.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
20 publications
Vetrivel, Iyanar; Mahajan, Swapnil; Tyagi, Manoj; Hoffmann, Lionel; Sanejouand, Yves-Henri; Srinivasan, Narayanaswamy; Brevern, Alexandre G De; Cadet, Frédéric; Offmann, Bernard
Knowledge-based prediction of protein backbone conformation using a structural alphabet Article de journal
Dans: PLoS ONE, vol. 12, no. 11, 2017, ISSN: 19326203.
@article{Vetrivel2017,
title = {Knowledge-based prediction of protein backbone conformation using a structural alphabet},
author = {Iyanar Vetrivel and Swapnil Mahajan and Manoj Tyagi and Lionel Hoffmann and Yves-Henri Sanejouand and Narayanaswamy Srinivasan and Alexandre G {De Brevern} and Frédéric Cadet and Bernard Offmann},
doi = {10.1371/journal.pone.0186215},
issn = {19326203},
year = {2017},
date = {2017-11-01},
journal = {PLoS ONE},
volume = {12},
number = {11},
publisher = {Public Library of Science},
abstract = {Libraries of structural prototypes that abstract protein local structures are known as structural alphabets and have proven to be very useful in various aspects of protein structure analyses and predictions. One such library, Protein Blocks, is composed of 16 standard 5-residues long structural prototypes. This form of analyzing proteins involves drafting its structure as a string of Protein Blocks. Predicting the local structure of a protein in terms of protein blocks is the general objective of this work. A new approach, PB-kPRED is proposed towards this aim. It involves (i) organizing the structural knowledge in the form of a database of pentapeptide fragments extracted from all protein structures in the PDB and (ii) applying a knowledge-based algorithm that does not rely on any secondary structure predictions and/ or sequence alignment profiles, to scan this database and predict most probable backbone conformations for the protein local structures. Though PB-kPRED uses the structural information from homologues in preference, if available. The predictions were evaluated rigorously on 15,544 query proteins representing a non-redundant subset of the PDB filtered at 30% sequence identity cut-off. We have shown that the kPRED method was able to achieve mean accuracies ranging from 40.8% to 66.3% depending on the availability of homologues. The impact of the different strategies for scanning the database on the prediction was evaluated and is discussed. Our results highlight the usefulness of the method in the context of proteins without any known structural homologues. A scoring function that gives a good estimate of the accuracy of prediction was further developed. This score estimates very well the accuracy of the algorithm (R2 of 0.82). An online version of the tool is provided freely for non-commercial usage at http://www.bo-protscience.fr/kpred/.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Sanejouand, Yves-Henri
Mutational dynamics of influenza A viruses: a principal component analysis of hemagglutinin sequences of subtype H1 Article de journal
Dans: 2017.
@article{Sanejouand2017b,
title = {Mutational dynamics of influenza A viruses: a principal component analysis of hemagglutinin sequences of subtype H1},
author = {Yves-Henri Sanejouand},
url = {http://arxiv.org/abs/1710.01594},
year = {2017},
date = {2017-10-01},
abstract = {A principal component analysis of a multiple sequence alignement of hemagglutinin sequences of subtype H1 has been performed, the sequences being encoded using the amino-acid property that maximizes the weight of the major component. In the case of this alignment, it happens to be a well-known hydrophobicity scale. Interestingly, sequences coming from human have large positive amplitudes along the major component before 2009, and large negative ones afterwards. This means that the 2009 pandemic was associated to a major change in the hydrophobicity pattern of hemagglutinin. The present analysis also highlights the high variability of viral sequences coming from swine. At a more general level, the method proposed in this paper allows to describe a sequence coming from an alignment with a set of numbers, the original point being that the choice of the corresponding property is driven by the data. This approach should allow the application of numerous methods to the study of large multiple sequence alignments.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Bosseboeuf, Adrien; Feron, Delphine; Tallet, Anne; Rossi, Cédric; Charlier, Cathy; Garderet, Laurent; Caillot, Denis; Moreau, Philippe; Cardó-Vila, Marina; Pasqualini, Renata; Arap, Wadih; Nelson, Alfreda Destea; Wilson, Bridget S; Perreault, Hélène; Piver, Eric; Weigel, Pierre; Girodon, François; Harb, Jean; Bigot-Corbel, Edith; Hermouet, Sylvie
Monoclonal IgG in MGUS and multiple myeloma targets infectious pathogens Article de journal
Dans: JCI Insight, vol. 2, no. 19, p. 1–18, 2017, ISSN: 0021-9738.
@article{Bosseboeuf2017,
title = {Monoclonal IgG in MGUS and multiple myeloma targets infectious pathogens},
author = {Adrien Bosseboeuf and Delphine Feron and Anne Tallet and Cédric Rossi and Cathy Charlier and Laurent Garderet and Denis Caillot and Philippe Moreau and Marina Cardó-Vila and Renata Pasqualini and Wadih Arap and Alfreda Destea Nelson and Bridget S Wilson and Hélène Perreault and Eric Piver and Pierre Weigel and François Girodon and Jean Harb and Edith Bigot-Corbel and Sylvie Hermouet},
doi = {10.1172/jci.insight.95367},
issn = {0021-9738},
year = {2017},
date = {2017-01-01},
journal = {JCI Insight},
volume = {2},
number = {19},
pages = {1--18},
abstract = {Subsets of mature B cell neoplasms are linked to infection with intracellular pathogens such as Epstein-Barr virus (EBV), hepatitis C virus (HCV), or Helicobacter pylori. However, the association between infection and the immunoglobulin-secreting (Ig-secreting) B proliferative disorders remains largely unresolved. We investigated whether the monoclonal IgG (mc IgG) produced by patients diagnosed with monoclonal gammopathy of undetermined significance (MGUS) or multiple myeloma (MM) targets infectious pathogens. Antigen specificity of purified mc IgG from a large patient cohort (n = 244) was determined using a multiplex infectious-antigen array (MIAA), which screens for reactivity to purified antigens or lysates from 9 pathogens. Purified mc IgG from 23.4% of patients (57 of 244) specifically recognized 1 pathogen in the MIAA. EBV was the most frequent target (15.6%), with 36 of 38 mc IgGs recognizing EBV nuclear antigen-1 (EBNA-1). MM patients with EBNA-1-specific mc IgG (14.0%) showed substantially greater bone marrow plasma cell infiltration and higher β2-microglobulin and inflammation/infection-linked cytokine levels compared with other smoldering myeloma/MM patients. Five other pathogens were the targets of mc IgG: herpes virus simplex-1 (2.9%), varicella zoster virus (1.6%), cytomegalovirus (0.8%), hepatitis C virus (1.2%), and H. pylori (1.2%). We conclude that a dysregulated immune response to infection may underlie disease onset and/or progression of MGUS and MM for subsets of patients.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Yaremenko, Ivan A; Syroeshkin, Mikhail A; Levitsky, Dmitri O; Fleury, Fabrice; Terent'ev, Alexander O
Cyclic peroxides as promising anticancer agents: in vitro cytotoxicity study of synthetic ozonides and tetraoxanes on human prostate cancer cell lines Article de journal
Dans: Medicinal Chemistry Research, vol. 26, no. 1, p. 170–179, 2017, ISSN: 1554-8120.
@article{Yaremenko2017,
title = {Cyclic peroxides as promising anticancer agents: in vitro cytotoxicity study of synthetic ozonides and tetraoxanes on human prostate cancer cell lines},
author = {Ivan A Yaremenko and Mikhail A Syroeshkin and Dmitri O Levitsky and Fabrice Fleury and Alexander O Terent'ev},
url = {https://doi.org/10.1007/s00044-016-1736-2},
doi = {10.1007/s00044-016-1736-2},
issn = {1554-8120},
year = {2017},
date = {2017-01-01},
journal = {Medicinal Chemistry Research},
volume = {26},
number = {1},
pages = {170--179},
abstract = {Synthetic ozonides and tetraoxanes were shown to have high cytotoxicity in vitro when tested on androgen-independent prostate cancer cell lines DU145 and PC3, which is in some cases was higher than that of doxorubicin, cisplatin, etoposide, artemisinin, and artesunate. Activity of ozonide stereoisomers differs from each other. This difference in activity and absence of correlation between activity of stereoisomers and their oxidative properties allow us to suggest existence of a quite specific mechanism of cytotoxicity of these endoperoxides different from a traditional mechanism based mainly on oxidative properties of peroxides.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Levitsky, Dmitri O; Gloriozova, Tatyana A; Poroikov, Vladimir V; Valery, M
ANABOLIC CYANOSTEROIDS AND THEIR BIOLOGICAL ACTIVITIES – A BRIEF REVIEW Article de journal
Dans: vol. 6, no. 12, p. 127–151, 2017, ISBN: 2017121061.
@article{Levitsky2017,
title = {ANABOLIC CYANOSTEROIDS AND THEIR BIOLOGICAL ACTIVITIES – A BRIEF REVIEW},
author = {Dmitri O Levitsky and Tatyana A Gloriozova and Vladimir V Poroikov and M Valery},
doi = {10.20959/wjpps201712-10618},
isbn = {2017121061},
year = {2017},
date = {2017-01-01},
volume = {6},
number = {12},
pages = {127--151},
abstract = {The present review describes the biological activities of synthetic anabolic cyanosteroids. More than forty biologically active compounds have shown confirmed anti-tumour, anti-inflammatory, antiviral and other activities. The structures and reported and predicted activities of synthetic cyanosteroids are available. With the computer programme PASS and based on structure–activity relationships (SAR), some additional activities are also predicted, which point towards new possible applications of these lipids. This review emphasizes the role of cyanosteroids as an important source and potential leads for drug discovery and they are of great interest to chemists, physicians, biologists, pharmacologists and the pharmaceutical industry. KEYWORDS:},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Faucon, Adrien; Benhelli-Mokrani, Houda; Fleury, Fabrice; Dutertre, Stéphanie; Tramier, Marc; Boucard, Joanna; Lartigue, Lénaïc; Nedellec, Steven; Hulin, Philippe; Ishow, Eléna
Bioconjugated fluorescent organic nanoparticles targeting EGFR-overexpressing cancer cells Article de journal
Dans: Nanoscale, vol. 9, no. 45, p. 18094–18106, 2017, ISSN: 20403372.
@article{Faucon2017,
title = {Bioconjugated fluorescent organic nanoparticles targeting EGFR-overexpressing cancer cells},
author = {Adrien Faucon and Houda Benhelli-Mokrani and Fabrice Fleury and Stéphanie Dutertre and Marc Tramier and Joanna Boucard and Lénaïc Lartigue and Steven Nedellec and Philippe Hulin and Eléna Ishow},
doi = {10.1039/c7nr06533g},
issn = {20403372},
year = {2017},
date = {2017-01-01},
journal = {Nanoscale},
volume = {9},
number = {45},
pages = {18094--18106},
publisher = {Royal Society of Chemistry},
abstract = {The field of optical bioimaging has considerably flourished with the advent of sophisticated microscopy techniques and ultra-bright fluorescent tools. Fluorescent organic nanoparticles (FONs) have thus recently appeared as very attractive labels for their high payload, absence of cytotoxicity and eventual biodegradation. Nevertheless, their bioconjugation to target specific receptors with high imaging contrast is scarcely performed. Moreover, assessing the reality of bioconjugation represents high challenges given the sub-nanomolar concentrations resulting from the commonly adopted nanoprecipitation fabrication process. Here, we describe how the combination of a magnetic shell allows us to easily generate red-emitting FONs conjugated with the epidermal growth factor ligand (EGF), a small protein promoting cancer cell proliferation by activating the EGF receptor (EGFR) pathway. Dual color fluorescence correlation spectroscopy combined with immunofluorescence is originally harnessed in its time trace mode to unambiguously demonstrate covalent attachment between the FON and EGF at sub-nanomolar concentrations. Strong asymmetric clustering of EGF-conjugated FONs is observed at the membrane of MDA-MB-468 human breast cancer cells overexpressing EGF receptors using super-resolution fluorescence microscopy. Such high recruitment of EGF-conjugated FONs is attributed to their EGF multivalency (4.7 EGF per FON) which enables efficient EGFR activation and subsequent phosphorylation. The large hydrodynamic diameter (DH ∼ 301 nm) of EGF-conjugated FONs prevents immediate engulfment of the sequestered receptors, which provides very bright and localized spots in less than 30 minutes. The reported bioconjugated nanoassemblies could thus serve as ultra-bright probes of breast cancer cells with EGFR-overexpression that is often associated with poor prognosis.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Alligand, Brendan; Breton, Magali Le; Marquis, Damien; Vallette, François; Fleury, Fabrice
Functional effects of diphosphomimetic mutations at cAbl-mediated phosphorylation sites on Rad51 recombinase activity Article de journal
Dans: Biochimie, vol. 139, p. 115–124, 2017, ISSN: 61831638.
@article{Alligand2017,
title = {Functional effects of diphosphomimetic mutations at cAbl-mediated phosphorylation sites on Rad51 recombinase activity},
author = {Brendan Alligand and Magali {Le Breton} and Damien Marquis and François Vallette and Fabrice Fleury},
url = {http://dx.doi.org/10.1016/j.biochi.2017.05.020},
doi = {10.1016/j.biochi.2017.05.020},
issn = {61831638},
year = {2017},
date = {2017-01-01},
journal = {Biochimie},
volume = {139},
pages = {115--124},
publisher = {Elsevier Ltd},
abstract = {Homologous Recombination enables faithful repair of the deleterious double strand breaks of DNA. This pathway relies on Rad51 to catalyze homologous DNA strand exchange. Rad51 is known to be phosphorylated in a sequential manner on Y315 and then on Y54, but the effect of such phosphorylation on Rad51 function remains poorly understood. We have developed a phosphomimetic model in order to study all the phosphorylation states. With the purified phosphomimetic proteins we performed in vitro assays to determine the activity of Rad51. Here we demonstrate the inhibitory effect of the double phosphomimetic mutant and suggest that it may be due to a defect in nucleofilament formation.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Dion, Johann; Deshayes, Frédérique; Storozhylova, Nataliya; Advedissian, Tamara; Lambert, Annie; Viguier, Mireille; Tellier, Charles; Dussouy, Christophe; Poirier, Françoise; Grandjean, Cyrille
Lactosamine-Based Derivatives as Tools to Delineate the Biological Functions of Galectins: Application to Skin Tissue Repair Article de journal
Dans: ChemBioChem, vol. 18, no. 8, p. 782–789, 2017, ISSN: 14397633.
@article{Dion2017c,
title = {Lactosamine-Based Derivatives as Tools to Delineate the Biological Functions of Galectins: Application to Skin Tissue Repair},
author = {Johann Dion and Frédérique Deshayes and Nataliya Storozhylova and Tamara Advedissian and Annie Lambert and Mireille Viguier and Charles Tellier and Christophe Dussouy and Françoise Poirier and Cyrille Grandjean},
doi = {10.1002/cbic.201600673},
issn = {14397633},
year = {2017},
date = {2017-01-01},
journal = {ChemBioChem},
volume = {18},
number = {8},
pages = {782--789},
abstract = {Galectins have been recognized as potential novel therapeutic targets for the numerous fundamental biological processes in which they are involved. Galectins are key players in homeostasis, and as such their expression and function are finely tuned in vivo. Thus, their modes of action are complex and remain largely unexplored, partly because of the lack of dedicated tools. We thus designed galectin inhibitors from a lactosamine core, functionalized at key C2 and C3′ positions by aromatic substituents to ensure both high affinity and selectivity, and equipped with a spacer that can be modified on demand to further modulate their physico-chemical properties. As a proof-of-concept, galectin-3 was selectively targeted. The efficacy of the synthesized di-aromatic lactosamine tools was shown in cellular assays to modulate collective epithelial cell migration and to interfere with actin/cortactin localization.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Coppin, Lucie; Vincent, Audrey; Frénois, Frédéric; Duchêne, Belinda; Lahdaoui, Fatima; Stechly, Laurence; Renaud, Florence; Villenet, Céline; Seuningen, Isabelle Van; Leteurtre, Emmanuelle; Dion, Johann; Grandjean, Cyrille; Poirier, Françoise; Figeac, Martin; Delacour, Delphine; Porchet, Nicole; Pigny, Pascal
Galectin-3 is a non-classic RNA binding protein that stabilizes the mucin MUC4 mRNA in the cytoplasm of cancer cells Article de journal
Dans: Scientific Reports, vol. 7, no. March, p. 1–14, 2017, ISSN: 20452322.
@article{Coppin2017,
title = {Galectin-3 is a non-classic RNA binding protein that stabilizes the mucin MUC4 mRNA in the cytoplasm of cancer cells},
author = {Lucie Coppin and Audrey Vincent and Frédéric Frénois and Belinda Duch{ê}ne and Fatima Lahdaoui and Laurence Stechly and Florence Renaud and Céline Villenet and Isabelle Van Seuningen and Emmanuelle Leteurtre and Johann Dion and Cyrille Grandjean and Fran{ç}oise Poirier and Martin Figeac and Delphine Delacour and Nicole Porchet and Pascal Pigny},
doi = {10.1038/srep43927},
issn = {20452322},
year = {2017},
date = {2017-01-01},
journal = {Scientific Reports},
volume = {7},
number = {March},
pages = {1--14},
abstract = {Pancreatic cancer cells express high levels of MUC1, MUC4 and MUC16 mRNAs that encode membrane-bound mucins. These mRNAs share unusual features such as a long half-life. However, it remains unknown how mucin mRNA stability is regulated. Galectin-3 (Gal-3) is an endogenous lectin playing important biological functions in epithelial cells. Gal-3 is encoded by LGALS3 which is up-regulated in pancreatic cancer. Despite the absence of a RNA-recognition motif, Gal-3 interacts indirectly with pre-mRNAs in the nucleus and promotes constitutive splicing. However a broader role of Gal-3 in mRNA fate is unexplored. We report herein that Gal-3 increases MUC4 mRNA stability through an intermediate, hnRNP-L which binds to a conserved CA repeat element in the 3′UTR in a Gal-3 dependent manner and also controls Muc4 mRNA levels in epithelial tissues of Gal3-/- mice. Gal-3 interacts with hnRNP-L in the cytoplasm, especially during cell mitosis, but only partly associates with protein markers of P-Bodies or Stress Granules. By RNA-IP plus RNA-seq analysis and imaging, we demonstrate that Gal-3 binds to mature spliced MUC4 mRNA in the perinuclear region, probably in hnRNP-L-containing RNA granules. Our findings highlight a new role for Gal-3 as a non-classic RNA-binding protein that regulates MUC4 mRNA post-transcriptionally.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Alvarez-Dorta, Dimitri; Brissonnet, Yoan; Saumonneau, Amélie; Deniaud, David; Bernard, Julien; Yan, Xibo; Tellier, Charles; Daligault, Franck; Gouin, Sébastien G
Magnetic Nanoparticles Coated with Thiomannosides or Iminosugars to Switch and Recycle Galactosidase Activity Article de journal
Dans: ChemistrySelect, vol. 2, no. 29, p. 9552–9556, 2017, ISSN: 23656549.
@article{Alvarez-Dorta2017,
title = {Magnetic Nanoparticles Coated with Thiomannosides or Iminosugars to Switch and Recycle Galactosidase Activity},
author = {Dimitri Alvarez-Dorta and Yoan Brissonnet and Amélie Saumonneau and David Deniaud and Julien Bernard and Xibo Yan and Charles Tellier and Franck Daligault and Sébastien G Gouin},
doi = {10.1002/slct.201702063},
issn = {23656549},
year = {2017},
date = {2017-01-01},
journal = {ChemistrySelect},
volume = {2},
number = {29},
pages = {9552--9556},
abstract = {Glycosidase effectors have rarely been reported despite their great potential interest in pharmaceutical sciences and industry. Magnetic nanoparticles were coated with thiomannosides (SMan@Fe3O4) or the broad spectrum glycosidase inhibitor deoxynojirimycin (DNJ@Fe3O4). The coated ligands were shown to exert a fully reverse effect on a model galactosidase (AgaB), with SMan@Fe3O4 or DNJ@Fe3O4 ligands acting as an enzyme inhibitor (Ki=3.7 µM) or a strong activator (250% higher AgaB velocity at 50 µM), respectively. This is striking considering that monovalent soluble SMan and DNJ analogues do not interact with AgaB at millimolar concentrations. The AgaB-DNJ@Fe3O4 enzyme-effector complex could be magnetically recycled and still showed a higher activity compared to free AgaB after four catalytic cycles. The “boost and recycle” procedure may provide interesting perspectives in glycosidase biocatalysis.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Legentil, Laurent; Cabezas, Yari; Tasseau, Olivier; Tellier, Charles; Daligault, Franck; Ferrières, Vincent
Regioselective Galactofuranosylation for the Synthesis of Disaccharide Patterns Found in Pathogenic Microorganisms Article de journal
Dans: Journal of Organic Chemistry, vol. 82, no. 14, p. 7114–7122, 2017, ISSN: 15206904.
@article{Legentil2017,
title = {Regioselective Galactofuranosylation for the Synthesis of Disaccharide Patterns Found in Pathogenic Microorganisms},
author = {Laurent Legentil and Yari Cabezas and Olivier Tasseau and Charles Tellier and Franck Daligault and Vincent Ferri{è}res},
doi = {10.1021/acs.joc.7b00565},
issn = {15206904},
year = {2017},
date = {2017-01-01},
journal = {Journal of Organic Chemistry},
volume = {82},
number = {14},
pages = {7114--7122},
abstract = {Koenigs-Knorr glycosylation of acceptors with more than one free hydroxyl group by 2,3,5,6-tetrabenzoyl galactofuranosyl bromide was performed using diphenylborinic acid 2-aminoethyl ester (DPBA) as inducer of regioselectivity. High regioselectivity for the glycosylation on the equatorial hydroxyl group of the acceptor was obtained thanks to the transient formation of a borinate adduct of the corresponding 1,2-cis diol. Nevertheless formation of orthoester byproducts hampered the efficiency of the method. Interestingly electron-withdrawing groups on O-6 or on C-1 of the acceptor displaced the reaction in favor of the desired galactofuranosyl containing disaccharide. The best yield was obtained for the furanosylation of p-nitrophenyl 6-O-acetyl mannopyranoside. Precursors of other disaccharides, found in the glycocalix of some pathogens, were synthesized according to the same protocol with yields ranging from 45 to 86%. This is a good alternative for the synthesis of biologically relevant glycoconjugates.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Sanejouand, Yves-Henri
A singular mutation in the hemagglutinin of the 1918 pandemic virus Article de journal
Dans: Archives of Biochemistry and Biophysics, vol. 625-626, p. 13–16, 2017, ISSN: 0003-9861.
@article{SANEJOUAND201713,
title = {A singular mutation in the hemagglutinin of the 1918 pandemic virus},
author = {Yves-Henri Sanejouand},
url = {http://www.sciencedirect.com/science/article/pii/S0003986117302576},
doi = {https://doi.org/10.1016/j.abb.2017.05.013},
issn = {0003-9861},
year = {2017},
date = {2017-01-01},
journal = {Archives of Biochemistry and Biophysics},
volume = {625-626},
pages = {13--16},
abstract = {The influenza pandemic of 1918–1919 killed at least 50 million people. The reasons why this pandemic was so deadly remain largely unknown [9]. However, It has been shown that the 1918 viral hemagglutinin allows to reproduce the hallmarks of the illness observed during the original pandemic [11]. Thanks to the wealth of hemagglutinin sequences accumulated over the last decades, amino-acid substitutions that are found in the 1918–1919 sequences but rare otherwise can be identified with high confidence. Noteworthy, Gly 188, which is located within a key motif of the receptor binding site, has never been observed again in sequences of human viruses of subtype H1. Monitoring this singular mutation in viral sequences may help prevent another dramatic pandemic.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Mahajan, Swapnil; Sanejouand, Yves-Henri
Jumping between protein conformers using normal modes Article de journal
Dans: Journal of Computational Chemistry, vol. 38, no. 18, p. 1622–1630, 2017, ISSN: 1096987X.
@article{Mahajan2017,
title = {Jumping between protein conformers using normal modes},
author = {Swapnil Mahajan and Yves-Henri Sanejouand},
doi = {10.1002/jcc.24803},
issn = {1096987X},
year = {2017},
date = {2017-01-01},
journal = {Journal of Computational Chemistry},
volume = {38},
number = {18},
pages = {1622--1630},
abstract = {The relationship between the normal modes of a protein and its functional conformational change has been studied for decades. However, using this relationship in a predictive context remains a challenge. In this work, we demonstrate that, starting from a given protein conformer, it is possible to generate in a single step model conformers that are less than 1 Å (Cα-RMSD) from the conformer which is the known endpoint of the conformational change, particularly when the conformational change is collective in nature. Such accurate model conformers can be generated by following either the so-called robust or the 50 lowest-frequency modes obtained with various Elastic Network Models (ENMs). Interestingly, the quality of many of these models compares well with actual crystal structures, as assessed by the ROSETTA scoring function and PROCHECK. The most accurate and best quality conformers obtained in the present study were generated by using the 50 lowest-frequency modes of an all-atom ENM. However, with less than ten robust modes, which are identified without any prior knowledge of the nature of the conformational change, nearly 90% of the motion described by the 50 lowest-frequency modes of a protein can be captured. Such results strongly suggest that exploring the robust modes of ENMs may prove efficient for sampling the functionally relevant conformational repertoire of many proteins. textcopyright 2017 Wiley Periodicals, Inc.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Atmanene, Cédric; Ronin, Céline; Téletchéa, Stéphane; Gautier, François Moana; Djedaïni-Pilard, Florence; Ciesielski, Fabrice; Vivat, Valérie; Grandjean, Cyrille
Biophysical and structural characterization of mono/di-arylated lactosamine derivatives interaction with human galectin-3 Article de journal
Dans: Biochemical and Biophysical Research Communications, vol. 489, no. 3, p. 281–286, 2017, ISSN: 10902104.
@article{Atmanene2017,
title = {Biophysical and structural characterization of mono/di-arylated lactosamine derivatives interaction with human galectin-3},
author = {Cédric Atmanene and Céline Ronin and Stéphane Téletchéa and François Moana Gautier and Florence Djedaïni-Pilard and Fabrice Ciesielski and Valérie Vivat and Cyrille Grandjean},
doi = {10.1016/j.bbrc.2017.05.150},
issn = {10902104},
year = {2017},
date = {2017-01-01},
journal = {Biochemical and Biophysical Research Communications},
volume = {489},
number = {3},
pages = {281--286},
abstract = {Combination of biophysical and structural techniques allowed characterizing and uncovering the mechanisms underlying increased binding affinity of lactosamine derivatives for galectin 3. In particular, complementing information gathered from X-ray crystallography, native mass spectrometry and isothermal microcalorimetry showed favorable enthalpic contribution of cation-π interaction between lactosamine aryl substitutions and arginine residues from the carbohydrate recognition domain, which resulted in two log increase in compound binding affinity. This incrementing strategy allowed individual contribution of galectin inhibitor moieties to be dissected. Altogether, our results suggest that core and substituents of these saccharide-based inhibitors can be optimized separately, providing valuable tools to study the role of galectins in diseases.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Labbé, Pauline; Faure, Emilie; Lecointe, Simon; Scouarnec, Solena Le; Kyndt, Florence; Marrec, Marie; Tourneau, Thierry Le; Offmann, Bernard; Duplaà, Cécile; Zaffran, Stéphane; Schott, Jean Jacques; Merot, Jean
The alternatively spliced LRRFIP1 Isoform-1 is a key regulator of the Wnt/β-catenin transcription pathway Article de journal
Dans: Biochimica et Biophysica Acta - Molecular Cell Research, vol. 1864, no. 7, p. 1142–1152, 2017, ISSN: 18792596.
@article{Labbe2017,
title = {The alternatively spliced LRRFIP1 Isoform-1 is a key regulator of the Wnt/β-catenin transcription pathway},
author = {Pauline Labbé and Emilie Faure and Simon Lecointe and Solena {Le Scouarnec} and Florence Kyndt and Marie Marrec and Thierry {Le Tourneau} and Bernard Offmann and Cécile Duplaà and Stéphane Zaffran and Jean Jacques Schott and Jean Merot},
doi = {10.1016/j.bbamcr.2017.03.008},
issn = {18792596},
year = {2017},
date = {2017-01-01},
journal = {Biochimica et Biophysica Acta - Molecular Cell Research},
volume = {1864},
number = {7},
pages = {1142--1152},
abstract = {The GC-rich Binding Factor 2/Leucine Rich Repeat in the Flightless 1 Interaction Protein 1 gene (GCF2/LRRFIP1) is predicted to be alternatively spliced in five different isoforms. Although important peptide sequence differences are expected to result from this alternative splicing, to date, only the gene transcription regulator properties of LRRFIP1-Iso5 were unveiled. Based on molecular, cellular and biochemical data, we show here that the five isoforms define two molecular entities with different expression profiles in human tissues, subcellular localizations, oligomerization properties and transcription enhancer properties of the canonical Wnt pathway. We demonstrated that LRRFIP1-Iso3, -4 and -5, which share over 80% sequence identity, are primarily located in the cell cytoplasm and form homo and hetero-multimers between each other. In contrast, LRRFIP1-Iso1 and -2 are primarily located in the cell nucleus in part thanks to their shared C-terminal domain. Furthermore, we showed that LRRFIP1-Iso1 is preferentially expressed in the myocardium and skeletal muscle. Using the in vitro Topflash reporter assay we revealed that among LRRFIP1 isoforms, LRRFIP1-Iso1 is the strongest enhancer of the β-catenin Wnt canonical transcription pathway thanks to a specific N-terminal domain harboring two critical tryptophan residues (W76, 82). In addition, we showed that the Wnt enhancer properties of LRRFIP1-Iso1 depend on its homo-dimerisation which is governed by its specific coiled coil domain. Together our study identified LRRFIP1-Iso1 as a critical regulator of the Wnt canonical pathway with a potential role in myocyte differentiation and myogenesis.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
David, Benoit; Irague, Romain; Jouanneau, Diane; Daligault, Franck; Czjzek, Mirjam; Sanejouand, Yves-Henri; Tellier, Charles
Internal Water Dynamics Control the Transglycosylation/Hydrolysis Balance in the Agarase (AgaD) of Zobellia galactanivorans Article de journal
Dans: ACS Catalysis, vol. 7, no. 5, p. 3357–3367, 2017, ISSN: 21555435.
@article{David2017a,
title = {Internal Water Dynamics Control the Transglycosylation/Hydrolysis Balance in the Agarase (AgaD) of Zobellia galactanivorans},
author = {Benoit David and Romain Irague and Diane Jouanneau and Franck Daligault and Mirjam Czjzek and Yves-Henri Sanejouand and Charles Tellier},
doi = {10.1021/acscatal.7b00348},
issn = {21555435},
year = {2017},
date = {2017-01-01},
journal = {ACS Catalysis},
volume = {7},
number = {5},
pages = {3357--3367},
abstract = {In retaining glycoside hydrolases (GHs), transglycosylase activity is often low due to the natural hydrolytic activity that is favored in water. Improving the relative transglycosylase activity of these enzymes is of particular interest to obtain enzymes suitable for the synthesis of oligosaccharides. We explored the effect of engineering the water dynamics within the endo-β-agarase AgaD on the transglycosylation/hydrolysis (T/H) balance. By mutating three amino acids (D341, Q342, and S351), which could control water access to a putative water channel ending close to the active site, we obtained AgaD variants with an inverted T/H balance. For the best mutant, D341L/Q342H/S351F, the hydrolysis activity was reduced 50-fold in comparison to the wild type, while the transglycosylase activity was maintained and even slightly improved. This variant produced a large amount of oligo-agaroses by a disproportionation reaction with deca-agarose as the substrate. Molecular dynamics simulations showed that these enzymatic modifications were correlated with higher water dynamics, as revealed by a marked reduction in the water survival time and a decrease in the purge time of water in a channel ending close to the active site. These results suggest that modifying the water dynamics in GHs could be a rational basis for engineering of transglycosylase activity.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Shahsavarian, Melody A; Chaaya, Nancy; Costa, Narciso; Boquet, Didier; Atkinson, Alexandre; Offmann, Bernard; Kaveri, Srini V; Lacroix-Desmazes, Sébastien; Friboulet, Alain; Avalle, Bérangère; Padiolleau-Lefèvre, Séverine
Multitarget selection of catalytic antibodies with β-lactamase activity using phage display Article de journal
Dans: FEBS Journal, vol. 284, no. 4, p. 634–653, 2017, ISSN: 17424658.
@article{Shahsavarian2017,
title = {Multitarget selection of catalytic antibodies with β-lactamase activity using phage display},
author = {Melody A Shahsavarian and Nancy Chaaya and Narciso Costa and Didier Boquet and Alexandre Atkinson and Bernard Offmann and Srini V Kaveri and Sébastien Lacroix-Desmazes and Alain Friboulet and Bérangère Avalle and Séverine Padiolleau-Lefèvre},
doi = {10.1111/febs.14012},
issn = {17424658},
year = {2017},
date = {2017-01-01},
journal = {FEBS Journal},
volume = {284},
number = {4},
pages = {634--653},
abstract = {β-lactamase enzymes responsible for bacterial resistance to antibiotics are among the most important health threats to the human population today. Understanding the increasingly vast structural motifs responsible for the catalytic mechanism of β-lactamases will help improve the future design of new generation antibiotics and mechanism-based inhibitors of these enzymes. Here we report the construction of a large murine single chain fragment variable (scFv) phage display library of size 2.7 × 109 with extended diversity by combining different mouse models. We have used two molecularly different inhibitors of the R-TEM β-lactamase as targets for selection of catalytic antibodies with β-lactamase activity. This novel methodology has led to the isolation of five antibody fragments, which are all capable of hydrolyzing the β-lactam ring. Structural modeling of the selected scFv has revealed the presence of different motifs in each of the antibody fragments potentially responsible for their catalytic activity. Our results confirm (a) the validity of using our two target inhibitors for the in vitro selection of catalytic antibodies endowed with β-lactamase activity, and (b) the plasticity of the β-lactamase active site responsible for the wide resistance of these enzymes to clinically available inhibitors and antibiotics.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Dion, Johann; Advedissian, Tamara; Storozhylova, Nataliya; Dahbi, Samir; Lambert, Annie; Deshayes, Frédérique; Viguier, Mireille; Tellier, Charles; Poirier, Françoise; Téletchéa, Stéphane; Dussouy, Christophe; Tateno, Hiroaki; Hirabayashi, Jun; Grandjean, Cyrille
Development of a Sensitive Microarray Platform for the Ranking of Galectin Inhibitors: Identification of a Selective Galectin-3 Inhibitor Article de journal
Dans: ChemBioChem, vol. 18, no. 24, p. 2428–2440, 2017, ISSN: 14397633.
@article{Dion2017a,
title = {Development of a Sensitive Microarray Platform for the Ranking of Galectin Inhibitors: Identification of a Selective Galectin-3 Inhibitor},
author = {Johann Dion and Tamara Advedissian and Nataliya Storozhylova and Samir Dahbi and Annie Lambert and Frédérique Deshayes and Mireille Viguier and Charles Tellier and Françoise Poirier and Stéphane Téletchéa and Christophe Dussouy and Hiroaki Tateno and Jun Hirabayashi and Cyrille Grandjean},
doi = {10.1002/cbic.201700544},
issn = {14397633},
year = {2017},
date = {2017-01-01},
journal = {ChemBioChem},
volume = {18},
number = {24},
pages = {2428--2440},
abstract = {Glycan microarrays are useful tools for lectin glycan profiling. The use of a glycan microarray based on evanescent-field fluorescence detection was herein further extended to the screening of lectin inhibitors in competitive experiments. The efficacy of this approach was tested with 2/3′-mono- and 2,3′-diaromatic type II lactosamine derivatives and galectins as targets and was validated by comparison with fluorescence anisotropy proposed as an orthogonal protein interaction measurement technique. We showed that subtle differences in the architecture of the inhibitor could be sensed that pointed out the preference of galectin-3 for 2′-arylamido derivatives over ureas, thioureas, and amines and that of galectin-7 for derivatives bearing an α substituent at the anomeric position of glucosamine. We eventually identified a diaromatic oxazoline as a highly specific inhibitor of galectin-3 versus galectin-1 and galectin-7.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
David, Benoît
Conception rationnelle dénzyme: conversion de glycoside hydrolases en transglycosidases Thèse
Université de Nantes, 2017.
@phdthesis{david2017conception,
title = {Conception rationnelle dénzyme: conversion de glycoside hydrolases en transglycosidases},
author = {Benoît David},
url = {https://www.theses.fr/2017NANT1044},
year = {2017},
date = {2017-01-01},
school = {Université de Nantes},
abstract = {Catalyseurs de la dégradation de polysaccharides dans le cadre de diverses applications industrielles, de nombreuses glycoside hydrolases (GH) possèdent également une activité de transglycosylation qui peut être exploitée pour la synthèse dóligosaccharides. Afin dáugmenter cette activité, minoritaire par rapport à l'hydrolyse, des expériences de mutagenèse rationnelle peuvent être employées. Toutefois, lénsemble des bases moléculaires régissant l’équilibre entre ces deux activités reste en revanche difficile a élucider. L'étude de quatre GH (Ttβgly, AgaD, TcTS, TrSA) par simulation de dynamique moléculaire a permis la découverte de canaux déau internes à leurs structures et connectant le site actif au milieu. Cette observation suggère que les canaux déau internes aux GH pourraient être impliqués dans leur activité d'hydrolyse. Plusieurs paires de résidus bordant deux de ces canaux ont été mis en évidence chez Ttβgly et AgaD et semblent contrôler le passage de léau du canal vers le site actif. La mutagenèse de ces résidus a été entreprise afin de tenter dáugmenter láctivité de transglycosylation chez ces deux enzymes. Une réduction de l'hydrolyse d'un facteur 7 et 50 au profit de láctivité de transglycosylation a été caractérisée chez les deux meilleurs mutants de Ttβgly et AgaD, respectivement. Lánalyse des simulations a révélé que ces résultats étaient corrélés à une augmentation de la dynamique des molécules déau internes aux deux canaux étudiés. Cette étude souligne ainsi límportance fonctionnelle de léau interne aux hydrolases et suggère que língénierie de sa dynamique peut constituer une approche originale pour convertir les GH en transglycosidases.},
keywords = {},
pubstate = {published},
tppubtype = {phdthesis}
}
Goyet, Vincent; Billard, Estelle; Pouvreau, Jean-Bernard; Lechat, Marc-Marie; Pelletier, Sandra; Bahut, Muriel; Monteau, Fabrice; Spíchal, Lukas; Delavault, Philippe; Montiel, Grégory; Simier, Philippe
Haustorium initiation in the obligate parasitic plant Phelipanche ramosa involves a host-exudated cytokinin signal Article de journal
Dans: J Exp Bot, vol. 68, no. 20, p. 5539-5552, 2017, ISSN: 0022-0957 (Print) 0022-0957.
@article{RN11,
title = {Haustorium initiation in the obligate parasitic plant Phelipanche ramosa involves a host-exudated cytokinin signal},
author = {Vincent Goyet and Estelle Billard and Jean-Bernard Pouvreau and Marc-Marie Lechat and Sandra Pelletier and Muriel Bahut and Fabrice Monteau and Lukas Spíchal and Philippe Delavault and Grégory Montiel and Philippe Simier},
url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5853424/pdf/erx359.pdf},
doi = {10.1093/jxb/erx359},
issn = {0022-0957 (Print) 0022-0957},
year = {2017},
date = {2017-01-01},
urldate = {2017-01-01},
journal = {J Exp Bot},
volume = {68},
number = {20},
pages = {5539-5552},
abstract = {The heterotrophic lifestyle of parasitic plants relies on the development of the haustorium, a specific infectious organ required for attachment to host roots. While haustorium development is initiated upon chemodetection of host-derived molecules in hemiparasitic plants, the induction of haustorium formation remains largely unknown in holoparasitic species such as Phelipanche ramosa. This work demonstrates that the root exudates of the host plant Brassica napus contain allelochemicals displaying haustorium-inducing activity on P. ramosa germinating seeds, which increases the parasite aggressiveness. A de novo assembled transcriptome and microarray approach with P. ramosa during early haustorium formation upon treatment with B. napus root exudates allowed the identification of differentially expressed genes involved in hormone signaling. Bioassays using exogenous cytokinins and the specific cytokinin receptor inhibitor PI-55 showed that cytokinins induced haustorium formation and increased parasite aggressiveness. Root exudates triggered the expression of cytokinin-responsive genes during early haustorium development in germinated seeds, and bio-guided UPLC-ESI(+)-/MS/MS analysis showed that these exudates contain a cytokinin with dihydrozeatin characteristics. These results suggest that cytokinins constitutively exudated from host roots play a major role in haustorium formation and aggressiveness in P. ramosa.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
16 publications
Silva, Viviane A O; Lafont, Florian; Benhelli-Mokrani, Houda; Breton, Magali Le; Hulin, Philippe; Chabot, Thomas; Paris, François; Sakanyan, Vehary; Fleury, Fabrice
Rapid diminution in the level and activity of DNA-dependent protein kinase in cancer cells by a reactive nitro-benzoxadiazole compound Article de journal
Dans: International Journal of Molecular Sciences, vol. 17, no. 5, 2016, ISSN: 14220067.
@article{Silva2016,
title = {Rapid diminution in the level and activity of DNA-dependent protein kinase in cancer cells by a reactive nitro-benzoxadiazole compound},
author = {Viviane A O Silva and Florian Lafont and Houda Benhelli-Mokrani and Magali {Le Breton} and Philippe Hulin and Thomas Chabot and Fran{ç}ois Paris and Vehary Sakanyan and Fabrice Fleury},
doi = {10.3390/ijms17050703},
issn = {14220067},
year = {2016},
date = {2016-05-01},
journal = {International Journal of Molecular Sciences},
volume = {17},
number = {5},
publisher = {MDPI AG},
abstract = {The expression and activity of DNA-dependent protein kinase (DNA-PK) is related to DNA repair status in the response of cells to exogenous and endogenous factors. Recent studies indicate that Epidermal Growth Factor Receptor (EGFR) is involved in modulating DNA-PK. It has been shown that a compound 4-nitro-7-[(1-oxidopyridin-2-yl)sulfanyl]-2,1,3-benzoxadiazole (NSC), bearing a nitro-benzoxadiazole (NBD) scaffold, enhances tyrosine phosphorylation of EGFR and triggers downstream signaling pathways. Here, we studied the behavior of DNA-PK and other DNA repair proteins in prostate cancer cells exposed to compound NSC. We showed that both the expression and activity of DNA-PKcs (catalytic subunit of DNA-PK) rapidly decreased upon exposure of cells to the compound. The decline in DNA-PKcs was associated with enhanced protein ubiquitination, indicating the activation of cellular proteasome. However, pretreatment of cells with thioglycerol abolished the action of compound NSC and restored the level of DNA-PKcs. Moreover, the decreased level of DNA-PKcs was associated with the production of intracellular hydrogen peroxide by stable dimeric forms of Cu/Zn SOD1 induced by NSC. Our findings indicate that reactive oxygen species and electrophilic intermediates, generated and accumulated during the redox transformation of NBD compounds, are primarily responsible for the rapid modulation of DNA-PKcs functions in cancer cells.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Liu, Guoxia; Ma, Hongmei; Xie, Hongyan; Xuan, Ning; Guo, Xia; Fan, Zhongxue; Rajashekar, Balaji; Arnaud, Philippe; Offmann, Bernard; Picimbon, Jean François
Biotype characterization, developmental profiling, insecticide response and binding property of Bemisia tabaci chemosensory proteins: Role of CSP in insect defense Article de journal
Dans: PLoS ONE, vol. 11, no. 5, 2016, ISSN: 19326203.
@article{Liu2016,
title = {Biotype characterization, developmental profiling, insecticide response and binding property of Bemisia tabaci chemosensory proteins: Role of CSP in insect defense},
author = {Guoxia Liu and Hongmei Ma and Hongyan Xie and Ning Xuan and Xia Guo and Zhongxue Fan and Balaji Rajashekar and Philippe Arnaud and Bernard Offmann and Jean François Picimbon},
doi = {10.1371/journal.pone.0154706},
issn = {19326203},
year = {2016},
date = {2016-05-01},
journal = {PLoS ONE},
volume = {11},
number = {5},
publisher = {Public Library of Science},
abstract = {Chemosensory proteins (CSPs) are believed to play a key role in the chemosensory process in insects. Sequencing genomic DNA and RNA encoding CSP1, CSP2 and CSP3 in the sweet potato whitefly Bemisia tabaci showed strong variation between B and Q biotypes. Analyzing CSP-RNA levels showed not only biotype, but also age and developmental stage-specific expression. Interestingly, applying neonicotinoid thiamethoxam insecticide using twenty-five different dose/time treatments in B and Q young adults showed that Bemisia CSP1, CSP2 and CSP3 were also differentially regulated over insecticide exposure. In our study one of the adult-specific gene (CSP1) was shown to be significantly up-regulated by the insecticide in Q, the most highly resistant form of B. tabaci. Correlatively, competitive binding assays using tryptophan fluorescence spectroscopy and molecular docking demonstrated that CSP1 protein preferentially bound to linoleic acid, while CSP2 and CSP3 proteins rather associated to another completely different type of chemical, i.e. α-pentyl-cinnamaldehyde (jasminaldehyde). This might indicate that some CSPs in whiteflies are crucial to facilitate the transport of fatty acids thus regulating some metabolic pathways of the insect immune response, while some others are tuned to much more volatile chemicals known not only for their pleasant odor scent, but also for their potent toxic insecticide activity.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Krylov, Igor B; Kompanets, Mykhailo O; Novikova, Katerina V; Opeida, Iosip O; Kushch, Olga V; Shelimov, Boris N; Nikishin, Gennady I; Levitsky, Dmitri O; Terent'ev, Alexander O
Well-Known Mediators of Selective Oxidation with Unknown Electronic Structure: Metal-Free Generation and EPR Study of Imide-N-oxyl Radicals Article de journal
Dans: Journal of Physical Chemistry A, vol. 120, no. 1, p. 68–73, 2016, ISSN: 15205215.
@article{Krylov2016,
title = {Well-Known Mediators of Selective Oxidation with Unknown Electronic Structure: Metal-Free Generation and EPR Study of Imide-N-oxyl Radicals},
author = {Igor B Krylov and Mykhailo O Kompanets and Katerina V Novikova and Iosip O Opeida and Olga V Kushch and Boris N Shelimov and Gennady I Nikishin and Dmitri O Levitsky and Alexander O Terent'ev},
doi = {10.1021/acs.jpca.5b10722},
issn = {15205215},
year = {2016},
date = {2016-01-01},
journal = {Journal of Physical Chemistry A},
volume = {120},
number = {1},
pages = {68--73},
abstract = {Nitroxyl radicals are widely used in chemistry, materials sciences, and biology. Imide-N-oxyl radicals are subclass of unique nitroxyl radicals that proved to be useful catalysts and mediators of selective oxidation and CH-functionalization. An efficient metal-free method was developed for the generation of imide-N-oxyl radicals from N-hydroxyimides at room temperature by the reaction with (diacetoxyiodo)benzene. The method allows for the production of high concentrations of free radicals and provides high resolution of their EPR spectra exhibiting the superhyperfine structure from benzene ring protons distant from the radical center. An analysis of the spectra shows that, regardless of the electronic effects of the substituents in the benzene ring, the superhyperfine coupling constant of an unpaired electron with the distant protons at positions 4 and 5 of the aromatic system is substantially greater than that with the protons at positions 3 and 6 that are closer to the N-oxyl radical center. This is indicative of an unusual character of the spin density distribution of the unpaired electron in substituted phthalimide-N-oxyl radicals. Understanding of the nature of the electron density distribution in imide-N-oxyl radicals may be useful for the development of commercial mediators of oxidation based on N-hydroxyimides.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Mansuroglu, Zeyni; Benhelli-Mokrani, Houda; Marcato, Vasco; Sultan, Audrey; Violet, Marie; Chauderlier, Alban; Delattre, Lucie; Loyens, Anne; Talahari, Smail; Bégard, Séverine; Nesslany, Fabrice; Colin, Morvane; Souès, Sylvie; Lefebvre, Bruno; Buée, Luc; Galas, Marie Christine; Bonnefoy, Eliette
Loss of Tau protein affects the structure, transcription and repair of neuronal pericentromeric heterochromatin Article de journal
Dans: Scientific Reports, vol. 6, no. September, p. 1–16, 2016, ISSN: 20452322.
@article{Mansuroglu2016,
title = {Loss of Tau protein affects the structure, transcription and repair of neuronal pericentromeric heterochromatin},
author = {Zeyni Mansuroglu and Houda Benhelli-Mokrani and Vasco Marcato and Audrey Sultan and Marie Violet and Alban Chauderlier and Lucie Delattre and Anne Loyens and Smail Talahari and Séverine Bégard and Fabrice Nesslany and Morvane Colin and Sylvie Souès and Bruno Lefebvre and Luc Buée and Marie Christine Galas and Eliette Bonnefoy},
doi = {10.1038/srep33047},
issn = {20452322},
year = {2016},
date = {2016-01-01},
journal = {Scientific Reports},
volume = {6},
number = {September},
pages = {1--16},
publisher = {Nature Publishing Group},
abstract = {Pericentromeric heterochromatin (PCH) gives rise to highly dense chromatin sub-structures rich in the epigenetic mark corresponding to the trimethylated form of lysine 9 of histone H3 (H3K9me3) and in heterochromatin protein 1α (HP1α), which regulate genome expression and stability. We demonstrate that Tau, a protein involved in a number of neurodegenerative diseases including Alzheimer's disease (AD), binds to and localizes within or next to neuronal PCH in primary neuronal cultures from wild-type mice. Concomitantly, we show that the clustered distribution of H3K9me3 and HP1α, two hallmarks of PCH, is disrupted in neurons from Tau-deficient mice (KOTau). Such altered distribution of H3K9me3 that could be rescued by overexpressing nuclear Tau protein was also observed in neurons from AD brains. Moreover, the expression of PCH non-coding RNAs, involved in PCH organization, was disrupted in KOTau neurons that displayed an abnormal accumulation of stress-induced PCH DNA breaks. Altogether, our results demonstrate a new physiological function of Tau in directly regulating neuronal PCH integrity that appears disrupted in AD neurons.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Jaunet-Lahary, Titouan; Goupille, Anaïs; Jacquemin, Denis; Fleury, Fabrice; Graton, Jérôme; Laurent, Adèle D
A Joint Theoretical and Experimental Study of the Behavior of the DIDS Inhibitor and its Derivatives Article de journal
Dans: ChemPhysChem, vol. 3, p. 2434–2445, 2016, ISSN: 14397641.
@article{Jaunet-Lahary2016,
title = {A Joint Theoretical and Experimental Study of the Behavior of the DIDS Inhibitor and its Derivatives},
author = {Titouan Jaunet-Lahary and Anaïs Goupille and Denis Jacquemin and Fabrice Fleury and Jérôme Graton and Adèle D Laurent},
doi = {10.1002/cphc.201600107},
issn = {14397641},
year = {2016},
date = {2016-01-01},
journal = {ChemPhysChem},
volume = {3},
pages = {2434--2445},
abstract = {4,4′-Diisothiocyanostilbene-2,2′-disulfonic acid (DIDS) is a well-known ion-exchange inhibitor targeting cardiac functions and indirectly impeding both radio- and chemo-resistance. A joint computational and experimental study is presented to provide deeper insights into DIDS and other members of this family of compounds. To this end, we applied state-of-the-art density functional theory (DFT) and time-dependent DFT methods, in addition to measuring the optical properties. The experimental data show that such compounds are highly sensitive to their environment and that the optical properties change within as little time as 7 h. However, the optical properties of DIDS are similar in various acidic/basic environments, which were confirmed by pKa computations on both cis and trans isomers. The protonation analysis also highlights that the singly protonated form of DIDS behaves like a proton sponge compound. The experimentally observed redshift that can be seen when going from water to DMSO was reproduced solely by using the solvation model based on density, although the polarization continuum model and implicit/explicit hybrid schemes were also tested. The characteristic broadening of the absorption peak in water and the vibronic fine structure in DMSO were also reproduced thanks to vibronic coupling simulations associated with the solvent reorganization energy. For other stilbene derivatives, a correlation is found between the maximum absorption wavelength and the Hammett parameters.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Terent'Ev, Alexander O; Pastukhova, Zhanna Yu; Yaremenko, Ivan A; Novikov, Roman A; Demchuk, Dmitry V; Bruk, Lev G; Levitsky, Dmitri O; Fleury, Fabrice; Nikishin, Gennady I
Selective transformation of tricyclic peroxides with pronounced antischistosomal activity into 2-hydroxy-1,5-diketones using iron (II) salts Article de journal
Dans: Tetrahedron, vol. 72, no. 24, p. 3421–3426, 2016, ISSN: 14645416.
@article{TerentEv2016,
title = {Selective transformation of tricyclic peroxides with pronounced antischistosomal activity into 2-hydroxy-1,5-diketones using iron (II) salts},
author = {Alexander O Terent'Ev and Zhanna Yu Pastukhova and Ivan A Yaremenko and Roman A Novikov and Dmitry V Demchuk and Lev G Bruk and Dmitri O Levitsky and Fabrice Fleury and Gennady I Nikishin},
url = {http://dx.doi.org/10.1016/j.tet.2016.04.054},
doi = {10.1016/j.tet.2016.04.054},
issn = {14645416},
year = {2016},
date = {2016-01-01},
journal = {Tetrahedron},
volume = {72},
number = {24},
pages = {3421--3426},
publisher = {Elsevier Ltd},
abstract = {The present work deals with selective transformations of peroxides into organic compounds via the cleavage of the O-O bond using variable valence metals. A selective transformation of tricyclic peroxides promoted by Fe2+ salts was discovered. This selective transformation is unexpected for compounds with structural features which allow diverse decomposition pathways. 2-Hydroxy-1,5-diketones are prepared in yields up to 92% in the reactions of tricyclic peroxides with FeSO4, Fe(ClO4)2, or FeCl2. This is a new preparative method for the synthesis of 1,5-diketones. 2-Hydroxy-1,5-diketones in CDCl3 at 25 °C exist mainly in the open-chain form of the hydroxyketone over the cyclic hemiacetal. The results of this work can be of interest to understand the mechanism of the antiparasitic action of peroxides.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Levitsky, Dmitri O; Gloriozova, Tatyana A; Poroikov, Vladimir V; Dembitsky, Valery M
Mathews Journal of Pharmaceutical Science Naturally Occurring Isocyano / Isothiocyanato Compounds : Their Pharmacological and SAR Activities Article de journal
Dans: MATHEWS, Open Access Journals, vol. 1, no. 1, p. 1–15, 2016.
@article{Levitsky2016,
title = {Mathews Journal of Pharmaceutical Science Naturally Occurring Isocyano / Isothiocyanato Compounds : Their Pharmacological and SAR Activities},
author = {Dmitri O Levitsky and Tatyana A Gloriozova and Vladimir V Poroikov and Valery M Dembitsky},
year = {2016},
date = {2016-01-01},
journal = {MATHEWS, Open Access Journals},
volume = {1},
number = {1},
pages = {1--15},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Zdvizhkov, Alexander T; Terent'Ev, Alexander O; Radulov, Peter S; Novikov, Roman A; Tafeenko, Viktor A; Chernyshev, Vladimir V; Ilovaisky, Alexey I; Levitsky, Dmitri O; Fleury, Fabrice; Nikishin, Gennady I
Transformation of 2-allyl-1,3-diketones to bicyclic compounds containing 1,2-dioxolane and tetrahydrofuran rings using the I2/H2O2 system Article de journal
Dans: Tetrahedron Letters, vol. 57, no. 8, p. 949–952, 2016, ISSN: 18733581.
@article{Zdvizhkov2016,
title = {Transformation of 2-allyl-1,3-diketones to bicyclic compounds containing 1,2-dioxolane and tetrahydrofuran rings using the I2/H2O2 system},
author = {Alexander T Zdvizhkov and Alexander O Terent'Ev and Peter S Radulov and Roman A Novikov and Viktor A Tafeenko and Vladimir V Chernyshev and Alexey I Ilovaisky and Dmitri O Levitsky and Fabrice Fleury and Gennady I Nikishin},
url = {http://dx.doi.org/10.1016/j.tetlet.2016.01.061},
doi = {10.1016/j.tetlet.2016.01.061},
issn = {18733581},
year = {2016},
date = {2016-01-01},
journal = {Tetrahedron Letters},
volume = {57},
number = {8},
pages = {949--952},
publisher = {Elsevier Ltd},
abstract = {A one-pot procedure was developed for the assembly of bicyclic compounds containing 1,2-dioxolane and tetrahydrofuran rings based on the reaction of 2-allyl-1,3-diketones with the I2/H2O2 system. A fivefold molar excess of H2O2 and a twofold excess of I2 are required for the selective formation of tetrahydrofurodioxoles. The synthesis of these structurally complex molecules is unusual in that it does not produce the expected bridged tetraoxanes, products of the addition of several H2O2 molecules to a carbonyl group, or the products of double bond iodoperoxidation.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Sakanyan, Vehary; Hulin, Philippe; Sousa, Rodolphe Alves De; Silva, Viviane A O; Hambardzumyan, Artur; Nedellec, Steven; Tomasoni, Christophe; Logé, Cédric; Pineau, Charles; Roussakis, Christos; Fleury, Fabrice; Artaud, Isabelle
Activation of EGFR by small compounds through coupling the generation of hydrogen peroxide to stable dimerization of Cu/Zn SOD1 Article de journal
Dans: Scientific Reports, vol. 6, no. January, p. 1–14, 2016, ISSN: 20452322.
@article{Sakanyan2016,
title = {Activation of EGFR by small compounds through coupling the generation of hydrogen peroxide to stable dimerization of Cu/Zn SOD1},
author = {Vehary Sakanyan and Philippe Hulin and Rodolphe {Alves De Sousa} and Viviane A O Silva and Artur Hambardzumyan and Steven Nedellec and Christophe Tomasoni and Cédric Logé and Charles Pineau and Christos Roussakis and Fabrice Fleury and Isabelle Artaud},
url = {http://dx.doi.org/10.1038/srep21088},
doi = {10.1038/srep21088},
issn = {20452322},
year = {2016},
date = {2016-01-01},
journal = {Scientific Reports},
volume = {6},
number = {January},
pages = {1--14},
publisher = {Nature Publishing Group},
abstract = {Activation of cell signaling by reactive chemicals and pollutants is an important issue for human health. It has been shown that lipophilic nitro-benzoxadiazole (NBD) compounds rapidly move across the plasma membrane and enhance Epidermal Growth Factor Receptor (EGFR) tyrosine phosphorylation in cancer cells. Unlike ligand-dependent activation, the mechanism of this induction relies on the generation of hydrogen peroxide, which is involved in the activation of the catalytic site of the receptor and the inactivation of protein tyrosine phosphatase PTP-1B. Production of H 2 O 2 during redox transformation of NBD compounds is associated with the transition of a monomeric form of Cu/Zn superoxide dismutase 1 (SOD1) to stable dimers. The highly stable and functionally active SOD1 dimer, in the absence of adequate activities in downstream reactions, promotes the disproportionate production and accumulation of intracellular hydrogen peroxide shortly after exposure to NBD compounds. The intrinsic fluorescence of small compounds was used to demonstrate their binding to SOD1. Our data indicate that H 2 O 2 and concomitantly generated electrophilic intermediates behave as independent entities, but all contribute to the biological reactivity of NBD compounds. This study opens a promising path to identify new biomarkers of oxidative/electrophilic stress in the progression of cancer and other diseases.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Faucon, Adrien; Benhelli-Mokrani, Houda; Fleury, Fabrice; Dubreil, Laurence; Hulin, Philippe; Nedellec, Steven; Doussineau, Tristan; Antoine, Rodolphe; Orlando, Tomas; Lascialfari, Alessandro; Fresnais, Jérôme; Lartigue, Lénaïc; Ishow, Eléna
Tuning the architectural integrity of high-performance magneto-fluorescent core-shell nanoassemblies in cancer cells Article de journal
Dans: Journal of Colloid and Interface Science, vol. 479, p. 139–149, 2016, ISSN: 10957103.
@article{Faucon2016,
title = {Tuning the architectural integrity of high-performance magneto-fluorescent core-shell nanoassemblies in cancer cells},
author = {Adrien Faucon and Houda Benhelli-Mokrani and Fabrice Fleury and Laurence Dubreil and Philippe Hulin and Steven Nedellec and Tristan Doussineau and Rodolphe Antoine and Tomas Orlando and Alessandro Lascialfari and Jér{ô}me Fresnais and Léna{ï}c Lartigue and Eléna Ishow},
url = {http://dx.doi.org/10.1016/j.jcis.2016.06.064},
doi = {10.1016/j.jcis.2016.06.064},
issn = {10957103},
year = {2016},
date = {2016-01-01},
journal = {Journal of Colloid and Interface Science},
volume = {479},
pages = {139--149},
publisher = {Elsevier Inc.},
abstract = {High-density nanoarchitectures, endowed with simultaneous fluorescence and contrast properties for MRI and TEM imaging, have been obtained using a simple self-assembling strategy based on supramolecular interactions between non-doped fluorescent organic nanoparticles (FON) and superparamagnetic nanoparticles. In this way, a high-payload core-shell structure FON@mag has been obtained, protecting the hydrophobic fluorophores from the surroundings as well as from emission quenching by the shell of magnetic nanoparticles. Compared to isolated nanoparticles, maghemite nanoparticles self-assembled as an external shell create large inhomogeneous magnetic field, which causes enhanced transverse relaxivity and exacerbated MRI contrast. The magnetic load of the resulting nanoassemblies is evaluated using magnetic sedimentation and more originally electrospray mass spectrometry. The role of the stabilizing agents (citrate versus polyacrylate anions) revealed to be crucial regarding the cohesion of the resulting high-performance magneto-fluorescent nanoassemblies, which questions their use after cell internalization as nanocarriers or imaging agents for reliable correlative light and electron microcopy.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Forato, Florian; Liu, Hao; Benoit, Roland; Fayon, Franck; Charlier, Cathy; Fateh, Amina; Defontaine, Alain; Tellier, Charles; Talham, Daniel R; Queffélec, Clémence; Bujoli, Bruno
Comparison of Zirconium Phosphonate-Modified Surfaces for Immobilizing Phosphopeptides and Phosphate-Tagged Proteins Article de journal
Dans: Langmuir, vol. 32, no. 22, p. 5480–5490, 2016, ISSN: 15205827.
@article{Forato2016,
title = {Comparison of Zirconium Phosphonate-Modified Surfaces for Immobilizing Phosphopeptides and Phosphate-Tagged Proteins},
author = {Florian Forato and Hao Liu and Roland Benoit and Franck Fayon and Cathy Charlier and Amina Fateh and Alain Defontaine and Charles Tellier and Daniel R Talham and Clémence Queffélec and Bruno Bujoli},
doi = {10.1021/acs.langmuir.6b01020},
issn = {15205827},
year = {2016},
date = {2016-01-01},
journal = {Langmuir},
volume = {32},
number = {22},
pages = {5480--5490},
abstract = {Different routes for preparing zirconium phosphonate-modified surfaces for immobilizing biomolecular probes are compared. Two chemical-modification approaches were explored to form self-assembled monolayers on commercially available primary amine-functionalized slides, and the resulting surfaces were compared to well-characterized zirconium phosphonate monolayer-modified supports prepared using Langmuir-Blodgett methods. When using POCl3 as the amine phosphorylating agent followed by treatment with zirconyl chloride, the result was not a zirconium-phosphonate monolayer, as commonly assumed in the literature, but rather the process gives adsorbed zirconium oxide/hydroxide species and to a lower extent adsorbed zirconium phosphate and/or phosphonate. Reactions giving rise to these products were modeled in homogeneous-phase studies. Nevertheless, each of the three modified surfaces effectively immobilized phosphopeptides and phosphopeptide tags fused to an affinity protein. Unexpectedly, the zirconium oxide/hydroxide modified surface, formed by treating the amine-coated slides with POCl3/Zr4+, afforded better immobilization of the peptides and proteins and efficient capture of their targets.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Goux, Marine; Fateh, Amina; Defontaine, Alain; Cinier, Mathieu; Tellier, Charles
In vivo phosphorylation of a peptide tag for protein purification Article de journal
Dans: Biotechnology Letters, vol. 38, no. 5, p. 767–772, 2016, ISSN: 1573-6776.
@article{Goux2016,
title = {In vivo phosphorylation of a peptide tag for protein purification},
author = {Marine Goux and Amina Fateh and Alain Defontaine and Mathieu Cinier and Charles Tellier},
url = {https://doi.org/10.1007/s10529-016-2040-4},
doi = {10.1007/s10529-016-2040-4},
issn = {1573-6776},
year = {2016},
date = {2016-01-01},
journal = {Biotechnology Letters},
volume = {38},
number = {5},
pages = {767--772},
abstract = {To design a new system for the in vivo phosphorylation of proteins in Escherichia coli using the co-expression of the α-subunit of casein kinase II (CKIIα) and a target protein, (Nanofitin) fused with a phosphorylatable tag.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Verhaeghe, Tom; Winter, Karel De; Berland, Magali; Vreese, Rob De; D'Hooghe, Matthias; Offmann, Bernard; Desmet, Tom
Converting bulk sugars into prebiotics: Semi-rational design of a transglucosylase with controlled selectivity Article de journal
Dans: Chemical Communications, vol. 52, no. 18, p. 3687–3689, 2016, ISSN: 1364548X.
@article{Verhaeghe2016,
title = {Converting bulk sugars into prebiotics: Semi-rational design of a transglucosylase with controlled selectivity},
author = {Tom Verhaeghe and Karel {De Winter} and Magali Berland and Rob {De Vreese} and Matthias D'Hooghe and Bernard Offmann and Tom Desmet},
doi = {10.1039/c5cc09940d},
issn = {1364548X},
year = {2016},
date = {2016-01-01},
journal = {Chemical Communications},
volume = {52},
number = {18},
pages = {3687--3689},
publisher = {Royal Society of Chemistry},
abstract = {Despite the growing importance of prebiotics in nutrition and gastroenterology, their structural variety is currently still very limited. The lack of straightforward procedures to gain new products in sufficient amounts often hampers application testing and further development. Although the enzyme sucrose phosphorylase can be used to produce the rare disaccharide kojibiose (α-1,2-glucobiose) from the bulk sugars sucrose and glucose, the target compound is only a side product that is difficult to isolate. Accordingly, for this biocatalyst to become economically attractive, the formation of other glucobioses should be avoided and therefore we applied semi-rational mutagenesis and low-throughput screening, which resulted in a double mutant (L341I-Q345S) with a selectivity of 95% for kojibiose. That way, an efficient and scalable production process with a yield of 74% could be established, and with a simple yeast treatment and crystallization step over a hundred grams of highly pure kojibiose (textgreater99.5%) was obtained.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Brahmi, Ines; Mabrouk, Yassine; Brun, Guillaume; Delavault, Philippe; Belhadj, Omrane; Simier, Philippe
Phenotypical and biochemical characterisation of resistance for parasitic weed (Orobanche foetida Poir.) in radiation-mutagenised mutants of chickpea Article de journal
Dans: Pest Manag Sci, vol. 72, no. 12, p. 2330-2338, 2016, ISSN: 1526-498x.
@article{RN16,
title = {Phenotypical and biochemical characterisation of resistance for parasitic weed (Orobanche foetida Poir.) in radiation-mutagenised mutants of chickpea},
author = {Ines Brahmi and Yassine Mabrouk and Guillaume Brun and Philippe Delavault and Omrane Belhadj and Philippe Simier},
url = {https://onlinelibrary.wiley.com/doi/10.1002/ps.4278},
doi = {10.1002/ps.4278},
issn = {1526-498x},
year = {2016},
date = {2016-01-01},
urldate = {2016-01-01},
journal = {Pest Manag Sci},
volume = {72},
number = {12},
pages = {2330-2338},
abstract = {BACKGROUND: Some radiation-mutagenised chickpea mutants potentially resistant to the broomrape, Orobanche foetida Poir., were selected through field trials. The objectives of this work were to confirm resistance under artificial infestation, in pots and mini-rhizotron systems, and to determine the developmental stages of broomrape affected by resistance and the relevant resistance mechanisms induced by radiation mutagenesis. RESULTS: Among 30 mutants tested for resistance to O. foetida, five shared strong resistance in both pot experiments and mini-rhizotron systems. Resistance was not complete, but the few individuals that escaped resistance displayed high disorders of shoot development. Results demonstrated a 2-3-fold decrease in stimulatory activity of root exudates towards broomrape seed germination in resistant mutants in comparison with non-irradiated control plants and susceptible mutants. Resistance was associated with an induction of broomrape necrosis early during infection. When infested, most of the resistant mutants shared enhanced levels of soluble phenolic contents, phenylalanine ammonia lyase activity, guaiacol peroxidase activity and polyphenol oxidase activity, in addition to glutathione and notably ascorbate peroxidase gene expression in roots. CONCLUSION: Results confirmed enhanced resistance in chickpea radiation-mutagenised mutants, and demonstrated that resistance is based on alteration of root exudation, presumed cell-wall reinforcement and change in root oxidative status in response to infection. © 2016 Society of Chemical Industry.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Péron, Thomas; Candat, Adrien; Montiel, Grégory; Veronesi, Christophe; Macherel, David; Delavault, Philippe; Simier, Philippe
New Insights into Phloem Unloading and Expression of Sucrose Transporters in Vegetative Sinks of the Parasitic Plant Phelipanche ramosa L. (Pomel) Article de journal
Dans: Front Plant Sci, vol. 7, p. 2048, 2016, ISSN: 1664-462X (Print) 1664-462x.
@article{RN23,
title = {New Insights into Phloem Unloading and Expression of Sucrose Transporters in Vegetative Sinks of the Parasitic Plant Phelipanche ramosa L. (Pomel)},
author = {Thomas Péron and Adrien Candat and Grégory Montiel and Christophe Veronesi and David Macherel and Philippe Delavault and Philippe Simier},
url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5220101/pdf/fpls-07-02048.pdf},
doi = {10.3389/fpls.2016.02048},
issn = {1664-462X (Print) 1664-462x},
year = {2016},
date = {2016-01-01},
urldate = {2016-01-01},
journal = {Front Plant Sci},
volume = {7},
pages = {2048},
abstract = {The plant-parasitic plant interaction is a interesting model to study sink-source relationship and phloem unloading. The parasitic plants, such as the achlorophyllous plant Phelipanche ramosa, connect to the host phloem through the haustorium and act as supernumerary sinks for the host-derived photoassimilates, primarily sucrose. The application of the fluorescent symplastic tracer, carboxyfluorescein (CF) derived from carboxyfluorescein diacetate (CFDA), to the leaves of the host plant (Brassica napus) showed direct phloem connections at the host-parasite interface. These experiments also evidenced the dominant apoplastic pathway for phloem unloading in major vegetative sinks of the parasite, including tubercles and shoots, except the adventitious root apices. The CF experiments showed also the symplastic isolation of the phloem tissues from the sink tissues in tubercle and shoot of the parasite, then suggesting the pivotal role of sucrose transporters in sucrose unloading in P. ramosa sinks. Three cDNAs encoding sucrose transporters (PrSUT) were isolated from the parasitic plant. PrSUT1 transcripts accumulated at the same level in the tubercle throughout the parasite growth while a significant increase in transcript accumulation occurred after emergence in the flowering shoot, notably in the growing apical part. The in situ hybridization experiments revealed the PrSUT1 transcript accumulation in the mature phloem cells of both subterranean and flowering shoots, as well as in shoot terminal sinks corresponding to apical meristem, scale leaf primordia and immature vasculature. The transient expression experiments in Arabidopsis protoplasts showed that PrSUT1 was localized at the plasma membrane, suggesting its role in phloem functioning and sucrose uptake by the sink cells in P. ramosa. Conversely, the PrSUT2 transcript accumulation was constantly low in tubercles and shoots but PrSUT3 transcripts accumulated markedly in the subterranean and flowering shoots, in concordance with the PrSUT3 mRNA accumulation in multiple sink areas including apical meristem, scale-leaf primordia, immature vasculature and even storage parenchyma. However, the PrSUT3 transcripts did not accumulate in the mature phloem cells. The transient expression experiments in Arabidopsis protoplasts suggested a tonoplast localization of PrSUT3, for which nevertheless the involvement in intracellular sucrose transport needs clarification.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Rolland, Mathieu; Dupuy, Aurélie; Pelleray, Aude; Delavault, Philippe
Molecular Identification of Broomrape Species from a Single Seed by High Resolution Melting Analysis Article de journal
Dans: Front Plant Sci, vol. 7, p. 1838, 2016, ISSN: 1664-462X (Print) 1664-462x.
@article{RN12,
title = {Molecular Identification of Broomrape Species from a Single Seed by High Resolution Melting Analysis},
author = {Mathieu Rolland and Aurélie Dupuy and Aude Pelleray and Philippe Delavault},
url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5149549/pdf/fpls-07-01838.pdf},
doi = {10.3389/fpls.2016.01838},
issn = {1664-462X (Print) 1664-462x},
year = {2016},
date = {2016-01-01},
urldate = {2016-01-01},
journal = {Front Plant Sci},
volume = {7},
pages = {1838},
abstract = {Broomrapes are holoparasitic plants spreading through seeds. Each plant produces hundreds of thousands of seeds which remain viable in the soils for decades. To limit their spread, drastic measures are being taken and the contamination of a commercial seed lot by a single broomrape seed can lead to its rejection. Considering that broomrapes species identification from a single seed is extremely difficult even for trained botanists and that among all the described species, only a few are really noxious for the crops, numerous seed lots are rejected because of the contamination by seeds of non-noxious broomrape species. The aim of this study was to develop and evaluate a High Resolution Melting assay identifying the eight most noxious and common broomrape species (Phelipanche aegyptiaca, Orobanche cernua, O. crenata, O. cumana, O. foetida, O. hederae, O. minor, and P. ramosa) from a single seed. Based on trnL and rbcL plastidial genes amplification, the designed assay successfully identifies O. cumana, O. cernua, O. crenata, O. minor, O. hederae, and O. foetida; P. ramosa, and P. aegyptiaca can be differentiated from other species but not from each other. Tested on 50 seed lots, obtained results perfectly matched identifications performed by sequencing. Through the analysis of common seed lots by different analysts, the reproducibility of the assay was evaluated at 90%. Despite an original sample preparation process it was not possible to extract enough DNA from some seeds (10% of the samples). The described assay fulfills its objectives and allows an accurate identification of the targeted broomrape species. It can be used to identify contaminants in commercial seed lots or for any other purpose. The assay might be extended to vegetative material.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
24 publications
Goux, Marine
Université de Nantes, 2015.
@phdthesis{goux2015fonctionnalisation,
title = {Fonctionnalisation de protéines alternatives aux anticorps appliquée à límagerie médicale en oncologie},
author = {Marine Goux},
url = {https://www.theses.fr/2015NANT2040},
year = {2015},
date = {2015-12-04},
school = {Université de Nantes},
abstract = {La tomographie par émission de positon (TEP) est une technique d’imagerie médicale permettant le diagnostic et le suivi de patient en oncologie. L’utilisation des anticorps et de leurs fragments pour le ciblage de biomarqueurs en TEP présente de nombreuses difficultés liées notamment à leur clairance lente (taille >100 kDa). Leur marquage, faisant intervenir principalement des réactions peu spécifiques, conduit à un mélange hétérogène de produits et parfois à l’inactivation des protéines. Le développement d’un nouvel outil de suivi in vivo des patients à l’aide de petites protéines alternatives aux anticorps, les Nanofitines (NF), permet de s’affranchir des contraintes liées à la taille (NF ≈ 10 kDa). La mise en place d’une stratégie de marquage originale et site-spécifique d’une NF sans étape de couplage chimique a d’abord été envisagée dans cette étude. L’approche est basée sur la capacité naturelle des phosphates à fixer des cations métalliques. L’insertion génétique d’une étiquette peptidique phosphorylable, in vivo ou in vitro, a permis la chélation d’un lanthanide en solution, le Tb(III), avec une affinité de l’ordre du μM. La seconde génération d’étiquettes peptidiques obtenues par mutagenèse a permis la chélation du Tb(III) avec une affinité d’environ 500 nM à pH7 et 50 nM à pH5,5, et une affinité pour le Ga(III) de l’ordre du μM à pH5,5. Parallèlement, la biodistribution et le ciblage spécifique in vivo d’une NF anti-EGFR radiomarquée à l’aide du 18F-FBEM ont été évalués dans un double modèle tumoral murin. Les images TEP obtenues avec un bon contraste ont permis de valider la preuve de concept quant à l’utilisation des NF en tant qu’outil en imagerie médicale.},
keywords = {},
pubstate = {published},
tppubtype = {phdthesis}
}
Martin-Jézéquel, Véronique; Calu, Guillaume; Candela, Leo; Amzil, Zouher; Jauffrais, Thierry; Séchet, Véronique; Weigel, Pierre
Effects of organic and inorganic nitrogen on the growth and production of domoic acid by pseudo-nitzschia multiseries and p. Australis (bacillariophyceae) in culture Article de journal
Dans: Marine Drugs, vol. 13, no. 12, p. 7067–7086, 2015, ISSN: 16603397.
@article{Martin-Jezequel2015,
title = {Effects of organic and inorganic nitrogen on the growth and production of domoic acid by pseudo-nitzschia multiseries and p. Australis (bacillariophyceae) in culture},
author = {Véronique Martin-Jézéquel and Guillaume Calu and Leo Candela and Zouher Amzil and Thierry Jauffrais and Véronique Séchet and Pierre Weigel},
doi = {10.3390/md13127055},
issn = {16603397},
year = {2015},
date = {2015-12-01},
journal = {Marine Drugs},
volume = {13},
number = {12},
pages = {7067--7086},
publisher = {MDPI AG},
abstract = {Over the last century, human activities have altered the global nitrogen cycle, and anthropogenic inputs of both inorganic and organic nitrogen species have increased around the world, causing significant changes to the functioning of aquatic ecosystems. The increasing frequency of Pseudo-nitzschia spp. in estuarine and coastal waters reinforces the need to understand better the environmental control of its growth and domoic acid (DA) production. Here, we document Pseudo-nitzschia spp. growth and toxicity on a large set of inorganic and organic nitrogen (nitrate, ammonium, urea, glutamate, glutamine, arginine and taurine). Our study focused on two species isolated from European coastal waters: P. multiseries CCL70 and P. australis PNC1. The nitrogen sources induced broad differences between the two species with respect to growth rate, biomass and cellular DA, but no specific variation could be attributed to any of the inorganic or organic nitrogen substrates. Enrichment with ammonium resulted in an enhanced growth rate and cell yield, whereas glutamate did not support the growth of P. multiseries. Arginine, glutamine and taurine enabled good growth of P. australis, but without toxin production. The highest DA content was produced when P. multiseries grew with urea and P. australis grew with glutamate. For both species, growth rate was not correlated with DA content but more toxin was produced when the nitrogen source could not sustain a high biomass. A significant negative correlation was found between cell biomass and DA content in P. australis. This study shows that Pseudo-nitzschia can readily utilize organic nitrogen in the form of amino acids, and confirms that both inorganic and organic nitrogen affect growth and DA production. Our results contribute to our understanding of the ecophysiology of Pseudo-nitzschia spp. and may help to predict toxic events in the natural environment.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Alligand, Brendan
Étude du rôle des phosphorylations de Rad51 en Y54 et en Y315 sur son fonctionnement Thèse
Université de Nantes, 2015.
@phdthesis{alligand2015etude,
title = {Étude du rôle des phosphorylations de Rad51 en Y54 et en Y315 sur son fonctionnement},
author = {Brendan Alligand},
url = {https://www.theses.fr/2015NANT2033},
year = {2015},
date = {2015-11-26},
school = {Université de Nantes},
abstract = {La Recombinaison Homologue (RH) permet la réparation des dommages à l’ADN les plus délétères : les Cassures double brin. L’étape centrale de la RH est basée sur l’activité d’échange de brins de RAD51. Ainsi, l’activité de RAD51 est cruciale pour le maintien de l’intégrité génomique. Toutefois, cette protéine possède également un côté sombre. En effet, la surexpression de RAD51 permet aux cellules cancéreuses de résister aux traitements. Ce qui en fait une cible thérapeutique potentielle pour sensibiliser les cellules cancéreuses au traitement. Une meilleure compréhension du contrôle de l’activité de RAD51 aiderait sûrement à développer des stratégies thérapeutiques. L’activité de RAD51 est régulée par des phosphorylations et plusieurs kinases sont connues pour cibler RAD51. C’est le cas de la kinase c-Abl qui phosphoryle les tyrosines Y54 et Y315 en réponse aux dommages à l’ADN. Mais le rôle de ces phosphorylations est peu connu. C’est pourquoi nous nous sommes intéressés à l’effet de ces phosphorylations sur RAD51. Dans ce but, nous avons produit des mutants de RAD51 mimant la phosphorylation. Leur activité a été analysée et comparée in vitro. Nous avons démontré que le mutant équivalent à une double phosphorylation est incapable de réaliser l’échange de brins. Un défaut de polymérisation de RAD51 serait à l’origine de cette inhibition. Par la suite, la régulation a été étudiée dans le contexte cellulaire. Les résultats préliminaires montrent un effet de la double phosphorylation sur la localisation cellulaire de RAD51. L’inactivation de RAD51 par cette double phosphorylation pourrait participer à la régulation de la voie de la Recombinaison Homologue et serait une étape clef dans la compréhension de la réponse aux dommages à l’ADN.},
keywords = {},
pubstate = {published},
tppubtype = {phdthesis}
}
Ségaliny, Aude I; Brion, Régis; Brulin, Bénédicte; Maillasson, Mike; Charrier, Céline; Téletchéa, Stéphane; Heymann, Dominique
IL-34 and M-CSF form a novel heteromeric cytokine and regulate the M-CSF receptor activation and localization Article de journal
Dans: Cytokine, vol. 76, no. 2, p. 170–181, 2015, ISSN: 10960023.
@article{Segaliny2015,
title = {IL-34 and M-CSF form a novel heteromeric cytokine and regulate the M-CSF receptor activation and localization},
author = {Aude I Ségaliny and Régis Brion and Bénédicte Brulin and Mike Maillasson and Céline Charrier and Stéphane Téletchéa and Dominique Heymann},
doi = {10.1016/j.cyto.2015.05.029},
issn = {10960023},
year = {2015},
date = {2015-01-01},
journal = {Cytokine},
volume = {76},
number = {2},
pages = {170--181},
abstract = {Interleukin-34 (IL-34) is a newly-discovered homodimeric cytokine that regulates, like Macrophage Colony-Stimulating Factor (M-CSF), the differentiation of the myeloid lineage through M-CSF receptor (M-CSFR) signaling pathways. To date, both cytokines have been considered as competitive cytokines with regard to the M-CSFR. The aim of the present work was to study the functional relationships of these cytokines on cells expressing the M-CSFR. We demonstrate that simultaneous addition of M-CSF and IL-34 led to a specific activation pattern on the M-CSFR, with higher phosphorylation of the tyrosine residues at low concentrations. Similarly, both cytokines showed an additive effect on cellular proliferation or viability. In addition, BIAcore experiments demonstrated that M-CSF binds to IL-34, and molecular docking studies predicted the formation of a heteromeric M-CSF/IL-34 cytokine. A proximity ligation assay confirmed this interaction between the cytokines. Finally, co-expression of the M-CSFR and its ligands differentially regulated M-CSFR trafficking into the cell. This study establishes a new foundation for the understanding of the functional relationship between IL-34 and M-CSF, and gives a new vision for the development of therapeutic approaches targeting the IL-34/M-CSF/M-CSFR axis.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Faucon, Adrien; Benhelli-Mokrani, Houda; w Córdova, Luis A; Brulin, Bénédicte; Heymann, Dominique; Hulin, Philippe; Nedellec, Steven; Ishow, Eléna
Are Fluorescent Organic Nanoparticles Relevant Tools for Tracking Cancer Cells or Macrophages? Article de journal
Dans: Advanced Healthcare Materials, vol. 4, no. 17, p. 2727–2734, 2015, ISSN: 21922659.
@article{Faucon2015,
title = {Are Fluorescent Organic Nanoparticles Relevant Tools for Tracking Cancer Cells or Macrophages?},
author = {Adrien Faucon and Houda Benhelli-Mokrani and Luis A w Córdova and Bénédicte Brulin and Dominique Heymann and Philippe Hulin and Steven Nedellec and Eléna Ishow},
doi = {10.1002/adhm.201500562},
issn = {21922659},
year = {2015},
date = {2015-01-01},
journal = {Advanced Healthcare Materials},
volume = {4},
number = {17},
pages = {2727--2734},
abstract = {Strongly solvatochromic fluorophores are devised, containing alkyl chains and enable to self-assemble as very bright fluorescent organic nanoparticles (FONs) in water (φf = 0.28). The alkyl chains impart each fluorophore with strongly hydrophobic surroundings, causing distinct emission colors between FONs where the fluorophores are associated, and their disassembled state. Such color change is harnessed to assess the long-term fate of FONs in both cancer cells and monocytes/macrophages. Disintegration of the orange-emitting FONs by monocytes/macrophages is evidenced through the formation of micrometer green-yellowish emitting vesicles. By contrast, cancer cells retain longer the integrity of organic nanoparticles. In both cases, no significant toxicity is detected, making FONs as valuable bioimaging agents for cell tracking with weak risks of deleterious accumulation and low degradation rate. Long-term fate of fluorescent organic nanoparticles (FONs), known as very bright imaging agents and made of self-assembled solvatochromic fluorophores, is explored in both cancer cells and monocytes/macrophages. Disintegration of the orange-emitting FONs by monocytes/macrophages is evidenced through the formation of micrometer green-yellowish emitting vesicles. By contrast, cancer cells retain longer the integrity of organic nanoparticles.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Qi, Haoling; Cantrelle, François Xavier; Benhelli-Mokrani, Houda; Smet-Nocca, Caroline; Buée, Luc; Lippens, Guy; Bonnefoy, Eliette; Galas, Marie Christine; Landrieu, Isabelle
Nuclear magnetic resonance spectroscopy characterization of interaction of Tau with DNA and its regulation by phosphorylation Article de journal
Dans: Biochemistry, vol. 54, no. 7, p. 1525–1533, 2015, ISSN: 15204995.
@article{Qi2015,
title = {Nuclear magnetic resonance spectroscopy characterization of interaction of Tau with DNA and its regulation by phosphorylation},
author = {Haoling Qi and François Xavier Cantrelle and Houda Benhelli-Mokrani and Caroline Smet-Nocca and Luc Buée and Guy Lippens and Eliette Bonnefoy and Marie Christine Galas and Isabelle Landrieu},
doi = {10.1021/bi5014613},
issn = {15204995},
year = {2015},
date = {2015-01-01},
journal = {Biochemistry},
volume = {54},
number = {7},
pages = {1525--1533},
abstract = {The capacity of endogenous Tau to bind DNA has been recently identified in neurons under physiological or oxidative stress conditions. Characterization of the protein domains involved in Tau-DNA complex formation is an essential first step in clarifying the contribution of Tau-DNA interactions to neurological biological processes. To identify the amino acid residues involved in the interaction of Tau with oligonucleotides, we have characterized a Tau-DNA complex using nuclear magnetic resonance spectroscopy. Interaction of an AT-rich or GC-rich 22 bp oligonucleotide with Tau showed multiple points of anchoring along the intrinsically disordered Tau protein. The main sites of contact characterized here correspond to the second half of the proline-rich domain (PRD) of Tau and the R2 repeat in the microtubule binding domain. This latter interaction site includes the PHF6∗ sequence known to govern Tau aggregation. The characterization was pursued by studying the binding of phosphorylated forms of Tau, displaying multiple phosphorylation sites mainly in the PRD, to the same oligonucleotide. No interaction of phospho-Tau with the oligonucleotide was detected, suggesting that pathological Tau phosphorylation could affect the physiological function of Tau mediated by DNA binding.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Terent'ev, Alexander O; Zdvizhkov, Alexander T; Levitsky, Dmitri O; Fleury, Fabrice; Pototskiy, Roman A; Kulakova, Alena N; Nikishin, Gennady I
Organocatalytic peroxidation of malonates, β-ketoesters, and cyanoacetic esters using n-Bu4NI/t-BuOOH-mediated intermolecular oxidative C(sp3)-O coupling Article de journal
Dans: Tetrahedron, vol. 71, no. 47, p. 8985–8990, 2015, ISSN: 14645416.
@article{Terentev2015,
title = {Organocatalytic peroxidation of malonates, β-ketoesters, and cyanoacetic esters using n-Bu4NI/t-BuOOH-mediated intermolecular oxidative C(sp3)-O coupling},
author = {Alexander O Terent'ev and Alexander T Zdvizhkov and Dmitri O Levitsky and Fabrice Fleury and Roman A Pototskiy and Alena N Kulakova and Gennady I Nikishin},
url = {http://dx.doi.org/10.1016/j.tet.2015.09.047},
doi = {10.1016/j.tet.2015.09.047},
issn = {14645416},
year = {2015},
date = {2015-01-01},
journal = {Tetrahedron},
volume = {71},
number = {47},
pages = {8985--8990},
publisher = {Elsevier Ltd},
abstract = {A new organocatalytic approach for the synthesis of peroxides based on CH activation of a sp3-hybridized carbon atom is reported. Peroxides were prepared in 31-89% yield by the reaction of malonates, β-ketoesters, and cyanoacetic esters with a Bu4NI/tert-butyl hydroperoxide system. The formation of the expected hydroxylation products was not observed. In the discovered reaction, tert-butyl hydroperoxide plays a dual role by acting as the oxidant and the O-reagent for the C-O coupling. The synthesis can be scaled up to generate gram quantities of the target products.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Arab-Jaziri, Faten; Bissaro, Bastien; Tellier, Charles; Dion, Michel; Fauré, Régis; O'Donohue, Michael J
Enhancing the chemoenzymatic synthesis of arabinosylated xylo-oligosaccharides by GH51 α-l-arabinofuranosidase Article de journal
Dans: Carbohydrate Research, vol. 401, p. 64–72, 2015, ISSN: 1873426X.
@article{Arab-Jaziri2015,
title = {Enhancing the chemoenzymatic synthesis of arabinosylated xylo-oligosaccharides by GH51 α-l-arabinofuranosidase},
author = {Faten Arab-Jaziri and Bastien Bissaro and Charles Tellier and Michel Dion and Régis Fauré and Michael J O'Donohue},
doi = {10.1016/j.carres.2014.10.029},
issn = {1873426X},
year = {2015},
date = {2015-01-01},
journal = {Carbohydrate Research},
volume = {401},
pages = {64--72},
publisher = {Elsevier Ltd},
abstract = {Random mutagenesis was performed on the α-l-arabinofuranosidase of Thermobacillus xylanilyticus in order to enhance its ability to perform transarabinofuranosylation using natural xylo-oligosaccharides as acceptors. To achieve this goal, a two-step, high-throughput digital imaging protocol involving a colorimetric substrate was used to screen a library of 30,000 mutants. In the first step this screen selected for hydrolytically-impaired mutants, and in the second step the screen identified mutants whose global activity was improved in the presence of a xylo-oligosaccharide mixture. Thereby, 199 mutants displaying lowered hydrolytic activity and modified properties were detected. In the presence of these xylo-oligosaccharides, most of the 199 (i.e., 70%) enzymes were less inhibited and some (18) mutants displayed an unambiguous alleviation of inhibition (textless25% loss of activity). More precise monitoring of reactions catalyzed by the most promising mutants revealed a significant improvement of the synthesis yields of transglycosylation products (up to 18% compared to 9% for the parental enzyme) when xylobiose was present in the reaction. Genetic analysis of improved mutants revealed that many of the amino acid substitutions that correlate with the modified phenotype are located in the vicinity of the active site, particularly in subsite -1. Consequently, we hypothesize that these mutations modify the active site topology or the molecular interaction network of the l-arabinofuranoside donor substrate, thus impairing the hydrolysis and concomitantly favoring transglycosylation onto natural acceptors.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
André-Miral, Corinne; Koné, Fankroma Mt; Solleux, Claude; Grandjean, Cyrille; Dion, Michel; Tran, Vinh; Tellier, Charles
De novo design of a trans-β-N-acetylglucosaminidase activity from a GH1 β-glycosidase by mechanism engineering Article de journal
Dans: Glycobiology, vol. 25, no. 4, p. 394–402, 2015, ISSN: 14602423.
@article{Andre-Miral2015,
title = {De novo design of a trans-β-N-acetylglucosaminidase activity from a GH1 β-glycosidase by mechanism engineering},
author = {Corinne André-Miral and Fankroma Mt Koné and Claude Solleux and Cyrille Grandjean and Michel Dion and Vinh Tran and Charles Tellier},
doi = {10.1093/glycob/cwu121},
issn = {14602423},
year = {2015},
date = {2015-01-01},
journal = {Glycobiology},
volume = {25},
number = {4},
pages = {394--402},
abstract = {Glycoside hydrolases are particularly abundant in all areas of metabolism as they are involved in the degradation of natural polysaccharides and glycoconjugates. These enzymes are classified into 133 families (CAZy server, http://www.cazy.org) in which members of each family have a similar structure and catalytic mechanism. In order to understand better the structure/function relationships of these enzymes and their evolution and to develop new robust evolved glycosidases, we undertook to convert a Family 1 thermostable β-glycosidase into an exo-β-N-acetylglucosaminidase. This latter activity is totally absent in Family 1, while natural β-hexosaminidases belong to CAZy Families 3, 20 and 84. Using molecular modeling, we first showed that the docking of N-acetyl-d-glucosamine in the subsite -1 of the β-glycosidase from Thermus thermophilus (TtβGly) suggested several steric conflicts with active site amino-acids (N163, E338) induced by the N-acetyl group. Both N163A and N163D-E338G mutations induced significant N-acetylglucosaminidase activity in TtβGly. The double mutant N163D-E338G was also active on the bicyclic oxazoline substrate, suggesting that this mutated enzyme uses a catalytic mechanism involving a substrate-assisted catalysis with a noncovalent oxazoline intermediate, similar to the N-acetylglucosaminidases from Families 20 and 84. Furthermore, a very efficient trans-N-acetylglucosaminidase activity was observed when the double mutant was incubated in the presence of NAG-oxazoline as a donor and N-methyl-O-benzyl-N-(β-d-glucopyranosyl)-hydroxylamine as an acceptor. More generally, this work demonstrates that it is possible to exchange the specificities and catalytic mechanisms with minimal changes between phylogenetically distant protein structures.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Brissonnet, Yoan; Ladevèze, Simon; Teze, David; Fabre, Emeline; Deniaud, David; Daligault, Franck; Tellier, Charles; Šesták, Sergej; Remaud-Simeon, Magali; Potocki-Veronese, Gabrielle; Gouin, Sébastien G
Polymeric iminosugars improve the activity of carbohydrate-processing enzymes Article de journal
Dans: Bioconjugate Chemistry, vol. 26, no. 4, p. 766–772, 2015, ISSN: 15204812.
@article{Brissonnet2015,
title = {Polymeric iminosugars improve the activity of carbohydrate-processing enzymes},
author = {Yoan Brissonnet and Simon Ladevèze and David Teze and Emeline Fabre and David Deniaud and Franck Daligault and Charles Tellier and Sergej Šesták and Magali Remaud-Simeon and Gabrielle Potocki-Veronese and Sébastien G Gouin},
doi = {10.1021/acs.bioconjchem.5b00081},
issn = {15204812},
year = {2015},
date = {2015-01-01},
journal = {Bioconjugate Chemistry},
volume = {26},
number = {4},
pages = {766--772},
abstract = {Multivalent iminosugars have recently emerged as powerful tools to inhibit the activities of specific glycosidases. In this work, biocompatible dextrans were coated with iminosugars to form linear and ramified polymers with unprecedently high valencies (from 20 to 900) to probe the evolution of the multivalent inhibition as a function of ligand valency. This study led to the discovery that polyvalent iminosugars can also significantly enhance, not only inhibit, the enzymatic activity of specific glycoside-hydrolase, as observed on two galactosidases, a fucosidase, and a bacterial mannoside phosphorylase for which an impressive 70-fold activation was even reached. The concept of glycosidase activation is largely unexplored, with a unique recent example of small-molecules activators of a bacterial O-GlcNAc hydrolase. The possibility of using these polymers as "artificial enzyme effectors may therefore open up new perspectives in therapeutics and biocatalysis.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Advedissian, Tamara; Deshayes, Frédérique; Poirier, Françoise; Grandjean, Cyrille; Viguier, Mireille
Les galectines: Des lectines pas comme les autres Article de journal
Dans: Medecine/Sciences, vol. 31, no. 5, p. 499–505, 2015, ISSN: 19585381.
@article{Advedissian2015,
title = {Les galectines: Des lectines pas comme les autres},
author = {Tamara Advedissian and Frédérique Deshayes and Françoise Poirier and Cyrille Grandjean and Mireille Viguier},
doi = {10.1051/medsci/20153105011},
issn = {19585381},
year = {2015},
date = {2015-01-01},
journal = {Medecine/Sciences},
volume = {31},
number = {5},
pages = {499--505},
abstract = {Galectins constitute a family of soluble animal lectins defined by their evolutionary conserved carbohydrate recognition domain and their affinity for β-galactosides containing glycoconjugates. Each galectin is characterized by a specific spatio-temporal distribution and a unique set of ligands and molecular partners. Interestingly, galectins are found both extracellularly and intracellularly and modulate various cellular processes. Knock-out mutant mice for galectins-1, 3 or 7 are viable but display a wide range of defects under various stress conditions. Indeed, galectins are multifunctional proteins involved in cell-cell and cell-extracellular matrix interactions, organization of membrane domains, cell signalling and also in intracellular trafficking, apoptosis, regulation of cell cycle. Galectins represent potential therapeutic targets, especially in the context of cancer and inflammatory diseases.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Cabezas, Yari; Legentil, Laurent; Robert-Gangneux, Florence; Daligault, Franck; Belaz, Sorya; Nugier-Chauvin, Caroline; Tranchimand, Sylvain; Tellier, Charles; Gangneux, Jean Pierre; Ferrières, Vincent
Leishmania cell wall as a potent target for antiparasitic drugs. A focus on the glycoconjugates Article de journal
Dans: Organic and Biomolecular Chemistry, vol. 13, no. 31, p. 8393–8404, 2015, ISSN: 14770520.
@article{Cabezas2015,
title = {Leishmania cell wall as a potent target for antiparasitic drugs. A focus on the glycoconjugates},
author = {Yari Cabezas and Laurent Legentil and Florence Robert-Gangneux and Franck Daligault and Sorya Belaz and Caroline Nugier-Chauvin and Sylvain Tranchimand and Charles Tellier and Jean Pierre Gangneux and Vincent Ferri{è}res},
doi = {10.1039/c5ob00563a},
issn = {14770520},
year = {2015},
date = {2015-01-01},
journal = {Organic and Biomolecular Chemistry},
volume = {13},
number = {31},
pages = {8393--8404},
publisher = {Royal Society of Chemistry},
abstract = {Although leishmaniasis has been studied for over a century, the fight against cutaneous, mucocutaneous and visceral forms of the disease remains a hot topic. This review refers to the parasitic cell wall and more particularly to the constitutive glycoconjugates. The structures of the main glycolipids and glycoproteins, which are species-dependent, are described. The focus is on the disturbance of the lipid membrane by existing drugs and possible new ones, in order to develop future therapeutic agents.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Mahajan, Swapnil; Brevern, Alexandre G De; Sanejouand, Yves-Henri; Srinivasan, Narayanaswamy; Offmann, Bernard
Use of a structural alphabet to find compatible folds for amino acid sequences Article de journal
Dans: Protein Science, vol. 24, no. 1, p. 145–153, 2015, ISSN: 1469896X.
@article{Mahajan2015a,
title = {Use of a structural alphabet to find compatible folds for amino acid sequences},
author = {Swapnil Mahajan and Alexandre G {De Brevern} and Yves-Henri Sanejouand and Narayanaswamy Srinivasan and Bernard Offmann},
doi = {10.1002/pro.2581},
issn = {1469896X},
year = {2015},
date = {2015-01-01},
journal = {Protein Science},
volume = {24},
number = {1},
pages = {145--153},
abstract = {The structural annotation of proteins with no detectable homologs of known 3D structure identified using sequence-search methods is a major challenge today. We propose an original method that computes the conditional probabilities for the amino-acid sequence of a protein to fit to known protein 3D structures using a structural alphabet, known as "Protein Blocks" (PBs). PBs constitute a library of 16 local structural prototypes that approximate every part of protein backbone structures. It is used to encode 3D protein structures into 1D PB sequences and to capture sequence to structure relationships. Our method relies on amino acid occurrence matrices, one for each PB, to score global and local threading of query amino acid sequences to protein folds encoded into PB sequences. It does not use any information from residue contacts or sequence-search methods or explicit incorporation of hydrophobic effect. The performance of the method was assessed with independent test datasets derived from SCOP 1.75A. With a Z-score cutoff that achieved 95% specificity (i.e., less than 5% false positives), global and local threading showed sensitivity of 64.1% and 34.2%, respectively. We further tested its performance on 57 difficult CASP10 targets that had no known homologs in PDB: 38 compatible templates were identified by our approach and 66% of these hits yielded correctly predicted structures. This method scales-up well and offers promising perspectives for structural annotations at genomic level. It has been implemented in the form of a web-server that is freely available at http://www.bo-protscience.fr/forsa.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Mahajan, Swapnil; Sanejouand, Yves-Henri
On the relationship between low-frequency normal modes and the large-scale conformational changes of proteins Article de journal
Dans: Archives of Biochemistry and Biophysics, vol. 567, p. 59–65, 2015, ISSN: 10960384.
@article{Mahajan2015b,
title = {On the relationship between low-frequency normal modes and the large-scale conformational changes of proteins},
author = {Swapnil Mahajan and Yves-Henri Sanejouand},
url = {http://dx.doi.org/10.1016/j.abb.2014.12.020},
doi = {10.1016/j.abb.2014.12.020},
issn = {10960384},
year = {2015},
date = {2015-01-01},
journal = {Archives of Biochemistry and Biophysics},
volume = {567},
pages = {59--65},
publisher = {Elsevier Inc.},
abstract = {Normal mode analysis is a computational technique that allows to study the dynamics of biological macromolecules. It was first applied to small protein cases, more than thirty years ago. The interest in this technique then raised when it was realized that it can provide insights about the large-scale conformational changes a protein can experience, for instance upon ligand binding. As it was also realized that studying highly simplified protein models can provide similar insights, meaning that this kind of analysis can be both quick and simple to handle, several applications were proposed, in the context of various structural biology techniques. This review focuses on these applications, as well as on how the functional relevance of the lowest-frequency modes of proteins was established.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Teze, David; Daligault, Franck; Ferrières, Vincent; Sanejouand, Yves-Henri; Tellier, Charles
Semi-rational approach for converting a GH36 α-glycosidase into an α-transglycosidase Article de journal
Dans: Glycobiology, vol. 25, no. 4, p. 420–427, 2015, ISSN: 14602423.
@article{Teze2015,
title = {Semi-rational approach for converting a GH36 α-glycosidase into an α-transglycosidase},
author = {David Teze and Franck Daligault and Vincent Ferrières and Yves-Henri Sanejouand and Charles Tellier},
doi = {10.1093/glycob/cwu124},
issn = {14602423},
year = {2015},
date = {2015-01-01},
journal = {Glycobiology},
volume = {25},
number = {4},
pages = {420--427},
abstract = {A large number of retaining glycosidases catalyze both hydrolysis and transglycosylation reactions. In order to use them as catalysts for oligosaccharide synthesis, the balance between these two competing reactions has to be shifted toward transglycosylation. We previously designed a semi-rational approach to convert the Thermus thermophilus β-glycosidases into transglycosidases by mutating highly conserved residues located around the -1 subsite. In an attempt to verify that this strategy could be a generic approach to turn glycosidases into transglycosidases, Geobacillus stearothermophilus α-galactosidase (AgaB) was selected in order to obtain α-transgalactosidases. This is of particular interest as, to date, there are no efficient α-galactosynthases, despite the considerable importance of α-galactooligosaccharides. Thus, by site-directed mutagenesis on 14 AgaB residues, 26 single mutants and 22 double mutants were created and screened, of which 11 single mutants and 6 double mutants exhibited improved synthetic activity, producing 4-nitrophenyl α-d-galactopyranosyl-(1,6)-α-d-galactopyranoside in 26-57% yields against only 22% when native AgaB was used. It is interesting to note that the best variant was obtained by mutating a second-shell residue, with no direct interaction with the substrate or a catalytic amino acid. As this approach has proved to be efficient with both α- and β-glycosidases, it is a promising route to convert retaining glycosidases into transglycosidases.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Saumonneau, Amélie; Champion, Elise; Peltier-Pain, Pauline; Molnar-Gabor, Dora; Hendrickx, Johann; Tran, Vinh; Hederos, Markus; Dekany, Gyula; Tellier, Charles
Design of an α-l-transfucosidase for the synthesis of fucosylated HMOs Article de journal
Dans: Glycobiology, vol. 26, no. 3, p. 261–269, 2015, ISSN: 14602423.
@article{Saumonneau2015a,
title = {Design of an α-l-transfucosidase for the synthesis of fucosylated HMOs},
author = {Amélie Saumonneau and Elise Champion and Pauline Peltier-Pain and Dora Molnar-Gabor and Johann Hendrickx and Vinh Tran and Markus Hederos and Gyula Dekany and Charles Tellier},
doi = {10.1093/glycob/cwv099},
issn = {14602423},
year = {2015},
date = {2015-01-01},
journal = {Glycobiology},
volume = {26},
number = {3},
pages = {261--269},
abstract = {Human milk oligosaccharides (HMOs) are recognized as benefiting breast-fed infants in multiple ways. As a result, there is growing interest in the synthesis of HMOs mimicking their natural diversity. Most HMOs are fucosylated oligosaccharides. α-l-Fucosidases catalyze the hydrolysis of α-l-fucose from the non-reducing end of a glucan. They fall into the glycoside hydrolase GH29 and GH95 families. The GH29 family fucosidases display a classic retaining mechanism and are good candidates for transfucosidase activity. We recently demonstrated that the α-l-fucosidase from Thermotoga maritima (TmαFuc) from the GH29 family can be evolved into an efficient transfucosidase by directed evolution (Osanjo et al. 2007). In this work, we developed semi-rational approaches to design an α-l-transfucosidase starting with the α-l-fucosidase from commensal bacteria Bifidobacterium longum subsp. infantis (BiAfcB, Blon-2336). Efficient fucosylation was obtained with enzyme mutants (L321P-BiAfcB and F34I/L321P-BiAfcB) enabling in vitro synthesis of lactodifucotetraose, lacto-N-fucopentaose II, lacto-N-fucopentaose III and lacto-N-difucohexaose I. The enzymes also generated more complex HMOs like fucosylated para-lacto-N-neohexaose (F-p-LNnH) and mono- or difucosylated lacto-N-neohexaose (F-LNnH-I, F-LNnH-II and DF-LNnH). It is worth noting that mutation at these two positions did not result in a strong decrease in the overall activity of the enzyme, which makes these variants interesting candidates for large-scale transfucosylation reactions. For the first time, this work provides an efficient enzymatic method to synthesize the majority of fucosylated HMOs.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Craveur, Pierrick; Joseph, Agnel P; Esque, Jeremy; Narwani, Tarun J; Noël, Floriane; Shinada, Nicolas; Goguet, Matthieu; Leonard, Sylvain; Poulain, Pierre; Bertrand, Olivier; Faure, Guilhem; Rebehmed, Joseph; Ghozlane, Amine; Swapna, Lakshmipuram S; Bhaskara, Ramachandra M; Barnoud, Jonathan; Téletchéa, Stéphane; Jallu, Vincent; Cerny, Jiri; Schneider, Bohdan; Etchebest, Catherine; Srinivasan, Narayanaswamy; Gelly, Jean Christophe; de Brevern, Alexandre G
Protein flexibility in the light of structural alphabets Article de journal
Dans: Frontiers in Molecular Biosciences, vol. 2, no. MAY, p. 1–20, 2015, ISSN: 2296889X.
@article{Craveur2015,
title = {Protein flexibility in the light of structural alphabets},
author = {Pierrick Craveur and Agnel P Joseph and Jeremy Esque and Tarun J Narwani and Floriane Noël and Nicolas Shinada and Matthieu Goguet and Sylvain Leonard and Pierre Poulain and Olivier Bertrand and Guilhem Faure and Joseph Rebehmed and Amine Ghozlane and Lakshmipuram S Swapna and Ramachandra M Bhaskara and Jonathan Barnoud and Stéphane Téletchéa and Vincent Jallu and Jiri Cerny and Bohdan Schneider and Catherine Etchebest and Narayanaswamy Srinivasan and Jean Christophe Gelly and Alexandre G de Brevern},
doi = {10.3389/fmolb.2015.00020},
issn = {2296889X},
year = {2015},
date = {2015-01-01},
journal = {Frontiers in Molecular Biosciences},
volume = {2},
number = {MAY},
pages = {1--20},
abstract = {Protein structures are valuable tools to understand protein function. Nonetheless, proteins are often considered as rigid macromolecules while their structures exhibit specific flexibility, which is essential to complete their functions. Analyses of protein structures and dynamics are often performed with a simplified three-state description, i.e., the classical secondary structures. More precise and complete description of protein backbone conformation can be obtained using libraries of small protein fragments that are able to approximate every part of protein structures. These libraries, called structural alphabets (SAs), have been widely used in structure analysis field, from definition of ligand binding sites to superimposition of protein structures. SAs are also well suited to analyze the dynamics of protein structures. Here, we review innovative approaches that investigate protein flexibility based on SAs description. Coupled to various sources of experimental data (e.g., B-factor) and computational methodology (e.g., Molecular Dynamic simulation), SAs turn out to be powerful tools to analyze protein dynamics, e.g., to examine allosteric mechanisms in large set of structures in complexes, to identify order/disorder transition. SAs were also shown to be quite efficient to predict protein flexibility from amino-acid sequence. Finally, in this review, we exemplify the interest of SAs for studying flexibility with different cases of proteins implicated in pathologies and diseases.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Fontaine, Nicolas; Grondin-perez, Brigitte; Cadet, Frédéric; Offmann, Bernard; Fontaine, Nicolas; Grondin-perez, Brigitte; Cadet, Frédéric; Offmann, Bernard; Fontaine, Nicolas; Grondin-perez, Brigitte; Cadet, Frédéric; Offmann, Bernard
Modeling of a Cell-Free Synthetic System for Biohydrogen Production Article de journal
Dans: Journal of Computer Science & Systems Biology, vol. 8, no. 3, 2015, ISSN: 09747230.
@article{Fontaine2015,
title = {Modeling of a Cell-Free Synthetic System for Biohydrogen Production},
author = {Nicolas Fontaine and Brigitte Grondin-perez and Frédéric Cadet and Bernard Offmann and Nicolas Fontaine and Brigitte Grondin-perez and Frédéric Cadet and Bernard Offmann and Nicolas Fontaine and Brigitte Grondin-perez and Frédéric Cadet and Bernard Offmann},
doi = {10.4172/jcsb.1000181},
issn = {09747230},
year = {2015},
date = {2015-01-01},
journal = {Journal of Computer Science & Systems Biology},
volume = {8},
number = {3},
abstract = {Hydrogen is a good candidate for the next generation fuel with a high energy density and an environment friendly behavior in the energy production phase. Micro-organism based biological production of hydrogen currently suffers low hydrogen production yields because the living cells must sustain different cellular activities other than the hydrogen production to survive. To circumvent this, teams have explored the synthetic assembly of enzymes in-vitro in cell-free systems with specific functions. Such a synthetic cell-free system was recently devised by combining 13 different enzymes to synthesize hydrogen from cellulose or cellobiose with better yield than microorganism-based systems. We used methods based on differential equations calculations to investigate how the initial conditions and the kinetic parameters of the enzymes influenced the productivity of a such system and, through simulations, identified those conditions that would optimize hydrogen production starting with cellobiose as substrate. Further, if the kinetic parameters of the component enzymes of such a system are not known, we showed how, using artificial neural network, it is possible to identify alternative models that account for the rate of production of hydrogen. This work demonstrates how modeling can help in designing and characterizing cell-free systems in synthetic biology. A web-based simulator implementing our differential equations based model is provided freely as a service for non- commercial usage at http://www.bo-protscience.fr/h2.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Le-Bail, Patricia; Lorentz, C; Pencreac'h, G; Soultani-Vigneron, S; Pontoire, B; Giraldo, J. López L; Villeneuve, P; Hendrickx, Johann; Tran, Vinh
Trapping by amylose of the aliphatic chain grafted onto chlorogenic acid: Importance of the graft position Article de journal
Dans: Carbohydrate Polymers, vol. 117, p. 910–916, 2015, ISSN: 01448617.
@article{Le-Bail2015,
title = {Trapping by amylose of the aliphatic chain grafted onto chlorogenic acid: Importance of the graft position},
author = {Patricia Le-Bail and C Lorentz and G Pencreac'h and S Soultani-Vigneron and B Pontoire and J.López L Giraldo and P Villeneuve and Johann Hendrickx and Vinh Tran},
url = {http://dx.doi.org/10.1016/j.carbpol.2014.10.029},
doi = {10.1016/j.carbpol.2014.10.029},
issn = {01448617},
year = {2015},
date = {2015-01-01},
journal = {Carbohydrate Polymers},
volume = {117},
pages = {910--916},
publisher = {Elsevier Ltd.},
abstract = {5-Caffeoylquinic acid (chlorogenic acid), is classified in acid-phenols family and as polyphenolic compounds it possesses antioxidant activity. The oxydative modification of chlorogenic acid in foods may lead to alteration of their qualities; to counteract these degradation effects, molecular encapsulation was used to protect chlorogenic acid. Amylose can interact strongly with a number of small molecules, including lipids. In order to enable chlorogenic acid complexation by amylose, a C16 aliphatic chain was previously grafted onto the cycle of quinic acid. This work showed that for the two lipophilic derivatives of chlorogenic acid: hexadecyl chlorogenate obtained by alkylation and 3-O-palmitoyl chlorogenic acid obtained by acylation; only the 3-O-palmitoyl chlorogenic acid complexed amylose. The chlorogenic acid derivatives were studied by X-ray diffraction, differential scanning calorimetry and NMR to elucidate the interaction. By comparing the results with previous work on the complexation of amylose by 4-O-palmitoyl chlorogenic acid, the importance of the aliphatic chain position on the cycle of the quinic acid is clearly highlighted. A study in molecular modeling helped to understand the difference in behavior relative to amylose of these three derivatives of chlorogenic acid.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Sanejouand, Yves-Henri
Simplified flexibility analysis of proteins Chapitre d'ouvrage
Dans: Fuxreiter, Monika (Ed.): Computational Approaches to Protein Dynamics: From Quantum to Coarse-Grained Methods, Chapitre 5, p. 153–182, CRC Press, 2015.
@inbook{EQ1:SANEJOUAND:2015,
title = {Simplified flexibility analysis of proteins},
author = {Yves-Henri Sanejouand},
editor = {Monika Fuxreiter},
url = {http://arxiv.org/abs/1312.5639},
year = {2015},
date = {2015-01-01},
booktitle = {Computational Approaches to Protein Dynamics: From Quantum to Coarse-Grained Methods},
pages = {153--182},
publisher = {CRC Press},
chapter = {5},
abstract = {A simple way to get insights about the possible functional motions of a protein is to perform a normal mode analysis (NMA). Indeed, it has been shown that low-frequency modes thus obtained are often closely related to domain motions involved in protein function. Moreover, because protein low-frequency modes are known to be robust, NMA can be performed using coarse-grained models. As a consequence, it can be done for large ensembles of conformations as well as for large systems, like the ribosome, whole virus capsids, etc. Unexpectedly, on the high-frequency side, modes obtained with cutoff-based coarse-grained models also seem able to provide useful insights on protein dynamical properties.},
keywords = {},
pubstate = {published},
tppubtype = {inbook}
}
Velic, Denis; Couturier, Anthony M; Ferreira, Maria Tedim; Rodrigue, Amélie; Poirier, Guy G; Fleury, Fabrice; Masson, Jean-Yves
DNA Damage Signalling and Repair Inhibitors: The Long-Sought-After Achilles’ Heel of Cancer Article de journal
Dans: Biomolecules, vol. 5, no. 4, p. 3204–3259, 2015, ISSN: 2218-273X.
@article{biom5043204,
title = {DNA Damage Signalling and Repair Inhibitors: The Long-Sought-After Achilles’ Heel of Cancer},
author = {Denis Velic and Anthony M Couturier and Maria Tedim Ferreira and Amélie Rodrigue and Guy G Poirier and Fabrice Fleury and Jean-Yves Masson},
url = {https://www.mdpi.com/2218-273X/5/4/3204},
doi = {10.3390/biom5043204},
issn = {2218-273X},
year = {2015},
date = {2015-01-01},
journal = {Biomolecules},
volume = {5},
number = {4},
pages = {3204--3259},
abstract = {For decades, radiotherapy and chemotherapy were the two only approaches exploiting DNA repair processes to fight against cancer. Nowadays, cancer therapeutics can be a major challenge when it comes to seeking personalized targeted medicine that is both effective and selective to the malignancy. Over the last decade, the discovery of new targeted therapies against DNA damage signalling and repair has offered the possibility of therapeutic improvements in oncology. In this review, we summarize the current knowledge of DNA damage signalling and repair inhibitors, their molecular and cellular effects, and future therapeutic use.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Delavault, Philippe
Knowing the Parasite: Biology and Genetics of Orobanche Article de journal
Dans: Helia, vol. 38, no. 62, p. 15-29, 2015.
@article{RN33,
title = {Knowing the Parasite: Biology and Genetics of Orobanche},
author = {Philippe Delavault},
url = {https://doi.org/10.1515/helia-2014-0030},
doi = {doi:10.1515/helia-2014-0030},
year = {2015},
date = {2015-01-01},
urldate = {2015-01-01},
journal = {Helia},
volume = {38},
number = {62},
pages = {15-29},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Lechat, Marc-Marie; Brun, Guillaume; Montiel, Grégory; Véronési, Christophe; Simier, Philippe; Thoiron, Séverine; Pouvreau, Jean-Bernard; Delavault, Philippe
Seed response to strigolactone is controlled by abscisic acid-independent DNA methylation in the obligate root parasitic plant, Phelipanche ramosa L. Pomel Article de journal
Dans: J Exp Bot, vol. 66, no. 11, p. 3129-40, 2015, ISSN: 0022-0957 (Print) 0022-0957.
@article{RN22,
title = {Seed response to strigolactone is controlled by abscisic acid-independent DNA methylation in the obligate root parasitic plant, Phelipanche ramosa L. Pomel},
author = {Marc-Marie Lechat and Guillaume Brun and Grégory Montiel and Christophe Véronési and Philippe Simier and Séverine Thoiron and Jean-Bernard Pouvreau and Philippe Delavault},
url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4449535/pdf/erv119.pdf},
doi = {10.1093/jxb/erv119},
issn = {0022-0957 (Print) 0022-0957},
year = {2015},
date = {2015-01-01},
urldate = {2015-01-01},
journal = {J Exp Bot},
volume = {66},
number = {11},
pages = {3129-40},
abstract = {Seed dormancy release of the obligate root parasitic plant, Phelipanche ramosa, requires a minimum 4-day conditioning period followed by stimulation by host-derived germination stimulants, such as strigolactones. Germination is then mediated by germination stimulant-dependent activation of PrCYP707A1, an abscisic acid catabolic gene. The molecular mechanisms occurring during the conditioning period that silence PrCYP707A1 expression and regulate germination stimulant response are almost unknown. Here, global DNA methylation quantification associated with pharmacological approaches and cytosine methylation analysis of the PrCYP707A1 promoter were used to investigate the modulation and possible role of DNA methylation during the conditioning period and in the PrCYP707A1 response to GR24, a synthetic strigolactone analogue. Active global DNA demethylation occurs during the conditioning period and is required for PrCYP707A1 activation by GR24 and for subsequent seed germination. Treatment with 5-azacytidine, a DNA-hypomethylating molecule, reduces the length of the conditioning period. Conversely, hydroxyurea, a hypermethylating agent, inhibits PrCYP707A1 expression and seed germination. Methylated DNA immunoprecipitation followed by PCR experiments and bisulfite sequencing revealed that DNA demethylation particularly impacts a 78-nucleotide sequence in the PrCYP707A1 promoter. The results here demonstrate that the DNA methylation status during the conditioning period plays a crucial role independently of abscisic acid in the regulation of P. ramosa seed germination by controlling the strigolactone-dependent expression of PrCYP707A1.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Molinero-Ruiz, Leire; Delavault, Philippe; Pérez-Vich, Begoña; Pacureanu-Joita, Maria; Bulos, Mariano; Altieri, Emiliano; Domínguez, Juan
History of the race structure of Orobanche cumana and the breeding of sunflower for resistance to this parasitic weed: A review Article de journal
Dans: Spanish Journal of Agricultural Research, vol. 13, no. 4, p. e10R01, 2015.
@article{RN34,
title = {History of the race structure of Orobanche cumana and the breeding of sunflower for resistance to this parasitic weed: A review},
author = {Leire Molinero-Ruiz and Philippe Delavault and Begoña Pérez-Vich and Maria Pacureanu-Joita and Mariano Bulos and Emiliano Altieri and Juan Domínguez},
url = {https://revistas.inia.es/index.php/sjar/article/view/8080
https://revistas.inia.es/index.php/sjar/article/download/8080/2588},
doi = {10.5424/sjar/2015134-8080},
year = {2015},
date = {2015-01-01},
urldate = {2015-01-01},
journal = {Spanish Journal of Agricultural Research},
volume = {13},
number = {4},
pages = {e10R01},
abstract = {Broomrape, caused by Orobanche cumana, has affected sunflowers since the early 20th century in Eastern Europe. Currently, it limits sunflower oil production in Southern and Eastern Europe and in some areas of Asia, causing around 50% seed losses when susceptible hybrids are grown. Covered in this review are aspects such as: biological processes that are common to Orobanche spp. and/or particular to O. cumana in sunflower, genetic resistance and its mechanisms, races of the parasite identified in different countries throughout the time and their increasing virulence, and breeding for resistance to some herbicides as a novel control option. The main purpose is to present an updated and, as far as possible, complete picture of the way both the parasitic weed and its host crop have evolved in time, and how they co-exist in the current agriculture. Additionally, we propose a system for determining the races of the parasite that can be internationally adopted from now. In the context of minimal harmful effects on the environment, changing patterns of land use in farming systems, and global environment changes, the final goal of this work is to provide all those interested in parasites from field crops and their integrated management compiled information on the sunflower – O. cumana system as a case study.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}