Éditeur(s) : HAL CCSD Ecole nationale du génie rural
Résumé :  
La zoochorie (transport des graines par les animaux) joue un rôle prépondérant dans les forêts tropicales. L'action de la faune sur la régénération forestière est analysée en fonction des co-évolutions s'étant développées entre plantes et animaux frugivores. Différentes associations entre certains types de fruits et certains groupes de mammifères ou d'oiseaux sont décrites, en insistant sur la spécificité de la dissémination qui en résulte. Celle-ci est le plus souvent hétérogène dans des sites plutôt favorables au développement des plantules. Ces diverses modalités de dissémination concourent autant à la colonisation de sites nouveaux qu'au maintien des espèces végétales dans un environnement donné. Dans le cas des plantes pionnières, la distribution est plus homogène et contribue à alimenter la banque de graines du sol. Ces graines entrent en dormance et ne germeront qu'après une ouverture de la canopée. La chasse des animaux frugivores pourrait avoir de lourdes conséquences pour certaines espèces végétales notamment.
ISSN: 0035-2829

hal-01032118
https://hal.archives-ouvertes.fr/hal-01032118

Éditeur(s) : HAL CCSD Society for the Study of Reproduction
Résumé : International audience
Transcription factor GATA4 is required for the development and function of the mammalian gonads. We first reported that the GATA4 gene in both human and rodents is expressed as two major alternative transcripts that differ solely in their first untranslated exon (exon 1a vs. exon 1b). We had also showed by quantitative PCR that in mouse tissues, both Gata4 exon 1a- and 1b-containing transcripts are present in all sites that are normally positive for GATA4 protein. In adult tissues, exon 1a-containing transcripts generally predominate. A notable exception, however, is the testis where the Gata4 exon 1a and 1b transcripts exhibit a similar level of expression. We now confirm by in situ hybridization analysis that each transcript is also strongly expressed during gonad differentiation in both sexes in the rat. To gain further insights into how Gata4 gene expression is controlled, we characterized the mouse Gata4 promoter sequence located upstream of exon 1b. In vitro studies revealed that the Gata4 1b promoter is less active than the 1a promoter in several gonadal cell lines tested. Whereas we have previously shown that endogenous Gata4 transcription driven by the 1a promoter is dependent on a proximally located Ebox motif, we now show using complementary in vitro and in vivo approaches that Gata4 promoter 1b-directed expression is regulated by GATA4 itself. Thus, Gata4 transcription in the gonads and other tissues is ensured by distinct promoters that are regulated differentially and independently.
ISSN: 0006-3363

hal-01010626
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01010626
DOI : 10.1095/biolreprod.113.113290
PUBMED : 24352556

Éditeur(s) : HAL CCSD SAGE Publications (UK and US)
Résumé : International audience
Molecular evolutionary analysis is an efficient method to predict and/or validate amino acid substitutions that could lead to a genetic disease and to highlight residues and motifs that could play an important role in the protein structure and/or function. We have applied such analysis to amelotin (AMTN), a recently identified enamel protein in the rat, mouse, and humans. An in silico search for AMTN provided 42 new mammalian sequences that were added to the 3 published sequences with which we performed the analysis using a dataset representative of all lineages (circa 220 million years of evolution), including 2 enamel-less species, sloth and armadillo. During evolution, of the 209 residues of human AMTN, 17 were unchanged and 34 had conserved their chemical properties. Substituting these important residues could lead to amelogenesis imperfecta (AI). Also, AMTN possesses a well-conserved signal peptide, 2 conserved motifs whose function is certainly important but unknown, and a putative phosphorylation site (SXE). In addition, the sequences of the 2 enamel-less species display mutations revealing that AMTN underwent pseudogenization, which suggests that AMTN is an enamel-specific protein.
ISSN: 0022-0345

hal-01545488
https://hal.archives-ouvertes.fr/hal-01545488
DOI : 10.1177/0022034512460551

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The strikingly complex structural organization of the mammalian testis in vivo creates particular difficulties for studies of its organization, function and regulation. These difficulties are particularly pronounced for investigations of the molecular communication networks within the seminiferous tubules that govern spermatogenesis. The use of classical molecular and cell biology approaches to unravel this complexity has proved problematic, due to difficulties in maintaining differentiated germ cells in vitro, in particular. The lack of a suitable testing ground has led to a greater reliance on high-quality proteomic and genomic analyses as a prelude to the in vitro antx1d in vivo testing of hypotheses. In this study, we highlight the options currently available for research, as used in our laboratory, in which proteomic and integrative genomic strategies are applied to the study of spermatogenesis in mammals. We will comment on results providing insight into the molecular mechanisms underlying normal and pathological spermatogenesis and new perspectives for the treatment of male infertility in humans. Finally, we will discuss the relevance of our strategies and the unexpected potential and perspectives they offer to teams involved in the study of male reproduction, within the framework of the Human Proteome Project. SIGNIFICANCE: Integrative genomics is becoming a powerful strategy for discovering the biological significance hidden in proteomic datasets. This work introduces some of the integrative genomic concepts and works used by our team to gain new insight into mammalian spermatogenesis, a remarkably sophisticated process. We demonstrate the relevance of these integrative approaches to understand the cellular cross talks established between the somatic Sertoli cells and the germ cell lineage, within the seminiferous epithelium. Our work also contributes to new knowledge on the pathophysiology of testicular function, with promising clinical applications. This article is part of a Special Issue entitled: 20years of Proteomics in memory of Viatliano Pallini. Guest Editors: Luca Bini, Juan J. Calvete, Natacha Turck, Denis Hochstrasser and Jean-Charles Sanchez.
ISSN: 1874-3919

hal-01063931
https://hal.archives-ouvertes.fr/hal-01063931
DOI : 10.1016/j.jprot.2014.04.013
PUBMED : 24751586

Éditeur(s) : HAL CCSD Universidad Complutense de Madrid
Résumé : The Lodève Permian synrift sequence is represented by thick stacked climate-controled playa cycles which have been constrained by structural, sedimentological, geochemical and paleontological processes. The present paper merges the different results in order to better constrain the dynamics and palaeoecologycal evolution of the playa system from Late Cisuralian to Early Lopingian time. In this depositional environment, thining upwards sheet-flood sequences represent flooding events; they are relayed by ephemeral ponding, suspension settling and limited carbonate precipitation accompanied by large amounts of shallow to subaerial sedimentary structures... (Ver más) (current and wind ripples, desiccation cracks, rain drops, etc.). The aridity of the climate contrasts with the surprising abundance of the fauna encountered into carbonate-rich silty-clay playa-lake deposits. Ephemeral pools are colonized by numerous shellfish: Choncostraca, Triopsids, and Insects, which led to intense burrowing of the overbank deposits (Scoyenia facies). Tetrapods are common and dominated by several types of reptiles after footprints: Pelycosauria, Parareptilia and Lepidosauria in the Rabejac Fm, and Mammalian reptiles (Therapsida) on the top of the fluvial deposits of the Salagou Fm near La Lieude farm. In addition, elements of a weighty herbivorous Pelycosaurian and a small amphibian Tupilakosaurid, only described in the Triassic before, have been also found in the Upper part of the Permian series of this sector.
ISSN: 1698-6180

hal-00411539
https://hal.archives-ouvertes.fr/hal-00411539

Éditeur(s) : HAL CCSD
Résumé : International audience
The epigenetic mark 5-hydroxymethylcytosine (5hmC) is a cytosine modification that is abundant in the central nervous system of mammals and which results from 5-methylcytosine oxidation by TET enzymes. Such a mark is suggested to play key roles in the regulation of chromatin structure and gene expression. However, its precise functions still remain poorly understood and information about its distribution in non-mammalian species is still lacking. Here, the distribution of 5hmC was investigated in the brain of adult zebrafish, African claw frog, and mouse in a comparative manner. We show that zebrafish neurons are endowed with high levels of 5hmC, whereas quiescent or proliferative neural progenitors show low to undetectable levels of the modified cytosine. In the brain of larval and juvenile Xenopus, 5hmC is also detected in neurons, while ventricular proliferative cells do not display this epigenetic mark. Similarly, 5hmC is enriched in neurons compared to neural progenitors of the ventricular zone in the mouse developing cortex. Interestingly, 5hmC colocalized with the methylated DNA binding protein MeCP2 and with the active chromatin histone modification H3K4me2 in mouse neurons. Taken together, our results show an evolutionarily conserved cerebral distribution of 5hmC between fish and tetrapods and reinforce the idea that 5hmC fulfills major functions in the control of chromatin activity in vertebrate neurons. J. Comp. Neurol. 525:478-497, 2017. © 2016 Wiley Periodicals, Inc.
Journal of Comparative Neurology

hal-01439354
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01439354
DOI : 10.1002/cne.24077
PUBMED : 27414756

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
Mammalian spermatogenesis, which takes place in complex testicular structures called seminiferous tubules, is a highly specialized process controlled by the integration of juxtacrine, paracrine and endocrine information. Within the seminiferous tubules, the germ cells and Sertoli cells are surrounded by testicular fluid (TF), which probably contains most of the secreted proteins involved in crosstalk between these cells. It has already been established that germ cells can modulate somatic Sertoli cell function through the secretion of diffusible factors. We studied the germ cell secretome, which was previously considered inaccessible, by analyzing the TF collected by microsurgery in an "integrative omics" strategy combining proteomics, transcriptomics, genomics and interactomics data. This approach identified a set of proteins preferentially secreted by Sertoli cells or germ cells. An interaction network analysis revealed complex, interlaced cell-cell dialog between the secretome and membranome of seminiferous cells, mediated via the TF. We then focused on germ cell-secreted candidate proteins, and we identified several potential interacting partners located on the surface of Sertoli cells. Two interactions, APOH/CDC42 and APP/NGFR, were validated in situ, in a proximity ligation assay (PLA). Our results provide new insight into the crosstalk between germ cells and Sertoli cells occurring during spermatogenesis. Our findings also demonstrate that this "integrative omics" strategy is powerful enough for data mining and highlighting meaningful cell-cell communication events between different types of cells in a complex tissue, via a biological fluid. This integrative strategy could be applied more widely, to gain access to secretomes that have proved difficult to study whilst avoiding the limitations of in vitro culture.
ISSN: 1932-6203

hal-01129957
https://hal.archives-ouvertes.fr/hal-01129957
https://hal.archives-ouvertes.fr/hal-01129957/document
https://hal.archives-ouvertes.fr/hal-01129957/file/2014_FChalmel_PlosOne_%7B1236BFCE-4830-400D-B816-4B6651311900%7D.pdf
DOI : 10.1371/journal.pone.0104418

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
Tuftelin (TUFT1) is an acidic, phosphorylated glycoprotein, initially discovered in developing enamel matrix. TUFT1 is expressed in many mineralized and non-mineralized tissues. We performed an evolutionary analysis of 82 mammalian TUFT1 sequences to identify residues and motifs that were conserved during 220 million years (Ma) of evolution. We showed that 168 residues (out of the 390 residues composing the human TUFT1 sequence) are under purifying selection. Our analyses identified several, new, putatively functional domains and confirmed previously described functional domains, such as the TIP39 interaction domain, which correlates with nuclear localization of the TUFT1 protein, that was demonstrated in several tissues. We also identified several sites under positive selection, which could indicate evolutionary changes possibly related to the functional diversification of TUFT1 during evolution in some lineages. We discovered that TUFT1 and MYZAP (myocardial zonula adherens protein) share a common ancestor that was duplicated circa 500 million years ago. Taken together, these findings expand our knowledge of TUFT1 evolution and provide new information that will be useful for further investigation of TUFT1 functions.
ISSN: 0022-2844

hal-01516886
http://hal.upmc.fr/hal-01516886
http://hal.upmc.fr/hal-01516886/document
http://hal.upmc.fr/hal-01516886/file/Delgado_2017_Evolutionary.pdf
DOI : 10.1007/s00239-017-9789-5

Éditeur(s) : HAL CCSD Taylor & Francis
Résumé : International audience
The functional organization of the circadian system and the location of the main circadian oscillators vary through phylogeny. Present study investigates by in situ hybridization the anatomical location of the clock gene gPer1b in forebrain and midbrain, pituitary, and in two peripheral locations, the anterior intestine and liver, in a teleost fish, the goldfish (Carassius auratus). Moreover, the daily expression profiles of this gene were also studied by quantitative Real Time-PCR. Goldfish were maintained under a 12L–12D photoperiod and fed daily at 2 h after lights were switched on. A wide distribution of gPer1b mRNA in goldfish brain and pituitary was found in telencephalon, some hypothalamic nuclei (including the homologous to mammalian SCN), habenular nucleus, optic tectum, cerebellum and torus longitudinalis. Moreover, gPer1b expression was observed, for the first time in teleosts, in the pituitary, liver and anterior intestine. Day/night differences in gper1b mRNA abundance were found by in situ hybridization, with higher signal at nighttime that correlates with the results obtained by RT-PCR, where a rhythmic gPer1b expression was found in all tissues with acrophases at the end of the night. Amplitudes of gper1b rhythms vary among tissues, being higher in liver and intestine than in the brain, maybe because different cues entrain clocks in these locations. These results support the existence of functional clocks in many central and peripheral locations in goldfish coordinated, ticking at the same time
ISSN: 0742-0528

hal-01197353
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01197353
DOI : 10.3109/07420528.2015.1049615
PUBMED : 26171989

Éditeur(s) : HAL CCSD
Résumé : International audience
Studying the ecology of Leishmania parasites is essential for understanding and controlling the epidemiology of the diseases they cause. Despite their abundance and diversity in neotropical forests, few studies have been conducted to investigate the potential involvement of Chiroptera in the Leishmania pathogenic complexes. However, phlebotomine sand flies are known to colonize the same anthropized habitat, are attracted to bats, and are able to transmit trypanosomatids. Thus, 216 bats representing 29 species were sampled in the field in different primary and secondary forests of French Guiana where human cutaneous leishmaniases have been reported, together with 62 non-volant mammals. A series of 411 tissue samples representing 47 mammalian species were cultured and screened for the presence of Leishmania spp. by a genus-specific polymerase chain reaction. All 278 individuals surveyed were negative. Thus, bats do not appear to be involved in the Lishmania parasitic cycles in the Guyanas.
The American journal of tropical medicine and hygiene

halsde-00339305
https://hal.archives-ouvertes.fr/halsde-00339305

Éditeur(s) : HAL CCSD
Résumé : International audience
The study of complex biological processes requires to forgo simplified models for extensive ones. Yet, these models' size and complexity place them beyond understanding. Their analysis requires new methods for identifying general patterns. The Transforming Growth Factor TGF-β is a multifunctional cytokine that regulates mammalian cell development , differentiation, and homeostasis. Depending on the context, it can play the antagonistic roles of growth inhibitor or of tumor promoter. Its context-dependent pleiotropic nature is associated with complex sig-naling pathways. The most comprehensive model of TGF-β-dependent signaling is composed of 15,934 chains of reactions (trajectories) linking TGF-β to at least one of its 159 target genes. Identifying functional patterns in such a network requires new automated methods. This article presents a framework for identifying groups of similar trajec-tories composed of the same molecules using an exhaustive and without prior assumptions approach. First, the trajectories were clustered using the Relevant Set Correlation model, a shared nearest-neighbors clustering method. Five groups of trajectories were identified. Second, for each cluster the over-represented molecules were determined by scoring the frequency of each molecule implicated in trajectories. Third, Gene set enrichment analysis on the clusters of trajectories revealed some specific TGF-β-dependent biological processes, with different clusters associated to the antagonists roles of TGF-β. This confirms that our approach yields biologically-relevant results. We developed a web interface that facilitates graph visualization and analysis. Our clustering-based method is suitable for identifying families of functionally-similar trajectories in the TGF-β signaling network. It can be generalized to explore any large-scale biological pathways.
CMSB 2017 - 15th International Conference on Computational Methods in Systems Biology
Darmstadt, France

hal-01559249
https://hal.archives-ouvertes.fr/hal-01559249
https://hal.archives-ouvertes.fr/hal-01559249/document
https://hal.archives-ouvertes.fr/hal-01559249/file/JeanCoquet_CMSB.pdf

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
From 15 to 17 June 2011, a dedicated workshop was held on the subject of in vitro models for mammalian spermatogenesis and their applications in toxicological hazard and risk assessment. The workshop was sponsored by the Dutch ASAT initiative (Assuring Safety without Animal Testing), which aims at promoting innovative approaches toward toxicological hazard and risk assessment on the basis of human and in vitro data, and replacement of animal studies. Participants addressed the state of the art regarding human and animal evidence for compound mediated testicular toxicity, reviewed existing alternative assay models, and brainstormed about future approaches, specifically considering tissue engineering. The workshop recognized the specific complexity of testicular function exemplified by dedicated cell types with distinct functionalities, as well as different cell compartments in terms of microenvironment and extracellular matrix components. This complexity hampers quick results in the realm of alternative models. Nevertheless, progress has been achieved in recent years, and innovative approaches in tissue engineering may open new avenues for mimicking testicular function in vitro. Although feasible, significant investment is deemed essential to be able to bring new ideas into practice in the laboratory. For the advancement of in vitro testicular toxicity testing, one of the most sensitive end points in regulatory reproductive toxicity testing, such an investment is highly desirable.
ISSN: 0890-6238

hal-00876979
https://hal.archives-ouvertes.fr/hal-00876979
DOI : 10.1016/j.reprotox.2013.04.004
PUBMED : 23612449

Éditeur(s) : HAL CCSD
Résumé : Due to their phylogenetic position outside from Bilateria, cnidarians and ctenophores are key phyla to understanding the origin and early evolution of molecular mechanisms, cell types, or body plan features at the level of Metazoa. Unlike other non-bilaterian phyla (sponges and placozoans), they possess neurons and muscle cells. The first part of my work relates to the problem of the origin of the metazoan nervous system. Recent studies have suggested a dual origin for nerve cells, with ctenophore neurons having emerged independently from those of cnidarians and bilaterians. This hypothesis relies on phylogenomic analyses supporting ctenophores as sister-group to all other metazoans, and on the purported absence in ctenophores of almost all well-known neuro-transmission systems, including the cholinergic system. Refuting this claim, I present substantial evidence in favour of acetylcholine (Ach) being used in the ctenophore Pleurobrachia pileus as an extra-cellular messenger, including within the nervous system. This conclusion arises from the conjunction of multiple approaches at the molecular scale (orthology analyses, Ach immuno-localisation, gene in situ hybridisation), at the cellular scale (calcium imaging on muscle cells exposed to Ach) and at the organism scale (pharmacological treatments with an Ach analogue and Ach antagonists). In the second part of my thesis, I address the conservation of molecular mechanisms involved in the control of cellular proliferation. Notably, the Hippo pathway is known for its role in bilaterians in the negative control of cellular proliferation. I show that components of this pathway are conserved in Pleurobrachia pileus and in Clytia hemisphaerica and that the nuclear vs. cytoplasmic localisation of the transcriptional co-factor Yorkie is correlated to the extent of proliferation within C. hemisphaerica tissues. Finally, RNAseq differential gene expression analyses along a cellular conveyor belt of the C. hemisphaerica medusa suggests a tendency for conservation of function among a set of genes whose mammalian orthologues have documented roles in the arrest of cellular proliferation.
Les Cnidaires et les Cténaires sont deux embranchements extérieurs aux Bilatériens qui, de par leur position phylogénétique, constituent des modèles d'étude cruciaux pour comprendre l'origine et l'évolution de mécanismes moléculaires ou encore de types cellulaires à grande échelle chez les Métazoaires. Ils sont les deux seuls embranchements non-Bilatériens à posséder des cellules nerveuses ainsi que des cellules musculaires. La première partie de mon travail de thèse s'inscrit dans le contexte de la compréhension de l'origine du système nerveux des Métazoaires. Des études récentes suggèrent une origine double du système nerveux ; ainsi celui des Cténaires aurait été acquis de manière convergente par rapport à celui des Cnidaires et des Bilatériens. Cela repose sur des données récentes de phylogénomique proposant les Cténaires en tant que groupe-frère de tous les autres Métazoaires et sur l'absence supposée chez les Cténaires de quasiment tous les systèmes de neurotransmission connus y compris le système cholinergique. A l'encontre de ces hypothèses, j'ai pu mettre en évidence l'existence d'un système cholinergique chez le Cténaire Pleurobrachia pileus ainsi que son étroite association avec le système nerveux. Cette conclusion repose sur une multiplicité d'approches à l'échelle moléculaire (analyses d'orthologie, immunolocalisation, hybridations in situ), cellulaire (imagerie calcique) et de l'organisme (approche pharmacologique). Dans la seconde partie de ma thèse, j'aborde la question de la conservation des mécanismes moléculaires impliqués dans le contrôle de la prolifération cellulaire à l'échelle des Métazoaires. J'ai pu mettre en évidence la conservation des acteurs.
https://tel.archives-ouvertes.fr/tel-01633223

NNT : 2015PA066629
tel-01633223
https://tel.archives-ouvertes.fr/tel-01633223
https://tel.archives-ouvertes.fr/tel-01633223v2/document
https://tel.archives-ouvertes.fr/tel-01633223/file/2015PA066629.pdf

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
Mammalian spermatogenesis, which takes place in complex testicular structures called seminiferous tubules, is a highly specialized process controlled by the integration of juxtacrine, paracrine and endocrine information. Within the seminiferous tubules, the germ cells and Sertoli cells are surrounded by testicular fluid (TF), which probably contains most of the secreted proteins involved in crosstalk between these cells. It has already been established that germ cells can modulate somatic Sertoli cell function through the secretion of diffusible factors. We studied the germ cell secretome, which was previously considered inaccessible, by analyzing the TF collected by microsurgery in an "integrative omics" strategy combining proteomics, transcriptomics, genomics and interactomics data. This approach identified a set of proteins preferentially secreted by Sertoli cells or germ cells. An interaction network analysis revealed complex, interlaced cell-cell dialog between the secretome and membranome of seminiferous cells, mediated via the TF. We then focused on germ cell-secreted candidate proteins, and we identified several potential interacting partners located on the surface of Sertoli cells. Two interactions, APOH/CDC42 and APP/NGFR, were validated in situ, in a proximity ligation assay (PLA). Our results provide new insight into the crosstalk between germ cells and Sertoli cells occurring during spermatogenesis. Our findings also demonstrate that this "integrative omics" strategy is powerful enough for data mining and highlighting meaningful cell-cell communication events between different types of cells in a complex tissue, via a biological fluid. This integrative strategy could be applied more widely, to gain access to secretomes that have proved difficult to study whilst avoiding the limitations of in vitro culture.
PLoS ONE

hal-01063901
https://hal.archives-ouvertes.fr/hal-01063901
DOI : 10.1371/journal.pone.0104418
PUBMED : 25111155

Éditeur(s) : HAL CCSD
Résumé : International audience
Spermatogenesis is a highly sophisticated process involved in the transmission of genetic heritage. It includes halving ploidy, repackaging of the chromatin for transport, and the equipment of developing spermatids and eventually spermatozoa with the advanced apparatus (e.g., tightly packed mitochondrial sheat in the mid piece, elongating of the tail, reduction of cytoplasmic volume) to elicit motility once they reach the epididymis. Mammalian spermatogenesis is divided into three phases. In the first the primitive germ cells or spermatogonia undergo a series of mitotic divisions. In the second the spermatocytes undergo two consecutive divisions in meiosis to produce haploid spermatids. In the third the spermatids differentiate into spermatozoa in a process called spermiogenesis. Paracrine, autocrine, juxtacrine, and endocrine pathways all contribute to the regulation of the process. The array of structural elements and chemical factors modulating somatic and germ cell activity is such that the network linking the various cellular activities during spermatogenesis is unimaginably complex. Over the past two decades, advances in genomics have greatly improved our knowledge of spermatogenesis, by identifying numerous genes essential for the development of functional male gametes. Large-scale analyses of testicular function have deepened our insight into normal and pathological spermatogenesis. Progress in genome sequencing and microarray technology have been exploited for genome-wide expression studies, leading to the identification of hundreds of genes differentially expressed within the testis. However, although proteomics has now come of age, the proteomics-based investigation of spermatogenesis remains in its infancy. Here, we review the state-of-the-art of large-scale proteomic analyses of spermatogenesis, from germ cell development during sex determination to spermatogenesis in the adult. Indeed, a few laboratories have undertaken differential protein profiling expression studies and/or systematic analyses of testicular proteomes in entire organs or isolated cells from various species. We consider the pros and cons of proteomics for studying the testicular germ cell gene expression program. Finally, we address the use of protein datasets, through integrative genomics (i.e., combining genomics, transcriptomics, and proteomics), bioinformatics, and modelling.
Systems Biology in Reproductive Medicine

hal-00877749
https://hal.archives-ouvertes.fr/hal-00877749
DOI : 10.3109/19396368.2012.691943
PUBMED : 22788530

Éditeur(s) : HAL CCSD National Academy of Sciences
Résumé : International audience
We applied single-molecule photobleaching to investigate the stoichiometry of human Orai1 and Orai3 channels tagged with eGFP and expressed in mammalian cells. Orai1 was detected predominantly as dimers under resting conditions and as tetramers when coexpressed with C-STIM1 to activate Ca(2+) influx. Orai1 was also found to be tetrameric when coexpressed with STIM1 and evaluated following fixation. We show that fixation rapidly causes release of Ca(2+), redistribution of STIM1 to the plasma membrane, and STIM1/Orai1 puncta formation, and may cause the channel to be in the activated state. Consistent with this possibility, Orai1 was found predominantly as a dimer when coexpressed with STIM1 in living cells under resting conditions. We further show that Orai3, like Orai1, is dimeric under resting conditions and is predominantly tetrameric when activated by C-STIM1. Interestingly, a dimeric Orai3 stoichiometry was found both before and during application of 2-aminoethyldiphenyl borate (2-APB) to activate a nonselective cation conductance in its STIM1-independent mode. We conclude that the human Orai1 and Orai3 channels undergo a dimer-to-tetramer transition to form a Ca(2+)-selective pore during store-operated activation and that Orai3 forms a dimeric nonselective cation pore upon activation by 2-APB.
ISSN: 0027-8424

hal-00873833
https://hal.archives-ouvertes.fr/hal-00873833
DOI : 10.1073/pnas.1114814108
PUBMED : 21987805

Éditeur(s) : HAL CCSD Histochemical Society
Résumé : International audience
The galectin-4 protein is mostly expressed in the digestive tract and is associated with lipid raft stabilization, protein apical trafficking, wound healing, and inflammation. While most mammalian species, including humans, have a single Lgals4 gene, some mice have two paralogues: Lgals4 and Lgals6. So far, their significant similarities have hindered the analysis of their respective expression and function. We took advantage of two antibodies that discriminate between the galectin-4 and galectin-6 proteins to document their patterns of expression in the normal and the dextran sodium sulfate (DSS)-damaged digestive tract in the mouse. In the normal digestive tract, their pattern of expression from tongue to colon is quite similar, which suggests functional redundancy. However, the presence of galectin-4, but not galectin-6, in the lamina propria of the DSS-damaged colon, its association with luminal colonic bacteria, and differences in subcellular localization of these proteins suggest that they also have distinct roles in the normal and the damaged mouse digestive tract. Our results provide a rare example of ancestral and derived functions evolving after tandem gene duplication.
ISSN: 0022-1554

hal-01544764
https://hal.archives-ouvertes.fr/hal-01544764
DOI : 10.1369/0022155413478612

Éditeur(s) : HAL CCSD National Academy of Sciences
Résumé : International audience
Stem cells are pivotal for development and tissue homeostasis of multicellular animals, and the quest for a gene toolkit associated with the emergence of stem cells in a common ancestor of all metazoans remains a major challenge for evolutionary biology. We reconstructed the conserved gene repertoire of animal stem cells by transcriptomic profiling of totipotent archeocytes in the demosponge Ephydatia fluviatilis and by tracing shared molecular signatures with flatworm and Hydra stem cells. Phylostratigraphy analyses indicated that most of these stem-cell genes predate animal origin, with only few metazoan innovations, notably including several partners of the Piwi machinery known to promote genome stability. The ancestral stem-cell transcriptome is strikingly poor in transcription factors. Instead, it is rich in RNA regulatory actors, including components of the ``germ-line multipotency program'' and many RNA-binding proteins known as critical regulators of mammalian embryonic stem cells.
ISSN: 0027-8424

hal-01544480
https://hal.archives-ouvertes.fr/hal-01544480
DOI : 10.1073/pnas.1514789112