Éditeur(s) : Université des Antilles AREBio Groupe de recherche BIOSPHERES : BIOlogie, Sciences Physiques & Humaines pour les énergies Renouvelables, l
Extrait de : 1er colloque international BIOSPHERES, du 18 au 20 juin 2019. Université des Antilles
Description : Drosophila often offers many advantages as an experimental organism. The dead ringer (dri) gene of drosophila melanogaster is a member of the recently discovered ARID-box family of eukaryotic genes that encodes proteins with a conserved DNA-binding domain. dri itself is highly well conserved with specific orthologs from human to yeast genomes. This family include ARID3A, 3B and 3C with have role in embryonic pattening, cell lineage gene regulation, cell cycle control, transcriptional regulation and chromatin structure modification. We first showed that the gene encoding ARID3A also known as Bright (B cell regulator of immunoglobulin heavy chain transcription) play critical roles in B-cell development and SATB1 in T-cell transcription regulation. In this international workshops we will expose a comprehensive understanding of these molecules and better knowledge of their specific targets and function-interactions in controlling cell fate decisions and development. In addition, dri have homology with the Aedes aegypti mosquitoes which had ability to carry and spread disease to human. More than half of the world?s population live in areas where this mosquito species is present, including Martinique. Sustained mosquito control efforts are important to prevent outbreaks from Dengue, Chikungunya, malaria, zika diseases. Discovering the functions of AT-rich genes in preventing illness from mosquito is the central goal for raising working progress hypothesis.

Droits : CC-BY-NC-ND - Attribution - Pas d'utilisation commerciale - Pas de modification
Permalien : http://www.manioc.org/fichiers/V19077
V19077

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
Defining homologous genes is important in many evolutionary studies but raises obvious issues. Some of these issues are conceptual and stem from our assumptions of how a gene evolves, others are practical, and depend on the algorithmic decisions implemented in existing software. Therefore, to make progress in the study of homology, both ontological and epistemological questions must be considered. In particular, defining homologous genes cannot be solely addressed under the classic assumptions of strong tree thinking, according to which genes evolve in a strictly tree-like fashion of vertical descent and divergence and the problems of homology detection are primarily methodological. Gene homology could also be considered under a different perspective where genes evolve as ``public goods,'' subjected to various introgressive processes. In this latter case, defining homologous genes becomes a matter of designing models suited to the actual complexity of the data and how such complexity arises, rather than trying to fit genetic data to some a priori tree-like evolutionary model, a practice that inevitably results in the loss of much information. Here we show how important aspects of the problems raised by homology detection methods can be overcome when even more fundamental roots of these problems are addressed by analyzing public goods thinking evolutionary processes through which genes have frequently originated. This kind of thinking acknowledges distinct types of homologs, characterized by distinct patterns, in phylogenetic and nonphylogenetic unrooted or multirooted networks. In addition, we define `` family resemblances'' to include genes that are related through intermediate relatives, thereby placing notions of homology in the broader context of evolutionary relationships. We conclude by presenting some payoffs of adopting such a pluralistic account of homology and family relationship, which expands the scope of evolutionary analyses beyond the traditional, yet relatively narrow focus allowed by a strong tree-thinking view on gene evolution.
ISSN: 0737-4038

hal-01544794
https://hal.archives-ouvertes.fr/hal-01544794
DOI : 10.1093/molbev/mst228

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
Background: Microbial genetic diversity is often investigated via the comparison of relatively similar 16S molecules through multiple alignments between reference sequences and novel environmental samples using phylogenetic trees, direct BLAST matches, or phylotypes counts. However, are we missing novel lineages in the microbial dark universe by relying on standard phylogenetic and BLAST methods? If so, how can we probe that universe using alternative approaches? We performed a novel type of multi-marker analysis of genetic diversity exploiting the topology of inclusive sequence similarity networks. Results: Our protocol identified 86 ancient gene families, well distributed and rarely transferred across the 3 domains of life, and retrieved their environmental homologs among 10 million predicted ORFs from human gut samples and other metagenomic projects. Numerous highly divergent environmental homologs were observed in gut samples, although the most divergent genes were over-represented in non-gut environments. In our networks, most divergent environmental genes grouped exclusively with uncultured relatives, in maximal cliques. Sequences within these groups were under strong purifying selection and presented a range of genetic variation comparable to that of a prokaryotic domain. Conclusions: Many genes families included environmental homologs that were highly divergent from cultured homologs: in 79 gene families (including 18 ribosomal proteins), Bacteria and Archaea were less divergent than some groups of environmental sequences were to any cultured or viral homologs. Moreover, some groups of environmental homologs branched very deeply in phylogenetic trees of life, when they were not too divergent to be aligned. These results underline how limited our understanding of the most diverse elements of the microbial world remains, and encourage a deeper exploration of natural communities and their genetic resources, hinting at the possibility that still unknown yet major divisions of life have yet to be discovered.
ISSN: 1745-6150

Droits : http://creativecommons.org/licenses/by/
hal-01257771
http://hal.upmc.fr/hal-01257771
http://hal.upmc.fr/hal-01257771/document
http://hal.upmc.fr/hal-01257771/file/s13062-015-0092-3.pdf
DOI : 10.1186/s13062-015-0092-3

Éditeur(s) : Université de Bretagne Occidentale
Résumé : The objective of the present work is to study the formation of the passive continental margins of the Central Segment of the South Atlantic, most particularly the Congo and Angola margins. We propose a combined approach, which integrates structural constraints based on geological cross-sections (based on seismic data) and global constraints based on plate kinematic reconstructions. The structural study is based on : i) MCS and refraction data collected during the ZaiAngo programme (a joint project conducted by Ifremer and Total) ; ii) proprietary, industrial seismic data (courtesy of Total) from the Angola margin and iii) on all available seismic lines from the Africa and Brazil conjugated margins, between Walvis Ridge and the Equatorial Fracture Zones. Based on theses data, three structural domains (continental, transitional and oceanic) have been defined, the major characteristics of which are : Crustal thinning occurs abruptly, mostly below the continental slope, over a lateral distance of less than 50 km. The top of the crust deepens as the Moho shallows. Only a few extensional structures are observed ; tilted blocks are very few (one or two, depending on the profile), found only on the upper part of the slope and sealed by a discordance prior to salt deposition. The transitional domain is characterized by the existence of a pre-salt basin lying over a thin crustal layer. No tilted blocks are observed in this domain and reflectors within the pre-salt sediment series are parallel to the base of the Aptian salt, over distances greater than 100 km, precluding the possibility of any significant deformation that would imply large horizontal motions. Two types of crust are observed in the transitional domain. "Type I" crust is found below the undeformed pre-salt sediment series located below the eastern part of the basin ; it is characterized by an upper layer of thickness greater than 5 km and a abnormal velocity layer (7.2 - 7.6 km/s), up to 6 km thick. "Type II" crust is less than 5 km thick and found below the salt compressive front that affects the western part of the basin. The salt cover is continuous (no erosion surface is observed), from the continental shelf to the western termination of the basin. Salt was not deposited in a confined environment (like in the Mediterranean), but in a shallow water, lagunal environment. This imposes the zero-level and constrains the paleo-bathymetry at the time of salt deposition, which dates the latest stage of margin formation. Understanding the formation of a margin cannot be approached without studying the homolog margin. Therefore, it is of major importance to reconstruct the closure of the ocean bordered by these homolog margins and take into account the constraints imposed by the kinematic reconstructions on the lateral motions of the lithospheric plates. In order to assess the relative position of the plates at the ocean closure (prior to crustal thinning), a global study was thus performed, integrating all geophysical and geological constraints, in the ocean and on land. The role of african intra-plate deformation and its limits and their consequences have been thoroughly studied. To juxtapose the margins of the central segment of the Southern Atlantic, it is all the margins bordering the Equatorial Atlantic that need to be adjuste precisely. The kinematic study of this last region shows that the reconstruction obtained are reliable, unambiguous with a quantifiable precision The best fitting poles (obtained using the PLACA software), show that it is impossible to close the margins beyond the superposition of the salt fronts, from the Angola and Brazil margins. The geological cross-sections based on seismic data from the homolog margins indicate that a 330 km wide basin with thin (< 12 km) crust was present at the time of the fit. This basin cannot result from horizontal movement related to pure stretching or simple shear, or any model implying conservative volume. This conclusion is consistent with the existence of presalt reflectors parallel to the salt layer wich extends to the platform: the formation of the pre-salt basin must be related to vertical motions. The scenario that we propose for the evolution of the Congo-Angola margin consist in four stages: the first phase corresponds to extensional deformation limited to the few tilted blocks observed on the upper part of the slope. During the second phase, the main crustal thinning occurs, vertical motions prevailes, resulting in the formation of the continental slope and in the subsidence of the basin. The third phase corresponds to the first stress striction: deformation is concentrated in a limited section of the basin, which corresponds to the salt compression front. A proto-oceanic crust is formed, probably composed of thinned continental crust intruded by mantle material. The second stress striction corresponds to the finale phase, resulting in oceanisation senso stricto. The evolution described shows that we can not apply conservative models for margin formation (such as McKenzie and Wernicke or any of their avatars). In order to explain this thinning, one should investigate non-conservative models (implying geochemical transformation, small scale convection, intrusion...) such as those proposed in marginal or continental basins with no horizontal movments.
Ce travail de thèse aborde la formation des marges continentales passives dans le segment central de l'océan Atlantique Sud (plus particulièrement au Congo et en Angola), en intégrant une étude en coupe (étude structurale à partir des coupes sismiques) et une étude en plan (étude cinématique). L'étude structurale de la marge a été réalisée à partir des données de sismique réflexion et réfraction de la campagne Zaïango et d'une compilation de données sismiques réflexion existantes sur toutes les marges africaine et brésilienne entre les zones de fracture équatoriales et la ride de Walvis. L'interprétation de ces données a permis d'individualiser la structure de la marge en trois domaines : continental, transitionnel et océanique et de déterminer quelques points majeurs sur la structuration de la marge. L'amincissement est abrupt, localisé dans la zone de pente continentale et restreint à 50 km. La marge montre peu de structures distensives : seuls un ou deux blocs basculés sont observés en haut de pente continentale. Le domaine transitionnel est caractérisé par la géométrie particulière de la sédimentation anté-salifère, l'absence de blocs basculés et la faible épaisseur de croûte. La couche sédimentaire anté-salifère montre des réflecteurs plans jusqu'à la base du sel, continus sur 100 km, éliminant toutes possibilités de déformation du socle pendant et après son dépôt. La croûte du domaine transitionnel peut-être divisée en deux types : une croûte de type I sur laquelle se déposent les sédiments non déformés, et une croûte de type II sur laquelle se superposent les limites du « front compressif salifère » bien exprimé dans les séries postsalifères. Enfin le sel, que l'on observe depuis la plate-forme jusqu'au bassin profond, ne se dépose pas dans un bassin confiné (comme en Méditerranée) mais à un niveau proche de 0 m (ressemblant probablement à un dépôt de type lagunaire) et donne la paléo-bathymétrie au moment de son dépôt qui marque la fin de la période de formation de la marge. La compréhension de la genèse d'une marge ne peut être approchée sans son homologue. Cette simple constatation, cette évidence, montre toute l'importance que l'on doit apporter à la reconstruction cinématique initiale de l'océan qui borde ces marges homologues et aux contraintes imposées par les reconstructions cinématiques sur les mouvements horizontaux des plaques lithosphériques. Afin d'étudier la position des marges au moment de cette fermeture, c'est-à-dire avant amincissement, une étude globale intégrant l'ensemble des données disponibles, géophysiques et géologiques, océaniques et continentales, a été réalisée. Le rôle de la déformation intraplaque africaine, ses limites et leurs conséquences a, en particulier, été l'objet d'une attention poussée. Pour juxtaposer les marges du segment central, ce sont toutes les marges de l'océan Atlantique Equatorial qui doivent être ajustées précisément. L'étude cinématique réalisée de la région équatoriale montre que l'on obtient une reconstruction fiable et sans ambiguïté, avec une précision que l'on peut quantifier. Les pôles issus de cette étude (et calculés avec le Logiciel PLACA) indiquent qu'il est impossible d'obtenir une fermeture plus serrée que celle qui conduit à la superposition des fronts salifères brésilien et angolais : les coupes issues de la sismique réflexion des deux marges indiquent qu'il subsiste un bassin aminci, large de plus de 330 km et dont la croûte n'excède jamais 13 kilomètres d'épaisseur. La formation de ce bassin ne peut résulter de mouvements horizontaux, ce qui exclut un amincissement par étirement (pure stretching) ou par l'existence d'une faille de détachement (simple shear) ou par quelque modèle conservatif que ce soit. Cette constatation corrobore l'observation de la présence d'horizons anté-salifère parallèles, entre eux et au sel, couche salifère que l'on retrouve sur la plate-forme : la création de ce bassin anté-salifère ne peut être que liée à un mouvement vertical. Le schéma d'évolution que nous proposons à partir des données structurales et des contraintes cinématiques présente quatre étapes : le premier stade correspond à une phase de déformation distensive limitée aux quelques rares blocs basculés observés en haut de pente continentale. C'est durant la deuxième étape que se déroule la phase d'amincissement principal, les mouvements verticaux prévalent, aboutissant à la formation de la pente continentale et à la subsidence du bassin. La troisième phase correspond à une première striction des contraintes : la déformation se concentre sur une partie réduite du bassin, coïncidant avec le front salifère compressif. Une proto-croûte océanique se forme, probablement composée de croûte continentale amincie et intrudée de matériel mantellique. La seconde striction correspond à la phase finale de formation de la marge et aboutit à l'océanisation sensu stricto. L'étude cinématique et la description de l'évolution de la marge à partir des données sismiques montre donc que l'on ne peut envisager l'application d'un modèle de genèse des marges avec conservation de volume (type McKenzie ou Wernicke et leurs avatars) : pour expliquer l'amincissement du bassin, il faudrait probablement nous intéresser aux modèles non-conservatifs (impliquant transformation, convection à petite échelle, ...) qui sont déjà invoqués pour la formation des bassins marginaux ou continentaux, sans mouvements horizontaux.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/2003/these-82.pdf
http://archimer.ifremer.fr/doc/00000/82/

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
A set-valued upper semi-continuous map is called an Rδ -map if each of its values is an Rδ -set (we recall that an Rδ -set is a space that can be represented as the intersection of a decreasing sequence of compact AR-spaces). We prove that a compact set-valued map of an AR-space into itself has a fixed point provided it can be factorized by an arbitrary finite number of Rδ -maps through ANR-spaces. This fact is a consequence of a more general result which is the main goal of this note. The proof relies on a refinement of the approximation technique and does not make use of homological tools.
ISSN: 0166-8641

hal-00699222
https://hal.archives-ouvertes.fr/hal-00699222

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
BackgroundFor a long time biologists and linguists have been noticing surprising similarities between the evolution of life forms and languages. Most of the proposed analogies have been rejected. Some, however, have persisted, and some even turned out to be fruitful, inspiring the transfer of methods and models between biology and linguistics up to today. Most proposed analogies were based on a comparison of the research objects rather than the processes that shaped their evolution. Focusing on process-based analogies, however, has the advantage of minimizing the risk of overstating similarities, while at the same time reflecting the common strategy to use processes to explain the evolution of complexity in both fields.ResultsWe compared important evolutionary processes in biology and linguistics and identified processes specific to only one of the two disciplines as well as processes which seem to be analogous, potentially reflecting core evolutionary processes. These new process-based analogies support novel methodological transfer, expanding the application range of biological methods to the field of historical linguistics. We illustrate this by showing (i) how methods dealing with incomplete lineage sorting offer an introgression-free framework to analyze highly mosaic word distributions across languages; (ii) how sequence similarity networks can be used to identify composite and borrowed words across different languages; (iii) how research on partial homology can inspire new methods and models in both fields; and (iv) how constructive neutral evolution provides an original framework for analyzing convergent evolution in languages resulting from common descent (Sapir’s drift).ConclusionsApart from new analogies between evolutionary processes, we also identified processes which are specific to either biology or linguistics. This shows that general evolution cannot be studied from within one discipline alone. In order to get a full picture of evolution, biologists and linguists need to complement their studies, trying to identify cross-disciplinary and discipline-specific evolutionary processes. The fact that we found many process-based analogies favoring transfer from biology to linguistics further shows that certain biological methods and models have a broader scope than previously recognized. This opens fruitful paths for collaboration between the two disciplines.
ISSN: 1745-6150

Droits : http://creativecommons.org/licenses/by/
hal-01378396
http://hal.upmc.fr/hal-01378396
http://hal.upmc.fr/hal-01378396/document
http://hal.upmc.fr/hal-01378396/file/unity.pdf
DOI : 10.1186/s13062-016-0145-2

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
BACKGROUND: Homologous recombination is the key process that generates genetic diversity and drives evolution. SPO11 protein triggers recombination by introducing DNA double stranded breaks at discreet areas of the genome called recombination hotspots. The hotspot locations are largely determined by the DNA binding specificity of the PRDM9 protein in human, mice and most other mammals. In budding yeast Saccharomyces cerevisae, which lacks a Prdm9 gene, meiotic breaks are formed opportunistically in the regions of accessible chromatin, primarily at gene promoters. The genome-wide distribution of hotspots in this organism can be altered by tethering Spo11 protein to Gal4 recognition sequences in the strain expressing Spo11 attached to the DNA binding domain of the Gal4 transcription factor. To establish whether similar re-targeting of meiotic breaks can be achieved in PRDM9-containing organisms we have generated a Gal4BD-Spo11 mouse that expresses SPO11 protein joined to the DNA binding domain of yeast Gal4. RESULTS: We have mapped the genome-wide distribution of the recombination initiation sites in the Gal4BD-Spo11 mice. More than two hundred of the hotspots in these mice were novel and were likely defined by Gal4BD, as the Gal4 consensus motif was clustered around the centers in these hotspots. Surprisingly, meiotic DNA breaks in the Gal4BD-Spo11 mice were significantly depleted near the ends of chromosomes. The effect is particularly striking at the pseudoautosomal region of the X and Y chromosomes -- normally the hottest region in the genome. CONCLUSIONS: Our data suggest that specific, yet-unidentified factors influence the initiation of meiotic recombination at subtelomeric chromosomal regions.
ISSN: 1471-2164

inserm-00849779
http://www.hal.inserm.fr/inserm-00849779
http://www.hal.inserm.fr/inserm-00849779/document
http://www.hal.inserm.fr/inserm-00849779/file/1471-2164-14-493.pdf
DOI : 10.1186/1471-2164-14-493

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Mitochondrial DNA integrity is ensured by several nuclear-encoded proteins in vertebrates, and a number of mtDNA alterations in human diseases, including deletions and duplications, have been suspected to result from errors in the mitochondrial recombination pathway. However, the presence of the latter system is still a matter of controversy as RecA proteins display various functions in vitro. In Escherichia coli, RecA plays a central role in homologous recombination by pairing and transferring a single strand to a homologous duplex DNA. To address indirectly the issue of a mitochondrial recombination pathway in vivo, we have constructed a chimeric gene containing an N terminal mitochondrial targeting sequence and the E. coli RecA gene. Cells were transfected by the recombinant plasmid, then tested for their mtDNA repair upon bleomycin treatment. We found an increased repair rate of the mitochondrial DNA in cells expressing RecA as compared to control cells. These results indicate that the transfected cells display an improved mtDNA repair replication pathway due to the exogenous RecA, likely in synergy with an endogenous rate-limiting mitochondrial recombination pathway.
ISSN: 0027-5107

hal-01680533
https://hal.univ-antilles.fr/hal-01680533
PUBMED : 11356332

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
The evolutionary origin of teeth from dermal denticles (odontodes) that developed in the mouth cavity, designated as outside-in hypothesis, has long been undisputed. The outside-in hypothesis is based on the conclusion that dermal denticles and teeth fulfil the criteria of homology in an exemplary manner. Over the past 15 years, this hypothesis has been challenged. Proponents of the alternative inside-out hypothesis suggest that teeth did not evolve from dermal denticles, that they are of endodermal origin (forming in conjunction with neural crest-derived mesenchyme) and that they evolved several times independently in different lineages of vertebrates. Key arguments for the inside-out hypothesis are mineralized structures of conodonts that are accepted as teeth, the exclusive acceptance of placoderm pharyngeal denticles as teeth, together with the rejection of the presence of teeth in basal placoderms. We summarize the results of recent studies that have been triggered by the fruitful discussion between the two conflicting hypotheses. New findings support the traditional outside-in hypothesis: the mineralized elements of conodonts are not teeth, and the oral cusps in basal placoderms are true teeth. Furthermore, new developmental and molecular data clarify homology between teeth and dermal denticles. Today a new synthesis is emerging about the evolutionary origin of teeth from dermal denticles and about the unity of the elements of the dermal skeleton.
ISSN: 0175-8659

hal-01545480
https://hal.archives-ouvertes.fr/hal-01545480
DOI : 10.1111/jai.12532

Éditeur(s) : Society for General Microbiology
Résumé : A novel piezotolerant, mesophilic, facultatively anaerobic, organotrophic, polarly flagellated bacterium (strain LT13a(T)) was isolated from a deep sediment layer in the Nankai Trough (Leg 190, Ocean Drilling Program) off the coast of Japan. This organism used a wide range of organic substrates as sole carbon and energy sources: pyruvate, glutamate, succinate, fumarate, lactate, citrate, peptone and tryptone. Oxygen, nitrate, fumarate, ferric iron and cystine were used as electron acceptors. Maximal growth rates were observed at a hydrostatic pressure of 10 MPa. Hydrostatic pressure for growth was in the range 0.1-50 MPa. Predominant cellular fatty acids were 16:1 omega7c, 15: 0 iso, 16: 0 and 13: 0 iso. The G + C content of the DNA was 44.9 mol%. On the basis of 16S rRNA gene sequences, strain LT13a(T) was shown to belong to the gamma-Proteobacteria, being closely related to Shewanella putrefaciens (98%), Shewanella oneidensis (97%) and Shewanella baltica (96 %). Levels of DNA homology between strain LT13a(T) and S. putrefaciens, S. oneidensis and S. baltica were < 20 %, indicating that strain LT13a(T) represents a novel species. Genetic evidence and phenotypic characteristics showed that isolate LT13a(T) constitutes a novel species of the genus Shewanella, Because of the deep origin of the strain, the name Shewanella profunda sp. nov. is proposed, with LT13a(T) (= DSM 15900(T)-JCM 12080(T)) as the type strain.
International journal of systematic and evolutionary microbiology (1466-5026) (Society for General Microbiology), 2004-11 , Vol. 54 , N. 6 , P. 1943-1949

Droits : 2004 International Union of Microbiological Societies
http://archimer.ifremer.fr/doc/2004/publication-590.pdf
DOI:10.1099/ijs.0.03007-0
http://archimer.ifremer.fr/doc/00000/590/

Éditeur(s) : HAL CCSD
Résumé : contient des versions PDF d'articles scientifiques (versions éditeur)
Spectrins are actin binding proteins that constitute the main components of membrane skeletons, the protein network located under the plasma membrane. Erythroid or non erythroid (in this case, they are called fodrins), spectrins play an important structural function in the membrane as demonstrated in the red blood cell. Spectrins are composed of two long α and β chains, associated in tetramers (αβ)2, forming the long flexible filaments of the network. Both chains are composed of repeating units which are folded in a triple helical arrangement (A, B and C helices), except for segment α10 which corresponds to a Src Homology 3 domain (SH3). The head-to-head interaction between dimers implies the N-terminal end of α chain and the C-terminal end of β chain. A model was proposed for the tetramerization site of spectrin : the two A and B helices of the last repeat of α chain interact with the C helix of the β chain in order to constitute a triple-helical structure similar to the repeats along the remainder of spectrin molecule. This model was first inferred from the relationship between the severity of the spectrin self-association defect and the location of the underlying mutations found in hereditary elliptocytosis (HE). Using recombinant peptides we defined the region, on both chains, which was sufficient and necessary to generate a fully functional tetramerization site. Producing peptides carrying a βHE mutation, we reproduced the tetramerization defect as observed in red blood cells of patients.
Finally, the presence of an SH3 domain probably gives to spectrins new functions which are different from the stability of the membrane. After contesting the existence of interaction between the fodrin SH3 domain and the α subunit of epithelial sodium channel sensitive to amiloride, we searched for partners of this domain, by screening a rat kidney library with the yeast two-hybrid system. We identified severals proteins implicated in the actin polymerization asoociated with motility or cell differenciation, suggesting that SH3 domain could play a part in this process.
Les spectrines, protéines liant l'actine, sont des constituants majeurs du squelette membranaire, réseau multiprotéique localisé sous la membrane plasmique. Érythroïdes ou non érythroïdes (dans ce cas, on les appelle fodrines), les spectrines ont un rôle structural important dans la membrane comme cela a déjà été démontré, pour la spectrine, dans le globule rouge. Elles sont constituées de deux longues chaînes a et ß associées côte à côte en tétramères (aß)2 qui forment les longs filaments du réseau. Chacune des chaînes est composée par la répétition de segments homologues, 22 pour a et 17 pour ß. Ces segments sont constitués de trois hélices a (hélices A, B et C) repliées sur elles-mêmes. Cette succession de structures trihélicoïdales est parfois interrompue par un domaine particulier comme le domaine SH3 (Src Homology 3) présent au milieu de la chaîne a. Les tétramères (aß)2 de spectrine constituent les filaments du squelette membranaire. L'interaction tête-à-tête de deux dimères aß implique les extrémités NH2 de la chaîne a et COOH de la chaîne ß. D'une part la sévérité du défaut d'auto-association et la localisation des mutations associées à celui-ci et d'autre part, les séquences en acides aminés des extrémités impliquées dans le site d'auto-association ont permis de proposer un modèle : la première hélice C isolée de la chaîne a pourrait s'associer aux deux dernières hélices A et B de la chaîne ß pour reconstituer une unité conformationnelle trihélicoïdale semblable à celles observées le long de la molécule. Un défaut dans la formation du tétramère est le support moléculaire le plus fréquemment observé dans les elliptocytoses héréditaires (HE). À l'aide de peptides recombinants, nous avons défini, sur les deux chaînes, les régions nécessaires et suffisantes possédant les caractéristiques pleinement fonctionnelles du site de tétramérisation. Nous avons ensuite, par mutagenèse dirigée, reproduit le lien entre la présence de mutations HE localisées dans les hélices A ou B et le défaut d'auto-association observé dans les globules rouges de patients HE. La présence d'un domaine SH3 localisé au milieu de la chaîne a confère probablement aux spectrine des fonctions autres que le maintien et la stabilité de la membrane. Les SH3, petits domaines protéiques, participent aux interactions protéine/protéine. Le seul partenaire connu du domaine SH3 de la fodrine était la sous-unité a du canal sodium sensible à l'amiloride (ENaC) mais la fonction de ce complexe n'était pas encore caractérisée. À l'aide de différentes méthodes, nous avons remis en cause l'interaction directe entre ENaC et le SH3 de la fodrine. La fonction de ce domaine SH3 étant liée à la nature de son ligand, nous avons donc recherché les partenaires putatifs du domaine SH3 de la fodrine par la technique du double-hybride. 29 partenaires ont été identifiés, regroupés en 19 familles et 10 clones isolés. La spécificité des interactions a été étudiée à la fois par double-hybride, à l'aide de mutants du domaine SH3 de la fodrine produits par mutagenèse dirigée. Les interactions vis-à-vis d'autres domaines SH3 (spectrine ou une protéine de levure non relatée Scd2) ont été également analysées. Enfin, la spécificité de certains partenaires a été confirmée par des études d'interactions in vitro. Deux des protéines les plus spécifiques du domaine SH3 de la fodrine sont des protéines tyrosine-phosphatase PTP. La première est l'isoforme A de PTP de faible poids moléculaire (LMPTPA) mais l'interaction n'a pas été confirmée in vitro. La deuxième, TD14, est une nouvelle PTP dont la seule fonction connue est d'inhiber la formation des foyers tumoraux des cellules surexprimant l'oncogène Ha-ras. Ces PTP pourraient soit déphosphoryler la fodrine, soit être recrutées sous la membrane pour déphosphoryler une autre cible. Nous avons également identifié trois partenaires (N-WASP, Evl et une protéine de la famille des formines) suggérant que les domaines SH3 des spectrines pourraient être impliqués dans les processus de polymérisation de l'actine liés à la mobilité ou la différenciation cellulaire. Mot clés : spectrine, fodrine, tétramérisation, SH3, double-hybride, polymérisation de l'actine
https://tel.archives-ouvertes.fr/tel-00284819

Droits : info:eu-repo/semantics/OpenAccess
tel-00284819
https://tel.archives-ouvertes.fr/tel-00284819
https://tel.archives-ouvertes.fr/tel-00284819/document
https://tel.archives-ouvertes.fr/tel-00284819/file/Nicolas_1999_-_These.pdf

Éditeur(s) : HAL CCSD Cold Spring Harbor Laboratory Press
Résumé : International audience
Meiotic recombination is required for the segregation of homologous chromosomes and is essential for fertility. In most mammals, the DNA double-strand breaks (DSBs) that initiate meiotic recombination are directed to a subset of genomic loci (hot spots) by sequence-specific binding of the PRDM9 protein. Rapid evolution of the DNA-binding specificity of PRDM9 and gradual erosion of PRDM9-binding sites by gene conversion will alter the recombination landscape over time. To better understand the evolutionary turnover of recombination hot spots and its consequences, we mapped DSB hot spots in four major subspecies of Mus musculus with different Prdm9 alleles and in their F1 hybrids. We found that hot spot erosion governs the preferential usage of some Prdm9 alleles over others in hybrid mice and increases sequence diversity specifically at hot spots that become active in the hybrids. As crossovers are disfavored at such hot spots, we propose that sequence divergence generated by hot spot turnover may create an impediment for recombination in hybrids, potentially leading to reduced fertility and, eventually, speciation
ISSN: 0890-9369

hal-01281480
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01281480
DOI : 10.1101/gad.270009.115
PUBMED : 26833728

Éditeur(s) : Natl Marine Fisheries Service Scientific Publ Office
Résumé : Twenty homologous microsatellite markers, or simple sequence repeats (SSRs), were developed for blackfin tuna (Thunnus atlanticus) through the use of a direct Seq-to-SSR approach. The number of alleles per locus ranged between 5 and 26, and the expected heterozygosity ranged between 0.640 and 0.969. Three loci displayed significant departure from Hardy-Weinberg equilibrium expectations, likely reflecting occurrence of null alleles. Another locus showed consecutive alleles that differed by one base pair only. Consequently, this locus may be prone to elevated rates of scoring errors. The remaining 16 loci will be valuable for studies in conservation genetics of blackfin tuna.
Fishery Bulletin (0090-0656) (Natl Marine Fisheries Service Scientific Publ Office), 2014-10 , Vol. 112 , N. 4 , P. 322-325

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/00239/34999/33529.pdf
DOI:10.7755/FB.112.4.8
http://archimer.ifremer.fr/doc/00239/34999/

Éditeur(s) : HAL CCSD Ecological Society of America
Résumé : Tropical plant diversity is extraordinarily high at both local and regional scales. Many studies have demonstrated that natural enemies maintain local diversity via negative density dependence, but we know little about how natural enemies influence beta-diversity across habitats and/or regions. One way herbivores could influence plant beta-diversity is by driving allocation trade-offs that promote habitat specialization across resource gradients. We therefore predicted that increasing resource availability should be accompanied by increasing herbivory rates and decreasing plant allocation to defense. Second, relative abundances within plant lineages are predicted to reflect patterns of habitat specialization and allocation trade-offs. A phylogenetic context is vital not only to compare homologous plant traits (including defense strategies) across habitat types, but also to connect evolutionary trade-offs to patterns of species diversification in each phylogenetic lineage. We tested these predictions for trees in white-sand, clay terra firme, and seasonally flooded forests in Peru and French Guiana that represent the range of soil fertility, forest structure, and floristic compositions found throughout the Amazon region. We established 74 0.5-ha plots in these habitats and sampled all trees. Within 12 representative plots we marked newly expanding leaves of 394 saplings representing 68 species, including the most abundant species in each plot in addition to species from five focal lineages: Swartzia and Inga (Fabaceae), Protieae (Burseracaeae), Bombacoideae (Malvaceae), and Micropholis (Sapotaceae). We measured total leaf production rates for each sapling and calculated relative herbivory impact as the ratio between herbivory rate and leaf production rate. Herbivory rates averaged 2.1% per month, did not correlate with leaf production rate, and were similar across habitats. Relative herbivore impacts exceeded leaf production rates for most species. Leaf production rate averaged 2.8%, was significantly higher in seasonally flooded forests than the other two habitats, and exhibited significant correlations with specific leaf area. Species with high herbivory rates exhibited significantly lower relative abundances in terra firme forests. Overall, focal species within lineages present contrasting patterns regarding their herbivory rates and leaf production rate within habitats. These results highlight why a lineage-based approach is necessary when attempting to connect hypotheses regarding evolutionary trade-offs to community assembly patterns.
ISSN: 0012-9658

hal-01032418
https://hal.archives-ouvertes.fr/hal-01032418

Éditeur(s) : Elsevier
Résumé : Polyploids can be defined as organisms with one or more additional chromosome sets with respect to the number most frequently found in nature for a given species. Triploids, organisms with three sets of homologous chromosomes, are found spontaneously in both wild and cultured populations and can be easily induced in many commercially relevant species of fish and shellfish. The major consequence of triploidy is gonadal sterility, which is of advantage in the aquaculture of molluscs since it can result in superior growth. In fish, the induction of triploidy is mainly used to avoid problems associated with sexual maturation such as lower growth rates, increased incidence of diseases and deterioration of the organoleptic properties. Triploidy can also be used to increase the viability of some hybrids, and is regarded as a potential method for the genetic containment of farmed shellfish and fish. This review focuses on some current issues related to the application of induced polyploidy in aquaculture, namely: 1) the artificial induction of polyploidy and the effectiveness of current triploidisation techniques, including the applicability of tetraploidy to generate auto- and allotriploids; 2) the performance capacity of triploids with respect to diploids; 3) the degree and permanence of gonadal sterility in triploids; and 4) the prospects for the potential future generalised use of triploids to avoid the genetic impact of escapees of farmed fish and shellfish on wild populations. Finally, directions for future research on triploids and their implementation are discussed. (C) 2009 Elsevier B.V. All rights reserved.
Aquaculture (0044-8486) (Elsevier), 2009-08 , Vol. 293 , N. 3-4 , P. 125-156

Droits : 2009 Elsevier Ltd All rights reserved.
http://archimer.ifremer.fr/doc/2009/publication-6648.pdf
DOI:10.1016/j.aquaculture.2009.04.036
http://archimer.ifremer.fr/doc/00000/6648/

Éditeur(s) : Elsevier Science Bv
Résumé : The opening of the Equatorial and South Atlantic Oceans is still a matter of debate, particularly as concerns the locations of the intraplate deformation. We propose here a critical review of the kinematic models published since Bullard et al., 1965, based on a series of constraints: new interpretation of the magnetic anomalies, seafloor isochrons, flow lines, fracture zones, continental and oceanic homologous structures and radiometric dating of igneous rocks. All of these models present numerous unexplained misfits (gaps, overlaps and misalignments). We present here a new evolution of the Equatorial and South Atlantic Ocean from the tightest reconstruction to Chron C34. This new model confirms the hypothesis of a northward propagation of the South American deformation proposed by Eagles, but rejuvenates slightly the ages for this propagation and refines the plate reconstructions. In particular, we highlight the role of the kinematic "buffer" Santos block, located between the salty Aptian Central segment in the North and the Volcanic Hauterivian Austral segment in the South. The new initial fit presented in this study represents the tightest reconstruction that could be obtained and constitutes the base canvas on which the problem of the continental margin genesis should be addressed.
Earth Science Reviews (0012-8252) (Elsevier Science Bv), 2010 , Vol. 98 , N. 1-2 , P. 1-37

Droits : 2010 Elsevier B.V. All rights reserved.
http://archimer.ifremer.fr/doc/00000/11160/7883.pdf
DOI:10.1016/j.earscirev.2009.08.001
http://archimer.ifremer.fr/doc/00000/11160/

Éditeur(s) : HAL CCSD Elsevier
Résumé : The Duffy antigen/receptor for chemokine (DARC) is an erythrocyte receptor for malaria parasites (Plasmodium vivax and Plasmodium knowlesi) and for chemokines. In contrast to other chemokine receptors, DARC is a promiscuous receptor that binds chemokines of both CC and CXC classes. The four extracellular domains (ECDs) of DARC are essential for its interaction with chemokines, whilst the first (ECD1) is sufficient for the interaction with malaria erythrocyte-binding protein. In this study, we elaborate and analyze structural models of the DARC. The construction of the 3D models is based on a comparative modeling process and on the use of many procedures to predict transmembrane segments and to detect far homologous proteins with known structures. Threading, ab initio, secondary structure and Protein Blocks approaches are used to build a very large number of models. The conformational exploration of the ECDs is performed with simulated annealing. The second and fourth ECDs are strongly constrained. On the contrary, the ECD1 is highly flexible, but seems composed of three consecutive regions: a small beta-sheet, a linker region and a structured loop. The chosen structural models encompass most of the biochemical features and reflect the known experimental data. They may be used to analyze functional interaction properties.
ISSN: 0006-3002

inserm-00143373
http://www.hal.inserm.fr/inserm-00143373
http://www.hal.inserm.fr/inserm-00143373/document
http://www.hal.inserm.fr/inserm-00143373/file/de_Brevern_BBA_2005.pdf
DOI : 10.1016/j.bbagen.2005.05.016

Éditeur(s) : Academic Press Ltd- Elsevier Science Ltd
Résumé : Extracellular products (ECPs) of the pathogenic Vibrio aestuarianus 01/32 were previously reported to display lethality in Crassostrea gigas oysters and to cause morphological changes and immunosuppression in oyster hemocytes. To identify the source of this toxicity, biochemical and genetic approaches were developed. ECP protease activity and lethality were shown to be significantly reduced following incubation with metal chelators, suggesting the involvement of a zinc metalloprotease. An open reading frame of 1836 bp encoding a 611-aa metalloprotease (designated yam) was identified. The deduced protein sequence showed high homology to other Vibrio metalloproteases reported to be involved in pathogenicity. To further confirm the role of this enzyme in ECP toxicity, a plasmid carrying the yarn gene under the control of an araC-P-BAD expression cassette was transferred to a Vibrio splendidus related strain, LMC20012(T), previously characterized as non-pathogenic to oysters. Expression of Vam conferred a toxic phenotype to LMG20012(T) ECPs in vivo and cytotoxicity to oyster hemocytes in vitro. Collectively, these data suggest that the Vam metalloprotease is a major contributor to the toxicity induced by V aestuarianus ECPs and is involved in the impairment of oyster hemocyte functions. (C) 2010 Elsevier Ltd. All rights reserved.
Fish & Shellfish Immunology (1050-4648) (Academic Press Ltd- Elsevier Science Ltd), 2010-11 , Vol. 29 , N. 5 , P. 753-758

Droits : 2010 Elsevier Ltd All rights reserved.
http://archimer.ifremer.fr/doc/00015/12649/9588.pdf
DOI:10.1016/j.fsi.2010.07.007
http://archimer.ifremer.fr/doc/00015/12649/

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
Vertebrate genomes contain around 20,000 protein-encoding genes, of which a large fraction is still not associated with specific functions. A major task in future genomics will thus be to assign physiological roles to all open reading frames revealed by genome sequencing. Here we show that C2orf62, a highly conserved protein with little homology to characterized proteins, is strongly expressed in testis in zebrafish and mammals, and in various types of ciliated cells during zebrafish development. By yeast two hybrid and GST pull-down, C2orf62 was shown to interact with TTC17, another uncharacterized protein. Depletion of either C2orf62 or TTC17 in human ciliated cells interferes with actin polymerization and reduces the number of primary cilia without changing their length. Zebrafish embryos injected with morpholinos against C2orf62 or TTC17, or with mRNA coding for the C2orf62 C-terminal part containing a RII dimerization/docking (R2D2) - like domain show morphological defects consistent with imperfect ciliogenesis. We provide here the first evidence for a C2orf62-TTC17 axis that would regulate actin polymerization and ciliogenesis.
ISSN: 1932-6203

hal-00955242
https://hal-univ-rennes1.archives-ouvertes.fr/hal-00955242
https://hal-univ-rennes1.archives-ouvertes.fr/hal-00955242/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-00955242/file/C2orf62_and_TTC17-accepted.pdf
DOI : 10.1371/journal.pone.0086476

Éditeur(s) : HAL CCSD Oxford University Press (OUP): Policy C - Option B
Résumé : International audience
We report the characterization of a DNA primase/ polymerase protein (PolpTN2) encoded by the pTN2 plasmid from Thermococcus nautilus. Sequence analysis revealed that this protein corresponds to a fusion between an N-terminal domain homologous to the small catalytic subunit PriS of heterodimeric archaeal and eukaryotic primases (AEP) and a C-terminal domain related to their large regulatory subunit PriL. This unique domain configuration is not found in other virus-and plasmid-encoded primases in which PriS-like domains are typically fused to different types of helicases. PolpTN2 exhibited primase, polymerase and nucleotidyl transferase activities and specifically incorporates dNTPs, to the exclusion of rNTPs. PolpTN2 could efficiently prime DNA synthesis by the T. nautilus PolB DNA polymerase, suggesting that it is used in vivo as a primase for pTN2 plasmid replication. The N-terminal PriS-like domain of PolpTN2 exhibited all activities of the full-length enzyme but was much less efficient in priming cellular DNA polymerases. Surprisingly, the N-terminal domain possesses reverse transcriptase activity. We speculate that this activity could reflect an ancestral function of AEP proteins in the transition from the RNA to the DNA world.
ISSN: 0305-1048

Droits : http://creativecommons.org/licenses/by/
hal-01332620
http://hal.upmc.fr/hal-01332620
http://hal.upmc.fr/hal-01332620/document
http://hal.upmc.fr/hal-01332620/file/Nucl.%20Acids%20Res.-2014-Gill-3707-19.pdf
DOI : 10.1093/nar/gkt1385