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) : Edp Sciences S A
Résumé : Reared sea bass were submitted to six stressful situations: hyperoxia with or without hypercapnia, increased stocking density in an open flow or recirculating system, transfer to another tank and nodavirus injection. The potentially negative impact of these factors on the lives of sea bass was investigated by measuring 9 water parameters and 19 fish parameters including total serum protein (TSP). TSP has already been used to evaluate stress. The present study investigates data of previous and new experiments, concentrating on the potential use of TSP as a routine indicator to assess welfare in sea bass reared on fish farms. In the current experiment, oxygen and carbon dioxide were seen to affect levels of TSP, but alterations were too erratic to enable proper comparison, probably because they are normal components of the fish environment and become toxic only by dose increase. TSP decreased when stocking density increased. After transfer to another tank, TSP decreased to 14% for three weeks and then increased during the fourth week through compensative overproduction, before returning to normal levels after 2 months. The results confirmed that transfer is an important stress factor for fish, with cumulative effects for successive transfers. TSP alteration of nodavirus-injected fish depends on the type of symptoms, which can be divided into 3 groups: (i) dying fish, in which TSP increased sharply due to over-production of protein involved in non-specific defences and inflammation, then decreased dramatically before death; (ii) whirling fish, a group that included both fish that later died, in which TSP decreased, and fish that subsequently survived, in which TSP increased due to development of specific immunity; and (iii) asymptomatic fish, in which TPS was similar to control levels and which were probably insensitive to nodavirus and/or had developed defences. In this paper, different mechanisms of TSP alteration are proposed and the interest of TSP as a field parameter is discussed. TSP is a non-destructive parameter that is robust, easy to measure everywhere and cheap, representing a suitable way of monitoring the overall welfare of fish by its regular increase. It can be used only as a "warning" of poor rearing conditions, however, and further investigations would be needed to identify the specific stress or health disorder.
Aquatic Living Resources (0990-7440) (Edp Sciences S A), 2011-04 , Vol. 24 , N. 2 , P. 121-127

Droits : EDP Sciences, IFREMER, IRD 2011
http://archimer.ifremer.fr/doc/00043/15382/12740.pdf
DOI:10.1051/alr/2011130
http://archimer.ifremer.fr/doc/00043/15382/

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
In this paper, we consider a direct protein transfer process between cells in co-culture. Assuming that cells continually encounter each other, and from some hypotheses on cell-to-cell rules of transfer, we derive discrete and continuous Boltzmann-like integrodifferential equations. The novelty of this model is to take into account multiple transfer rules. This new transfer model is used to fit the experimental data of cell-to-cell protein transfer in breast cancer.
ISSN: 0092-8240

Droits : info:eu-repo/semantics/OpenAccess
hal-01683780
https://hal.univ-antilles.fr/hal-01683780
https://hal.univ-antilles.fr/hal-01683780/document
https://hal.univ-antilles.fr/hal-01683780/file/MNPZF%20Bull%20Math%20Biol%202017.pdf
DOI : 10.1007/s11538-017-0319-9

Éditeur(s) : HAL CCSD
Résumé : International audience
Despite their dynamic nature, certain chromatin marks must be maintained over the long term. This is particulary true for histone 3 lysine 9 (H3K9) trimethylation, that is involved in the maintenance of healthy differentiated cellular states by preventing inappropriate gene expression, and has been recently identified as the most efficient barrier to cellular reprogramming in nuclear transfer experiments. We propose that the capacity of the enzymes SUV39H1/2 to rebind to a minor fraction of their products, either directly or via HP1α/β, contributes to the solidity of this mark through (i) a positive feedback involved in its establishment by the mutual enforcement of H3K9me3 and SUV39H1/2 and then (ii) a negative feedback sufficient to strongly stabilize H3K9me3 heterochromatin in post-mitotic cells by generating local enzyme concentrations capable of counteracting transient bursts of demethylation. This model does not require direct molecular interactions with adjacent nucleosomes and is favoured by a series of additional mechanisms including (i) the protection of chromatin-bound SUV39H1/2 from the turnovers of soluble proteins, which can explain the uncoupling between the cellular contents in SUV39H1 mRNA and protein; (ii) the cooperative dependence on the local density of the H3K9me3 of HP1α/β-dependent heterochomatin condensation and, dispensably (iii) restricted enzyme exchanges with chromocenters confining the reactive bursts of SUV39H1/2 in heterochromatin. This mechanism illustrates how seemingly static epigenetic states can be firmly maintained by dynamic and reversible modifications. © 2016 Elsevier B.V.
Biochimica et Biophysica Acta - Gene Regulatory Mechanisms

hal-01467548
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01467548
DOI : 10.1016/j.bbagrm.2016.11.006
PUBMED : 27876670

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-Blackwell
Résumé : International audience
Based on their small size and genomic properties, ultrasmall prokaryotic groups like the Candidate Phyla Radiation have been proposed as possible symbionts dependent on other bacteria or archaea. In this study, we use a bipartite graph analysis to examine patterns of sequence similarity between draft and complete genomes from ultrasmall bacteria and other complete prokaryotic genomes, assessing whether the former group might engage in significant gene transfer (or even endosymbioses) with other community members. Our results provide preliminary evidence for many lateral gene transfers with other prokaryotes, including members of the archaea, and report the presence of divergent, membrane-associated proteins among these ultrasmall taxa. In particular, these divergent genes were found in TM6 relatives of the intracellular parasite Babela massiliensis.
ISSN: 1462-2912

Droits : http://creativecommons.org/licenses/by/
hal-01480348
http://hal.upmc.fr/hal-01480348
http://hal.upmc.fr/hal-01480348/document
http://hal.upmc.fr/hal-01480348/file/emi13477.pdf
DOI : 10.1111/1462-2920.13477

Résumé : Les biofilms électroactifs (EA) sont des consortia bactériens mono ou pluri-espèces, qui ont la faculté d’échanger des électrons provenant de leur métabolisme avec les surfaces solides conductrices des électrodes. Cette découverte est à l’origine d’un nouveau dispositif énergétique : la pile à combustible microbienne (PACM). Depuis les années 2000, la littérature scientifique sur les biofilms EA et sur les PACM explose, notamment grâce à la découverte de bactéries capables de transférer par voie directe – par des pili ou protéines transmembranaires – des électrons vers les électrodes. Plusieurs sources de bactéries EA ont été à ce jour découvertes, allant de cultures pures à des communautés bactériennes plus complexes. Ces dernières sont issues de milieux aqueux naturels (milieux marins ou d’eau douce), industriels ou urbains (effluents d’industrie, eaux usées domestiques). La plupart de ces sources bactériennes proviennent d’environnements de climat tempéré. Dans ce travail de thèse, plusieurs sols de milieux humides de la Guyane ont été identifiés comme étant de sources de bactéries EA. Les expériences menées sous potentiel d’électrode imposé et constant ont permis d’étudier l’adhésion à la surface d’électrode des biofilms EA issus de la flore endogène des milieux sélectionnés. La formation de bioanodes et de biocathodes a été possible en présence respectivement d’acétate et d’oxygène dans les milieux. Une étude par voltammétrie cyclique a mis en évidence les pics d’oxydo-réduction en lien avec les échanges électroniques du biofilm EA et de l’électrode. En optimisant la procédure de formation des biofilms EA par chronoampérométrie (surface d’électrode plus importante, apport en continu et progressif du substrat), une densité de courant maximale de 12 A/m2 et un rendement faradique de 24 % ont été obtenus. Une autre méthode pour former des biofilms EA à partir d’un milieu choisi, la mangrove, a consisté à utiliser deux prototypes de PACM : une pile à compartiment unique et à cathode à air, et une pile benthique. Dans les deux cas, les biofilms EA ont pu être formés et étudiés, complétant certaines observations faites sous potentiel imposé. La PACM benthique s’est avérée être la plus proche d’une application à grande échelle puisqu’elle a été complètement autonome : anode et cathode utilisant uniquement le milieu pour fonctionner. Elle a pu être étudiée en laboratoire comme sur le terrain.
Electroactive biofilms (EA) are mono or multi-species bacterial consortia, which have the ability to exchange electrons from their metabolism with solid surfaces of conductive electrodes. This discovery is the basis for a device of energy production: microbial fuel cell (MFC). Since the 2000s, the scientific literature on EA biofilms and MFC explodes, thanks to the discovery of bacteria that are able to transfer directly – by pili or trans-membrane proteins – electrons to electrodes. Several sources of EA bacteria were discovered to date, ranging from pure cultures to more complex bacterial communities. Those last are from natural (marine and freshwater), industrial or urban (industrial effluents, domestic wastewater) aqueous environments. However, the vast majority of these are from temperate environments.In this thesis, several wetland soils of French Guiana have been identified as sources of EA bacteria. Experiments under poised and constant electrode potential were used to examine adherence to the electrode surface of EA biofilms from the endogenous flora of selected environments. Formation of bioanodes and biocathodes was possible in the presence respectively of acetate and oxygen in the media. A study by cyclic voltammetry showed the redox peaks related to electronic exchanges between EA biofilm and electrode. By optimizing the process of EA biofilm formation by chronoamperometry (larger electrode surface, providing continuous and progressive substrate), a maximum current density of 12 A/m2 and a coulombic efficiency of 24% were obtained.Another method to form EA biofilms from a chosen medium (mangrove) was to use two MFC prototypes: a single compartment and air cathode one, and a benthic one. In both cases, the EA biofilms have been trained and studied supplementing certain observations made under poised polarization. MFC benthic proved to be the closest to a wide application since it was completely autonomous, anode and cathode only using the medium to function. It has been studied in the laboratory and in the field.

http://www.theses.fr/2012AGUY0560/document

Éditeur(s) : Nature Publishing Group
Résumé : Vibrio nigripulchritudo is an emerging pathogen of farmed shrimp in New Caledonia and other regions in the Indo-Pacific. The molecular determinants of V. nigripulchritudo pathogenicity are unknown; however, molecular epidemiological studies have suggested that pathogenicity is linked to particular lineages. Here, we performed high-throughput sequencing-based comparative genome analysis of 16 V. nigripulchritudo strains to explore the genomic diversity and evolutionary history of pathogen-containing lineages and to identify pathogen-specific genetic elements. Our phylogenetic analysis revealed three pathogen-containing V. nigripulchritudo clades, including two clades previously identified from New Caledonia and one novel clade comprising putatively pathogenic isolates from septicemic shrimp in Madagascar. The similar genetic distance between the three clades indicates that they have diverged from an ancestral population roughly at the same time and recombination analysis indicates that these genomes have, in the past, shared a common gene pool and exchanged genes. As each contemporary lineage is comprised of nearly identical strains, comparative genomics allowed differentiation of genetic elements specific to shrimp pathogenesis of varying severity. Notably, only a large plasmid present in all highly pathogenic (HP) strains encodes a toxin. Although less/non-pathogenic strains contain related plasmids, these are differentiated by a putative toxin locus. Expression of this gene by a non-pathogenic V. nigripulchritudo strain resulted in production of toxic culture supernatant, normally an exclusive feature of HP strains. Thus, this protein, here termed 'nigritoxin', is implicated to an extent that remains to be precisely determined in the toxicity of V. nigripulchritudo.
Isme Journal (1751-7362) (Nature Publishing Group), 2013-10 , Vol. 7 , N. 10 , P. 1985-1996

Droits : 2013 International Society for Microbial Ecology All rights reserved 1751-7362/13
http://archimer.ifremer.fr/doc/00160/27117/28369.pdf
DOI:10.1038/ismej.2013.90
http://archimer.ifremer.fr/doc/00160/27117/

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) : 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 Wiley
Résumé : International audience
Analysis of microbial biodiversity is hampered by a lack of reference genomes from most bacteria, viruses, and algae. This necessitates either the cultivation of a restricted number of species for standard sequencing projects or the analysis of highly complex environmental DNA metagenome data. Single-cell genomics (SCG) offers a solution to this problem by constraining the studied DNA sample to an individual cell and its associated symbionts, prey, and pathogens. We used SCG to study marine heterotrophic amoebae related to Paulinella ovalis (A. Wulff) P.W. Johnson, P.E. Hargraves & J.M. Sieburth (Rhizaria). The genus Paulinella is best known for its photosynthetic members such as P.chromatophora Lauterborn that is the only case of plastid primary endosymbiosis known outside of algae and plants. Here, we studied the phagotrophic sister taxa of P.chromatophora that are related to P.ovalis and found one SCG assembly to contain -cyanobacterial DNA. These cyanobacterial contigs are presumably derived from prey. We also uncovered an associated cyanophage lineage (provisionally named phage PoL_MC2). Phylogenomic analysis of the fragmented genome assembly suggested a minimum genome size of 200Kbp for phage PoL_MC2 that encodes 179 proteins and is most closely related to Synechococcus phage S-SM2. For this phage, gene network analysis demonstrates a highly modular genome structure typical of other cyanophages. Our work demonstrates that SCG is a powerful approach for discovering algal and protist biodiversity and for elucidating biotic interactions in natural samples.
ISSN: 0022-3646

hal-01544797
https://hal.archives-ouvertes.fr/hal-01544797
DOI : 10.1111/jpy.12028

Éditeur(s) : HAL CCSD Nature Publishing Group
Résumé : International audience
Iron is an essential micronutrient involved in many biological processes and is often limiting for primary production in large regions of the World Ocean. Metagenomic and physiological studies have identified clades or ecotypes of marine phytoplankton that are specialized in iron depleted ecological niches. Although less studied, eukaryotic picophytoplankton does contribute significantly to primary production and carbon transfer to higher trophic levels. In particular, metagenomic studies of the green picoalga Ostreococcus have revealed the occurrence of two main clades distributed along coast-offshore gradients, suggesting niche partitioning in different nutrient regimes. Here, we present a study of the response to iron limitation of four Ostreococcus strains isolated from contrasted environments. Whereas the strains isolated in nutrient-rich waters showed high iron requirements, the oceanic strains could cope with lower iron concentrations. The RCC802 strain, in particular, was able to maintain high growth rate at low iron levels. Together physiological and transcriptomic data indicate that the competitiveness of RCC802 under iron limitation is related to a lowering of iron needs though a reduction of the photosynthetic machinery and of protein content, rather than to cell size reduction. Our results overall suggest that iron is one of the factors driving the differentiation of physiologically specialized Ostreococcus strains in the ocean.
ISSN: 2045-2322

Droits : http://creativecommons.org/licenses/by/
hal-01502140
http://hal.upmc.fr/hal-01502140
http://hal.upmc.fr/hal-01502140/document
http://hal.upmc.fr/hal-01502140/file/acclimation.pdf
DOI : 10.1038/s41598-017-00216-6