Phylogénomique des Archées

Les transferts horizontaux de gènes (THG) ont été démontrés pour jouer un rôle important dans l'évolution des procaryotes. Leur impact a été le sujet de débats intenses, ceux-ci allant même jusqu'à l'abandon de l'arbre des espèces. Selon certaines études, un signal historique dominant est présent chez les procaryotes, puisque les transmissions horizontales stables et fonctionnelles semblent beaucoup plus rares que les transmissions verticales (des dizaines contre des milliards). Cependant, l'effet cumulatif des THG est non-négligeable et peut potentiellement affecter l'inférence phylogénétique. Conséquemment, la plupart des chercheurs basent leurs inférences phylogénétiques sur un faible nombre de gènes rarement transférés, comme les protéines ribosomales. Ceux-ci n'accordent cependant pas autant d'importance au modèle d'évolution utilisé, même s'il a été démontré que celui-ci est important lorsqu'il est question de résoudre certaines divergences entre ancêtres d'espèces, comme pour les animaux par exemple. Dans ce mémoire, nous avons utilisé des simulations et analyser des jeux de données d'Archées afin d'étudier l'impact relatif des THG ainsi que l'impact des modèles d'évolution sur la précision phylogénétique. Nos simulations prouvent que (1) les THG ont un impact limité sur les phylogénies, considérant un taux de transferts réaliste et que (2) l'approche super-matrice est plus précise que l'approche super-arbre. Nous avons également observé que les modèles complexes expliquent non seulement mieux les données que les modèles standards, mais peuvent avoir un impact direct sur différents groupes phylogénétiques et sur la robustesse de l'arbre obtenu. Nos résultats contredisent une publication récente proposant que les Thaumarchaeota apparaissent à la base de l'arbre des Archées.Horizontal gene transfer (HGT) had been demonstrated to play an important role in the evolution of prokaryotes. Their impact on phylogeny was the subject of a heated debate, with some proposing that the concept of a species tree should be abandoned. The phylogeny of prokaryotes does contain a major part of the historical signal, because stable and functional horizontal transmissions appear to be by far rarer than vertical transmissions (tens versus billions). However, the cumulative effect of HGT is non-negligible and can potentially affect phylogenetic inference. Therefore, most researchers base their phylogenetic inference on a low number of rarely transferred genes such as ribosomal proteins, but they assume the selection of the model of evolution as less important, this despite the fact that it has been shown of prime importance for much less deep divergences, e.g. like animals. Here, we used a combination of simulations and of real data from Archaea to study the relative impact of HGT and of the inference methods on the phylogenetic accuracy. Our simulations prove that (1) HGTs have a limited impact on phylogeny, assuming a realistic rate and (2) the supermatrix is much more accurate than the supertree approach. We also observed that more complex models of evolution not only have a better fit to the data, but can also have a direct impact on different phylogenetic groups and on the robustness of the tree. Our results are in contradiction to a recent publication proposing that the Thaumarchaeota are at the base of the Archaeal tree

Dimérisation photocatalytique d’alcynes pour la synthèse de 1,3-énynes

Ce mémoire présente une nouvelle méthode pour la synthèse de 1,3-énynes par dimérisation d’alcynes terminaux. La méthode de synthèse utilisée est la métallaphotorédox, une technologie qui s’est largement développée au cours des dernières années. Celle-ci nécessite l’utilisation de la lumière visible comme source d’énergie, un photocatalyseur qui peut absorber la lumière ainsi qu’un catalyseur métallique qui peut interagir avec le photocatalyseur. La dimérisation d’alcyne peut être achevée en soumettant un alcyne terminal face à de la lumière bleue en présence du photocatalyseur 4CzIPN, du catalyseur Co(BF4)2·6H2O, du ligand DPPP et de la base DIPEA qui fait office d’anode sacrificielle, dans l’acétonitrile. Les réactions d’homo-dimérisation (un alcyne avec un autre alcyne identique) fournissent des rendements de 48 à 90 % avec un rapport E:Z de >99:1 pour l’ényne formé. Des réactions d’hétéro-dimérisation (un alcyne avec un alcyne différent) peuvent également être effectuées entre un alcyne aliphatique ou aromatique et un alcyne de silyle (TMS ou TIPS) et les rendements varient de 47 à 99 % avec un rapport E:Z de >99:1 pour l’ényne formé. Cette méthodologie a ensuite été appliquée pour des réactions de macrocyclisation. Trois macrocycles à 17, 18 et 19 chaînons ont pu être synthétisés de cette manière avec des rendements respectifs de 25, 91 et 37 %.This thesis presents a new methodology for the synthesis of 1,3-enynes by dimerization of terminal alkynes. The synthetic method used is based on metallaphotoredox, a technology that was largely developed during the last few years. The latter uses visible light as an energy source, a photocatalyst that can absorb the light and a metal-based catalyst that interacts with the photocatalyst. The dimerization of alkyne can be achieved by submitting a terminal alkyne under blue light irradiation in the presence of the photocatalyst 4CzIPN, the catalyst Co(BF4)2·6H2O, the ligand DPPP and the base DIPEA which is used as a sacrificial anode, in acetonitrile. The reactions of homo-dimerization (one alkyne with an identical alkyne) provides yields ranging from 48 to 90 % and a E:Z ratio of >99:1 for the resulting enyne. Reactions of hetero-dimerization (one alkyne with a different alkyne) can also be achieve with an aliphatic or aromatic alkyne and a silyl alkyne (TMS or TIPS) with yields ranging from 47 to 99 % and a E:Z ratio of >99:1 for the resulting enyne. This methodology was then applied for macrocyclization reactions. Macrocycles with 17-, 18- and 19- members ring were synthesized that way, with yield of 25, 91 and 37 % respectively

Gene activation precedes DNA demethylation in response to infection in human dendritic cells

DNA methylation is considered to be a relatively stable epigenetic mark. However, a growing body of evidence indicates that DNA methylation levels can change rapidly; for example, in innate immune cells facing an infectious agent. Nevertheless, the causal relationship between changes in DNA methylation and gene expression during infection remains to be elucidated. Here, we generated time-course data on DNA methylation, gene expression, and chromatin accessibility patterns during infection of human dendritic cells with Mycobacterium tuberculosis. We found that the immune response to infection is accompanied by active demethylation of thousands of CpG sites overlapping distal enhancer elements. However, virtually all changes in gene expression in response to infection occur before detectable changes in DNA methylation, indicating that the observed losses in methylation are a downstream consequence of transcriptional activation. Footprinting analysis revealed that immune-related transcription factors (TFs), such as NF-κB/Rel, are recruited to enhancer elements before the observed losses in methylation, suggesting that DNA demethylation is mediated by TF binding to cis-acting elements. Collectively, our results show that DNA demethylation plays a limited role to the establishment of the core regulatory program engaged upon infection

Primate innate immune responses to bacterial and viral pathogens reveals an evolutionary trade-off between strength and specificity

Despite their close genetic relatedness, apes and African and Asian monkeys (AAMs) differ in their susceptibility to severe bacterial and viral infections that are important causes of human disease. Such differences between humans and other primates are thought to be a result, at least in part, of interspecies differences in immune response to infection. However, because of the lack of comparative functional data across species, it remains unclear in what ways the immune systems of humans and other primates differ. Here, we report the whole-genome transcriptomic responses of ape species (human and chimpanzee) and AAMs (rhesus macaque and baboon) to bacterial and viral stimulation. We find stark differences in the responsiveness of these groups, with apes mounting a markedly stronger early transcriptional response to both viral and bacterial stimulation, altering the transcription of ∼40% more genes than AAMs. Additionally, we find that genes involved in the regulation of inflammatory and interferon responses show the most divergent early transcriptional responses across primates and that this divergence is attenuated over time. Finally, we find that relative to AAMs, apes engage a much less specific immune response to different classes of pathogens during the early hours of infection, up-regulating genes typical of anti-viral and anti-bacterial responses regardless of the nature of the stimulus. Overall, these findings suggest apes exhibit increased sensitivity to bacterial and viral immune stimulation, activating a broader array of defense molecules that may be beneficial for early pathogen killing at the potential cost of increased energy expenditure and tissue damage

Morphological assessment of non-human primate models of osteoarthritis: Comparisons of HR-MRI with CT arthrography (CTA)

International audienc

A Short-Term High-Fat Diet Alters Glutathione Levels and IL-6 Gene Expression in Oxidative Skeletal Muscles of Young Rats

Obesity and ensuing disorders are increasingly prevalent worldwide. High-fat diets (HFD) and diet-induced obesity have been shown to induce oxidative stress and inflammation while altering metabolic homeostasis in many organs, including the skeletal muscle. We previously observed that 14 days of HFD impairs contractile functions of the soleus (SOL) oxidative skeletal muscle. However, the mechanisms underlying these effects are not clarified. In order to determine the effects of a short-term HFD on skeletal muscle glutathione metabolism, young male Wistar rats (100–125 g) were fed HFD or a regular chow diet (RCD) for 14 days. Reduced (GSH) and disulfide (GSSG) glutathione levels were measured in the SOL. The expression of genes involved in the regulation of glutathione metabolism, oxidative stress, antioxidant defense and inflammation were measured by RNA-Seq. We observed a significant 25% decrease of GSH levels in the SOL muscle. Levels of GSSG and the GSH:GSSG ratio were similar in both groups. Further, we observed a 4.5 fold increase in the expression of pro-inflammatory cytokine interleukin 6 (IL-6) but not of other cytokines or markers of inflammation and oxidative stress. We hereby demonstrate that a short-term HFD significantly lowers SOL muscle GSH levels. This effect could be mediated through the increased expression of IL-6. Further, the skeletal muscle antioxidant defense could be impaired under cellular stress. We surmise that these early alterations could contribute to HFD-induced insulin resistance observed in longer protocols

Chronic inflammation permanently reshapes tissue-resident immunity in celiac disease

Tissue-resident lymphocytes play a key role in immune surveillance, but it remains unclear how these inherently stable cell populations respond to chronic inflammation. In the setting of celiac disease (CeD), where exposure to dietary antigen can be controlled, gluten-induced inflammation triggered a profound depletion of naturally occurring Vγ4+/Vδ1+ intraepithelial lymphocytes (IELs) with innate cytolytic properties and specificity for the butyrophilin-like (BTNL) molecules BTNL3/BTNL8. Creation of a new niche with reduced expression of BTNL8 and loss of Vγ4+/Vδ1+ IELs was accompanied by the expansion of gluten-sensitive, interferon-γ-producing Vδ1+ IELs bearing T cell receptors (TCRs) with a shared non-germline-encoded motif that failed to recognize BTNL3/BTNL8. Exclusion of dietary gluten restored BTNL8 expression but was insufficient to reconstitute the physiological Vγ4+/Vδ1+ subset among TCRγδ+ IELs. Collectively, these data show that chronic inflammation permanently reconfigures the tissue-resident TCRγδ+ IEL compartment in CeD

Plasma amyloid β levels are driven by genetic variants near APOE, BACE1, APP, PSEN2: A genome-wide association study in over 12,000 non-demented participants

INTRODUCTION: There is increasing interest in plasma amyloid beta (Aβ) as an endophenotype of Alzheimer's disease (AD). Identifying the genetic determinants of plasma Aβ levels may elucidate important biological processes that determine plasma Aβ measures. METHODS: We included 12,369 non-demented participants from eight population-based studies. Imputed genetic data and measured plasma Aβ1-40, Aβ1-42 levels and Aβ1-42/Aβ1-40 ratio were used to perform genome-wide association studies, and gene-based and pathway analyses. Significant variants and genes were followed up for their association with brain positron emission tomography Aβ deposition and AD risk. RESULTS: Single-variant analysis identified associations with apolipoprotein E (APOE) for Aβ1-42 and Aβ1-42/Aβ1-40 ratio, and BACE1 for Aβ1-40. Gene-based analysis of Aβ1-40 additionally identified associations for APP, PSEN2, CCK, and ZNF397. There was suggestive evidence for interaction between a BACE1 variant and APOE ε4 on brain Aβ deposition. DISCUSSION: Identification of variants near/in known major Aβ-processing genes strengthens the relevance of plasma-Aβ levels as an endophenotype of AD

Convergent genetic and expression data implicate immunity in Alzheimer's disease

Background Late–onset Alzheimer's disease (AD) is heritable with 20 genes showing genome wide association in the International Genomics of Alzheimer's Project (IGAP). To identify the biology underlying the disease we extended these genetic data in a pathway analysis. Methods The ALIGATOR and GSEA algorithms were used in the IGAP data to identify associated functional pathways and correlated gene expression networks in human brain. Results ALIGATOR identified an excess of curated biological pathways showing enrichment of association. Enriched areas of biology included the immune response (p = 3.27×10-12 after multiple testing correction for pathways), regulation of endocytosis (p = 1.31×10-11), cholesterol transport (p = 2.96 × 10-9) and proteasome-ubiquitin activity (p = 1.34×10-6). Correlated gene expression analysis identified four significant network modules, all related to the immune response (corrected p 0.002 – 0.05). Conclusions The immune response, regulation of endocytosis, cholesterol transport and protein ubiquitination represent prime targets for AD therapeutics