Evolutionary and ecological significance of non-shivering thermogenesis in the common vole

La production endogène à long terme de chaleur, même au repos, est une adaptation que l'on retrouve chez les animaux à sang chaud (les oiseaux et les mammifères). Cette production de chaleur a comme but le maintien d'une température constante du corps indépendamment de la température extérieure. A cette fin, les mammifères ont développé une forme de tissu spécialisé nommé tissu adipeux brun (BAT). Ce tissu est responsable de la conversion de nourriture en chaleur, procédé appelé thermogenèse sans frisson (NST = non-shivering thermogenesis). Durant ce procédé la uncoupling protein 1 (UCP1) convertit, au sein des mitochondries, la nourriture en chaleur au lieu de produire de l'ATP, molécule utilisée comme énergie cellulaire. On suppose que cette inefficacité de la conversion de la nourriture en ATP dans le BAT influence l'homéostasie de l'énergie, l'allocation des ressources ainsi que la régulation de processus gourmant en énergie comme la croissance et la reproduction. Afin de maintenir une température du corps constante, les mammifères doivent ajuster leur NST en fonction de la température ambiante. La NST devrait être donc plus importante que la croissance et la reproduction durant l'hiver que lors l'été/à haute altitude qu'à basse altitude. En effet, plusieurs études ont déjà démontré la dépendance de la NST aux divers paramètres environnementaux. Par contre, l'héritabilité de la NST ainsi que sa relation avec d'autres traits de caractère, ne sont que très peu connus, ceci malgré l'importance d'une telle information afin de pouvoir comprendre son potentiel évolutif. L'étude de l'importance évolutive et écologique sur la NST chez les campagnols des champs (Microtus arvalis) fut donc le but cette thèse de doctorat. Grâce aux informations collectées sur 4 générations de campagnols (chapitre 1), une dépendance saisonnière et journalière de la NST a été démontrée: elle augmente lors des périodes froides et diminue lors de la lactation. On a démontré que bien qu'étant plastique, la variation de la NST a une composante génétique significative. Elle est corrélée avec le taux d'activité métabolique au repos indiquant des contraintes intrinsèques. A l'aide d'une expérience de jardin commune, on a pu démontrer dans le chapitre 2 que les campagnols habitant en altitude ont une capacité génétique de thermogenèse sans frisson plus haute que celles de basse altitude. Ils produisent des portées plus petites et leur descendance grandit moins vite, surtout à partir du 10ème jour ce qui coïncide avec le début de la production de chaleur endogène. En choisissant artificiellement des campagnols avec une NST faible ou grande, on a pu démontrer une relation entre la NST et la développement de la masse corporelle. Les campagnols avec une haute NST grandissent plus lentement et sont plus légères à l'âge adulte que celles ayant une basse NST. A l'aide d'un croisement interligne entre les campagnols sélectionnés (avec basse et haute NST), on a pu montrer dans le chapitre 3 des effets « parent-of-origin >> du développement massique de la descendance, indiquant une empreinte génétique parentale. Cela veut dire que l'expression d'un allele dépend de l'origine parentale. De plus, des effets « parent-of-origin » des taux de base de norépinephrine et d'irisine ont pu être trouvés. Ces hormones sont connues pour influencer non seulement la TSF mais aussi d'autres caractéristiques. Ces influences ouvrent la voie à de nouvelles études sur la relation entre la TSF et l'histoire de vie. Dans le chapitre 4 on a démontré des effets à long terme de l'allocation des ressources en manipulant la taille des portées qui ont abouti à des différences dans l'investissement dans la reproduction et de la croissance de la descendance à la fois dans le cas de la reproduction manipulé et aussi dans le non - manipulée entre les femelles avec portées agrandies et réduites. Ensemble, ces résultats mettent en évidence le rôle central de la NST dans l'allocation des ressources sur la base d'un compromis entre le maintien et la croissance et ainsi transforme l'histoire de vie des mammifères. Ces études montrent comment les mammifères peuvent répondre rapidement à court et à long terme (c'est-à-dire par des réponses génétiques ou plastiques) à un changement rapide du climat. On montre aussi qu'il y a probablement une corrélation entre l'histoire de vie et des changements du comportement. Finalement mes résultats ont montré un lien étroit entre la NST et la croissance et les dimensions du corps. Ces résultats indiquent que le tissu adipeux brun et la NST pourraient être une cible thérapeutique intéressante pour traiter l'obésité.

Symbiotic effectiveness and ecological characterization of indigenous Rhizobium loti populations in Uruguay

The objectives of this work were to describe the distribution, density and seasonal variation of the indigenous populations of Rhizobium loti in different Uruguayan soils and to determine the symbiotic effectiveness and stress tolerance factors of different isolates, both with the aim of obtaining selected strains to re-introduce as inoculants in Lotus pastures. R. loti was present in ten soils studied and their densities varied from year to year and within each soil. All the isolates nodulated Lotus corniculatus effectively. The nodules in Lotus pedunculatus and Lotus subbiflorus were small, red on the surface and ineffective in nitrogen fixation. The study of 50 isolates from the ten soils showed high variability in their symbiotic efficiency and tolerance to pH. The indigenous population was acid tolerant in culture medium (pH 4.5), 83% of them could grow at pH 4.5 in 3 days. This work showed that there was a great diversity between the strains of R. loti isolated from Uruguayan soils and supports the importance of selecting among them the most efficient and resistant strains to be included in the inoculants.

Comparative genomics suggests that the human pathogenic fungus Pneumocystis jirovecii acquired obligate biotrophy through gene loss.

Pneumocystis jirovecii is a fungal parasite that colonizes specifically humans and turns into an opportunistic pathogen in immunodeficient individuals. The fungus is able to reproduce extracellularly in host lungs without eliciting massive cellular death. The molecular mechanisms that govern this process are poorly understood, in part because of the lack of an in vitro culture system for Pneumocystis spp. In this study, we explored the origin and evolution of the putative biotrophy of P. jirovecii through comparative genomics and reconstruction of ancestral gene repertoires. We used the maximum parsimony method and genomes of related fungi of the Taphrinomycotina subphylum. Our results suggest that the last common ancestor of Pneumocystis spp. lost 2,324 genes in relation to the acquisition of obligate biotrophy. These losses may result from neutral drift and affect the biosyntheses of amino acids and thiamine, the assimilation of inorganic nitrogen and sulfur, and the catabolism of purines. In addition, P. jirovecii shows a reduced panel of lytic proteases and has lost the RNA interference machinery, which might contribute to its genome plasticity. Together with other characteristics, that is, a sex life cycle within the host, the absence of massive destruction of host cells, difficult culturing, and the lack of virulence factors, these gene losses constitute a unique combination of characteristics which are hallmarks of both obligate biotrophs and animal parasites. These findings suggest that Pneumocystis spp. should be considered as the first described obligate biotrophs of animals, whose evolution has been marked by gene losses.

Genomics: more than genes

The fundamentals of Real-time Polymerase Chain Reaction,Automated capillary electrophoresis -Sanger sequencing and Fragmentanalysis- and "Next-generation" sequencing are reviewed. An overview ofapplications is presented using our own examples carried out in our facility.

Ecological niche overlap in sister species: how do oil-collecting bees Macropis europaea and M. fulvipes (Hymenoptera: Melittidae) avoid competition and hybridization?

Oil-collecting bees are found worldwide and always in association with particular oil-producing flowers. In the Western Palearctic, three oil-collecting bee species within the genus Macropis (Hymenoptera, Melittidae) interact in a tight pollination mutualism with species of the only European oil-producing plant genus Lysimachia L. (Myrsinaceae). Two of these oil-collecting bees (Macropis europaea and Macropis fulvipes) show overlapping geographic distributions, comparable morphologies, and similar ecological characteristics (e.g., habitat type, floral preferences). In view of these similarities, we presume that hybridization should occur between the two species unless potential variation among the species' ecological niches prevents it, simultaneously decreasing competition for resources. Using modern genetic analyses and ecological niche modeling on a large bee sampling throughout Europe, we discuss new perspectives on the ecology and evolutionary history of this mutualism.

Evolutionary insights on C4 photosynthetic subtypes in grasses from genomics and phylogenetics

In plants, an oligogene family encodes NADP-malic enzymes (NADP-me), which are responsible for various functions and exhibit different kinetics and expression patterns. In particular, a chloroplast isoform of NADP-me plays a key role in one of the three biochemical subtypes of C4 photosynthesis, an adaptation to warm environments that evolved several times independently during angiosperm diversification. By combining genomic and phylogenetic approaches, this study aimed at identifying the molecular mechanisms linked to the recurrent evolutions of C4-specific NADP-me in grasses (Poaceae). Genes encoding NADP-me (nadpme) were retrieved from genomes of model grasses and isolated from a large sample of C3 and C4 grasses. Genomic and phylogenetic analyses showed that 1) the grass nadpme gene family is composed of four main lineages, one of which is expressed in plastids (nadpme-IV), 2) C4-specific NADP-me evolved at least five times independently from nadpme-IV, and 3) some codons driven by positive selection underwent parallel changes during the multiple C4 origins. The C4 NADP-me being expressed in chloroplasts probably constrained its recurrent evolutions from the only plastid nadpme lineage and this common starting point limited the number of evolutionary paths toward a C4 optimized enzyme, resulting in genetic convergence. In light of the history of nadpme genes, an evolutionary scenario of the C4 phenotype using NADP-me is discussed.

Spatial Polarization of the Ecological Footprint distribution

The international allocation of natural resources is determined, not by any ethical or ecological criteria, but by the dominance of market mechanisms. From a core-periphery perspective, this allocation may even be driven by historically determined structural patterns, with a core group of countries whose consumption appropriates most available natural resources, and another group, having low natural resource consumption, which plays a peripheral role. This article consists of an empirical distributional analysis of natural resource consumption (as measured by Ecological Footprints) whose purpose is to assess the extent to which the distribution of consumption responds to polarization (as opposed to mere inequality). To assess this, we estimate and decompose different polarization indices for a balanced sample of 119 countries over the period 1961 to 2007. Our results points toward a polarized distribution which is consistent with a core-periphery framework.

Functional genomics of intracellular bacteria.

During the genomic era, a large amount of whole-genome sequences accumulated, which identified many hypothetical proteins of unknown function. Rapidly, functional genomics, which is the research domain that assign a function to a given gene product, has thus been developed. Functional genomics of intracellular pathogenic bacteria exhibit specific peculiarities due to the fastidious growth of most of these intracellular micro-organisms, due to the close interaction with the host cell, due to the risk of contamination of experiments with host cell proteins and, for some strict intracellular bacteria such as Chlamydia, due to the absence of simple genetic system to manipulate the bacterial genome. To identify virulence factors of intracellular pathogenic bacteria, functional genomics often rely on bioinformatic analyses compared with model organisms such as Escherichia coli and Bacillus subtilis. The use of heterologous expression is another common approach. Given the intracellular lifestyle and the many effectors that are used by the intracellular bacteria to corrupt host cell functions, functional genomics is also often targeting the identification of new effectors such as those of the T4SS of Brucella and Legionella.

Modelling ecological niches with support vector machines

1. The ecological niche is a fundamental biological concept. Modelling species' niches is central to numerous ecological applications, including predicting species invasions, identifying reservoirs for disease, nature reserve design and forecasting the effects of anthropogenic and natural climate change on species' ranges. 2. A computational analogue of Hutchinson's ecological niche concept (the multidimensional hyperspace of species' environmental requirements) is the support of the distribution of environments in which the species persist. Recently developed machine-learning algorithms can estimate the support of such high-dimensional distributions. We show how support vector machines can be used to map ecological niches using only observations of species presence to train distribution models for 106 species of woody plants and trees in a montane environment using up to nine environmental covariates. 3. We compared the accuracy of three methods that differ in their approaches to reducing model complexity. We tested models with independent observations of both species presence and species absence. We found that the simplest procedure, which uses all available variables and no pre-processing to reduce correlation, was best overall. Ecological niche models based on support vector machines are theoretically superior to models that rely on simulating pseudo-absence data and are comparable in empirical tests. 4. Synthesis and applications. Accurate species distribution models are crucial for effective environmental planning, management and conservation, and for unravelling the role of the environment in human health and welfare. Models based on distribution estimation rather than classification overcome theoretical and practical obstacles that pervade species distribution modelling. In particular, ecological niche models based on machine-learning algorithms for estimating the support of a statistical distribution provide a promising new approach to identifying species' potential distributions and to project changes in these distributions as a result of climate change, land use and landscape alteration.

Contribution of electrostatic interactions, compactness and quaternary structure to protein thermostability: lessons from structural genomics of Thermotoga maritima.

Studies of the structural basis of protein thermostability have produced a confusing picture. Small sets of proteins have been analyzed from a variety of thermophilic species, suggesting different structural features as responsible for protein thermostability. Taking advantage of the recent advances in structural genomics, we have compiled a relatively large protein structure dataset, which was constructed very carefully and selectively; that is, the dataset contains only experimentally determined structures of proteins from one specific organism, the hyperthermophilic bacterium Thermotoga maritima, and those of close homologs from mesophilic bacteria. In contrast to the conclusions of previous studies, our analyses show that oligomerization order, hydrogen bonds, and secondary structure play minor roles in adaptation to hyperthermophily in bacteria. On the other hand, the data exhibit very significant increases in the density of salt-bridges and in compactness for proteins from T.maritima. The latter effect can be measured by contact order or solvent accessibility, and network analysis shows a specific increase in highly connected residues in this thermophile. These features account for changes in 96% of the protein pairs studied. Our results provide a clear picture of protein thermostability in one species, and a framework for future studies of thermal adaptation.

Natural genetic variation in Arabidopsis: tools, traits and prospects for evolutionary ecology.

BACKGROUND: The model plant Arabidopsis thaliana (Arabidopsis) shows a wide range of genetic and trait variation among wild accessions. Because of its unparalleled biological and genomic resources, the potential of Arabidopsis for molecular genetic analysis of this natural variation has increased dramatically in recent years. SCOPE: Advanced genomics has accelerated molecular phylogenetic analysis and gene identification by quantitative trait loci (QTL) mapping and/or association mapping in Arabidopsis. In particular, QTL mapping utilizing natural accessions is now becoming a major strategy of gene isolation, offering an alternative to artificial mutant lines. Furthermore, the genomic information is used by researchers to uncover the signature of natural selection acting on the genes that contribute to phenotypic variation. The evolutionary significance of such genes has been evaluated in traits such as disease resistance and flowering time. However, although molecular hallmarks of selection have been found for the genes in question, a corresponding ecological scenario of adaptive evolution has been difficult to prove. Ecological strategies, including reciprocal transplant experiments and competition experiments, and utilizing near-isogenic lines of alleles of interest will be a powerful tool to measure the relative fitness of phenotypic and/or allelic variants. CONCLUSIONS: As the plant model organism, Arabidopsis provides a wealth of molecular background information for evolutionary genetics. Because genetic diversity between and within Arabidopsis populations is much higher than anticipated, combining this background information with ecological approaches might well establish Arabidopsis as a model organism for plant evolutionary ecology.