Candidate genes revealed by a genome scan for mosquito resistance to a bacterial insecticide: sequence and gene expression variations

<p>Abstract</p> <p>Background</p> <p>Genome scans are becoming an increasingly popular approach to study the genetic basis of adaptation and speciation, but on their own, they are often helpless at identifying the specific gene(s) or mutation(s) targeted by selection. This shortcoming is hopefully bound to disappear in the near future, thanks to the wealth of new genomic resources that are currently being developed for many species. In this article, we provide a foretaste of this exciting new era by conducting a genome scan in the mosquito <it>Aedes aegypti </it>with the aim to look for candidate genes involved in resistance to <it>Bacillus thuringiensis </it>subsp. <it>israelensis </it>(<it>Bti</it>) insecticidal toxins.</p> <p>Results</p> <p>The genome of a <it>Bti</it>-resistant and a <it>Bti</it>-susceptible strains was surveyed using about 500 MITE-based molecular markers, and the loci showing the highest inter-strain genetic differentiation were sequenced and mapped on the <it>Aedes aegypti </it>genome sequence. Several good candidate genes for <it>Bti</it>-resistance were identified in the vicinity of these highly differentiated markers. Two of them, coding for a cadherin and a leucine aminopeptidase, were further examined at the sequence and gene expression levels. In the resistant strain, the cadherin gene displayed patterns of nucleotide polymorphisms consistent with the action of positive selection (e.g. an excess of high compared to intermediate frequency mutations), as well as a significant under-expression compared to the susceptible strain.</p> <p>Conclusion</p> <p>Both sequence and gene expression analyses agree to suggest a role for positive selection in the evolution of this cadherin gene in the resistant strain. However, it is unlikely that resistance to <it>Bti </it>is conferred by this gene alone, and further investigation will be needed to characterize other genes significantly associated with <it>Bti </it>resistance in <it>Ae. aegypti</it>. Beyond these results, this article illustrates how genome scans can build on the body of new genomic information (here, full genome sequence and MITE characterization) to finally hold their promises and help pinpoint candidate genes for adaptation and speciation.</p

A MITE-based genotyping method to reveal hundreds of DNA polymorphisms in an animal genome after a few generations of artificial selection

<p>Abstract</p> <p>Background</p> <p>For most organisms, developing hundreds of genetic markers spanning the whole genome still requires excessive if not unrealistic efforts. In this context, there is an obvious need for methodologies allowing the low-cost, fast and high-throughput genotyping of virtually any species, such as the Diversity Arrays Technology (DArT). One of the crucial steps of the DArT technique is the genome complexity reduction, which allows obtaining a genomic representation characteristic of the studied DNA sample and necessary for subsequent genotyping. In this article, using the mosquito <it>Aedes aegypti </it>as a study model, we describe a new genome complexity reduction method taking advantage of the abundance of miniature inverted repeat transposable elements (MITEs) in the genome of this species.</p> <p>Results</p> <p><it>Ae. aegypti </it>genomic representations were produced following a two-step procedure: (1) restriction digestion of the genomic DNA and simultaneous ligation of a specific adaptor to compatible ends, and (2) amplification of restriction fragments containing a particular MITE element called <it>Pony </it>using two primers, one annealing to the adaptor sequence and one annealing to a conserved sequence motif of the <it>Pony </it>element. Using this protocol, we constructed a library comprising more than 6,000 DArT clones, of which at least 5.70% were highly reliable polymorphic markers for two closely related mosquito strains separated by only a few generations of artificial selection. Within this dataset, linkage disequilibrium was low, and marker redundancy was evaluated at 2.86% only. Most of the detected genetic variability was observed between the two studied mosquito strains, but individuals of the same strain could still be clearly distinguished.</p> <p>Conclusion</p> <p>The new complexity reduction method was particularly efficient to reveal genetic polymorphisms in <it>Ae. egypti</it>. Overall, our results testify of the flexibility of the DArT genotyping technique and open new prospects as regards its application to a wider range of species, including animals which have been refractory to it so far. DArT has also a role to play in the current burst of whole-genome scans carried out in various organisms, which track signatures of selection in order to unravel the basis of genetic adaptation.</p

Promoting collaboration between livestock and wildlife conservation genetics communities

The collaboration between livestock and wildlife conservation genetics communities has the potential to help promote shared priorities, with respect to emerging technologies and new analytical approaches such as next generation sequencing incorporating adaptive variation. The GLOBALDIV Consortium recently organized an international workshop held at the Ecole Polytechnique Fédérale de Lausanne (Switzerland) including a whole-day session with contributions aimed at taking stock of the situation regarding the extent of information and methodology exchange between the two communities. Discussions permitted the identification of potential benefits of further promoting cooperation in the context of genetic monitoring in particular, a central concept to current concerns for both the livestock and wildlife conservation communitie

Review of Actinide Decorporation with Chelating Agents

International audienceIn case of accidental release of radionuclides in a nuclear facility or in the environment, internal contamination (inhalation, in-gestion or wound) with actinides represents a severe health risk to human beings. It is therefore important to provide effective che-lation therapy or decorporation to reduce acute radiation damage, chemical toxicity, and late radiation effects. Speciation governs bioavailability and toxicity of elements and it is a prerequisite tool for the design and success of new ligands or chelating agents. The purpose of this review is to present the state-of-the-art of actinide decorporation within biological media, to recall briefly actinide metabolism, to list the basic constraints of actinideeligand for development, to describe main tools developed and used for decorporation studies, to review mainly the chelating agents tested for actinides, and finally to conclude on the future trends in this field. To cite this article: E ´. Ansoborlo et al., C. R. Chimie X 33 (2007). Ó 2007 Académie des sciences. Published by Elsevier Masson SAS. All rights reserved.En cas de rejet accidentel de radionucléides dans une installation nucléaire ou dans l'environnement, il existe un risque de contamination interne (inhalation, ingestion ou blessure) pour l'homme et il est important de pouvoir fournir un traitement thérapeutique par des agents chélatants ou décorporation permettant de réduire la dose, la toxicité chimique et les effets retardés des radiations.La spéciation domine la biodisponibilité et la toxicité des éléments et représente un outil indispensable pour la conception et l'efficacité de nouveaux ligands ou chélatants. Le but de cet article est de présenter l'état de l'art sur la décorporation des actinides en milieu biologique, de rappeler les grandes lignes du métabolisme des actinides, de lister les contraintes indispensables actinide–ligands pour la décorporation, de décrire succinctement les principaux outils expérimentaux ou analytiques utilisés, de passer en revue les principaux ligands testés pour les actinides et de présenter les orientations du futur dans ce domaine

Metabarcoding data reveal vertical multitaxa variation in topsoil communities during the colonization of deglaciated forelands

Ice-free areas are expanding worldwide due to dramatic glacier shrinkage and are undergoing rapid colonization by multiple lifeforms, thus representing key environments to study ecosystem development. It has been proposed that the colonization dynamics of deglaciated terrains is different between surface and deep soils but that the heterogeneity between communities inhabiting surface and deep soils decreases through time. Nevertheless, tests of this hypothesis remain scarce, and it is unclear whether patterns are consistent among different taxonomic groups. Here, we used environmental DNA metabarcoding to test whether community diversity and composition of six groups (Eukaryota, Bacteria, Mycota, Collembola, Insecta, and Oligochaeta) differ between the surface (0–5 cm) and deeper (7.5–20 cm) soil at different stages of development and across five Alpine glaciers. Taxonomic diversity increased with time since glacier retreat and with soil evolution. The pattern was consistent across groups and soil depths. For Eukaryota and Mycota, alpha-diversity was highest at the surface. Time since glacier retreat explained more variation of community composition than depth. Beta-diversity between surface and deep layers decreased with time since glacier retreat, supporting the hypothesis that the first 20 cm of soil tends to homogenize through time. Several molecular operational taxonomic units of bacteria and fungi were significant indicators of specific depths and/or soil development stages, confirming the strong functional variation of microbial communities through time and depth. The complexity of community patterns highlights the importance of integrating information from multiple taxonomic groups to unravel community variation in response to ongoing global changes

Relations between climatic fluctuations, carbon cycle perturbations and carbonate production crises : focus on the early cretaceous

Le Crétacé inférieur est ponctué de perturbations du cycle du carbone associées à des épisodes de préservation de matière organique et à des crises de la production carbonatée néritique et pélagique. Ces évènements coïncident également avec des refroidissements à très court terme (<1Ma) dont l’origine et les conséquences sont encore imprécises en raison de la faible résolution des courbes de températures dans les eaux de surface. Les études récentes réalisées à partir de modèles climatiques couplés à des modèles géochimiques laissent penser qu’une crise de la production carbonatée pourrait engendrer un refroidissement climatique sur une échelle de temps inférieure à 1 Ma (Donnadieu et al., accepté). Basées sur les dépôts d’âge Valanginien des coupes de La Charce–Vergol et d’Ollioules (Sud-est de la France) et sur les sédiments de l’Aptien du sous-Bassin de Galvé (Nord-est de l’Espagne), des études stratigraphiques, paléoécologiques et géochimiques ont été menées pour établir les relations entre la production carbonatée et le climat au cours du Valanginien et de l’Aptien. Pour cela, des courbes de température à haute résolution pour les eaux de surface ont été établies et mises en regard des évolutions des producteurs néritiques et pélagiques de carbonate. Le Valanginien et l’Aptien présentent tous deux des arrêts polyphasés de la production carbonatée néritique. Certains arrêts précèdent des refroidissements à court terme, dont ceux datés du Valanginien supérieur, du début et de la fin de l’Aptien inférieur. Cette succession suggérerait un lien de cause à effet entre les crises de la production et les fluctuations climatiques. Toutefois, les refroidissements du Valanginien supérieur et de la fin de l’Aptien inférieur sont respectivement précédés par un enfouissement de matière organique continentale et océanique, qui est un processus pouvant également générer une diminution de CO2 et un refroidissement. Ce travail a permis de mettre en évidence les répercutions des changements climatiques sur la production carbonatée par l’intermédiaire de changements de producteurs dans les domaines néritiques et pélagiques. Dans un premier temps, la mise en place de conditions froides au Valanginien supérieur et à la fin de l’Aptien inférieur est suivie de remplacements floro-fauniques caractérisés par l’évolution de communautés hétérozoaires à photozoaires. Les bouleversements observés suggèrent un changement drastique des conditions trophiques sous le développement de conditions arides relatives au refroidissement. Dans un second temps, l’évolution des communautés pélagiques au Valanginien répondraient également aux changements climatiques : ces communautés marquées d’un déclin depuis la fin du Valanginien inférieur présentent une courte reprise du début au milieu du Valanginien supérieur. Cette reprise coïncide avec le développement de conditions froides et plus arides occasionnant des conditions trophiques plus faiblesThe Early Cretaceous is punctuated by carbon cycle perturbations, associated with organic matter burial episodes and carbonate production crises. These events coincide with short-term cooling (<1Ma), yet the mechanisms are still unclear, because of low resolution in sea surface temperature reconstructions. Recent climatic models suggest that carbonate-platform-collapse events may trigger a short-term ocean cooling episode (Donnadieu et al., accepted). In order to establish relations between climates and carbonate productions, we performed stratigraphic, palaeoecologic and geochemical analyses on Valanginian sediments from the La Charce-Vergol and the Ollioules sections (South-East France) and Aptian sedimentary record of the Galvé subasin (North East Spain). Therefore, high-resolution sea surface temperature curves were reconstructed with regard to the pelagic and neritic carbonate producer evolution. Both Valanginian and Aptian stages are marked by polyphased neritic production drawdown. Moreover, the Late Valanginian, basal and latest Early Aptian carbonate-platform demises predate a short-term cooling occurrence. The chronology of these events may imply that carbonate production decrease may have affected the atmospheric CO2 pool and the climate. Nevertheless, the decreases of water temperature that took place in the Late Valanginian and the latest Early Aptian are also prior to episodes of continental and oceanic organic matter burial, respectively. This process is also known as a CO2 drawdown and cooling generator. The present study allowed establishing climate feedbacks on the pelagic and neritic carbonate producers triggering fluctuations of the carbonate production fluxes. At first, cooler conditions during the Late Valanginien and latest Early Aptian are posterior to floro-faunal changes characterised by heterozoan to photozoan replacements. These suggest a trophic level decrease relative to cool and dryer climatic condition. Subsequently, nannoconid communities seem to record a response to the Late Valanginian climatic change: these producers are characterised by a decline from the latest Early Valanginian onward, interrupted by a recovery from the earliest Late Valanginian up to the mid-Late Valanginian. This recovery coincides with the development of cooling and dryer conditions, triggering low trophic level and thus promoting a subsequent pelagic production recovery

Relations entre les variations climatiques, les perturbations du cycle du carbone et les crises de la production carbonatée : application au Crétacé inférieur

The Early Cretaceous is punctuated by carbon cycle perturbations, associated with organic matter burial episodes and carbonate production crises. These events coincide with short-term cooling (<1Ma), yet the mechanisms are still unclear, because of low resolution in sea surface temperature reconstructions. Recent climatic models suggest that carbonate-platform-collapse events may trigger a short-term ocean cooling episode (Donnadieu et al., accepted). In order to establish relations between climates and carbonate productions, we performed stratigraphic, palaeoecologic and geochemical analyses on Valanginian sediments from the La Charce-Vergol and the Ollioules sections (South-East France) and Aptian sedimentary record of the Galvé subasin (North East Spain). Therefore, high-resolution sea surface temperature curves were reconstructed with regard to the pelagic and neritic carbonate producer evolution. Both Valanginian and Aptian stages are marked by polyphased neritic production drawdown. Moreover, the Late Valanginian, basal and latest Early Aptian carbonate-platform demises predate a short-term cooling occurrence. The chronology of these events may imply that carbonate production decrease may have affected the atmospheric CO2 pool and the climate. Nevertheless, the decreases of water temperature that took place in the Late Valanginian and the latest Early Aptian are also prior to episodes of continental and oceanic organic matter burial, respectively. This process is also known as a CO2 drawdown and cooling generator. The present study allowed establishing climate feedbacks on the pelagic and neritic carbonate producers triggering fluctuations of the carbonate production fluxes. At first, cooler conditions during the Late Valanginien and latest Early Aptian are posterior to floro-faunal changes characterised by heterozoan to photozoan replacements. These suggest a trophic level decrease relative to cool and dryer climatic condition. Subsequently, nannoconid communities seem to record a response to the Late Valanginian climatic change: these producers are characterised by a decline from the latest Early Valanginian onward, interrupted by a recovery from the earliest Late Valanginian up to the mid-Late Valanginian. This recovery coincides with the development of cooling and dryer conditions, triggering low trophic level and thus promoting a subsequent pelagic production recovery.Le Crétacé inférieur est ponctué de perturbations du cycle du carbone associées à des épisodes de préservation de matière organique et à des crises de la production carbonatée néritique et pélagique. Ces évènements coïncident également avec des refroidissements à très court terme (<1Ma) dont l’origine et les conséquences sont encore imprécises en raison de la faible résolution des courbes de températures dans les eaux de surface. Les études récentes réalisées à partir de modèles climatiques couplés à des modèles géochimiques laissent penser qu’une crise de la production carbonatée pourrait engendrer un refroidissement climatique sur une échelle de temps inférieure à 1 Ma (Donnadieu et al., accepté). Basées sur les dépôts d’âge Valanginien des coupes de La Charce–Vergol et d’Ollioules (Sud-est de la France) et sur les sédiments de l’Aptien du sous-Bassin de Galvé (Nord-est de l’Espagne), des études stratigraphiques, paléoécologiques et géochimiques ont été menées pour établir les relations entre la production carbonatée et le climat au cours du Valanginien et de l’Aptien. Pour cela, des courbes de température à haute résolution pour les eaux de surface ont été établies et mises en regard des évolutions des producteurs néritiques et pélagiques de carbonate. Le Valanginien et l’Aptien présentent tous deux des arrêts polyphasés de la production carbonatée néritique. Certains arrêts précèdent des refroidissements à court terme, dont ceux datés du Valanginien supérieur, du début et de la fin de l’Aptien inférieur. Cette succession suggérerait un lien de cause à effet entre les crises de la production et les fluctuations climatiques. Toutefois, les refroidissements du Valanginien supérieur et de la fin de l’Aptien inférieur sont respectivement précédés par un enfouissement de matière organique continentale et océanique, qui est un processus pouvant également générer une diminution de CO2 et un refroidissement. Ce travail a permis de mettre en évidence les répercutions des changements climatiques sur la production carbonatée par l’intermédiaire de changements de producteurs dans les domaines néritiques et pélagiques. Dans un premier temps, la mise en place de conditions froides au Valanginien supérieur et à la fin de l’Aptien inférieur est suivie de remplacements floro-fauniques caractérisés par l’évolution de communautés hétérozoaires à photozoaires. Les bouleversements observés suggèrent un changement drastique des conditions trophiques sous le développement de conditions arides relatives au refroidissement. Dans un second temps, l’évolution des communautés pélagiques au Valanginien répondraient également aux changements climatiques : ces communautés marquées d’un déclin depuis la fin du Valanginien inférieur présentent une courte reprise du début au milieu du Valanginien supérieur. Cette reprise coïncide avec le développement de conditions froides et plus arides occasionnant des conditions trophiques plus faible