Environmental and geographical factors structure soil microbial diversity in New Caledonian ultramafic substrates: A metagenomic approach

Soil microorganisms play key roles in ecosystem functioning and are known to be influenced by biotic and abiotic factors, such as plant cover or edaphic parameters. New Caledonia, a biodiversity hotspot located in the southwest Pacific, is one-third covered by ultramafic substrates. These types of soils are notably characterised by low nutrient content and high heavy metal concentrations. Ultramafic outcrops harbour diverse vegetation types and remarkable plant diversity. In this study, we aimed to assess soil bacterial and fungal diversity in New Caledonian ultramafic substrates and to determine whether floristic composition, edaphic parameters and geographical factors affect this microbial diversity. Therefore, four plant formation types at two distinct sites were studied. These formations represent different stages in a potential chronosequence. Soil cores, according to a given sampling procedure, were collected to assess microbial diversity using a metagenomic approach, and to characterise the physico-chemical parameters. A botanical inventory was also performed. Our results indicated that microbial richness, composition and abundance were linked to the plant cover type and the dominant plant species. Furthermore, a large proportion of Ascomycota phylum (fungi), mostly in non-rainforest formations, and Planctomycetes phylum (bacteria) in all formations were observed. Interestingly, such patterns could be indicators of past disturbances that occurred on different time scales. Furthermore, the bacteria and fungi were influenced by diverse edaphic parameters as well as by the interplay between these two soil communities. Another striking finding was the existence of a site effect. Differences in microbial communities between geographical locations may be explained by dispersal limitation in the context of the biogeographical island theory. In conclusion, each plant formation at each site possesses is own microbial community resulting from multiple interactions between abiotic and biotic factors. (Résumé d'auteur

IWGSC Sequence Repository: Moving towards tools to facilitate data integration for the reference sequence of wheat

URGI is a genomics and bioinformatics research unit at INRA (French National institute for Agricultural Research), dedicated to plants and crop parasites. We develop and maintain a genomic and genetic Information System called GnpIS that manages multiple types of wheat data. Under the umbrella of the IWGSC (International Wheat Genome Sequencing Consortium), we have set up a Sequence Repository on the Wheat@URGI website to store, browse and BLAST the data being generated by the wheat genome project: http://wheat-urgi.versailles.inra.fr/Seq-Repository. The repository holds the wheat physical maps, the chromosome survey sequence data for the individual chromosomes of breadwheat, draft sequences for diploid and tetraploid wheats and provides browsable access to the BAC-based reference sequence for chromosome 3B, the first of the chromosomes to be completed by the consortium. I will highlight the new features and data available in the Sequence Repository (e.g., new BLAST functionalities) and, in particular, present what we have done to address needs and concerns raised during the IWGSC S&P workshop last year. In addition, I will open the discussion about the future needs for tools to facilitate the integration of data to produce the reference sequence

The BioMart community portal: an innovative alternative to large, centralized data repositories.

The BioMart Community Portal (www.biomart.org) is a community-driven effort to provide a unified interface to biomedical databases that are distributed worldwide. The portal provides access to numerous database projects supported by 30 scientific organizations. It includes over 800 different biological datasets spanning genomics, proteomics, model organisms, cancer data, ontology information and more. All resources available through the portal are independently administered and funded by their host organizations. The BioMart data federation technology provides a unified interface to all the available data. The latest version of the portal comes with many new databases that have been created by our ever-growing community. It also comes with better support and extensibility for data analysis and visualization tools. A new addition to our toolbox, the enrichment analysis tool is now accessible through graphical and web service interface. The BioMart community portal averages over one million requests per day. Building on this level of service and the wealth of information that has become available, the BioMart Community Portal has introduced a new, more scalable and cheaper alternative to the large data stores maintained by specialized organizations

Shifting the limits in wheat research and breeding using a fully annotated reference genome

Introduction: Wheat (Triticum aestivum L.) is the most widely cultivated crop on Earth, contributing about a fifth of the total calories consumed by humans. Consequently, wheat yields and production affect the global economy, and failed harvests can lead to social unrest. Breeders continuously strive to develop improved varieties by fine-tuning genetically complex yield and end-use quality parameters while maintaining stable yields and adapting the crop to regionally specific biotic and abiotic stresses. Rationale: Breeding efforts are limited by insufficient knowledge and understanding of wheat biology and the molecular basis of central agronomic traits. To meet the demands of human population growth, there is an urgent need for wheat research and breeding to accelerate genetic gain as well as to increase and protect wheat yield and quality traits. In other plant and animal species, access to a fully annotated and ordered genome sequence, including regulatory sequences and genome-diversity information, has promoted the development of systematic and more time-efficient approaches for the selection and understanding of important traits. Wheat has lagged behind, primarily owing to the challenges of assembling a genome that is more than five times as large as the human genome, polyploid, and complex, containing more than 85% repetitive DNA. To provide a foundation for improvement through molecular breeding, in 2005, the International Wheat Genome Sequencing Consortium set out to deliver a high-quality annotated reference genome sequence of bread wheat. Results: An annotated reference sequence representing the hexaploid bread wheat genome in the form of 21 chromosome-like sequence assemblies has now been delivered, giving access to 107,891 high-confidence genes, including their genomic context of regulatory sequences. This assembly enabled the discovery of tissue- and developmental stage–related gene coexpression networks using a transcriptome atlas representing all stages of wheat development. The dynamics of change in complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. Aspects of the future value of the annotated assembly for molecular breeding and research were exemplarily illustrated by resolving the genetic basis of a quantitative trait locus conferring resistance to abiotic stress and insect damage as well as by serving as the basis for genome editing of the flowering-time trait. Conclusion: This annotated reference sequence of wheat is a resource that can now drive disruptive innovation in wheat improvement, as this community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding. Importantly, the bioinformatics capacity developed for model-organism genomes will facilitate a better understanding of the wheat genome as a result of the high-quality chromosome-based genome assembly. By necessity, breeders work with the genome at the whole chromosome level, as each new cross involves the modification of genome-wide gene networks that control the expression of complex traits such as yield. With the annotated and ordered reference genome sequence in place, researchers and breeders can now easily access sequence-level information to precisely define the necessary changes in the genomes for breeding programs. This will be realized through the implementation of new DNA marker platforms and targeted breeding technologies, including genome editing

31st Annual Meeting and Associated Programs of the Society for Immunotherapy of Cancer (SITC 2016) : part two

Background The immunological escape of tumors represents one of the main ob- stacles to the treatment of malignancies. The blockade of PD-1 or CTLA-4 receptors represented a milestone in the history of immunotherapy. However, immune checkpoint inhibitors seem to be effective in specific cohorts of patients. It has been proposed that their efficacy relies on the presence of an immunological response. Thus, we hypothesized that disruption of the PD-L1/PD-1 axis would synergize with our oncolytic vaccine platform PeptiCRAd. Methods We used murine B16OVA in vivo tumor models and flow cytometry analysis to investigate the immunological background. Results First, we found that high-burden B16OVA tumors were refractory to combination immunotherapy. However, with a more aggressive schedule, tumors with a lower burden were more susceptible to the combination of PeptiCRAd and PD-L1 blockade. The therapy signifi- cantly increased the median survival of mice (Fig. 7). Interestingly, the reduced growth of contralaterally injected B16F10 cells sug- gested the presence of a long lasting immunological memory also against non-targeted antigens. Concerning the functional state of tumor infiltrating lymphocytes (TILs), we found that all the immune therapies would enhance the percentage of activated (PD-1pos TIM- 3neg) T lymphocytes and reduce the amount of exhausted (PD-1pos TIM-3pos) cells compared to placebo. As expected, we found that PeptiCRAd monotherapy could increase the number of antigen spe- cific CD8+ T cells compared to other treatments. However, only the combination with PD-L1 blockade could significantly increase the ra- tio between activated and exhausted pentamer positive cells (p= 0.0058), suggesting that by disrupting the PD-1/PD-L1 axis we could decrease the amount of dysfunctional antigen specific T cells. We ob- served that the anatomical location deeply influenced the state of CD4+ and CD8+ T lymphocytes. In fact, TIM-3 expression was in- creased by 2 fold on TILs compared to splenic and lymphoid T cells. In the CD8+ compartment, the expression of PD-1 on the surface seemed to be restricted to the tumor micro-environment, while CD4 + T cells had a high expression of PD-1 also in lymphoid organs. Interestingly, we found that the levels of PD-1 were significantly higher on CD8+ T cells than on CD4+ T cells into the tumor micro- environment (p < 0.0001). Conclusions In conclusion, we demonstrated that the efficacy of immune check- point inhibitors might be strongly enhanced by their combination with cancer vaccines. PeptiCRAd was able to increase the number of antigen-specific T cells and PD-L1 blockade prevented their exhaus- tion, resulting in long-lasting immunological memory and increased median survival

Epidemiology of pestivirus infection in wild ungulates of the French South Alps

&lt;p&gt;Inter-species transmission is often incriminated in the epidemiology of Pestivirus diseases. The purpose of this study was to investigate the prevalence of Pestivirus in some mountain wild ungulates and to determine their role in Pestivirus transmission, as mountain pastures are a place where cohabitations between wild and domestic ungulates are particularly high. Between 2003 and 2007, a longitudinal epidemiological study was carried out on hunted ungulates in the French Hautes-Alpes department. Pestivirus-specific antibodies against p80 protein (also named NS3) common to all Bovine Viral Diarrhea Virus (BVDV) and Border Disease Virus (BDV) were found in 45.9% (95% confidence interval [CI95%]: 40.5-51.3%) of the 343 tested chamois (Rupicapra rupicapra). In addition, mouflons (Ovis gmelinii musimon) were shown for the first time to be strongly infected (61.1%; CI95%: 38.6-83.6) by a Pestivirus. These serological ELISA results were confirmed by comparative virus neutralization tests, performed on seven Pestivirus strains by using 15 seropositive samples. The highest antibody titers were directed against 2 BDV strains (Av and 33s strains), rather than BDV-4, a strain responsible for Pyrenean-chamois epizooties. Virus neutralization tests confirm a BDV circulation in wild ungulates in the French South Alps. However, no Pestivirus RNA was detected by reverse-transcriptase polymerase chain reaction in serum and spleen samples from seronegative animals and no virus was isolated from those samples either. Efforts should be made to improve the protocol in order to be able to isolate and characterize the local strain. Finally, the oldness (age) and femaleness (gender) increase the risk of seroconversion in chamois.&lt;/p&gt;</p

Les troubles du langage inauguraux et démence : étude des troubles lexicaux auprès de 28 patients au stade débutant de la maladie d'Alzheimer

Les troubles du langage font partie, avec les troubles de la mémoire, des premiers signes cliniques cognitifs de la maladie d’Alzheimer. Au début de la maladie, ces troubles essentiellement expressifs touchent surtout le lexique, les autres aspects du langage (phonologie, syntaxe) restant préservés plus longtemps. Afin de mieux caractériser ces troubles du langage inauguraux, nous avons évalué ces troubles auprès de 28 sujets (12 hommes et 16 femmes), âgés de 52 à 90 ans (moyenne d’âge : 73 ans), présentant une maladie d’Alzheimer au stade débutant (MMS > ou = à 20, moyenne = 23,79). Aucun de ces sujets ne présentait de troubles auditifs ou visuels non corrigés ni de troubles gnosiques visuels. L’examen des troubles lexicaux a consisté en la passation de 3 épreuves (dénomination, désignation et appariement d’images) permettant d’évaluer conjointement pour les mêmes 54 items (contrôlés en termes de fréquence, longueur et catégorie sémantique) la production et la compréhension lexicale ainsi que le traitement sémantique non verbal. Les résultats à ces épreuves ont été analysés en fonction des scores et temps seuils établis auprès d’une population contrôle de 369 sujets. Les résultats montrent que 62% des sujets examinés présente des troubles de la production lexicale caractérisés par la présence de paraphasies lexicales sémantiques et visuo-sémantiques, de circonlocutions et de dénominations vides et des délais dans les réponses, dans l’épreuve de dénomination d’images. Ces troubles expressifs s’accompagnent de troubles sémantiques dans la mesure 72% des sujets présentent des scores pathologiques à l’épreuve d’appariement sémantique et dans une moindre proportion, sont associés à des troubles de la compréhension lexicale (44% de scores pathologiques en désignation). Ces chiffres, plus élevés que ceux de la littérature, confortent l’hypothèse de troubles lexico-sémantiques propres à la maladie d’Alzheimer qui peuvent être identifiés précocement si l’on dispose d’outils d’évaluation adaptés à cette population

Les troubles du langage inauguraux et démence : étude des troubles lexicaux auprès de 28 patients au stade débutant de la maladie d'Alzheimer

Les troubles du langage font partie, avec les troubles de la mémoire, des premiers signes cliniques cognitifs de la maladie d’Alzheimer. Au début de la maladie, ces troubles essentiellement expressifs touchent surtout le lexique, les autres aspects du langage (phonologie, syntaxe) restant préservés plus longtemps. Afin de mieux caractériser ces troubles du langage inauguraux, nous avons évalué ces troubles auprès de 28 sujets (12 hommes et 16 femmes), âgés de 52 à 90 ans (moyenne d’âge : 73 ans), présentant une maladie d’Alzheimer au stade débutant (MMS > ou = à 20, moyenne = 23,79). Aucun de ces sujets ne présentait de troubles auditifs ou visuels non corrigés ni de troubles gnosiques visuels. L’examen des troubles lexicaux a consisté en la passation de 3 épreuves (dénomination, désignation et appariement d’images) permettant d’évaluer conjointement pour les mêmes 54 items (contrôlés en termes de fréquence, longueur et catégorie sémantique) la production et la compréhension lexicale ainsi que le traitement sémantique non verbal. Les résultats à ces épreuves ont été analysés en fonction des scores et temps seuils établis auprès d’une population contrôle de 369 sujets. Les résultats montrent que 62% des sujets examinés présente des troubles de la production lexicale caractérisés par la présence de paraphasies lexicales sémantiques et visuo-s��mantiques, de circonlocutions et de dénominations vides et des délais dans les réponses, dans l’épreuve de dénomination d’images. Ces troubles expressifs s’accompagnent de troubles sémantiques dans la mesure 72% des sujets présentent des scores pathologiques à l’épreuve d’appariement sémantique et dans une moindre proportion, sont associés à des troubles de la compréhension lexicale (44% de scores pathologiques en désignation). Ces chiffres, plus élevés que ceux de la littérature, confortent l’hypothèse de troubles lexico-sémantiques propres à la maladie d’Alzheimer qui peuvent être identifiés précocement si l’on dispose d’outils d’évaluation adaptés à cette population