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There are connections between apparent spatial shifts in the skipjack tuna population in the Pacific Ocean and large zonal displacements of the western equatorial Pacific warm pool that take place during El Nino Southern Oscillation (ENSO) events. Observations of skipjack relative abundance were correlated with a proxy for location of the zone of convergence of surface-layer water masses on the eastern edge of the western Pacific warm pool, the 29 degrees C sea surface temperature isotherm, and with the southern oscillation index.

The World Conference on Stock Assessment Methods (July 2013) included a workshop on testing assessment methods through simulations. The exercise was made up of two steps applied to datasets from 14 representative fish stocks from around the world. Step 1 involved applying stock assessments to datasets with varying degrees of effort dedicated to optimizing fit. Step 2 was applied to a subset of the stocks and involved characteristics of given model fits being used to generate pseudo-data with error. These pseudo-data were then provided to assessment modellers and fits to the pseudo-data provided consistency checks within (self-tests) and among (cross-tests) assessment models. Although trends in biomass were often similar across models, the scaling of absolute biomass was not consistent across models. Similar types of models tended to perform similarly (e.g. age based or production models). Self-testing and cross-testing of models are a useful diagnostic approach, and suggested that estimates in the most recent years of time-series were the least robust. Results from the simulation exercise provide a basis for guidance on future large-scale simulation experiments and demonstrate the need for strategic investments in the evaluation and development of stock assessment methods. [ABSTRACT FROM PUBLISHER]

The adaptive immune system, along with the innate immune system, are the two main biological processes that protect an organism from pathogens. The adaptive immune system is characterized by the specificity and extreme diversity of its antigen receptors. These antigen receptors are the immunoglobulins (IG) or antibodies of the B cells and the T cell receptors (TR) of the T cells. The IG are proteins that have a dual role in immunity: they recognize antigens and trigger elimination mechanisms, to rid the body of foreign cells. The synthesis of the immunoglobulin heavy and light chains requires gene rearrangements at the DNA level in the IGH, IGK, and IGL loci. The rhesus monkey ( Macaca mulatta ) is one of the most widely used nonhuman primate species in biomedical research. In this manuscript, we provide a thorough analysis of the three IG loci of the Mmul_10 assembly of rhesus monkey, integrating IMGT previously existing data. Detailed characterization of IG genes includes their localization and position in the loci, the determination of the allele functionality, and the description of the regulatory elements of their promoters as well as the sequences of the conventional recombination signals (RS). This complete annotation of the genomic IG loci of Mmul_10 assembly and the highly detailed IG gene characterization could be used as a model, in additional rhesus monkey assemblies, for the analysis of the IG allelic polymorphism and structural variation, which have been described in rhesus monkeys.

IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org/, is at the forefront of the immunogenetics and immunoinformatics fields with more than 30 years of experience. IMGT® makes available databases and tools to the scientific community pertaining to the adaptive immune response, based on the IMGT-ONTOLOGY. We focus on the recent features of the IMGT® databases, tools, reference directories and web resources, within the three main axes of IMGT® research and development. Axis I consists in understanding the adaptive immune response, by deciphering the identification and characterization of the immunoglobulin (IG) and T cell receptor (TR) genes in jawed vertebrates. It is the starting point of the two other axes, namely the analysis and exploration of the expressed IG and TR repertoires based on comparison with IMGT reference directories in normal and pathological situations (Axis II) and the analysis of amino acid changes and functions of 2D and 3D structures of antibody and TR engineering (Axis III)., (© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.)

The adaptive immune response provides the vertebrate immune system with the ability to recognize and remember specific pathogens to generate immunity, and mount stronger attacks each time the pathogen is encountered. T cell receptors are the antigen receptors of the adaptive immune response expressed by T cells, which specifically recognize processed antigens, presented as peptides by the highly polymorphic major histocompatibility (MH) proteins. T cell receptors (TR) are divided into two groups, αβ and γδ, which express distinct TR containing either α and β, or γ and δ chains, respectively. The TRα locus (TRA) and TRδ locus (TRD) of bovine ( Bos taurus ) and the sheep ( Ovis aries ) have recently been described and annotated by IMGT ® biocurators. The aim of the present study is to present the results of the biocuration and to compare the genes of the TRA/TRD loci among these ruminant species based on the Homo sapiens repertoire. The comparative analysis shows similarities but also differences, including the fact that these two species have a TRA/TRD locus about three times larger than that of humans and therefore have many more genes which may demonstrate duplications and/or deletions during evolution.

IMGT®, the international ImMunoGeneTics information system® is the global reference in immunogenetics and immunoinformatics. By its creation in 1989 by Marie-Paule Lefranc (Université de Montpellier and CNRS), IMGT® marked the advent of immunoinformatics, which emerged at the interface between immunogenetics and bioinformatics. IMGT® is specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility (MH), and proteins of the IgSF and MhSF superfamilies. T cell receptors are divided into two groups, αβ and γδ TR, which express distinct TR containing either α and β, or γ and δ chains, respectively. The TRβ locus (TRB) was recently described and annotated by IMGT® biocurators for several veterinary species, i.e., cat ( Felis catus ), dog ( Canis lupus familiaris ), ferret ( Mustela putorius furo ), pig ( Sus scrofa ), rabbit ( Oryctolagus cuniculus ), rhesus monkey ( Macaca mulatta ), and sheep ( Ovis aries ). The aim of the present study is to compare the genes of the TRB locus among these different veterinary species based on Homo sapiens . The results reveal that there are similarities but also differences including the number of genes by subgroup which may demonstrate duplications and/or deletions during evolution., (Copyright © 2020 Pégorier, Bertignac, Chentli, Nguefack Ngoune, Folch, Jabado-Michaloud, Hadi-Saljoqi, Giudicelli, Duroux, Lefranc and Kossida.)

Malassezia restricta, one of the predominant basidiomycetous yeasts present on human skin, is involved in scalp disorders. Here, we report the complete genome sequence of the lipophilic Malassezia restricta CBS 7877 strain, which will facilitate the study of the mechanisms underlying its commensal and pathogenic roles within the skin microbiome.

In the context of the Common Fisheries Policy Reform, the implementation of multiannual management plans for fisheries and the annual quota negotiations between EU member states has generated a growing demand from stakeholders and managers for integrated advice that goes beyond the usual biological advice. This has led to the emergence of bio-economic tools and methods for the comparison of the biological, economic and social tradeoffs associated with alternative options for fisheries management. A Decision Support Framework (DSF) has been developed in this context, with the objective to tackle technical and methodological challenges to be able to provide bio-economic advices to support decision at national and European level. It is based on a partnership approach involving the fishing industry, managers and scientists and on technical protocols. We present the development of a partnership DSF within three local case studies, highlighting key challenges and lessons learnt regarding appropriateness and application of a DSF. The data processing methods and collaborative platform were pivotal for scoping out objectives and management options, and for aligning DSF outcomes with decision makers' needs and agendas. Definition of common standards and institutionalization of the use of partnership DSF are still required to operationalize the integrated advice process at national and European levels., (Copyright © 2018 Elsevier Ltd. All rights reserved.)