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Le réseau français REPAMO a été créé en 1992 pour répondre aux directives européennes relatives aux conditions de police sanitaire des animaux d'aquaculture et au contrôle de certaines maladies affectant les mollusques bivalves. Ses missions sont : 1) la surveillance des maladies à déclaration obligatoire présentes en France, 2) l'étude des mortalités anormales, 3) la surveillance du statut zoosanitaire des populations de mollusques sauvages ou cultivés. Le réseau REPANUI a été créé plus récemment pour répondre à des buts similaires, en insistant plus particulièrement sur le suivi de la santé des huîtres perlières en appui à la filière d'élevage polynésienne. Created in 1992, the French network REPAMO is in charge of the surveillance and monitoring of the mollusc health status along the French coast according to European legislation. The missions of the network are the following: (1) the surveillance of notifiable diseases present in France, (2) the study of abnormal mortalities, (3) the surveillance of health status of cultivated and natural mollusc populations. The more recent network REPANUI has similar goals mainly focused on the pearl oyster health status to support the oyster farming industry in French Polynesia.

International audience; In wild Atlantic salmon, Salmo salar, of Armorican rivers, precocious maturity occurred at <5% at age 0+ (males only). At 1+ (in both sexes) the percentage occurrence varied between years and stretches of river. Spawning marks on scales of smolts and anadromous adults confirmed that such fish smoltify after spawning. From back-calculation from scales of R. Scorff salmon it was found that: (1) mature parr were larger than immature fish at 1+ in autumn and at smolting; (2) mature 1+ parr had been intermediate in length between upper and lower modal group fish in their first autumn. It is suggested that in western France a holobiotic cycle for the Atlantic salmon can occur before the amphibiotic one as an adaptive strategy.

We investigate the mechanical behavior of wet granular agglomerates composed of spherical particles by means of molecular dynamics simulations. The capillary cohesion force is modeled as an attraction force at the contact between two particles and expressed as an explicit function of the gap and volume of the liquid bridge. We are interested in the effect of the friction coefficient between primary particles. The agglomerates are subjected to diametrical compression tests. We find that the deformation is ductile involving particle rearrangements. However, a well-defined stress peak is observed and the peak stress is used as a measure of the compressive strength of the agglomerate. The strength increases with friction coefficient but levels off at friction coefficients above 0.4. Furthermore, the compressive strength is an increasing function of particle size span.

Abstract Background The Marburg virus (MARV) has a negative-sense single-stranded RNA genome, belongs to the family Filoviridae, and is responsible for several outbreaks of highly fatal hemorrhagic fever. Codon usage patterns of viruses reflect a series of evolutionary changes that enable viruses to shape their survival rates and fitness toward the external environment and, most importantly, their hosts. To understand the evolution of MARV at the codon level, we report a comprehensive analysis of synonymous codon usage patterns in MARV genomes. Multiple codon analysis approaches and statistical methods were performed to determine overall codon usage patterns, biases in codon usage, and influence of various factors, including mutation pressure, natural selection, and its two hosts, Homo sapiens and Rousettus aegyptiacus. Results Nucleotide composition and relative synonymous codon usage (RSCU) analysis revealed that MARV shows mutation bias and prefers U- and A-ended codons to code amino acids. Effective number of codons analysis indicated that overall codon usage among MARV genomes is slightly biased. The Parity Rule 2 plot analysis showed that GC and AU nucleotides were not used proportionally which accounts for the presence of natural selection. Codon usage patterns of MARV were also found to be influenced by its hosts. This indicates that MARV have evolved codon usage patterns that are specific to both of its hosts. Moreover, selection pressure from R. aegyptiacus on the MARV RSCU patterns was found to be dominant compared with that from H. sapiens. Overall, mutation pressure was found to be the most important and dominant force that shapes codon usage patterns in MARV. Conclusions To our knowledge, this is the first detailed codon usage analysis of MARV and extends our understanding of the mechanisms that contribute to codon usage and evolution of MARV.

Abstract The persistence of DNA over archaeological and paleontological timescales in diverse environments has led to a revolutionary body of paleogenomic research, yet the dynamics of DNA degradation are still poorly understood. We analyzed 185 paleogenomic datasets and compared DNA survival with environmental variables and sample ages. We find cytosine deamination follows a conventional thermal age model, but we find no correlation between DNA fragmentation and sample age over the timespans analyzed, even when controlling for environmental variables. We propose a model for ancient DNA decay wherein fragmentation rapidly reaches a threshold, then subsequently slows. The observed loss of DNA over time may be due to a bulk diffusion process in many cases, highlighting the importance of tissues and environments creating effectively closed systems for DNA preservation. This model of DNA degradation is largely based on mammal bone samples due to published genomic dataset availability. Continued refinement to the model to reflect diverse biological systems and tissue types will further improve our understanding of ancient DNA breakdown dynamics.

ABSTRACTPhylogenetic trees are an important analytical tool for evaluating community diversity and evolutionary history. In the case of microorganisms, the decreasing cost of sequencing has enabled researchers to generate ever-larger sequence datasets, which in turn have begun to fill gaps in the evolutionary history of microbial groups. However, phylogenetic analyses of these types of datasets create complex trees that can be challenging to interpret. Scientific inferences made by visual inspection of phylogenetic trees can be simplified and enhanced by customizing various parts of the tree. Yet, manual customization is time-consuming and error prone, and programs designed to assist in batch tree customization often require programming experience or complicated file formats for annotation. Iroki, a user-friendly web interface for tree visualization, addresses these issues by providing automatic customization of large trees based on metadata contained in tab-separated text files. Iroki’s utility for exploring biological and ecological trends in sequencing data was demonstrated through a variety of microbial ecology applications in which trees with hundreds to thousands of leaf nodes were customized according to extensive collections of metadata. The Iroki web application and documentation are available at https://www.iroki.net or through the VIROME portal (http://virome.dbi.udel.edu). Iroki’s source code is released under the MIT license and is available at https://github.com/mooreryan/iroki.

The authors study, for the use in artificial insemination, the mobility and the metabolism of sperm and its senescence during the reproduction period in fishes.