Evolution and diversity of the Microviridae viral family through a collection of 81 new complete genomes assembled from virome reads.

International audienceRecent studies suggest that members of the Microviridae (a family of ssDNA bacteriophages) might play an important role in a broad spectrum of environments, as they were found in great number among the viral fraction from seawater and human gut samples. 24 completely sequenced Microviridae have been described so far, divided into three distinct groups named Microvirus, Gokushovirinae and Alpavirinae, this last group being only composed of prophages. In this study, we present the analysis of 81 new complete Microviridae genomes, assembled from viral metagenomes originating from various ecosystems. The phylogenetic analysis of the core genes highlights the existence of four groups, confirming the three sub-families described so far and exhibiting a new group, named Pichovirinae. The genomic organizations of these viruses are strikingly coherent with their phylogeny, the Pichovirinae being the only group of this family with a different organization of the three core genes. Analysis of the structure of the major capsid protein reveals the presence of mushroom-like insertions conserved within all the groups except for the microviruses. In addition, a peptidase gene was found in 10 Microviridae and its analysis indicates a horizontal gene transfer that occurred several times between these viruses and their bacterial hosts. This is the first report of such gene transfer in Microviridae. Finally, searches against viral metagenomes revealed the presence of highly similar sequences in a variety of biomes indicating that Microviridae probably have both an important role in these ecosystems and an ancient origin

Integrating heterogeneous information within a social network for detecting communities

International audienceAttributed graphs can be described using two dimensions: first a structural dimension that contains the social graph, e.g. the actors and the relationships between them, and second a compositional dimension describing the actors, e.g. their profile, their textual publications, the metadata of the videos they share, etc. Each of these dimensions can be used to explain different phenomena occurring on the social network, whether from a connectivity or an thematic perspective. This paper claims that the integration of both dimensions would allow researchers to analyze real social networks from different perspectives. We present here a novel approach to the community detection problem with the integration of the two dimensions composing an attributed graph. We show how to integrate but also how to control the integration of two different partitions, one based on the links, the other one based on the attributes. The resulting partition exhibits interesting properties, such as dense and homogeneous groups of actors, revealing new types of communities to the analyst. Because we use a contingency matrix, and because the analyst may invent new ways of combining rows and columns, we open new perspectives for the exploration of attributed social networks

Étude d'une souche Marocaine du virus de la Peste Porcine (Association du virus pestique et d’un virus agent d’une Pneumonie à virus du Porc).

Girard H. C., Mackowiak Czesław, Goret Pierre, Joubert L., Lucam François, Poulet M.-J. Étude d’une souche Marocaine du virus de la peste porcine. In: Bulletin de l'Académie Vétérinaire de France tome 106 n°10, 1953. pp. 555-568

The histone H3.1 variant regulates TONSOKU-mediated DNA repair during replication

The tail of replication-dependent histone H3.1 varies from that of replication-independent H3.3 at the amino acid located at position 31 in plants and animals, but no function has been assigned to this residue to demonstrate a unique and conserved role for H3.1 during replication. Here, we show that TONSOKU (TSK/TONSL), which rescues broken replication forks, specifically interacts with H3.1 via recognition of alanine 31 by its tetratricopeptide repeat domain. Our results indicate that genomic instability in the absence of ATXR5/ATXR6-catalyzed H3K27me1 in plants depends on H3.1, TSK and DNA polymerase theta (Pol θ). Overall, this work reveals an H3.1-specific function during replication and the common strategy used in multicellular eukaryotes for regulating post-replicative chromatin maturation and TSK, which relies on histone mono-methyltransferases and reading the H3.1 variant

Stability of hydrated minerals on Mars

The validity of recent identification of various hydrated minerals (kieserite, gypsum, hexahydrite, nontronite, chamosite, and montmorillonite) on Mars was assessed by exposing these minerals to simulated Martian surface conditions of atmospheric composition and pressure, temperature, and ultraviolet light irradiation. When exposed to such conditions the hydrated minerals exhibit in general, greater losses of interlayer H2O than structural OH. Minerals such as gypsum that contain structural H2O are more resistant to H2O loss than phyllosilicates. The partial loss of OH in some of the phyllosilicates is not accompanied by a measurable and systematic change in the wavelength position or intensity of metal-OH absorption bands. The characteristic absorption features that allow for identification of these minerals on Mars may be reduced in intensity, but are nevertheless largely preserved.This study was supported with grants from the University of Winnipeg, the Canadian Space Agency. Funding for our spectrometer and Mars environment chamber facility at the University of Winnipeg (HOSERLab) was provided by the Canada Foundation for Innovation, the Manitoba Research and Innovation Fund and the Canadian Space Agency.https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2007GL03126

Evaluation of Three Sampling Methods to Monitor Outcomes of Antiretroviral Treatment Programmes in Low- and Middle-Income Countries

BACKGROUND: Retention of patients on antiretroviral therapy (ART) over time is a proxy for quality of care and an outcome indicator to monitor ART programs. Using existing databases (Antiretroviral in Lower Income Countries of the International Databases to Evaluate AIDS and Médecins Sans Frontières), we evaluated three sampling approaches to simplify the generation of outcome indicators. METHODS AND FINDINGS: We used individual patient data from 27 ART sites and included 27,201 ART-naive adults (≥15 years) who initiated ART in 2005. For each site, we generated two outcome indicators at 12 months, retention on ART and proportion of patients lost to follow-up (LFU), first using all patient data and then within a smaller group of patients selected using three sampling methods (random, systematic and consecutive sampling). For each method and each site, 500 samples were generated, and the average result was compared with the unsampled value. The 95% sampling distribution (SD) was expressed as the 2.5(th) and 97.5(th) percentile values from the 500 samples. Overall, retention on ART was 76.5% (range 58.9-88.6) and the proportion of patients LFU, 13.5% (range 0.8-31.9). Estimates of retention from sampling (n = 5696) were 76.5% (SD 75.4-77.7) for random, 76.5% (75.3-77.5) for systematic and 76.0% (74.1-78.2) for the consecutive method. Estimates for the proportion of patients LFU were 13.5% (12.6-14.5), 13.5% (12.6-14.3) and 14.0% (12.5-15.5), respectively. With consecutive sampling, 50% of sites had SD within ±5% of the unsampled site value. CONCLUSIONS: Our results suggest that random, systematic or consecutive sampling methods are feasible for monitoring ART indicators at national level. However, sampling may not produce precise estimates in some sites