Human Herpesvirus 8, Southern Siberia

International audienceLette

The epigenomic landscape of African rainforest hunter-gatherers and farmers

International audienceThe genetic history of African populations is increasingly well documented, yet their patterns of epigenomic variation remain uncharacterized. Moreover, the relative impacts of DNA sequence variation and temporal changes in lifestyle and habitat on the human epigenome remain unknown. Here we generate genome-wide genotype and DNA methylation profiles for 362 rainforest hunter-gatherers and sedentary farmers. We find that the current habitat and historical lifestyle of a population have similarly critical impacts on the methylome, but the biological functions affected strongly differ. Specifically, methylation variation associated with recent changes in habitat mostly concerns immune and cellular functions, whereas that associated with historical lifestyle affects developmental processes. Furthermore, methylation variation—particularly that correlated with historical lifestyle—shows strong associations with nearby genetic variants that, moreover, are enriched in signals of natural selection. Our work provides new insight into the genetic and environmental factors affecting the epigenomic landscape of human populations over time

Uniparental markers in Italy reveal a sex-biased genetic structure and different historical strata

University of Adelaide Genographic Consortium contributers: Christina J. Adler, Alan Cooper, Clio S. I. Der Sarkissian, Wolfgang Haak.Located in the center of the Mediterranean landscape and with an extensive coastal line, the territory of what is today Italy has played an important role in the history of human settlements and movements of Southern Europe and the Mediterranean Basin. Populated since Paleolithic times, the complexity of human movements during the Neolithic, the Metal Ages and the most recent history of the two last millennia (involving the overlapping of different cultural and demic strata) has shaped the pattern of the modern Italian genetic structure. With the aim of disentangling this pattern and understanding which processes more importantly shaped the distribution of diversity, we have analyzed the uniparentally-inherited markers in ~900 individuals from an extensive sampling across the Italian peninsula, Sardinia and Sicily. Spatial PCAs and DAPCs revealed a sex-biased pattern indicating different demographic histories for males and females. Besides the genetic outlier position of Sardinians, a North West–South East Y-chromosome structure is found in continental Italy. Such structure is in agreement with recent archeological syntheses indicating two independent and parallel processes of Neolithisation. In addition, date estimates pinpoint the importance of the cultural and demographic events during the late Neolithic and Metal Ages. On the other hand, mitochondrial diversity is distributed more homogeneously in agreement with older population events that might be related to the presence of an Italian Refugium during the last glacial period in Europe.Alessio Boattini, Begoña Martinez-Cruz, Stefania Sarno, Christine Harmant, Antonella Useli, Paula Sanz, Daniele Yang-Yao, Jeremy Manry, Graziella Ciani, Donata Luiselli, Lluis Quintana- Murci, David Comas, Davide Pettener, the Genographic Consortiu

Electrophoretic Patterns of Esterases and Lactate-and L-Malate-Dehydrogenases from Flavobacterium Species

International audienceEsterases and lactate-(LDH) and L-malate-(MDH) dehydrogenases of 64 strains of 13 species of Flavobacterium (particularly 46 strains of F. meningosepticum belonging to 15 different serotypes) were analyzed by horizontal polyacrylamide-agarose gel electrophoresis. Twenty-five esterase types were detected; these enzymes were distinguished by their spectra of hydrolytic activity towards five synthetic substrates (hydrolytic type) and their electrolytic mobilities (electrophoretic type). No variant of LDH was detected in all the strains of Flavobacterium. No variant of MDH was detected in three species: F. aquatile, F. branchiophilum, and F. breve and in serotype I, J and L. of F. meningosepticum. These results within the genus Flavobacterium permit precise identification, which may be useful for characterization of strains kept in collections as well as for epidemiological studies

Identification of Strains of <i>Alcaligenes</i> and <i>Agrobacterium</i> by a Polyphasic Approach

International audienceThe number of stable discriminant biochemical characters is limited in the genera Alcaligenes and Agrobacterium, whose species are consequently difficult to distinguish from one another by conventional tests. Moreover, genomic studies have recently drastically modified the nomenclature of these genera; for example, Alcaligenes xylosoxidans was transferred to the genus Achromobacter in 1998. Twenty-five strains of Achromobacter xylosoxidans, three strains of an Agrobacterium sp., five strains of an Alcaligenes sp., and four unnamed strains belonging to the Centers for Disease Control and Prevention group IVc-2 were examined. These strains were characterized by conventional tests, including biochemical tests. The assimilation of 99 carbohydrates, organic acids, and amino acids was studied by using Biotype-100 strips, and rRNA gene restriction patterns were obtained with the automated Riboprinter microbial characterization system after cleavage of total DNA with EcoRI or PstI restriction endonuclease. This polyphasic approach allowed the two subspecies of A. xylosoxidans to be clearly separated. Relationships between five strains and the Ralstonia paucula type strain were demonstrated. Likewise, three strains were found to be related to the Ochrobactrum anthropi type strain. We showed that substrate assimilation tests and automated ribotyping provide a simple, rapid, and reliable means of identifying A. xylosoxidans subspecies and that these two methods can be used as alternative methods to characterize unidentified strains rapidly when discriminant biochemical characters are missing

Identification of Strains of <i>Alcaligenes</i> and <i>Agrobacterium</i> by a Polyphasic Approach

International audienceThe number of stable discriminant biochemical characters is limited in the genera Alcaligenes and Agrobacterium, whose species are consequently difficult to distinguish from one another by conventional tests. Moreover, genomic studies have recently drastically modified the nomenclature of these genera; for example, Alcaligenes xylosoxidans was transferred to the genus Achromobacter in 1998. Twenty-five strains of Achromobacter xylosoxidans, three strains of an Agrobacterium sp., five strains of an Alcaligenes sp., and four unnamed strains belonging to the Centers for Disease Control and Prevention group IVc-2 were examined. These strains were characterized by conventional tests, including biochemical tests. The assimilation of 99 carbohydrates, organic acids, and amino acids was studied by using Biotype-100 strips, and rRNA gene restriction patterns were obtained with the automated Riboprinter microbial characterization system after cleavage of total DNA with EcoRI or PstI restriction endonuclease. This polyphasic approach allowed the two subspecies of A. xylosoxidans to be clearly separated. Relationships between five strains and the Ralstonia paucula type strain were demonstrated. Likewise, three strains were found to be related to the Ochrobactrum anthropi type strain. We showed that substrate assimilation tests and automated ribotyping provide a simple, rapid, and reliable means of identifying A. xylosoxidans subspecies and that these two methods can be used as alternative methods to characterize unidentified strains rapidly when discriminant biochemical characters are missing

Characterization of the Type Strain of Campylobacter coli, CIP 70.80, by Plasmid Typing

International audienceA 1.9-kb plasmid DNA fragment from the type strain of Campylobacter coli, CIP 70.80, was used as a probe to characterize this type strain, other C. coli type strains obtained from several culture collections, and other C. coli strains. A specific hybridization pattern was obtained, and this pattern can be used to identify, characterize, and follow up C. coli type strains in culture collections

Identification of Rhodococcus, Gordona and Dietzia species using carbon source utilization tests ("Biotype-100" strips)

International audienceThe "Biotype-NW identification system (BioMerieux, La Balme-les-Grottes, France) based on carbon source utilization was evaluated for 'its ability to discriminate among 10 species of Rhodococcus, 7 species of Gordona and one species of Dietzia. The type strains of three species of Tsukamurella and 8 species of Nocardia were also included in the study. Results were compared with chemotaxonomic and conventional data. Carbon source utilization was shown to be reliable, rapid and easy to use when compared with standard identification methods. The 29 species tested were unambiguously separated by carbon source utilization tests. Rhodococcus egui was found to be heterogenous.Les galeries “Biotype-100” (BioMérieux) ont été utilisées pour différencier 10 espèces du genre Rhodococcus, 7 espèces du genre Gordona et 1 espèce du genre Dietzia entre elles. Les souchestypes de 3 espèces du genre Tsukamurella et 8 espèces du genre Nocardia ont été incluses dans cette étude. Les résultats ont été comparés avec ceux des études chimiotaxonomiques et ceux obtenus avec les galeries d'identification classiques. Les galeries Biotype-100 sont sûres, rapides et faciles à utiliser par rapport aux galeries classiques. Les 29 espèces étudiées ont été identifiées sans aucune difficulté. L'espèce Rhodococcus equi s'est révélée hétérogène

L’expérience professionnelle de soins entraves par les mesures de distanciation physique enpsychiatrie

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Recent Adaptive Acquisition by African Rainforest Hunter-Gatherers of the Late Pleistocene Sickle-Cell Mutation Suggests Past Differences in Malaria Exposure

International audienceThe hemoglobin βS sickle mutation is a textbook case in which natural selection maintains a deleterious mutation at high frequency in the human population. Homozygous individuals for this mutation develop sickle-cell disease, whereas heterozygotes benefit from higher protection against severe malaria. Because the overdominant βS allele should be purged almost immediately from the population in the absence of malaria, the study of the evolutionary history of this iconic mutation can provide important information about the history of human exposure to malaria. Here, we sought to increase our understanding of the origins and time depth of the βS mutation in populations with different lifestyles and ecologies, and we analyzed the diversity of HBB in 479 individuals from 13 populations of African farmers and rainforest hunter-gatherers. Using an approximate Bayesian computation method, we estimated the age of the βS allele while explicitly accounting for population subdivision, past demography, and balancing selection. When the effects of balancing selection are taken into account, our analyses indicate a single emergence of βS in the ancestors of present-day agriculturalist populations ∼22,000 years ago. Furthermore, we show that rainforest hunter-gatherers have more recently acquired the βS mutation from the ancestors of agriculturalists through adaptive gene flow during the last ∼6,000 years. Together, our results provide evidence for a more ancient exposure to malarial pressures among the ancestors of agriculturalists than previously appreciated, and they suggest that rainforest hunter-gatherers have been increasingly exposed to malaria during the last millennia