Le concept de maladies virales émergentes : quel risque de zoonose pour La Réunion ?

A La Réunion, le risque d'émergence de maladies virales est constitué par plusieurs zoonoses virales qu'il convient de surveiller: infections à virus Sindbis, virus de l'encéphalite japonaise, virus Wesselsbron, virus Nipah, virus Zika, virus West Nile, virus de la fièvre de la vallée du Rift. La lutte contre ces maladies virales émergentes (MVE) passe par une détection précoce des cas et donc un système de surveillance doté d'un véritable réseau d'information, d'alerte et de prévention international. (Résumé d'auteur

Benchmarking long-read genome sequence alignment tools for human genomics applications

Background The utility of long-read genome sequencing platforms has been shown in many fields including whole genome assembly, metagenomics, and amplicon sequencing. Less clear is the applicability of long reads to reference-guided human genomics, which is the foundation of genomic medicine. Here, we benchmark available platform-agnostic alignment tools on datasets from nanopore and single-molecule real-time platforms to understand their suitability in producing a genome representation. Results For this study, we leveraged publicly-available data from sample NA12878 generated on Oxford Nanopore and sample NA24385 on Pacific Biosciences platforms. We employed state of the art sequence alignment tools including GraphMap2, long-read aligner (LRA), Minimap2, CoNvex Gap-cost alignMents for Long Reads (NGMLR), and Winnowmap2. Minimap2 and Winnowmap2 were computationally lightweight enough for use at scale, while GraphMap2 was not. NGMLR took a long time and required many resources, but produced alignments each time. LRA was fast, but only worked on Pacific Biosciences data. Each tool widely disagreed on which reads to leave unaligned, affecting the end genome coverage and the number of discoverable breakpoints. No alignment tool independently resolved all large structural variants (1,001–100,000 base pairs) present in the Database of Genome Variants (DGV) for sample NA12878 or the truthset for NA24385. Conclusions These results suggest a combined approach is needed for LRS alignments for human genomics. Specifically, leveraging alignments from three tools will be more effective in generating a complete picture of genomic variability. It should be best practice to use an analysis pipeline that generates alignments with both Minimap2 and Winnowmap2 as they are lightweight and yield different views of the genome. Depending on the question at hand, the data available, and the time constraints, NGMLR and LRA are good options for a third tool. If computational resources and time are not a factor for a given case or experiment, NGMLR will provide another view, and another chance to resolve a case. LRA, while fast, did not work on the nanopore data for our cluster, but PacBio results were promising in that those computations completed faster than Minimap2. Due to its significant burden on computational resources and slow run time, Graphmap2 is not an ideal tool for exploration of a whole human genome generated on a long-read sequencing platform

Adaptation méthodologique de l’indicateur PH2 - Phytoplancton en Méditerranée - 1ère partie. Synthèse des spécificités de la Méditerranée : paramètres abiotiques et biomasse phytoplanctonique totale (chl a).

L’évaluation DCSMM de l’état écologique des Habitats pélagiques repose sur le seul critère D1C6 dans les 4 sous-régions marines françaises (Manche - Mer du Nord, Mers Celtiques, Golfe de Gascogne et Méditerranée Occidentale). Les 3 indicateurs utilisés (PH1, PH2 et PH3) ont été développés par OSPAR pour l’Atlantique Nord-Est. Ils ciblent les caractéristiques des communautés phyto- et zooplanctoniques dont l’organisation est contrôlée par les facteurs abiotiques et biotiques propres à chaque sous-région marine. Les fortes spécificités du milieu pélagique méditerranéen n’ont pas été prises en compte lors de l’évaluation 2018. Cette note synthétise les principales caractéristiques abiotiques de la Méditerranée et leurs impacts sur le développement de la biomasse phytoplanctonique totale (chl a). Il est rappelé en particulier que : • La Méditerranée est un bassin d’évaporation, où les apports d’eau douce ne compensent pas les pertes dues à l’évaporation. Le déficit en eau (≈ 1 m par an) est comblé par une entrée d’Eau Atlantique qui pénètre en surface en Méditerranée par le détroit de Gibraltar. Le flux entrant d’Eau Atlantique, le stress lié aux vents et la bathymétrie contrôlent la circulation de surface de toute la Méditerranée. • Les forçages hydrodynamiques contraignent les distributions horizontale et verticale de la biomasse phytoplanctonique. La distribution horizontale du phytoplancton est caractérisée par une hétérogénéité spatiale importante. • L’oligotrophie de la Méditerranée augmente d’Ouest en Est. En Méditerranée Occidentale, elle est modulée par une série de processus physiques (gyres, systèmes frontaux, ondes internes, …) qui agissent à différentes échelles spatiales et temporelles et enrichissent la couche de surface en nutriments. • Dans la ZEE française, et à l’exception de la région du delta du Rhône, les eaux du large sont plus riches en nutriments et en phytoplancton que les eaux côtières. • Du printemps à la fin de l’automne, une thermocline saisonnière isole les eaux chaudes de surface des eaux froides présentes en profondeur. Durant cette période, les eaux situées au-dessus de la thermocline sont épuisées en nutriments et en phytoplancton dans toutes les zones du large. • Une caractéristique majeure du phytoplancton méditerranéen est la présence d’un maximum profond de chlorophylle (« Deep Chlorophyll Maximum », DCM) pendant toute la période stratifiée. Le DCM est observé dans toute la Méditerranée. Il est situé sous la thermocline et n’est pas détecté par les satellites. Le DCM est une entité dynamique dont les caractéristiques sont contrôlées par les variables abiotiques du milieu. Il constitue la source de nourriture principale pour le zooplancton 6 à 8 mois par an, et attire une partie de l’ichtyoplancton qui s’y rassemble pour profiter de l’agrégation de nourriture. Le DCM a donc un rôle essentiel dans le fonctionnement du milieu pélagique méditerranéen. Les éléments présentés dans ce travail montrent la nécessité : (i) d’intégrer la dimension verticale de la colonne d’eau dans l’évaluation DCSMM de l’état écologique des Habitats pélagiques méditerranéens, (ii) d’adapter l’indicateur PH2-Phytoplancton en intégrant la dimension verticale afin de tendre vers une évaluation réaliste de l’état des Habitats pélagiques méditerranéens

Mutations in the PCNA-binding site of CDKN1C inhibit cell proliferation by impairing the entry into S phase

Abstract\ud \ud CDKN1C (also known as P57\ud \ud kip2\ud ) is a cyclin-dependent kinase inhibitor that functions as a negative regulator of cell proliferation through G1 phase cell cycle arrest. Recently, our group described gain-of-function mutations in the PCNA-binding site of CDKN1C that result in an undergrowth syndrome called IMAGe Syndrome (Intrauterine Growth Restriction, Metaphyseal dysplasia, Adrenal hypoplasia, and Genital anomalies), with life-threatening consequences. Loss-of-function mutations in CDKN1C have been identified in 5-10% of individuals with Beckwith-Wiedemann syndrome (BWS), an overgrowth disorder with features that are the opposite of IMAGe syndrome. Here, we investigate the effects of IMAGe-associated mutations on protein stability, cell cycle progression and cell proliferation. Mutations in the PCNA-binding site of CDKN1C significantly increase CDKN1C protein stability and prevent cell cycle progression into the S phase. Overexpression of either wild-type or BWS-mutant CDKN1C inhibited cell proliferation. However, the IMAGe-mutant CDKN1C protein decreased cell growth significantly more than both the wild-type or BWS protein. These findings bring new insights into the molecular events underlying IMAGe syndrome.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP process number 2012/09391-0

Genomic surveys by methylation-sensitive SNP analysis identify sequence-dependent allele-specific DNA methylation

Allele-specific DNA methylation (ASM) is a hallmark of imprinted genes, but ASM in the larger nonimprinted fraction of the genome is less well characterized. Using methylation-sensitive SNP analysis (MSNP), we surveyed the human genome at 50K and 250K resolution, identifying ASM as recurrent genotype call conversions from heterozygosity to homozygosity when genomic DNAs were predigested with the methylation-sensitive restriction enzyme HpaII. Using independent assays, we confirmed ASM at 16 SNP-tagged loci distributed across various chromosomes. At 12 of these loci (75%), the ASM tracked strongly with the sequence of adjacent SNPs. Further analysis showed allele-specific mRNA expression at two loci from this methylation-based screen—the vanin and CYP2A6-CYP2A7 gene clusters—both implicated in traits of medical importance. This recurrent phenomenon of sequence-dependent ASM has practical implications for mapping and interpreting associations of noncoding SNPs and haplotypes with human phenotypes

The importance of having two X chromosomes

Historically, it was thought that the number of X chromosomes plays little role in causing sex differences in traits. Recently, selected mouse models have been used increasingly to compare mice with the same type of gonad but with one versus two copies of the X chromosome. Study of these models demonstrates that mice with one X chromosome can be strikingly different from those with two X chromosomes, when the differences are not attributable to confounding group differences in gonadal hormones. The number of X chromosomes affects adiposity and metabolic disease, cardiovascular ischaemia/reperfusion injury and behaviour. The effects of X chromosome number are likely the result of inherent differences in expression of X genes that escape inactivation, and are therefore expressed from both X chromosomes in XX mice, resulting in a higher level of expression when two X chromosomes are present. The effects of X chromosome number contribute to sex differences in disease phenotypes, and may explain some features of X chromosome aneuploidies such as in Turner and Klinefelter syndromes

The Effects of Perinatal Testosterone Exposure on the DNA Methylome of the Mouse Brain Are Late-Emerging

Background The biological basis for sex differences in brain function and disease susceptibility is poorly understood. Examining the role of gonadal hormones in brain sexual differentiation may provide important information about sex differences in neural health and development. Permanent masculinization of brain structure, function, and disease is induced by testosterone prenatally in males, but the possible mediation of these effects by long-term changes in the epigenome is poorly understood. Methods We investigated the organizational effects of testosterone on the DNA methylome and transcriptome in two sexually dimorphic forebrain regions—the bed nucleus of the stria terminalis/preoptic area and the striatum. To study the contribution of testosterone to both the establishment and persistence of sex differences in DNA methylation, we performed genome-wide surveys in male, female, and female mice given testosterone on the day of birth. Methylation was assessed during the perinatal window for testosterone\u27s organizational effects and in adulthood. Results The short-term effect of testosterone exposure was relatively modest. However, in adult animals the number of genes whose methylation was altered had increased by 20-fold. Furthermore, we found that in adulthood, methylation at a substantial number of sexually dimorphic CpG sites was masculinized in response to neonatal testosterone exposure. Consistent with this, testosterone\u27s effect on gene expression in the striatum was more apparent in adulthood. Conclusion Taken together, our data imply that the organizational effects of testosterone on the brain methylome and transcriptome are dramatic and late-emerging. Our findings offer important insights into the long-term molecular effects of early-life hormonal exposure

The Sex Chromosome Trisomy mouse model of XXY and XYY: metabolism and motor performance

BACKGROUND: Klinefelter syndrome (KS), caused by XXY karyotype, is characterized by low testosterone, infertility, cognitive deficits, and increased prevalence of health problems including obesity and diabetes. It has been difficult to separate direct genetic effects from hormonal effects in human studies or in mouse models of KS because low testosterone levels are confounded with sex chromosome complement. METHODS: In this study, we present the Sex Chromosome Trisomy (SCT) mouse model that produces XXY, XYY, XY, and XX mice in the same litters, each genotype with either testes or ovaries. The independence of sex chromosome complement and gonadal type allows for improved recognition of sex chromosome effects that are not dependent on levels of gonadal hormones. All mice were gonadectomized and treated with testosterone for 3 weeks. Body weight, body composition, and motor function were measured. RESULTS: Before hormonal manipulation, XXY mice of both sexes had significantly greater body weight and relative fat mass compared to XY mice. After gonadectomy and testosterone replacement, XXY mice (both sexes) still had significantly greater body weight and relative fat mass, but less relative lean mass compared to XY mice. Liver, gonadal fat pad, and inguinal fat pad weights were also higher in XXY mice, independent of gonadal sex. In several of these measures, XX mice also differed from XY mice, and gonadal males and females differed significantly on almost every metabolic measure. The sex chromosome effects (except for testis size) were also seen in gonadally female mice before and after ovariectomy and testosterone treatment, indicating that they do not reflect group differences in levels of testicular secretions. XYY mice were similar to XY mice on body weight and metabolic variables but performed worse on motor tasks compared to other groups. CONCLUSIONS: We find that the new SCT mouse model for XXY and XYY recapitulates features found in humans with these aneuploidies. We illustrate that this model has significant promise for unveiling the role of genetic effects compared to hormonal effects in these syndromes, because many phenotypes are different in XXY vs. XY gonadal female mice which have never been exposed to testicular secretions