Recombinational Landscape and Population Genomics of Caenorhabditis elegans

Recombination rate and linkage disequilibrium, the latter a function of population genomic processes, are the critical parameters for mapping by linkage and association, and their patterns in Caenorhabditis elegans are poorly understood. We performed high-density SNP genotyping on a large panel of recombinant inbred advanced intercross lines (RIAILs) of C. elegans to characterize the landscape of recombination and, on a panel of wild strains, to characterize population genomic patterns. We confirmed that C. elegans autosomes exhibit discrete domains of nearly constant recombination rate, and we show, for the first time, that the pattern holds for the X chromosome as well. The terminal domains of each chromosome, spanning about 7% of the genome, exhibit effectively no recombination. The RIAILs exhibit a 5.3-fold expansion of the genetic map. With median marker spacing of 61 kb, they are a powerful resource for mapping quantitative trait loci in C. elegans. Among 125 wild isolates, we identified only 41 distinct haplotypes. The patterns of genotypic similarity suggest that some presumed wild strains are laboratory contaminants. The Hawaiian strain, CB4856, exhibits genetic isolation from the remainder of the global population, whose members exhibit ample evidence of intercrossing and recombining. The population effective recombination rate, estimated from the pattern of linkage disequilibrium, is correlated with the estimated meiotic recombination rate, but its magnitude implies that the effective rate of outcrossing is extremely low, corroborating reports of selection against recombinant genotypes. Despite the low population, effective recombination rate and extensive linkage disequilibrium among chromosomes, which are techniques that account for background levels of genomic similarity, permit association mapping in wild C. elegans strains

CIDMEF-Sciences® : Deux ans d’existence, quel bilan ?

Contexte et problématique : CIDMEF-Sciences® est une plateforme internet d’aide en ligne à la rédaction médicale et à la publication d’articles scientifiques médicaux. Emanation du conseil scientifique de la Conférence internationale des doyens et des facultés de médecine d’expression française (CIDMEF), son but est d’aider les enseignants isolés moins favorisés à diffuser leurs activités de recherche. C’est un complément des séminaires de méthodologie de la recherche, qui ont lieu plus en amont, et plus largement des formations pédagogiques. Description : Avec des ressources documentaires et de méthodologie sur le site et l’organisation d’un tutorat personnalisé, l’auteur est aidé par CIDMEF-Sciences® dans l’élaboration et la finalisation de son travail avant la proposition pour publication. Bilan et résultats : Le bilan à presque deux ans d’existence est encourageant. Une plus large diffusion de l’existence de cet outil d’aide à la rédaction médicale semble indispensable afin que cette plateforme éducative serve à un plus grand nombre. Cette action bénévole de savoir partagé intéresse toute la francophonie y compris les pays non adhérents à la CIDMEF, mais aussi tous ceux qui souhaitent publier en français bien qu’étant dans des pays non francophones (Amérique du Sud)

High syphilis prevalence and incidence in people living with HIV and Preexposure Prophylaxis users: A retrospective review in the French Dat’AIDS cohort

International audienceBackground In the past years, we observed a sharp increase of Syphilis, especially among male who have sex with male (MSM), either HIV-infected, or on pre-exposure prophylaxis (PrEP). Our aim was to assess syphilis prevalence and incidence among people living with HIV (PLWH) and PrEP users.Methods PLWH were included from 2010 to 2020 and PrEP users from 2016 to 2020 from the Dat’AIDS French cohort. We calculated syphilis prevalence and incidences for first infections, re-infections, and iterative infections (> 2 times). T-Tests, Wilcoxon tests and Chi2 test were used for descriptive analysis and multivariate logistic regression models were used to estimate Odds ratios (OR) and 95% confidence intervals (95% CI) for factors associated with syphilis.Results Among the 8 583 PLWH, prevalence of subject with past or present syphilis was 19.9%. These subjects were more likely MSM or transgender and aged over 35 years, but prevalence was lower in AIDS subjects. Same pattern was seen for incident infection and re-infection. Incidence was 3.8 per 100 person-years for infection and 6.5 per 100 person-years for re-infection. Among 1 680 PrEP users, syphilis prevalence was 25.8%, with an estimated 7.2% frequency of active syphilis. Risk of syphilis infection was higher in male and increased with age. Incidence was 11.2 per 100 person-years for infection and 11.1 per 100 person-years for re-infection.Conclusion Syphilis prevalence and incidence were high, especially in older MSM with controlled HIV infection and PrEP users, enhancing the need to improve syphilis screening and behavioral risk reduction counseling among high-risk subjects

Switch to Ritonavir-Boosted versus Unboosted Atazanavir plus Raltegravir Dual-Drug Therapy Leads to Similar Efficacy and Safety Outcomes in Clinical Practice.

To assess immunovirological response, safety and pharmacokinetic of NRTI-sparing regimen dual therapy of atazanavir (ATV) and raltegravir (RAL) in maintenance strategy.A retrospective analysis was conducted on a cohort of HIV-infected adults followed in French centers (Dat'AIDS cohort), comparing the proportions of virological and therapeutic failures between ATV + RAL and ATV/ritonavir + RAL dual therapy regimens.283 patients were assessed: 185 switched for ATV + RAL and 98 for ATV/ritonavir + RAL dual therapy. Virological failure rate at week 96 was 13.8% (95% CI, 9.8-17.8), without difference between the two groups (Log-rank Test, p = 0.87). The cumulative percentages of patients remaining free of therapeutic failure at week 24, 48 and 96 of dual therapy were 74.9% (95% CI, 69.9-80.0), 65.4% (95% CI, 59.8-70.9) and 53.4% (95% CI, 47.5-59.2), respectively. Four out of 39 confirmed virological failures developed RAL resistance. By multivariate analysis, virological failure was associated with high HIV-1 RNA zenith (p = 0.02), low CD4+ T-cell count at baseline (p<0.001) and short duration on antiretroviral therapy (p<0.001). Before week 96, dual therapy was discontinued in 44 patients (16%) because of various adverse events, with no difference between the two groups. Minimal plasma levels were targeted in 84% and 87% of patients for ATV and RAL, respectively, and both were significantly higher in ritonavir-boosted regimen.Emerging RAL-resistance and discontinuations for adverse events resulted in moderate efficacy rates of ATV and RAL dual therapy in heavily pretreated patients

Full-genome evolutionary histories of selfing, splitting, and selection in Caenorhabditis

The nematode Caenorhabditis briggsae is a model for comparative developmental evolution with C. elegans. Worldwide collections of C. briggsae have implicated an intriguing history of divergence among genetic groups separated by latitude, or by restricted geography, that is being exploited to dissect the genetic basis to adaptive evolution and reproductive incompatibility; yet, the genomic scope and timing of population divergence is unclear. We performed high-coverage whole-genome sequencing of 37 wild isolates of the nematode C. briggsae and applied a pairwise sequentially Markovian coalescent (PSMC) model to 703 combinations of genomic haplotypes to draw inferences about population history, the genomic scope of natural selection, and to compare with 40 wild isolates of C. elegans. We estimate that a diaspora of at least six distinct C. briggsae lineages separated from one another approximately 200,000 generations ago, including the "Temperate" and "Tropical" phylogeographic groups that dominate most samples worldwide. Moreover, an ancient population split in its history approximately 2 million generations ago, coupled with only rare gene flow among lineage groups, validates this system as a model for incipient speciation. Low versus high recombination regions of the genome give distinct signatures of population size change through time, indicative of widespread effects of selection on highly linked portions of the genome owing to extreme inbreeding by self-fertilization. Analysis of functional mutations indicates that genomic context, owing to selection that acts on long linkage blocks, is a more important driver of population variation than are the functional attributes of the individually encoded genes

Metabolic syndrome in french HIV-infected patients: prevalence and predictive factors after 3 years of antiretroviral therapy

EA MERS CT3 Enjeu 3International audienceTreatment of HIV infection with highly active antiretroviral therapy can induce metabolic complications and increase the risk of developing the metabolic syndrome (MS). The purpose of this study was to report the prevalence and the risk factors for MS in HIV-infected patients who started highly active antiretroviral therapy (HAART) after 2000. SYMET is a prospective, multicentric, cohort study evaluating the prevalence of MS in 269 patients who had received continuous HAART for 1 to 4 years up to September 2007. MS was defined according to the American Heart Association (AHA) and the National Heart, Lung, and Blood Institute (NHLBI) 2005 criteria. Cross-sectional assessment included clinical examination and fasting evaluation of metabolic, inflammatory, and oxidative parameters. Data were analyzed with Chi-square, Student, or Wilcoxon tests. Univariate and multivariate logistic regressions were performed to identify predictive factors for MS. The prevalence of MS was 18.2% after a median duration of HAART of 29.8 months. In multivariate analysis, predictive factors of MS were high non-HDL-cholesterol (OR=1.87; p<0.0001), high-sensitivity C-reactive protein levels (hsCRP) (OR=1.56; p=0.01), coinfection with hepatitis C virus (HCV) (OR=5.67; p=0.02), as well as age (OR=1.04; p=0.02) and duration of exposure to protease inhibitors (PI) (OR=1.03; p=0.02) or to abacavir (ABC) (OR=1.03; p=0.02). In this cohort of patients exposed to less than 4 years of HAART, MS prevalence was 18.2%. Older age, high hsCRP, HCV coinfection, and elevated non-HDL-cholesterol were risk factors for the MS. There was also a moderate significant association of increased risk of MS with cumulative PI and ABC exposure