SNP mining in C. clementina BAC end sequences; transferability in the Citrus genus (Rutaceae), phylogenetic inferences and perspectives for genetic mapping

<p>Abstract</p> <p>Background</p> <p>With the increasing availability of EST databases and whole genome sequences, SNPs have become the most abundant and powerful polymorphic markers. However, SNP chip data generally suffers from ascertainment biases caused by the SNP discovery and selection process in which a small number of individuals are used as discovery panels. The ongoing International Citrus Genome Consortium sequencing project of the highly heterozygous Clementine and sweet orange genomes will soon result in the release of several hundred thousand SNPs. The primary goals of this study were: (i) to estimate the transferability within the genus <it>Citrus </it>of SNPs discovered from Clementine BACend sequencing (BES), (ii) to estimate bias associated with the very narrow discovery panel, and (iii) to evaluate the usefulness of the Clementine-derived SNP markers for diversity analysis and comparative mapping studies between the different cultivated <it>Citrus </it>species.</p> <p>Results</p> <p>Fifty-four accessions covering the main <it>Citrus </it>species and 52 interspecific hybrids between pummelo and Clementine were genotyped on a GoldenGate array platform using 1,457 SNPs mined from Clementine BES and 37 SNPs identified between and within <it>C. maxima, C. medica, C. reticulata </it>and <it>C. micrantha</it>. Consistent results were obtained from 622 SNP loci. Of these markers, 116 displayed incomplete transferability primarily in <it>C. medica, C. maxima </it>and wild <it>Citrus </it>species. The two primary biases associated with the SNP mining in Clementine were an overestimation of the <it>C. reticulata </it>diversity and an underestimation of the interspecific differentiation. However, the genetic stratification of the gene pool was high, with very frequent significant linkage disequilibrium. Furthermore, the shared intraspecific polymorphism and accession heterozygosity were generally enough to perform interspecific comparative genetic mapping.</p> <p>Conclusions</p> <p>A set of 622 SNP markers providing consistent results was selected. Of the markers mined from Clementine, 80.5% were successfully transferred to the whole <it>Citrus </it>gene pool. Despite the ascertainment biases in relation to the Clementine origin, the SNP data confirm the important stratification of the gene pools around <it>C. maxima, C. medica </it>and <it>C. reticulata </it>as well as previous hypothesis on the origin of secondary species. The implemented SNP marker set will be very useful for comparative genetic mapping in <it>Citrus </it>and genetic association in <it>C. reticulata</it>.</p

Environmental and socioeconomic correlates of extinction risk in endemic species

Aim Our current understanding of the causes of global extinction risk is mostly informed by the expert knowledge-based “threats classification scheme” of the IUCN Red List of Threatened Species. Studies based on this dataset came to different conclusions about the relative importance of threats to species, depending on which taxonomic groups and levels of extinction risk were considered, and which version of the database was used. A key reason may lie in data limitations as causes of threat are well known for charismatic and well-studied species, but not for the majority of species assessed. Here, we aim to fill current knowledge gaps about the importance of drivers of global extinction risks by focusing on endemic species. Location Global. Methods We examined country-level variation in the proportion of globally threatened and extinct endemic species (Index of Threat, IoT) with a range of spatially explicit information about anthropogenic pressures, mitigation measures and data limitations. Results IoT coincided with several anthropogenic pressures, with substantial differences among kingdoms, life-forms, levels of extinction risk and geographic locations. IoT of plants, particularly tropical woody plants of moderate extinction risk, was higher in countries with higher GDP and more invasive species. Furthermore, IoT of animals, particularly tropical mammals and invertebrates of moderate extinction risk, was higher in countries with higher GDP and smaller roadless areas. Main conclusions The extinction crisis for endemic species is associated with a complex network of potential drivers that need to be considered in concert in conservation policy and practice. Although our results require careful interpretation and remain sensitive to data limitations, we encourage similar studies at smaller scales to identify potential drivers of extinction risk at a higher resolution, particularly in regions where species assessments have been conducted consistently or on organisms with a uniform response time to pressures

Modelling human choices: MADeM and decision‑making

Research supported by FAPESP 2015/50122-0 and DFG-GRTK 1740/2. RP and AR are also part of the Research, Innovation and Dissemination Center for Neuromathematics FAPESP grant (2013/07699-0). RP is supported by a FAPESP scholarship (2013/25667-8). ACR is partially supported by a CNPq fellowship (grant 306251/2014-0)

Effect of angiotensin-converting enzyme inhibitor and angiotensin receptor blocker initiation on organ support-free days in patients hospitalized with COVID-19

IMPORTANCE Overactivation of the renin-angiotensin system (RAS) may contribute to poor clinical outcomes in patients with COVID-19. Objective To determine whether angiotensin-converting enzyme (ACE) inhibitor or angiotensin receptor blocker (ARB) initiation improves outcomes in patients hospitalized for COVID-19. DESIGN, SETTING, AND PARTICIPANTS In an ongoing, adaptive platform randomized clinical trial, 721 critically ill and 58 non–critically ill hospitalized adults were randomized to receive an RAS inhibitor or control between March 16, 2021, and February 25, 2022, at 69 sites in 7 countries (final follow-up on June 1, 2022). INTERVENTIONS Patients were randomized to receive open-label initiation of an ACE inhibitor (n = 257), ARB (n = 248), ARB in combination with DMX-200 (a chemokine receptor-2 inhibitor; n = 10), or no RAS inhibitor (control; n = 264) for up to 10 days. MAIN OUTCOMES AND MEASURES The primary outcome was organ support–free days, a composite of hospital survival and days alive without cardiovascular or respiratory organ support through 21 days. The primary analysis was a bayesian cumulative logistic model. Odds ratios (ORs) greater than 1 represent improved outcomes. RESULTS On February 25, 2022, enrollment was discontinued due to safety concerns. Among 679 critically ill patients with available primary outcome data, the median age was 56 years and 239 participants (35.2%) were women. Median (IQR) organ support–free days among critically ill patients was 10 (–1 to 16) in the ACE inhibitor group (n = 231), 8 (–1 to 17) in the ARB group (n = 217), and 12 (0 to 17) in the control group (n = 231) (median adjusted odds ratios of 0.77 [95% bayesian credible interval, 0.58-1.06] for improvement for ACE inhibitor and 0.76 [95% credible interval, 0.56-1.05] for ARB compared with control). The posterior probabilities that ACE inhibitors and ARBs worsened organ support–free days compared with control were 94.9% and 95.4%, respectively. Hospital survival occurred in 166 of 231 critically ill participants (71.9%) in the ACE inhibitor group, 152 of 217 (70.0%) in the ARB group, and 182 of 231 (78.8%) in the control group (posterior probabilities that ACE inhibitor and ARB worsened hospital survival compared with control were 95.3% and 98.1%, respectively). CONCLUSIONS AND RELEVANCE In this trial, among critically ill adults with COVID-19, initiation of an ACE inhibitor or ARB did not improve, and likely worsened, clinical outcomes. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT0273570

Effect of sylvicultural practices on chemical and microbiological properties of forest soils : a multiscalar approach in the mediterranean context

Les sols forestiers contiennent des stocks de C importants et la gestion de tels espaces naturels est donc cruciale dans le contexte du changement climatique. Ce travail s’attache à comprendre quels leviers (facteurs environnementaux, pratiques sylvicoles) contrôlent le fonctionnement microbien des sols de peuplements représentatifs de Provence calcaire en considérant différentes échelles spatiales. La hiérarchisation des facteurs modulant le fonctionnement des sols forestiers a mis en évidence une structuration des communautés fonctionnelles microbiennes à l’échelle régionale par les conditions bioclimatiques (bioclimats sub-humide vs. humide), et une modulation des activités enzymatiques à l’échelle locale par la MO définie par le peuplement (Quercus ilex et Pinus halepensis vs. Q. pubescens et P. sylvestris en composition pure ou mixte). Les effets de la mixité forestière (décrite via les surfaces terrières et les densités des troncs) sur le fonctionnement du sol a été évaluée dans les deux contextes bioclimatiques: la complémentarité des essences en peuplements mixtes sous bioclimat humide favorise le recyclage de la MO et induit une diminution des stocks de C et N, cet effet non-additif des essences n’est pas observé sous bioclimat sub-humide. L’addition de différents types de rémanents (feuilles/aiguilles vs. bois) a été testée en mésocosmes : les équilibres entre les populations fongiques et bactériennes sont conditionnés par le ratio C/N, lui-même dépendant du type de rémanents apporté. Ainsi, ces résultats indiquent que les pratiques sylvicoles pourraient orienter les dynamiques des flux de C dans les sols forestiers.Since forest soils can store large carbon amounts, the management of such ecosystem is of major importance considering the forecasted climate change. This work aims at understanding which drivers (environmental factors and sylvicultural practices) control soil microbial functioning in forest stands of Provence (South of France) considering different spatial scales. The hierarchization of drivers showed that microbial functional diversity is driven at the regional scale by bioclimatic conditions (sub-humid vs. humid bioclimate) and enzyme activities at the local scale by the organic matter print defined by stand composition (Quercus ilex and Pinus halepensis vs. Q. pubescens and P. sylvestris in pure or mixed stand). Mixed forest composition and structure (described through basal area and density of trunks of pines and oaks) influenced soil functioning differently depending on the bioclimate: the complementarity of species in mixed stands in humid bioclimate favoured organic matter recycling and induced a decrease in C and N stocks, while an additive effect of tree species was found in sub-humid bioclimate. Amendments with different types of logging residues (leaves / needles vs. wood) were tested in mesocosms: the balance between fungal and bacterial populations was conditioned by the C to N ratio, C and N amounts varying with the type of residue. Thus, these results indicate that forest management - through the choice of adapted practices - has the potential to drive microbial functioning in forest soils

Pratiques d'élevages et bien-être animal (l'épointage des dents du porcelet)

TOULOUSE3-BU Santé-Centrale (315552105) / SudocTOULOUSE3-BU Santé-Allées (315552109) / SudocPARIS-BIUM (751062103) / SudocSudocFranceF

« Ateliers, groupes techniques et mains d'artistes : les cercueils à fond jaune de la Troisième Période intermédiaire »

International audienc

« Ateliers, groupes techniques et mains d'artistes : les cercueils à fond jaune de la Troisième Période intermédiaire »

International audienc