Introgression reshapes recombination distribution in grapevine interspecific hybrids

In grapevine interspecific hybrids, meiotic recombination is suppressed in homeologous regions and enhanced in homologous regions of recombined chromosomes, whereas crossover rate remains unchanged when chromosome pairs are entirely homeologous

A High-Quality Grapevine Downy Mildew Genome Assembly Reveals Rapidly Evolving and Lineage-Specific Putative Host Adaptation Genes

Downy mildews are obligate biotrophic oomycete pathogens that cause devastating plant diseases on economically important crops. Plasmopara viticola is the causal agent of grapevine downy mildew, a major disease in vineyards worldwide. We sequenced the genome of Pl. viticola with PacBio long reads and obtained a new 92.94 Mb assembly with high contiguity (359 scaffolds for a N50 of 706.5 kb) due to a better resolution of repeat regions. This assembly presented a high level of gene completeness, recovering 1,592 genes encoding secreted proteins involved in plant–pathogen interactions. Plasmopara viticola had a two-speed genome architecture, with secreted protein-encoding genes preferentially located in gene-sparse, repeat-rich regions and evolving rapidly, as indicated by pairwise dN/dS values. We also used short reads to assemble the genome of Plasmopara muralis, a closely related species infecting grape ivy (Parthenocissus tricuspidata). The lineage-specific proteins identified by comparative genomics analysis included a large proportion of RxLR cytoplasmic effectors and, more generally, genes with high dN/dS values. We identified 270 candidate genes under positive selection, including several genes encoding transporters and components of the RNA machinery potentially involved in host specialization. Finally, the Pl. viticola genome assembly generated here will allow the development of robust population genomics approaches for investigating the mechanisms involved in adaptation to biotic and abiotic selective pressures in this species

VvNPR1.1 est l’orthologue d’AtNPR1 et sa surexpression provoque l’activation constitutive des gènes PR et la résistance à Erysiphe necator chez Vitis vinifera

La compréhension des bases moléculaires des mécanismes de résistance de la Vigne aux agresseurs biotiques constitue un prérequis à la recherche de moyens de lutte alternatifs aux pesticides. Chez Arabidopsis, NPR1 (Non expressor of PR genes 1) joue un rôle clé dans la voie de signalisation régulée par l’acide salicylique et responsable de la mise en place de la résistance aux agents pathogènes biotrophes et de la résistance systémique acquise (SAR). Nous avons identifié deux gènes homologues d’AtNPR1 chez la Vigne : VvNPR1.1 et VvNPR1.2. La caractérisation fonctionnelle de ces deux gènes montre que la surexpression de VvNPR1.1 dans le mutant npr1-2 d’Arabidopsis permet, contrairement `a VvNPR1.2, de restaurer l’expression de PR1 après traitement par du SA ou inoculation bactérienne, ainsi que la résistance à Pseudomonas syringae pv. maculicola, un agent pathogène virulent. VvNPR1.1 apparaît donc comme l’orthologue fonctionnel d’AtNPR1, alors que VvNPR1.2 assure vraisemblablement une fonction différente. La surexpression stable de VvNPR1.1 en fusion avec la GFP a également pu être réalisée chez V. vinifera cv. Chardonnay, grâce à une technique de transformation par A. tumefaciens de cals embryogènes de Vigne. Les résultats obtenus sur les plantules transformées montrent une localisation constitutive de VvNPR1-GFP dans le noyau, ainsi qu’une expression élevée des protéines PR en l’absence d’infection. De plus, les vignes surexprimant VvNPR1-GFP montrent clairement une augmentation de la r´esistance vis-à-vis de l’infection par Erysiphe necator, l’agent de l’oïdium. La forte conservation de séquence des gènes VvNPR1 chez les Vitaceae ainsi que l’ensemble de ces résultats souligne l’importance de la voie régulée par le SA et NPR1 pour la résistance aux agents pathogènes biotrophes chez la Vigne

Effectiveness of habitat management in the recovery of low-density populations of wild rabbit.

Understanding the relationship between spatial patterns of landscape attributes and population presence and abundance is essential for understanding population processes as well as supporting management and conservation strategies. This study evaluates the influence of three factors: environment, habitat management, and season on the presence and abundance of the wild rabbit (Oryctolagus cuniculus), an important prey species for Mediterranean endangered predator species. To address this issue, we estimated wild rabbit presence and abundance by latrine counting in transects located in 45 plots within a 250×250 m grid from June 2007 until June 2009 in a 1,200 ha hunting area in southern Portugal.We then analyzed how wild rabbit presence and abundance correlatewith the aforementioned factors. Our results showed that the main variable influencing wild rabbit presence and abundance was the distance to the artificial warrens. North and northeast slope directions were negatively related to wild rabbit presence. Conversely, rabbit presence was positively correlated with short distances to ecotone, artificial warrens, and spring. Regarding rabbit abundance, in addition to artificial warrens, soft soils, bushes, and season also had a positive effect. We found that environmental variables, management practices, and season each affect wild rabbit presence and abundance differently at a home range scale in low-density population. Thus, our major recommendations are reducing the distance to artificial warrens and ecotone, ideally to less than 100 m, and promoting habitat quality improvement on slopes with plenty of sun exposure

Implementation of a knowledge mobilization model to prevent peripheral venous catheter-related adverse events: PREBACP study-a multicenter cluster-randomized trial protocol.

BACKGROUND: Peripheral venous catheters are the most commonly used invasive devices in hospitals worldwide. Patients can experience multiple adverse events during the insertion, maintenance, and management of these devices. Health professionals aim to resolve the challenges of care variability in the use of peripheral venous catheter through adherence to clinical practice guidelines. The aim of this cluster-randomized controlled trial is to determine the efficacy of a multimodal intervention on incidence of adverse events associated with the use of peripheral venous catheters in adult hospital patients. Additional aims are to analyze the fidelity of nurses and the relationship between contextual factors on the use of best available and the outcomes of the intervention. METHODS: Five public hospitals in the Spanish National Health System, with diverse profiles, including one university hospital and four second-level hospitals, will be included. In total, 20 hospitalization wards will be randomized for this study by ward to one of two groups. Those in the first group receive an intervention that lasts 12 months implementing evidence-based practice in healthcare related to peripheral catheters through a multimodal strategy, which will contain updated and poster protocols insertion, maintenance and removal of peripheral venous catheters, technologies applied to e-learning, feedback on the results, user and family information related to peripheral catheter, and facilitation of the best evidence by face-to-face training session. PRIMARY OUTCOME MEASURES: Incidence of adverse events associated with the use of peripheral venous catheters is measured by assessing hospital records. SECONDARY OUTCOME MEASURES: Nurses' adherence to clinical practice guidelines, clinical outcomes, and the cost of implementing the multimodal intervention. DISCUSSION: Clinical implementation is a complex, multifaceted phenomenon which requires a deep understanding of decision-making, knowledge mobilization, and sense making in routine clinical practice. Likewise, the inclusion of strategies that promote fidelity to recommendations through multicomponent and multimodal intervention must be encouraged. The use of a transfer model could counterbalance one of the greatest challenges for organizations, the evaluation of the impact of the implementation of evidence in the professional context through quality indicators associated with prevention and control of infections. TRIAL REGISTRATION: Current Controlled Trials ISRCTN10438530 . Registered 20 March 2018

MAMMALS IN PORTUGAL : A data set of terrestrial, volant, and marine mammal occurrences in P ortugal

Mammals are threatened worldwide, with 26% of all species being includedin the IUCN threatened categories. This overall pattern is primarily associatedwith habitat loss or degradation, and human persecution for terrestrial mam-mals, and pollution, open net fishing, climate change, and prey depletion formarine mammals. Mammals play a key role in maintaining ecosystems func-tionality and resilience, and therefore information on their distribution is cru-cial to delineate and support conservation actions. MAMMALS INPORTUGAL is a publicly available data set compiling unpublishedgeoreferenced occurrence records of 92 terrestrial, volant, and marine mam-mals in mainland Portugal and archipelagos of the Azores and Madeira thatincludes 105,026 data entries between 1873 and 2021 (72% of the data occur-ring in 2000 and 2021). The methods used to collect the data were: live obser-vations/captures (43%), sign surveys (35%), camera trapping (16%),bioacoustics surveys (4%) and radiotracking, and inquiries that represent lessthan 1% of the records. The data set includes 13 types of records: (1) burrowsjsoil moundsjtunnel, (2) capture, (3) colony, (4) dead animaljhairjskullsjjaws, (5) genetic confirmation, (6) inquiries, (7) observation of live animal (8),observation in shelters, (9) photo trappingjvideo, (10) predators dietjpelletsjpine cones/nuts, (11) scatjtrackjditch, (12) telemetry and (13) vocalizationjecholocation. The spatial uncertainty of most records ranges between 0 and100 m (76%). Rodentia (n=31,573) has the highest number of records followedby Chiroptera (n=18,857), Carnivora (n=18,594), Lagomorpha (n=17,496),Cetartiodactyla (n=11,568) and Eulipotyphla (n=7008). The data setincludes records of species classified by the IUCN as threatened(e.g.,Oryctolagus cuniculus[n=12,159],Monachus monachus[n=1,512],andLynx pardinus[n=197]). We believe that this data set may stimulate thepublication of other European countries data sets that would certainly contrib-ute to ecology and conservation-related research, and therefore assisting onthe development of more accurate and tailored conservation managementstrategies for each species. There are no copyright restrictions; please cite thisdata paper when the data are used in publications.info:eu-repo/semantics/publishedVersio

The Variant rs1867277 in FOXE1 Gene Confers Thyroid Cancer Susceptibility through the Recruitment of USF1/USF2 Transcription Factors

In order to identify genetic factors related to thyroid cancer susceptibility, we adopted a candidate gene approach. We studied tag- and putative functional SNPs in genes involved in thyroid cell differentiation and proliferation, and in genes found to be differentially expressed in thyroid carcinoma. A total of 768 SNPs in 97 genes were genotyped in a Spanish series of 615 cases and 525 controls, the former comprising the largest collection of patients with this pathology from a single population studied to date. SNPs in an LD block spanning the entire FOXE1 gene showed the strongest evidence of association with papillary thyroid carcinoma susceptibility. This association was validated in a second stage of the study that included an independent Italian series of 482 patients and 532 controls. The strongest association results were observed for rs1867277 (OR[per-allele] = 1.49; 95%CI = 1.30–1.70; P = 5.9×10−9). Functional assays of rs1867277 (NM_004473.3:c.−283G>A) within the FOXE1 5′ UTR suggested that this variant affects FOXE1 transcription. DNA-binding assays demonstrated that, exclusively, the sequence containing the A allele recruited the USF1/USF2 transcription factors, while both alleles formed a complex in which DREAM/CREB/αCREM participated. Transfection studies showed an allele-dependent transcriptional regulation of FOXE1. We propose a FOXE1 regulation model dependent on the rs1867277 genotype, indicating that this SNP is a causal variant in thyroid cancer susceptibility. Our results constitute the first functional explanation for an association identified by a GWAS and thereby elucidate a mechanism of thyroid cancer susceptibility. They also attest to the efficacy of candidate gene approaches in the GWAS era