Genomic scans for selection and runs of homozygosity in southern Italian turkey populations.

Basilicata and Apulian (BAS-APU) turkeys, a native population in the Basilicata and Puglia regions of southern Italy, are known for their high meat quality and tolerance to local conditions. Understanding the genomic patterns of BAS-APU turkeys is critical for effective breeding and preservation strategies. In this study, we characterized runs of homozygosity (ROH), and selection signatures using the integrated haplotype score (iHS) and ROH approaches.

Ligand-Directed Labeling of the Adenosine A Receptor in Living Cells.

The study of protein function and dynamics in their native cellular environment is essential for progressing fundamental science. To overcome the requirement of genetic modification of the protein or the limitations of dissociable fluorescent ligands, ligand-directed (LD) chemistry has most recently emerged as a complementary, bioorthogonal approach for labeling native proteins. Here, we describe the rational design, development, and application of the first ligand-directed chemistry approach for labeling the AAR in living cells.

Expression genome-wide association study identifies key regulatory variants enriched with metabolic and immune functions in four porcine tissues.

Background: Integration of high throughput DNA genotyping and RNA-sequencing data enables the discovery of genomic regions that regulate gene expression, known as expression quantitative trait loci (eQTL). In pigs, efforts to date have been mainly focused on purebred lines for traits with commercial relevance as such growth and meat quality. However, little is known on genetic variants and mechanisms associated with the robustness of an animal, thus its overall health status.

The genomics of adaptation to climate in European great tit () populations.

The recognition that climate change is occurring at an unprecedented rate means that there is increased urgency in understanding how organisms can adapt to a changing environment. Wild great tit () populations represent an attractive ecological model system to understand the genomics of climate adaptation. They are widely distributed across Eurasia and they have been documented to respond to climate change.

Corrigendum: A novel loss-of-function variant in transmembrane protein 263 (TMEM263) of autosomal dwarfism in chicken.

[This corrects the article DOI: 10.3389/fgene.2018.

Role of endothelin ET receptors in the hypertension induced by the VEGFR-2 kinase inhibitors axitinib and lenvatinib in conscious freely-moving rats.

Receptor tyrosine kinase inhibitors (RTKIs) suppress tumour growth by targeting vascular endothelial growth factor receptor 2 (VEGFR-2) which is an important mediator of angiogenesis. Here, we demonstrate that two potent RTKIs, axitinib and lenvatinib, are associated with hypertensive side effects. Doppler flowmetry was used to evaluate regional haemodynamic profiles of axitinib and lenvatinib.

Swine global genomic resources: insights into wild and domesticated populations.

Suids, both domesticated and wild, are found on all continents except for Antarctica and provide valuable food resources for humans in addition to serving as important models for biomedical research. Continuing advances in genome sequencing have allowed researchers to compare the genomes from diverse populations of suids helping to clarify their evolution and dispersal. Further analysis of these samples may provide clues to improve disease resistance/resilience and productivity in domestic suids as well as better ways of classifying and conserving genetic diversity within wild and captive suids.

Symmetric expression of ohnologs encoding conserved antiviral responses in tetraploid common carp suggest absence of subgenome dominance after whole genome duplication.

Allopolyploids often experience subgenome dominance, with one subgenome showing higher levels of gene expression and greater gene retention. Here, we address the functionality of both subgenomes of allotetraploid common carp (Cyprinus carpio) by analysing a functional network of interferon-stimulated genes (ISGs) crucial in anti-viral immune defence. As an indicator of subgenome dominance we investigated retainment of a core set of ohnologous ISGs.

The rate of de novo structural variation is increased in in vitro-produced offspring and preferentially affects the paternal genome.

Assisted reproductive technologies (ARTs), including in vitro maturation and fertilization (IVF), are increasingly used in human and animal reproduction. Whether these technologies directly affect the rate of de novo mutation (DNM), and to what extent, has been a matter of debate. Here we take advantage of domestic cattle, characterized by complex pedigrees that are ideally suited to detect DNMs and by the systematic use of ART, to study the rate of de novo structural variation (dnSV) in this species and how it is impacted by IVF.

External Validity and Consistency over Time of Patient Segmentation Based on Disease Acceptance and Perceived Control in Inflammatory Bowel Disease.

Background And Aims: The patient segmentation model based on disease acceptance and perceived control may guide personalized care in inflammatory bowel disease (IBD). We aimed to investigate the external validity of the segmentation model and its consistency over time.

Methods: This is a multicenter longitudinal cohort study of adult IBD patients with questionnaires on disease acceptance and perceived control (6-items, 7-point Likert scale) and health-related quality of life (HRQoL) (Short IBD questionnaire, range 10-70).

Potential selection for lipid kinase activity and spermatogenesis in Henan native pig breeds and growth shaping by introgression of European genes.

Background: China has one third of the worldwide indigenous pig breeds. The Henan province is one of the earliest pig domestication centers of China (about 8000 years ago). However, the precise genetic characteristics of the Henan local pig breeds are still obscure.

A new haplotype-resolved turkey genome to enable turkey genetics and genomics research.

Background: The domesticated turkey (Meleagris gallopavo) is a species of significant agricultural importance and is the second largest contributor, behind broiler chickens, to world poultry meat production. The previous genome is of draft quality and partly based on the chicken (Gallus gallus) genome. A high-quality reference genome of M.

Baseline dependent minimally important differences for clinical outcomes of pulmonary rehabilitation in people with COPD.

Introduction: Minimally important differences (MIDs) for common outcomes of pulmonary rehabilitation are well documented for people with chronic obstructive pulmonary disease (COPD). It is not known whether MIDs differ based on COPD disease characteristics. This study aimed to estimate MIDs for clinical outcomes of pulmonary rehabilitation dependent upon baseline characteristics.

Mucosal α4β7+ Lymphocytes and MAdCAM+ Venules Predict Response to Vedolizumab in Ulcerative Colitis.

Background: Therapeutic strategies for patients with ulcerative colitis (UC) are based on patient- and disease-related factors in combination with drug characteristics but fail to predict success in individual patients. A considerable proportion of UC patients do not respond to the biological vedolizumab. Therefore, pretreatment biomarkers for therapeutic efficacy are urgently needed.

Integrative metabolomic and transcriptomic analysis reveals difference in glucose and lipid metabolism in the longissimus muscle of Luchuan and Duroc pigs.

Luchuan pig, an obese indigenous Chinese porcine breed, has a desirable meat quality and reproductive capacity. Duroc, a traditional western breed, shows a faster growth rate, high feed efficiency and high lean meat rate. Given the unique features these two porcine breeds have, it is of interest to investigate the underlying molecular mechanisms behind their distinctive nature.

Identification and characterisation of de novo germline structural variants in two commercial pig lines using trio-based whole genome sequencing.

Background: De novo mutations arising in the germline are a source of genetic variation and their discovery broadens our understanding of genetic disorders and evolutionary patterns. Although the number of de novo single nucleotide variants (dnSNVs) has been studied in a number of species, relatively little is known about the occurrence of de novo structural variants (dnSVs). In this study, we investigated 37 deeply sequenced pig trios from two commercial lines to identify dnSVs present in the offspring.

Assessing the relationship between the in silico predicted consequences of 97 missense mutations mapping to 68 genes related to lipid metabolism and their association with porcine fatness traits.

In general, the relationship between the predicted functional consequences of missense mutations mapping to genes known to be involved in human diseases and the severity of disease manifestations is weak. In this study, we tested in pigs whether missense single nucleotide polymorphisms (SNPs), predicted to have consequences on the function of genes related to lipid metabolism are associated with lipid phenotypes. Association analysis demonstrated that nine out of 72 nominally associated SNPs were classified as "highly" or "very highly consistent" in silico-predicted functional mutations and did not show association with lipid traits expected to be affected by inactivation of the corresponding gene.

Distinct traces of mixed ancestry in western commercial pig genomes following gene flow from Chinese indigenous breeds.

Studying gene flow between different livestock breeds will benefit the discovery of genes related to production traits and provide insight into human historical breeding. Chinese pigs have played an indispensable role in the breeding of Western commercial pigs. However, the differences in the timing and volume of the contribution of pigs from different Chinese regions to Western pigs are not yet apparent.

Genomic insight into the influence of selection, crossbreeding, and geography on population structure in poultry.

Background: In poultry, the population structure of local breeds is usually complex mainly due to unrecorded breeding. Local chicken breeds offer an interesting proxy to understand the complexity of population structure in the context of human-mediated development of diverse morphologies and varieties. We studied 37 traditional Dutch chicken breeds to investigate population structure and the corresponding genomic impact using whole-genome sequence data.