Compilation of a panel of informative single nucleotide polymorphisms for bovine identification in the Northern Irish cattle population

<p>Abstract</p> <p>Background</p> <p>Animal identification is pivotal in governmental agricultural policy, enabling the management of subsidy payments, movement of livestock, test scheduling and control of disease. Advances in bovine genomics have made it possible to utilise inherent genetic variability to uniquely identify individual animals by DNA profiling, much as has been achieved with humans over the past 20 years. A DNA profiling test based on bi-allelic single nucleotide polymorphism (SNP) markers would offer considerable advantages over current short tandem repeat (STR) based industry standard tests, in that it would be easier to analyse and interpret. In this study, a panel of 51 genome-wide SNPs were genotyped across panels of semen DNA from 6 common breeds for the purposes of ascertaining allelic frequency. For SNPs on the same chromosome, the extent of linkage disequilbrium was determined from genotype data by Expectation Maximization (EM) algorithm. Minimum probabilities of unique identification were determined for each breed panel. The usefulness of this SNP panel was ascertained by comparison to the current bovine STR Stockmarks II assay. A statistically representative random sampling of bovine animals from across Northern Ireland was assembled for the purposes of determining the population allele frequency for these STR loci and subsequently, the minimal probability of unique identification they conferred in sampled bovine animals from Northern Ireland.</p> <p>Results</p> <p>6 SNPs exhibiting a minor allele frequency of less than 0.2 in more than 3 of the breed panels were excluded. 2 Further SNPs were found to reside in coding areas of the cattle genome and were excluded from the final panel. The remaining 43 SNPs exhibited genotype frequencies which were in Hardy Weinberg Equilibrium. SNPs on the same chromosome were observed to have no significant linkage disequilibrium/allelic association. Minimal probabilities of uniquely identifying individual animals from each of the breeds were obtained and were observed to be superior to those conferred by the industry standard STR assay.</p> <p>Conclusions</p> <p>The 43 SNPs characterised herein may constitute a starting point for the development of a SNP based DNA identification test for European cattle.</p

Continent-wide analysis of how urbanization affects bird-window collision mortality in North America

Characteristics of buildings and land cover surrounding buildings influence the number of bird-window collisions, yet little is known about whether bird-window collisions are associated with urbanization at large spatial scales. We initiated a continent-wide study in North America to assess how bird-window collision mortality is influenced by building characteristics, landscaping around buildings, and regional urbanization. In autumn 2014, researchers at 40 sites (N = 281 buildings) used standardized protocols to document collision mortality of birds, evaluate building characteristics, and measure local land cover and regional urbanization. Overall, 324 bird carcasses were observed (range = 0–34 per site) representing 71 species. Consistent with previous studies, we found that building size had a strong positive effect on bird-window collision mortality, but the strength of the effect on mortality depended on regional urbanization. The positive relationship between collision mortality and building size was greatest at large buildings in regions of low urbanization, locally extensive lawns, and low-density structures. Collision mortality was consistently low for small buildings, regardless of large-scale urbanization. The mechanisms shaping broad-scale variation in collision mortality during seasonal migration may be related to habitat selection at a hierarchy of scales and behavioral divergence between urban and rural bird populations. These results suggest that collision prevention measures should be prioritized at large buildings in regions of low urbanization throughout North America

Continent-wide analysis of how urbanization affects bird-window collision mortality in North America

Characteristics of buildings and land cover surrounding buildings influence the number of bird-window collisions, yet little is known about whether bird-window collisions are associated with urbanization at large spatial scales. We initiated a continent-wide study in North America to assess how bird-window collision mortality is influenced by building characteristics, landscaping around buildings, and regional urbanization. In autumn 2014, researchers at 40 sites (N = 281 buildings) used standardized protocols to document collision mortality of birds, evaluate building characteristics, and measure local land cover and regional urbanization. Overall, 324 bird carcasses were observed (range = 0–34 per site) representing 71 species. Consistent with previous studies, we found that building size had a strong positive effect on bird-window collision mortality, but the strength of the effect on mortality depended on regional urbanization. The positive relationship between collision mortality and building size was greatest at large buildings in regions of low urbanization, locally extensive lawns, and low-density structures. Collision mortality was consistently low for small buildings, regardless of large-scale urbanization. The mechanisms shaping broad-scale variation in collision mortality during seasonal migration may be related to habitat selection at a hierarchy of scales and behavioral divergence between urban and rural bird populations. These results suggest that collision prevention measures should be prioritized at large buildings in regions of low urbanization throughout North America

Alternative genomic diagnoses for individuals with a clinical diagnosis of Dubowitz syndrome

Abstract Dubowitz syndrome (DubS) is considered a recognizable syndrome characterized by a distinctive facial appearance and deficits in growth and development. There have been over 200 individuals reported with Dubowitz or a “Dubowitz-like” condition, although no single gene has been implicated as responsible for its cause. We have performed exome (ES) or genome sequencing (GS) for 31 individuals clinically diagnosed with DubS. After genome-wide sequencing, rare variant filtering and computational and Mendelian genomic analyses, a presumptive molecular diagnosis was made in 13/27 (48%) families. The molecular diagnoses included biallelic variants in SKIV2L, SLC35C1, BRCA1, NSUN2; de novo variants in ARID1B, ARID1A, CREBBP, POGZ, TAF1, HDAC8, and copy-number variation at1p36.11(ARID1A), 8q22.2(VPS13B), Xp22, and Xq13(HDAC8). Variants of unknown significance in known disease genes, and also in genes of uncertain significance, were observed in 7/27 (26%) additional families. Only one gene, HDAC8, could explain the phenotype in more than one family (N = 2). All but two of the genomic diagnoses were for genes discovered, or for conditions recognized, since the introduction of next-generation sequencing. Overall, the DubS-like clinical phenotype is associated with extensive locus heterogeneity and the molecular diagnoses made are for emerging clinical conditions sharing characteristic features that overlap the DubS phenotype

Is perioperative COVID-19 really associated with worse surgical outcomes? A nationwide COVIDSurg propensity-matched analysis

BACKGROUND: Patients undergoing surgery with perioperative COVID-19 are suggested to have worse outcomes, but whether this is COVID-related or due to selection bias remains unclear. We aimed to compare the postoperative outcomes of patients with and without perioperative COVID-19. METHODS: Patients with perioperative COVID-19 diagnosed within 7 days before or 30 days after surgery between February and July 2020 from 68 US hospitals in COVIDSurg, an international multicenter database, were 1:1 propensity score matched to patients without COVID-19 undergoing similar procedures in the 2012 American College of Surgeons National Surgical Quality Improvement Program database. The matching criteria included demographics (e.g., age, sex), comorbidities (e.g., diabetes, chronic obstructive pulmonary disease, chronic kidney disease), and operation characteristics (e.g., type, urgency, complexity). The primary outcome was 30-day hospital mortality. Secondary outcomes included hospital length of stay and 13 postoperative complications (e.g., pneumonia, renal failure, surgical site infection). RESULTS: A total of 97,936 patients were included, 1,054 with and 96,882 without COVID-19. Prematching, COVID-19 patients more often underwent emergency surgery (76.1% vs. 10.3%, p &lt; 0.001). A total of 843 COVID-19 and 843 non-COVID-19 patients were successfully matched based on demographics, comorbidities, and operative characteristics. Postmatching, COVID-19 patients had a higher mortality (12.0% vs. 8.1%, p = 0.007), longer length of stay (6 [2-15] vs. 5 [1-12] days), and higher rates of acute renal failure (19.3% vs. 3.0%, p &lt; 0.001), sepsis (13.5% vs. 9.0%, p = 0.003), and septic shock (11.8% vs. 6.0%, p &lt; 0.001). They also had higher rates of thromboembolic complications such as deep vein thrombosis (4.4% vs. 1.5%, p &lt; 0.001) and pulmonary embolism (2.5% vs. 0.4%, p &lt; 0.001) but lower rates of bleeding (11.6% vs. 26.1%, p &lt; 0.001). CONCLUSION: Patients undergoing surgery with perioperative COVID-19 have higher rates of 30-day mortality and postoperative complications, especially thromboembolic, compared with similar patients without COVID-19 undergoing similar surgeries. Such information is crucial for the complex surgical decision making and counseling of these patients. (J Trauma Acute Care Surg. 2023;94: 513-524. Copyright (C) 2023 American Association for the Surgery of Trauma.)LEVEL OF EVIDENCE: Prognostic and Epidemiologic; Level IV