2,335 research outputs found

    Animal board invited review: Practical applications of genomic information in livestock

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    Access to high-dimensional genomic information in many livestock species is accelerating. This has been greatly aided not only by continual reductions in genotyping costs but also an expansion in the services available that leverage genomic information to create a greater return-on-investment. Genomic information on individual animals has many uses including (1) parentage verification and discovery, (2) traceability, (3) karyotyping, (4) sex determination, (5) reporting and monitoring of mutations conferring major effects or congenital defects, (6) better estimating inbreeding of individuals and coancestry among individuals, (7) mating advice, (8) determining breed composition, (9) enabling precision management, and (10) genomic evaluations; genomic evaluations exploit genome-wide genotype information to improve the accuracy of predicting an animal’s (and by extension its progeny’s) genetic merit. Genomic data also provide a huge resource for research, albeit the outcome from this research, if successful, should eventually be realised through one of the ten applications already mentioned. The process for generating a genotype all the way from sample procurement to identifying erroneous genotypes is described, as are the steps that should be considered when developing a bespoke genotyping panel for practical application

    Within- and across-breed imputation of high-density genotypes in dairy and beef cattle from medium- and low-density genotypes

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    peer-reviewedFinancial support of the Irish Department of Agriculture Research Stimulus Fund (RSF-06-0353; RSF-06-0428; 11/SF/311), Science Foundation Ireland (09/IN.1/B2642) and the Irish dairy and beef industry are gratefully acknowledged.The objective of this study was to evaluate, using three different genotype density panels, the accuracy of imputation from lower- to higher-density genotypes in dairy and beef cattle. High-density genotypes consisting of 777 962 single-nucleotide polymorphisms (SNP) were available on 3122 animals comprised of 269, 196, 710, 234, 719, 730 and 264 Angus, Belgian Blue, Charolais, Hereford, Holstein-Friesian, Limousin and Simmental bulls, respectively. Three different genotype densities were generated: low density (LD; 6501 autosomal SNPs), medium density (50K; 47 770 autosomal SNPs) and high density (HD; 735 151 autosomal SNPs). Imputation from lower- to higher-density genotype platforms was undertaken within and across breeds exploiting population-wide linkage disequilibrium. The mean allele concordance rate per breed from LD to HD when undertaken using a single breed or multiple breed reference population varied from 0.956 to 0.974 and from 0.947 to 0.967, respectively. The mean allele concordance rate per breed from 50K to HD when undertaken using a single breed or multiple breed reference population varied from 0.987 to 0.994 and from 0.987 to 0.993, respectively. The accuracy of imputation was generally greater when the reference population was solely comprised of the breed to be imputed compared to when the reference population comprised of multiple breeds, although the impactDepartment of Agriculture, Food and the MarineScience Foundation Irelan

    First-Pass Meconium Samples from Healthy Term Vaginally-Delivered Neonates : An Analysis of the Microbiota

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    Acknowledgments The authors would like to thank the parents who consented to provide samples with limited notice at an emotional and stressful time. This work was supported entirely from personal donations to the neonatal endowments fund at Aberdeen Maternity Hospital and we thank families for their continued generosity, year-on-year. The Rowett Institute of Nutrition and Health receives funding from the Scottish Government (SG-RESAS). Funding: This work was funded from NHS Grampian Neonatal Endowments. The Rowett Institute receives funding from the Rural and Environmental Science and Analytical Services programme of the Scottish Government. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Peer reviewedPublisher PD

    Institutional Merit-Based Aid and Student Departure: A Longitudinal Analysis

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    The use of merit criteria in awarding institutional aid has grown considerably and, some argue, is supplanting need as the central factor in awarding aid. Concurrently, the accountability movement in higher education has placed greater emphasis on retention and graduation as indicators of institutional success and quality. In this context, this study explores the relationship between institutional merit aid and student departure from a statewide system of higher education. We found that, once we account for self-selection to the extent possible, there was no significant relationship. By contrast, need-based aid was consistently related to decreased odds of departure

    Black Hole Genealogy: Identifying Hierarchical Mergers with Gravitational Waves

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    In dense stellar environments, the merger products of binary black hole mergers may undergo additional mergers. These hierarchical mergers are naturally expected to have higher masses than the first generation of black holes made from stars. The components of hierarchical mergers are expected to have significant characteristic spins, imprinted by the orbital angular momentum of the previous mergers. However, since the population properties of first-generation black holes are uncertain, it is difficult to know if any given merger is first-generation or hierarchical. We use observations of gravitational waves to reconstruct the binary black hole mass and spin spectrum of a population including the possibility of hierarchical mergers. We employ a phenomenological model that captures the properties of merging binary black holes from simulations of globular clusters. Inspired by recent work on the formation of low-spin black holes, we include a zero-spin subpopulation. We analyze binary black holes from LIGO and Virgo's first two observing runs, and find that this catalog is consistent with having no hierarchical mergers. We find that the most massive system in this catalog, GW170729, is mostly likely a first-generation merger, having a 4% probability of being a hierarchical merger assuming a 5 × 10⁵ M_⊙ globular cluster mass. Using our model, we find that 99% of first-generation black holes in coalescing binaries have masses below 44 M_⊙, and the fraction of binaries with near-zero component spins is less than 0.16 (90% probability). Upcoming observations will determine if hierarchical mergers are a common source of gravitational waves

    Sensitivity and threshold dynamics of Pinus strobus and Quercus spp. in response to experimental and naturally-occurring severe droughts

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    Increased drought frequency and severity are a pervasive global threat, yet the capacity of mesic temperate forests to maintain resilience in response to drought remains poorly understood. We deployed a throughfall removal experiment to simulate a once in a century drought in New Hampshire, USA, which coupled with the region-wide 2016 drought, intensified moisture stress beyond that experienced in the lifetimes of our study trees. To assess the sensitivity and threshold dynamics of two dominant northeastern tree genera (Quercus and Pinus), we monitored sap flux density (Js), leaf water potential and gas exchange, growth, and intrinsic water use efficiency (iWUE) for one pretreatment year (2015) and two treatment years (2016-17). Results showed that Js in pine (P. strobus) declined abruptly at a soil moisture threshold of 0.15 m3m-3 , while oak’s (Q. rubra and Q. velutina) threshold was 0.11 m3m-3 — a finding consistent with pine’s more isohydric strategy. Nevertheless, once oaks’ moisture threshold was surpassed, Js declined abruptly, suggesting that while oaks are well-adapted to moderate drought, they are highly susceptible to extreme drought. The radial growth reduction in response to the 2016 drought was more than twice as great for pine than for oaks (50% vs. 18% respectively). Despite relatively high precipitation in 2017, the oaks’ growth continued to decline (low recovery), whereas pine showed neutral (treatment) or improved (control) growth. iWUE increased in 2016 for both treatment and control pines, but only in treatment oaks. Notably, pines exhibited a significant linear relationship between iWUE and precipitation across years, whereas the oaks only showed a response during the driest conditions, further underscoring the different sensitivity thresholds for these species. Our results provide new insights into how interactions between temperate forest tree species’ contrasting physiologies and soil moisture thresholds influence their responses and resilience to extreme drought

    Genetic selection to reduce lameness in dairy cattle

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    The high prevalence of lameness in dairy cattle is a critical issue for the industry. Despite having a low heritability, considerable genetic variability is associated with the risk of lameness; therefore, genetic selection can be used to complement management-based approaches to reduce lameness in dairy herds. The Lameness Advantage genetic index, available for all recorded and evaluated dairy animals in the UK, is an estimate of an animal's genetic predisposition to lameness. It has been shown that cows with higher Lameness Advantage values had a reduced incidence of sole lesions, digital dermatitis, and lameness; therefore, breeding to increase the average Lameness Advantage value of a herd could be beneficial. This can be readily achieved by breeding replacements from bulls with a Lameness Advantage value that is above the herd average; this is a low-cost and effective strategy that all farms could implement almost immediately to improve foot health. It is important to ensure a balanced approach to genetic selection by first selecting the parents of the next generation on their overall profitability index (eg £PLI, £SCI or £ACI), followed by secondary selection criteria to address specific breeding goals. </jats:p

    Conformational control of structure and guest uptake by a tripeptide-based porous material

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    Chemical processes often rely on the selective sorting and transformation of molecules according to their size, shape and chemical functionality. For example, porous materials such as zeolites achieve the required selectivity through the constrained pore dimensions of a single structure.1 In contrast, proteins function by navigating between multiple metastable structures using bond rotations of the polypeptide,2,3 where each structure lies in one of the minima of a conformational energy landscape and can be selected according to the chemistry of the molecules interacting with the protein.3 Here we show that rotation about covalent bonds in a peptide linker can change a flexible metal-organic framework (MOF) to afford nine distinct crystal structures, revealing a conformational energy landscape characterised by multiple structural minima. The uptake of small molecule guests by the MOF can be chemically triggered by inducing peptide conformational change. This change transforms the material from a minimum on the landscape that is inactive for guest sorption to an active one. Chemical control of the conformation of a flexible organic linker offers a route to modify the pore geometry and internal surface chemistry and thus the function of open-framework materials
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