Effects of Zilpaterol Hydrochloride Supplementation on Growth Performance,Carcass Characteristics and Production Economics of SteersDiffering in Breed Composition

The β–adrenergic agonist zilpaterol hydrochloride (ZH) affects skeletal muscle growth, but little is known if this response is influenced by differences in genetic background of cattle. The objective of this study was to determine the effects of ZH on growth, carcass characteristics and production economic responses of Angus-sired (ANG) and SimAngus-sired (SIMANG) steers. Pens within each block × breed composition were randomly assigned to either ZH (8.3 ppm of DM; fed for the final 20 d before slaughter) or control (CON; 0 ppm ZH). Steers were ultrasounded before ZH inclusion and following withdrawal to determine the influence of ZH on change in ribeye area (REA), fat thickness and percent intramuscular fat (IMF). Carcass and feedlot performance data were collected and used to determine breed composition and ZH effects on economic responses. The interaction of breed composition × ZH had no influence on measured responses. Breed composition did not influence change in ultrasound measurements during the ZH feeding period or feedlot performance. Carcasses from SIMANG steers had larger REA and improved YG, while ANG steers had increased marbling scores. SimAngus-sired steers produced a greater percentage of YG 2 and a lower percentage of YG 3 carcasses than ANG steers. A greater proportion of ANG carcasses were classified as upper 2/3 Choice while a greater proportion of SIMANG carcasses were included in the lower 1/3 Choice designation. Carcass value per cwt was greater for ANG compared to SIMANG carcasses while other economic responses were similar. Feeding ZH improved ADG, YG, and REA and resulted in increased YG 2 carcasses. Total carcass value was greater for ZH compared to CON. While CON had increased IMF during ZH feeding, this did not manifest into differences in QG. Breed composition influenced carcass grid premiums, but not overall carcass value. Feeding ZH improved carcass value by increasing HCW. Responses among breed composition were as expected for ANG vs SIMANG cattle types. The resultant economic effect was that grid premiums for higher-grading ANG cattle were offset by larger HCW for SIMANG, leading to similar overall carcass values. Finally, the influence of ZH on growth and carcass traits was as expected with increased carcass value being realized through heavier HCW

Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel

A major use of the 1000 Genomes Project (1000GP) data is genotype imputation in genome-wide association studies (GWAS). Here we develop a method to estimate haplotypes from low-coverage sequencing data that can take advantage of single-nucleotide polymorphism (SNP) microarray genotypes on the same samples. First the SNP array data are phased to build a backbone (or 'scaffold') of haplotypes across each chromosome. We then phase the sequence data 'onto' this haplotype scaffold. This approach can take advantage of relatedness between sequenced and non-sequenced samples to improve accuracy. We use this method to create a new 1000GP haplotype reference set for use by the human genetic community. Using a set of validation genotypes at SNP and bi-allelic indels we show that these haplotypes have lower genotype discordance and improved imputation performance into downstream GWAS samples, especially at low-frequency variants. © 2014 Macmillan Publishers Limited. All rights reserved

Semi-automated assembly of high-quality diploid human reference genomes

The current human reference genome, GRCh38, represents over 20 years of effort to generate a high-quality assembly, which has benefitted society. However, it still has many gaps and errors, and does not represent a biological genome as it is a blend of multiple individuals. Recently, a high-quality telomere-to-telomere reference, CHM13, was generated with the latest long-read technologies, but it was derived from a hydatidiform mole cell line with a nearly homozygous genome. To address these limitations, the Human Pangenome Reference Consortium formed with the goal of creating high-quality, cost-effective, diploid genome assemblies for a pangenome reference that represents human genetic diversity. Here, in our first scientific report, we determined which combination of current genome sequencing and assembly approaches yield the most complete and accurate diploid genome assembly with minimal manual curation. Approaches that used highly accurate long reads and parent-child data with graph-based haplotype phasing during assembly outperformed those that did not. Developing a combination of the top-performing methods, we generated our first high-quality diploid reference assembly, containing only approximately four gaps per chromosome on average, with most chromosomes within ±1% of the length of CHM13. Nearly 48% of protein-coding genes have non-synonymous amino acid changes between haplotypes, and centromeric regions showed the highest diversity. Our findings serve as a foundation for assembling near-complete diploid human genomes at scale for a pangenome reference to capture global genetic variation from single nucleotides to structural rearrangements

A draft human pangenome reference

Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals. These assemblies cover more than 99% of the expected sequence in each genome and are more than 99% accurate at the structural and base pair levels. Based on alignments of the assemblies, we generate a draft pangenome that captures known variants and haplotypes and reveals new alleles at structurally complex loci. We also add 119 million base pairs of euchromatic polymorphic sequences and 1,115 gene duplications relative to the existing reference GRCh38. Roughly 90 million of the additional base pairs are derived from structural variation. Using our draft pangenome to analyse short-read data reduced small variant discovery errors by 34% and increased the number of structural variants detected per haplotype by 104% compared with GRCh38-based workflows, which enabled the typing of the vast majority of structural variant alleles per sample

Seroprevalence of canine herpesvirus in breeding kennels in the Gauteng Province of South Africa

Canine herpesvirus (CHV-1) causes neonatal deaths as well as infertility due to embryonal death, abortion and stillbirths in breeding kennels. The aim of this study was to determine the prevalence of antibodies against canine herpesvirus in the serum of dogs older than 1 year in breeding kennels in the Gauteng Province of South Africa. A serum neutralization test (SNT) and a newly developed enzyme linked immunosorbent assay (ELISA) were used to test the serum samples of 328 dogs in 38 breeding kennels. With SNT as well as ELISA, 22% of sera were positive (P > 0.9). Seventeen kennels (45% of total kennels) each had at least one positive dog on SNT compared with twenty kennels (53% of total kennels) that each had at least one positive dog on ELISA (P = 0.6). The prevalence of positive dogs in positive kennels was 42 26% (n = 17 kennels) for SNT and 39 26% (n = 20 kennels) for ELISA. Pairwise comparison of kennels showed that the prevalence of SNT positive dogs was similar to the prevalence of ELISA positive dogs (P = 0.3, n = 38 kennels). Seroprevalence was independent of age, gender or colony size. This study suggests that canine herpesvirus is sufficiently common in breeding dogs in the Gauteng Province of South Africa to pose a threat to neonatal survival and fertility

Antibodies against Entamoeba histolytica in individuals with intestinal amoebiasis presenting cysts and/or trophozoites in the feces Anticorpos anti-Entamoeba histolylica em indivíduos com amebíase intestinal apresentando cistos e/ou trofozoitas nas fezes

Serum samples were obtained from 154 individuals infected with Entamoeba histolytica (78 symptomatic and 76 asymptomatic). Twelve had trophozoites in the feces whereas 142 had only cysts. The sera were used to test the existence of antibodies anti-Entamoeba histolytica employing the Indirect Hemagglutination (IHA), Indirect Immunofluoresccnce (IFAT), Complement Fixation Reaction (CFR) and Counterimmunoelectrophoresis (CIEP). For those individuals with trophozoites in their feces, 75.0 were positive by IHA and IFAT, 83.0 by CFR and 41.7 by CIEP. In individuals who had only cysts, positive results by the same tests were respectively, 5.6%, 12.0%, 19.0% and 5.6%. The difference in relation to the tilers of antibodies detected through IHA, IFAT, CFR and CIEP and in relation to the presence of trophozoites or cysts in the feces was significative for four immunological reactions when X², was employed (P < 0.05).<br>Amostras de soros foram obtidas de 154 indivíduos comprovadamente parasitados pela Entamoeba histolytica (78 sintomáticos c 76 assintomáticos). Doze apresentavam trofozoitas nas fezes, enquanto 142 tinham apenas cistos. Os soros foram utilizados para testar a ocorrência de anticorpos anti-Entamoeba histolytica, empregando-se para tal, Reação de Hemaglutinação Indireta (HAI), Reação de Imunofluorescência Indireta (RIFI), Reação de Fixação de Complemento (RFC) e Contraimunoeletroforese (CIEP). Entre os soros dos indivíduos com trofozoitas em suas fezes, 75,0% foram positivos para HAI e RIFI, 83,3% por RFC, e 41,7% por CIEP. Nos indivíduos que tinham apenas cistos, resultados positivos pelos mesmos testes foram respectivamente, 5,6%; 12,0%; 19,0% c 5,6%. A diferença cm relação aos títulos de anticorpos detectados através de HAI, RIFI, RFC e CIEP e em relação à presença de trofozoitas ou cistos nas fezes foi significativa para as quatro reações imunológicas, quando X² foi empregado (P < 0,05)