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https://www.readbyqxmd.com/read/28211150/genomic-prediction-of-reproduction-traits-for-merino-sheep
#1
S Bolormaa, D J Brown, A A Swan, J H J van der Werf, B J Hayes, H D Daetwyler
Economically important reproduction traits in sheep, such as number of lambs weaned and litter size, are expressed only in females and later in life after most selection decisions are made, which makes them ideal candidates for genomic selection. Accurate genomic predictions would lead to greater genetic gain for these traits by enabling accurate selection of young rams with high genetic merit. The aim of this study was to design and evaluate the accuracy of a genomic prediction method for female reproduction in sheep using daughter trait deviations (DTD) for sires and ewe phenotypes (when individual ewes were genotyped) for three reproduction traits: number of lambs born (NLB), litter size (LSIZE) and number of lambs weaned...
February 17, 2017: Animal Genetics
https://www.readbyqxmd.com/read/28208220/allergic-respiratory-disease-different-allergens-different-symptoms
#2
Antonio Valero, Santiago Quirce, Ignacio Dávila, Julio Delgado, Javier Domínguez-Ortega
BACKGROUND: Spanish population is rather homogeneous in its genetic and socio-cultural characteristics, but allergen sensitization shows wide geographical variations. We aimed at assessing whether sensitization to different allergens in the diverse geographical areas induced different clinical and quality of life characteristics in adult patients with a first-time diagnosis of rhinitis and/or asthma. METHODS: Two sequential, identically designed studies were carried out to evaluate such associations (PERFILAR I and II)...
February 16, 2017: Allergy
https://www.readbyqxmd.com/read/28204911/selection-of-transformation-efficient-barley-genotypes-based-on-tfa-transformation-amenability-haplotype-and-higher-resolution-mapping-of-the-tfa-loci
#3
Hiroshi Hisano, Brigid Meints, Matthew J Moscou, Luis Cistue, Begoña Echávarri, Kazuhiro Sato, Patrick M Hayes
The genetic substitution of transformation amenability alleles from 'Golden Promise' can facilitate the development of transformation-efficient lines from recalcitrant barley cultivars. Barley (Hordeum vulgare) cv. 'Golden Promise' is one of the most useful and well-studied cultivars for genetic manipulation. In a previous report, we identified several transformation amenability (TFA) loci responsible for Agrobacterium-mediated transformation using the F2 generation of immature embryos, derived from 'Haruna Nijo' × 'Golden Promise,' as explants...
February 15, 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/28199149/a-genetic-method-to-evaluate-the-prevalence-of-unique-dna-profiles-between-sequential-ground-beef-batches
#4
G Peters, B Cleveland, J Higgins, F Butler, C Meghen
The delineation of ground beef batches has implications for the management of product disposition policies in the event of Shiga toxin-producing Escherichia coli contamination. Analysis of individual contributor animal-specific DNA profiles can provide valuable empirical data for understanding the dynamics of ground meat production processes and can act as a surrogate for cross-contamination. A genetic method was developed for characterizing the source raw material flow and carryover between discrete batches of ground beef in a large-scale commercial beef grinding operation...
February 15, 2017: Journal of Food Protection
https://www.readbyqxmd.com/read/28196537/characterization-of-a-novel-disease-causing-mutation-in-exon-1-of-sh2d1a-gene-through-amplicon-sequencing-a-case-report-on-hlh
#5
Shiyuan Zhou, Hongyu Ma, Bo Gao, Guangming Fang, Yi Zeng, Qing Zhang, GaoFu Qi
BACKGROUND: Hemophagocytic lymphohistocytosis (HLH) is a rare but fatal hyperinflammatory syndrome caused by uncontrolled proliferation of activated macrophages and T lymphocytes secreting high amounts of inflammatory cytokines. Genetic defect is a common cause of HLH. HLH is complicated to be diagnosed as there are many common symptoms with other disorders. CASE PRESENTATION: Here we report on an HLH case caused by 1 bp deletion in gene SH2D1A. Patient was a 3-years-old boy and had fever for more than 8 days...
February 14, 2017: BMC Medical Genetics
https://www.readbyqxmd.com/read/28194132/molecular-imaging-markers-to-track-huntington-s-disease-pathology
#6
REVIEW
Heather Wilson, Rosa De Micco, Flavia Niccolini, Marios Politis
Huntington's disease (HD) is a progressive, monogenic dominant neurodegenerative disorder caused by repeat expansion mutation in the huntingtin gene. The accumulation of mutant huntingtin protein, forming intranuclear inclusions, subsequently leads to degeneration of medium spiny neurons in the striatum and cortical areas. Genetic testing can identify HD gene carriers before individuals develop overt cognitive, psychiatric, and chorea symptoms. Thus, HD gene carriers can be studied in premanifest stages to understand and track the evolution of HD pathology...
2017: Frontiers in Neurology
https://www.readbyqxmd.com/read/28187888/a-survey-of-nature-inspired-algorithms-for-feature-selection-to-identify-parkinson-s-disease
#7
Prashant Shrivastava, Anupam Shukla, Praneeth Vepakomma, Neera Bhansali, Kshitij Verma
BACKGROUND AND OBJECTIVES: Parkinson's disease is a chronic neurological disorder that directly affects human gait. It leads to slowness of movement, causes muscle rigidity and tremors. Analyzing human gait serves to be useful in studies aiming at early recognition of the disease. In this paper we perform a comparative analysis of various nature inspired algorithms to select optimal features/variables required for aiding in the classification of affected patients from the rest. METHODS: For the experiments, we use a real life dataset of 166 people containing both healthy controls and affected people...
February 2017: Computer Methods and Programs in Biomedicine
https://www.readbyqxmd.com/read/28184244/solid-binding-peptides-for-immobilisation-of-thermostable-enzymes-to-hydrolyse-biomass-polysaccharides
#8
Andrew Care, Kerstin Petroll, Emily S Y Gibson, Peter L Bergquist, Anwar Sunna
BACKGROUND: Solid-binding peptides (SBPs) bind strongly to a diverse range of solid materials without the need for any chemical reactions. They have been used mainly for the functionalisation of nanomaterials but little is known about their use for the immobilisation of thermostable enzymes and their feasibility in industrial-scale biocatalysis. RESULTS: A silica-binding SBP sequence was fused genetically to three thermostable hemicellulases. The resulting enzymes were active after fusion and exhibited identical pH and temperature optima but differing thermostabilities when compared to their corresponding unmodified enzymes...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28182345/a-cross-validation-design-using-age-and-hla-alleles-for-the-assessment-of-clinical-schizophrenia-risk
#9
Song Laiyu, Zhang Lei, Xie Soufu, Xv Junting, Zhou Jie, Liu Hui
BACKGROUND: Schizophrenia (SCH) is a highly heritable disease that occurs mostly in young adults. Genetic factors usually play important roles in the onset of SCH. Human leukocyte antigen complex (HLA) genes are considered to be the important genetic predisposition factor and the genetic markers in SCH and other diseases. METHODS: To screen SCH-associated HLA alleles, alleles for HLA-DRB1 and HLA-DQB1 loci were determined using the PCR-SSP typing kit. Statistically significant differences between observed and expected frequencies of allele combinations were identified...
February 1, 2017: Clinical Laboratory
https://www.readbyqxmd.com/read/28181240/cytochrome-p450-genetic-variations-can-predict-mrna-expression-cyclophosphamide-4-hydroxylation-and-treatment-outcomes-in-chinese-patients-with-non-hodgkin-s-lymphoma
#10
Wenying Shu, Lingyan Chen, Xiaoye Hu, Meimei Zhang, Wensheng Chen, Lei Ma, Xiaoyan Liu, Jianing Huang, Tingyuan Pang, Jia Li, Yu Zhang
To investigate the impact of cytochrome P450 (CYP) genetic polymorphisms CYP2B6, CYP2C19, and CYP3A5 on mRNA expression, cyclophosphamide/4-hydroxycyclophosphamide pharmacokinetics, and treatment outcomes of the R-CHOP regimen (rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone) in Chinese patients with non-Hodgkin's lymphoma, 567 cases were investigated. Plasma concentrations of cyclophosphamide/4-hydroxycyclophosphamide were determined using liquid chromatography-tandem mass spectrometry and pharmacokinetic parameters calculated...
February 9, 2017: Journal of Clinical Pharmacology
https://www.readbyqxmd.com/read/28176359/detecting-association-of-rare-and-common-variants-based-on-cross-validation-prediction-error
#11
Xinlan Yang, Shuaichen Wang, Shuanglin Zhang, Qiuying Sha
Despite the extensive discovery of disease-associated common variants, much of the genetic contribution to complex traits remains unexplained. Rare variants may explain additional disease risk or trait variability. Although sequencing technology provides a supreme opportunity to investigate the roles of rare variants in complex diseases, detection of these variants in sequencing-based association studies presents substantial challenges. In this article, we propose novel statistical tests to test the association between rare and common variants in a genomic region and a complex trait of interest based on cross-validation prediction error (PE)...
February 8, 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/28152098/genome-wide-association-analysis-for-heat-tolerance-at-flowering-detected-a-large-set-of-genes-involved-in-adaptation-to-thermal-and-other-stresses
#12
Tanguy Lafarge, Crisanta Bueno, Julien Frouin, Laval Jacquin, Brigitte Courtois, Nourollah Ahmadi
Fertilization sensitivity to heat in rice is a major issue within climate change scenarios in the tropics. A panel of 167 indica landraces and improved varieties was phenotyped for spikelet sterility (SPKST) under 38°C during anthesis and for several secondary traits potentially affecting panicle micro-climate and thus the fertilization process. The panel was genotyped with an average density of one marker per 29 kb using genotyping by sequencing. Genome-wide association analyses (GWAS) were conducted using three methods based on single marker regression, haplotype regression and simultaneous fitting of all markers, respectively...
2017: PloS One
https://www.readbyqxmd.com/read/28148241/a-predictive-assessment-of-genetic-correlations-between-traits-in-chickens-using-markers
#13
Mehdi Momen, Ahmad Ayatollahi Mehrgardi, Ayoub Sheikhy, Ali Esmailizadeh, Masood Asadi Fozi, Andreas Kranis, Bruno D Valente, Guilherme J M Rosa, Daniel Gianola
BACKGROUND: Genomic selection has been successfully implemented in plant and animal breeding programs to shorten generation intervals and accelerate genetic progress per unit of time. In practice, genomic selection can be used to improve several correlated traits simultaneously via multiple-trait prediction, which exploits correlations between traits. However, few studies have explored multiple-trait genomic selection. Our aim was to infer genetic correlations between three traits measured in broiler chickens by exploring kinship matrices based on a linear combination of measures of pedigree and marker-based relatedness...
February 1, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28144390/predictors-for-advanced-fibrosis-in-morbidly-obese-non-alcoholic-fatty-liver-patients
#14
Shira Zelber-Sagi, Dafna Shoham, Isabel Zvibel, Subhi Abu-Abeid, Oren Shibolet, Sigal Fishman
AIM: To investigate predictors for fibrosis specifically in a high risk population of morbidly obese patients, including detailed evaluation of lifestyle. METHODS: We conducted a cross-sectional study among morbidly obese patients attending the bariatric clinic at the Tel-Aviv Medical Center between the years 2013-2014 with body mass index (BMI) above 40 or above 35 with co-morbidity. Patients with serum hepatitis B surface antigen or anti-hepatitis C virus antibodies, genetic liver diseases, autoimmune disease or high alcohol intake (≥ 30 g/d in men or ≥ 20 g/d in women) were excluded from the study...
January 18, 2017: World Journal of Hepatology
https://www.readbyqxmd.com/read/28143593/the-use-of-genomic-information-increases-the-accuracy-of-breeding-value-predictions-for-sea-louse-caligus-rogercresseyi-resistance-in-atlantic-salmon-salmo-salar
#15
Katharina Correa, Rama Bangera, René Figueroa, Jean P Lhorente, José M Yáñez
Sea lice infestations caused by Caligus rogercresseyi are a main concern to the salmon farming industry due to associated economic losses. Resistance to this parasite was shown to have low to moderate genetic variation and its genetic architecture was suggested to be polygenic. The aim of this study was to compare accuracies of breeding value predictions obtained with pedigree-based best linear unbiased prediction (P-BLUP) methodology against different genomic prediction approaches: genomic BLUP (G-BLUP), Bayesian Lasso, and Bayes C...
January 31, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28143402/genomic-predictions-can-accelerate-selection-for-resistance-against-piscirickettsia-salmonis-in-atlantic-salmon-salmo-salar
#16
Rama Bangera, Katharina Correa, Jean P Lhorente, René Figueroa, José M Yáñez
BACKGROUND: Salmon Rickettsial Syndrome (SRS) caused by Piscirickettsia salmonis is a major disease affecting the Chilean salmon industry. Genomic selection (GS) is a method wherein genome-wide markers and phenotype information of full-sibs are used to predict genomic EBV (GEBV) of selection candidates and is expected to have increased accuracy and response to selection over traditional pedigree based Best Linear Unbiased Prediction (PBLUP). Widely used GS methods such as genomic BLUP (GBLUP), SNPBLUP, Bayes C and Bayesian Lasso may perform differently with respect to accuracy of GEBV prediction...
January 31, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28133611/diagnostic-method-of-diabetes-based-on-support-vector-machine-and-tongue-images
#17
Jianfeng Zhang, Jiatuo Xu, Xiaojuan Hu, Qingguang Chen, Liping Tu, Jingbin Huang, Ji Cui
Objective. The purpose of this research is to develop a diagnostic method of diabetes based on standardized tongue image using support vector machine (SVM). Methods. Tongue images of 296 diabetic subjects and 531 nondiabetic subjects were collected by the TDA-1 digital tongue instrument. Tongue body and tongue coating were separated by the division-merging method and chrominance-threshold method. With extracted color and texture features of the tongue image as input variables, the diagnostic model of diabetes with SVM was trained...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28129567/response-surface-methodology-in-drug-design-a-case-study-on-docking-analysis-of-a-potent-antifungal-fluconazole
#18
Fatemeh Bohlooli, Saghi Sepehri, Nima Razzaghi-Asl
Molecular docking is a valuable in silico technique for discovery/design of bioactive compounds. A current challenge within docking simulations is the incorporation of receptor flexibility. A useful strategy toward solving such problem would be the docking of a typical ligand into the multiple conformations of the target. In this study, a multifactor response surface model was constructed to estimate the AutoDock based binding free energy of fluconazole within multiple conformations of 14α-demethylase (CYP51) (cross docking) as a validated antifungal target...
January 19, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28125086/utilization-of-genetic-tests-analysis-of-gene-specific-billing-in-medicare-claims-data
#19
Julie A Lynch, Brygida Berse, W David Dotson, Muin J Khoury, Nicole Coomer, John Kautter
PURPOSE: We examined the utilization of precision medicine tests among Medicare beneficiaries through analysis of gene-specific tier 1 and 2 billing codes developed by the American Medical Association in 2012. METHODS: We conducted a retrospective cross-sectional study. The primary source of data was 2013 Medicare 100% fee-for-service claims. We identified claims billed for each laboratory test, the number of patients tested, expenditures, and the diagnostic codes indicated for testing...
January 26, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28122512/prediction-of-genomic-breeding-values-for-growth-carcass-and-meat-quality-traits-in-a-multi-breed-sheep-population-using-a-hd-snp-chip
#20
Luiz F Brito, Shannon M Clarke, John C McEwan, Stephen P Miller, Natalie K Pickering, Wendy E Bain, Ken G Dodds, Mehdi Sargolzaei, Flávio S Schenkel
BACKGROUND: New Zealand has some unique Terminal Sire composite sheep breeds, which were developed in the last three decades to meet commercial needs. These composite breeds were developed based on crossing various Terminal Sire and Maternal breeds and, therefore, present high genetic diversity compared to other sheep breeds. Their breeding programs are focused on improving carcass and meat quality traits. There is an interest from the industry to implement genomic selection in this population to increase the rates of genetic gain...
January 26, 2017: BMC Genetics
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