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Genetics cross validation

Marion I Boldingh, Angelina H Maniaol, Cathrine Brunborg, Harald Weedon-Fekjær, Jan J G M Verschuuren, Chantal M E Tallaksen
OBJECTIVE: To study the risk of clinical onset of myasthenia gravis (MG) in pregnancy and during the first 6 months postpartum because an association between pregnancy or the postpartum period and the onset of autoimmune MG is widely assumed but not proven. METHODS: The design was a cross-sectional population-based cohort study of 2 MG cohorts (Norway and the Netherlands) with 1,038 healthy controls from Norway. Data were obtained on 246 women with MG (age at onset 15-45 years)...
October 21, 2016: Neurology
Jan Scott, Pierre Alexis Geoffroy, Sarah Sportiche, Clara Brichant-Petit-Jean, Sebastien Gard, Jean-Pierre Kahn, Jean-Michel Azorin, Chantal Henry, Bruno Etain, Frank Bellivier
BACKGROUND: It is increasingly recognised that reliable and valid assessments of lithium response are needed in order to target more efficiently the use of this medication in bipolar disorders (BD) and to identify genotypes, endophenotypes and biomarkers of response. METHODS: In a large, multi-centre, clinically representative sample of 300 cases of BD, we assess external clinical validators of lithium response phenotypes as defined using three different recommended approaches to scoring the Alda lithium response scale...
October 11, 2016: Journal of Affective Disorders
Youxin Wang, Siqi Ge, Yuxiang Yan, Anxin Wang, Zhongyao Zhao, Xinwei Yu, Jing Qiu, Mohamed Ali Alzain, Hao Wang, Honghong Fang, Qing Gao, Manshu Song, Jie Zhang, Yong Zhou, Wei Wang
BACKGROUND: Suboptimal health status (SHS) is a physical state between health and disease, characterized by the perception of health complaints, general weakness, chronic fatigue and low energy levels. SHS is proposed by the ancient concept of traditional Chinese medicine (TCM) from the perspective of preservative, predictive and personalized (precision) medicine. We previously created the suboptimal health status questionnaire 25 (SHSQ-25), a novel instrument to measure SHS, validated in various populations...
October 13, 2016: Journal of Translational Medicine
Toby Fountain, Mark Ravinet, Richard Naylor, Klaus Reinhardt, Roger K Butlin
The rapid evolution of insecticide resistance remains one of the biggest challenges in the control of medically and economically important pests. Insects have evolved a diverse range of mechanisms to reduce the efficacy of the commonly used classes of insecticides and finding the genetic basis of resistance is a major aid to management. In a previously unstudied population, we performed an F2 resistance mapping cross for the common bed bug, Cimex lectularius, for which insecticide resistance is increasingly widespread...
October 12, 2016: G3: Genes—Genomes—Genetics
Trevor Humby, Ellen S Cross, Lauren Messer, Silvia Guerrero, William Davies
Postpartum psychosis (PP) is a severe psychiatric disorder affecting a small proportion of new mothers shortly after childbirth. The molecular pathophysiology underlying the disorder is currently poorly understood, and there are no amenable animal models for the condition; maternal deficiency for the enzyme steroid sulfatase has been proposed as a potential risk mechanism. Here we show that inhibition of steroid sulfatase with 667-COUMATE (10mg/kg p.o.) in new mouse mothers results in behavioural abnormalities that can be partially alleviated by the administration of the clinically-efficacious antipsychotic ziprasidone (0...
September 28, 2016: Psychoneuroendocrinology
L Maes, T Carolus, V De Preter, S Ignoul, R Cartuyvels, L Braeken, P-J D'Huys, V Saegeman, B Kabamba, M Raymaekers
This study reports the evaluation of the technical and clinical validation of the O-DiaBorburg kit (DIA), Borrelia burgdorferi PCR kit, ISEX (GENE), and Borrelia burgdorferi sensu lato Real-TM (SAC) for the diagnosis of neuroborreliosis in cerebrospinal fluid based on both Borrelia DNA and CSF samples from patients with clinical suspicion of neuroborreliosis. This validation study was done by analysing the kits on the Rotorgene Q (RGQ), CFX96, and LightCycler480 (LC480). For all kits, the linear range was larger on RGQ than on CFX96 and LC480...
October 6, 2016: European Journal of Clinical Microbiology & Infectious Diseases
Suzanne M McDermott, Jie Luo, Jason Carnes, Jeff A Ranish, Kenneth Stuart
Uridine insertion and deletion RNA editing generates functional mitochondrial mRNAs in Trypanosoma brucei Editing is catalyzed by three distinct ∼20S editosomes that have a common set of 12 proteins, but are typified by mutually exclusive RNase III endonucleases with distinct cleavage specificities and unique partner proteins. Previous studies identified a network of protein-protein interactions among a subset of common editosome proteins, but interactions among the endonucleases and their partner proteins, and their interactions with common subunits were not identified...
October 5, 2016: Proceedings of the National Academy of Sciences of the United States of America
Rasmus Hare Jensen
Antifungal drug resistance is a multifaceted clinical challenge, and when present, a primary cause of treatment failure in patients with severe fungal infections. Changing epidemiology, increasing resistance rates and a narrow antifungal armamentarium may further underline the required attention on resistance particularly within the most prevalent invasive fungal infections caused by Candida yeasts and Aspergillus moulds. In Denmark, the resistance epidemiology remains to be fully elucidated. This thesis sought to address this demand as well as provide insight into the landscape of underlying molecular resistance mechanisms...
October 2016: Danish Medical Journal
Teresa B De Leon, Steven Linscombe, Prasanta K Subudhi
BACKGROUND: Salinity is one of the many abiotic stresses limiting rice production worldwide. Several studies were conducted to identify quantitative trait loci (QTLs) for traits associated to salinity tolerance. However, due to large confidence interval for the position of QTLs, utility of reported QTLs and the associated markers has been limited in rice breeding programs. The main objective of this study is to construct a high-density rice genetic map for identification QTLs and candidate genes for salinity tolerance at seedling stage...
December 2016: Rice
Xiaoqing Yu, Xianran Li, Tingting Guo, Chengsong Zhu, Yuye Wu, Sharon E Mitchell, Kraig L Roozeboom, Donghai Wang, Ming Li Wang, Gary A Pederson, Tesfaye T Tesso, Patrick S Schnable, Rex Bernardo, Jianming Yu
The 7.4 million plant accessions in gene banks are largely underutilized due to various resource constraints, but current genomic and analytic technologies are enabling us to mine this natural heritage. Here we report a proof-of-concept study to integrate genomic prediction into a broad germplasm evaluation process. First, a set of 962 biomass sorghum accessions were chosen as a reference set by germplasm curators. With high throughput genotyping-by-sequencing (GBS), we genetically characterized this reference set with 340,496 single nucleotide polymorphisms (SNPs)...
October 3, 2016: Nature Plants
Fan Zhang, Chunyan Ren, Hengqiang Zhao, Lei Yang, Fei Su, Ming-Ming Zhou, Junwei Han, Eric A Sobie, Martin J Walsh
Triple negative breast cancers (TNBCs) are highly heterogeneous and aggressive without targeted treatment. Here, we aim to systematically dissect TNBCs from a prognosis point of view by building a subnetwork atlas for TNBC prognosis through integrating multi-dimensional cancer genomics data from The Cancer Genome Atlas (TCGA) project and the interactome data from three different interaction networks. The subnetworks are represented as the protein-protein interaction modules perturbed by multiple genetic and epigenetic interacting mechanisms contributing to patient survival...
September 27, 2016: Oncotarget
Zheng Chen, Yuncheng Deng, Renchao Zhou, Shaoyun He
PREMISE OF THE STUDY: To examine patterns of genetic diversity and test possible hybridization events, microsatellite markers were identified and characterized in Hoya ledongensis (Apocynaceae), and cross-amplification was tested in a congener, H. jianfenglingensis. METHODS AND RESULTS: Based on the transcriptome data of H. ledongensis, 46 microsatellite primer pairs were randomly selected for initial validation. From these, 28 primer pairs were successfully amplified, 12 of which were polymorphic in 36 individuals across three populations of H...
September 2016: Applications in Plant Sciences
Georgia Kapatai, Carmen L Sheppard, Ali Al-Shahib, David J Litt, Anthony P Underwood, Timothy G Harrison, Norman K Fry
Streptococcus pneumoniae typically express one of 92 serologically distinct capsule polysaccharide (cps) types (serotypes). Some of these serotypes are closely related to each other; using the commercially available typing antisera, these are assigned to common serogroups containing types that show cross-reactivity. In this serotyping scheme, factor antisera are used to allocate serotypes within a serogroup, based on patterns of reactions. This serotyping method is technically demanding, requires considerable experience and the reading of the results can be subjective...
2016: PeerJ
William D Gilliland, Dennis P May, Eileen M Colwell, James A Kennison
Drosophila stocks bearing compound chromosomes, single molecules of DNA that carry the genomic complement of two chromosomes, are useful tools for studying meiosis and mitosis. However, these stocks cannot easily be crossed to stocks with regular chromosomes, due to the lethality of the resulting whole-chromosome aneuploidy. This prevents the examination of interesting genetic variants in a compound chromosome background. Methods to circumvent this difficulty have included the use of triploid females or nondisjunction (caused by either cold-induced microtubule depolymerization or meiotic mutants...
September 26, 2016: G3: Genes—Genomes—Genetics
S Mookprom, W Boonkum, S Kunhareang, S Siripanya, M Duangjinda
The objective of this research is to investigate appropriate random regression models with various covariance functions, for the genetic evaluation of test-day egg production. Data included 7,884 monthly egg production records from 657 Thai native chickens (Pradu Hang Dam) that were obtained during the first to sixth generation and were born during 2007 to 2014 at the Research and Development Network Center for Animal Breeding (Native Chickens), Khon Kaen University. Average annual and monthly egg productions were 117 ± 41 and 10...
September 24, 2016: Poultry Science
Noemie Prat, Camille Guilbert, Ursa Prah, Elisabeth Wachter, Barbara Steiner, Thierry Langin, Olivier Robert, Hermann Buerstmayr
The QTL Fhb1 was successfully introgressed and validated in three durum wheat populations. The novel germplasm and the QTL detected will support improvement of Fusarium resistance in durum wheat. Durum wheat (Triticum durum Desf.) is particularly susceptible to Fusarium head blight (FHB) and breeding for resistance is hampered by limited genetic variation within this species. To date, resistant sources are mainly available in a few wild relative tetraploid wheat accessions. In this study, the effect of the well-known hexaploid wheat (Triticum aestivum L...
September 23, 2016: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
Likai Chen, Weiwei Gao, Siping Chen, Liping Wang, Jiyong Zou, Yongzhu Liu, Hui Wang, Zhiqiang Chen, Tao Guo
BACKGROUND: Grain appearance quality is a main determinant of market value in rice and one of the highly important traits requiring improvement in breeding programs. The genetic basis of grain shape and endosperm chalkiness have been given significant attention because of their importance in affecting grain quality. Meanwhile, the introduction of NGS (Next Generation Sequencing) has a significant part to play in the area of genomics, and offers the possibility for high-resolution genetic map construction, population genetics analysis and systematic expression profile study...
December 2016: Rice
Y Li, R Hawken, R Sapp, A George, S A Lehnert, J M Henshall, A Reverter
Genome-wide association mapping and genomic predictions of phenotype of individuals in livestock are predominately based on the detection and estimation of additive genetic effects. Non-additive genetic effects are largely ignored. Studies in animals, plants, and humans to assess the impact of non-additive genetic effects in genetic analyses have led to differing conclusions. In this paper, we examined the consequences of including non-additive genetic effects in genome-wide association mapping and genomic prediction of total genetic values in a commercial population of 5,658 broiler chickens genotyped for 45,176 single nucleotide polymorphism (SNP) markers...
September 19, 2016: Poultry Science
Pamela J Kaisaki, Georg W Otto, Karène Argoud, Stephan C Collins, Robert H Wallis, Steven P Wilder, Anthony C Y Yau, Christophe Hue, Sophie Calderari, Marie-Thérèse Bihoreau, Jean-Baptiste Cazier, Richard Mott, Dominique Gauguier
To test the impact of genetic heterogeneity on cis- and trans-mediated mechanisms of gene expression regulation, we profiled the transcriptome of adipose tissue in 20 inbred congenic strains derived from diabetic Goto-Kakizaki (GK) rats and Brown-Norway (BN) controls, which contain well-defined blocks (1Mb-183Mb) of genetic polymorphisms, and in 123 genetically heterogeneous rats of an (GKxBN)F2 offspring. Within each congenic we identified 73 to 1,351 differentially expressed genes (DEG), only 7.7% of which mapped within the congenic blocks, and which may be regulated in cis The remainder localised outside the blocks, and therefore must be regulated in trans Most trans-regulated genes exhibited approximately two-fold expression changes, consistent with mono-allelic expression...
September 19, 2016: G3: Genes—Genomes—Genetics
Maolong Xi, Jun Sun, Li Liu, Fangyun Fan, Xiaojun Wu
This paper focuses on the feature gene selection for cancer classification, which employs an optimization algorithm to select a subset of the genes. We propose a binary quantum-behaved particle swarm optimization (BQPSO) for cancer feature gene selection, coupling support vector machine (SVM) for cancer classification. First, the proposed BQPSO algorithm is described, which is a discretized version of original QPSO for binary 0-1 optimization problems. Then, we present the principle and procedure for cancer feature gene selection and cancer classification based on BQPSO and SVM with leave-one-out cross validation (LOOCV)...
2016: Computational and Mathematical Methods in Medicine
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