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https://www.readbyqxmd.com/read/28098149/characterising-private-and-shared-signatures-of-positive-selection-in-37-asian-populations
#1
Xuanyao Liu, Dongsheng Lu, Woei-Yuh Saw, Philip J Shaw, Pongsakorn Wangkumhang, Chumpol Ngamphiw, Suthat Fucharoen, Worachart Lert-Itthiporn, Kwanrutai Chin-Inmanu, Tran Nguyen Bich Chau, Katie Anders, Anuradhani Kasturiratne, H Janaka de Silva, Tomohiro Katsuya, Ryosuke Kimura, Toru Nabika, Takayoshi Ohkubo, Yasuharu Tabara, Fumihiko Takeuchi, Ken Yamamoto, Mitsuhiro Yokota, Dolikun Mamatyusupu, Wenjun Yang, Yeun-Jun Chung, Li Jin, Boon-Peng Hoh, Ananda R Wickremasinghe, RickTwee-Hee Ong, Chiea-Chuen Khor, Sarah J Dunstan, Cameron Simmons, Sissades Tongsima, Prapat Suriyaphol, Norihiro Kato, Shuhua Xu, Yik-Ying Teo
The Asian Diversity Project (ADP) assembled 37 cosmopolitan and ethnic minority populations in Asia that have been densely genotyped across over half a million markers to study patterns of genetic diversity and positive natural selection. We performed population structure analyses of the ADP populations and divided these populations into four major groups based on their genographic information. By applying a highly sensitive algorithm haploPS to locate genomic signatures of positive selection, 140 distinct genomic regions exhibiting evidence of positive selection in at least one population were identified...
January 18, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28097517/in-utero-exposure-of-hyperlipidemic-mice-to-diesel-exhaust-lack-of-effects-on-atherosclerosis-in-adult-offspring-fed-a-regular-chow-diet
#2
Jenna Harrigan, Divya Ravi, Jerry Ricks, Michael E Rosenfeld
Uterine stress is associated with an increased risk of later life metabolic diseases. In this study, we investigated the effect of diesel exhaust (DE) exposure in utero on adult susceptibility to atherosclerosis in genetically hyperlipidemic mice. Pregnant apolipoprotein E-deficient mice received either DE exposure (~250-300 μg/m(3) PM2.5 for 6 h/day, 5 days/week) or filtered air (FA) throughout gestation. Treatment effects on litter size and gender distribution were recorded. Plasma cholesterol and triglycerides were measured at 8, 12 and 16 weeks of age...
January 17, 2017: Cardiovascular Toxicology
https://www.readbyqxmd.com/read/28097398/mapping-quantitative-trait-loci-for-root-development-under-hypoxia-conditions-in-soybean-glycine-max-l-merr
#3
Loc Van Nguyen, Ryoji Takahashi, Stephen Mwangi Githiri, Tito O Rodriguez, Nobuko Tsutsumi, Sayuri Kajihara, Takasi Sayama, Masao Ishimoto, Kyuya Harada, Keisuke Suematsu, Tomomi Abiko, Toshihiro Mochizuki
Greatest potential, QTLs for hypoxia and waterlogging tolerance in soybean roots were detected using a new phenotypic evaluation method. Waterlogging is a major environmental stress limiting soybean yield in wet parts of the world. Root development is an important indicator of hypoxia tolerance in soybean. However, little is known about the genetic control of root development under hypoxia. This study was conducted to identify quantitative trait loci (QTLs) responsible for root development under hypoxia. Recombinant inbred lines (RILs) developed from a cross between a hypoxia-sensitive cultivar, Tachinagaha, and a tolerant landrace, Iyodaizu, were used...
January 17, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28097204/genomics-implicates-adaptive-and-innate-immunity-in-alzheimer-s-and-parkinson-s-diseases
#4
Sarah A Gagliano, Jennie G Pouget, John Hardy, Jo Knight, Michael R Barnes, Mina Ryten, Michael E Weale
OBJECTIVES: We assessed the current genetic evidence for the involvement of various cell types and tissue types in the etiology of neurodegenerative diseases, especially in relation to the neuroinflammatory hypothesis of neurodegenerative diseases. METHODS: We obtained large-scale genome-wide association study (GWAS) summary statistics from Parkinson's disease (PD), Alzheimer's disease (AD), and amyotrophic lateral sclerosis (ALS). We used multiple sclerosis (MS), an autoimmune disease of the central nervous system, as a positive control...
December 2016: Annals of Clinical and Translational Neurology
https://www.readbyqxmd.com/read/28097170/microsatellite-ssr-amplification-by-pcr-usually-led-to-polymorphic-bands-evidence-which-shows-replication-slippage-occurs-in-extend-or-nascent-dna-strands
#5
Abasalt Hosseinzadeh-Colagar, Mohammad Javad Haghighatnia, Zahra Amiri, Maryam Mohadjerani, Majid Tafrihi
Microsatellites or simple sequence repeats (SSRs) are very effective molecular markers in population genetics, genome mapping, taxonomic study and other large-scale studies. Variation in number of tandem repeats within microsatellite refers to simple sequence length polymorphism (SSLP); but there are a few studies that are showed SSRs replication slippage may be occurred during in vitro amplification which are produced 'stutter products' differing in length from the main products. The purpose of this study is introducing a reliable method to realize SSRs replication slippage...
September 2016: Molecular Biology Research Communications
https://www.readbyqxmd.com/read/28096648/identification-of-genetic-and-epigenetic-variants-associated-with-breast-cancer-prognosis-by-integrative-bioinformatics-analysis
#6
Arunima Shilpi, Yingtao Bi, Segun Jung, Samir K Patra, Ramana V Davuluri
INTRODUCTION: Breast cancer being a multifaceted disease constitutes a wide spectrum of histological and molecular variability in tumors. However, the task for the identification of these variances is complicated by the interplay between inherited genetic and epigenetic aberrations. Therefore, this study provides an extrapolate outlook to the sinister partnership between DNA methylation and single-nucleotide polymorphisms (SNPs) in relevance to the identification of prognostic markers in breast cancer...
2017: Cancer Informatics
https://www.readbyqxmd.com/read/28096076/a-landscape-of-synthetic-viable-interactions-in-cancer
#7
Yunyan Gu, Ruiping Wang, Yue Han, Wenbin Zhou, Zhangxiang Zhao, Tingting Chen, Yuanyuan Zhang, Fuduan Peng, Haihai Liang, Lishuang Qi, Wenyuan Zhao, Da Yang, Zheng Guo
Synthetic viability, which is defined as the combination of gene alterations that can rescue the lethal effects of a single gene alteration, may represent a mechanism by which cancer cells resist targeted drugs. Approaches to detect synthetic viable (SV) interactions in cancer genome to investigate drug resistance are still scarce. Here, we present a computational method to detect synthetic viability-induced drug resistance (SVDR) by integrating the multidimensional data sets, including copy number alteration, whole-exome mutation, expression profile and clinical data...
January 17, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28095895/genome-wide-snp-analysis-using-2b-rad-sequencing-identifies-the-candidate-genes-putatively-associated-with-resistance-to-ivermectin-in-haemonchus-contortus
#8
Xiaoping Luo, Xiaona Shi, Chunxiu Yuan, Min Ai, Cheng Ge, Min Hu, Xingang Feng, Xiaoye Yang
BACKGROUND: The excessive and uncontrolled use of anthelmintics, e.g. ivermectin (IVM) for the treatment of livestock parasites has led to widespread resistance in gastrointestinal nematodes, such as Haemonchus contortus. There is an urgent need for better management of drug-use in nematode control and development of novel anthelmintics. Discovery and identification of anthelmintic resistance-associate molecules/markers can provide a basis for rational anthelmintics-use and development of novel drugs...
January 17, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28095743/adult-murine-pancreatic-progenitors-require-egf-and-nicotinamide-for-self-renewal-and-differentiation-in-a-serum-and-conditioned-medium-free-culture
#9
Lena Wedeken, Angela Luo, Jacob R Tremblay, Jeffrey Rawson, Liang Jin, Dan Gao, Janine Quijano, Hsun Teresa Ku
Adult pancreatic stem and progenitor cells may serve as an alternative source of insulin-secreting endocrine cells in cell replacement therapy for type 1 diabetes, but much remained unknown about these cells. We previously identified adult murine pancreatic progenitor-like cells that displayed in vitro self-renewal and tri-lineage differentiation activities in a 3-dimensional colony/organoid assay containing 1% methylcellulose and 5% Matrigel. However, the presence of other undefined culture components, such as serum and conditioned medium, has prevented a complete understanding of the signals required for progenitor cell growth...
January 17, 2017: Stem Cells and Development
https://www.readbyqxmd.com/read/28095669/complete-mitochondrial-genome-of-a-tongue-worm-armillifer-agkistrodontis
#10
Jian Li, Fu-Nan He, Hong-Xiang Zheng, Rui-Xiang Zhang, Yi-Jing Ren, Wei Hu
Armillifer agkistrodontis (Ichthyostraca: Pantastomida) is a parasitic pathogen, only reported in China, which can cause a zoonotic disease, pentastomiasis. A complete mitochondrial (mt) genome was 16,521 bp comprising 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and 1 non-coding region (NCR). A phylogenetic tree drawn with the concatenated amino acid sequences of the 6 conserved PCGs (atp6, cox1-3, and nad2) showed that A. agkistrodontis and Armillifer armillatus constituted a clade Pentastomida which was a sister group of the Branchiura...
December 2016: Korean Journal of Parasitology
https://www.readbyqxmd.com/read/28094982/bacterial-genome-editing-via-a-designed-toxin-antitoxin-cassette
#11
Jie Wu, Aihua Deng, Qinyun Sun, Hua Bai, Zhaopeng Sun, Xiuling Shang, Yun Zhang, Qian Liu, Yong Liang, Shuwen Liu, Yongsheng Che, Tingyi Wen
Manipulating the bacterial genomes in an efficient manner is essential to biological and biotechnological research. Despite usage of various modules for genomic editing with counter-selectable markers including the toxin genes, an easy-to-use and highly designable toxin-antitoxin (TA) cassette without causing any leakages is urgently needed for efficient genome editing of the Gram-positive bacteria. Here, we reprogramed the bacterial TA systems as a toxin counter-selectable cassette regulated by an antitoxin switch (TCCRAS) for genetic modifications in the extensively studied and utilized Gram-positive bacteria, B...
January 17, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28094814/meta-analysis-reveals-associations-between-genetic-variation-in-the-5-and-3-regions-of-neuregulin-1-and-schizophrenia
#12
M S Mostaid, S G Mancuso, C Liu, S Sundram, C Pantelis, I P Everall, C A Bousman
Genetic, post-mortem and neuroimaging studies repeatedly implicate neuregulin-1 (NRG1) as a critical component in the pathophysiology of schizophrenia. Although a number of risk haplotypes along with several genetic polymorphisms in the 5' and 3' regions of NRG1 have been linked with schizophrenia, results have been mixed. To reconcile these conflicting findings, we conducted a meta-analysis examining 22 polymorphisms and two haplotypes in NRG1 among 16 720 cases, 20 449 controls and 2157 family trios. We found significant associations for three polymorphisms (rs62510682, rs35753505 and 478B14-848) at the 5'-end and two (rs2954041 and rs10503929) near the 3'-end of NRG1...
January 17, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/28094539/genetic-diversity-and-population-structure-of-castor-ricinus-communis-l-germplasm-within-the-us-collection-assessed-with-est-ssr-markers
#13
M L Wang, M Dzievit, Z Chen, J B Morris, J E Norris, N A Barkley, B Tonnis, G A Pederson, J Yu
Castor is an important oilseed crop and although its oil is inedible, it has multiple industrial and pharmaceutical applications. The entire US castor germplasm collection was previously screened for oil content and fatty acid composition, but its genetic diversity and population structure has not been determined. Based on the screening results of oil content, fatty acid composition, and country origins, 574 accessions were selected and genotyped with 22 polymorphic EST-SSR markers. The results from cluster analysis, population structure, and principal component analysis were consistent, and partitioned accessions into four subpopulations...
October 14, 2016: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28094451/development-of-diversity-arrays-technology-markers-as-a-tool-for-rapid-genomic-assessment-in-nile-tilapia-oreochromis-niloticus
#14
C E Lind, A Kilian, J A H Benzie
The development of genomic markers is described for Nile tilapia, Oreochromis niloticus, using the Diversity Arrays Technology (DArT) genotype-by-sequencing platform. A total of 13 215 single nucleotide polymorphism (SNP) markers and 12 490 silicoDArT (dominant) markers were identified from broodstock of two selective breeding programs [Genetically Improved Farmed Tilapia (GIFT) strain from Malaysia and the Abbassa strain from Egypt]. Over 10 000 SNPs were polymorphic in either strain, and 2985 and 3087 showed strain-specific polymorphisms for the GIFT and Abbassa strains respectively...
January 17, 2017: Animal Genetics
https://www.readbyqxmd.com/read/28094105/sonographic-alteration-of-substantia-nigra-is-related-to-parkinsonism-predominant-course-of-x-linked-dystonia-parkinsonism
#15
Uwe Walter, Raymond Rosales, Alessandro Rocco, Ana Westenberger, Aloysius Domingo, Criscely L Go, Norbert Brüggemann, Christine Klein, Lillian V Lee, Dirk Dressler
INTRODUCTION: X-linked recessive dystonia-parkinsonism (XDP, DYT3) is highly prevalent in the Philippines and manifests with varying phenotype. We sought to evaluate the significance of transcranial brain sonography as a biomarker for parkinsonism-predominant phenotype. METHODS: 90 Filipino participants were enrolled into a cross-sectional study: 39 patients with XDP, 21 asymptomatic first-degree relatives of XDP patients, and 30 healthy control subjects. Echogenicity of the substantia nigra and the lenticular nuclei was digitally quantified...
January 10, 2017: Parkinsonism & related Disorders
https://www.readbyqxmd.com/read/28094097/diverse-genotypes-of-bradyrhizobium-nodulate-herbaceous-chamaecrista-moench-fabaceae-caesalpinioideae-species-in-brazil
#16
José Miguel Ferreira Dos Santos, Patricia Alves Casaes Alves, Verônica Cordeiro Silva, Mariana Ferreira Kruschewsky Rhem, Euan K James, Eduardo Gross
The genus Chamaecrista comprises more than 330 species which are mainly distributed across tropical America, especially in Brazil (256 spp.), the main center of radiation. In this study, nodulation of herbaceous Chamaecrista species that are commonly found growing in different vegetation types in the north eastern Brazilian state of Bahia was assessed together with the diversity of rhizobia isolated from their root nodules. Genetic characterization of the isolates was performed using molecular markers to examine the phylogeny of their "core" (16S rRNA, ITS, recA, glnII, dnaK and gyrB) and symbiosis-related (nifH, nodC) genomes...
January 10, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/28093362/hypoxia-inducible-factor-1%C3%AE-inhibition-modulates-airway-hyperresponsiveness-and-nitric-oxide-levels-in-a-balb-c-mouse-model-of-asthma
#17
Carola Dewitz, Elisa McEachern, Stephanie Shin, Kathryn Akong, Dale G Nagle, David H Broide, Praveen Akuthota, Laura E Crotty Alexander
: Hypoxia inducible factor (HIF)-1α is a master regulator of inflammation and is upregulated in alveolar macrophages and lung parenchyma in asthma. HIF-1α regulates select pathways in allergic inflammation, and thus may drive particular asthma phenotypes. This work examines the role of pharmacologic HIF-1α inhibition in allergic inflammatory airway disease (AIAD) pathogenesis in BALB/c mice, which develop an airway hyperresponsiveness (AHR) asthma phenotype. Systemic treatment with HIF-1α antagonist YC-1 suppressed the increase in HIF-1α expression seen in control AIAD mice...
January 13, 2017: Clinical Immunology: the Official Journal of the Clinical Immunology Society
https://www.readbyqxmd.com/read/28093353/vitamin-d-metabolites-in-captivity-should-we-measure-free-or-total-25-oh-d-to-assess-vitamin-d-status
#18
REVIEW
Daniel Bikle, Roger Bouillon, Ravi Thadhani, Inez Schoenmakers
There is general consensus that serum 25(OH)D is the best biochemical marker for nutritional vitamin D status. Whether free 25(OH)D would be a better marker than total 25(OH)D is so far unclear. Free 25(OH)D can either be calculated based on the measurement of the serum concentrations of total 25(OH)D, vitamin D-binding protein (DBP), albumin, and the affinity between 25(OH)D and its binding proteins in physiological situations. Free 25(OH)D can also be measured directly by equilibrium dialysis, ultrafitration or immunoassays...
January 13, 2017: Journal of Steroid Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28093278/similar-patterns-of-brain-activation-abnormalities-during-emotional-and-non-emotional-judgments-of-faces-in-a-schizophrenia-family-study
#19
Michael J Spilka, Vina M Goghari
Schizophrenia patients have impaired performance and abnormal brain activation during facial emotion recognition, which may represent a marker of genetic liability to schizophrenia. However, it remains unclear whether the impairment is specific to recognizing emotion from faces or is instead attributable to more generalized dysfunction. The current study aimed to distinguish between specific and generalized neural dysfunction underlying impaired facial emotion recognition in schizophrenia and examine associations with genetic liability...
January 13, 2017: Neuropsychologia
https://www.readbyqxmd.com/read/28093217/abnormal-cd161-immune-cells-and-ror%C3%AE-t-mediated-enhanced-il-17f-expression-in-genetic-hypertension
#20
Madhu V Singh, Michael Z Cicha, Santosh Kumar, David K Meyerholz, Kaikobad Irani, Mark W Chapleau, François M Abboud
BACKGROUND: Hypertension is considered an immunological disorder. However, the role of IL-17 family in genetic hypertension of the spontaneously hypertensive rat (SHR) has not been investigated. OBJECTIVE: We tested the hypothesis that enhanced Th17 programming and IL-17 expression in abundant CD161+ immune cells in SHR represent an abnormal proinflammatory adaptive immune response. Furthermore, we propose that this response is driven by the master regulator RORγt and a nicotinic proinflammatory innate immune response...
January 13, 2017: Journal of Allergy and Clinical Immunology
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