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genetic differentiation

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https://www.readbyqxmd.com/read/28335009/open-chromatin-profiling-of-human-postmortem-brain-infers-functional-roles-for-non-coding-schizophrenia-loci
#1
John F Fullard, Claudia Giambartolomei, Mads E Hauberg, Ke Xu, Georgios Voloudakis, Zhiping Shao, Christopher Bare, Joel T Dudley, Manuel Mattheisen, Nikolaos K Robakis, Vahram Haroutunian, Panos Roussos
Open chromatin provides access to DNA binding proteins for the correct spatiotemporal regulation of gene expression. Mapping chromatin accessibility has been widely used to identify the location of cis regulatory elements (CREs) including promoters and enhancers. CREs show tissue- and cell-type specificity and disease-associated variants are often enriched for CREs in the tissues and cells that pertain to a given disease. To better understand the role of CREs in neuropsychiatric disorders we applied the Assay for Transposase Accessible Chromatin followed by sequencing (ATAC-seq) to neuronal and non-neuronal nuclei isolated from frozen postmortem human brain by fluorescence-activated nuclear sorting (FANS)...
March 14, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28334933/disrupted-in-schizophrenia-1is-essential-for-normal-hypothalamic-pituitary-interrenal-hpi-axis-function
#2
Helen Eachus, Charlotte Bright, Vincent T Cunliffe, Marysia Placzek, Jonathan D Wood, Penelope J Watt
Psychiatric disorders arise due to an interplay of genetic and environmental factors, including stress. Studies in rodents have shown that mutants for Disrupted-In-Schizophrenia-1 (DISC1), a well-accepted genetic risk factor for mental illness, display abnormal behaviours in response to stress, but the mechanisms through which DISC1 affects stress responses remain poorly understood. Using two lines of zebrafish homozygous mutant for disc1, we investigated behaviour and functioning of the hypothalamic-pituitary-interrenal (HPI) axis, the fish equivalent of the hypothalamic-pituitary-adrenal (HPA) axis...
March 1, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28334820/high-resolution-time-course-mapping-of-early-transcriptomic-molecular-and-cellular-phenotypes-in-huntington-s-disease-cag-knock-in-mice-across-multiple-genetic-backgrounds
#3
Seth A Ament, Jocelynn R Pearl, Andrea Grindeland, Jason St Claire, John C Earls, Marina Kovalenko, Tammy Gillis, Jayalakshmi Mysore, James F Gusella, Jong-Min Lee, Seung Kwak, David Howland, Min Young Lee, David Baxter, Kelsey Scherler, Kai Wang, Donald Geman, Jeffrey B Carroll, Marcy E MacDonald, George Carlson, Vanessa C Wheeler, Nathan D Price, Leroy E Hood
Huntington's disease is a dominantly inherited neurodegenerative disease caused by the expansion of a CAG repeat in the HTT gene. In addition to the length of the CAG expansion, factors such as genetic background have been shown to contribute to the age at onset of neurological symptoms. A central challenge in understanding the disease progression that leads from the HD mutation to massive cell death in the striatum is the ability to characterize the subtle and early functional consequences of the CAG expansion longitudinally...
February 27, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28334803/statistical-analysis-of-genetic-interactions-in-tn-seq-data
#4
Michael A DeJesus, Subhalaxmi Nambi, Clare M Smith, Richard E Baker, Christopher M Sassetti, Thomas R Ioerger
Tn-Seq is an experimental method for probing the functions of genes through construction of complex random transposon insertion libraries and quantification of each mutant's abundance using next-generation sequencing. An important emerging application of Tn-Seq is for identifying genetic interactions, which involves comparing Tn mutant libraries generated in different genetic backgrounds (e.g. wild-type strain versus knockout strain). Several analytical methods have been proposed for analyzing Tn-Seq data to identify genetic interactions, including estimating relative fitness ratios and fitting a generalized linear model...
February 22, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334792/gwas-identifies-population-specific-new-regulatory-variants-in-fut6-associated-with-plasma-b12-concentrations-in-indians
#5
Suraj S Nongmaithem, Charudatta V Joglekar, Ghattu V Krishnaveni, Sirazul A Sahariah, Meraj Ahmad, Swetha Ramachandran, Meera Gandhi, Harsha Chopra, Anand Pandit, Ramesh D Potdar, Caroline Hd Fall, Chittaranjan S Yajnik, Giriraj R Chandak
Vitamin B12 is an important cofactor in one-carbon metabolism whose dysregulation is associated with various clinical conditions. Indians have a high prevalence of B12 deficiency but little is known about the genetic determinants of circulating B12 concentrations in Indians. We performed a genome-wide association study in 1001 healthy participants in the Pune Maternal Nutrition Study (PMNS), replication studies in 3418 individuals from other Indian cohorts and by meta-analysis identified new variants, rs3760775 (p = 1...
February 27, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28334784/testing-the-ret-and-sema3d-genetic-interaction-in-mouse-enteric-nervous-system-development
#6
Ashish Kapoor, Dallas R Auer, Dongwon Lee, Sumantra Chatterjee, Aravinda Chakravarti
For most multigenic disorders, clinical manifestation (penetrance) and presentation (expressivity) are likely to be an outcome of genetic interaction between multiple susceptibility genes. Here, using gene knockouts in mice we evaluated genetic interaction between loss of Ret and loss of Sema3d, two Hirschsprung disease susceptibility genes. We intercrossed Ret and Sema3d double null heterozygotes to generate mice with the nine possible genotypes and assessed survival by counting various genotypes, myenteric plexus presence by acetylcholinesterase staining and embryonic day 12...
March 7, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28334284/genomic-diversity-guides-conservation-strategies-among-rare-terrestrial-orchid-species-when-taxonomy-remains-uncertain
#7
Collin W Ahrens, Megan A Supple, Nicola C Aitken, David J Cantrill, Justin O Borevitz, Elizabeth A James
Background and Aims: Species are often used as the unit for conservation, but may not be suitable for species complexes where taxa are difficult to distinguish. Under such circumstances, it may be more appropriate to consider species groups or populations as evolutionarily significant units (ESUs). A population genomic approach was employed to investigate the diversity within and among closely related species to create a more robust, lineage-specific conservation strategy for a nationally endangered terrestrial orchid and its relatives from south-eastern Australia...
March 15, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28334280/origin-and-genetic-differentiation-of-pink-flowered-sorbus-hybrids-in-the-western-carpathians
#8
Veronika Uhrinová, Judita Zozomová-Lihová, Dana Bernátová, Juraj Paule, Ladislav Paule, Dušan Gömöry
Background and Aims: Diversity of the genus Sorbus has been affected by interspecific hybridizations. Pink-flowered hybrid species have been insufficiently studied so far. They comprise bigenomic hybrid species derived from crosses S. aria s.l. × S. chamaemespilus and trigenomic ones, where S. aucuparia was involved as well. The main objective of the present study was to reconstruct their hybrid origins as well as to assess genetic distinction among several morphologically recognized hybrid species...
March 13, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28334234/breast-cancer-risk-associated-variants-at-6q25-1-influence-risk-of-hepatocellular-carcinoma-in-a-chinese-population
#9
Jiaoyuan Li, Ying Wang, Ying Zhu, Yajie Gong, Yang Yang, Jianbo Tian, Yi Zhang, Danyi Zou, Xiating Peng, Juntao Ke, Jing Gong, Rong Zhong, Jiang Chang
The gender disparity observed in the incidence of hepatocellular carcinoma (HCC) suggests an important role of estrogens in HCC pathogenesis. In this study, we conducted a case-control study to investigate whether breast cancer risk-associated single nucleotide polymorphisms (SNPs) located at estrogens loci identified by genome-wide association studies (GWASs) also predispose to HCC in a Chinese population. Three candidate SNPs at 6q25.1 were genotyped in 2,025 HCC cases and 2,032 healthy controls. Differential expression analyses and expression quantitative trait loci (eQTL) analyses were conducted to further explore the role of significant SNPs and genes they reside in...
March 3, 2017: Carcinogenesis
https://www.readbyqxmd.com/read/28334183/comparative-transcriptional-analysis-of-the-host-specialized-aphids-aphis-gossypii-hemiptera-aphididae
#10
Yuan-Chen Zhang, Hai-Xia Lei, Ning-Hui Miao, Xiang-Dong Liu
Host specialization is an ubiquitous character in aphid populations. Many polyphagous aphid populations usually consist of several subpopulations that have strong fidelity to a specific host or a subset of host range. Host specialization is an evolutional result of food habit of insects. However, genetic basis and molecular mechanism of host specialization are still unclear. In this study, we presented a comparative analysis on global gene expression profiles of three lineages of Aphis gossypii Glover: cotton-specialized (CO), cucurbit-specialized (CU), and CU reared on cowpea (CU-cowpea), using RNA-Seq method...
February 17, 2017: Journal of Economic Entomology
https://www.readbyqxmd.com/read/28334098/untangling-the-reticulate-history-of-species-complexes-and-horticultural-breeds-in-abelia-caprifoliaceae
#11
Sven Landrein, Sven Buerki, Hua-Feng Wang, James J Clarkson
Background and Aims: The genetic and morphological consequences of natural selection and selective breeding are explored in the genus Abelia . The genus consists of ornamental shrubs endemic to China, which have been bred to create attractive and diverse cultivars. Methods: DNA fingerprinting (AFLP) and DNA sequence data are used to investigate the genetic diversity among 46 accessions of Abelia (22 natural taxa and 24 horticultural breeds). In the cultivated varieties these data are used to explore taxon boundaries, hybridisation and backcrossing...
February 20, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28334085/environmental-niche-divergence-among-three-dune-shrub-sister-species-with-parapatric-distributions
#12
Sergio Chozas, Rosa M Chefaoui, Otília Correia, Raúl Bonal, Joaquín Hortal
Background and Aims: The geographical distributions of species are constrained by their ecological requirements. The aim of this work was to analyse the effects of environmental conditions, historical events and biogeographical constraints on the diversification of the three species of the western Mediterranean shrub genus Stauracanthus , which have a parapatric distribution in the Iberian Peninsula. Methods: Ecological niche factor analysis and generalized linear models were used to measure the response of all Stauracanthus species to the environmental gradients and map their potential distributions in the Iberian Peninsula...
February 20, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28334007/a-functional-variant-in-neph3-gene-confers-high-risk-of-renal-failure-in-primary-hematuric-glomerulopathies-evidence-for-predisposition-to-microalbuminuria-in-the-general-population
#13
Konstantinos Voskarides, Charalambos Stefanou, Myrtani Pieri, Panayiota Demosthenous, Kyriakos Felekkis, Maria Arsali, Yiannis Athanasiou, Dimitris Xydakis, Kostas Stylianou, Eugenios Daphnis, Giorgos Goulielmos, Petros Loizou, Judith Savige, Martin Höhne, Linus A Völker, Thomas Benzing, Patrick H Maxwell, Daniel P Gale, Mathias Gorski, Carsten Böger, Barbara Kollerits, Florian Kronenberg, Bernhard Paulweber, Michalis Zavros, Alkis Pierides, Constantinos Deltas
BACKGROUND: Recent data emphasize that thin basement membrane nephropathy (TBMN) should not be viewed as a form of benign familial hematuria since chronic renal failure (CRF) and even end-stage renal disease (ESRD), is a possible development for a subset of patients on long-term follow-up, through the onset of focal and segmental glomerulosclerosis (FSGS). We hypothesize that genetic modifiers may explain this variability of symptoms. METHODS: We looked in silico for potentially deleterious functional SNPs, using very strict criteria, in all the genes significantly expressed in the slit diaphragm (SD)...
2017: PloS One
https://www.readbyqxmd.com/read/28333993/integrated-transcriptomic-and-proteomic-analysis-of-the-molecular-cargo-of-extracellular-vesicles-derived-from-porcine-adipose-tissue-derived-mesenchymal-stem-cells
#14
Alfonso Eirin, Xiang-Yang Zhu, Amrutesh S Puranik, John R Woollard, Hui Tang, Surendra Dasari, Amir Lerman, Andre J van Wijnen, Lilach O Lerman
BACKGROUND: Mesenchymal stromal/stem cell (MSC) transplantation is a promising therapy for tissue regeneration. Extracellular vesicles (EVs) released by MSCs act as their paracrine effectors by delivering proteins and genetic material to recipient cells. To assess how their cargo mediates biological processes that drive their therapeutic effects, we integrated miRNA, mRNA, and protein expression data of EVs from porcine adipose tissue-derived MSCs. METHODS: Simultaneous expression profiles of miRNAs, mRNAs, and proteins were obtained by high-throughput sequencing and LC-MS/MS proteomic analysis in porcine MSCs and their daughter EVs (n = 3 each)...
2017: PloS One
https://www.readbyqxmd.com/read/28333931/differential-gene-expression-in-patients-with-subsyndromal-symptomatic-depression-and-major-depressive-disorder
#15
Chengqing Yang, Guoqin Hu, Zezhi Li, Qingzhong Wang, Xuemei Wang, Chengmei Yuan, Zuowei Wang, Wu Hong, Weihong Lu, Lan Cao, Jun Chen, Yong Wang, Shunying Yu, Yimin Zhou, Zhenghui Yi, Yiru Fang
BACKGROUND: Subsyndromal symptomatic depression (SSD) is a subtype of subthreshold depressive and can lead to significant psychosocial functional impairment. Although the pathogenesis of major depressive disorder (MDD) and SSD still remains poorly understood, a set of studies have found that many same genetic factors play important roles in the etiology of these two disorders. Nowadays, the differential gene expression between MDD and SSD is still unknown. In our previous study, we compared the expression profile and made the classification with the leukocytes by using whole-genome cRNA microarrays among drug-free first-episode subjects with SSD, MDD and matched healthy controls (8 subjects in each group), and finally determined 48 gene expression signatures...
2017: PloS One
https://www.readbyqxmd.com/read/28333377/circadian-rhythms-in-adipose-tissue-physiology
#16
Jana-Thabea Kiehn, Anthony H Tsang, Isabel Heyde, Brinja Leinweber, Isa Kolbe, Alexei Leliavski, Anthony H Tsang
The different types of adipose tissues fulfill a wide range of biological functions-from energy storage to hormone secretion and thermogenesis-many of which show pronounced variations over the course of the day. Such 24-h rhythms in physiology and behavior are coordinated by endogenous circadian clocks found in all tissues and cells, including adipocytes. At the molecular level, these clocks are based on interlocked transcriptional-translational feedback loops comprised of a set of clock genes/proteins. Tissue-specific clock-controlled transcriptional programs translate time-of-day information into physiologically relevant signals...
March 16, 2017: Comprehensive Physiology
https://www.readbyqxmd.com/read/28333213/x-chromosome-wide-association-study-identifies-a-susceptibility-locus-for-inflammatory-bowel-disease-in-koreans
#17
Ho-Su Lee, Hyunjung Oh, Jiwon Baek, Seulgi Jung, Myunghee Hong, Kyung Mo Kim, Hyoung Doo Shin, Kyung-Jo Kim, Sang Hyoung Park, Byong Duk Ye, Buhm Han, Suk-Kyun Yang, Kyuyoung Song
Background and Aims: Genome-wide association studies of inflammatory bowel disease identified >200 susceptibility loci only in autosomes. This study aimed to identify inflammatory bowel disease susceptibility loci on the X chromosome. Methods: We performed an X chromosome-wide association study in Korean patients with inflammatory bowel disease. We analyzed X chromosome data from our recent genome-wide association studies, including 1,505 cases (922 Crohn's disease and 583 ulcerative colitis) and 4,041 controls during the discovery phase, followed by replication in additional 1,989 cases (993 Crohn's disease, 996 ulcerative colitis) and 3,491 controls...
February 22, 2017: Journal of Crohn's & Colitis
https://www.readbyqxmd.com/read/28333195/genome-wide-genetic-analyses-highlight-mitogen-activated-protein-kinase-mapk-signaling-in-the-pathogenesis-of-endometriosis
#18
Outi Uimari, Nilufer Rahmioglu, Dale R Nyholt, Katy Vincent, Stacey A Missmer, Christian Becker, Andrew P Morris, Grant W Montgomery, Krina T Zondervan
STUDY QUESTION: Do genome-wide association study (GWAS) data for endometriosis provide insight into novel biological pathways associated with its pathogenesis? SUMMARY ANSWER: GWAS analysis uncovered multiple pathways that are statistically enriched for genetic association signals, analysis of Stage A disease highlighted a novel variant in MAP3K4, while top pathways significantly associated with all endometriosis and Stage A disease included several mitogen-activated protein kinase (MAPK)-related pathways...
February 9, 2017: Human Reproduction
https://www.readbyqxmd.com/read/28332369/gender-specific-associations-between-chgb-genetic-variants-and-schizophrenia-in-a-korean-population
#19
Joong Gon Shin, Jeong Hyun Kim, Chul Soo Park, Bong Jo Kim, Jae Won Kim, Ihn Geun Choi, Jaeuk Hwang, Hyoung Doo Shin, Sung Il Woo
PURPOSE: Schizophrenia is a devastating mental disorder and is known to be affected by genetic factors. The chromogranin B (CHGB), a member of the chromogranin gene family, has been proposed as a candidate gene associated with the risk of schizophrenia. The secretory pathway for peptide hormones and neuropeptides in the brain is regulated by chromogranin proteins. The aim of this study was to investigate the potential associations between genetic variants of CHGB and schizophrenia susceptibility...
May 2017: Yonsei Medical Journal
https://www.readbyqxmd.com/read/28331934/microarray-analysis-of-differential-gene-expression-profile-between-human-fetal-and-adult-heart
#20
Zhimin Geng, Jue Wang, Lulu Pan, Ming Li, Jitai Zhang, Xueli Cai, Maoping Chu
Although many changes have been discovered during heart maturation, the genetic mechanisms involved in the changes between immature and mature myocardium have only been partially elucidated. Here, gene expression profile changed between the human fetal and adult heart was characterized. A human microarray was applied to define the gene expression signatures of the fetal (13-17 weeks of gestation, n = 4) and adult hearts (30-40 years old, n = 4). Gene ontology analyses, pathway analyses, gene set enrichment analyses, and signal transduction network were performed to predict the function of the differentially expressed genes...
March 22, 2017: Pediatric Cardiology
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