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Gene Mapping

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https://www.readbyqxmd.com/read/28227870/identifying-disease-network-perturbations-through-regression-on-gene-expression-and-pathway-topology-analysis
#1
Georgios N Dimitrakopoulos, Panos Balomenos, Aristidis G Vrahatis, Kyriakos Sgarbas, Anastasios Bezerianos, Georgios N Dimitrakopoulos, Panos Balomenos, Aristidis G Vrahatis, Kyriakos Sgarbas, Anastasios Bezerianos, Kyriakos Sgarbas, Panos Balomenos, Georgios N Dimitrakopoulos, Anastasios Bezerianos, Aristidis G Vrahatis
In Systems Biology, network-based approaches have been extensively used to effectively study complex diseases. An important challenge is the detection of network perturbations which disrupt regular biological functions as a result of a disease. In this regard, we introduce a network based pathway analysis method which isolates casual interactions with significant regulatory roles within diseased-perturbed pathways. Specifically, we use gene expression data with Random Forest regression models to assess the interactivity strengths of genes within disease-perturbed networks, using KEGG pathway maps as a source of prior-knowledge pertaining to pathway topology...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226767/place-field-detection-using-grid-based-clustering-in-a-large-scale-computational-model-of-the-rat-dentate-gyrus
#2
Gene J Yu, Dong Song, Theodore W Berger, Gene J Yu, Dong Song, Theodore W Berger, Dong Song, Gene J Yu, Theodore W Berger
Place cells are neurons in the hippocampus that are sensitive to location within an environment. Simulations of a large-scale, computational model of the rat dentate gyrus using grid cell input have been performed resulting in granule cells that express multiple place fields. The typical method of detecting place fields using a global threshold on this data is unreliable as the characteristics of the place fields from a single neuron can be highly variable. A grid-based implementation of DENCLUE has been developed to calculate local thresholds to identify each place field...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226236/new-strategies-and-tools-in-quantitative-genetics-how-to-go-from-the-phenotype-to-the-genotype
#3
C Bazakos, M Hanemian, C Trontin, J M Jiménez-Gómez, O Loudet
Quantitative genetics has a long history in plants: It has been used to study specific biological processes, identify the factors important for trait evolution, and breed new crop varieties. These classical approaches to quantitative trait locus mapping have naturally improved with technology. In this review, we show how quantitative genetics has evolved recently in plants and how new developments in phenotyping, population generation, sequencing, gene manipulation, and statistics are rejuvenating both the classical linkage mapping approaches (for example, through nested association mapping) as well as the more recently developed genome-wide association studies...
February 6, 2017: Annual Review of Plant Biology
https://www.readbyqxmd.com/read/28226195/global-transcriptional-response-of-human-liver-cells-to-ethanol-stress-of-different-strength-reveals-hormetic-behavior
#4
Wolfgang Schmidt-Heck, Eva C Wönne, Thomas Hiller, Uwe Menzel, Dirk Koczan, Georg Damm, Daniel Seehofer, Fanny Knöspel, Nora Freyer, Reinhard Guthke, Steven Dooley, Katrin Zeilinger
BACKGROUND: The liver is the major site for alcohol metabolism in the body and therefore, the primary target organ for ethanol-induced toxicity. In this study, we investigated the in vitro response of human liver cells to different ethanol concentrations in a perfused bioartificial liver device that mimics the complex architecture of the natural organ. METHODS: Primary human liver cells were cultured in the bioartificial liver device and treated for 24 hours with medium containing 150 mM (low), 300 mM (medium) or 600 mM (high) ethanol, while a control culture was kept untreated...
February 22, 2017: Alcoholism, Clinical and Experimental Research
https://www.readbyqxmd.com/read/28225770/a-distal-intergenic-region-controls-pancreatic-endocrine-differentiation-by-acting-as-a-transcriptional-enhancer-and-as-a-polycomb-response-element
#5
Joris van Arensbergen, Sebastien Dussaud, Corinne Pardanaud-Glavieux, Javier García-Hurtado, Claire Sauty, Aline Guerci, Jorge Ferrer, Philippe Ravassard
Lineage-selective expression of developmental genes is dependent on the interplay between activating and repressive mechanisms. Gene activation is dependent on cell-specific transcription factors that recognize transcriptional enhancer sequences. Gene repression often depends on the recruitment of Polycomb group (PcG) proteins, although the sequences that underlie the recruitment of PcG proteins, also known as Polycomb response elements (PREs), remain poorly understood in vertebrates. While distal PREs have been identified in mammals, a role for positive-acting enhancers in PcG-mediated repression has not been described...
2017: PloS One
https://www.readbyqxmd.com/read/28224915/characterization-of-small-rna-populations-in-non-transgenic-and-aflatoxin-reducing-transformed-peanut
#6
Imana L Power, Phat M Dang, Victor S Sobolev, Valerie A Orner, Joseph L Powell, Marshall C Lamb, Renee S Arias
Aflatoxin contamination is a major constraint in food production worldwide. In peanut (Arachis hypogaea L.), these toxic and carcinogenic aflatoxins are mainly produced by Aspergillus flavus Link and A. parasiticus Speare. The use of RNA interference (RNAi) is a promising method to reduce or prevent the accumulation of aflatoxin in peanut seed. In this study, we performed high-throughput sequencing of small RNA populations in a control line and in two transformed peanut lines that expressed an inverted repeat targeting five genes involved in the aflatoxin-biosynthesis pathway and that showed up to 100% less aflatoxin B1 than the controls...
April 2017: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/28224495/hidden-markov-models-in-bioinformatics-snv-inference-from-next-generation-sequence
#7
Jiawen Bian, Xiaobo Zhou
The rapid development of next generation sequencing (NGS) technology provides a novel avenue for genomic exploration and research. Hidden Markov models (HMMs) have wide applications in pattern recognition as well as Bioinformatics such as transcription factor binding sites and cis-regulatory modules detection. An application of HMM is introduced in this chapter with the in-deep developing of NGS. Single nucleotide variants (SNVs) inferred from NGS are expected to reveal gene mutations in cancer. However, NGS has lower sequence coverage and poor SNV detection capability in the regulatory regions of the genome...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28224059/identification-of-downy-mildew-resistance-gene-candidates-by-positional-cloning-in-maize-zea-mays-subsp-mays-poaceae
#8
Jae Yoon Kim, Jun-Cheol Moon, Hyo Chul Kim, Seungho Shin, Kitae Song, Kyung-Hee Kim, Byung-Moo Lee
PREMISE OF THE STUDY: Positional cloning in combination with phenotyping is a general approach to identify disease-resistance gene candidates in plants; however, it requires several time-consuming steps including population or fine mapping. Therefore, in the present study, we suggest a new combined strategy to improve the identification of disease-resistance gene candidates. METHODS AND RESULTS: Downy mildew (DM)-resistant maize was selected from five cultivars using a spreader row technique...
February 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28223989/ufgt-the-key-enzyme-associated-with-the-petals-variegation-in-japanese-apricot
#9
Xinxin Wu, Qinghua Gong, Xiaopeng Ni, Yong Zhou, Zhihong Gao
Japanese apricot (Prunus mume Sieb.et Zucc.) is an important ornamental plant in China. One of the traits of petals color variegation is attractive, but its formation mechanism is unclear. In our study, RNA-seq technology was employed to characterize the transcriptome response to the mutation of "Fuban Tiaozhi" associated with petals variegation in Japanese apricot. As a result, 4,579,040 (white-flowered, WF) and 7,269,883 (red-flowered, RF) reads were mapped to P. persica genes, while 5,006,676 (WF) and 7,907,436 (RF) were mapped to P...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28223811/risk-assessment-of-aggressive-behavior-in-chinese-patients-with-schizophrenia-by-fmri-and-comt-gene
#10
Xiaoli Tang, Jun Jin, Yi Tang, Jinbo Cao, Junjie Huang
BACKGROUND: Blood-oxygen-level dependent functional magnetic resonance imaging (BOLD-fMRI) maps cerebral activity by the hemodynamic response. Catechol-O-methyltransferase (COMT) gene is involved in the metabolism of dopamine. It is reported that both of these can be used to assess the aggression risk in patients with schizophrenia. However, these methods to assess the aggression risk patients with schizophrenia have not been established in China. Therefore, we deliver here a systematic review and meta-analysis based on the studies dealing with Chinese patients...
2017: Neuropsychiatric Disease and Treatment
https://www.readbyqxmd.com/read/28223457/the-source-and-evolutionary-history-of-a-microbial-contaminant-identified-through-soil-metagenomic-analysis
#11
Matthew R Olm, Cristina N Butterfield, Alex Copeland, T Christian Boles, Brian C Thomas, Jillian F Banfield
In this study, strain-resolved metagenomics was used to solve a mystery. A 6.4-Mbp complete closed genome was recovered from a soil metagenome and found to be astonishingly similar to that of Delftia acidovorans SPH-1, which was isolated in Germany a decade ago. It was suspected that this organism was not native to the soil sample because it lacked the diversity that is characteristic of other soil organisms; this suspicion was confirmed when PCR testing failed to detect the bacterium in the original soil samples...
February 21, 2017: MBio
https://www.readbyqxmd.com/read/28223312/natural-variation-and-dosage-of-the-hei10-meiotic-e3-ligase-control-arabidopsis-crossover-recombination
#12
Piotr A Ziolkowski, Charles J Underwood, Christophe Lambing, Marina Martinez-Garcia, Emma J Lawrence, Liliana Ziolkowska, Catherine Griffin, Kyuha Choi, F Chris H Franklin, Robert A Martienssen, Ian R Henderson
During meiosis, homologous chromosomes undergo crossover recombination, which creates genetic diversity and balances homolog segregation. Despite these critical functions, crossover frequency varies extensively within and between species. Although natural crossover recombination modifier loci have been detected in plants, causal genes have remained elusive. Using natural Arabidopsis thaliana accessions, we identified two major recombination quantitative trait loci (rQTLs) that explain 56.9% of crossover variation in Col×Ler F2 populations...
February 21, 2017: Genes & Development
https://www.readbyqxmd.com/read/28222720/birt-hogg-dub%C3%A3-syndrome-a-literature-review-and-case-study-of-a-chinese-woman-presenting-a-novel-flcn-mutation
#13
Shengyu Hao, Fei Long, Fenglan Sun, Teng Liu, Daowei Li, Shujuan Jiang
BACKGROUND: The Birt-Hogg-Dubé (BHD) syndrome is a very rare autosomal dominant form of genodermatosis caused by germline mutations in the folliculin (FLCN) gene, which is mapped to the p11.2 region in chromosome 17. BHD commonly presents cutaneous fibrofolliculomas, pulmonary cysts, renal cell carcinoma, and recurrent pneumothoraxes. The disease is easily ignored or misdiagnosed as pneumothorax, pulmonary lymphangiomyomatosis (LAM), or emphysema. Follow-up and guidelines for managing recurrent pneumothoraxes in these patients are lacking...
February 21, 2017: BMC Pulmonary Medicine
https://www.readbyqxmd.com/read/28222718/abnormal-epigenetic-changes-during-differentiation-of-human-skeletal-muscle-stem-cells-from-obese-subjects
#14
Cajsa Davegårdh, Christa Broholm, Alexander Perfilyev, Tora Henriksen, Sonia García-Calzón, Lone Peijs, Ninna Schiøler Hansen, Petr Volkov, Rasmus Kjøbsted, Jørgen F P Wojtaszewski, Maria Pedersen, Bente Klarlund Pedersen, Dov B Ballak, Charles A Dinarello, Bas Heinhuis, Leo A B Joosten, Emma Nilsson, Allan Vaag, Camilla Scheele, Charlotte Ling
BACKGROUND: Human skeletal muscle stem cells are important for muscle regeneration. However, the combined genome-wide DNA methylation and expression changes taking place during adult myogenesis have not been described in detail and novel myogenic factors may be discovered. Additionally, obesity is associated with low relative muscle mass and diminished metabolism. Epigenetic alterations taking place during myogenesis might contribute to these defects. METHODS: We used Infinium HumanMethylation450 BeadChip Kit (Illumina) and HumanHT-12 Expression BeadChip (Illumina) to analyze genome-wide DNA methylation and transcription before versus after differentiation of primary human myoblasts from 14 non-obese and 14 obese individuals...
February 22, 2017: BMC Medicine
https://www.readbyqxmd.com/read/28222204/comparative-transcriptome-and-potential-antiviral-signaling-pathways-analysis-of-the-gills-in-the-red-swamp-crayfish-procambarus-clarkii-infected-with-white-spot-syndrome-virus-wssv
#15
Zhi-Qiang Du, Yan-Hui Jin
Red swamp crayfish is an important model organism for research of the invertebrate innate immunity mechanism. Its excellent disease resistance against bacteria, fungi, and viruses is well-known. However, the antiviral mechanisms of crayfish remain unclear. In this study, we obtained high-quality sequence reads from normal and white spot syndrome virus (WSSV)-challenged crayfish gills. For group normal (GN), 39,390,280 high-quality clean reads were randomly assembled to produce 172,591 contigs; whereas, 34,011,488 high-quality clean reads were randomly assembled to produce 182,176 contigs for group WSSV-challenged (GW)...
February 20, 2017: Genetics and Molecular Biology
https://www.readbyqxmd.com/read/28222102/anln-truncation-causes-a-familial-fatal-acute-respiratory-distress-syndrome-in-dalmatian-dogs
#16
Saila Holopainen, Marjo K Hytönen, Pernilla Syrjä, Meharji Arumilli, Anna-Kaisa Järvinen, Minna Rajamäki, Hannes Lohi
Acute respiratory distress syndrome (ARDS) is the leading cause of death in critical care medicine. The syndrome is typified by an exaggerated inflammatory response within the lungs. ARDS has been reported in many species, including dogs. We have previously reported a fatal familial juvenile respiratory disease accompanied by occasional unilateral renal aplasia and hydrocephalus, in Dalmatian dogs. The condition with a suggested recessive mode of inheritance resembles acute exacerbation of usual interstitial pneumonia in man...
February 21, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28222096/metacoder-an-r-package-for-visualization-and-manipulation-of-community-taxonomic-diversity-data
#17
Zachary S L Foster, Thomas J Sharpton, Niklaus J Grünwald
Community-level data, the type generated by an increasing number of metabarcoding studies, is often graphed as stacked bar charts or pie graphs that use color to represent taxa. These graph types do not convey the hierarchical structure of taxonomic classifications and are limited by the use of color for categories. As an alternative, we developed metacoder, an R package for easily parsing, manipulating, and graphing publication-ready plots of hierarchical data. Metacoder includes a dynamic and flexible function that can parse most text-based formats that contain taxonomic classifications, taxon names, taxon identifiers, or sequence identifiers...
February 21, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28222092/the-genetic-basis-of-resistance-and-matching-allele-interactions-of-a-host-parasite-system-the-daphnia-magna-pasteuria-ramosa-model
#18
Gilberto Bento, Jarkko Routtu, Peter D Fields, Yann Bourgeois, Louis Du Pasquier, Dieter Ebert
Negative frequency-dependent selection (NFDS) is an evolutionary mechanism suggested to govern host-parasite coevolution and the maintenance of genetic diversity at host resistance loci, such as the vertebrate MHC and R-genes in plants. Matching-allele interactions of hosts and parasites that prevent the emergence of host and parasite genotypes that are universally resistant and infective are a genetic mechanism predicted to underpin NFDS. The underlying genetics of matching-allele interactions are unknown even in host-parasite systems with empirical support for coevolution by NFDS, as is the case for the planktonic crustacean Daphnia magna and the bacterial pathogen Pasteuria ramosa...
February 21, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28221953/comparative-evaluation-of-genomic-and-laboratory-approaches-for-determination-of-shiga-toxin-subtypes-in-escherichia-coli
#19
Catherine D Carrillo, Adam G Koziol, Amit Mathews, Noriko Goji, Dominic Lambert, George Huszczynski, Martine Gauthier, Kingsley Amoako, Burton W Blais
The determination of Shiga toxin (ST) subtypes can be an important element in the risk characterization of foodborne ST-producing Escherichia coli (STEC) isolates for making risk management decisions. ST subtyping methods include PCR techniques based on electrophoretic or pyrosequencing analysis of amplicons and in silico techniques based on whole genome sequence analysis using algorithms that can be readily incorporated into bioinformatics analysis pipelines for characterization of isolates by their genetic composition...
December 2016: Journal of Food Protection
https://www.readbyqxmd.com/read/28221285/genome-wide-methylation-analysis-of-a-large-population-sample-shows-neurological-pathways-involvement-in-chronic-widespread-musculoskeletal-pain-cwp
#20
Gregory Livshits, Ida Malkin, Maxim B Freidin, Yudong Xia, Fei Gao, Jun Wang, Timothy D Spector, Alex MacGregor, Jordana T Bell, Frances Mk Williams
Chronic widespread musculoskeletal pain (CWP), has a considerable heritable component, which remains to be explained. Epigenetic factors may contribute to and account for some of the heritability estimate. We analysed epigenome-wide methylation using MeDIPseq in whole blood DNA from 1708 monozygotic (MZ) and dizygotic (DZ) Caucasian twins having CWP prevalence of 19.9%. Longitudinally stable methylation bins (lsBINs), were established by testing repeated measurements conducted ≥3 years apart, n=292. DNA methylation variation at lsBINs was tested for association with CWP in a discovery set of 50 MZ twin pairs discordant for CWP, and in an independent dataset (n=1608 twins), and the results from the two samples were combined using Fisher's method...
February 15, 2017: Pain
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