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Bioinformatics & pathogenicity prediction

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https://www.readbyqxmd.com/read/28524153/transcriptome-analysis-of-mirna-lncrna-mrna-interactions-in-the-malignant-transformation-process-of-gastric-cancer-initiation
#1
Y Mao, R Liu, H Zhou, S Yin, Q Zhao, X Ding, H Wang
Gastric cancer is a common heterogeneous malignancy that is pathologically characterized by the development of chronic atrophic gastritis and dysplasia of the epithelium. The pathogenic mechanisms at the molecular level are completely unclear. In the present study, we first address the expression network and miRNA-lncRNA-mRNA interaction in the malignant transformation process from normal mucosa and atrophic gastritis to a tumor. First, the long non-coding RNA (lncRNA), micro RNA (miRNA) and messenger RNA (mRNA) expression profiles of normal gastric mucosa, atrophic gastritis, gastric cancer and the peri-tumor tissues were analyzed using microarrays...
May 19, 2017: Cancer Gene Therapy
https://www.readbyqxmd.com/read/28520167/kmt2b-rare-missense-variants-in-generalized-dystonia
#2
Michael Zech, Robert Jech, Petra Havránková, Anna Fečíková, Riccardo Berutti, Dušan Urgošík, David Kemlink, Tim M Strom, Jan Roth, Evžen Růžička, Juliane Winkelmann
BACKGROUND: Recently a novel syndrome of childhood-onset generalized dystonia originating from mutations in lysine-specific methyltransferase 2B (KMT2B) has been reported. METHODS: We sequenced the exomes of 4 generalized dystonia-affected probands recruited from a Prague movement disorders center (Czech Republic). Bioinformatics analyses were conducted to select candidate causal variants in described dystonia-mutated genes. After cosegregation testing, checklists from the American College of Medical Genetics and Genomics were adopted to judge variant pathogenicity...
May 18, 2017: Movement Disorders: Official Journal of the Movement Disorder Society
https://www.readbyqxmd.com/read/28506932/refined-annotation-of-the-complete-genome-of-the-phytopathogenic-and-xanthan-producing-xanthomonas-campestris-pv-campestris-strain-b100-based-on-rna-sequence-data
#3
Rabeaa S Alkhateeb, Christian Rückert, Oliver Rupp, Boas Pucker, Gerd Hublik, Daniel Wibberg, Karsten Niehaus, Alfred Pühler, Frank-Jörg Vorhölter
Bioinformatics tools and gene expression data were applied to identify new genes and to enhance the accuracy in genomic feature predictions for Xanthomonas campestris pv. campestris B100, a pathogen of cruciferous plants and model strain for the biosynthesis of xanthan, a polysaccharide with a multitude of commercial applications as a thickening agent. Results from 5'-enriched RNA end-sequencing and total transcriptome RNA-seq experiments were used for this purpose. Functional gene annotations were updated where new evidence had emerged and start codon predictions were enhanced for 153 protein-coding genes (CDS)...
May 12, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28506204/antibiotic-effects-of-loperamide-homology-of-human-targets-of-loperamide-with-targets-in-acanthamoeba-spp
#4
Abdul Mannan Baig, Zohaib Rana, M Mohsin Mannan, S Sumayya Tariq, H R Ahmad
BACKGROUND: Loperamide is an anti-diarrheal drug prescribed for non-infectious diarrhea. The drug is an opioid receptor agonist, a blocker of voltage-dependent calcium channel (Cav) and a calmodulin (CaM) inhibitor on human cells. Loperamide has been reported to exert anti-amoebic effects against pathogenic strains of Acanthamoeba castellanii. OBJECTIVES: The precise mode of antibiotic action, cellular target homology with human counterparts and the pattern of cell death induced by loperamide in Acanthamoeba castellanii remain to be established...
April 25, 2017: Recent Patents on Anti-infective Drug Discovery
https://www.readbyqxmd.com/read/28496441/discovery-of-novel-leptospirosis-vaccine-candidates-using-reverse-and-structural-vaccinology
#5
André Alex Grassmann, Frederico Schmitt Kremer, Júlia Cougo Dos Santos, Jéssica Dias Souza, Luciano da Silva Pinto, Alan John Alexander McBride
Leptospira spp. are diderm (two membranes) bacteria that infect mammals causing leptospirosis, a public health problem with global implications. Thousands of people die every year due to leptospirosis, especially in developing countries with tropical climates. Prophylaxis is difficult due to multiple factors, including the large number of asymptomatic hosts that transmit the bacteria, poor sanitation, increasing numbers of slum dwellers, and the lack of an effective vaccine. Several leptospiral recombinant antigens were evaluated as a replacement for the inactivated (bacterin) vaccine; however, success has been limited...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28494495/mutations-in-lrp5-fzd4-tspan12-ndp-znf408-or-kif11-genes-account-for-38-7-of-chinese-patients-with-familial-exudative-vitreoretinopathy
#6
Feng-Qin Rao, Xue-Bi Cai, Fei-Fei Cheng, Wan Cheng, Xiao-Long Fang, Na Li, Xiu-Feng Huang, Li-Hong Li, Zi-Bing Jin
Purpose: Familial exudative vitreoretinopathy (FEVR) is a severe hereditary retinal disorder characterized by defects in retinal vascular development. To date, six genes have been reported to be responsible for this disease, including LRP5, FZD4, TSPAN12, NDP, ZNF408, and KIF11. The purpose of our study was to investigate the genetic defects in Chinese patients with FEVR through mutational analyses of 31 pedigrees. Methods: Clinical data and peripheral blood were collected from 31 pedigrees with FEVR...
May 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/28484437/a-novel-raym_rs09735-raym_rs09740-two-component-signaling-system-regulates-gene-expression-and-virulence-in-riemerella-anatipestifer
#7
Ying Wang, Ti Lu, Xuehuan Yin, Zutao Zhou, Shaowen Li, Mei Liu, Sishun Hu, Dingren Bi, Zili Li
The Gram-negative bacterium Riemerella anatipestifer is an important waterfowl pathogen, causing major economic losses to the duck-producing industry. However, little is known of the virulence factors that mediate pathogenesis during R. anatipestifer infection. In this study, RAYM_RS09735 and RAYM_RS09740 were predicted to form a two-component signaling system (TCS) through bioinformatics analysis. This TCS was highly conserved across the Flavobacteriaceae. A mutant YMΔRS09735/RS09740 strain was constructed to investigate the role of the RAYM_RS09735/RAYM_RS09740 TCS in R...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28480143/analysis-of-microsatellites-from-the-transcriptome-of-downy-mildew-pathogens-and-their-application-for-characterization-of-pseudoperonospora-populations
#8
Emma C Wallace, Lina M Quesada-Ocampo
Downy mildew pathogens affect several economically important crops worldwide but, due to their obligate nature, few genetic resources are available for genomic and population analyses. Draft genomes for emergent downy mildew pathogens such as the oomycete Pseudoperonospora cubensis, causal agent of cucurbit downy mildew, have been published and can be used to perform comparative genomic analysis and develop tools such as microsatellites to characterize pathogen population structure. We used bioinformatics to identify 2,738 microsatellites in the P...
2017: PeerJ
https://www.readbyqxmd.com/read/28479507/complete-genome-sequence-and-bioinformatics-analyses-of-bacillus-thuringiensis-strain-bm-bt15426
#9
Junyan Liu, Lin Li, Brian M Peters, Bing Li, Dingqiang Chen, Zhenbo Xu, Mark E Shirtliff
OBJECTIVES: This study aimed to investigate the genetic characteristics of Bacillus thuringiensis strain BM-BT15426. METHODS: B. thuringiensis strain was identified by sequencing the PCR product (amplifying 16S rRNA gene) using ABI Prism 377 DNA Sequencer. The genome was sequenced using PacBio RS II sequencers and assembled de novo using HGAP. Also, further genome annotation was performed. RESULTS: The genome of B. thuringiensis strain BM-BT15426 has a length of 5,246,329 bp and contains 5409 predicted genes with an average G + C content of 35...
May 4, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/28475857/mutations-in-epigenetic-regulation-genes-are-a-major-cause-of-overgrowth-with-intellectual-disability
#10
Katrina Tatton-Brown, Chey Loveday, Shawn Yost, Matthew Clarke, Emma Ramsay, Anna Zachariou, Anna Elliott, Harriet Wylie, Anna Ardissone, Olaf Rittinger, Fiona Stewart, I Karen Temple, Trevor Cole, Shazia Mahamdallie, Sheila Seal, Elise Ruark, Nazneen Rahman
To explore the genetic architecture of human overgrowth syndromes and human growth control, we performed experimental and bioinformatic analyses of 710 individuals with overgrowth (height and/or head circumference ≥+2 SD) and intellectual disability (OGID). We identified a causal mutation in 1 of 14 genes in 50% (353/710). This includes HIST1H1E, encoding histone H1.4, which has not been associated with a developmental disorder previously. The pathogenic HIST1H1E mutations are predicted to result in a product that is less effective in neutralizing negatively charged linker DNA because it has a reduced net charge, and in DNA binding and protein-protein interactions because key residues are truncated...
May 4, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28472130/novel-compound-heterozygous-myo7a-mutations-in-moroccan-families-with-autosomal-recessive-non-syndromic-hearing-loss
#11
Amina Bakhchane, Majida Charif, Amale Bousfiha, Redouane Boulouiz, Halima Nahili, Hassan Rouba, Hicham Charoute, Guy Lenaers, Abdelhamid Barakat
The MYO7A gene encodes a protein belonging to the unconventional myosin super family. Mutations within MYO7A can lead to either non syndromic hearing loss or to the Usher syndrome type 1B (USH1B). Here, we report the results of genetic analyses performed on Moroccan families with autosomal recessive non syndromic hearing loss that identified two families with compound heterozygous MYO7A mutations. Five mutations (c.6025delG, c.6229T>A, c.3500T>A, c.5617C>T and c.4487C>A) were identified in these families, the latter presenting two differently affected branches...
2017: PloS One
https://www.readbyqxmd.com/read/28451820/analysis-of-the-potato-calcium-dependent-protein-kinase-family-and-characterization-of-stcdpk7-a-member-induced-upon-infection-with-phytophthora-infestans
#12
Elisa Fantino, María Eugenia Segretin, Franco Santin, Federico Gabriel Mirkin, Rita M Ulloa
We describe the potato CDPK family and place StCDPK7 as a player in potato response to Phytophthora infestans infection, identifying phenylalanine ammonia lyase as its specific phosphorylation target in vitro. Calcium-dependent protein kinases (CDPKs) decode calcium (Ca(2+)) signals and activate different signaling pathways involved in hormone signaling, plant growth, development, and both abiotic and biotic stress responses. In this study, we describe the potato CDPK/CRK multigene family; bioinformatic analysis allowed us to identify 20 new CDPK isoforms, three CDPK-related kinases (CRKs), and a CDPK-like kinase...
April 27, 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/28444906/carbamoyl-phosphate-synthetase-1-deficiency-diagnosed-by-whole-exome-sequencing
#13
Guoqing Zhang, Yulin Chen, Huiqun Ju, Fei Bei, Jing Li, Jian Wang, Jianhua Sun, Jun Bu
BACKGROUND: Carbamoyl Phosphate Synthetase 1 deficiency (CPS1D) is a rare autosomal recessive inborn metabolic disease characterized mainly by hyperammonemia. The fatal nature of CPS1D and its similar symptoms with other urea cycle disorders (UCDs) make its diagnosis difficult, and the molecular diagnosis is hindered due to the large size of the causative gene CPS1. Therefore, the objective of the present study was to investigate the clinical applicability of exome sequencing in molecular diagnosis of CPS1D in Chinese population...
April 26, 2017: Journal of Clinical Laboratory Analysis
https://www.readbyqxmd.com/read/28439188/next-generation-sequencing-reveals-high-prevalence-of-brca1-and-brca2-variants-of-unknown-significance-in-early-onset-breast-cancer-in-african-american-women
#14
Luisel Ricks-Santi, J Tyson McDonald, Bert Gold, Michael Dean, Nicole Thompson, Muneer Abbas, Bradford Wilson, Yasmine Kanaan, Tammey J Naab, Georgia Dunston
BACKGROUND: Variants of unknown significance (VUSs) have been identified in BRCA1 and BRCA2 and account for the majority of all identified sequence alterations. Notably, VUSs occur disproportionately in people of African descent hampering breast cancer (BCa) management and prevention efforts in the population. Our study sought to identify and characterize mutations associated with increased risk of BCa at young age. METHODS: In our study, the spectrum of mutations in BRCA1 and BRCA2 was enumerated in a cohort of 31 African American women of early age at onset breast cancer, with a family history of breast or cancer in general and/or with triple negative breast cancer...
2017: Ethnicity & Disease
https://www.readbyqxmd.com/read/28433619/lack-of-pathogenic-mutations-in-sos1-gene-in-phenytoin-induced-gingival-overgrowth-patients
#15
Katia Margiotti, Giulia Pascolini, Federica Consoli, Valentina Guida, Carlo Di Bonaventura, Anna Teresa Giallonardo, Antonio Pizzuti, Alessandro De Luca
OBJECTIVE: Gingival overgrowth is a side effect associated with some distinct classes of drugs, such as anticonvulsants, immunosuppressants, and calcium channel blockers. One of the main drugs associated with gingival overgrowth is the antiepileptic phenytoin, which affects gingival tissues by altering extracellular matrix metabolism. It has been shown that mutation of human SOS1 gene is responsible for a rare hereditary gingival fibromatosis type 1, a benign gingival overgrowth. The aim of the present study is to evaluate the possible contribution of SOS1 mutation to gingival overgrowth-related phenotype...
April 5, 2017: Archives of Oral Biology
https://www.readbyqxmd.com/read/28423643/pole-and-pold1-screening-in-155-patients-with-multiple-polyps-and-early-onset-colorectal-cancer
#16
Clara Esteban-Jurado, David Giménez-Zaragoza, Jenifer Muñoz, Sebastià Franch-Expósito, Miriam Álvarez-Barona, Teresa Ocaña, Miriam Cuatrecasas, Sabela Carballal, María López-Cerón, Maria Marti-Solano, Marcos Díaz-Gay, Tom van Wezel, Antoni Castells, Luis Bujanda, Judith Balmaña, Victoria Gonzalo, Gemma Llort, Clara Ruiz-Ponte, Joaquín Cubiella, Francesc Balaguer, Rosa Aligué, Sergi Castellví-Bel
Germline mutations in POLE and POLD1 have been shown to cause predisposition to colorectal multiple polyposis and a wide range of neoplasms, early-onset colorectal cancer being the most prevalent. In order to find additional mutations affecting the proofreading activity of these polymerases, we sequenced its exonuclease domain in 155 patients with multiple polyps or an early-onset colorectal cancer phenotype without alterations in the known hereditary colorectal cancer genes. Interestingly, none of the previously reported mutations in POLE and POLD1 were found...
April 18, 2017: Oncotarget
https://www.readbyqxmd.com/read/28422960/predicting-the-impact-of-lynch-syndrome-causing-missense-mutations-from-structural-calculations
#17
Sofie V Nielsen, Amelie Stein, Alexander B Dinitzen, Elena Papaleo, Michael H Tatham, Esben G Poulsen, Maher M Kassem, Lene J Rasmussen, Kresten Lindorff-Larsen, Rasmus Hartmann-Petersen
Accurate methods to assess the pathogenicity of mutations are needed to fully leverage the possibilities of genome sequencing in diagnosis. Current data-driven and bioinformatics approaches are, however, limited by the large number of new variations found in each newly sequenced genome, and often do not provide direct mechanistic insight. Here we demonstrate, for the first time, that saturation mutagenesis, biophysical modeling and co-variation analysis, performed in silico, can predict the abundance, metabolic stability, and function of proteins inside living cells...
April 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28421333/identification-of-putative-second-genetic-hits-in-schizophrenia-carriers-of-high-risk-copy-number-variants-and-resequencing-in-additional-samples
#18
Julio Rodríguez-López, Beatriz Sobrino, Jorge Amigo, Noa Carrera, Julio Brenlla, Santiago Agra, Eduardo Paz, Ángel Carracedo, Mario Páramo, Manuel Arrojo, Javier Costas
Copy number variants (CNVs) conferring risk of schizophrenia present incomplete penetrance, suggesting the existence of second genetic hits. Identification of second hits may help to find genes with rare variants of susceptibility to schizophrenia. The aim of this work was to search for second hits of moderate/high risk in schizophrenia carriers of risk CNVs and resequencing of the relevant genes in additional samples. To this end, ten patients with risk CNVs at cytobands 15q11.2, 15q11.2-13.1, 16p11.2, or 16p13...
April 18, 2017: European Archives of Psychiatry and Clinical Neuroscience
https://www.readbyqxmd.com/read/28416776/clinical-value-of-mir-101-3p-and-biological-analysis-of-its-prospective-targets-in-breast-cancer-a-study-based-on-the-cancer-genome-atlas-tcga-and-bioinformatics
#19
Chun-Yao Li, Dan-Dan Xiong, Chun-Qin Huang, Rong-Quan He, Hai-Wei Liang, Deng-Hua Pan, Han-Lin Wang, Yi-Wen Wang, Hua-Wei Zhu, Gang Chen
BACKGROUND MiR-101-3p can promote apoptosis and inhibit proliferation, invasion, and metastasis in breast cancer (BC) cells. However, its mechanisms in BC are not fully understood. Therefore, a comprehensive analysis of the target genes, pathways, and networks of miR-101-3p in BC is necessary. MATERIAL AND METHODS The miR-101 profiles for 781 patients with BC from The Cancer Genome Atlas (TCGA) were analyzed. Gene expression profiling of GSE31397 with miR-101-3p transfected MCF-7 cells and scramble control cells was downloaded from Gene Expression Omnibus (GEO), and the differentially expressed genes (DEGs) were identified...
April 18, 2017: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
https://www.readbyqxmd.com/read/28391287/identification-of-2-potentially-relevant-gene-mutations-involved-in-strabismus-using-whole-exome-sequencing
#20
Xiangrong Min, Haiying Fan, Guiqiu Zhao, Guixiang Liu
BACKGROUND The etiology of strabismus has a genetic component. Our study aimed to localize the candidate causative gene mutant in a Chinese family with strabismus and to describe its underlying etiology. MATERIAL AND METHODS Genomic DNA was extracted from the affected individual and his parents in a Chinese pedigree with strabismus. The resulting exomes were sequenced by whole-exome sequencing. After variant calling and filtering, the candidate causative gene mutations were selected for the rarity and predicted damaging effect, which complied with the model of recessive disease transmission...
April 9, 2017: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
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