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Bioinformatics & pathogenicity prediction

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https://www.readbyqxmd.com/read/28068479/secretable-small-rnas-via-outer-membrane-vesicles-in-periodontal-pathogens
#1
J-W Choi, S-C Kim, S-H Hong, H-J Lee
MicroRNAs (miRNAs) have been shown to be major regulators of eukaryotic gene expression. However, bacterial RNAs comparable in size to eukaryotic miRNAs (18-22 nucleotides) have received little attention. Recently, a novel class of small RNAs similar in size to miRNAs (miRNA-size, small RNAs or msRNAs) have also been found in several bacteria. Like miRNAs, msRNAs are approximately 15 to 25 nucleotides in length, and their precursors are predicted to form a hairpin loop secondary structure. Here, we identified msRNAs in the periodontal pathogens Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, and Treponema denticola...
January 1, 2017: Journal of Dental Research
https://www.readbyqxmd.com/read/28055186/antimicrobials-inspired-by-nonribosomal-peptide-synthetase-gene-clusters
#2
Xavier Vila-Farres, John Chu, Daigo Inoyama, Melinda A Ternei, Christophe Lemetre, Louis J Cohen, Wooyoung Cho, Boojala Vijay B Reddy, Henry A Zebroski, Joel Stephen Freundlich, David S Perlin, Sean F Brady
Bacterial culture broth extracts have been the starting point for the development of numerous therapeutics. However, only a small fraction of bacterial biosynthetic diversity is accessible using this strategy. Here, we apply a discovery approach that bypasses the culturing step entirely by bioinformatically predicting small molecule structures from the primary sequences of the biosynthetic gene clusters. These structures are then chemically synthesized to give synthetic-bioinformatic natural products (syn-BNPs)...
January 5, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28040530/correlation-of-cell-surface-proteins-of-distinct-beauveria-bassiana-cell-types-and-adaption-to-varied-environment-and-interaction-with-the-host-insect-cell-surface-associated-proteins-of-b-bassiana
#3
Zhi Yang, Hongyan Jiang, Xin Zhao, Zhuoyue Lu, Zhibing Luo, Xuebing Li, Jing Zhao, Yongjun Zhang
The insect fungal pathogen Beauveria bassiana produces a number of distinct cell types that include aerial conidia, blastospores and haemolymph-derived cells, termed hyphal bodies, to adapt varied environment niches and within the host insect. These cells display distinct biochemical properties and surface structures, and a highly ordered outermost brush-like structure uniquely present on hyphal bodies, but not on any in vitro cells. Here, we found that the outermost structure on the hyphal bodies mainly consisted of proteins associated to structural wall components in that most of it could be removed by dithiothreitol (DTT) or proteinase K...
December 28, 2016: Fungal Genetics and Biology: FG & B
https://www.readbyqxmd.com/read/28039165/pbit-pipeline-builder-for-identification-of-drug-targets-for-infectious-diseases
#4
Gauri Shende, Harshala Haldankar, Ram Shankar Barai, Mohammed Husain Bharmal, Vinit Shetty, Susan Idicula-Thomas
: PBIT (Pipeline Builder for Identification of drug Targets) is an online webserver that has been developed for screening of microbial proteomes for critical features of human drug targets such as being non-homologous to human proteome as well as the human gut microbiota, essential for the pathogen's survival, participation in pathogen-specific pathways etc. The tool has been validated by analyzing 57 putative targets of Candida albicans documented in literature. PBIT integrates various in silico approaches known for drug target identification and will facilitate high-throughput prediction of drug targets for infectious diseases, including multi-pathogenic infections...
December 30, 2016: Bioinformatics
https://www.readbyqxmd.com/read/28031184/svscore-an-impact-prediction-tool-for-structural-variation
#5
Liron Ganel, Haley J Abel, Ira M Hall
: Here we present SVScore, a tool for in silico structural variation (SV) impact prediction. SVScore aggregates per-base single nucleotide polymorphism (SNP) pathogenicity scores across relevant genomic intervals for each SV in a manner that considers variant type, gene features and positional uncertainty. We show that the allele frequency spectrum of high-scoring SVs is strongly skewed toward lower frequencies, suggesting that they are under purifying selection, and that SVScore identifies deleterious variants more effectively than alternative methods...
December 28, 2016: Bioinformatics
https://www.readbyqxmd.com/read/28028452/burkholderia-pseudomallei-type-iii-secreted-protein-bipc-role-in-actin-modulation-and-translocation-activities-required-for-the-bacterial-intracellular-lifecycle
#6
Wen Tyng Kang, Kumutha Malar Vellasamy, Lakshminarayanan Rajamani, Roger W Beuerman, Jamuna Vadivelu
Melioidosis, an infection caused by the facultative intracellular pathogen Burkholderia pseudomallei, has been classified as an emerging disease with the number of patients steadily increasing at an alarming rate. B. pseudomalleipossess various virulence determinants that allow them to invade the host and evade the host immune response, such as the type III secretion systems (TTSS). The products of this specialized secretion system are particularly important for the B. pseudomallei infection. Lacking in one or more components of the TTSS demonstrated different degrees of defects in the intracellular lifecycle of B...
2016: PeerJ
https://www.readbyqxmd.com/read/28009814/a-novel-pathogenic-brca1-splicing-variant-produces-partial-intron-retention-in-the-mature-messenger-rna
#7
Maria Valeria Esposito, Marcella Nunziato, Flavio Starnone, Antonella Telese, Alessandra Calabrese, Giuseppe D'Aiuto, Pietro Pucci, Massimiliano D'Aiuto, Francisco Baralle, Valeria D'Argenio, Francesco Salvatore
About 10% of all breast cancers arise from hereditary mutations that increase the risk of breast and ovarian cancers; and about 25% of these are associated with the BRCA1 or BRCA2 genes. The identification of BRCA1/BRCA2 mutations can enable physicians to better tailor the clinical management of patients; and to initiate preventive measures in healthy carriers. The pathophysiological significance of newly identified variants poses challenges for genetic counseling. We characterized a new BRCA1 variant discovered in a breast cancer patient during BRCA1/2 screening by next-generation sequencing...
December 21, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28004519/antimicrobial-assay-and-genetic-screening-of-selected-freshwater-cyanobacteria-and-identification-of-a-biomolecule-dihydro-2h-pyran-2-one-derivative
#8
A Srivastava, V K Singh, S Patnaik, J Tripathi, P Singh, G Nath, R K Asthana
AIMS: Explorations of freshwater cyanobacteria as antimicrobial (bacteria, fungi and MRSA strains) drug resource using bioassay, NRPS (non-ribosomal polypeptide synthetase) and PKS (polyketide synthase) genes, as well as in silico approach. METHODS AND RESULTS: We have bioassayed the extracts of Phormidium CCC727, Geitlerinema CCC728, Arthrospira CCC729, Leptolyngbya CCC732, Phormidium CCC730, Phormidium CCC731 against six pathogenic bacteria Gram (+ve): Staphylococcus aureus including seven clinical methicillin-resistant S...
December 22, 2016: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/27997716/collagen-like-proteins-of-pathogenic-streptococci
#9
REVIEW
Slawomir Lukomski, Beth A Bachert, Flavia Squeglia, Rita Berisio
The collagen domain, which is defined by the presence of the Gly-X-Y triplet repeats, is amongst the most versatile and widespread known structures found in proteins from organisms representing all three domains of life. The streptococcal collagen-like (Scl) proteins are widely present in pathogenic streptococci, including Streptococcus pyogenes, S. agalactiae, S. pneumoniae, and S. equi. Experiments and bioinformatic analyses support the hypothesis that all Scl proteins are homotrimeric and cell wall-anchored...
December 20, 2016: Molecular Microbiology
https://www.readbyqxmd.com/read/27989580/the-promises-and-challenges-of-exome-sequencing-in-familial-non-syndromic-congenital-heart-disease
#10
Gillian M Blue, David Humphreys, Justin Szot, Joelene Major, Gavin Chapman, Alexis Bosman, Edwin P Kirk, Gary F Sholler, Richard P Harvey, Sally L Dunwoodie, David S Winlaw
BACKGROUND: Exome sequencing is an established strategy to identify causal variants in families with two or more members affected by congenital heart disease (CHD). This unbiased approach, in which both rare and common variants are identified, makes it suitable to research complex, heterogeneous diseases such as CHD. METHODS AND RESULTS: Exome sequencing was performed on two affected members of a three generation family with atrial septal defects (ASD), suggesting a dominant inheritance pattern...
December 13, 2016: International Journal of Cardiology
https://www.readbyqxmd.com/read/27986864/microrna-322-inhibits-inflammatory-cytokine-expression-and-promotes-cell-proliferation-in-lps-stimulated-murine-macrophages-by-targeting-nf-%C3%AE%C2%BAb1-p50
#11
Kai Zhang, Fengling Song, Xiaoxia Lu, Wenxun Chen, Chunxiao Huang, Lexing Li, Danyang Liang, Shengbo Cao, Hanchuan Dai
Inflammation is the body's normal self-protection mechanism to eliminate pathogens and resist pathogen invasion. The excessive inflammatory response may lead to inflammatory lesions. The mechanisms accounting for inflammation remain hazy. miRNAs have been proposed to have crucial effects on inflammation. In the present study, we reported that lipopolysaccharide (LPS)-stimulation increased the expression levels of inflammatory cytokines and the cell-cycle progression was suppressed in RAW264.7 cells. Meanwhile, the expression of miR-322 was significantly down-regulated after LPS treatment...
February 28, 2017: Bioscience Reports
https://www.readbyqxmd.com/read/27984190/mutation-screening-of-pdgfb-gene-in-chinese-population-with-primary-familial-brain-calcification
#12
Xiang-Ping Yao, Chong- Wang, Hui-Zhen Su, Xin-Xin Guo, Ying-Qian Lu, Miao Zhao, Yao-Bin Liu, Jing-Hui Lai, Hai-Ting Chen, Ning Wang, Wan-Jin Chen
BACKGROUND: Until recently, primary familial brain calcification (PFBC) has been determined by four genes, SLC20A2, PDGFRB, PDGFB and XPR1. No studies have been carried out to analyze the gene mutation of PDGFB in Chinese population. OBJECTIVE: To screen mutations of PDGFB gene in a large cohort of Chinese PFBC patients with no SLC20A2 mutations. METHODS: We recruited 192 PFBC patients, including 21 index cases and 171 sporadic cases, in our study...
October 28, 2016: Gene
https://www.readbyqxmd.com/read/27966633/structure-based-activity-prediction-of-cyp21a2-stability-variants-a-survey-of-available-gene-variations
#13
Carlos D Bruque, Marisol Delea, Cecilia S Fernández, Juan V Orza, Melisa Taboas, Noemí Buzzalino, Lucía D Espeche, Andrea Solari, Verónica Luccerini, Liliana Alba, Alejandro D Nadra, Liliana Dain
Congenital adrenal hyperplasia due to 21-hydroxylase deficiency accounts for 90-95% of CAH cases. In this work we performed an extensive survey of mutations and SNPs modifying the coding sequence of the CYP21A2 gene. Using bioinformatic tools and two plausible CYP21A2 structures as templates, we initially classified all known mutants (n = 343) according to their putative functional impacts, which were either reported in the literature or inferred from structural models. We then performed a detailed analysis on the subset of mutations believed to exclusively impact protein stability...
December 14, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27931036/clinical-exome-sequencing-reveals-mkrn3-pathogenic-variants-in-familial-and-nonfamilial-idiopathic-central-precocious-puberty
#14
Nelmar Valentina Ortiz-Cabrera, Rosa Riveiro-Álvarez, Miguel Ángel López-Martínez, Pilar Pérez-Segura, Isabel Aragón-Gómez, María José Trujillo-Tiebas, Leandro Soriano-Guillén
BACKGROUND/AIMS: Idiopathic central precocious puberty (ICPP) is the premature activation of the hypothalamic-pituitary-gonadal axis in the absence of organic disease. Up to now, just gain-of-function mutations of KISS1/KISS1R and loss-of-function mutations of the maternally imprinted gene MKRN3 are the known genetic causes of ICPP. Our intention is to evaluate variants present in genes related to the pubertal onset pathway that could act as disease-causing or predisposing variants. METHODS: We studied the clinical exome of 20 patients diagnosed with ICPP using the Illumina platform...
December 9, 2016: Hormone Research in Pædiatrics
https://www.readbyqxmd.com/read/27922074/resistance-gene-identification-from-larimichthys-crocea-with-machine-learning-techniques
#15
Yinyin Cai, Zhijun Liao, Ying Ju, Juan Liu, Yong Mao, Xiangrong Liu
The research on resistance genes (R-gene) plays a vital role in bioinformatics as it has the capability of coping with adverse changes in the external environment, which can form the corresponding resistance protein by transcription and translation. It is meaningful to identify and predict R-gene of Larimichthys crocea (L.Crocea). It is friendly for breeding and the marine environment as well. Large amounts of L.Crocea's immune mechanisms have been explored by biological methods. However, much about them is still unclear...
December 6, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27914961/expanding-the-clinical-and-genetic-spectrum-of-g6pd-deficiency-the-occurrence-of-bcgitis-and-novel-missense-mutation
#16
Taj Ali Khan, Humaira Mazhar, Mehboob Nawaz, Kalsoom Kalsoom, Muhammad Ishfaq, Huma Asif, Hazir Rahman, Muhammad Qasim, Farkhanda Naz, Mubashir Hussain, Baharullah Khattak, Waheed Ullah, Otavio Cabral-Marques, Jawad Butt, Asif Iqbal
Glucose-6-phosphate dehydrogenase (G6PD) is a key enzyme in the pentose phosphate pathway that ensures sufficient production of coenzyme nicotinamide adenine dinucleotide phosphate (NADPH) by catalyzing the reduction of NADP+ to NADPH. Noteworthy, the latter mediates the production of reactive oxygen species (ROS) by phagocytic cells such as neutrophils and monocytes. Therefore, patients with severe forms of G6PD deficiency may present impaired NADPH oxidase activity and become susceptible to recurrent infections...
January 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/27904804/mining-snps-in-extracellular-vesicular-transcriptome-of-trypanosoma-cruzi-a-step-closer-to-early-diagnosis-of-neglected-chagas-disease
#17
Pallavi Gaur, Anoop Chaturvedi
One of the newest and strongest members of intercellular communicators, the Extracellular vesicles (EVs) and their enclosed RNAs; Extracellular RNAs (exRNAs) have been acknowledged as putative biomarkers and therapeutic targets for various diseases. Although a very deep insight has not been possible into the physiology of these vesicles, they are believed to be involved in cell-to-cell communication and host-pathogen interactions. EVs might be significantly helpful in discovering biomarkers for possible target identification as well as prognostics, diagnostics and developing vaccines...
2016: PeerJ
https://www.readbyqxmd.com/read/27899486/functional-investigations-of-hnf1a-identify-rare-variants-as-risk-factors-for-type-2-diabetes-in-the-general-population
#18
Laeya Abdoli Najmi, Ingvild Aukrust, Jason Flannick, Janne Molnes, Noel Burtt, Anders Molven, Leif Groop, David Altshuler, Stefan Johansson, Lise Bjørkhaug, Pål Rasmus Njølstad
Variants in HNF1A encoding hepatocyte nuclear factor-1A are associated with maturity-onset diabetes of the young (MODY3) and type 2 diabetes. We investigated whether functional classification of HNF1A rare coding variants can inform models of diabetes risk prediction in the general population by analyzing the effect of 27 HNF1A variants identified in well-phenotyped populations (n = 4115). Bioinformatics tools classified 11 variants as likely pathogenic and showed no association with diabetes risk (combined MAF = 0...
November 29, 2016: Diabetes
https://www.readbyqxmd.com/read/27898768/transcriptome-and-small-rnaome-dynamics-during-a-resistant-and-susceptible-interaction-between-cucumber-and-downy-mildew
#19
Alyssa Burkhardt, Brad Day
Cucumber ( L.) downy mildew, caused by the obligate oomycete pathogen (Berk. and Curt.) Rostov., is the primary factor limiting cucumber production. Although sources of resistance have been identified, such as plant introduction line PI 197088, the genes and processes involved in mediating resistance are still unknown. In the current study, we conducted a comprehensive transcriptome and small RNAome analysis of a resistant (PI 197088) and susceptible ('Vlaspik') cucumber during a time course of infection using Illumina sequencing...
March 2016: Plant Genome
https://www.readbyqxmd.com/read/27895760/prioritization-of-non-coding-disease-causing-variants-and-long-non-coding-rnas-in-liver-cancer
#20
Hua Li, Zekun He, Yang Gu, Lin Fang, Xin Lv
There are multiple bioinformatics tools available for the detection of coding driver mutations in cancers. However, the prioritization of pathogenic non-coding variants remains a challenging and demanding task. The present study was performed to discriminate non-coding disease-causing mutations and prioritize potential cancer-implicated long non-coding RNAs (lncRNAs) in liver cancer using a logistic regression model. A logistic regression model was constructed by combining 19,153 disease-associated ClinVar and human gene mutation database pathogenic variants as the response variable and non-coding features as the predictor variable...
November 2016: Oncology Letters
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