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https://www.readbyqxmd.com/read/28316117/how-consistent-are-we-interlaboratory-comparison-study-in-fathead-minnows-using-the-model-estrogen-17%C3%AE-ethinylestradiol-to-develop-recommendations-for-environmental-transcriptomics
#1
April Feswick, Meghan Isaacs, Adam Biales, Robert W Flick, David C Bencic, Rong-Lin Wang, Chris Vulpe, Marianna Brown-Augustine, Alex Loguinov, Francesco Falciani, Philipp Antczak, John Herbert, Lorraine Brown, Nancy D Denslow, Kevin J Kroll, Candice Lavelle, Viet Dang, Lynn Escalon, Natàlia Garcia-Reyero, Christopher J Martyniuk, Kelly R Munkittrick
Fundamental questions remain about the application of omics in environmental risk assessments, such as the consistency of data across laboratories. The objective of this study was to determine the congruence of transcript data across six independent laboratories. Male fathead minnows (FHM) were exposed to a measured concentration of 15.8 ng /L EE2 for 96 h. Livers were divided equally and sent to the participating laboratories for transcriptomic analysis using the same FHM microarray. Each laboratory was free to apply bioinformatics pipelines of their choice...
March 18, 2017: Environmental Toxicology and Chemistry
https://www.readbyqxmd.com/read/28315224/an-overview-of-bioinformatics-tools-and-resources-in-allergy
#2
Zhiyan Fu, Jing Lin
The rapidly increasing number of characterized allergens has created huge demands for advanced information storage, retrieval, and analysis. Bioinformatics and machine learning approaches provide useful tools for the study of allergens and epitopes prediction, which greatly complement traditional laboratory techniques. The specific applications mainly include identification of B- and T-cell epitopes, and assessment of allergenicity and cross-reactivity. In order to facilitate the work of clinical and basic researchers who are not familiar with bioinformatics, we review in this chapter the most important databases, bioinformatic tools, and methods with relevance to the study of allergens...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28293298/rapid-development-of-entity-based-data-models-for-bioinformatics-with-persistence-object-oriented-design-and-structured-interfaces
#3
Elishai Ezra Tsur
Databases are imperative for research in bioinformatics and computational biology. Current challenges in database design include data heterogeneity and context-dependent interconnections between data entities. These challenges drove the development of unified data interfaces and specialized databases. The curation of specialized databases is an ever-growing challenge due to the introduction of new data sources and the emergence of new relational connections between established datasets. Here, an open-source framework for the curation of specialized databases is proposed...
2017: BioData Mining
https://www.readbyqxmd.com/read/28286226/microrna-297-promotes-cardiomyocyte-hypertrophy-via-targeting-sigma-1-receptor
#4
Qinxue Bao, Mingyue Zhao, Li Chen, Yu Wang, Siyuan Wu, Wenchao Wu, Xiaojing Liu
AIMS: Sigma-1 receptor (Sig-1R) is a ligand-regulated endoplasmic reticulum (ER) chaperone involved in cardiac hypertrophy, but it is not known whether Sig-1R is regulated by microRNAs (miRNAs). According to bioinformatic analysis, miR-297 was suggested as a potential target miRNA for Sig-1R. Therefore, we verified whether miR-297 could target Sig-1R and investigated the possible mechanisms underlying the role of miR-297 in cardiac hypertrophy. MAIN METHODS: Bioinformatic analysis combined with laboratory experiments, including quantitative RT-PCR, Western blotting, and luciferase assay, were performed to identify the target miRNA of Sig-1R...
March 10, 2017: Life Sciences
https://www.readbyqxmd.com/read/28280605/next-generation-sequencing-identifies-interactome-signatures-in-relapsed-and-refractory-metastatic-colorectal-cancer
#5
Benny Johnson, Laurence Cooke, Daruka Mahadevan
BACKGROUND: In the management of metastatic colorectal cancer (mCRC), KRAS, NRAS and BRAF mutational status individualizes therapeutic options and identify a cohort of patients (pts) with an aggressive clinical course. We hypothesized that relapsed and refractory mCRC pts develop unique mutational signatures that may guide therapy, predict for a response and highlight key signaling pathways important for clinical decision making. METHODS: Relapsed and refractory mCRC pts (N=32) were molecularly profiled utilizing commercially available next generation sequencing (NGS) platforms...
February 2017: Journal of Gastrointestinal Oncology
https://www.readbyqxmd.com/read/28253235/simple-multiplexed-pcr-based-barcoding-of-dna-for-ultrasensitive-mutation-detection-by-next-generation-sequencing
#6
Anders Ståhlberg, Paul M Krzyzanowski, Matthew Egyud, Stefan Filges, Lincoln Stein, Tony E Godfrey
Detection of extremely rare variant alleles within a complex mixture of DNA molecules is becoming increasingly relevant in many areas of clinical and basic research, such as the detection of circulating tumor DNA in the plasma of cancer patients. Barcoding of DNA template molecules early in next-generation sequencing (NGS) library construction provides a way to identify and bioinformatically remove polymerase errors that otherwise make detection of these rare variants very difficult. Several barcoding strategies have been reported, but all require long and complex library preparation protocols...
April 2017: Nature Protocols
https://www.readbyqxmd.com/read/28251763/a-13-week-research-based-biochemistry-laboratory-curriculum
#7
Scott T Lefurgy, Emily C Mundorff
Here, we present a 13-week research-based biochemistry laboratory curriculum designed to provide the students with the experience of engaging in original research while introducing foundational biochemistry laboratory techniques. The laboratory experience has been developed around the directed evolution of an enzyme chosen by the instructor, with mutations designed by the students. Ideal enzymes for this curriculum are able to be structurally modeled, solubly expressed, and monitored for activity by UV/Vis spectroscopy, and an example curriculum for haloalkane dehalogenase is given...
March 2, 2017: Biochemistry and Molecular Biology Education
https://www.readbyqxmd.com/read/28249815/advances-in-the-application-of-high-throughput-sequencing-in-invertebrate-virology
#8
R Van Aerle, E M Santos
Over the last decade, advances in high-throughput sequencing technologies have revolutionised biological research, making it possible for DNA/RNA sequencing of any organism of interest to be undertaken. Sequencing approaches are now routinely used in the detection and characterisation of (novel) viruses, investigation of host-pathogen interactions, and effective development of disease treatment strategies. For the sequencing and identification of viruses of interest, metagenomics approaches using infected host tissue are frequently used, as it is not always possible to culture and isolate these pathogens...
February 26, 2017: Journal of Invertebrate Pathology
https://www.readbyqxmd.com/read/28247913/cellular-proteomic-analysis-of-porcine-circovirus-type-2-and-classical-swine-fever-virus-coinfection-in-porcine-kidney-15-cells-using-isobaric-tags-for-relative-and-absolute-quantitation-coupled-lc-ms-ms
#9
Niu Zhou, Chunmei Fan, Song Liu, Jianwei Zhou, Yulan Jin, Xiaojuan Zheng, Qin Wang, Jue Liu, Hanchun Yang, Jinyan Gu, Jiyong Zhou
Viral coinfection or superinfection in host has caused public health concern and huge economic losses of farming industry. The influence of viral coinfection on cellular protein abundance is essential for viral pathogenesis. Based on a coinfection model for porcine circovirus type 2 (PCV2) and classical swine fever virus (CSFV) developed previously by our laboratory, isobaric tags for relative and absolute quantitation (iTRAQ)-coupled LC-MS/MS proteomic profiling was performed to explore the host cell responses to PCV2-CSFV coinfection...
March 1, 2017: Electrophoresis
https://www.readbyqxmd.com/read/28242148/-next-generation-dna-sequencing-in-clinical-diagnostics
#10
C Lacoste, A Fabre, C Pécheux, N Lévy, M Krahn, P Malzac, N Bonello-Palot, C Badens, P Bourgeois
The advent of next generation sequencing (NGS) technologies is so scale-changing that it modifies molecular diagnostics indications and induces laboratories to rethink their diagnostic strategies, until now based on the Sanger sequencing routine. Several high-throughput approaches are available from the sequencing of a gene panel, to an exome, or even a genome. In all cases, a tremendous amount of data is generated, which has to be filtered, interpreted and analyzed using powerful bioinformatics tools. In parallel, ethical considerations are raised to avoid the potential drifts of these powerful approaches...
February 24, 2017: Archives de Pédiatrie: Organe Officiel de la Sociéte Française de Pédiatrie
https://www.readbyqxmd.com/read/28228490/short-read-whole-genome-sequencing-for-laboratory-based-surveillance-of-bordetella-pertussis
#11
Alex Marchand-Austin, Raymond S W Tsang, Jennifer L Guthrie, Jennifer H Ma, Gillian Lim, Natasha S Crowcroft, Shelley L Deeks, David J Farrell, Frances B Jamieson
Bordetella pertussis (BP) is a Gram-negative bacterium that causes respiratory infections in humans. Ongoing molecular surveillance of BP acellular vaccine (aP) antigens is critical for understanding the interaction between evolutionary pressures, disease pathogenesis, and vaccine effectiveness. Methods currently used to characterize aP components are relatively labour intensive and low throughput. To address this challenge, we sought to derive aP antigen genotypes from minimally processed short-read whole genome sequencing data generated from 40 clinical BP isolates and analyzed using the SRST2 bioinformatic package...
February 22, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28223374/enterobacter-cloacae-complex-isolates-harboring-blanmc-a-or-blaimi-type-class-a-carbapenemase-genes-on-novel-chromosomal-integrative-elements-and-plasmids
#12
David A Boyd, Laura F Mataseje, Ross Davidson, Johannes A Delport, Jeff Fuller, Linda Hoang, Brigitte Lefebvre, Paul Levett, Diane L Roscoe, Barbara M Willey, Michael R Mulvey
Carbapenem-resistant Enterobacter cloacae complex isolates submitted to a reference laboratory from 2010 to 2015 were screened by PCR for seven common carbapenemase gene groups, namely, KPC, NDM, OXA-48, VIM, IMP, GES, and NMC-A/IMI. Nineteen of the submitted isolates (1.7%) were found to harbor Ambler class A blaNMC-A or blaIMI-type carbapenemases. All 19 isolates were resistant to at least one carbapenem but susceptible to aminoglycosides, trimethoprim-sulfamethoxazole, tigecycline, and ciprofloxacin. Most isolates (17/19) gave positive results with the Carba-NP test for phenotypic carbapenemase detection...
February 21, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28221970/genomic-tools-for-customized-recovery-and-detection-of-foodborne-shiga-toxigenic-escherichia-coli
#13
Michael Knowles, Sara Stinson, Dominic Lambert, Catherine Carrillo, Adam Koziol, Martine Gauthier, Burton Blais
Genomic antimicrobial resistance (AMR) prediction tools have the potential to support foodborne illness outbreak investigations through their application in the analysis of bacterial genomes from causative strains. The AMR marker profile of a strain of interest, initially identified in outbreak-associated clinical samples, may serve as the basis for customization of selective enrichment media, facilitating its recovery from samples in a food safety investigation. Different possibilities for AMR analyses include the use of comprehensive AMR gene databases such as the Comprehensive Antibiotic Resistance Database, which can be mined with in-house bioinformatics alignment tools (e...
December 2016: Journal of Food Protection
https://www.readbyqxmd.com/read/28221953/comparative-evaluation-of-genomic-and-laboratory-approaches-for-determination-of-shiga-toxin-subtypes-in-escherichia-coli
#14
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/28221883/enrichment-amplification-and-sequence-based-typing-of-salmonella-enterica-and-other-foodborne-pathogens
#15
Tom Edlind, Jeffrey D Brewster, George C Paoli
Detection of Salmonella enterica in foods typically involves microbiological enrichment, molecular-based assay, and subsequent isolation and identification of a pure culture. This is ideally followed by strain typing, which provides information critical to the investigation of outbreaks and the attribution of their sources. Pulsed-field gel electrophoresis is the "gold standard" for S. enterica strain typing, but its limitations have encouraged the search for alternative methods, including whole genome sequencing...
January 2017: Journal of Food Protection
https://www.readbyqxmd.com/read/28221002/computational-biology-and-chemistry-in-mti-emphasis-on-the-prediction-of-some-admet-properties
#16
REVIEW
Maria A Miteva, Bruno O Villoutreix
Our research and teaching group called MTi (Molécules Thérapeutiques in silico) has developed numerous applications available online, thanks to the RPBS platform (Ressource Parisienne en Bioinformatique Structurale), in the field of chemoinformatics, structural bioinformatics and drug design. Since its opening in 2009, over 200 articles/reviews have been reported and involve virtual screening studies, prediction of druggability, analysis of protein-protein interaction inhibitors, development of databases, data mining and knowledge discovery, as well as combined in silico-in vitro work to search for new hits and chemical probes acting on original targets in several therapeutic areas...
February 21, 2017: Molecular Informatics
https://www.readbyqxmd.com/read/28218974/molecular-cloning-bioinformatics-analysis-and-transcriptional-profiling-of-jaz1-and-jaz2-from-salvia-miltiorrhiza
#17
Yangyun Zhou, Xun Zhou, Qing Li, Junfeng Chen, Ying Xiao, Lei Zhang, Wansheng Chen
Production of major effective metabolites, tanshinones and lithospermic acid B (LAB), was dramatically enhanced by exogenous jasmonate (JA) treatment in Salvia miltiorrhiza. However, the molecular mechanism of such metabolic activation in S. miltiorrhiza has not been elucidated yet. Here, we focused on jasmonate ZIM-domain (JAZ) proteins that act as repressors of JA signaling. Open reading frames of two novel genes, SmJAZ1 and SmJAZ2, from S. miltiorrhiza were amplified according to the annotation of S. miltiorrhiza transcriptome...
January 2017: Biotechnology and Applied Biochemistry
https://www.readbyqxmd.com/read/28218742/mirna-expression-profiles-reveal-the-involvement-of-mir-26a-mir-548l-and-mir-34a-in-hepatocellular-carcinoma-progression-through-regulation-of-st3gal5
#18
Hongjiao Cai, Huimin Zhou, Yuan Miao, Nana Li, Lifen Zhao, Li Jia
MicroRNAs (miRNAs) have key roles in comprehensive physiological and pathological processes by targeting specific genes through translational repression. Identification of miRNAs related to metastasis enables us to obtain better insight into cancer development. In the current study, we investigated the miRNA expressional profiles in the highly invasive human hepatocellular carcinoma cell line MHCC97-H and MHCC97-L with lower metastatic potential using miRNA microarrays. By quantitative real-time PCR, we confirmed the results of miRNA experiments...
February 20, 2017: Laboratory Investigation; a Journal of Technical Methods and Pathology
https://www.readbyqxmd.com/read/28218741/identification-of-micrornas-associated-with-invasive-and-aggressive-phenotype-in-cutaneous-melanoma-by-next-generation-sequencing
#19
Sankhiros Babapoor, Rong Wu, James Kozubek, Donna Auidi, Jane M Grant-Kels, Soheil S Dadras
A comprehensive repertoire of human microRNAs (miRNAs) that could be involved in early melanoma invasion into the dermis remains unknown. To this end, we sequenced small RNAs (18-30 nucleotides) isolated from an annotated series of invasive melanomas (average invasive depth, 2.0 mm), common melanocytic nevi, and matched normal skin (n=28). Our previously established bioinformatics pipeline identified 765 distinct mature known miRNAs and defined a set of top 40 list that clearly segregated melanomas into thin (0...
February 20, 2017: Laboratory Investigation; a Journal of Technical Methods and Pathology
https://www.readbyqxmd.com/read/28214999/e6-associated-protein-dependent-estrogen-receptor-regulation-of-protein-kinase-a-regulatory-subunit-r2a-expression-in-neuroblastoma
#20
Jean-Pierre Obeid, Youssef H Zeidan, Nawal Zafar, Jimmy El Hokayem
E6ap is a known transcriptional coregulator for estrogen receptor alpha (Er, Erα) in the presence of estrogen. Protein kinase A (PKA) contains two regulatory subunits derived from four genes. Recent evidence demonstrates that PKA regulates E6ap activity. Data generated in our lab indicated estrogen dependent regulation of Pkar2a levels. Our project sets to investigate a possible feedback mechanism constituting of Erα and E6ap transcriptional regulation of Pkar2a expression. Western blot evaluated protein regulation correlations with E2 in mouse neuroblastoma lines...
February 18, 2017: Molecular Neurobiology
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