keyword
MENU ▼
Read by QxMD icon Read
search

bioinformatics lab

keyword
https://www.readbyqxmd.com/read/28228490/short-read-whole-genome-sequencing-for-laboratory-based-surveillance-of-bordetella-pertussis
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
https://www.readbyqxmd.com/read/28202748/rna-splicing-in-human-disease-and-in-the-clinic
#11
REVIEW
Diana Baralle, Emanuele Buratti
Defects at the level of the pre-mRNA splicing process represent a major cause of human disease. Approximately 15-50% of all human disease mutations have been shown to alter functioning of basic and auxiliary splicing elements. These elements are required to ensure proper processing of pre-mRNA splicing molecules, with their disruption leading to misprocessing of the pre-mRNA molecule and disease. The splicing process is a complex process, with much still to be uncovered before we are able to accurately predict whether a reported genomic sequence variant (GV) represents a splicing-associated disease mutation or a harmless polymorphism...
March 1, 2017: Clinical Science (1979-)
https://www.readbyqxmd.com/read/28187415/estimation-of-biomass-composition-from-genomic-and-transcriptomic-information
#12
Sophia Santos, Isabel Rocha
Given the great potential impact of the growing number of complete genome-scale metabolic network reconstructions of microorganisms, bioinformatics tools are needed to simplify and accelerate the course of knowledge in this field. One essential component of a genome-scale metabolic model is its biomass equation, whose maximization is one of the most common objective functions used in Flux Balance Analysis formulations. Some components of biomass, such as amino acids and nucleotides, can be estimated from genome information, providing reliable data without the need of performing lab experiments...
November 27, 2016: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28182618/the-evolving-landscape-of-hiv-drug-resistance-diagnostics-for-expanding-testing-in-resource-limited-settings
#13
Seth C Inzaule, Raph L Hamers, Roger Paredes, Chunfu Yang, Rob Schuurman, Tobias F Rinke de Wit
Global scale-up of antiretroviral treatment (ART) has dramatically changed the prospects of HIV/AIDS disease rendering life-long chronic care and treatment a reality for millions of HIV-infected patients. Affordable technologies to monitor ART are needed to ensure long-term durability of limited available drug regimens. HIV drug resistance tests can complement existing strategies in optimizing clinical decision-making for patients with treatment failure, in addition to facilitating population-based surveillance of HIV drug resistance...
February 9, 2017: AIDS Reviews
https://www.readbyqxmd.com/read/28174235/an-integrated-approach-identifies-mediators-of-local-recurrence-in-head-neck-squamous-carcinoma
#14
Francesca Citron, Joshua Armenia, Giovanni Franchin, Jerry Polesel, Renato Talamini, Sara D'Andrea, Sandro Sulfaro, Carlo M Croce, William Klement, Dave Otasek, Chiara Pastrello, Tomas Tokar, Igor Jurisica, Deborah French, Riccardo Bomben, Emanuela Vaccher, Diego Serraino, Barbara Belletti, Andrea Vecchione, Luigi Barzan, Gustavo Baldassarre
PURPOSE: Head and Neck Squamous Cell Carcinomas (HNSCC) cause more than 300,000 deaths worldwide each year. Locoregional and distant recurrences represent worse prognostic events and accepted surrogate markers of patients' survival. No valid biomarker and salvage therapy exist to identify and treat patients at high-risk of recurrence. We aimed to verify if selected microRNAs (miRs) could be used as biomarkers of recurrence in HNSCC. EXPERIMENTAL DESIGN: A Nanostring array was used to identify miRs associated with locoregional recurrence in 44 HNSCC patients...
February 7, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28171857/the-iona%C3%A2-test-development-of-an-automated-cell-free-dna-based-screening-test-for-fetal-trisomies-13-18-and-21-that-employs-the-ion-proton-semiconductor-sequencing-platform
#15
Francesco Crea, Matthew Forman, Rachel Hulme, Robert W Old, Dan Ryan, Rosalyn Mazey, Michael D Risley
OBJECTIVE: To develop a screening test for fetal trisomy 13, 18, and 21 using cell-free DNA from maternal blood with an automated workflow using the Ion Proton sequencing platform. METHODS: An automated next-generation sequencing workflow was developed using the Ion Proton sequencing platform and software developed for straightforward bioinformatic analysis. An algorithm was developed using 239 samples to determine the likelihood of trisomy, using DNA fragment counts and a fetal fraction validity check; the results were compared with those from invasive diagnostic procedures...
February 8, 2017: Fetal Diagnosis and Therapy
https://www.readbyqxmd.com/read/28169558/validation-of-metagenomic-next-generation-sequencing-tests-for-universal-pathogen-detection
#16
Robert Schlaberg, Charles Y Chiu, Steve Miller, Gary W Procop, George Weinstock
CONTEXT: -Metagenomic sequencing can be used for detection of any pathogens using unbiased, shotgun next-generation sequencing (NGS), without the need for sequence-specific amplification. Proof-of-concept has been demonstrated in infectious disease outbreaks of unknown causes and in patients with suspected infections but negative results for conventional tests. Metagenomic NGS tests hold great promise to improve infectious disease diagnostics, especially in immunocompromised and critically ill patients...
February 7, 2017: Archives of Pathology & Laboratory Medicine
https://www.readbyqxmd.com/read/28161601/messages-from-the-first-international-conference-on-clinical-metagenomics-iccmg
#17
Etienne Ruppé, Gilbert Greub, Jacques Schrenzel
Metagenomics is recently entering in the clinical microbiology and an increasing number of diagnostic laboratories are now proposing the sequencing & annotation of bacterial genomes and/or the analysis of clinical samples by direct or PCR-based metagenomics with short time to results. In this context, the first International Conference on Clinical Metagenomics (ICCMg) was held in Geneva in October 2016 and several key aspects have been discussed including: i) the need for improved resolution, ii) the importance of interpretation given the common occurrence of sequence contaminants, iii) the need for improved bioinformatic pipelines, iv) the bottleneck of DNA extraction, v) the importance of gold standards, vi) the need to further reduce time to results, vii) how to improve data sharing, viii) the applications of bacterial genomics and clinical metagenomics in better adapting therapeutics and ix) the impact of metagenomics and new sequencing technologies in discovering new microbes...
February 1, 2017: Microbes and Infection
https://www.readbyqxmd.com/read/28134443/challenges-and-opportunities-for-whole-genome-sequencing-based-surveillance-of-antibiotic-resistance
#18
Anita C Schürch, Willem van Schaik
Infections caused by drug-resistant bacteria are increasingly reported across the planet, and drug-resistant bacteria are recognized to be a major threat to public health and modern medicine. In this review, we discuss how whole-genome sequencing (WGS)-based approaches can contribute to the surveillance of the emergence and spread of antibiotic resistance. We outline the characteristics of sequencing technologies that are currently most used for WGS (Illumina short-read technologies and the long-read sequencing platforms developed by Pacific Biosciences and Oxford Nanopore)...
January 2017: Annals of the New York Academy of Sciences
https://www.readbyqxmd.com/read/28112756/long-noncoding-rna-ftx-is-upregulated-in-gliomas-and-promotes-proliferation-and-invasion-of-glioma-cells-by-negatively-regulating-mir-342-3p
#19
Weiguang Zhang, Yunke Bi, Jianhua Li, Fei Peng, Hui Li, Chenguang Li, Laizang Wang, Fubin Ren, Chen Xie, Pengwei Wang, Weiwei Liang, Zhi Wang, Dan Zhu
Gliomas remain a major public health challenge, posing a high risk for brain tumor-related morbidity and mortality. However, the mechanisms that drive the development of gliomas remain largely unknown. Emerging evidence has shown that long noncoding RNAs are key factors in glioma pathogenesis. qRT-PCR analysis was used to assess the expression of FTX and miR-342-3p in the different stages of gliomas in tissues. Bioinformatics tool DIANA and TargetSCan were used to predict the targets of FTX and miR-342-3p, respectively...
January 23, 2017: Laboratory Investigation; a Journal of Technical Methods and Pathology
https://www.readbyqxmd.com/read/28110668/a-novel-thermophilic-and-halophilic-esterase-from-janibacter-sp-r02-the-first-member-of-a-new-lipase-family-family-xvii
#20
Agustín Castilla, Paola Panizza, Diego Rodríguez, Luis Bonino, Pilar Díaz, Gabriela Irazoqui, Sonia Rodríguez Giordano
Janibacter sp. strain R02 (BNM 560) was isolated in our laboratory from an Antarctic soil sample. A remarkable trait of the strain was its high lipolytic activity, detected in Rhodamine-olive oil supplemented plates. Supernatants of Janibacter sp. R02 displayed superb activity on transesterification of acyl glycerols, thus being a good candidate for lipase prospection. Considering the lack of information concerning lipases of the genus Janibacter, we focused on the identification, cloning, expression and characterization of the extracellular lipases of this strain...
March 2017: Enzyme and Microbial Technology
keyword
keyword
98359
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"