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https://www.readbyqxmd.com/read/28090096/a-bioinformatics-practicum-to-develop-student-understanding-of-immunological-rejection-of-protein-drugs
#1
Lauren A O'Donnell, Wilson S Meng, Benjamin J Andrick, Alexa M Borello
Objectives. To design and implement a bioinformatics exercise that applies immunological principles to predicting rejection of protein drugs based upon patient genotype. Design. Doctor of pharmacy (PharmD) students used the Immune Epitope Database, a freely available bioinformatics tool. Over a 2-week laboratory, students interrogated whether a protein drug would be predicted to induce an immune response based upon patient genotype. Results were presented at the last laboratory session, and students completed reports discussing their findings...
November 25, 2016: American Journal of Pharmaceutical Education
https://www.readbyqxmd.com/read/28077566/duplicates-redundancies-and-inconsistencies-in-the-primary-nucleotide-databases-a-descriptive-study
#2
Qingyu Chen, Justin Zobel, Karin Verspoor
GenBank, the EMBL European Nucleotide Archive and the DNA DataBank of Japan, known collectively as the International Nucleotide Sequence Database Collaboration or INSDC, are the three most significant nucleotide sequence databases. Their records are derived from laboratory work undertaken by different individuals, by different teams, with a range of technologies and assumptions and over a period of decades. As a consequence, they contain a great many duplicates, redundancies and inconsistencies, but neither the prevalence nor the characteristics of various types of duplicates have been rigorously assessed...
2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/28068515/comparative-analysis-of-amino-acid-composition-in-the-active-site-of-nirk-gene-encoding-copper-containing-nitrite-reductase-cunir-in-bacterial-spp
#3
Utpal Kumar Adhikari, M Mizanur Rahman
The nirk gene encoding the copper-containing nitrite reductase (CuNiR), a key catalytic enzyme in the environmental denitrification process that helps to produce nitric oxide from nitrite. The molecular mechanism of denitrification process is definitely complex and in this case a theoretical investigation has been conducted to know the sequence information and amino acid composition of the active site of CuNiR enzyme using various Bioinformatics tools. 10 Fasta formatted sequences were retrieved from the NCBI database and the domain and disordered regions identification and phylogenetic analyses were done on these sequences...
December 31, 2016: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28066818/microbiome-helper-a-custom-and-streamlined-workflow-for-microbiome-research
#4
André M Comeau, Gavin M Douglas, Morgan G I Langille
Sequence-based approaches to study microbiomes, such as 16S rRNA gene sequencing and metagenomics, are uncovering associations between microbial taxa and a myriad of factors. A drawback of these approaches is that the necessary sequencing library preparation and bioinformatic analyses are complicated and continuously changing, which can be a barrier for researchers new to the field. We present three essential components to conducting a microbiome experiment from start to finish: first, a simplified and step-by-step custom gene sequencing protocol that requires limited lab equipment, is cost-effective, and has been thoroughly tested and utilized on various sample types; second, a series of scripts to integrate various commonly used bioinformatic tools that is available as a standalone installation or as a single downloadable virtual image; and third, a set of bioinformatic workflows and tutorials to provide step-by-step guidance and education for those new to the microbiome field...
January 2017: MSystems
https://www.readbyqxmd.com/read/28064023/identification-and-characterization-of-a-gamma-interferon-inducible-lysosomal-thiol-reductase-homolog-from-guinea-pig-cavia-porcellus-that-exhibits-thiol-reductase-activity-in-vitro
#5
Lei Ma, Fang Cao, Runze Tang, Jiaxin Zhang, Shuangquan Zhang
Gamma-interferon-inducible lysosomal thiol reductase (GILT) is a key enzyme in the antigen processing and presentation pathway whereby it reduces disulfide bonds at an acidic pH. In this study, a homolog of GILT from guinea pigs (designated gpGILT) was identified and characterized using bioinformatic methods and bioactivity assays. The open reading frame of gpGILT is 705bp in length and encodes 234 amino acids, with a putative molecular weight of about 25.85kDa. The structure of gpGILT is similar to those of humans and zebrafish, containing six introns and seven exons...
December 28, 2016: Research in Veterinary Science
https://www.readbyqxmd.com/read/28062316/discovery-of-streptococcus-pneumoniae-serogroup-35-variants-in-australian-patients
#6
Megan Staples, Rikki M A Graham, Vicki Hicks, Janet Strachan, Anders Gonçalves da Silva, Jade Peverall, Veyatie Wicks, Amy V Jennison
OBJECTIVES: S. pneumoniae isolates from Australian invasive pneumococcal disease cases displaying an atypical 35B phenotype. Whole genome sequencing was used to analyse these strains and identify changes to the capsule gene regions. METHODS: Four atypical serogroup 35 isolates from Australian reference laboratories were unable to be assigned to one of the four known group 35 serotypes by the Quellung serotyping method. Genetic characterisation of the capsule locus was performed by bioinformatic analysis of whole genome sequencing data for all isolates RESULTS: Genetic analysis identified four independent disruptions to the wciG gene, which encodes an O-acetyltransferase responsible for the O-acetylation of the 6Galβ1 residue in the capsular polysaccharide repeat unit of serotype 35B...
January 3, 2017: Clinical Microbiology and Infection
https://www.readbyqxmd.com/read/28057679/spot-ligand-2-improving-structure-based-virtual-screening-by-binding-homology-search-on-an-expanded-structural-template-library
#7
Thomas Litfin, Yaoqi Zhou, Yuedong Yang
MOTIVATION: The high cost of drug discovery motivates the development of accurate virtual screening tools. Binding-homology, which takes advantage of known protein-ligand binding pairs, has emerged as a powerful discrimination technique. In order to exploit all available binding data, modelled structures of ligand-binding sequences may be used to create an expanded structural binding template library. RESULTS: SPOT-Ligand 2 has demonstrated significantly improved screening performance over its previous version by expanding the template library 15 times over the previous one...
January 5, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28057186/identification-of-genomic-somatic-variants-in-cancer-from-discovery-to-actionability
#8
G L Fawcett, A Karina Eterovic
The perfect method to discover and validate actionable somatic variants in cancer has not yet been developed, yet significant progress has been made toward this goal. There have been huge increases in the throughput and cost of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) sequencing technologies that have led to the burgeoning possibility of using sequencing data in clinical settings. Discovery of somatic mutations is relatively simple and has been improved recently due to laboratory methods optimization, bioinformatics algorithms development, and the expansion of various databases of population genomic information...
2017: Advances in Clinical Chemistry
https://www.readbyqxmd.com/read/28054304/comparative-analysis-of-drosophila-melanogaster-gut-microbiota-with-respect-to-host-strain-sex-and-age
#9
Gangsik Han, Hyo Jung Lee, Sang Eun Jeong, Che Ok Jeon, Seogang Hyun
Microbiota has a significant impact on the health of the host individual. The complexity of the interactions between mammalian hosts and their microbiota highlights the value of using Drosophila melanogaster as a model organism, because of its relatively simple microbial community and ease of physiological and genetic manipulation. However, highly variable and sometimes inconsistent results regarding the microbiota of D. melanogaster have been reported for host samples collected from different geographical locations; discrepancies that may be because of the inherent physiological conditions of the D...
January 4, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28043601/best-approaches-to-drug-resistance-surveillance-at-the-country-level
#10
A M Cabibbe, D M Cirillo
In 2014, the World Health Organization (WHO) recommendation to include the endorsed rapid molecular technologies (Xpert MTB/RIF, line probe assays) into surveillance systems and surveys allowed the testing of more tuberculosis (TB) patients for drug resistance at country level than ever before. The whole genome sequencing (WGS) approach is emerging as a more powerful tool for epidemiological and drug-resistant routine surveillances, promising a rapid and simultaneous screening of all the clinically-relevant mutations for the determination of resistance to the first-, second-line, and new anti-TB drugs...
December 2016: International Journal of Mycobacteriology
https://www.readbyqxmd.com/read/28035420/argininosuccinate-lyase-interacts-with-cyclin-a2-in-cytoplasm-and-modulates-growth-of-liver-tumor-cells
#11
Yu-Hsuan Hung, Hau-Lun Huang, Wei-Ching Chen, Meng-Chi Yen, Chien-Yu Cho, Tzu-Yang Weng, Chih-Yang Wang, Yi-Ling Chen, Li-Tzong Chen, Ming-Derg Lai
Arginine is a critical amino acid in specific cancer types including hepatocellular carcinoma (HCC) and melanoma. Novel molecular mechanisms and therapeutic targets in arginine metabolism-mediated cancer formation await further identification. Our laboratory has previously demonstrated that arginine metabolic enzyme argininosuccinate lyase (ASL) promoted HCC formation in part via maintenance of cyclin A2 protein expression and arginine production for channeling to nitric oxide synthase. In this study, we investigated the mechanism by which ASL regulates cyclin A2 expression...
February 2017: Oncology Reports
https://www.readbyqxmd.com/read/28035028/sexy-a-tool-for-sex-inference-from-genotype-arrays
#12
David C Qian, Jonathan A Busam, Xiangjun Xiao, Tracy A O'Mara, Rosalind A Eeles, Frederick R Schumacher, Catherine M Phelan, Christopher I Amos
MOTIVATION: Checking concordance between reported sex and genotype-inferred sex is a crucial quality control measure in genome-wide association studies (GWAS). However, limited insights exist regarding the true accuracy of software that infer sex from genotype array data. RESULTS: We present seXY, a logistic regression model trained on both X chromosome heterozygosity and Y chromosome missingness, that consistently demonstrated >99.5% sex inference accuracy in cross-validation for 889 males and 5,361 females enrolled in prostate cancer and ovarian cancer GWAS...
December 28, 2016: Bioinformatics
https://www.readbyqxmd.com/read/28031438/integrating-advanced-molecular-technologies-into-public-health
#13
Marta Gwinn, Duncan R MacCannell, Rima F Khabbaz
Advances in laboratory and information technologies are transforming public health microbiology. High-throughput genome sequencing and bioinformatics are enhancing our ability to investigate and control outbreaks, detect emerging infectious diseases, develop vaccines, and combat antimicrobial resistance-all with increased accuracy, timeliness, and efficiency. The Advanced Molecular Detection (AMD) initiative has allowed the Centers for Disease Control and Prevention (CDC) to provide leadership and coordination in integrating new technologies into routine practice throughout the US public health laboratory system...
December 28, 2016: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28011785/wright-fisher-exact-solver-wfes-scalable-analysis-of-population-genetic-models-without-simulation-or-diffusion-theory
#14
Ivan Krukov, Bianca de Sanctis, A P Jason de Koning
MOTIVATION: The simplifying assumptions that are used widely in theoretical population genetics may not always be appropriate for empirical population genetics. General computational approaches that do not require the assumptions of classical theory are therefore quite desirable. One such general approach is provided by the theory of absorbing Markov chains, which can be used to obtain exact results by directly analyzing population genetic Markov models, such as the classic bi-allelic Wright-Fisher model...
December 23, 2016: Bioinformatics
https://www.readbyqxmd.com/read/28011771/improving-protein-disorder-prediction-by-deep-bidirectional-long-short-term-memory-recurrent-neural-networks
#15
Jack Hanson, Yuedong Yang, Kuldip Paliwal, Yaoqi Zhou
MOTIVATION: Capturing long-range interactions between structural but not sequence neighbors of proteins is a long-standing challenging problem in bioinformatics. Recently, long short-term memory (LSTM) networks have significantly improved the accuracy of speech and image classification problems by remembering useful past information in long sequential events. Here, we have implemented deep bidirectional LSTM recurrent neural networks in the problem of protein intrinsic disorder prediction...
December 22, 2016: Bioinformatics
https://www.readbyqxmd.com/read/28009051/a-brief-primer-on-genomic-epidemiology-lessons-learned-from-mycobacterium-tuberculosis
#16
Jennifer L Guthrie, Jennifer L Gardy
Genomics is now firmly established as a technique for the investigation and reconstruction of communicable disease outbreaks, with many genomic epidemiology studies focusing on revealing transmission routes of Mycobacterium tuberculosis. In this primer, we introduce the basic techniques underlying transmission inference from genomic data, using illustrative examples from M. tuberculosis and other pathogens routinely sequenced by public health agencies. We describe the laboratory and epidemiological scenarios under which genomics may or may not be used, provide an introduction to sequencing technologies and bioinformatics approaches to identifying transmission-informative variation and resistance-associated mutations, and discuss how variation must be considered in the light of available clinical and epidemiological information to infer transmission...
December 23, 2016: Annals of the New York Academy of Sciences
https://www.readbyqxmd.com/read/28008714/bioinformatic-tools-for-analysis-of-clip-ribonucleoprotein-data
#17
REVIEW
Supriyo De, Myriam Gorospe
Investigating the interactions of RNA-binding proteins (RBPs) with RNAs is a complex task for molecular and computational biologists. The molecular biology techniques and the computational approaches to understand RBP-RNA (or ribonucleoprotein, RNP) interactions have advanced considerably over the past few years and numerous and diverse software tools have been developed to analyze these data. Accordingly, laboratories interested in RNP biology face the challenge of choosing adequately among the available software tools those that best address the biological problem they are studying...
December 23, 2016: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/28007010/genetic-analysis-of-a-hereditary-factor-xii-deficiency-pedigree-of-a-consanguineous-marriage-due-to-a-homozygous-f12-gene-mutation-gly341arg
#18
Xiaoli Cheng, Lihong Yang, Guoyong Huang, Yanhui Jin, Xiuping Hao, Mingshan Wang
OBJECTIVE AND IMPORTANCE: To study the gene mutations of factor XII (FXII) in a Chinese family of consanguineous marriage with FXII deficiency and illuminate the possible molecular pathogenic mechanism. It will contribute to our comprehension of the pathogenesis of the disease. CLINICAL PRESENTATION: The proband was a 26-year-old Chinese pregnant woman who was discovered, in a pregnancy test, with a prolonged activated partial thromboplastin time (APTT) at 61.6s (reference range, 29...
December 22, 2016: Hematology (Amsterdam, Netherlands)
https://www.readbyqxmd.com/read/28003256/recycler-an-algorithm-for-detecting-plasmids-from-de-novo-assembly-graphs
#19
Roye Rozov, Aya Brown Kav, David Bogumil, Naama Shterzer, Eran Halperin, Itzhak Mizrahi, Ron Shamir
MOTIVATION: Plasmids and other mobile elements are central contributors to microbial evolution and genome innovation. Recently, they have been found to have important roles in antibiotic resistance and in affecting production of metabolites used in industrial and agricultural applications. However, their characterization through deep sequencing remains challenging, in spite of rapid drops in cost and throughput increases for sequencing. Here, we attempt to ameliorate this situation by introducing a new circular element assembly algorithm, leveraging assembly graphs provided by a conventional de novo assembler and alignments of paired-end reads to assemble cyclic sequences likely to be plasmids, phages and other circular elements...
December 21, 2016: Bioinformatics
https://www.readbyqxmd.com/read/27993789/spadevizr-an-r-package-for-visualization-analysis-and-integration-of-spade-results
#20
Guillaume Gautreau, David Pejoski, Roger Le Grand, Antonio Cosma, Anne-Sophie Beignon, Nicolas Tchitchek
MOTIVATION: Flow, hyperspectral and mass cytometry are experimental techniques measuring cell marker expressions at the single cell level. The recent increase of the number of markers simultaneously measurable has led to the development of new automatic gating algorithms. Especially, the SPADE algorithm has been proposed as a novel way to identify clusters of cells having similar phenotypes in high-dimensional cytometry data. While SPADE or other cell clustering algorithms are powerful approaches, complementary analysis features are needed to better characterize the identified cell clusters...
December 19, 2016: Bioinformatics
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