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nucleic acid databases

Sean M Mythen, Saravanan Devendran, Celia Méndez-García, Isaac Cann, Jason M Ridlon
Gut metagenomic sequences provide a rich source of microbial genes, the majority of which are annotated by homology or unknown. Genes and gene pathways that encode enzymes catalyzing biotransformation of host bile acids are important to identify in gut metagenomic sequences due to the importance of bile acids on gut microbiome structure and host physiology. Hydroxysteroid dehydrogenases (HSDH) are pyridine nucleotide-dependent enzymes with stereo-specificity and regio-specificity for bile acid and steroid hydroxyl groups...
January 12, 2018: Applied and Environmental Microbiology
Daniel J Rigden, Xosé M Fernández
The 2018 Nucleic Acids Research Database Issue contains 181 papers spanning molecular biology. Among them, 82 are new and 84 are updates describing resources that appeared in the Issue previously. The remaining 15 cover databases most recently published elsewhere. Databases in the area of nucleic acids include 3DIV for visualisation of data on genome 3D structure and RNArchitecture, a hierarchical classification of RNA families. Protein databases include the established SMART, ELM and MEROPS while GPCRdb and the newcomer STCRDab cover families of biomedical interest...
January 4, 2018: Nucleic Acids Research
Z Dou, Z Jiang, P L Pan, W L Song, J Xu, Z Y Wu
Objective: To compare the community viral load (CVL) among MSM in 15 cities in China using standardized national reference sources. Methods: The study analyzed the existing database of National Major Science and Technology Project of China. The database was established with serial random survey of MSM HIV CVL among MSM in 15 cities from 2013 to 2015. VL tests were conducted in 15 laboratories with different equipment and methods, including RT-PCR, nucleic acid sequence based amplification (NASBA), branched DNA testing (bDNA) and Abbott M2000 RealTime system (M2000)...
December 10, 2017: Zhonghua Liu Xing Bing Xue za Zhi, Zhonghua Liuxingbingxue Zazhi
Fredmoore L Orosco, Arturo O Lluisma
Marine animals typically harbor a community of viruses, a number of which are known to cause diseases. In shrimp aquaculture, viral pathogens are the principal causes of major economic losses. However, the composition of the viral load of shrimps in wild population is poorly known. In this study, we explored the viral diversity in the microbiome of wild Penaeus monodon collected from six sites in the Philippines, with a view to detecting pathogenic forms. We employed a metagenomic approach via particle-associated nucleic acid isolation, sequence-independent single primer amplification, and pyrosequencing...
September 2017: Virusdisease
Leonie J Barnett, Terrence L Miller
Species-level relationships of a complex of six putative acanthocolpid cercariae with ventral keels from nassariid gastropods from Capricornia, Queensland (Cercaria capricornia I-VI) were explored using mitochondrial and nuclear DNA sequence data. Analysis of the large subunit of nuclear ribosomal DNA (rDNA), the internal transcribed spacer 2 rDNA and subunit 3 of the nicotinamide-adenine-dinucleotide dehydrogenase mitochondrial gene indicates that the six distinct morphotypes previously identified relate to only three discrete genotypes...
December 26, 2017: Parasitology International
Kerri Basile, Jen Kok, Dominic E Dwyer
Successful treatment outcomes for viral respiratory tract infections presenting from primary health care to quaternary hospitals will only be achieved with rapid, sensitive and specific identification of pathogens to allow effective pathogen-specific antiviral therapy and infection control measures. Areas Covered: This review aims to explore the different point-of-care tests currently available to diagnose viral respiratory tract infections, discuss the advantages and limitations of point-of-care testing, and provide insights into the future of point-of-care tests...
December 18, 2017: Expert Review of Molecular Diagnostics
Nelson Gil, Andras Fiser
Motivation: Multiple sequence alignments (MSAs) can provide essential input to many bioinformatics applications, including protein structure prediction and functional annotation. However, the optimal selection of sequences to obtain a biologically informative MSAs for such purposes is poorly-explored, and has traditionally been performed manually. Results: We present SAMMI, an automated, sequence-based approach to objectively select an optimal MSA from a large set of alternatives sampled from a general sequence database search...
December 1, 2017: Bioinformatics
Priscyla Maria Vieira Mendes, Daila Leite Chaves Bezerra, Loanne Rocha Dos Santos, Raísa de Oliveira Santos, Stéfany Rodrigues de Sousa Melo, Jennifer Beatriz Silva Morais, Juliana Soares Severo, Sabas Carlos Vieira, Dilina do Nascimento Marreiro
Breast cancer is a disease of high mortality, characterized by the progressive accumulation of mutations that contribute to the uncontrolled development of breast tissue cells. Literature shows that disturbances in mineral homeostasis, such as magnesium, may interfere with tumor progression. The objective of this study is to provide updated information about magnesium's role in the pathogenesis of breast cancer. A review of literature was carried out from a search for articles in the PubMed and CAPES Periodicals databases published between 1995 and 2016 with the cross-references of the descriptors "magnesium," "breast neoplasms," and "oxidative stress" and the corresponding words in Portuguese...
December 2, 2017: Biological Trace Element Research
Claudio Campa, Carla Enrica Gallenga, Elena Bolletta, Paolo Perri
Background: Gene therapy represents the therapeutic delivery of nucleic acid polymers into a patient's cells with the aim of treating an underlying disease. Over the past 2 decades this new therapy has made substantial progress owing to better understanding of the pathobiologic basis of various diseases coupled with growth of gene transfer biotechnologies. The eye, in particular, represents a suitable target for such therapy due to the immune privilege provided by the blood-ocular barrier, the ability to directly visualize, access and locally treat the cells and the minimal amount of vector needed given the size of this organ...
November 16, 2017: Current Gene Therapy
Ali Amini, Olivia Varsaneux, Helen Kelly, Weiming Tang, Wen Chen, Debrah I Boeras, Jane Falconer, Joseph D Tucker, Roger Chou, Azumi Ishizaki, Philippa Easterbrook, Rosanna W Peeling
BACKGROUND: Chronic Hepatitis B Virus (HBV) infection is characterised by the persistence of hepatitis B surface antigen (HBsAg). Expanding HBV diagnosis and treatment programmes into low resource settings will require high quality but inexpensive rapid diagnostic tests (RDTs) in addition to laboratory-based enzyme immunoassays (EIAs) to detect HBsAg. The purpose of this review is to assess the clinical accuracy of available diagnostic tests to detect HBsAg to inform recommendations on testing strategies in 2017 WHO hepatitis testing guidelines...
November 1, 2017: BMC Infectious Diseases
Weiming Tang, Wen Chen, Ali Amini, Debi Boeras, Jane Falconer, Helen Kelly, Rosanna Peeling, Olivia Varsaneux, Joseph D Tucker, Philippa Easterbrook
BACKGROUND: Although direct-acting antivirals can achieve sustained virological response rates greater than 90% in Hepatitis C Virus (HCV) infected persons, at present the majority of HCV-infected individuals remain undiagnosed and therefore untreated. While there are a wide range of HCV serological tests available, there is a lack of formal assessment of their diagnostic performance. We undertook a systematic review and meta-analysis to evaluate he diagnostic accuracy of available rapid diagnostic tests (RDT) and laboratory based EIA assays in detecting antibodies to HCV...
November 1, 2017: BMC Infectious Diseases
Azumi Ishizaki, Julie Bouscaillou, Niklas Luhmann, Stephanie Liu, Raissa Chua, Nick Walsh, Sarah Hess, Elena Ivanova, Teri Roberts, Philippa Easterbrook
BACKGROUND: There have been few reports on programmatic experience of viral hepatitis testing and treatment in resource-limited settings. To inform the development of the 2017 World Health Organization (WHO) viral hepatitis testing guidance and in particular the feasibility of proposed recommendations, we undertook a survey across a range of organisations engaged with hepatitis testing in low- and middle-income countries (LMICs). Our objective was to describe current hepatitis B and C testing practices across a range of settings in different countries, as well as key barriers or challenges encountered and proposed solutions to promote testing scale-up...
November 1, 2017: BMC Infectious Diseases
(no author information available yet)
The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed database of citations and abstracts for published life science journals. The Entrez system provides search and retrieval operations for most of these data from 39 distinct databases. The E-utilities serve as the programming interface for the Entrez system. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets...
November 13, 2017: Nucleic Acids Research
Welkin H Pope, Deborah Jacobs-Sera
Current sequencing technologies allow for the rapid and inexpensive sequencing of complete bacteriophage genomes, using small quantities of nucleic acid as starting material. Determination of the location and function of the gene features within the genome sequence, or annotation, is a necessary next step prior to submission to a public database, publication in a scientific journal, or advanced comparative genomic and proteomic studies. Gene prediction can be largely accomplished through the use of several freely available programs...
2018: Methods in Molecular Biology
Hui Liu, Huaizhi Wang, Zhen Wei, Songyao Zhang, Gang Hua, Shao-Wu Zhang, Lin Zhang, Shou-Jiang Gao, Jia Meng, Xing Chen, Yufei Huang
Methyltranscriptome is an exciting new area that studies the mechanisms and functions of methylation in transcripts. A knowledge base with the systematic collection and curation of context specific transcriptome-wide methylations is critical for elucidating their biological functions as well as for developing bioinformatics tools. Since its inception in 2014, the Met-DB (Liu, H., Flores, M.A., Meng, J., Zhang, L., Zhao, X., Rao, M.K., Chen, Y. and Huang, Y. (2015) MeT-DB: a database of transcriptome methylation in mammalian cells...
November 8, 2017: Nucleic Acids Research
Chang Chen, Shadi Zabad, Haipeng Liu, Wangfei Wang, Constance Jeffery
MoonProt 2.0 ( is an updated, comprehensive and open-access database storing expert-curated annotations for moonlighting proteins. Moonlighting proteins contain two or more physiologically relevant distinct functions performed by a single polypeptide chain. Here, we describe developments in the MoonProt website and database since our previous report in the Database Issue of Nucleic Acids Research. For this V 2.0 release, we expanded the number of proteins annotated to 370 and modified several dozen protein annotations with additional or updated information, including more links to protein structures in the Protein Data Bank, compared with the previous release...
November 6, 2017: Nucleic Acids Research
Camilla Sekse, Arne Holst-Jensen, Ulrich Dobrindt, Gro S Johannessen, Weihua Li, Bjørn Spilsberg, Jianxin Shi
High-throughput sequencing (HTS) is becoming the state-of-the-art technology for typing of microbial isolates, especially in clinical samples. Yet, its application is still in its infancy for monitoring and outbreak investigations of foods. Here we review the published literature, covering not only bacterial but also viral and Eukaryote food pathogens, to assess the status and potential of HTS implementation to inform stakeholders, improve food safety and reduce outbreak impacts. The developments in sequencing technology and bioinformatics have outpaced the capacity to analyze and interpret the sequence data...
2017: Frontiers in Microbiology
Ulrike Wittig, Maja Rey, Andreas Weidemann, Renate Kania, Wolfgang Müller
SABIO-RK ( is a manually curated database containing data about biochemical reactions and their reaction kinetics. The data are primarily extracted from scientific literature and stored in a relational database. The content comprises both naturally occurring and alternatively measured biochemical reactions and is not restricted to any organism class. The data are made available to the public by a web-based search interface and by web services for programmatic access. In this update we describe major improvements and extensions of SABIO-RK since our last publication in the database issue of Nucleic Acid Research (2012)...
October 30, 2017: Nucleic Acids Research
Alejandro A Schäffer, Eric P Nawrocki, Yoon Choi, Paul A Kitts, Ilene Karsch-Mizrachi, Richard McVeigh
Motivation: Nucleic acid sequences in public databases should not contain vector contamination, but many sequences in GenBank do (or did) contain vectors. The National Center for Biotechnology Information (NCBI) uses the program VecScreen to screen submitted sequences for contamination. Additional tools are needed to distinguish true positive (contamination) from false positive (not contamination) VecScreen matches. Results: A principal reason for false positive VecScreen matches is that the sequence and the matching vector subsequence originate from closely related or identical organisms (for example, both originate in E...
October 23, 2017: Bioinformatics
Pierre Cappy, Alice Moisan, Fabienne De Oliveira, Jean-Christophe Plantier, Matteo Negroni
To generate the long-terminal repeats (LTR) that border the integrated viral genome, two-strand transfer steps must occur during reverse transcription. Analysis of the genetic polymorphisms that are present in the LTR of HIV-1 heterozygous virions in single infection cycle studies has revealed which of the two copies of genomic RNAs is used for each transfer event. Thus, the first event of strand transfer has been described to be either intra- or intermolecular, while the second event is generally intramolecular...
October 20, 2017: Scientific Reports
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