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nucleic acid databases

Lars Hahn, Chris-André Leimeister, Rachid Ounit, Stefano Lonardi, Burkhard Morgenstern
Many algorithms for sequence analysis rely on word matching or word statistics. Often, these approaches can be improved if binary patterns representing match and don't-care positions are used as a filter, such that only those positions of words are considered that correspond to the match positions of the patterns. The performance of these approaches, however, depends on the underlying patterns. Herein, we show that the overlap complexity of a pattern set that was introduced by Ilie and Ilie is closely related to the variance of the number of matches between two evolutionarily related sequences with respect to this pattern set...
October 2016: PLoS Computational Biology
Homa Hajjaran, Maryam Mahdi, Mehdi Mohebali, Katayoun Samimi-Rad, Angila Ataei-Pirkooh, Elham Kazemi-Rad, Saied Reza Naddaf, Reza Raoofian
Leishmania RNA virus (LRV) was first detected in members of the subgenus Leishmania (Viannia), and later, the virulence and metastasis of the New World species were attributed to this virus. The data on the presence of LRV in Old World species are confined to Leishmania major and a few Leishmania aethiopica isolates. The aim of this study was to survey the presence of LRV in various Iranian Leishmania species originating from patients and animal reservoir hosts. Genomic nucleic acids were extracted from 50 cultured isolates belonging to the species Leishmania major, Leishmania tropica, and Leishmania infantum...
December 2016: Archives of Virology
Martijn J C van Herwijnen, Marijke I Zonneveld, Soenita Goerdayal, Esther N M Nolte-'t Hoen, Johan Garssen, Bernd Stahl, A F Maarten Altelaar, Frank A Redegeld, Marca H M Wauben
Breast milk contains several macromolecular components with distinctive functions, whereby milk fat globules and casein micelles mainly provide nutrition to the newborn, while whey contains molecules that can stimulate the newborn's developing immune system and gastrointestinal tract. Although extracellular vesicles (EV) have been identified in breast milk, their physiological function and composition has not been addressed in detail. EV are submicron sized vehicles released by cells for intercellular communication via selectively incorporated lipids, nucleic acids and proteins...
September 6, 2016: Molecular & Cellular Proteomics: MCP
Indira Cruz-Plancarte, Adrián Cazares, Gabriel Guarneros
: Previously, a collection of virulent phages infecting Pseudomonas aeruginosa were isolated from open water reservoirs and residual waters. Here, we described the comparative genomics of a set of five related phages from the collection, the physical structure of the genome, the structural proteomics of the virion and the transcriptional program of archetypal phage PaMx41. The phage genomes were closely associated with each other and with those of two other P. aeruginosa phages, 119X and PaP2, previously filed in the databases...
September 2, 2016: Applied and Environmental Microbiology
Alexandra Paulo, Ana Paula Francisco
Nucleic acids are prone to structural polymorphism and a number of structures may be formed in addition to the well-known DNA double helix. Among these is a family of nucleic acid four-stranded structures known as G-quadruplexes (G4). These quadruplex structures can be formed by sequences containing repetitive guanine-rich tracks and the analysis of Non-B-DNA database indicated an enrichment of these sequences in genomic regions controlling cellular proliferation, such as for example in the promoter regions of c-MYC, k-RAS, c-KIT, HSP90 and VEGF among others...
August 29, 2016: Current Medicinal Chemistry
Roger Y Dodd, Edward P Notari, Diane Nelson, Gregory A Foster, David E Krysztof, Zhanna Kaidarova, Lisa Milan-Benson, Debra A Kessler, Beth H Shaz, Farnaz Vahidnia, Brian Custer, Susan L Stramer
BACKGROUND: The frequency of positive test results for transfusion-transmitted infections (TTIs) among blood donors is an important index of safety; thus, appropriate monitoring is critical, particularly when there are changes in policies affecting donor suitability. STUDY DESIGN AND METHODS: Testing algorithms from three large blood systems were reviewed and consensus definitions for a surveillance-positive result for hepatitis B virus (HBV), hepatitis C virus (HCV), human immunodeficiency virus (HIV), and human T-cell lymphotropic virus (HTLV) established...
August 25, 2016: Transfusion
Jeremy F Taylor, Lynsey K Whitacre, Jesse L Hoff, Polyana C Tizioto, JaeWoo Kim, Jared E Decker, Robert D Schnabel
BACKGROUND: Decreasing sequencing costs and development of new protocols for characterizing global methylation, gene expression patterns and regulatory regions have stimulated the generation of large livestock datasets. Here, we discuss experiences in the analysis of whole-genome and transcriptome sequence data. METHODS: We analyzed whole-genome sequence (WGS) data from 132 individuals from five canid species (Canis familiaris, C. latrans, C. dingo, C. aureus and C...
2016: Genetics, Selection, Evolution: GSE
Takeshi Kawabata
The HOMCOS server ( ) was updated for both searching and modeling the 3D complexes for all molecules in the PDB. As compared to the previous HOMCOS server, the current server targets all of the molecules in the PDB including proteins, nucleic acids, small compounds and metal ions. Their binding relationships are stored in the database. Five services are available for users. For the services "Modeling a Homo Protein Multimer" and "Modeling a Hetero Protein Multimer", a user can input one or two proteins as the queries, while for the service "Protein-Compound Complex", a user can input one chemical compound and one protein...
August 13, 2016: Journal of Structural and Functional Genomics
Marcin Kowiel, Dariusz Brzezinski, Mariusz Jaskolski
The refinement of macromolecular structures is usually aided by prior stereochemical knowledge in the form of geometrical restraints. Such restraints are also used for the flexible sugar-phosphate backbones of nucleic acids. However, recent highly accurate structural studies of DNA suggest that the phosphate bond angles may have inadequate description in the existing stereochemical dictionaries. In this paper, we analyze the bonding deformations of the phosphodiester groups in the Cambridge Structural Database, cluster the studied fragments into six conformation-related categories and propose a revised set of restraints for the O-P-O bond angles and distances...
September 30, 2016: Nucleic Acids Research
Ozge Cevik, Ahmet Tarik Baykal, Azize Sener
Platelets play a crucial role in the pathogenesis of stroke and antiplatelet agents exist for its treatment and prevention. Through the use of LC-MS based protein expression profiling, platelets from stroke patients were analyzed and then correlated with the proteomic analyses results in the context of this disease. This study was based on patients who post ischemic stroke were admitted to hospital and had venous blood drawn within 24 hrs of the incidence. Label-free protein expression analyses of the platelets' tryptic digest was performed in triplicate on a UPLC-ESI-qTOF-MS/MS system and ProteinLynx Global Server (v2...
2016: PloS One
J Morgan Freiman, Trang M Tran, Samuel G Schumacher, Laura F White, Stefano Ongarello, Jennifer Cohn, Philippa J Easterbrook, Benjamin P Linas, Claudia M Denkinger
BACKGROUND: Diagnosis of chronic hepatitis C virus (HCV) infection requires both a positive HCV antibody screen and confirmatory nucleic acid testing (NAT). Testing for hepatitis C virus core antigen (HCVcAg) is a potential alternative to NAT. PURPOSE: To evaluate the accuracy of diagnosis of active HCV infection among adults and children for 5 HCVcAg tests compared with NAT. DATA SOURCES: EMBASE, PubMed, Web of Science, Scopus, and Cochrane Database of Systematic Reviews from 1990 through 31 March 2016...
September 6, 2016: Annals of Internal Medicine
Taichiro Ishige, Hiromi Hara, Takashi Hirano, Tomohiro Kono, Kei Hanzawa
Liver-expressed antimicrobial peptide 2 (LEAP-2) is a cationic peptide that plays an important role in innate immunity for host defense. The aim of this study was to characterize the LEAP-2 gene in the Japanese quail (Coturnix japonica). Japanese quail LEAP-2 (CjLEAP-2) was identified from the Japanese quail draft genome database by a local BLAST analysis using chicken LEAP-2 (GgLEAP-2). The exon-intron structure of CjLEAP-2, analyzed from three quails, is composed of three exons, as is the chicken LEAP-2 homolog (GgLEAP-2)...
September 2016: Animal Science Journal, Nihon Chikusan Gakkaihō
Sunghwan Kim, Paul A Thiessen, Tiejun Cheng, Bo Yu, Benjamin A Shoemaker, Jiyao Wang, Evan E Bolton, Yanli Wang, Stephen H Bryant
BACKGROUND: PubChem is an open archive consisting of a set of three primary public databases (BioAssay, Compound, and Substance). It contains information on a broad range of chemical entities, including small molecules, lipids, carbohydrates, and (chemically modified) amino acid and nucleic acid sequences (including siRNA and miRNA). Currently (as of Nov. 2015), PubChem contains more than 150 million depositor-provided chemical substance descriptions, 60 million unique chemical structures, and 225 million biological activity test results provided from over 1 million biological assay records...
2016: Journal of Cheminformatics
Mohammed Fawaz, Periyasamy Vijayakumar, Anamika Mishra, Pradeep N Gandhale, Rupam Dutta, Nitin M Kamble, Shashi B Sudhakar, Parimal Roychoudhary, Himanshu Kumar, Diwakar D Kulkarni, Ashwin Ashok Raut
BACKGROUND: Ducks (Anas platyrhynchos) an economically important waterfowl for meat, eggs and feathers; is also a natural reservoir for influenza A viruses. The emergence of novel viruses is attributed to the status of co-existence of multiple types and subtypes of viruses in the reservoir hosts. For effective prediction of future viral epidemic or pandemic an in-depth understanding of the virome status in the key reservoir species is highly essential. METHODS: To obtain an unbiased measure of viral diversity in the enteric tract of ducks by viral metagenomic approach, we deep sequenced the viral nucleic acid extracted from cloacal swabs collected from the flock of 23 ducks which shared the water bodies with wild migratory birds...
2016: Gut Pathogens
Jin Zhu, Yuehua Zhang, Weichen Zhang, Wei Zhang, Linni Fan, Lu Wang, Yixiong Liu, Shasha Liu, Ying Guo, Yingmei Wang, Jun Yi, Qingguo Yan, Zhe Wang, Gaosheng Huang
BACKGROUND: MicroRNAs have the potential as diagnostic biomarkers and therapeutic targets in autoimmune diseases. However, very limited studies have evaluated the expression of microRNA profile in thyroid gland related to Hashimoto's thyroiditis (HT). METHODS: MicroRNA microarray expression profiling was performed and validated by quantitative RT-PCR. The expression pattern of miR-142-5p was detected using locked nucleic acid-in situ hybridization. The target gene was predicted and validated using miRNA targets prediction database, gene expression analysis, quantitative RT-PCR, western blot, and luciferase assay...
2016: Journal of Translational Medicine
Luciano A Abriata
This Briefing reviews the widely used, currently active, up-to-date databases derived from the worldwide Protein Data Bank (PDB) to facilitate browsing, finding and exploring its entries. These databases contain visualization and analysis tools tailored to specific kinds of molecules and interactions, often including also complex metrics precomputed by experts or external programs, and connections to sequence and functional annotation databases. Importantly, updates of most of these databases involves steps of curation and error checks based on specific expertise about the subject molecules or interactions, and removal of sequence redundancy, both leading to better data sets for mining studies compared with the full list of raw PDB entries...
June 5, 2016: Briefings in Bioinformatics
Ezra D Mirvish, Masahiro Shuda
Over 20% of human cancers worldwide are associated with infectious agents, including viruses, bacteria, and parasites. Various methods have been used to identify human tumor viruses, including electron microscopic observations of viral particles, immunologic screening, cDNA library screening, nucleic acid hybridization, consensus PCR, viral DNA array chip, and representational difference analysis. With the Human Genome Project, a large amount of genetic information from humans and other organisms has accumulated over the last decade...
2016: Frontiers in Microbiology
Maunank Shah, Colleen Hanrahan, Zhuo Yu Wang, Nandini Dendukuri, Stephen D Lawn, Claudia M Denkinger, Karen R Steingart
BACKGROUND: Rapid detection of tuberculosis (TB) among people living with human immunodeficiency virus (HIV) is a global health priority. HIV-associated TB may have different clinical presentations and is challenging to diagnose. Conventional sputum tests have reduced sensitivity in HIV-positive individuals, who have higher rates of extrapulmonary TB compared with HIV-negative individuals. The lateral flow urine lipoarabinomannan assay (LF-LAM) is a new, commercially available point-of-care test that detects lipoarabinomannan (LAM), a lipopolysaccharide present in mycobacterial cell walls, in people with active TB disease...
2016: Cochrane Database of Systematic Reviews
Katharina J Huber, Alicia M Geppert, Gerhard Wanner, Bärbel U Fösel, Pia K Wüst, Jörg Overmann
Members of the phylum Acidobacteria are abundant in a wide variety of soil environments. Despite this, previous cultivation attempts have frequently failed to retrieve representative phylotypes of Acidobacteria, which have, therefore, been discovered by culture-independent methods (13175 acidobacterial sequences in the SILVA database version 123; NR99) and only 47 species have been described so far. Strain Ac_5_C6T represents the first isolate of the globally widespread and abundant subdivision 6 Acidobacteria and is described in the present study...
August 2016: International Journal of Systematic and Evolutionary Microbiology
Jihoon Jo, Jongsun Park, Hyun-Gwan Lee, Elizabeth M A Kern, Seongmin Cheon, Soyeong Jin, Joong-Ki Park, Sung-Jin Cho, Chungoo Park
The sea cucumber Apostichopus japonicus Selenka 1867 represents an important resource in biomedical research, traditional medicine, and the seafood industry. Much of the commercial value of A. japonicus is determined by dorsal/ventral color variation (red, green, and black), yet the taxonomic relationships between these color variants are not clearly understood. We performed the first comparative analysis of de novo assembled transcriptome data from three color variants of A. japonicus. Using the Illumina platform, we sequenced nearly 177,596,774 clean reads representing a total of 18...
August 2016: Marine Genomics
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