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nucleic acid databases

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https://www.readbyqxmd.com/read/28291811/systematic-identification-and-characterization-of-long-non-coding-rnas-in-mouse-mature-sperm
#1
Xiaoning Zhang, Fengxin Gao, Jianbo Fu, Peng Zhang, Yuqing Wang, Xuhui Zeng
Increasing studies have shown that mature spermatozoa contain many transcripts including mRNAs and miRNAs. However, the expression profile of long non-coding RNAs (lncRNAs) in mammalian sperm has not been systematically investigated. Here, we used highly purified RNA to investigate lncRNA expression profiles in mouse mature sperm by stranded-specific RNA-seq. We identified 20,907 known and 4,088 novel lncRNAs transcripts, and the existence of intact lncRNAs was confirmed by RT-PCR and fluorescence in situ hybridization on two representative lncRNAs...
2017: PloS One
https://www.readbyqxmd.com/read/28287524/a-web-tool-for-generating-high-quality-machine-readable-biological-pathways
#2
Miguel Ramirez-Gaona, Ana Marcu, Allison Pon, Jason Grant, Anthony Wu, David S Wishart
PathWhiz is a web server built to facilitate the creation of colorful, interactive, visually pleasing pathway diagrams that are rich in biological information. The pathways generated by this online application are machine-readable and fully compatible with essentially all web-browsers and computer operating systems. It uses a specially developed, web-enabled pathway drawing interface that permits the selection and placement of different combinations of pre-drawn biological or biochemical entities to depict reactions, interactions, transport processes and binding events...
February 8, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28266272/multiscale-molecular-simulations-applied-to-nucleic-acid-dendrimer-interactions-studies
#3
Fernando Danilo González-Nilo, Ingrid Araya-Durán, Valeria Márquez-Miranda
BACKGROUND: Dendrimers are monodisperse, regular, three-dimensional and small-scale macromolecules that can be used to release substances such as drugs, markers, and genetic material into the cells. Among these substances, nucleic acids such as plasmid DNA, antisense oligonucleotides (asODN), and small-interfering RNA (siRNA) are widely used as therapeutic macromolecules for the treatment and prevention of diverse diseases. Several studies were focused on the modification of dendrimers aiming to improve their affinity for nucleic acids and their ability to release nucleic acids inside the cells...
March 5, 2017: Current Pharmaceutical Design
https://www.readbyqxmd.com/read/28263762/development-and-evaluation-of-taqman-real-time-pcr-assay-for-detection-of-beak-and-feather-disease-virus
#4
Lenka Černíková, Eliška Vitásková, Alexander Nagy
Psittacine beak and feather disease (PBFD) is one of the most significant viral diseases in psittacine birds. The aim of the presented study was to develop a highly specific and sensitive TaqMan real-time PCR assay for universal detection of beak and feather disease virus (BFDV). Primers and a hydrolysis probe were selected on the highly conserved regions belonging to the ORF1 of the BFDV genome which were identified by aligning 814 genomic sequences downloaded from the GenBank database. The evaluation of the reaction parameters suggested a reaction efficiency of 97...
March 2, 2017: Journal of Virological Methods
https://www.readbyqxmd.com/read/28188804/metabolite-profiling-of-infection-associated-metabolic-markers-of-onchocerciasis
#5
Sasisekhar Bennuru, Sara Lustigman, David Abraham, Thomas B Nutman
The global efforts for onchocerciasis elimination may require additional tools (safe micro and macrofilaricidal drugs, vaccines and biomarkers) as elimination efforts move toward the "end game". Efforts toward the identification of suitable biomarkers have focused on specific protein(s) and/or nucleic acids, but metabolites present an alternative option as they have limited half-lives and are the result of combinatorial effects. In comparison to previously used methodology of LC-MS for metabolomic approaches, we used a non-targeted capillary electrophoresis time-of-flight mass spectrometry (CE-TOFMS) to analyze the serum metabolic profiles of Ov-infected and -uninfected individuals (n=20)...
February 8, 2017: Molecular and Biochemical Parasitology
https://www.readbyqxmd.com/read/28165358/extending-immunological-profiling-in-the-gilthead-sea-bream-sparus-aurata-by-enriched-cdna-library-analysis-microarray-design-and-initial-studies-upon-the-inflammatory-response-to-pamps
#6
Sebastian Boltaña, Barbara Castellana, Giles Goetz, Lluis Tort, Mariana Teles, Victor Mulero, Beatriz Novoa, Antonio Figueras, Frederick W Goetz, Cristian Gallardo-Escarate, Josep V Planas, Simon Mackenzie
This study describes the development and validation of an enriched oligonucleotide-microarray platform for Sparus aurata (SAQ) to provide a platform for transcriptomic studies in this species. A transcriptome database was constructed by assembly of gilthead sea bream sequences derived from public repositories of mRNA together with reads from a large collection of expressed sequence tags (EST) from two extensive targeted cDNA libraries characterizing mRNA transcripts regulated by both bacterial and viral challenge...
February 3, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28100696/the-24th-annual-nucleic-acids-research-database-issue-a-look-back-and-upcoming-changes
#7
Michael Y Galperin, Xosé M Fernández-Suárez, Daniel J Rigden
No abstract text is available yet for this article.
January 18, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28093921/microbial-genomics-and-antimicrobial-susceptibility-testing
#8
W Michael Dunne, Magali Jaillard, Olivier Rochas, Alex Van Belkum
Antimicrobial susceptibility testing is key in modern clinical microbiology. With pandemic emergence of (multi-)antibiotic resistance, methods to detect and quantify resistance of clinically important bacterial species are imperative. Historically, antimicrobial susceptibility testing (AST) was mostly performed using methods relying on bacterial growth. Such methods may be time-consuming and more rapid alternatives have been actively sought for. Areas covered: Among the new AST methods there are many that focus on detection of causal resistance genes and/or gene mutations...
March 2017: Expert Review of Molecular Diagnostics
https://www.readbyqxmd.com/read/28065598/cas13b-is-a-type-vi-b-crispr-associated-rna-guided-rnase-differentially-regulated-by-accessory-proteins-csx27-and-csx28
#9
Aaron A Smargon, David B T Cox, Neena K Pyzocha, Kaijie Zheng, Ian M Slaymaker, Jonathan S Gootenberg, Omar A Abudayyeh, Patrick Essletzbichler, Sergey Shmakov, Kira S Makarova, Eugene V Koonin, Feng Zhang
CRISPR-Cas adaptive immune systems defend microbes against foreign nucleic acids via RNA-guided endonucleases. Using a computational sequence database mining approach, we identify two class 2 CRISPR-Cas systems (subtype VI-B) that lack Cas1 and Cas2 and encompass a single large effector protein, Cas13b, along with one of two previously uncharacterized associated proteins, Csx27 and Csx28. We establish that these CRISPR-Cas systems can achieve RNA interference when heterologously expressed. Through a combination of biochemical and genetic experiments, we show that Cas13b processes its own CRISPR array with short and long direct repeats, cleaves target RNA, and exhibits collateral RNase activity...
February 16, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28056497/taxonomic-distribution-repeats-and-functions-of-the-s1-domain-containing-proteins-as-members-of-the-ob-fold-family
#10
Evgeniia I Deryusheva, Andrey V Machulin, Olga M Selivanova, Oxana V Galzitskaya
Proteins of the nucleic acid-binding proteins superfamily perform such functions as processing, transport, storage, stretching, translation, and degradation of RNA. It is one of the 16 superfamilies containing the OB-fold in protein structures. Here, we have analyzed the superfamily of nucleic acid-binding proteins (the number of sequences exceeds 200,000) and obtained that this superfamily prevalently consists of proteins containing the cold shock DNA-binding domain (ca. 131,000 protein sequences). Proteins containing the S1 domain compose 57% from the cold shock DNA-binding domain family...
January 5, 2017: Proteins
https://www.readbyqxmd.com/read/28053169/nucleic-acids-research-volume-45-database-issue-january-4-2017
#11
(no author information available yet)
No abstract text is available yet for this article.
January 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28053160/the-24th-annual-nucleic-acids-research-database-issue-a-look-back-and-upcoming-changes
#12
Michael Y Galperin, Xosé M Fernández-Suárez, Daniel J Rigden
This year's Database Issue of Nucleic Acids Research contains 152 papers that include descriptions of 54 new databases and update papers on 98 databases, of which 16 have not been previously featured in NAR As always, these databases cover a broad range of molecular biology subjects, including genome structure, gene expression and its regulation, proteins, protein domains, and protein-protein interactions. Following the recent trend, an increasing number of new and established databases deal with the issues of human health, from cancer-causing mutations to drugs and drug targets...
January 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28050843/evaluating-the-probiotic-and-therapeutic-potentials-of-saccharomyces-cerevisiae-strain-obs2-isolated-from-fermented-nectar-of-toddy-palm
#13
Banoth Srinivas, Ganapathiwar Swarupa Rani, Bhukya Kiran Kumar, Banoth Chandrasekhar, Kommalapati Vamsi Krishna, Tangutur Anjana Devi, Bhukya Bhima
The purpose of this study is to evaluate the probiotic characteristics of 15 yeast strains isolated from nectar of toddy palm. Initially, the collected samples were inoculated on yeast extract peptone dextrose agar plates and the colonies so obtained were culturally and morphologically characterized. Commercial probiotic yeast, Saccharomyces boulardii served as the control in these experiments. Of the 15 yeast strains, the isolates that were resistant to antibiotics and worked synergistically with other cultures were considered for further evaluation...
December 2017: AMB Express
https://www.readbyqxmd.com/read/28039272/micafungin-alters-the-amino-acid-nucleic-acid-and-central-carbon-metabolism-of-candida-albicans-at-subinhibitory-concentrations-novel-insights-into-mechanisms-of-action
#14
Aspasia Katragkou, Michael Williams, Sandi Sternberg, Dennis Pantazatos, Emmanuel Roilides, Thomas J Walsh
BACKGROUND: Echinocandins are an important class of antifungal agents in the treatment of invasive candidiasis. However, little is known about the metabolomic effects of echinocandins on Candida We therefore performed LC-high-resolution MS (LC-HRMS)-based metabolomics profiling of the response of Candida albicans cells to increasing concentrations of micafungin to determine the metabolic response of Candida to micafungin subinhibitory injury. METHODS: Isolates of C...
December 30, 2016: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/28031034/uqlust-combining-profile-hashing-with-linear-time-ranking-for-efficient-clustering-and-analysis-of-big-macromolecular-data
#15
Rafal Adamczak, Jarek Meller
BACKGROUND: Advances in computing have enabled current protein and RNA structure prediction and molecular simulation methods to dramatically increase their sampling of conformational spaces. The quickly growing number of experimentally resolved structures, and databases such as the Protein Data Bank, also implies large scale structural similarity analyses to retrieve and classify macromolecular data. Consequently, the computational cost of structure comparison and clustering for large sets of macromolecular structures has become a bottleneck that necessitates further algorithmic improvements and development of efficient software solutions...
December 28, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28024397/mayachemtools-an-open-source-package-for-computational-drug-discovery
#16
Manish Sud
MayaChemTools is a growing collection of Perl scripts, modules, and classes to support a variety of computational drug discovery needs, such as manipulation and analysis of data, generation of two-dimensional (2D) fingerprints, similarity searching, and calculation of physicochemical properties. MayaChemTools provides command line scripts for the following tasks: manipulation and analysis of data in SD, CSV/TSV, sequence/alignments, and PDB files; calculation of a key set of physicochemical properties, such as molecular weight, hydrogen bond donors and acceptors, logP, and topological polar surface area; generation of 2D fingerprints corresponding to atom neighborhoods, atom types, E-state indices, extended connectivity, MACCS keys, path lengths, topological atom pairs, topological atom triplets, topological atom torsions, topological pharmacophore atom pairs, and topological pharmacophore atom triplets; similarity searching and calculation of similarity matrices using available 2D fingerprints; listing properties of elements in the periodic table, amino acids, and nucleic acids; and exporting data from relational databases...
December 27, 2016: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28009009/bacteriophage-t5-gene-d10-encodes-a-branch-migration-protein
#17
Io Nam Wong, Jon R Sayers, Cyril M Sanders
Helicases catalyze the unwinding of double-stranded nucleic acids where structure and phosphate backbone contacts, rather than nucleobase sequence, usually determines substrate specificity. We have expressed and purified a putative helicase encoded by the D10 gene of bacteriophage T5. Here we report that this hitherto uncharacterized protein possesses branch migration and DNA unwinding activity. The initiation of substrate unwinding showed some sequence dependency, while DNA binding and DNA-dependent ATPase activity did not...
December 23, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27997751/identifying-the-plant-associated-microbiome-across-aquatic-and-terrestrial-environments-the-effects-of-amplification-method-on-taxa-discovery
#18
Sara L Jackrel, Sarah M Owens, Jack A Gilbert, Catherine A Pfister
Plants in terrestrial and aquatic environments contain a diverse microbiome. Yet, the chloroplast and mitochondria organelles of the plant eukaryotic cell originate from free-living cyanobacteria and Rickettsiales. This represents a challenge for sequencing the plant microbiome with universal primers, as ~99% of 16S rRNA sequences may consist of chloroplast and mitochondrial sequences. Peptide nucleic acid clamps offer a potential solution by blocking amplification of host-associated sequences. We assessed the efficacy of chloroplast and mitochondria-blocking clamps against a range of microbial taxa from soil, freshwater, and marine environments...
December 20, 2016: Molecular Ecology Resources
https://www.readbyqxmd.com/read/27987046/matrix-assisted-laser-desorption-ionization-time-of-flight-mass-spectrometry-maldi-tof-ms-for-rapid-identification-of-micro-organisms-in-the-routine-clinical-microbiology-laboratory
#19
C Wattal, J K Oberoi, N Goel, R Raveendran, S Khanna
The study evaluates the utility of matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) Vitek MS for identification of microorganisms in the routine clinical microbiology laboratory. From May 2013 to April 2014, microbial isolates recovered from various clinical samples were identified by Vitek MS. In case of failure to identify by Vitek MS, the isolate was identified using the Vitek 2 system (bioMerieux, France) and serotyping wherever applicable or otherwise by nucleic acid-mediated methods...
December 16, 2016: European Journal of Clinical Microbiology & Infectious Diseases
https://www.readbyqxmd.com/read/27938328/combining-independent-de-novo-assemblies-optimizes-the-coding-transcriptome-for-nonconventional-model-eukaryotic-organisms
#20
Nicolas Cerveau, Daniel J Jackson
BACKGROUND: Next-generation sequencing (NGS) technologies are arguably the most revolutionary technical development to join the list of tools available to molecular biologists since PCR. For researchers working with nonconventional model organisms one major problem with the currently dominant NGS platform (Illumina) stems from the obligatory fragmentation of nucleic acid material that occurs prior to sequencing during library preparation. This step creates a significant bioinformatic challenge for accurate de novo assembly of novel transcriptome data...
December 9, 2016: BMC Bioinformatics
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