keyword
MENU ▼
Read by QxMD icon Read
search

nucleic acid databases

keyword
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
#1
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...
January 4, 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
#2
Evgeniia I Deryusheva, Andrey V Machulin, Olga M Selivanova, Oxana V Galzitskaya
Proteins of the nucleic acid-binding proteins superfamily perform such functions as of 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 200000) and obtained that this superfamily prevalently consists of proteins containing the cold shock DNA-binding domain (about 131000 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
#3
(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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
https://www.readbyqxmd.com/read/27936518/computational-investigation-of-proton-transfer-pka-shifts-and-ph-optimum-of-protein-dna-and-protein-rna-complexes
#13
Yunhui Peng, Emil Alexov
Protein-nucleic acid interactions play a crucial role in many biological processes. This work investigates the changes of pKa values and protonation states of ionizable groups (including nucleic acid bases) that may occur at protein-nucleic acid binding. Taking advantage of the recently developed pKa calculation tool DelphiPka, we utilize the large protein-nucleic acid interaction database (NPIDB database) to model pKa shifts caused by binding. It has been found that the protein's interfacial basic residues experience favorable electrostatic interactions while the protein acidic residues undergo proton uptake to reduce the energy cost upon the binding...
December 9, 2016: Proteins
https://www.readbyqxmd.com/read/27913843/molecular-evolution-in-historical-perspective
#14
Edna Suárez-Díaz
In the 1960s, advances in protein chemistry and molecular genetics provided new means for the study of biological evolution. Amino acid sequencing, nucleic acid hybridization, zone gel electrophoresis, and immunochemistry were some of the experimental techniques that brought about new perspectives to the study of the patterns and mechanisms of evolution. New concepts, such as the molecular evolutionary clock, and the discovery of unexpected molecular phenomena, like the presence of repetitive sequences in eukaryotic genomes, eventually led to the realization that evolution might occur at a different pace at the organismic and the molecular levels, and according to different mechanisms...
December 2016: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/27910033/cytogenetic-resources-and-information
#15
Etienne De Braekeleer, Jean-Loup Huret, Hossain Mossafa, Philippe Dessen
The main databases devoted stricto sensu to cancer cytogenetics are the "Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer" ( http://cgap.nci.nih.gov/Chromosomes/Mitelman ), the "Atlas of Genetics and Cytogenetics in Oncology and Haematology" ( http://atlasgeneticsoncology.org ), and COSMIC ( http://cancer.sanger.ac.uk/cosmic ).However, being a complex multistep process, cancer cytogenetics are broadened to "cytogenomics," with complementary resources on: general databases (nucleic acid and protein sequences databases; cartography browsers: GenBank, RefSeq, UCSC, Ensembl, UniProtKB, and Entrez Gene), cancer genomic portals associated with recent international integrated programs, such as TCGA or ICGC, other fusion genes databases, array CGH databases, copy number variation databases, and mutation databases...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27905517/g4ipdb-a-database-for-g-quadruplex-structure-forming-nucleic-acid-interacting-proteins
#16
Subodh Kumar Mishra, Arpita Tawani, Amit Mishra, Amit Kumar
Nucleic acid G-quadruplex structure (G4) Interacting Proteins DataBase (G4IPDB) is an important database that contains detailed information about proteins interacting with nucleic acids that forms G-quadruplex structures. G4IPDB is the first database that provides comprehensive information about this interaction at a single platform. This database contains more than 200 entries with details of interaction such as interacting protein name and their synonyms, their UniProt-ID, source organism, target name and its sequences, ∆Tm, binding/dissociation constants, protein gene name, protein FASTA sequence, interacting residue in protein, related PDB entries, interaction ID, graphical view, PMID, author's name and techniques that were used to detect their interactions...
December 1, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27901142/an-optimized-charge-penetration-model-for-use-with-the-amoeba-force-field
#17
Joshua A Rackers, Qiantao Wang, Chengwen Liu, Jean-Philip Piquemal, Pengyu Ren, Jay W Ponder
The principal challenge of using classical physics to model biomolecular interactions is capturing the nature of short-range interactions that drive biological processes from nucleic acid base stacking to protein-ligand binding. In particular most classical force fields suffer from an error in their electrostatic models that arises from an ability to account for the overlap between charge distributions occurring when molecules get close to each other, known as charge penetration. In this work we present a simple, physically motivated model for including charge penetration in the AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications) force field...
December 21, 2016: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/27899966/analysis-of-the-molecular-mechanism-of-osteosarcoma-using-a-bioinformatics-approach
#18
Jianxun Yang, Ning Wang
The aim of this study was to explore the underlying molecular mechanism related to the process and progression of osteosarcoma (OS). The differentially expressed genes (DEGs) were downloaded from the Gene Expression Omnibus database. The pathway and gene ontology (GO) enrichment analysis, as well as transcription factor, tumor-associated gene and tumor suppressor gene analyses were performed to investigate the functions of DEGs. Next, the protein-protein interaction (PPI) network was constructed and module analysis was further assessed by cluster analysis with the overlapping neighborhood expansion (Cluster ONE) cytoscape plug-in...
November 2016: Oncology Letters
https://www.readbyqxmd.com/read/27899635/interpro-in-2017-beyond-protein-family-and-domain-annotations
#19
Robert D Finn, Teresa K Attwood, Patricia C Babbitt, Alex Bateman, Peer Bork, Alan J Bridge, Hsin-Yu Chang, Zsuzsanna Dosztányi, Sara El-Gebali, Matthew Fraser, Julian Gough, David Haft, Gemma L Holliday, Hongzhan Huang, Xiaosong Huang, Ivica Letunic, Rodrigo Lopez, Shennan Lu, Aron Marchler-Bauer, Huaiyu Mi, Jaina Mistry, Darren A Natale, Marco Necci, Gift Nuka, Christine A Orengo, Youngmi Park, Sebastien Pesseat, Damiano Piovesan, Simon C Potter, Neil D Rawlings, Nicole Redaschi, Lorna Richardson, Catherine Rivoire, Amaia Sangrador-Vegas, Christian Sigrist, Ian Sillitoe, Ben Smithers, Silvano Squizzato, Granger Sutton, Narmada Thanki, Paul D Thomas, Silvio C E Tosatto, Cathy H Wu, Ioannis Xenarios, Lai-Su Yeh, Siew-Yit Young, Alex L Mitchell
InterPro (http://www.ebi.ac.uk/interpro/) is a freely available database used to classify protein sequences into families and to predict the presence of important domains and sites. InterProScan is the underlying software that allows both protein and nucleic acid sequences to be searched against InterPro's predictive models, which are provided by its member databases. Here, we report recent developments with InterPro and its associated software, including the addition of two new databases (SFLD and CDD), and the functionality to include residue-level annotation and prediction of intrinsic disorder...
January 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899602/the-human-phenotype-ontology-in-2017
#20
Sebastian Köhler, Nicole A Vasilevsky, Mark Engelstad, Erin Foster, Julie McMurry, Ségolène Aymé, Gareth Baynam, Susan M Bello, Cornelius F Boerkoel, Kym M Boycott, Michael Brudno, Orion J Buske, Patrick F Chinnery, Valentina Cipriani, Laureen E Connell, Hugh J S Dawkins, Laura E DeMare, Andrew D Devereau, Bert B A de Vries, Helen V Firth, Kathleen Freson, Daniel Greene, Ada Hamosh, Ingo Helbig, Courtney Hum, Johanna A Jähn, Roger James, Roland Krause, Stanley J F Laulederkind, Hanns Lochmüller, Gholson J Lyon, Soichi Ogishima, Annie Olry, Willem H Ouwehand, Nikolas Pontikos, Ana Rath, Franz Schaefer, Richard H Scott, Michael Segal, Panagiotis I Sergouniotis, Richard Sever, Cynthia L Smith, Volker Straub, Rachel Thompson, Catherine Turner, Ernest Turro, Marijcke W M Veltman, Tom Vulliamy, Jing Yu, Julie von Ziegenweidt, Andreas Zankl, Stephan Züchner, Tomasz Zemojtel, Julius O B Jacobsen, Tudor Groza, Damian Smedley, Christopher J Mungall, Melissa Haendel, Peter N Robinson
Deep phenotyping has been defined as the precise and comprehensive analysis of phenotypic abnormalities in which the individual components of the phenotype are observed and described. The three components of the Human Phenotype Ontology (HPO; www.human-phenotype-ontology.org) project are the phenotype vocabulary, disease-phenotype annotations and the algorithms that operate on these. These components are being used for computational deep phenotyping and precision medicine as well as integration of clinical data into translational research...
January 4, 2017: Nucleic Acids Research
keyword
keyword
69905
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"