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https://www.readbyqxmd.com/read/27913980/complete-nucleotide-sequences-and-construction-of-full-length-infectious-cdna-clones-of-cucumber-green-mottle-mosaic-virus-cgmmv-in-a-versatile-newly-developed-binary-vector-including-both-35s-and-t7-promoters
#1
Chan-Hwan Park, Hye-Kyoung Ju, Jae-Yeong Han, Jong-Seo Park, Ik-Hyun Kim, Eun-Young Seo, Jung-Kyu Kim, John Hammond, Hyoun-Sub Lim
Seed-transmitted viruses have caused significant damage to watermelon crops in Korea in recent years, with cucumber green mottle mosaic virus (CGMMV) infection widespread as a result of infected seed lots. To determine the likely origin of CGMMV infection, we collected CGMMV isolates from watermelon and melon fields and generated full-length infectious cDNA clones. The full-length cDNAs were cloned into newly constructed binary vector pJY, which includes both the 35S and T7 promoters for versatile usage (agroinfiltration and in vitro RNA transcription) and a modified hepatitis delta virus ribozyme sequence to precisely cleave RNA transcripts at the 3' end of the tobamovirus genome...
December 2, 2016: Virus Genes
https://www.readbyqxmd.com/read/27913251/unmapped-reads-from-cattle-rnaseq-data-a-source-for-missing-and-misassembled-sequences-in-the-reference-assemblies-and-for-detection-of-pathogens-in-the-host
#2
Tahir Usman, Frieder Hadlich, Wiebke Demasius, Rosemarie Weikard, Christa Kühn
Usually, reads from transcriptome sequencing data unmapped to the target species reference genome are disregarded. A recent RNAseq project on the new fatal disease Bovine Neonatal Pancytopenia had indicated an unexplained immune response signature to a double stranded RNA virus. To unravel its background, contigs were de novo assembled from unmapped RNAseq reads and aligned against the bovine genome assemblies and multispecies NCBI databases. Lack of genuine virus sequence contigs rejected the hypothesis of a live virus being causal for the unexplained immune response...
November 29, 2016: Genomics
https://www.readbyqxmd.com/read/27904520/a-diagnostic-one-step-real-time-reverse-transcription-polymerase-chain-reaction-method-for-accurate-detection-of-influenza-virus-type-a
#3
Mohammad Amin Behzadi, Mazyar Ziyaeyan, Abdolvahab Alborzi
INTRODUCTION: Influenza A is known as a public health concern worldwide. In this study, a novel one-step real-time reverse transcription polymerase chain reaction (rtRT-PCR) assay was designed and optimized for the detection of influenza A viruses. MATERIAL AND METHODS: The primers and probe were designed based on the analysis of 90 matrix nucleotide sequence data of influenza type A subtypes from the GenBank database of the National Center for Biotechnology Information (NCBI)...
December 1, 2016: Archives of Medical Science: AMS
https://www.readbyqxmd.com/read/27900493/mining-the-cicer-arietinum-genome-for-the-mildew-locus-o-mlo-gene-family-and-comparative-evolutionary-analysis-of-the-mlo-genes-from-medicago-truncatula-and-some-other-plant-species
#4
Reena Deshmukh, V K Singh, Brahma Deo Singh
The mildew locus O (Mlo) gene family is ubiquitous in land plants. Some members of this gene family are involved in negative regulation of powdery mildew resistance, while others are involved in several other biological functions. Mlo proteins have characteristic seven transmembrane domains and a calmodulin-binding domain at their C-termini, and are associated with plasma membrane. The Mlo gene family has been studied in several economically important cereals, but little information is available on this gene family in the important legumes, Medicago truncatula Gaertn...
November 30, 2016: Journal of Plant Research
https://www.readbyqxmd.com/read/27900265/complete-genome-sequence-of-the-biofilm-forming-microbacterium-sp-strain-bh-3-3-3-isolated-from-conventional-field-grown-lettuce-lactuca-sativa-in-norway
#5
Merete Wiken Dees, May Bente Brurberg, Erik Lysøe
The genus Microbacterium contains bacteria that are ubiquitously distributed in various environments and includes plant-associated bacteria that are able to colonize tissue of agricultural crop plants. Here, we report the 3,508,491 bp complete genome sequence of Microbacterium sp. strain BH-3-3-3, isolated from conventionally grown lettuce (Lactuca sativa) from a field in Vestfold, Norway. The nucleotide sequence of this genome was deposited into NCBI GenBank under the accession CP017674.
March 2017: Genomics Data
https://www.readbyqxmd.com/read/27899678/virus-variation-resource-improved-response-to-emergent-viral-outbreaks
#6
Eneida L Hatcher, Sergey A Zhdanov, Yiming Bao, Olga Blinkova, Eric P Nawrocki, Yuri Ostapchuck, Alejandro A Schäffer, J Rodney Brister
The Virus Variation Resource is a value-added viral sequence data resource hosted by the National Center for Biotechnology Information. The resource is located at http://www.ncbi.nlm.nih.gov/genome/viruses/variation/ and includes modules for seven viral groups: influenza virus, Dengue virus, West Nile virus, Ebolavirus, MERS coronavirus, Rotavirus A and Zika virus Each module is supported by pipelines that scan newly released GenBank records, annotate genes and proteins and parse sample descriptors and then map them to controlled vocabulary...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899674/cdd-sparcle-functional-classification-of-proteins-via-subfamily-domain-architectures
#7
Aron Marchler-Bauer, Yu Bo, Lianyi Han, Jane He, Christopher J Lanczycki, Shennan Lu, Farideh Chitsaz, Myra K Derbyshire, Renata C Geer, Noreen R Gonzales, Marc Gwadz, David I Hurwitz, Fu Lu, Gabriele H Marchler, James S Song, Narmada Thanki, Zhouxi Wang, Roxanne A Yamashita, Dachuan Zhang, Chanjuan Zheng, Lewis Y Geer, Stephen H Bryant
NCBI's Conserved Domain Database (CDD) aims at annotating biomolecular sequences with the location of evolutionarily conserved protein domain footprints, and functional sites inferred from such footprints. An archive of pre-computed domain annotation is maintained for proteins tracked by NCBI's Entrez database, and live search services are offered as well. CDD curation staff supplements a comprehensive collection of protein domain and protein family models, which have been imported from external providers, with representations of selected domain families that are curated in-house and organized into hierarchical classifications of functionally distinct families and sub-families...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899644/the-dbgap-data-browser-a-new-tool-for-browsing-dbgap-controlled-access-genomic-data
#8
Kira M Wong, Kristofor Langlais, Geoffrey S Tobias, Colette Fletcher-Hoppe, Donna Krasnewich, Hilary S Leeds, Laura Lyman Rodriguez, Georgy Godynskiy, Valerie A Schneider, Erin M Ramos, Stephen T Sherry
The database of Genotypes and Phenotypes (dbGaP) Data Browser (https://www.ncbi.nlm.nih.gov/gap/ddb/) was developed in response to requests from the scientific community for a resource that enable view-only access to summary-level information and individual-level genotype and sequence data associated with phenotypic features maintained in the controlled-access tier of dbGaP. Until now, the dbGaP controlled-access environment required investigators to submit a data access request, wait for Data Access Committee review, download each data set and locally examine them for potentially relevant information...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899620/mrprimerv-a-database-of-pcr-primers-for-rna-virus-detection
#9
Hyerin Kim, NaNa Kang, KyuHyeon An, Doyun Kim, JaeHyung Koo, Min-Soo Kim
Many infectious diseases are caused by viral infections, and in particular by RNA viruses such as MERS, Ebola and Zika. To understand viral disease, detection and identification of these viruses are essential. Although PCR is widely used for rapid virus identification due to its low cost and high sensitivity and specificity, very few online database resources have compiled PCR primers for RNA viruses. To effectively detect viruses, the MRPrimerV database (http://MRPrimerV.com) contains 152 380 247 PCR primer pairs for detection of 1818 viruses, covering 7144 coding sequences (CDSs), representing 100% of the RNA viruses in the most up-to-date NCBI RefSeq database...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899599/pubchem-bioassay-2017-update
#10
Yanli Wang, Stephen H Bryant, Tiejun Cheng, Jiyao Wang, Asta Gindulyte, Benjamin A Shoemaker, Paul A Thiessen, Siqian He, Jian Zhang
PubChem's BioAssay database (https://pubchem.ncbi.nlm.nih.gov) has served as a public repository for small-molecule and RNAi screening data since 2004 providing open access of its data content to the community. PubChem accepts data submission from worldwide researchers at academia, industry and government agencies. PubChem also collaborates with other chemical biology database stakeholders with data exchange. With over a decade's development effort, it becomes an important information resource supporting drug discovery and chemical biology research...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899596/chitars-3-1-the-enhanced-chimeric-transcripts-and-rna-seq-database-matched-with-protein-protein-interactions
#11
Alessandro Gorohovski, Somnath Tagore, Vikrant Palande, Assaf Malka, Dorith Raviv-Shay, Milana Frenkel-Morgenstern
Discovery of chimeric RNAs, which are produced by chromosomal translocations as well as the joining of exons from different genes by trans-splicing, has added a new level of complexity to our study and understanding of the transcriptome. The enhanced ChiTaRS-3.1 database (http://chitars.md.biu.ac.il) is designed to make widely accessible a wealth of mined data on chimeric RNAs, with easy-to-use analytical tools built-in. The database comprises 34 922: chimeric transcripts along with 11 714: cancer breakpoints...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899564/genbank
#12
Dennis A Benson, Mark Cavanaugh, Karen Clark, Ilene Karsch-Mizrachi, David J Lipman, James Ostell, Eric W Sayers
GenBank(®) (www.ncbi.nlm.nih.gov/genbank/) is a comprehensive database that contains publicly available nucleotide sequences for 370 000 formally described species. These sequences are obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole genome shotgun (WGS) and environmental sampling projects. Most submissions are made using the web-based BankIt or the NCBI Submission Portal. GenBank staff assign accession numbers upon data receipt...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899561/database-resources-of-the-national-center-for-biotechnology-information
#13
(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 37 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 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27896724/genomic-database-searching
#14
James R A Hutchins
The availability of reference genome sequences for virtually all species under active research has revolutionized biology. Analyses of genomic variations in many organisms have provided insights into phenotypic traits, evolution and disease, and are transforming medicine. All genomic data from publicly funded projects are freely available in Internet-based databases, for download or searching via genome browsers such as Ensembl, Vega, NCBI's Map Viewer, and the UCSC Genome Browser. These online tools generate interactive graphical outputs of relevant chromosomal regions, showing genes, transcripts, and other genomic landmarks, and epigenetic features mapped by projects such as ENCODE...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27896718/managing-sequence-data
#15
Christopher O'Sullivan, Benjamin Busby, Ilene Karsch Mizrachi
Nucleotide and protein sequences are the foundation for all bioinformatics tools and resources. Researchers can analyze these sequences to discover genes or predict the function of their products. The INSDC (International Nucleotide Sequence Database-DDBJ/ENA/GenBank + SRA) is an international, centralized primary sequence resource that is freely available on the Internet. This database contains all publicly available nucleotide and derived protein sequences. This chapter discusses the structure and history of the nucleotide sequence database resources built at NCBI, provides information on how to submit sequences to the databases, and explains how to access the sequence data...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27896071/draft-genome-sequence-of-thermoactinomyces-sp-gus2-1-isolated-from-the-hot-spring-gusikha-in-bargusin-valley-baikal-rift-zone-russia
#16
Aleksey S Rozanov, Alla V Bryanskaya, Anastasia V Kotenko, Sergey E Peltek
The Thermoactinomyces sp. strain Gus2-1 was isolated from hot-spring sediments sample from the hot-spring Gusikha in Bargusin Valley (Baikal Rift Zone, Russia). The sequenced and annotated genome is 2,623,309 bp and encodes 2513 genes. The draft genome sequence of the Thermoactinomyces sp. strain Gus2-1 has been deposited at DDBJ/EMBL/GenBank under the accession JPZM01000000 and the sequences could be found at the site https://www.ncbi.nlm.nih.gov/nuccore/JPZM01000000.
March 2017: Genomics Data
https://www.readbyqxmd.com/read/27896069/evaluation-of-de-novo-assembly-technique-in-the-south-african-abalone-haliotis-midae-transcriptome-a-comparison-from-illumina-and-454-systems
#17
Barbara Picone, Clint Rhode, Rouvay Roodt-Wilding
Next generation sequencing platforms have recently been used to rapidly characterize transcriptome sequences from a number of non-model organisms. The present study compares two of the most frequently used platforms, the Roche 454-pyrosequencing and the Illumina sequencing-by-synthesis (SBS), on the same RNA sample obtained from an intertidal gastropod mollusc species, Haliotis midae. All the sequencing reads were deposited in the Short Read Archive (SRA) database are retrievable under the accession number [SRR071314 (Illumina Genome Analyzer II)] and [SRR1737738, SRR1737737, SRR1737735, SRR1737734 (454 GS FLX)] in the SRA database of NCBI...
December 2016: Genomics Data
https://www.readbyqxmd.com/read/27896068/metagenomic-investigation-of-the-microbial-diversity-in-a-chrysotile-asbestos-mine-pit-pond-lowell-vermont-usa
#18
Heather E Driscoll, James J Vincent, Erika L English, Elizabeth D Dolci
Here we report on a metagenomics investigation of the microbial diversity in a serpentine-hosted aquatic habitat created by chrysotile asbestos mining activity at the Vermont Asbestos Group (VAG) Mine in northern Vermont, USA. The now-abandoned VAG Mine on Belvidere Mountain in the towns of Eden and Lowell includes three open-pit quarries, a flooded pit, mill buildings, roads, and > 26 million metric tons of eroding mine waste that contribute alkaline mine drainage to the surrounding watershed. Metagenomes and water chemistry originated from aquatic samples taken at three depths (0...
December 2016: Genomics Data
https://www.readbyqxmd.com/read/27893688/identification-of-genes-and-signaling-pathways-associated-with-diabetic-neuropathy-using-a-weighted-correlation-network-analysis-a-consort-study
#19
Ya Li, Weiguo Ma, Chuanqing Xie, Min Zhang, Xiaohong Yin, Fenfen Wang, Jie Xu, Bingyin Shi
BACKGROUND: The molecular mechanisms behind diabetic neuropathy remains to be investigated. METHODS: This is a secondary study on microarray dataset (GSE24290) downloaded from Gene Expression Omnibus (GEO) at the National Center for Biotechnology Information (NCBI), which included 18 nerve tissue samples of progressing diabetic neuropathy (fibers loss ≥500 fibers/mm) and 17 nerve tissue samples of nonprogressing diabetic neuropathy (fibers loss ≤100 fibers/mm)...
November 2016: Medicine (Baltimore)
https://www.readbyqxmd.com/read/27893553/healing-effects-of-platelet-rich-plasma-on-peripheral-nerve-injuries
#20
Farshid Bastami, Peyman Vares, Arash Khojasteh
Regeneration of peripheral nerve injuries (PNIs) has been a major challenging issue in regenerative medicine and tissue engineering. Inferior alveolar nerve and lingual nerve injuries are the major difficulties and complications of oral surgeries following dental implant placement, etc. The aim of this study was to systematically review the effects of platelet-rich plasma (PRP) on the regeneration of PNIs. Medline NCBI databases were searched for related articles up to and including May 2016. Being published in English papers, use of PRP in peripheral nerve regeneration, in vivo studies, and having histological evaluations was the inclusion criteria...
November 23, 2016: Journal of Craniofacial Surgery
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