Abstract:
:The Biodegradative Strain Database (BSD) is a freely-accessible, web-based database providing detailed information on degradative bacteria and the hazardous substances that they degrade, including corresponding literature citations, relevant patents and links to additional web-based biological and chemical data. The BSD (http://bsd.cme.msu.edu) is being developed within the phylogenetic framework of the Ribosomal Database Project II (RDPII: http://rdp.cme.msu.edu/html) to provide a biological complement to the chemical and degradative pathway data of the University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD: http://umbbd.ahc.umn.edu). Data is accessible through a series of strain, chemical and reference lists or by keyword search. The web site also includes on-line data submission and user survey forms to solicit user contributions and suggestions. The current release contains information on over 250 degradative bacterial strains and 150 hazardous substances. The transformation of xenobiotics and other environmentally toxic compounds by microorganisms is central to strategies for biocatalysis and the bioremediation of contaminated environments. However, practical, comprehensive, strain-level information on biocatalytic/biodegradative microbes is not readily available and is often difficult to compile. Similarly, for any given environmental contaminant, there is no single resource that can provide comparative information on the array of identified microbes capable of degrading the chemical. A web site that consolidates and cross-references strain, chemical and reference data related to biocatalysis, biotransformation, biodegradation and bioremediation would be an invaluable tool for academic and industrial researchers and environmental engineers.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Urbance JW,Cole J,Saxman P,Tiedje JMdoi
10.1093/nar/gkg032keywords:
subject
Has Abstractpub_date
2003-01-01 00:00:00pages
152-5issue
1eissn
0305-1048issn
1362-4962journal_volume
31pub_type
杂志文章abstract::Despite the large number of noncoding RNAs in human genome and their roles in many diseases include cancer, we know very little about them due to lack of structural clues. The centerpiece of the structural clues is the full RNA base-pairing structure of secondary and tertiary contacts that can be precisely obtained on...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz1192
更新日期:2020-02-20 00:00:00
abstract::We developed an algorithm named ViReMa (Viral-Recombination-Mapper) to provide a versatile platform for rapid, sensitive and nucleotide-resolution detection of recombination junctions in viral genomes using next-generation sequencing data. Rather than mapping read segments of pre-defined lengths and positions, ViReMa ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt916
更新日期:2014-01-01 00:00:00
abstract:UNLABELLED:Synonymous codon usage biases are associated with various biological factors, such as gene expression level, gene length, gene translation initiation signal, protein amino acid composition, protein structure, tRNA abundance, mutation frequency and patterns, and GC compositions. Quantification of codon usage ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm392
更新日期:2007-07-01 00:00:00
abstract::The Department of Energy (DOE) Joint Genome Institute (JGI) is a national user facility with massive-scale DNA sequencing and analysis capabilities dedicated to advancing genomics for bioenergy and environmental applications. Beyond generating tens of trillions of DNA bases annually, the Institute develops and maintai...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr947
更新日期:2012-01-01 00:00:00
abstract::Primers4clades is an easy-to-use web server that implements a fully automatic PCR primer design pipeline for cross-species amplification of novel sequences from metagenomic DNA, or from uncharacterized organisms, belonging to user-specified phylogenetic clades or taxa. The server takes a set of non-aligned protein cod...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp377
更新日期:2009-07-01 00:00:00
abstract::The InParanoid eukaryotic ortholog database (http://InParanoid.sbc.su.se/) has been updated to version 6 and is now based on 35 species. We collected all available 'complete' eukaryotic proteomes and Escherichia coli, and calculated ortholog groups for all 595 species pairs using the InParanoid program. This resulted ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm1020
更新日期:2008-01-01 00:00:00
abstract::Single nucleotide polymorphisms (SNPs) are, together with copy number variation, the primary source of variation in the human genome. SNPs are associated with altered response to drug treatment, susceptibility to disease and other phenotypic variation. Furthermore, during genetic screens for disease-associated mutatio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm979
更新日期:2008-01-01 00:00:00
abstract::The modified nucleoside, 7-(4,5-cis-dihydroxy-1-cyclopenten-3-yl-aminomethyl)-7-deazaguanosine, designated as Q, and its derivative, Q*, were found in tRNA's from various organisms, including several mammalian tissues, other animals such as starfish, lingula and hagfish, and wheat germ. Q isolated from rat liver tRNA ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/2.10.1931
更新日期:1975-10-01 00:00:00
abstract::The surface accessibility of macromolecules plays a key role in modulating molecular recognition events. RNA is a complex and dynamic molecule involved in many aspects of gene expression. However, there are few experimental methods available to measure the accessible surface of RNA. Here, we investigate the accessible...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm1062
更新日期:2008-03-01 00:00:00
abstract::Highly regulated induction systems enabling dose-dependent and reversible fine-tuning of protein expression output are beneficial for engineering complex biosynthetic pathways. To address this, we developed PhiReX, a novel red/far-red light-regulated protein expression system for use in Saccharomyces cerevisiae. PhiRe...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx610
更新日期:2017-09-06 00:00:00
abstract::Melanotransferrin (MTf) is a tumor associated antigen found in abundance on the surface of melanoma cells. It is a transferrin-like protein found in low amount in most adult tissues and whose gene is reminiscent of house-keeping genes. With the goal of understanding the regulatory mechanisms which might explain the en...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.11.2853
更新日期:1992-06-11 00:00:00
abstract::DNA double-strand breaks (DSBs) and their repair can cause extensive epigenetic changes. As a result, DSBs have been proposed to promote transcriptional and, ultimately, physiological dysfunction via both cell-intrinsic and cell-non-autonomous pathways. Studying the consequences of DSBs in higher organisms has, howeve...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv1482
更新日期:2016-04-20 00:00:00
abstract::The hammerhead self-cleaving motif occurs in a variety of RNAs that infect plants and consists of three non-conserved helices connected by a highly conserved central core. A variant hammerhead, called the extended hammerhead, is found in satellite 2 transcripts from a variety of caudate amphibians. The extended hammer...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.11.2189
更新日期:1997-06-01 00:00:00
abstract::More than 200 assembly factors (AFs) are required for the production of ribosomes in yeast. The stepwise association and dissociation of these AFs with the pre-ribosomal subunits occurs in a hierarchical manner to ensure correct maturation of the pre-rRNAs and assembly of the ribosomal proteins. Although decades of re...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz1079
更新日期:2020-01-10 00:00:00
abstract::Transcription of the human adenovirus 5 genome in transformed rat embryo cells (DFK3) was investigated using two different approaches. Preferential digestion of transcribed viral sequences by DNase I was analysed using kinetics of renaturation of 32P-labeled Ad5 HpaI restriction fragments in the presence of material w...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/5.1.1
更新日期:1978-01-01 00:00:00
abstract::S/MARt DB, the S/MAR transaction database, is a relational database covering scaffold/matrix attached regions (S/MARs) and nuclear matrix proteins that are involved in the chromosomal attachment to the nuclear scaffold. The data are mainly extracted from original publications, but a World Wide Web interface for direct...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.1.372
更新日期:2002-01-01 00:00:00
abstract::Apolipoprotein B (apoB) is a major protein component of low density and very low density lipoproteins. Because of its large size and heterogeneity, molecular studies of apoB have been difficult, and its structure and regulation remain poorly understood. We now report the identification of human apoB cDNA clones by ant...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.19.6937
更新日期:1985-10-11 00:00:00
abstract::We describe an interactive computer program (ANALYSEQ) that is used from a simple graphics terminal. The main purpose of the program is to determine the function of nucleic acid sequences but it also offers the simpler listing, searching and counting options. It contains methods to locate genes by looking for the effe...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.1part2.521
更新日期:1984-01-11 00:00:00
abstract::HinP1I recognizes and cleaves the palindromic tetranucleotide sequence G downward arrowCGC in DNA. We report three structures of HinP1I-DNA complexes: in the presence of Ca(2+) (pre-reactive complex), in the absence of metal ion (binary complex) and in the presence of Mg(2+) (post-reactive complex). HinP1I forms a bac...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkj484
更新日期:2006-02-09 00:00:00
abstract::A cDNA library was constructed from the mRNA of the ZR-75 oestrogen responsive human breast cancer cell line and screened for oestrogen regulated mRNA sequences. Of the recombinants isolated, 30 contained cDNA that corresponded to a single mRNA species of 2.1 kb that was induced between 10 and 15 fold by oestradiol tr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.9.3773
更新日期:1987-05-11 00:00:00
abstract::Escherichia coli MutY is an adenine and a weak guanine DNA glycosylase involved in reducing mutagenic effects of 7,8-dihydro-8-oxo-guanine (8-oxoG). The C-terminal domain of MutY is required for 8-oxoG recognition and is critical for mutation avoidance of oxidative damage. To determine which residues of this domain ar...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg434
更新日期:2003-06-15 00:00:00
abstract::The UCSC Genome Browser (https://genome.ucsc.edu) provides a web interface for exploring annotated genome assemblies. The assemblies and annotation tracks are updated on an ongoing basis-12 assemblies and more than 28 tracks were added in the past year. Two recent additions are a display of CRISPR/Cas9 guide sequences...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx1020
更新日期:2018-01-04 00:00:00
abstract::Muscleblind-like proteins (MBNLs) are regulators of RNA metabolism. During tissue differentiation the level of MBNLs increases, while their functional insufficiency plays a crucial role in myotonic dystrophy (DM). Deep sequencing of RNA molecules cross-linked to immunoprecipitated protein particles (CLIP-seq) revealed...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw1158
更新日期:2017-02-28 00:00:00
abstract::PlantGDB (http://www.plantgdb.org/) is a genomics database encompassing sequence data for green plants (Viridiplantae). PlantGDB provides annotated transcript assemblies for >100 plant species, with transcripts mapped to their cognate genomic context where available, integrated with a variety of sequence analysis tool...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm1041
更新日期:2008-01-01 00:00:00
abstract::Heteroduplexes between the viral DNA of phiX174 and DNA from the replicative form (RF) of phage G4 were examined by electron microscopy. The single Eco RI site of G4-RF was utilized as a physical marker by preparing the heteroduplexes from the denatured, linear DNA obtained by restricting G4-RF with Eco RI endonucleas...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/6.5.1979
更新日期:1979-01-01 00:00:00
abstract::The response to amino acid (AA) limitation of the entire aminoacyl-tRNA synthetase (ARS) gene family revealed that 16/20 of the genes encoding cytoplasmic-localized enzymes are transcriptionally induced by activating transcription factor 4 (Atf4) via C/ebp-Atf-Response-Element (CARE) enhancers. In contrast, only 4/19 ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw667
更新日期:2016-11-16 00:00:00
abstract::The mission of UniProt is to support biological research by providing a freely accessible, stable, comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and querying interfaces. UniProt is comprised of four major components, each optimized for ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr981
更新日期:2012-01-01 00:00:00
abstract::We describe a rapid fluorescence indicator displacement assay (R-FID) to evaluate the affinity and the selectivity of compounds binding to different DNA structures. We validated the assay using a library of 30 well-known nucleic acid binders containing a variety chemical scaffolds. We used a combination of principal c...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky019
更新日期:2018-04-20 00:00:00
abstract::Metagenomics is a relatively recently established but rapidly expanding field that uses high-throughput next-generation sequencing technologies to characterize the microbial communities inhabiting different ecosystems (including oceans, lakes, soil, tundra, plants and body sites). Metagenomics brings with it a number ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt961
更新日期:2014-01-01 00:00:00
abstract::A reporter assay was developed to detect and quantify nonsense codon suppression by chemically aminoacylated tRNAs in mammalian cells. It is based on the cellular expression of the enhanced green fluorescent protein (EGFP) as a reporter for the site-specific amino acid incorporation in its sequence using an orthogonal...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gnf128
更新日期:2002-12-01 00:00:00