Abstract:
:TcruziDB (http://TcruziDB.org) is an integrated genome database for the parasitic organism Trypanosoma cruzi, the causative agent of Chagas' disease. The database currently incorporates all available sequence data (Genomic, BAC, EST) in a single user-friendly location. The database contains a variety of tools specifically designed for searching unannotated draft sequence via BLAST, keyword searches of pre-computed BLAST results, and protein motif searches. Release 1.0 of the database contains nearly 730 million bp of genome sequence from 1.1 million sequence reads generated by the TIGR-Karolinska-SBRI Trypanosoma cruzi Genome Consortium and 15 million bp of clustered EST and genomic sequence obtained from other sources. As annotation, microarray and proteomic data become available, the database will incorporate and integrate these data using the GUS (http://www.gusdb. org) relational framework.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Luchtan M,Warade C,Weatherly DB,Degrave WM,Tarleton RL,Kissinger JCdoi
10.1093/nar/gkh049keywords:
subject
Has Abstractpub_date
2004-01-01 00:00:00pages
D344-6issue
Database issueeissn
0305-1048issn
1362-4962pii
32/suppl_1/D344journal_volume
32pub_type
杂志文章abstract::Plasmodium falciparum origin recognition complex 1 (ORC1) protein has been implicated in DNA replication and silencing var gene family. However, the mechanism and the domain structure of ORC1 related to the regulation of var gene family are unknown. Here we show that the unique N-terminus of PfORC1 (PfORC1N(1-238)) is...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks202
更新日期:2012-07-01 00:00:00
abstract::Stress response mechanisms that modulate the dynamics of tRNA degradation and accumulation from the cytoplasm to the nucleus have been studied in yeast, the rat hepatoma and human cells. In the current study, we investigated tRNA degradation and accumulation in HeLa cells under various forms of stress. We found that i...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt153
更新日期:2013-04-01 00:00:00
abstract::DNA helicases are required for virtually every aspect of DNA metabolism, including replication, repair, recombination and transcription. A comprehensive description of these essential biochemical processes requires detailed understanding of helicase mechanisms. These enzymes are ubiquitous, having been identified in v...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/gkl501
更新日期:2006-01-01 00:00:00
abstract::The chromatin-remodelling complex B-WICH, comprised of William syndrome transcription factor, the ATPase SNF2h and nuclear myosin, specifically activates RNA polymerase III transcription of the 5S rRNA and 7SL genes. However, the underlying mechanism is unknown. Using high-resolution MN walking we demonstrate here tha...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv312
更新日期:2015-05-19 00:00:00
abstract::Using a human interferon-alpha probe we have isolated recombinant phages containing murine interferon-alpha (Mu IFN-alpha) genes from a genomic library. One of these phages contained two complete Mu IFN-alpha genes and part of a third gene. The insert of a second phage held two IFN genes. This indicates that the Mu IF...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.3.791
更新日期:1985-02-11 00:00:00
abstract::Single-molecule force spectroscopy provides insight into how proteins bind to and move along DNA. Such studies often embed a single-stranded (ss) DNA region within a longer double-stranded (ds) DNA molecule. Yet, producing these substrates remains laborious and inefficient, particularly when using the traditional thre...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx761
更新日期:2017-10-13 00:00:00
abstract::The sequence of the 1173 nt 12S kinetoplast ribosomal RNA from Leishmania tarentolae was determined from the maxicircle DNA sequence, and the 5' and 3' ends localized by primer runoff and S1 nuclease protection experiments. The gene was shown to be free of introns by S1 nuclease analysis. A partial secondary structure...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.7.2337
更新日期:1985-04-11 00:00:00
abstract::It has been recently reported that the pR plasmid enhances the UV survival in E.coli c600. In order to test whether this function may be expressed also in mammalian cells, LTA (tk- aprt-) mouse cells were cotransformed with pR plasmid DNA and ptk1 plasmid as selectable marker. Tk+ transformants were analyzed for their...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.11.3679
更新日期:1983-06-11 00:00:00
abstract::Virulence factor database (VFDB) was set up in 2004 dedicated for providing current knowledge of virulence factors (VFs) from various medical significant bacterial pathogens to facilitate pathogenomic research. Nowadays, complete genome sequences of almost all the major pathogenic microbes have been determined, which ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm951
更新日期:2008-01-01 00:00:00
abstract::Efficient strategies for precise genome editing in human-induced pluripotent cells (hiPSCs) will enable sophisticated genome engineering for research and clinical purposes. The development of programmable sequence-specific nucleases such as Transcription Activator-Like Effectors Nucleases (TALENs) and Cas9-gRNA allows...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt555
更新日期:2013-10-01 00:00:00
abstract::The beta protein encoded by the Streptococcus pyogenes plasmid pSM19035 is a site-specific recombinase involved in both resolution of plasmid multimers into monomers and DNA inversion. It has been proposed that the DNA region to which the beta recombinase binds to mediate recombination includes a promoter from which o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.10.1855
更新日期:1994-05-25 00:00:00
abstract::The repAC operon of plasmid RSF1010 consists of the genes for proteins E, F, RepA (DNA helicase), and RepC (origin-binding initiator protein) and is transcriptionally initiated by a promoter called P4. We have studied the expression of the repAC operon in vivo by using fusions to the lacZ reporter gene. The results sh...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.21.6215
更新日期:1990-11-11 00:00:00
abstract::The three chromosomal DNAs of S. pombe have been fractionated by pulsed field gel electrophoresis. The resulting molecular karyotype will greatly speed gene mapping in this organism, and it indicates that the separation range of the technique extends to DNA molecules as large as 9,000,000 base pairs. ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.11.4481
更新日期:1987-06-11 00:00:00
abstract::DNA double-strand breaks are repaired by end-joining or homologous recombination. A key-committing step of recombination is DNA end resection. In resection, phosphorylated CtIP first promotes the endonuclease of MRE11-RAD50-NBS1 (MRN). Subsequently, CtIP also stimulates the WRN/BLM-DNA2 pathway, coordinating thus both...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa273
更新日期:2020-06-04 00:00:00
abstract::POGO-DB (http://pogo.ece.drexel.edu/) provides an easy platform for comparative microbial genomics. POGO-DB allows users to compare genomes using pre-computed metrics that were derived from extensive computationally intensive BLAST comparisons of >2000 microbes. These metrics include (i) average protein sequence ident...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt1094
更新日期:2014-01-01 00:00:00
abstract::More than 20 different heterogeneous nuclear ribonucleoproteins (hnRNPs) are associated with pre-mRNAs in the nucleus of mammalian cells and these proteins appear to influence pre-mRNA processing and other aspects of mRNA metabolism and transport. The arrangement of hnRNP proteins on pre-mRNAs is likely to be unique f...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.6.1059
更新日期:1994-03-25 00:00:00
abstract::Lambda-red system-based recombinogenic engineering is a powerful new method to engineer DNA without the need for restriction enzymes or ligases. Here, we report the use of a single selectable marker to enhance the usefulness of this approach. The strategy is to utilize the thymidylate synthase A (thyA) gene, which enc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gni059
更新日期:2005-03-30 00:00:00
abstract::Unoxidized crystalline silicon, characterized by high purity, high homogeneity, sturdiness and an atomically flat surface, offers many advantages for the construction of electronic miniaturized biosensor arrays upon attachment of biomolecules (DNA, proteins or small organic compounds). This allows to study the inciden...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gnj034
更新日期:2006-02-28 00:00:00
abstract::The Agrobacterium tumefaciens Ti plasmid contains at least six transcriptional units (designated vir loci) which are essential for efficient crown gall tumorigenesis. Mutations in one of these loci, virE, result in a sharply attenuated virulence phenotype. In the present communication, we have analyzed the virE operon...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.2.825
更新日期:1987-01-26 00:00:00
abstract::Using cyanoethyldiisopropylamino phosphoramidite chemistry, four oligonucleotides constituting a part of the sequence of the initiator t-RNA from B. subtilis were synthesized. For the protection of the exocyclic amino functions of bases, phenoxyacetyl group was used for adenine and guanine, and acetyl group was prefer...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.18.7381
更新日期:1989-09-25 00:00:00
abstract::Human foamy or spuma virus (HFV) codes for a distinct set of pol gen products. To determine the minimal requirements for the HFV enzymatic activities, defined residues of the reverse transcriptase (RT) and ribo-nuclease H (RNase H) domain of the HFV pol gene were mutated by site-specific PCR mutagenesis. The mutant ge...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.14.2621
更新日期:1995-07-25 00:00:00
abstract::Reverse transcription of HIV-1 RNA is initiated from the 3' end of a tRNA3Lys molecule annealed to the primer binding site (PBS). An additional interaction between the anticodon loop of tRNA3Lys and a viral A-rich loop is required for efficient initiation of reverse transcription of the HIV-1 MAL isolate. In the HIV-1...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg754
更新日期:2003-10-01 00:00:00
abstract::Scanning tunneling microscopy (STM) reveals nanometer scale details of hydrated DNA but the interpretation of the images is controversial because of substrate artifacts and the lack of a theory for image contrast. We demonstrate that we have overcome these problems by identifying five DNA samples by their STM images a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.25.5896
更新日期:1993-12-25 00:00:00
abstract::A restriction endonuclease, ApaI, has been partially purified from Acetobacter pasteurianus. This enzyme cleaves bacteriophage lambda DNA and Simian virus 40 DNA at one site, adenovirus-2 DNA at more than nine sites, but it does not cleave phi X174 DNA nor plasmid pBR322 DNA. This enzyme recognizes the sequence (formu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.13.4409
更新日期:1983-07-11 00:00:00
abstract::OligoArrayDb is a comprehensive database containing pangenomic oligonucleotide microarray probe sets designed for most of the sequenced genomes that are not covered by commercial catalog arrays. The availability of probe sequences, associated with custom microarray fabrication services offered by many companies and co...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn761
更新日期:2009-01-01 00:00:00
abstract::DNA polymerase III (DNA pol III) efficiently replicates the Escherichia coli genome, but it cannot bypass DNA damage. Instead, translesion synthesis (TLS) DNA polymerases are employed to replicate past damaged DNA; however, the exchange of replicative for TLS polymerases is not understood. The umuD gene products, whic...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks229
更新日期:2012-07-01 00:00:00
abstract::Expression of the wild-type p53 tumor suppressor gene has been found to play an important role in the regulation of cellular proliferation and differentiation. In addition, in many transformed cells and primary tumors, the gene has undergone allelic deletions and mutant forms of the p53 gene are expressed at elevated ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.2.345
更新日期:1993-01-25 00:00:00
abstract::Embryonic stem cells (ESCs) and meiosis are featured by relatively higher frequent homologous recombination associated with DNA double strand breaks (DSB) repair. Here, we show that Pold3 plays important roles in DSB repair, telomere maintenance and genomic stability of both ESCs and spermatocytes in mice. By attempti...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky098
更新日期:2018-04-20 00:00:00
abstract::Several plasmids which direct the expression of human interferon-gamma (IFN-gamma) cDNA in the yeast Saccharomyces cerevisiae under the transcriptional control of the 3-phosphoglycerate kinase (PGK) promoter have been constructed. Up to 25 x 10(6) units per liter culture of biologically active IFN-gamma are synthesize...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.6.1819
更新日期:1983-03-25 00:00:00
abstract::In the past year, DDBJ (http://www.ddbj.nig.ac.jp) collected and released 1,956,826 entries or 1,741,313,111 bases. The released data include approximately 90,000 ESTs and cDNAs of Macaca fascicularis, and 280 million bases of mouse GSS. In addition to the data collection, we have indexed the submitted data to the Int...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkj111
更新日期:2006-01-01 00:00:00