Abstract:
:We have developed a web-based resource (available at www.ciliate.org) for researchers studying the model ciliate organism Tetrahymena thermophila. Employing the underlying database structure and programming of the Saccharomyces Genome Database, the Tetrahymena Genome Database (TGD) integrates the wealth of knowledge generated by the Tetrahymena research community about genome structure, genes and gene products with the newly sequenced macronuclear genome determined by The Institute for Genomic Research (TIGR). TGD provides information curated from the literature about each published gene, including a standardized gene name, a link to the genomic locus in our graphical genome browser, gene product annotations utilizing the Gene Ontology, links to published literature about the gene and more. TGD also displays automatic annotations generated for the gene models predicted by TIGR. A variety of tools are available at TGD for searching the Tetrahymena genome, its literature and information about members of the research community.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Stover NA,Krieger CJ,Binkley G,Dong Q,Fisk DG,Nash R,Sethuraman A,Weng S,Cherry JMdoi
10.1093/nar/gkj054keywords:
subject
Has Abstractpub_date
2006-01-01 00:00:00pages
D500-3issue
Database issueeissn
0305-1048issn
1362-4962pii
34/suppl_1/D500journal_volume
34pub_type
杂志文章abstract::IStrons are chimeric genetic elements composed of a group I intron associated with an insertion sequence (IS). The group I intron is a catalytic RNA providing the IStron with self-splicing ability, which renders IStron insertions harmless to the host genome. The IS element is a DNA transposon conferring mobility, and ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku939
更新日期:2014-11-10 00:00:00
abstract::Two DNA hexadecamers containing one central 5'-GC-3' base step have been examined by footprinting methodology in the presence and absence of actinomycin D. The results of these studies, coupled with imino proton NMR measurements indicate that the antitumor drug causes a change in DNA conformation at a distance from th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.23.11125
更新日期:1988-12-09 00:00:00
abstract::The transcriptional regulator Spx plays a key role in maintaining the redox homeostasis of Bacillus subtilis cells exposed to disulfide stress. Defects in Spx were previously shown to lead to differential expression of numerous genes but direct and indirect regulatory effects could not be distinguished. Here we identi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks755
更新日期:2012-10-01 00:00:00
abstract::Horizontally acquired genes are typically regulated by ancestral regulators. This regulation enables expression of horizontally acquired genes to be coordinated with that of preexisting genes. Here, we report a singular example of the opposite regulation: a horizontally acquired gene that controls an ancestral regulat...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa813
更新日期:2020-11-04 00:00:00
abstract::Cell specific expression of the insulin gene is achieved through transcriptional mechanisms operating on 5' flanking DNA elements. In the enhancer of rat I insulin gene, two elements, the Nir and Far boxes, located at positions -104 and -233 respectively and containing the same octameric motif are essential for B cell...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.7.1595
更新日期:1993-04-11 00:00:00
abstract::The DNA-binding protein RdgC has been identified as an inhibitor of RecA-mediated homologous recombination in Escherichia coli. In Neisseria species, RdgC also has a role in virulence-associated antigenic variation. We have previously solved the crystal structure of the E. coli RdgC protein and shown it to form a toro...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq509
更新日期:2010-10-01 00:00:00
abstract::Cytokines are cell-to-cell signaling proteins that play a central role in immune development, pathogen responses, and diseases. Cytokines are highly regulated at the transcriptional level by combinations of transcription factors (TFs) that recruit cofactors and the transcriptional machinery. Here, we mined through thr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky787
更新日期:2018-10-12 00:00:00
abstract::We previously reported that O4-alkyl dTTPs could replace, for short times, dTTP in polymer synthesis [Singer et al., PNAS 83, 26-32, 1986]. The reasons for such early termination of synthesis could be either proofreading or the eventual formation of weakly paired primer termini. Utilizing the known 3'----5' exonucleol...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.16.6735
更新日期:1986-08-26 00:00:00
abstract::Aside from classical loops among G-quadruplexes, the unique leaped V-shape scaffold spans over three G-tetrads, without any intervening residues. This scaffold enables a sharp reversal of two adjacent strand directions and simultaneously participates in forming the G-tetrad core. These features make this scaffold itse...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky1167
更新日期:2019-02-20 00:00:00
abstract::The persistence of fetal hemoglobin in many patients with deletion type beta thalassemias and the expression patterns of human globin genes in transgenic mice suggest that gamma- to beta-globin gene switching results primarily from competition of gamma- and beta-globin genes for interaction with the beta-globin locus ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.14.2736
更新日期:2000-07-15 00:00:00
abstract::A physical mapping strategy has been developed to verify and accelerate the assembly and gap closure phase of a microbial genome shotgun-sequencing project. The protocol was worked out during the ongoing Pseudomonas putida KT2440 genome project. A macro-restriction map was constructed by linking probe hybridisation of...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.22.e110
更新日期:2001-11-15 00:00:00
abstract::Diethyl pyrocarbonate reacts with the single-stranded loops of cruciform structures with great selectivity. Adenine bases are carbethoxylated, as a result of which the backbone may be cleaved with piperidine, and the level of chemical modification at each base may be determined. We have studied the ColE1 and (A-T)34 c...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.10.3995
更新日期:1986-05-27 00:00:00
abstract::The TGGCA protein, the chicken homologue of HeLa cell NF-I, was purified to homogeneity from liver tissue by a procedure which includes preparative mobility shift electrophoresis (PMSE) as the final step. PMSE was here adjusted for the isolation of the TGGCA protein, but can be used as a general method to characterize...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.23.9707
更新日期:1987-12-10 00:00:00
abstract::The RNA-dependent RNA polymerases (RdRPs) encoded by RNA viruses represent a unique class of nucleic acid polymerases. RdRPs are essential in virus life cycle due to their central role in viral genome replication/transcription processes. However, their contribution in host adaption has not been well documented. By sol...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa1250
更新日期:2021-01-06 00:00:00
abstract::The polyadenylate binding protein 1 (PABPN1) is a ubiquitously expressed RNA binding protein vital for multiple steps in RNA metabolism. Although PABPN1 plays a critical role in the regulation of RNA processing, mutation of the gene encoding this ubiquitously expressed RNA binding protein causes a specific form of mus...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx786
更新日期:2017-10-13 00:00:00
abstract::Transcriptomics (at the level of single cells, tissues and/or whole organisms) underpins many fields of biomedical science, from understanding the basic cellular function in model organisms, to the elucidation of the biological events that govern the development and progression of human diseases, and the exploration o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq667
更新日期:2010-09-01 00:00:00
abstract::The function of non-coding RNA genes largely depends on their secondary structure and the interaction with other molecules. Thus, an accurate prediction of secondary structure and RNA-RNA interaction is essential for the understanding of biological roles and pathways associated with a specific RNA gene. We present web...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr248
更新日期:2011-07-01 00:00:00
abstract::Two similar, but not identical, models have been proposed for the amino acid-base pair contacts in the CAP-DNA complex ('Model I,' Weber, I. and Steitz, T., Proc. Natl. Acad. Sci. USA, 81, 3973-3977, 1984; 'Model II,' Ebright, et al., Proc. Natl. Acad. Sci. USA, 81, 7274-7278, 1984). One difference between the two mod...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.23.6853
更新日期:1990-12-11 00:00:00
abstract::Reactive oxygen species (ROS) have been implicated as the cause of cumulative damage to DNA, proteins and lipids that can ultimately result in cell death. A common problem when measuring oxidative DNA damage has been the introduction of modifications in the native state of the molecule by many DNA isolation methods. W...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.4.968
更新日期:2000-02-15 00:00:00
abstract::A recently reported cDNA clone coding for human promyelocytic L apoferritin, shows some differences with a liver L apoferritin cDNA. We have investigated if these differences are due to the expression of different genes or to an alternative transcription of an unique gene. In this paper we report data suggesting that ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.7.2863
更新日期:1986-04-11 00:00:00
abstract::The binding of nine aminoalkyl adenylates to isoleucyl-tRNA synthetase from Escherichia coli MRE 600 was measured and compared with the binding of the cognate amino acids. It was found that they bind rather tightly to the enzyme, the Kd's ranging from 3.1.10(-4) M with glycinol-AMP ester to 3.7.10(-9) M with L-isoleuc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/4.3.673
更新日期:1977-03-01 00:00:00
abstract::Immunotoxoin-mediated cell targeting (IMCT) is a technique for conditionally ablating specific cell types based on the cytotoxic activity of a recombinant immunotoxin anti-Tac (Fv)-PE40. To examine the feasibility of this technique for the negative selection in mouse embryonic stem (ES) cells, we investigated the resp...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.18.3653
更新日期:1996-09-15 00:00:00
abstract::Using an in vitro transcription system for Saccharomyces cerevisiae RNA polymerase I, we have analyzed Pol I promoter deletion mutants and mapped the boundaries of the promoter between positions -155 and +27. The 5'-boundary of the minimal core promoter capable of transcription initiation, however, was found to lie be...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.19.5363
更新日期:1991-10-11 00:00:00
abstract::The secondary structure of V4, the largest variable area of eukaryotic small subunit ribosomal RNA, was re-examined by comparative analysis of 3253 nucleotide sequences distributed over the animal, plant and fungal kingdoms and a diverse set of protist taxa. An extensive search for compensating base pair substitutions...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.23.4698
更新日期:2000-12-01 00:00:00
abstract::We have reported on the differences in site-specific cleavage between DNA and DNA-RNA hybrids by various prototypic DNA cleavers (accompanying paper). In the case of bleomycin (BLM), degradation at 5'-GC-3'sites was suppressed relative to the same sequence in double-stranded DNA, while 5'-GT-3' damage remained constan...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.9.1846
更新日期:1997-05-01 00:00:00
abstract::FANTOM DB, the database of Functional Annotation of RIKEN Mouse cDNA Clones, is designed to store sequence information of RIKEN full-length enriched mouse cDNA clones, graphical views of sequence analysis results, curated functional annotation information and additional descriptions, including Gene Ontology terms. RIK...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.1.116
更新日期:2002-01-01 00:00:00
abstract::Genes from yeast to mammals are frequently subject to non-coding transcription of their antisense strand; however the genome-wide role for antisense transcription remains elusive. As transcription influences chromatin structure, we took a genome-wide approach to assess which chromatin features are associated with nasc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv666
更新日期:2015-09-18 00:00:00
abstract::DNA polymerase mu is a member of the mammalian pol X family and reduces deletion during chromosome break repair by nonhomologous end joining (NHEJ). This biological role is linked to pol mu's ability to promote NHEJ of ends with noncomplementary 3' overhangs, but questions remain regarding how it performs this role. W...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn164
更新日期:2008-05-01 00:00:00
abstract::The putative role of double-strand breaks (DSBs) created in vitro by restriction enzyme cleavage in or near CGG*CCG or CTG*CAG repeat tracts on their genetic instabilities, both within the repeats and in their flanking sequences, was investigated in an Escherichia coli plasmid system. DSBs at TRS junctions with the ve...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl612
更新日期:2006-01-01 00:00:00
abstract::RecBCD enzyme acts in the major pathway of homologous recombination of linear DNA in Escherichia coli. The enzyme unwinds DNA and is an ATP-dependent double-strand and single-strand exonuclease and a single-strand endonuclease; it acts at Chi recombination hotspots (5'-GCTGGTGG-3') to produce a recombinogenic single-s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.9.2125
更新日期:1998-05-01 00:00:00