SEARCH · PubMed Health

Results for “Open data”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 721 records · Page 40Linked to original sources

PubMed2001

The plastid chromosome of spinach (Spinacia oleracea): complete nucleotide sequence and gene organization.

The chloroplast chromosome of spinach (Spinacia oleracea) is a double-stranded circular DNA molecule of 150,725 nucleotide pairs. A comparison of this chromosome with those of the three other autotrophic dicotyledons for which complete DNA sequences of plastid chromosomes are available confirms a conserved overall structure. Three classes of open reading frames were distinguished: (1) genes of known function which include 108 unique loci, (2) three hypothetical chloroplast reading frames (ycfs) that are highly conserved interspecifically, and (3) species-specific or rapidly diverging 'open reading frames'. A detailed transcript study of one of the latter (ycf15) shows that these loci may be transcribed, but do not constitute protein-coding genes.

Base Sequence↗

PubMed1997

Bovine papillomavirus type 5: partial sequence and comparison with other bovine papillomaviruses.

Two restriction fragments of bovine papillomavirus type 5 (BPV5), of a genomic size of 1.6 and 1.2 kb were subcloned and sequenced. One of them seemed to correspond to the 3' end of the E1 open reading frame (ORF) and the other to the region of the E7, E8 and 5' end of the E1 ORF. Alignments of these fragments with other BPVs showed that BPV5 is only distantly related to the other 5 BPVs.

Base Sequence↗

PubMed2004

Chromosome-encoded CTX-M-3 from Kluyvera ascorbata: a possible origin of plasmid-borne CTX-M-1-derived cefotaximases.

A gene identical to plasmid-borne bla(CTX-M-3) is present in the chromosome of one Kluyvera ascorbata strain. It is associated with a structure including an inverted repeat right and an open reading frame 477-like gene probably involved in the mobilization of bla(CTX-M-3). Two other K. ascorbata strains rendered the previously described bla(KLUA-9) gene.

Escherichia coli↗

PubMed2002

Identification of target genes regulated by the two-component system HP166-HP165 of Helicobacter pylori.

Two-component systems are signal transduction systems which enable bacteria to regulate cellular functions in response to changing environmental conditions. In most cases regulation is accomplished on the transcriptional level by a response regulator protein, which, according to the phosphorylation state of its receiver domain, displays different affinities for its target promoters. Here we describe identification of genes regulated by the two-component system HP166-HP165 of Helicobacter pylori and characterization of the corresponding target promoters. We demonstrated that expression of the HP166-HP165 two-component system is negatively autoregulated under conditions favoring autophosphorylation of the histidine kinase. Furthermore, we found that response regulator HP166 activates transcription of genes encoding a protein family with an unknown function present in H. pylori 26695, as well as an operon composed of five H. pylori-specific genes. While open reading frame HP166 is an essential gene, the target genes of the response regulator are not required for growth under in vitro culture conditions.

Base Sequence↗

PubMed1993

The rbcL gene sequence from chestnut indicates a slow rate of evolution in the Fagaceae.

The nucleotide sequence was obtained for the chloroplast gene coding for the large subunit of the ribulose 1,5-bisphosphate carboxylase (rbcL) of chestnut (Castanea sativa Mill.), a member of the woody family Fagaceae. Amplification primers downstream and upstream the rbcL open reading frame are also described. By comparing with other angiosperm sequences, we show that the rate of evolution of rbcL in the family Fagaceae is much slower than that observed for the families of annuals analyzed.

Base Sequence↗

PubMed1995

The complete sequence of a 9037 bp DNA fragment of the right arm of Saccharomyces cerevisiae chromosome VII.

We report the sequence of a 9037 bp fragment from the right arm of Saccharomyces cerevisiae chromosome VII. Analysis of the sequence revealed four complete open reading frames (ORFs), namely G7572, G7576, G7579 and G7584. The first three corresponded, respectively, to the previously cloned genes: HIP1, coding for a high-affinity histidine-specific permease, TDH1, one of the known genes coding for glyceraldehyde-3-phosphate dehydrogenase and ODPX, which encodes a precursor of protein X, a component of the pyruvate dehydrogenase complex. The ORF G7584 showed 35.8% identity with a hypothetical protein of Caenorhabditis elegans chromosome 3. The reported sequence has been deposited in the EMBL data library under Accession Number X82408.

ATP-Binding Cassette Transporters↗

PubMed1998

Evidence that whitefly-transmitted cowpea mild mottle virus belongs to the genus Carlavirus.

Two strains of whitefly-transmitted cowpea mild mottle virus (CPMMV) causing severe (CPMMV-S) and mild (CPMMV-M) disease symptoms in peanuts were collected from two distinct agro-ecological zones in India. The host-range of these strains was restricted to Leguminosae and Chenopodiaceae, and each could be distinguished on the basis of symptoms incited in different hosts. The 3'-terminal 2500 nucleotide sequence of the genomic RNA of both the strains was 70% identical and contains five open reading frames (ORFs). The first three (P25, P12 and P7) overlap to form a triple gene block of proteins, P32 encodes the coat protein, followed by P12 protein located at the 3' end of the genome. Genome organization and pair-wise comparisons of amino acid sequences of proteins encoded by these ORFs with corresponding proteins of known carlaviruses and potexviruses suggest that CPMMV-S and CPMMV-M are closely related to viruses in the genus Carlavirus. Based on the data, it is concluded that CPMMV is a distinct species in the genus Carlavirus.

Amino Acid Sequence↗

PubMed1998

A differentially expressed prion gene mRNA is found in prion-infected mouse brains and in N2A cells but not in uninfected mice.

The transmissible spongiform encephalopathies comprise a group of fatal neurodegenerative diseases that are characterized by the conversion of the normal host cellular prion protein (PrPC) to the abnormal protease-resistant isoform PrPSC. Distinct alterations of transcriptional regulation during disease progression could not be observed. The regulation of transcription 5' and 3' to the previously described cap sites of the prion gene mRNA as well as usage of internal short ORF's was investigated. We identified a mRNA species which is expressed differentially in prion-infected mice and in N2A cells. This mRNA is detectable neither in uninfected mice nor in early stages of the disease. The novel mRNA contains two short open reading frames which encode two small peptides with a calculated molecular weight of 2.1 kDA and 0.7 kDa. These peptides were also found to be expressed in vitro and in vivo.

Animals↗

PubMed1991

A bacterial homolog to HPRT.

The deduced 182 amino acid sequence of an open reading frame in the photosynthetic bacterium Rhodobacter capsulatus shows significant similarity to the hypoxanthine-guanine phosphoribosyltransferases of other organisms. This similarity includes conserved amino acid residues involved in Lesch-Nyhan syndrome.

Amino Acid Sequence↗

PubMed1991

Cloning and sequencing of the casein kinase 2 alpha subunit from Zea mays.

The nucleotide sequence of the cDNA coding for the alpha subunit of casein kinase 2 of Zea mays has been determined. The cDNA clone contains an open reading frame of 996 nucleotides encoding a polypeptide comprising 332 amino acids. The primary amino acid sequence exhibits 75% identity to the alpha subunit and 71% identity to the alpha' subunit of human casein kinase 2.

Amino Acid Sequence↗

PubMed2006

Extrachromosomal DNA isolated from tomato big bud and Candidatus Phytoplasma australiense phytoplasma strains.

The nucleotide sequences of two extrachromosomal elements from tomato big bud (TBB) and one extrachromosomal element from Candidatus Phytoplasma australiense (Ca. P. australiense) phytoplasmas were determined. Both TBB plasmids (3319 and 4092 bp) contained an open reading frame ( approximately 570 bp) with homology to the rolling circle replication initiator protein (Rep). This gene was shorter than the rep genes identified from other phytoplasma plasmids, geminiviruses and bacterial plasmids. Both TBB extrachromosomal DNAs (eDNAs) encoded a putative DNA primase (dnaG) gene, a chromosomal gene required for DNA replication and which contains the conserved topoisomerase/primase domain. We speculate that the replication mechanism for the TBB phytoplasma eDNA involves the dnaG gene instead of the rep gene. The Ca. P. australiense eDNA (3773 bp) was shown to be circular and contained four open reading frames. The rep gene was encoded on ORF 1 and had homology to both plasmid (pLS1) and geminivirus-like domains.

Amino Acid Sequence↗

PubMedDate not supplied

Sequence of a Euplotes crassus macronuclear DNA molecule encoding a protein with homology to a rat form-I phosphoinositide-specific phospholipase C.

A 604-base pair macronuclear DNA molecule from the hypotrichous ciliate Euplotes crassus was cloned and its DNA sequence determined. The DNA sequence contains an open reading frame capable of encoding a protein 141 amino acids in length. The putative protein contains significant sequence similarity to other eukaryotic proteins, including the rat form-I phosphoinositide-specific phospholipase-C.

Amino Acid Sequence↗

PubMed1994

Identification and sequencing of pyrG, the CTP synthetase gene of Azospirillum brasilense Sp7.

An 18.5-kb DNA fragment carrying the trpGDC cluster of Azospirillum brasilense Sp7 was previously cloned, yielding cosmid pAB1005. Attempts to identify trpA in the vicinity of trpGDC failed but led to the detection of a locus strongly homologous to pyrG, the structural gene for the CTP synthetase. The function of the A. brasilense pyrG gene was verified by complementation of the cytidine-requiring PyrG-deficient mutant JF646 of Escherichia coli. A second open reading frame was identified downstream of pyrG. The deduced amino acid sequence showed homology to dienelactone hydrolases of Pseudomonas and Alcaligenes, enzymes involved in utilization of halogenated aromatic compounds.

Amino Acid Sequence↗

PubMed1993

Component A2 of methylcoenzyme M reductase system from Methanobacterium thermoautotrophicum delta H: nucleotide sequence and functional expression by Escherichia coli.

The gene for component A2 of the methylcoenzyme M reductase system from Methanobacterium thermoautotrophicum delta H was cloned, and its nucleotide sequence was determined. The gene for A2, designated atwA, encodes an acidic protein of 59,335 Da. Amino acid sequence analysis revealed partial homology of A2 to a number of eucaryotic and bacterial proteins in the ATP-binding cassette (ABC) family of transport systems. Component A2 possesses two ATP-binding domains. A 2.2-kb XmaI-BamHI fragment containing atwA and the surrounding open reading frames was cloned into pGEM-7Zf(+). A cell extract from this strain replaced purified A2 from M. thermoautotrophicum delta H in an in vitro methylreductase assay.

Adenosine Triphosphate↗

PubMed1993

Expression and identification of hepatitis C virus polyprotein cleavage products.

Hepatitis C virus (HCV) is the major cause of transfusion-acquired non-A, non-B hepatitis. HCV is an enveloped positive-sense RNA virus which has been classified as a new genus in the flavivirus family. Like the other two genera in this family, the flaviviruses and the pestiviruses, HCV polypeptides appear to be produced by translation of a long open reading frame and subsequent proteolytic processing of this polyprotein. In this study, a cDNA clone encompassing the long open reading frame of the HCV H strain (3,011 amino acid residues) has been assembled and sequenced. This clone and various truncated derivatives were used in vaccinia virus transient-expression assays to map HCV-encoded polypeptides and to study HCV polyprotein processing. HCV polyproteins and cleavage products were identified by using convalescent human sera and a panel of region-specific polyclonal rabbit antisera. Similar results were obtained for several mammalian cell lines examined, including the human HepG2 hepatoma line. The data indicate that at least nine polypeptides are produced by cleavage of the HCV H strain polyprotein. Putative structural proteins, located in the N-terminal one-fourth of the polyprotein, include the capsid protein C (21 kDa) followed by two possible virion envelope proteins, E1 (31 kDa) and E2 (70 kDa), which are heavily modified by N-linked glycosylation. The remainder of the polyprotein probably encodes nonstructural proteins including NS2 (23 kDa), NS3 (70 kDa), NS4A (8 kDa), NS4B (27 kDa), NS5A (58 kDa), and NS5B (68 kDa). An 82- to 88-kDa glycoprotein which reacted with both E2 and NS2-specific HCV antisera was also identified (called E2-NS2). Preliminary results suggest that a fraction of E1 is associated with E2 and E2-NS2 via disulfide linkages.

Antigens, Viral↗

PubMed1992

Characterisation of genes encoding two novel members of the aldo-keto reductase superfamily.

The predicted amino acid sequence of the protein encoded by a cDNA clone isolated from the protozoan haemoparasite Babesia bovis has approximately 22% amino acid identity with the Pichia stipitis xylose reductase. There are similar levels of amino acid identity with other members of the aldo-keto reductase superfamily. The identities include many residues highly conserved in the superfamily. However, the amino acid sequence of the B. bovis protein (AKR1) clearly lies outside the cluster of the previously characterized members of the superfamily. A putative protein encoded by a previously undescribed partially characterized open reading frame at the igrA (increased glyphosate resistance) locus of Pseudomonas sp. strain PG2982 also exhibits similarity to AKR1 and the aldo-keto reductases.

Alcohol Oxidoreductases↗

PubMed1991

Purification of the alternative sigma factor, sigma 54, from Salmonella typhimurium and characterization of sigma 54-holoenzyme.

The alternative sigma factor sigma 54 of enteric bacteria, or its homologue in other purple bacteria, is required for transcription of genes whose products have diverse physiological roles. Previous studies have indicated that sigma 54 confers on core RNA polymerase the ability to recognize a specific class of promoters but not the ability to isomerize from closed to open complexes. Isomerization requires ATP and one member of a family of activator proteins, it being different activator proteins that allow this form of polymerase to respond to different physiological signals. We have developed a strategy for overproducing and purifying sigma 54 from Salmonella typhimurium and have studied several biochemical properties of reconstituted sigma 54-holoenzyme. The initial binding constant KB for the formation of closed complexes between this holoenzyme and the ginA promoter in our transcription buffer is approximately 3 x 10(8) M-1, which was determined from DNaseI protection assays at 37 degrees C. After the formation of open complexes, several properties of sigma 54-holoenzyme appear to be similar to those of sigma 70-holoenzyme. We have determined the complete nucleotide sequence of the gene encoding sigma 54 (ntrA) in Salmonella.

Amino Acid Sequence↗

PubMed1996

The sequence of a 30 kb fragment on the left arm of chromosome XV from Saccharomyces cerevisiae reveals 15 open reading frames, five of which correspond to previously identified genes.

We report the sequence of a 30,469 bp long DNA fragment on the left arm of chromosome XV of Saccharomyces cerevisiae. The fragment contains 15 open reading frames (ORFs) of at least 300 bp. Five previously sequenced yeast genes, PHO80, TIR2, SLG1, the gene encoding the subtilisin-like protease III precursor and the gene coding for ATP-dependent permease, are found among these ORFs. By DNA sequence comparison, two ORFs identified previously reported expressed sequence tags from yeast. Of the proteins encoded by the remaining eight ORFs, six show similarities to proteins from different organisms and two lack detectable similarity with any amino acid sequence described in public data banks.

Chromosomes, Fungal↗