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Results for “Sequence Analysis, DNA”

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At least 199 records · Page 11Linked to original sources

PubMed1986

Rat liver glutathione S-transferases. DNA sequence analysis of a Yb2 cDNA clone and regulation of the Yb1 and Yb2 mRNAs by phenobarbital.

We have constructed a cDNA clone, pGTA/C48, which is complementary to the rat liver glutathione S-transferase Yb2 mRNA. Recombinant clone pGTA/C48 contains a cDNA insert of 845 base pairs which overlaps nucleotides 108-952 of the Yb1 cDNA clone, pGTA/C44, described previously by our laboratory (Ding, G. J.-F., Lu, A. Y. H., and Pickett, C. B. (1985) J. Biol. Chem. 260, 13268-13271). Over the protein coding region of the Yb1 and Yb2 cDNA clones there is an 84% nucleotide sequence homology, whereas the 3' untranslated regions are only 32% homologous. The complete amino acid sequence of the Yb2 subunit has been determined from a combination of DNA sequence analysis of pGTA/C48 and conventional protein sequence analysis of the glutathione S-transferase Yb1 Yb2 heterodimer. The Yb2 subunit is comprised of 218 amino acids with a molecular weight of 25,705 and has an amino acid sequence which is 79% homologous to the sequence of the Yb1 subunit. We have utilized the divergent 3' untranslated regions of three rat liver glutathione S-transferase cDNA clones as specific probes to determine the effect of phenobarbital on the level of Yb1, Yb2, and Yc mRNAs. Our results clearly show that the Yb1 and Yb2 mRNAs are elevated approximately 5-6-fold by phenobarbital administration; whereas the Yc mRNA is only modestly elevated by this xenobiotic. Finally, our data suggest that the Yb2 subunit is encoded by a gene(s) which is distinct from the Yb1 gene(s) and provides direct evidence for the existence of multiple glutathione S-transferase Yb genes in the rat.

Amino Acid Sequence↗

PubMed2001

[DNA sequence analysis and expression of the recombinant plasmid pBX1 from Borrelia burgdorferi B31 strain].

OBJECTIVE: This study was to provide the target antigen for the development of a Lyme disease vaccine and serodiagnosis reagent. METHODS: We used the automatic DNA sequencing machine (Model 377) to detect the nucleotide sequence of the inserted part of the recombinant plasmid pBX1 from Borrelia burgdorferi B31 strain. The restriction enzyme map of the inserted part of pBX1 was analysed by using computer software. The expressed product of pBX1 in E. coli XLI-Blue MRF was analysed by using SDS-PAGE and western-blotting. RESULTS: 1. DNA sequencing showed that pBX1 contained a 477bp inserted gene fragment, and when it was compared with the published sequence of the specific region of the gene of the 83 kd antigen protein from Borrelia burgdorferi B31 strain, only one amino acid codon was different. 2. The restriction enzyme map of the inserted part of pBX1 was successfully constructed. 3. The recombinant plasmid pBX1 expressed a 29 kd fusion protein in E. coli XL1-Blue MRF' after induced with IPTG. The recombinant fusion protein could be recongnized by rabbit polyclonal antiserum against Borrelia burgdorferi B31 strain. CONCLUSION: A recombinant plasmid which contains the gene fragment encoding the specific region of the 83 kd antigen protein from Borrelia burgdorferi B31 strain has been successfully constructed. The recombinant plasmid can stably express 29 kd fusion protein in E. coli XL1-Blue MRF'. These results could serve as a base of further studies on the usefulness of the fusion protein in serodiagnosis and vaccine for Lyme disease.

Animals↗

PubMed1996

DNA sequence analysis of hprt mutations in lymphocytes from Sprague-Dawley rats treated with 7,12-dimethylbenz[a]anthracene.

Treatment of female Sprague-Dawley rats with the potent mammary gland carcinogen 7,12-dimethylbenz[a]anthracene (DMBA) results in the formation of DNA adducts with dG and dA and in the induction of 6-thioguanine-resistant (TGr) lymphocyte mutants. In this study, we have examined the types of mutations induced in TGr lymphocytes from DMBA-treated rats. DNA from 263 TGr lymphocyte clones was screened for mutations in exons 2, 3, and 8 of the hprt gene by polymerase chain reaction (PCR) amplification of the exons followed by heteroduplex analysis using denaturing gradient-gel electrophoresis. Twenty-five of the clones produced heteroduplexes in exon 2, 35 produced heteroduplexes in exon 3, and 36 produced heteroduplexes in exon 8. Direct sequence analysis of the heteroduplexes revealed 96 mutations, and at least 74 of these mutations were produced independently. Eighty-five of the total mutations were simple base pair (bp) substitutions, with A --> T and G --> T transversions being the predominant types. Seven mutations were deletions, three were complex bp substitutions, and one was an insertion. The results suggest that the types of mutations produced by DMBA in rat lymphocytes are specific to the DNA adducts produced by this compound.

9,10-Dimethyl-1,2-benzanthracene↗

PubMed2000

DNA sequence analysis of the photosynthesis region of Rhodobacter sphaeroides 2.4.1.

This paper describes the DNA sequence of the photosynthesis region of Rhodobacter sphaeroides 2.4.1 (T). The photosynthesis gene cluster is located within a approximately 73 kb Ase I genomic DNA fragment containing the puf, puhA, cycA and puc operons. A total of 65 open reading frames (ORFs) have been identified, of which 61 showed significant similarity to genes/proteins of other organisms while only four did not reveal any significant sequence similarity to any gene/protein sequences in the database. The data were compared with the corresponding genes/ORFs from a different strain of R.sphaeroides and Rhodobacter capsulatus, a close relative of R. sphaeroides. A detailed analysis of the gene organization in the photosynthesis region revealed a similar gene order in both species with some notable differences located to the pucBAC = cycA region. In addition, photosynthesis gene regulatory protein (PpsR, FNR, IHF) binding motifs in upstream sequences of a number of photosynthesis genes have been identified and shown to differ between these two species. The difference in gene organization relative to pucBAC and cycA suggests that this region originated independently of the photosynthesis gene cluster of R.sphaeroides.

Base Sequence↗

PubMed1993

DNA sequence analysis of serologically detected ELA class II haplotypes at the equine DQ beta locus.

The genetic diversity at the ELA DQ beta locus was investigated using polymerase chain reaction and DNA sequencing. Based upon serological methods 16 class II homozygous animals were selected and their genomic DNA was used. A DQ beta gene from an equine cDNA library was also sequenced. Our methodology and the similarity between the genomic and the cDNA sequences suggest that the studied locus is expressed on equine lymphocytes. In the predicted amino acid sequence the most extensive variation is located at residues 56-60. The pattern of these five amino acids is strongly correlated to the serological ELA class II specificities (W13, W22, W23, Be200). The alleles corresponding to the W23 specificity are the most divergent among the equine DQ beta alleles and also from other mammalian DQ beta sequences.

Alleles↗

PubMed2004

Complete mitochondrial DNA sequence analysis in a family with early-onset dystonia and optic atrophy.

The combination of optic atrophy and dystonia has been etiologically associated with mitochondrial DNA (mtDNA) mutations. We report here on the complete mtDNA sequence from the proband of a consanguineous family exhibiting "mitochondrial-like" optic atrophy and dystonia. A candidate tRNA(Gly) mutation was identified that was unique to the family. However, the mutation was homoplasmic in both affected and unaffected family members and we were unable to demonstrate a biochemical defect in patient mitochondria. Hence, it is unlikely that a mtDNA mutation accounts for the phenotype in this family.

Adult↗

PubMed1997

Gene identification and DNA sequence analysis in the GC-poor 20 megabase region of human chromosome 21.

In contrast to the distal half of the long arm of chromosome 21, the proximal half of approximately 20 megabases of DNA, including 21q11-21 bands, is low in GC content, CpG islands, and identified genes. Despite intensive searches, very few genes and cDNAs have been found in this region. Since the 21q11-21 region is associated with certain Down syndrome pathologies like mental retardation, the identification of relevant genes in this region is important. We used a different approach by constructing microdissection libraries specifically for this region and isolating unique sequence microclones for detailed molecular analysis. We found that this region is enriched with middle and low-copy repetitive sequences, and is also heavily methylated. By sequencing and homology analysis, we identified a significant number of genes/cDNAs, most of which appear to belong to gene families. In addition, we used unique sequence microclones in direct screening of cDNA libraries and isolated 12 cDNAs for this region. Thus, although the 21q11-21 region is gene poor, it is not completely devoid of genes/cDNAs. The presence of high proportions of middle and low-copy repetitive sequences in this region may have evolutionary significance in the genome organization and function of this region. Since 21q11-21 is heavily methylated, the expression of genes in this region may be regulated by a delicate balance of methylation and demethylation, and the presence of an additional copy of chromosome 21 may seriously disturb this balance and cause specific Down syndrome anomalies including mental retardation.

Chromosomes, Human, Pair 21↗

PubMed1999

[Analysis of kidney tumors in trichloroethylene exposed workers by comparative genomic hybridization and DNA sequence analysis].

Environmental and occupational mutagens such as chemical agents are suspected to be involved in cancer development. However, a direct link between carcinogen exposure and genetic alterations has been established only in a few examples. Carcinogen involvement in renal cell carcinoma (RCC) was recently supported by reports of an increased frequency of RCC among workers exposed to Trichloroethylene (TRI) in Germany. The aim of this study was to evaluate the phenotype and the genotype of renal tumors in occupationally TRI-exposed patients. Sporadic RCCs from TRI nonexposed patients served as control. Normal and renal tumor tissues from 12 patients with occupational histories of solvents and TRI exposure were histologically analyzed. Comparative Genomic Hybridization (CGH) was used to screen for genomic alterations along all chromosomal arms. Tumor DNA was analyzed for mutations of the von Hippel-Lindau gene (VHL) on 3p25.5 by PCR and sequencing analyses. The histological analysis revealed 9 clear cell (75%), 2 papillary RCC (18%) and 1 oncocytoma (8%). In clear cell RCC, DNA losses were frequently observed on 3p (66%), 6q (56%), 9p and 4q (44% each) and 2q (33%). DNA gains were detected on 9q, 17 (33% each) and 5q (22%). DNA gains were identified on chromosome 7 and 17 in papillary RCC. Four VHL gene mutations were found in three clear cell RCC (33%) with 3p loss. Comparisons of these results with data obtained from sporadic RCC revealed no unique phenotype, genotype or mutation pattern in the VHL gene of renal tumors after TRI exposure. Therefore, further studies on the relevance of dose and exposure time for the nephrocarcinogenic effect of TRI are indicated.

Base Sequence↗

PubMed2002

Expressed sequence tags for the chicken genome from a normalized 10-day-old white leghorn whole-embryo cDNA library. 3. DNA sequence analysis of genetic variation in commercial chicken populations.

Single nucleotide polymorphisms (SNPs) have emerged as a major class of DNA markers with the advantage of permitting the development of high-density genetic maps adequate for quantitative trait loci (QTL) identification by linkage-disequilibrium analysis. Here we describe results of a relatively high-depth survey of chicken broiler and layer populations for SNPs in targeted genomic regions of chicken expressed sequence tag (EST) sites. The sequences scanned, representing the composite sequence of 12 amplified fragments for a total of 6489 bp, were randomly distributed, occurring on six different chromosomes or linkage groups in the chicken genome. Although one of the genomic DNA sequences did not match the reference cDNA sequence, another contained an intron that separated two putative exons. The number of SNPs observed within each of the 12 EST-targeted genomic regions ranged from 0 to 10 for a total of 44 and a frequency of 0.7%. About 70% of the polymorphisms were shared between layer and broiler populations. The average heterozygosity within the populations ranged from 0.15 to 0.48, with the layer populations showing the higher heterozygosity. SNPs and oligonucleotides described will provide a resource for genetic analysis in commercial chicken populations. The data appear to indicate that the relative frequency of SNPs in the targeted regions scanned is higher than the frequency reported for any of the other regions scanned to date in other eukaryotic genomes. Additionally, the results suggest that the use of DNA pools may offer an efficient approach to SNP detection in chickens, as has been shown in other vertebrates.

Animals↗

PubMed1994

DNA sequence analysis of a 10.4 kbp region on the right arm of yeast chromosome XVI positions GPH1 and SGV1 adjacent to KRE6, and identifies two novel tRNA genes.

Determination of DNA sequence in the KRE6 region of the Saccharomyces cerevisiae genome completes a 10.4 kbp section on the extreme right arm of chromosome XVI. This segment contains two additional genes, GHP1 and SGV1 (Hwang et al., 1989; Irei et al., 1991) previously assigned physically to chromosome XVI, as well as a new tRNA(Gly) gene, and a novel tRNA(Ala) gene which is flanked by a sigma element.

Chromosome Mapping↗

PubMed2005

Quasi-interpenetrating network formed by polyacrylamide and poly(N,N-dimethylacrylamide) used in high-performance DNA sequencing analysis by capillary electrophoresis.

Quasi-interpenetrating network (IPN) formed by polyacrylamide and poly(N,N-dimethylacrylamide) was designed, synthesized, and tested as a high-performance DNA separation medium by capillary electrophoresis. The performance of quasi-IPN on DNA sequencing was determined by the acrylamide to dimethylacrylamide molar ratio, polyacrylamide molecular weight, and its size distribution. Under optimal operating conditions, quasi-IPN was able to achieve one-color DNA sequencing up to 1000 bases in 39 min, or 1200 bases in 60 min. Its performance was compared with some of the existing commercialized products, such as POP6 from Applied Biosystems and MegaBACE matrix from Amersham Biosciences. By using the ABI 310 Genetic Analyzer, even without optimized base-calling software, quasi-IPN yielded a read length of up to 700 bases of contiguous sequence (50-750 bases) in 35 min with 99.6% accuracy, or 750 bases of contiguous sequence (50-800 bases) in 37 min with 98.0% accuracy.

Acrylamides↗

PubMed1995

Zymomonas mobilis squalene-hopene cyclase gene (shc): cloning, DNA sequence analysis, and expression in Escherichia coli.

Using a DNA probe from the gene encoding squalene-hopene cyclase (SHC, EC 5.4.99.-) from the Gram-positive bacterium Alicyclobacillus acidocaldarius, we have cloned a 4.3 kb HindIII fragment of chromosomal DNA from Zymomonas mobilis. An open reading frame of 1977 bp was detected that could encode a protein of 658 amino acids with a calculated molecular mass of 74077 Da. Under the control of lac or tac promoters, this gene, shc, was expressed in Escherichia coli K12 strains and its product had squalene-hopene cyclase activity. Sequence alignments with the A. acidocaldarius SHC, the lanosterol cyclase of the yeast Candida albicans, and the cycloartenol synthase of the plant Arabidopsis thaliana revealed six highly conserved regions (mainly in the C-terminal part) of the proteins. These regions contained the core motif Gln-X-X-X-Gly-X-Trp.

Amino Acid Sequence↗

PubMed2001

16S ribosomal DNA sequence analysis distinguishes biotypes of Streptococcus bovis: Streptococcus bovis Biotype II/2 is a separate genospecies and the predominant clinical isolate in adult males.

We characterized 22 human clinical strains of Streptococcus bovis by genotypic (16S rRNA gene sequence analysis [MicroSeq]; Applied Biosystems, Foster City, Calif.) and phenotypic (API 20 Strep and Rapid ID32 Strep systems (bioMerieux Vitek, Hazelton, Mo.) methods. The strains, isolated from blood, cerebrospinal fluid (CSF), and urine, formed two distinct 16S ribosomal DNA sequence clusters. Three strains which were associated with endocarditis urinary tract infection (UTI), and sepsis clustered with the S. bovis type strain ATCC 33317 (cluster 1); other closely related type strains were S. equinus and S. infantarius. Nineteen strains clustered at a distance of about 2.5% dissimilarity to the S. bovis type strain (cluster 2) and were associated with central nervous system (CNS) disease in addition to endocarditis, UTI, and sepsis. All strains were distinct from S. gallolyticus. Within cluster 2, a single strain grouped with ATCC strain 43143 (cluster 2a) and may be phenotypically distinct. All the other strains formed a second subgroup (cluster 2b) that was biochemically similar to S. bovis biotype II/2 (mannitol negative and beta galactosidase, alpha galactosidase, beta glucuronidase, and trehalose positive). The API 20 Strep system identified isolates of cluster 2b as S. bovis biotype II/2, those of cluster 1 as S. bovis biotype II/1, and that of cluster 2a as S. bovis biotype I. There was an excellent correlation of biotype and genotype: S. bovis biotype II/2 isolates form a separate genospecies distinct from the S. bovis, S. gallolyticus, and S. infantarius type strains and are the most common isolates in adult males.

Adult↗

PubMed1984

DNA sequence analysis of the type-common glycoprotein-D genes of herpes simplex virus types 1 and 2.

The DNA sequences for the coding and flanking regions of the type-common glycoprotein-D (gD) genes of herpes simplex virus (HSV) types 1 and 2 have been determined. The resultant protein sequences are approximately 80% homologous. Both gD proteins are 393 amino acids long and both have maintained three identical potential glycosylation sites. Amino acid changes are found throughout the proteins, with the majority of changes located in the amino and carboxyl/termini. Most of the amino acid differences were found to be conservative. Hydropathy analysis, which determines hydrophobic and hydrophilic regions, reveals a remarkable structural similarity between the proteins. Examination of 5' flanking sequences demonstrates extensive DNA sequence homology adjacent to the start of gD gene transcription. In addition, another homologous noncoding region was found 3' to the gD gene. This second homologous sequence is 5' to a 1.6-kb transcription unit.

Amino Acid Sequence↗

PubMed1984

Location by DNA sequence analysis of cop mutations affecting the number of plasmid copies of prophage P1.

The DNA sequence of six P1 cop mutants, which are altered in the control of copy number of the plasmid prophage, was compared to that of P1 wild type. Each cop mutant differs from the wild type by a single base substitution. All of these substitutions are located within a 400 base pair region of P1 DNA that also encodes rep, a gene whose product is required for P1 replication.

Amino Acid Sequence↗

PubMed1995

Prediction of function in DNA sequence analysis.

Recognition of function of newly sequenced DNA fragments is an important area of computational molecular biology. Here we present an extensive review of methods for prediction of functional sites, tRNA, and protein-coding genes and discuss possible further directions of research in this area.

Algorithms↗

PubMed1984

Microcomputer programs for back translation of protein to DNA sequences and analysis of ambiguous DNA sequences.

Three computer programs are described which may be used to translate a DNA sequence into a protein sequence, back translate the protein sequence into an ambiguous DNA sequence, and then do pattern searching in the ambiguous sequence. The programs are written in the C programming language, have been compiled to run on a microcomputer under the CP/M 80 operating system, and may be copied in binary format through a modem. They are also to become available for the IBM/PC.

Amino Acid Sequence↗

PubMed1988

RNA splicing in yeast mitochondria: DNA sequence analysis of mit- mutants deficient in the excision of introns aI1 and aI2 of the gene for subunit I of cytochrome c oxidase.

We have characterized two yeast mutants deficient in the splicing of transcripts of the mitochondrial gene for cytochrome c oxidase subunit I (coxI). Both map to the first intron (aI1). RNA blot analysis shows that in addition to a reduced (mutant M15-190) or blocked (mutant M12-193) excision of the mutated intron aI1, the mutants are unable to excise the adjacent aI2 intron, the reading frame of which displays an amino acid sequence similarity to aI1. Splicing of the downstream introns is not affected, however. Sequence analysis of the first mutant DNA (M12-193) reveals a premature termination of the intron-encoded open reading frame, followed by two alterations at a short distance downstream. The other (M15-190) contains 11 separate changes. Although these occur in the intron reading frame, their main effect on RNA splicing may be exerted through the disturbance of intron secondary structure proposed for the 5' end of several group II introns. The implications of these findings in relation to maturase function and structure of intron aI1 are discussed.

Base Sequence↗