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At least 1,297 records · Page 72Linked to original sources
PubMed1982

Nucleotide sequences of cloned cDNA fragments specific for six Xenopus laevis ribosomal proteins.

We have previously constructed and selected six recombinant plasmids containing cDNA sequences specific for different ribosomal proteins of Xenopus laevis (Bozzoni et al., 1981). DNA cloned in these plasmids have been isolated and sequenced. Amino acid sequences of the corresponding portions of the proteins have been derived from DNA sequences; they are arginine- and lysine-rich as expected for ribosomal proteins. One of the cDNA sequences has an open reading frame also on the strand complementary to the one coding for the ribosomal protein; this fragment has inverted repeats twenty nucleotides lone at the two ends. The codon usage for the six sequences appears to be non-random with some differences among the ribosomal proteins analysed.

Animals↗
PubMed1997

Localization and intron usage analysis of the human CPT1B gene for muscle type carnitine palmitoyltransferase I.

We isolated and sequenced cDNA and genomic DNA fragments of the human CPT1B gene, encoding muscle type camitine palmitoyltransferase I. A recombinant P1 phage containing CPT1B was mapped to chromosome 22qter by fluorescent in situ hybridization. This finding supports the concept that 'liver type' and 'muscle type' isoforms of CPT I are encoded by different loci at separate chromosomal positions. Analysis of CPT1B cDNA sequences revealed the presence of an untranslated 5' exon and differential processing of introns 13 and 19. The alternative splicing of intron 13 causes an in-frame deletion leading to a 10 amino acid residues smaller protein. Using different splice acceptor sites, intron 19 is spliced in the majority of cases, but 4 out of 14 sequenced CPT1B 3' cDNA clones contain part of intron 19 in stead of exon 20. We found that differential polyadenylation is the mechanism behind the existence of these alternative 3' CPT1B mRNA forms.

Base Sequence↗
PubMed1997

Molecular cloning and sequencing of the cDNA encoding mouse glutamate-cysteine ligase regulatory subunit.

Reverse transcription-polymerase chain reaction (RT-PCR) was used to amplify and clone the regulatory subunit of mouse glutamate-cysteine ligase (Glclr) using primers adapted from the published rat Glclr cDNA sequence, and from mouse genomic DNA. Amplified cDNA was cloned into a plasmid vector, and additional RT-PCR reactions coupled with 3' RACE were used to amplify and sequence 3' regions covered by the rat primer. Comparison of the mouse Glclr cDNA sequence and predicted protein sequence with that of rat Glclr and human GLCLR revealed extensive homology in cDNA and amino acid sequences among these species.

Amino Acid Sequence↗
PubMed1996

MHCDB: database of the human MHC (release 2).

The second release of the human major histocompatibility complex (MHC) database is now publicly available. It contains an updated physical map and considerably more genomic sequence. cDNA sequences of all current alleles are accessible as individual sequence entries. The variability of different genes is displayed graphically as static and dynamic images accessible from the database. Known disease-serotype associations have also been incorporated, together with data from the MHCPEP database of eluted peptides.

Databases, Factual↗
PubMed1985

Alpha 1-antitrypsin and serum albumin mRNA accumulation in normal, acute phase and ZZ human liver.

Alpha 1-Antitrypsin and albumin mRNA levels of 4 human livers were assessed using a newly sequenced cDNA clone of the carboxyterminal third of alpha 1-antitrypsin and a previously cloned albumin cDNA sequence. The relative concentration of alpha 1-antitrypsin mRNA was the same in poly(A)-containing RNA isolated from acute phase (MM) and alpha1-antitrypsin deficient (ZZ) individuals. In the acute phase liver relative to the normal (MM) liver, total RNA extracts showed a marked decrease in albumin mRNA concentration but no increase in alpha 1-antitrypsin mRNA. The ZZ liver showed decreased total and poly(A)-containing RNA content but the same proportion of alpha 1-antitrypsin to albumin mRNA as in the normal (MM) liver. This supports other evidence that ZZ alpha 1-antitrypsin deficiency is due to a defect in polypeptide processing (secretion) rather than a deficiency in mRNA accumulation.

Adolescent↗
PubMed2004

Historical review: Endothelin.

Endothelin (ET) is a potent vasoconstrictive peptide that was isolated initially from the conditioned medium of cultured endothelial cells. In 1988, details of the isolation and identification, amino acid sequence, cDNA sequence and pharmacology of ET were published. Subsequently, ET isoforms, ET receptors and endothelin-converting enzyme (ECE) were cloned. Because ET was thought to be important in cardiovascular homeostasis, many investigators focused on the physiological and pathophysiological significance of ET. Accordingly, ET receptor antagonists and ECE inhibitors have been developed rapidly, mostly for the treatment of cardiovascular diseases. The field of molecular biology has provided valuable information about ET, including evidence that the ET system plays important roles in the early development of the neural crest and, thus, in the formation of organs. These results now present new avenues of ET research.

Cardiovascular Diseases↗
PubMed2003

Pathogen discovery from human tissue by sequence-based computational subtraction.

We have recently reported a new pathogen discovery approach, "computational subtraction". With this approach, non-human transcripts are detected by sequencing cDNA libraries from infected tissue and eliminating those transcripts that match the human genome. We show now that this method is experimentally feasible. We generated a cDNA library from a tissue sample of post-transplant lymphoproliferative disorder (PTLD). 27,840 independent cDNA sequences were filtered by computational subtraction against the known human sequence to identify 32 nonmatching transcripts. Of these, 22 (0.1%) were found to be amplifiable from both infected and noninfected samples and were inferred to be human DNA not yet contained in the available human genome sequence. The remaining 10 sequences could be amplified only from Epstein-Barr virus (EBV)-infected tissues. All 10 corresponded to the known EBV sequence. This proof-of-principle experiment demonstrates that computational subtraction can detect pathogenic microbes in primary human-diseased tissue.

DNA, Complementary↗
PubMed2001

Electrochemical detection of sequence-specific DNA using a DNA probe labeled with aminoferrocene and chitosan modified electrode immobilized with ssDNA.

The electrochemical detection of sequence-specific DNA using a DNA probe labeled with aminoferrocene (AFC) is reported. Sample ssDNA was immobilized on a chitosan modified glassy carbon electrode. A sequence-known DNA with 256 bp [obtained by polymerase chain reaction (PCR)] was successfully labeled with the electro-active reagent AFC by 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide for the first time. This DNA probe labeled with AFC was applied to hybridize with a sequence-unknown DNA sample. Only the complementary sequence (cDNA) could form a double-stranded DNA (dsDNA) with the DNA probe labeled with AFC. The anodic peak currents (ipa) of the AFC bound to the dsDNA by differential pulse voltammetry were used for the determination of cDNA. The ipa of AFC was linearly related to the concentration of cDNA sequence between 1.0 x 10(-8) and 6.0 x 10(-6) mol L-1. The detection limit was 2.0 x 10(-9) mol L-1 using 3 sigma (where sigma is the standard deviation of blank solution, n = 11). The probe showed high sensitivity and selectivity.

Animals↗
PubMed1989

Lc, a member of the maize R gene family responsible for tissue-specific anthocyanin production, encodes a protein similar to transcriptional activators and contains the myc-homology region.

Previous studies have suggested that the R locus of maize is responsible for determining the temporal and spatial pattern of anthocyanin pigmentation in the plant. In this report we demonstrate that three members of the R gene family, P, S, and Lc, encode homologous transcripts 2.5 kilobases in length. The structure of one R gene, Lc, was determined by sequencing cDNA and genomic clones. The putative Lc protein, deduced from the cDNA sequence, is composed of 610 amino acids and has homology to the helix-loop-helix DNA-binding/dimerization motif found in the L-myc gene product and other regulatory proteins. It also contains a large acidic domain that may be involved in transcriptional activation. Consistent with its proposed role as a transcriptional activator is our finding that a functional R gene is required for the accumulation of transcripts of at least two genes in the anthocyanin biosynthetic pathway. We discuss the possibility that the diverse patterns of anthocyanin pigmentation conditioned by different R genes reflect differences in the R gene promoters rather than their gene products.

Amino Acid Sequence↗
PubMed1992

Isolation and sequence of two genes associated with a CpG island 5' of the factor VIII gene.

Many disease loci have been linked to the telomeric end of the long arm of the human X-chromosome, Xq28. We have isolated and sequenced cDNA sequences corresponding to two novel genes that map to Xq28. These genes, c6.1A and c6.1B, are transcribed in opposite directions from a CpG island that lies approximately 70 kilobases (kb) upstream (5') of the factor VIII locus. One of these genes, c6.1A, is highly conserved between species and expressed abundantly in many human and mouse tissues, whereas, c6.1B is moderately conserved and has a restricted tissue distribution of expression. The Xq28 gene c6.1A has an autosomal homologue that is transcriptionally inactive in B-cell lines. An open reading frame (ORF) predicting a peptide of 293 amino acids is observed for c6.1A but c6.1B does not possess a single long ORF. No striking homologies to existing genes could be found for either of the two new loci. Expressed sequences that are physically close to the factor VIII gene are candidates for disease loci that map to this region of Xq28. The relevance of these genes to disease loci was investigated using DNA and RNA from hemophilia A patients bearing deletions that extend in a 5' direction away from factor VIII. The results imply that neither of these genes are primarily responsible for the development Xq28-linked diseases. However, c6.1A and c6.1B define a region of Xq28 that is deleted in two brothers that suffer from mental handicap and dysmorphism as well as hemophilia A. Thus, this region is likely to contain loci that are important for physical and mental development.

Amino Acid Sequence↗
PubMed1989

The nucleotide sequence of a soybean mosaic virus coat protein-coding region and its expression in Escherichia coli, Agrobacterium tumefaciens and tobacco callus.

A DNA complementary to the 3'-terminal 1168 nucleotides of the genome of the N strain of soybean mosaic virus (SMV) has been cloned and sequenced. cDNA sequence and coat protein analyses indicate that the SMV coat protein-coding region is at the 3' end of the genome, and that the coat protein is processed from a larger protein. The coat protein-coding sequence is predicted to be 795 nucleotides in length, encoding a protein of 265 amino acids with a calculated Mr of 29,857. The 3' untranslated region is 259 nucleotides in length and is followed by a polyadenylate tract. The SMV coat protein-coding region, along with a small amount of upstream sequence, has been expressed in Escherichia coli as a beta-galactosidase fusion protein. The size of the protein was less than predicted for the fusion protein, suggesting processing in E. coli. The coat protein-coding region has also been expressed in Agrobacterium tumefaciens and transgenic tobacco callus as an unfused protein under the control of the cauliflower mosaic virus 35S promoter. The coat protein produced in transgenic tobacco callus had an electrophoretic mobility identical to that of SMV coat protein and constituted approximately 0.05% (w/w) of the total extracted protein.

Amino Acid Sequence↗
PubMed1996

Hb Toranomon [beta 112(G14)Cys-->Trp]: a new unstable electrophoretically silent hemoglobin.

We describe a silent and unstable hemoglobin variant, Hb Toranomon, which was discovered by high performance liquid chromatography in an apparently healthy Japanese male during a Hb A1c assay. Isoelectrofocusing of his hemolysate and chromatographic separation of globin on a CM-cellulose column revealed no abnormality. The isopropanol precipitation test gave a positive result. Amino acid analysis of all peptides isolated from the tryptic digests of the aminoethylated and non-aminoethylated beta chain (beta A + beta X) by reversed phase high performance liquid chromatography indicated a substitution of Cys-->Trp at position 112 of the beta chain, which was confirmed by protein sequencing. cDNA sequencing showed the nucleotide sequence of the beta 112 codon to be TGG instead of TGT, confirming the amino acid substitution described above. The globin biosynthesis ratio (beta/alpha) was 1.00.

Adult↗
PubMed1983

Cloning and sequence analysis of cDNA for human renin precursor.

The primary structure of human renin precursor has been deduced from its cDNA sequence. A library of cDNA clones was constructed from human kidney poly(A)+ RNA by applying the vector/primer method of Okayama and Berg. The library was screened for human renin sequences by hybridization with the previously cloned mouse renin cDNA. Of the 240,000 colonies screened, 35 colonies that were positive for hybridization were isolated. Two recombinant plasmids containing long inserts of about 1,300 and 1,600 base pairs were selected for sequence analysis. The amino acid sequence predicted from the cDNA sequence shows that the human renin precursor consists of 406 amino acids with a pre and a pro segment carrying 20 and 46 amino acids, respectively. A high degree of sequence homology was found upon comparison of the mouse and human renins. Close similarities were also observed in the primary structures of renin and aspartyl proteinases that have known three-dimensional structures, suggesting a similar tertiary structure for renin.

Amino Acid Sequence↗
PubMed2006

Sequence analysis of cDNA encoding rabbit follicle-stimulating hormone beta-subunit precursor protein.

To understand the molecular basis of the rabbit's efficient superovulation, we determined the cDNA sequence of the follicle-stimulating hormone (FSH) beta-subunit precursor protein using a combination of 5'- and 3'-rapid amplification of cDNA ends (RACE) with pituitary cDNA libraries of the Japanese White rabbit and compared it with those of other mammals. RACE experiments detected at least three transcripts for the FSHbeta precursor protein in the libraries. The transcripts had lengths of 457, 1,621, and 1,767 bp, from the 5'-end to the poly(A) site. The shortest and mid-length transcripts had the putative polyadenylation signal sequence AATAAA at nucleotides 436 and 1,601, respectively, whereas the longest form had an ATTAAA sequence at nucleotide 1,745 of the cDNA sequence. These transcripts are likely to be polyadenylation variants of one large transcript because they share the same coding sequence for the precursor protein (130 amino acid residues in length). However, only a few shortest variants seem to be formed because the shortest variants were not detected by Northern blot analysis. Phylogenetic analysis of the deduced amino acid sequence indicates that the rabbit is phylogenetically closer to humans than to the other mammals, suggesting that an FSH preparation from human sources would be superior as a follicle stimulant for the induction of superovulation.

Amino Acid Sequence↗
PubMed1999

High-molecular-weight allergens of the house dust mite: an apolipophorin-like cDNA has sequence identity with the major M-177 allergen and the IgE-binding peptide fragments Mag1 and Mag3.

BACKGROUND: A 349-residue recombinant polypeptide of Dermatophagoides farinae, Mag 3, has been shown to represent part of a larger 177-kD (M-177) allergen with very high IgE-binding activity. METHODS: Cloning and sequencing of cDNA from the house dust mites Dermatophagoides pteronyssinus and Euroglyphus maynei was used to characterise the polypeptide containing the Mag 3 sequence. RESULTS: cDNA clones containing the complete sequence of the E. maynei homologue of the M-177 allergen were isolated and analysed. The translation contained not only an amino acid sequence with 90% identity to the 349-residue Mag-3 fragment but also a further sequence with 90% identity to another IgE-binding recombinant D. farinae polypeptide designated Mag 1. The complete sequence encoded a mature polypeptide of 1,650 residues and a molecular mass of 189.5 kD. cDNA clones from D. pteronyssinus also encoded sequences equivalent to the Mag 1 and 3 polypeptides. The M-177 sequence showed strong similarity to the lipid transport apolipophorins found in insect lipophorins. CONCLUSIONS: cDNA sequence data show that the D. pteronyssinus and E. maynei homologues of the M-177 high-molecular-weight D. farinae allergen contain sequences equivalent to both the Mag 1 and Mag 3 recombinant IgE-binding fragments. The N-terminal sequence of the full-length 1,650 amino-acid allergen showed strong similarity to the insect apolipophorins which are poorly soluble in aqueous extracts and exist in the lipid transport particles in haemolymph. It is proposed that presentation in lipid particles could be a factor which enhances the immunogenicity of this group of allergens.

Allergens↗
PubMed1987

Complete nucleotide sequence of cDNA and predicted amino acid sequence of rat acyl-CoA oxidase.

cDNA clones for rat acyl-CoA oxidase were isolated. The 3.8-kilobase mRNA sequence of the enzyme was completely covered by two overlapping clones. The composite cDNA sequence consisted of 3741 bases and contained a 1983-base open reading frame which encodes a polypeptide of 661 amino acid residues. Two species of acyl-CoA oxidase cDNA were identified. They differed in their coding nucleotide sequences, only within a small region. They contained the same number of nucleotides and can be translated in a common reading frame. They are 55% and 50% homologous in the above region at the nucleotide and the amino acid levels, respectively. Both types of cDNA were isolated from a library constructed from mRNA of a single rat, thereby suggesting the occurrence of two species of acyl-CoA oxidase in each rat. The amino terminus of the enzyme was determined to be N-acetylmethionine, which corresponds to the initiator methionine, thus confirming the absence of a terminal presequence. We reported previously that a purified preparation of the enzyme contained three polypeptide components, A, B, and C, and suggested that components B and C are produced by a proteolytic cleavage of component A (Osumi, T., Hashimoto, T., and Ui, N. (1980) J. Biochem. (Tokyo) 87, 1735-1746). We located components B and C on the amino- and the carboxyl-terminal sides of component A. Possible functional significances of several stretches of amino acids of the enzyme are discussed, based on the sequence comparison data between rat and yeast acyl-CoA oxidases.

Acyl-CoA Oxidase↗
PubMed1993

Synthesis, cloning and sequencing of glucoamylase cDNA from Aspergillus niger mutant T21.

Poly(A)+ RNA was isolated from Aspergillus niger T21, a glucoamylase overproducing strain and was used as template to synthesize double stranded cDNA. A cDNA library was then constructed. The E. coli transformants were screened for the glucoamylase cDNA by in situ colony hybridization with P-labeled fragment of glucoamylase gene as probe. The positive rate was 1.6%. Restriction analysis proved that 32% of the positive clones carried the inserts of 2.1 kb of full length glucoamylase cDNA. Sequence of the glucoamylase cDNA was determined and the result showed that the sequence of glucoamylase gene of the mutant T21 was almost the same as that reported previously. The high rate of glucoamylase cDNA-containing clones in the cDNA library of strain T21 provided evidence of high steady state level of glucoamylase mRNA in mycelium of mutant T21. Most likely it is one of the major causes for the high glucoamylase productivity of mutant T21.

Aspergillus niger↗