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At least 1,207 records · Page 67Linked to original sources
PubMed2002

Twenty single-nucleotide polymorphisms in four genes encoding cardiac ion channels.

We here report 20 novel single-nucleotide polymorphisms in four genes that are potentially involved in the excitement of cardiomyocytes: 1 in KCNA5 (encoding Kv1.5), 5 in KCNAB1 (encoding Kvbeta1.3), 5 in KCNIP2 (encoding KChIP2), and 9 in CACNA1C (encoding a cardiac L-type voltage-dependent calcium ion channel, dihydropyridine receptor). We also examined their allelic frequencies in Japanese individuals. These data will be useful for genetic association studies designed to investigate secondary long QT syndrome or other circulatory disorders.

Gene Frequency↗
PubMed2000

Cloning and Sequence Analysis of Vibrio halioticoli Genes Encoding Three Types of Polyguluronate Lyase.

The alginate lyase-coding genes of Vibrio halioticoli IAM 14596(T), which was isolated from the gut of the abalone Haliotis discus hannai, were cloned using plasmid vector pUC 18, and expressed in Escherichia coli. Three alginate lyase-positive clones, pVHB, pVHC, and pVHE, were obtained, and all clones expressed the enzyme activity specific for polyguluronate. Three genes, alyVG1, alyVG2, and alyVG3, encoding polyguluronate lyase were sequenced: alyVG1 from pVHB was composed of a 1056-bp open reading frame (ORF) encoding 352 amino acid residues; alyVG2 gene from pVHC was composed of a 993-bp ORF encoding 331 amino acid residues; and alyVG3 gene from pVHE was composed of a 705-bp ORF encoding 235 amino acid residues. Comparison of nucleotide and deduced amino acid sequences among AlyVG1, AlyVG2, and AlyVG3 revealed low homologies. The identity value between AlyVG1 and AlyVG2 was 18.7%, and that between AlyVG2 and AlyVG3 was 17.0%. A higher identity value (26.0%) was observed between AlyVG1 and AlyVG3. Sequence comparison among known polyguluronate lyases including AlyVG1, AlyVG2, and AlyVG3 also did not reveal an identical region in these sequences. However, AlyVG1 showed the highest identity value (36.2%) and the highest similarity (73.3%) to AlyA from Klebsiella pneumoniae. A consensus region comprising nine amino acid (YFKAGXYXQ) in the carboxy-terminal region previously reported by Mallisard and colleagues was observed only in AlyVG1 and AlyVG2.

Journal Article↗
PubMed2003

2D-RF-pulse-encoded curved-slice imaging.

A new approach to curved-slice imaging is described in which spatial resolution is achieved using 2D-RF-pulse- and conventional-frequency encoding. This approach offers the opportunity to image curved anatomical structures directly using curved single-slice MRI. A set of 2D-RF pulses is employed to excite transverse magnetization in an arbitrarily shaped curved-slice profile in three-dimensional space. Spatial resolution along the curved-slice direction is achieved by encoding the different volume elements of the slice using a set of specially designed RF pulses and an appropriate encoding scheme. The remaining spatial direction is measured using conventional-frequency encoding. Phantom and in vivo experiments were carried out to illustrate the basic feasibility and the limitations of this approach.

Anatomy, Cross-Sectional↗
PubMed2006

Nine 3-ketoacyl-CoA thiolases (KATs) and acetoacetyl-CoA thiolases (ACATs) encoded by five genes in Arabidopsis thaliana are targeted either to peroxisomes or cytosol but not to mitochondria.

The sub-cellular location of enzymes of fatty acid beta-oxidation in plants is controversial. In the current debate the role and location of particular thiolases in fatty acid degradation, fatty acid synthesis and isoleucine degradation are important. The aim of this research was to determine the sub-cellular location and hence provide information about possible functions of all the putative 3-ketoacyl-CoA thiolases (KAT) and acetoacetyl-CoA thiolases (ACAT) in Arabidopsis. Arabidopsis has three genes predicted to encode KATs, one of which encodes two polypeptides that differ at the N-terminal end. Expression in Arabidopsis cells of cDNAs encoding each of these KATs fused to green fluorescent protein (GFP) at their C-termini showed that three are targeted to peroxisomes while the fourth is apparently cytosolic. The four KATs are also predicted to have mitochondrial targeting sequences, but purified mitochondria were unable to import any of the proteins in vitro. Arabidopsis also has two genes encoding a total of five different putative ACATs. One isoform is targeted to peroxisomes as a fusion with GFP, while the others display no targeting in vivo as GFP fusions, or import into isolated mitochondria. Analysis of gene co-expression clusters in Arabidopsis suggests a role for peroxisomal KAT2 in beta-oxidation, while KAT5 co-expresses with genes of the flavonoid biosynthesis pathway and cytosolic ACAT2 clearly co-expresses with genes of the cytosolic mevalonate biosynthesis pathway. We conclude that KATs and ACATs are present in the cytosol and peroxisome, but are not found in mitochondria. The implications for fatty acid beta-oxidation and for isoleucine degradation in mitochondria are discussed.

Acetyl-CoA C-Acetyltransferase↗
PubMed1995

Multiple deficiencies of mitochondrial DNA- and nuclear-encoded subunits of respiratory NADH dehydrogenase detected with peptide- and subunit-specific antibodies in mitochondrial myopathies.

Antibodies have been raised against synthetic peptides corresponding to several computer-predicted epitopes of three mtDNA-encoded subunits, ND4, ND5 and ND6, of the human respiratory chain NADH dehydrogenase (Complex I). Antibodies were characterized by a sensitive immunoblotting assay using proteins from human skeletal muscle mitochondria and by immunoprecipitation of radio-labeled HeLa cell mitochondrial translation products. Only antibodies against two of six selected peptides of the ND4 subunit, i.e., the C-terminal peptide and an internal peptide close to the C-terminus, reacted in both assays with the subunit. Antibodies raised against an internal peptide close to the N-terminus of the ND5 subunit and antibodies raised against an internal epitope of the ND6 subunit also reacted in both the immunoblotting and immunoprecipitation assays. The antibodies described above and other Complex I subunit- or holoenzyme-specific antibodies were used to investigate the subunit deficiencies of the respiratory NADH dehydrogenase in the skeletal muscle of patients affected by mitochondrial myopathies associated with Complex I defects. The reduction in enzyme activity correlated in an immunoblot assay with a decrease of four mtDNA-encoded subunits of the enzyme, as well as with a decrease of other subunits of Complex I encoded in the nDNA. The present work provides the first evidence of a decrease in NADH dehydrogenase subunits encoded in the mitochondrial genome in myopathy patients.

Adolescent↗
PubMed1993

Nucleotide sequence encoding a novel member of the hydratase/dehydrogenase family.

The nucleotide sequence encoding a novel member of the family of fatty acid oxidation enzymes has been determined. Clones were generated from porcine gastric corpus cDNA by application of the polymerase chain reaction (PCR) using oligodeoxyribonucleotides based on the amino acid sequence of a 78 kDa gastrin-binding protein isolated from porcine gastric mucosal membranes (Baldwin et al., J. Biol. Chem. 261 (1986) 12252-12257). Clones encoding the 3' and 5' ends of the cDNA were then isolated by conventional screening of a porcine liver cDNA library, and by application of anchored PCR, respectively. The composite cDNA of 2744 nucleotides encoded a protein of 763 amino acids, the sequence of which was related to a rat peroxisomal trifunctional enzyme, delta 3, delta 2-enoyl-CoA isomerase/enoyl-CoA hydratase/3-hydroxyacyl-CoA dehydrogenase, and to other members of the same enzyme family. Northern blots indicated that the 3-kb mRNA encoding the novel protein was abundant in gastric corpus and liver, with lower amounts also present in gastric antrum and forestomach.

3-Hydroxyacyl CoA Dehydrogenases↗
PubMed1988

Cloning of cDNA encoding a new peptide C-terminal alpha-amidating enzyme having a putative membrane-spanning domain from Xenopus laevis skin.

A cDNA clone encoding a precursor of a peptide C-terminal alpha-amidating enzyme (AE-I) from Xenopus laevis skin was recently isolated and sequenced in our laboratory. In this study, by using the restriction fragment of this clone as a hybridization probe, we have identified the cDNA encoding another new peptide C-terminal alpha-amidating enzyme (tentatively named AE-II) distinct from AE-I. The cDNA encodes a polypeptide of 875 amino acid residues, which contains a region extensively homologous to AE-I precursor at N-terminus. The encoded protein characteristically has a putative membrane-spanning domain near C-terminus. Our results indicate that C-terminal alpha-amide formation of peptides in Xenopus skin is regulated by at least two distinct alpha-amidating enzymes.

Amino Acid Sequence↗
PubMed1992

The chimeric gene linked to glucocorticoid-suppressible hyperaldosteronism encodes a fused P-450 protein possessing aldosterone synthase activity.

Glucocorticoid-suppressible hyperaldosteronism (GSH) is one variety of primary aldosteronism with hypertension and is inherited in an autosomal dominant mode. A recent report has indicated that GSH is caused by a gene duplication arising from unequal crossing over between the two genes, CYP11B1 and CYP11B2, encoding P-450(11 beta) and P-450C18, respectively (Lifton et al. Nature (1992) 355, 262-265). The nucleotide sequence analysis in the present study has demonstrated that unequal crossing over in the chimeric gene formed by the gene duplication occurs within the region from the 3'-portion of exon 4 through the 5'-portion of intron 4 in Australian GSH patients. Namely, the chimeric gene encodes a fused P-450 protein consisting of the amino-terminal side of P-450(11 beta) (encoded by exons 1-4 of CYP11B1) and the carboxyl-terminal side of P-450C18 (encoded by exons 5-9 of CYP11B2). When a cDNA corresponding to the chimeric gene is transfected into COS-7 cells, the fused P-450 protein expressed in the mitochondria exhibits steroid 18-hydroxylase or aldosterone synthase activity. These results provide the molecular genetic basis for the characteristic biochemical phenotype of GSH patients.

Animals↗
PubMed1992

Investigation of phonological encoding through speech error analyses: achievements, limitations, and alternatives.

Phonological encoding in language production can be defined as a set of processes generating utterance forms on the basis of semantic and syntactic information. Most evidence about these processes stems from analyses of sound errors. In section 1 of this paper, certain important results of these analyses are reviewed. Two prominent models of phonological encoding, which are mainly based on speech error evidence, are discussed in section 2. In section 3, limitations of speech error analyses are discussed, and it is argued that detailed and comprehensive models of phonological encoding cannot be derived solely on the basis of error analyses. As is argued in section 4, a new research strategy is required. Instead of using the properties of errors to draw inferences about the generation of correct word forms, future research should directly investigate the normal process of phonological encoding.

Female↗
PubMed1991

Cloning and sequencing of the gene encoding the large (alpha-) subunit of the proteasome from Thermoplasma acidophilum.

The gene encoding the alpha-subunit of the proteasome from the archaebacterium Thermoplasma acidophilum was cloned and sequenced. The gene encodes for a polypeptide with 233 amino acid residues and a calculated molecular weight of 25870. Sequence similarity of the alpha-subunit with the Saccharomyces cerevisiae wild-type suppressor gene scll+ encoded polypeptide, which is probably identical with the subunit YC7-alpha of the yeast proteasome, lends support to a putative role of proteasomes in the regulation of gene expression. The significant sequence similarity to the various subunits of eukaryotic proteasomes make it likely that proteasomal proteins are encoded by one gene family of ancient origin.

Amino Acid Sequence↗
PubMed1989

Expression of substance P/neurokinin A-encoding preprotachykinin messenger ribonucleic acids in the rat enteric nervous system.

The cellular localization of substance P/neurokinin A-encoding preprotachykinin mRNAs in the rat enteric nervous system was studied by means of in situ hybridization histochemistry using 35S- or 3H-labeled single-stranded ribonucleic acid (RNA) probes which recognize all three preprotachykinin mRNA species, alpha, beta, and gamma. Substance P/neurokinin A-encoding mRNAs are expressed in neurons within the myenteric plexus of the esophagus and stomach, being more numerous in the latter, and in ganglion cells distributed to both the myenteric and submucosal plexuses of the intestine. Specificity of the hybridization was demonstrated by the lack of specific signal above background in sections incubated with a sense RNA probe or pretreated with ribonuclease A before hybridization. Ribonucleic acid blot hybridization analysis of RNA extracts from both the muscle layer-myenteric plexus and submucosal layer preparations of the duodenum demonstrated a single band of hybridization at 1.3 kb. Solution hybridization-nuclease protection assays showed multiple preprotachykinin-encoding transcripts in these RNA extracts, with an abundance level of gamma-mRNA greater than beta-mRNA much greater than alpha-mRNA, which is similar to that observed in the rat brain. Our results indicate that the preprotachykinin gene encoding the tachykinin peptides, substance P and neurokinin A, is transcribed in a population of enteric neurons that have a regional distribution comparable to the previously described tachykinin-like immunoreactive neurons, suggesting that specific mRNAs and the posttranslationally processed peptides are localized in the same structures.

Animals↗
PubMed1986

Complete nucleotide and encoded amino acid sequence of a mammalian myosin heavy chain gene. Evidence against intron-dependent evolution of the rod.

The complete nucleotide sequence and exon/intron structure of the rat embryonic skeletal muscle myosin heavy chain (MHC) gene has been determined. This gene comprises 24 X 10(3) bases of DNA and is split into 41 exons. The exons encode a 6035 nucleotide (nt) long mRNA consisting of 90 nt of 5' untranslated, 5820 nt of protein coding and 125 nt of 3' untranslated sequence. The rat embryonic MHC polypeptide is encoded by exons 3 to 41 and contains 1939 amino acid residues with a calculated Mr of 223,900. Its amino acid sequence displays the structural features typical for all sarcomeric MHCs, i.e. an amino-terminal "globular" head region and a carboxy-terminal alpha-helical rod portion that shows the characteristics of a coiled coil with a superimposed 28-residue repeat pattern interrupted at only four positions by "skip" residues. The complex structure of the rat embryonic MHC gene and the conservation of intron locations in this and other MHC genes are indicative of a highly split ancestral sarcomeric MHC gene. Introns in the rat embryonic gene interrupt the coding sequence at the boundaries separating the proteolytic subfragments of the head, but not at the head/rod junction or between the 28-residue repeats present within the rod. Therefore, there is little evidence for exon shuffling and intron-dependent evolution by gene duplication as a mechanism for the generation of the ancestral MHC gene. Rather, intron insertion into a previously non-split ancestral MHC rod gene consisting of multiple tandemly arranged 28-residue-encoding repeats, or convergent evolution of an originally non-repetitive ancestral MHC rod gene must account for the observed structure of the rod-encoding portion of present-day MHC genes.

Amino Acid Sequence↗
PubMed1987

Proteins encoded by the DpnII restriction gene cassette. Two methylases and an endonuclease.

Proteins encoded by three genes in the DpnII restriction enzyme cassette of Streptococcus pneumoniae were purified and characterized. Large amounts of the proteins were produced by subcloning the cassette in an Escherichia coli expression system. All three proteins appear to be dimers composed of identical polypeptide subunits. One is the DpnII endonuclease, and the other two are DNA adenine methylase active at 5' GATC 3' sites. Inactivation of enzyme activity by insertions into the genes and comparison of the DNA sequence with the amino-terminal sequence of amino acid residues in the proteins demonstrated the following correspondence between genes and enzymes. The promoter-proximal gene in the operon, dpnM, encodes a 33 X 10(3) Mr polypeptide that gives rise to a potent DNA methylase. The next gene, dpnA, encodes the 31 x 10(3) Mr polypeptide of a weaker and less-specific methylase. The third gene, dpnB, encodes the 34 x 10(3) Mr polypeptide of the endonuclease. Although the endonuclease polypeptide is initiated from an ordinary ribosome-binding site, each of the methylase polypeptide begins at an atypical site with a consensus sequence entirely different from that of Shine & Dalgarno. This presumptive novel ribosome-binding site is well recognized in both S. pneumoniae and E. coli.

Amino Acid Sequence↗
PubMed1994

Verbal recall and recognition as a function of depth of encoding in patients with unilateral temporal lobectomy.

The hypothesis that impairment in cognitive organization is a significant causal factor in the verbal memory impairment known to follow left anterior temporal (LT) lobectomy was tested by assessing verbal recall and recognition as a function of depth of encoding in 20 patients with LT lobectomy (19 in the recognition condition), 20 patients with right temporal lobectomy and 20 normal control subjects. Subjects first made decisions regarding either the physical, phonemic or semantic aspects of 48 words. After the encoding phase, a free recall test was given, followed by a recognition test. As expected, the verbal memory of the LT group was impaired in both the recall and recognition conditions. However, the LT group followed the pattern of the other two groups in recalling and recognizing more words which had been subjected to semantic analysis. These findings do not support the hypothesis that a disruption in the normal relationship between cognitive organization and memory contributes to the memory impairment following LT lobectomy. In contrast the verbal recall of the LT group failed to follow the pattern of the other two groups in that it did not benefit from phonemic encoding. Taken together, these findings support the notion that left anterior temporal-lobe cortical structures are more specialized for the evocation of the sound of a word than for those processes that underlie the recall of semantically encoded verbal material.

Adult↗
PubMed1986

Identification and structure of the gene encoding gpII, a major glycoprotein of varicella-zoster virus.

The genome of varicella-zoster virus (VZV) encodes three major families of glycoproteins (gpI, gpII, and gpIII). mRNA from VZV-infected cells was hybrid selected using a library of VZV recombinant plasmids and translated in vitro; polypeptide products were immunoprecipitated by polyclonal monospecific guinea pig antibodies to gpII. The mRNA encoding a 100-kD polypeptide precipitable by anti-gpII antibodies mapped to the HindIII D fragment near the center of the UL region. DNA sequence analysis of this region of the VZV genome revealed a 2.6-kbp open reading frame (ORF) potentially encoding a 98-kDa polypeptide possessing the characteristics of a glycoprotein. The 100-kDa polypeptide was specified by mRNA isolated by hybrid selection using a plasmid containing part of the 2.6-kbp ORF, and immunoprecipitation of this protein by anti-gpII antibodies and by convalescent zoster serum was blocked specifically by purified gpII. We conclude that the 2.6-kbp ORF encodes gpII. The imputed primary amino acid sequence of gpII shows a high degree of homology to that of herpes simplex virus type 1 (HSV-1) gB, a result consistent with the equivalent map locations of the respective genes in the HSV and VZV genomes and with the recently reported serological cross-reactivity of HSV-1 gB and VZV gpII. Unlike the mature gene products of gB, those of gpII have been described as a pair of glycoproteins with approximate molecular weights of 60 kDa in reducing gels, products of a single glycoprotein species with approximate mol mass of 125-140 kDa in nonreducing gels. Amino-terminal sequences of purified gpII were determined and compared to the imputed amino acid sequence. This comparison implies that the primary translational product is cleaved approximately into halves in vivo and suggests that mature gpII is a disulfide-linked heterodimer.

Amino Acid Sequence↗
PubMed1988

Characterization of a latent protein encoded by the large internal repeats and the BamHI Y fragment of the Epstein-Barr virus (EBV) genome.

Analysis of EBV nuclear antigen 1 (EBNA 1) encoding transcripts by cDNA characterization revealed a potentially polycistronic message generated by long-range splicing of several exons (Speck, S., and Strominger, J., Proc. Natl. Acad. Sci. USA 82, 8305-8309, 1985). Besides the open reading frame encoding EBNA 1, two other open reading frames are found in the EBNA 1-specific cDNA. The first reading frame consists of several exons from BamHI W and Y viral genome fragments (W1, W2, Y1, and Y2). In our experiments, the W1 exon was expressed in the tryptophan-regulated expression vector pATH11. Rabbit sera, raised against the bacterial fusion protein, recognized one or two proteins of molecular weights between 30,000 and 100,000 in several EBV genome harboring Burkitt lymphoma and EBV immortalized peripheral blood cell lines. Although, in a few cell lines from both groups no specific protein could be detected. Immunofluorescence analysis and characterization of subcellular distribution demonstrated that this W/Y fragment encoded latent protein is located, in part, in the cytoskeleton fraction, and in the chromatin. In addition, 2-D immunoblot analysis revealed post-translational modifications of this latent protein, probably due to phosphorylation. In DNA-binding studies on DNA cellulose columns, this W/Y encoded latent protein exhibited specific DNA binding activities.

Amino Acid Sequence↗
PubMed1990

Identification of two additional v-sea-encoded proteins in avian erythroblastosis virus, S13-infected fibroblasts.

Rabbit antibodies prepared against a v-sea-encoded polypeptide expressed in bacteria were used to characterize the v-sea-encoded proteins in cells transformed by the avian erythroblastosis virus, S13. In addition to the two previously described v-sea-encoded proteins, gp155 and gp70, two additional proteins were identified of molecular weights 38,000 and 36,000 Da. Interestingly, these two proteins were found only in fibroblasts infected with the S13 virus and not in S13-transformed erythroid cells. These two proteins were phosphoproteins, but, unlike the two previously characterized v-sea-encoded proteins, they did not appear to be modified by the addition of N-linked sugars. Possible mechanisms for the biosynthesis of these two new proteins are discussed.

Alpharetrovirus↗
PubMed1991

Proteolytic maturation of the 206-kDa nonstructural protein encoded by turnip yellow mosaic virus RNA.

The longest open reading frame of turnip yellow mosaic virus genomic RNA (ORF-206) encodes a 206-kDa nonstructural protein. The most prominent in vitro translation products of ORF-206 are the full-length p206 and a shorter N-coterminal 150-kDa protein. We have confirmed these assignments by immunoprecipitation of in vitro translation products with antisera raised to N-terminal and C-terminal regions encoded by ORF-206. The mechanism by which the 150-kDa protein arises from ORF-206 was investigated by in vitro translation of deletion and substitution derivatives transcribed from pTYMC, a cDNA clone of TYMV RNA. The following observations demonstrate that the 150-kDa protein and a C-terminal 70-kDa protein arise from ORF-206 by autoproteolysis: (1) Two regions encoded by ORF-206 were necessary for the formation of the 150-kDa protein: a domain between amino acids 555 and 1051, postulated to encode a protease, and the region between amino acids 1253 and 1261, thought to constitute the protease recognition and/or cleavage site. (2) Mutants with substitutions between amino acids 1253 and 1261 that produce low levels of the 150-kDa protein in in vitro translations also have high levels of p206 and low levels of the 70-kDa protein. (3) The rate of formation of the 150-kDa protein is dilution insensitive, suggesting that proteolysis occurs mainly in cis.

Amino Acid Sequence↗