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At least 1,351 records · Page 75Linked to original sources
PubMed2005

Identification of an interferon antagonist protein encoded by segment 7 of infectious salmon anaemia virus.

Infectious salmon anaemia virus (ISAV) is an orthomyxovirus and member of the genus Isavirus, which contains eight genomic segments coding for ten viral proteins. This study focussed on identifying the function of the largest protein encoded by ISAV genomic segment 7 (7i), which like influenza A segment 7 encodes two proteins, one of which is based on removal of an intron from the primary transcript. Using two independent methods, an Mx1 promoter-driven reporter system and real-time PCR of FACS-sorted transfected cells, we demonstrate that the non-structural ISAV 7i protein is an interferon-signalling antagonist. Other transfection studies indicated a predominantly cytoplasmic localisation of the expressed protein, which is consistent with this role. The demonstration that ISAV segment 7 encodes a putative non-structural IFN system antagonist reveals a difference with influenza A virus, where segment 7, which shares a similar coding strategy, encodes the structural matrix proteins.

Animals↗
PubMed2005

Sequences of avian reovirus M1, M2 and M3 genes and predicted structure/function of the encoded mu proteins.

We report the first sequence analysis of the entire complement of M-class genome segments of an avian reovirus (ARV). We analyzed the M1, M2 and M3 genome segment sequences, and sequences of the corresponding muA, muB and muNS proteins, of two virus strains, ARV138 and ARV176. The ARV M1 genes were 2,283 nucleotides in length and predicted to encode muA proteins of 732 residues. Alignment of the homologous mammalian reovirus (MRV) mu2 and ARV muA proteins revealed a relatively low overall amino acid identity ( approximately 30%), although several highly conserved regions were identified that may contribute to conserved structural and/or functional properties of this minor core protein (i.e. the MRV mu2 protein is an NTPase and a putative RNA-dependent RNA polymerase cofactor). The ARV M2 genes were 2158 nucleotides in length, encoding predicted muB major outer capsid proteins of 676 amino acids, more than 30 amino acids shorter than the homologous MRV mu1 proteins. In spite of the difference in size, the ARV/MRV muB/mu1 proteins were more conserved than any of the homologous proteins encoded by other M- or S-class genome segments, exhibiting percent amino acid identities of approximately 45%. The conserved regions included the residues involved in the maturation- and entry- specific proteolytic cleavages that occur in the MRV mu1 protein. Notably missing was a region recently implicated in MRV mu1 stabilization and in forming "hub and spokes" complexes in the MRV outer capsid. The ARV M3 genes were 1996 nucleotides in length and predicted to encode a muNS non-structural protein of 635 amino acids, significantly shorter than the homologous MRV muNS protein, which is attributed to several substantial deletions in the aligned ARV muNS proteins. Alignments of the ARV and MRV muNS proteins revealed a low overall amino acid identity ( approximately 25%), although several regions were relatively conserved.

Amino Acid Sequence↗
PubMed2006

Parapoxvirus of red deer in New Zealand encodes a variant of viral vascular endothelial growth factor.

Parapoxvirus of red deer in New Zealand (PVNZ), a species of the Parapoxvirus genus, causes scabby lesions on the skin and the velvet of red deer. The three other species of the genus have each been shown to encode homologs of vascular endothelial growth factor (VEGF). We report here that PVNZ strain RD86 also encodes a VEGF and that the predicted PVNZ protein shows only 37-54% amino acid identity to VEGFs encoded by the other species of the genus. Despite this extensive sequence divergence, assays of purified PVNZ VEGF (PVNZ(RD86)VEGF) demonstrated that it shares the unique VEGF receptor (VEGFR) binding profile of the other parapoxvirus VEGFs, in that it binds VEGFR-2 and induces VEGFR-2-mediated proliferation of Ba/F3-derived cells, but does not bind VEGFR-1 or VEGFR-3. In contrast to some other viral VEGFs, it does not bind neuropilin-1. Our results indicate that PVNZ(RD86)VEGF is a biologically active member of the VEGF family and is likely to contribute to the proliferative and highly vascularized nature of PVNZ lesions. Our data also reveal that all members of the genus encode a VEGF and that an extraordinary degree of inter-species sequence variation is a general feature of the parapoxvirus VEGFs.

Amino Acid Sequence↗
PubMed1995

Quantitation of cardiac output with velocity-encoded, phase-difference magnetic resonance imaging.

Velocity-encoded, phase-difference magnetic resonance imaging (MRI) previously has been used to measure flow in the aorta, as well as in the pulmonary, carotid, and renal arteries, but these measurements have not been validated against currently accepted invasive techniques. To determine the accuracy of velocity-encoded, phase-difference MRI measurements of cardiac output, 23 subjects (11 men and 12 women, aged 15 to 72 years) underwent velocity-encoded, phase-difference MRI measurements of cardiac output in the proximal aorta, followed immediately by cardiac catheterization, with measurement of cardiac output by the Fick principle and by thermodilution. For MRI, Fick, and thermodilution measurements, stroke volume was calculated by dividing cardiac output by heart rate. The magnetic resonance images were acquired in 1 to 3 minutes. For all patients, the agreement between measurements of stroke volume was 3 +/- 9 ml for MRI and Fick, -3 +/- 11 ml for MRI and thermodilution, and 0 +/- 8 ml for MRI and the average of Fick and thermodilution. Compared with standard invasive measurements, velocity-encoded, phase-difference MRI can accurately and rapidly determine cardiac output.

Adolescent↗
PubMed1998

Encoding of human basic and glycosylated proline-rich proteins by the PRB gene complex and proteolytic processing of their precursor proteins.

Proline-rich proteins (PRPs) constitute a family of about 20 members in human saliva that are encoded by six genes. Assignment of genomic DNA coding regions is complicated because of the occurrence of many alleles and the great similarity of amino acid sequences of PRPs. To overcome these problems, the nucleotide sequences of the genes encoding basic and glycosylated PRPs from one person were determined and then aligned with her previously determined protein sequences. This, together with additional protein data, has also resolved various discrepancies between corresponding protein and DNA sequences. For the first time in one person it is now possible to account for all the regions in the PRB genes encoding basic and glycosylated PRPs, and the primary structures of all secreted basic and glycosylated PRPs have been determined. Each gene encodes a precursor protein that subsequently undergoes proteolytic cleavage, thereby giving rise to the secreted proteins. The results have allowed identification of all the proteolytic cleavage sites in the precursor proteins, which all conform to a consensus cleavage site for furin. To evaluate if furin is responsible for the precursor protein cleavages, a recombinant precursor protein was synthesized by in vitro transcription translation of a PRB1 allele. The protein was shown to be correctly cleaved by furin, giving rise to the expected secreted proteins.

Alleles↗
PubMed2003

The nuclear encoded subunits of complex I from bovine heart mitochondria.

NADH:ubiquinone oxidoreductase (complex I) from bovine heart mitochondria is a complicated, multi-subunit, membrane-bound assembly. Recently, the subunit compositions of complex I and three of its subcomplexes have been reevaluated comprehensively. The subunits were fractionated by three independent methods, each based on a different property of the subunits. Forty-six different subunits, with a combined molecular mass of 980 kDa, were identified. The three subcomplexes, I alpha, I beta and I lambda, correlate with parts of the membrane extrinsic and membrane-bound domains of the complex. Therefore, the partitioning of subunits amongst these subcomplexes has provided information about their arrangement within the L-shaped structure. The sequences of 45 subunits of complex I have been determined. Seven of them are encoded by mitochondrial DNA, and 38 are products of the nuclear genome, imported into the mitochondrion from the cytoplasm. Post-translational modifications of many of the nuclear encoded subunits of complex I have been identified. The seven mitochondrially encoded subunits, and seven of the nuclear encoded subunits, are homologues of the 14 subunits found in prokaryotic complexes I. They are considered to be sufficient for energy transduction by complex I, and they are known as the core subunits. The core subunits bind a flavin mononucleotide (FMN) at the active site for NADH oxidation, up to eight iron-sulfur clusters, and one or more ubiquinone molecules. The locations of some of the cofactors can be inferred from the sequences of the core subunits. The remaining 31 subunits of bovine complex I are the supernumerary subunits, which may be important either for the stability of the complex, or for its assembly. Sequence relationships suggest that some of them carry out reactions unrelated to the NADH:ubiquinone oxidoreductase activity of the complex.

Animals↗
PubMed2002

Non-AUG translation initiation of mRNA encoding plastid-targeted phage-type RNA polymerase in Nicotiana sylvestris.

A third nuclear gene encoding a bacteriophage T7-type RNA polymerase, NsRpoT-C, was isolated and characterized from Nicotiana sylvestris. The gene, NsRpoT-C, consists of 21 exons and 20 introns and encodes a polypeptide of 977 amino acid residues. The predicted NsRpoT-C protein shows the highest identity (72% amino acid identity) with Arabidopsis thaliana RpoT;3 which is a plastid-targeted protein. Surprisingly, comparison of the deduced amino acid sequence of NsRpoT-C with that of A. thaliana RpoT;3 predicted that the NsRpoT-C starts at a CUG triplet, a rare translation initiation codon. Transient expression assays in protoplasts from tobacco leaves demonstrated that the putative N-terminal transit peptide of NsRpoT-C encodes a targeting signal directing the protein into chloroplasts. This strongly suggests that NsRpoT-C functions as an RNA polymerase transcribing plastid-encoded genes. We have designated this protein NsRpoTp.

Amino Acid Sequence↗
PubMed1988

Comparison of two independent cDNA clones reported to encode beta 1,4 galactosyltransferase.

The identity of cDNA encoding beta 1,4 galactosyltransferase (EC 2.4.1.38) has been controversial, since two independent and unrelated cDNAs have been cloned (GTcDNA-1 and -2), both of which are thought to encode beta 1,4 galactosyltransferase. We have resolved this issue by examining the expression of the corresponding mRNAs in tissues possessing varying levels of galactosyltransferase activity. The expression of GTcDNA-1 parallels the level of galactosyltransferase activity assayed enzymatically, while the expression of GTcDNA-2 is unrelated to the level of enzyme activity, being virtually undetectable in tissues with abundant galactosyltransferase activity. GTcDNA-2, therefore, does not likely encode beta 1,4 galactosyltransferase, but rather, encodes a product that indirectly influences enzyme activity following cellular transfection.

Animals↗
PubMed2002

The influence of attention on holistic face encoding.

We examined the influence of attention on the formation of holistic face representations using the composite effect (Perception 16 (1987) 747). In Experiment 1, stimuli composed of a face superimposed on a house were shown during encoding. Subjects delineated either the face or the house, thus manipulating attention away or toward the face. In Experiment 2, an intact face image was presented with letters scrolling from top to bottom. Subjects were asked to either ignore the letters or read them and decipher the words that they formed. Aligned and misaligned composites were shown at testing. Recognition performance was consistently better for misaligned than aligned stimuli, regardless of the allocation of attention during encoding. In Experiment 3, we show that the composite effect can be eliminated by a disruption in holistic processing at the time of encoding. We conclude that holistic encoding is one aspect of face analysis that occurs equally well with or without attention.

Adolescent↗
PubMed1999

The surface form x problem size interaction in cognitive arithmetic: evidence against an encoding locus.

Sixty-four university students received simple addition problems with operands presented as arabic digits (e.g. 2 + 3, 8 + 6) or as English number words (two + three, eight + six). Operands either were displayed simultaneously or sequentially with the left operand appearing 800 ms before the right operand. Consistent with previous findings, word problems were slower than digit problems and this word-format cost was larger for large- than small-number problems. The central question addressed by this experiment concerned whether this Format x Size interaction arises during problem encoding processes or in subsequent retrieval or production processes. In the simultaneous condition, both operands would contribute to format-related differences in encoding, whereas in the sequential condition encoding differences would arise only in connection with the second operand. Critically, however, the Format x Size interaction did not differ between the sequential and simultaneous conditions, although the experiment had ample power to detect such an effect. The results argue that the Format x Size interaction does not arise during encoding, but instead arises during calculation or production processes.

Adolescent↗
PubMed2001

Functional role of the HIV-1 Rev exon 1 encoded region in complex formation and trans-dominant inhibition.

To study functional aspects of the exon 1 encoded region of the human immunodeficiency virus type 1 Rev protein, the viral Tev protein which exhibits low Rev activity but lacks the rev exon 1 encoded region was examined. Neither Rev-Tev heteromer complex formation nor inhibition of Rev by an export deficient Tev mutant was observed. Insertion of the rev exon 1 encoded region into the Tev mutant allowed it to oligomerize with Rev and act as a trans-dominant negative mutant. This showed that the exon 1 encoded region of Rev is essential for oligomerization and that oligomerization is a prerequisite for trans-dominant inhibition.

Animals↗
PubMed2002

Molecular cloning of three cDNAs encoding different GnRHs in the brain of barfin flounder.

To examine the reproductive endocrinology of a large pleuronectiform fish, barfin flounder, Verasper moseri, a promising candidate for aquaculture and resource enhancement in northern Japan due to its high commercial value, three gonadotropin-releasing hormones (GnRHs) in the brain was identified by isolation of their cDNAs. This species had three molecular forms of GnRH; salmon GnRH (sGnRH), chicken GnRH-II (cGnRH-II), and seabream GnRH (sbGnRH). Each GnRH cDNA encoded a signal peptide (SP), GnRH, and a GnRH-associated peptide (GAP), which was connected to GnRH by a Gly-Lys-Arg sequence. The sGnRH cDNA encoded an SP composed of 23 amino acids and a GAP composed of 54 amino acids. The cGnRH-II cDNA encoded an SP of 23 amino acids and a GAP of 49 amino acids. The sbGnRH cDNA encoded an SP of 26 amino acids and a GAP of 57 amino acids. In situ hybridization showed that the genes for sGnRH, cGnRH-II, and sbGnRH are expressed in the ventromedial olfactory bulbs and the terminal nerve ganglion, the midbrain tegmentum, and the preoptic area, respectively. These results indicate that sbGnRH neurons in the preoptic area are involved in gonadotropin secretion in barfin flounder.

Amino Acid Sequence↗
PubMed2002

VSP417-6, a variant-specific surface protein encoded at a sixth locus within the vsp417 gene subfamily of Giardia intestinalis.

A sixth locus (vsp417-6) belonging to the vsp417 gene subfamily, a subset of the family of genes that encodes 'variant-specific' surface proteins (VSP) in Giardia, is described. The sequence of vsp417-6(A-I), the ortholog representing the vsp417-6 locus in isolates of the type A-I (Assemblage A, Group I) genotype of Giardia intestinalis, was determined from a cloned 5.5-kb Hind III fragment of genomic DNA derived from isolate Ad-1/C1. The gene encodes a 704 residue polypeptide (VSP417-6(A-I), Mr 71,674) that has 75% identity (92% similarity) over a 718 residue overlap with the prototype of the VSP417 subfamily, VSP417-1(A-I)-encoded by the vsp417-1 (syn. tsa417) locus in type A-I isolates. Alignment of VSP417-6(A-I) with the deduced sequences of other known members of this subfamily identified one polypeptide, encoded by a gene found in type A-II (Assemblage A, Group II) isolates, whose homology with VSP417-6(A-I) (91% identity, 98% similarity over 713-residues) indicated that it was VSP417-6(A-II), the VSP417-6 ortholog in type A-II isolates. Sequence-based phylogenetic analyses of known VSP417 subfamily members defined several loci that predate the emergence of the A-I and A-II sublineages of G. intestinalis. Related sequences that may correspond to additional, uncharacterised vsp417 subfamily genes were identified in genomic DNA by Southern hybridisation using subfamily- and locus-specific probes. Variant-specific expression of vsp417-1 and vsp417-6 within axenic cultures of G. intestinalis was detected by in situ mRNA hybridization, indicating that these genes are functional and that they are expressed in an alternative fashion with other vsp genes in these organisms.

Amino Acid Sequence↗
PubMed1990

Structure and complete nucleotide sequence of the gene encoding rat fibroblast tropomyosin 4.

We have isolated and determined the complete nucleotide sequence of the gene that encodes the 248 amino acid residue fibroblast tropomyosin, TM-4. The TM-4 sequence is encoded by eight exons, which span approximately 16,000 bases. The position of the intron-exon splice junctions relative to the final transcript are identical to those present in other vertebrate tropomyosin genes and the Drosophila melanogaster TMII gene. We have found no evidence that the rat TM-4 gene is alternatively spliced, unlike all the other tropomyosin genes from multicellular organisms that have been described. Typical vertebrate tropomyosin genes contain some, or all, of alternatively spliced exons 1a and 1b, 2a and 2b, 6a and 6b, and 9a, 9b, 9c and 9d in addition to common exons 3, 4, 5, 7 and 8. The rat fibroblast TM-4 mRNA is encoded by sequences most similar to exons 1b, 3, 4, 5, 6b, 7, 8 and 9d. Two exon-like sequences that are highly similar to alternatively spliced exons 2b and 9a of the rat beta-tropomyosin gene and the human TMnm gene have been located in the appropriate region of the gene encoding rat fibroblast TM-4. However, several mutations in these sequences render them non-functional as tropomyosin coding exons. We have termed these exon-like sequences, vestigial exons. The evolutionary relationship of the rat TM-4 gene relative to other vertebrate tropomyosin genes is discussed.

Amino Acid Sequence↗
PubMed1997

Word-stem completion priming for perceptually and conceptually encoded words in patients with Alzheimer's disease.

This study examined whether the frequently reported word-stem completion priming deficit of Alzheimer's disease (AD) patients could be characterized as either a semantic encoding deficit or a conceptual priming deficit. AD patients and normal elderly control subjects studied words in two conditions: (1) reading visually presented words aloud, which maximizes perceptual encoding of seen words, and (2) generating words aloud from definitions, which maximizes conceptual encoding of words not seen but retrieved on the basis of semantic context. Recognition accuracy was greater for words that were generated at study, and word-stem completion priming was greater for words that were read at study. For the AD patients, recognition accuracy was impaired and word-stem completion priming was intact for words encoded in both conditions. The findings are discussed in terms of discrepant results about word-stem completion priming in AD.

Aged↗
PubMed1996

Pentagastrin selectively modulates levels of mRNAs encoding apical H/K adenosine triphosphatase and basolateral Na-K-Cl cotransporter in rat gastric fundic mucosa.

BACKGROUND: Gastrin regulates gastric acid secretion and gastric mucosal cell proliferation. We hypothesized that pentagastrin administration would affect mRNA levels of two membrane proteins that are important during stimulated states of HCl secretion, the basolateral Na-K-Cl cotransporter (BSC) and the apical H/K adenosine triphosphatase (H/K). METHODS: Two groups of Fischer rats received intraperitoneal injections of pentagastrin (2.5 or 25 micrograms/kg) every 8 hours for three doses. A third group served as controls. An additional group received pentagastrin plus the gastrin receptor antagonist (GRA) L740,093. Fundic mucosae were subjected to semiquantitative Northern analysis of mRNAs encoding H/K and BSC. The mRNA for Na/K adenosine triphosphatase (Na/K), a transport protein not involved directly in acid secretion, also was evaluated. RESULTS: Administration of pentagastrin caused dose-dependent increases in levels of mRNAs encoding H/K and BSC but had no significant effect on levels of Na/K mRNA. Administration of GRA prevented the pentagastrin-induced changes in mRNA levels for these transporters. CONCLUSIONS: Pentagastrin administration selectively up-regulates levels of mRNA encoding membrane proteins involved in acid secretion. The up-regulation of the mRNAs encoding BSC during pentagastrin stimulation indicates that regulation of basolateral Cl- movement may be as important as the regulation of apical H+ movement under stimulated states.

Acids↗
PubMed1997

Cloning and characterization of cDNAs encoding three isoforms of phospholipase A2 in Malayan spitting cobra (Naja naja sputatrix) venom.

cDNAs encoding three phospholipase A2 (PLA2) isoforms in Naja naja sputatrix were cloned and characterized. One of them encoded an acidic PLA2 (APLA) while the others encoded neutral PLA2 (NPLA-1 and NPLA-2). The specific characteristics of APLA and NPLA were attributed to mutations at nt139 and nt328 from G to C and G to A, respectively, resulting in amino acid substitutions from Asp20 and 83 in APLA to His20 and Asn83 in NPLA. Amino acid sequencing of purified protein also showed the presence of this Asp20 and His20 in APLA and NPLA, respectively. The cDNA encoding one of the PLA2 (NAJPLA-2A), when expressed in Escherichia coli, yielded a protein that exhibited PLA2 activity.

Amino Acid Sequence↗
PubMed2003

Enhanced immunogenicity of DNA fusion vaccine encoding secreted hepatitis B surface antigen and chemokine RANTES.

To increase the potency of DNA vaccines, we constructed genetic fusion vaccines encoding antigen, secretion signal, and/or chemokine RANTES. The DNA vaccines encoding secreted hepatitis B surface antigen (HBsAg) were constructed by inserting HBsAg gene into an expression vector with an endoplasmic reticulum (ER)-targeting secretory signal sequence. The plasmid encoding secretory HBsAg (pER/HBs) was fused to cDNA of RANTES, generating pER/HBs/R. For comparison, HBsAg genes were cloned into pVAX1 vector with no signal sequence (pHBs), and further linked to the N-terminus of RANTES (pHBs/R). Immunofluorescence study showed the cytoplasmic localization of HBsAg protein expressed from pHBs and pHBs/R, but not from pER/HBs and pER/HBs/R at 48 h after transfection. In mice, RANTES-fused DNA vaccines more effectively elicited the levels of HBsAg-specific IgG antibodies than pHBs. All the DNA vaccines induced higher levels of IgG(2a) rather than IgG(1) antibodies. Of RANTES-fused vaccines, pER/HBs/R encoding the secreted fusion protein revealed much higher humoral and CD8(+) T cell-stimulating responses compared to pHBs/R. These results suggest that the immunogenicity of DNA vaccines could be enhanced by genetic fusion to a secretory signal peptide sequence and RANTES.

Animals↗