Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Predictive coding”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

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

At least 217 records · Page 12Linked to original sources
PubMed1995

At least four MHC class I genes are transcribed in the horse: phylogenetic analysis suggests an unusual evolutionary history for the MHC in this species.

Nineteen horse MHC class I specificities have been serologically identified previously at a single locus (ELA-A), and two other specificities appear to be coded at other loci. Biochemical studies indicate that there are at least two expressed loci. In order to establish the number of transcribed horse MHC class I genes, we made a cDNA library from a heterozygous animal (ELA-A3/A7), and screened for positive clones using a bovine class I probe. More than 200 class I clones were isolated in this way, and so far seven unique full length sequences have been identified. All of the sequences are predicted to code for surface expressed, functional molecules. The number of different sequences identified demonstrate that at least four genes are transcribed, although variations in transmembrane length (which is generally conserved in class I loci) suggest that five genes could be represented. Evolutionary analysis of these sequences (and two additional sequences known to represent different horse class I loci) reveals no firm relationships, such that the division between the different loci cannot be discerned. These results suggest an unusual evolutionary history for the horse MHC, the precise nature of which may be revealed only following further cross-species comparisons.

Amino Acid Sequence↗
PubMed1998

Temporal encoding as a determinant of overshadowing.

Three conditioned lick suppression experiments explored the effects on overshadowing of the temporal relationships of two conditioned stimuli (CSs) with an unconditioned stimulus (US). Assuming overshadowing is maximal when the potential information conveyed by two competing CSs is equivalent, the temporal coding hypothesis predicts that greater overshadowing will be observed when the CSs share the same temporal relationship with the US. Rats were exposed to an overshadowing CS that had either a forward, simultaneous, or backward relationship to the US. The relationship of the overshadowed CSs to the US was either forward (Experiment 1), simultaneous (Experiment 2), or backward (Experiment 3). The greatest amount of overshadowing was observed when both CSs had the same temporal relationship to the US. The data are discussed within the framework of the temporal coding hypothesis and of alternative models of Pavlovian conditioning based on the informational hypothesis.

Animals↗
PubMed1992

Characterization of the extracellular region of the human thyrotrophin receptor expressed as a recombinant protein.

DNA encoding the N-terminal 415 residues of the human thyrotrophin receptor (predicted to code for the large extracellular region) was introduced into Chinese hamster ovary (CHO) cells using the glutamine synthetase/cytomegalovirus amplifiable expression system, and into E. coli using the pGEX-3X expression vector. Substantial quantities of insoluble fusion protein product resulted from bacterial expression; by Western blot analysis, this was shown to be reactive with anti-receptor antibodies raised against a peptide corresponding to residues 313-330. Immunoreactivity was not retained by the solubilized protein. In eukaryotic expression, several successful CHO transfectants were observed and one (ExG2) was characterized thoroughly. Using agarose-bound Concanavalin A, a glycoprotein with an M(r) of approximately 60,000 was detected in a detergent extract of metabolically labelled ExG2 cells, agreeing with the predicted molecular size of 45,000, plus carbohydrate. The same protein could also be detected by immunoprecipitation using the experimental anti-peptide antisera and also sera from patients with Graves' disease. The protein was immunoreactive in Western blot analyses of ExG2 cells using the experimental antisera but not the pathological sera, supporting the view that linear sequences are not sufficient for autoantibody binding. These are the first studies in which visualization of eukaryotically expressed recombinant receptor by such immunological techniques has been possible, presumably because of the higher expression of the glutamine synthetase system. Surprisingly, the recombinant protein was retained within the cells rather than being secreted. The recombinant protein was very effective at absorbing the adenylate cyclase-stimulating activity of the sera from patients with Graves' disease, but not that of thyrotrophin. This suggests that the large N-terminal extracellular region contains epitopes for stimulatory autoantibodies, but that high affinity thyrotrophin binding requires additional components.

Adenylyl Cyclases↗
PubMedDate not supplied

An unusual coding sequence from a Drosophila clock gene is conserved in vertebrates.

The per locus has a fundamental involvement in the expression of biological rhythms in Drosophila. Mutations at this locus can shorten, lengthen or eliminate a variety of rhythmic activities that range from circadian behaviours, exemplified by eclosion and locomotor activities, to short-period behaviour such as the 55-s rhythm of courtship song. DNA from the per locus has been cloned, and we have used P-element-mediated DNA transformation to establish that a 7.1-kilobase(kb) HindIII fragment contains a functional copy of the gene. This transforming DNA contains a single transcription unit which gives rise to a 4.5-kb poly(A)+ RNA. Here we report the results of a search for sequences homologous to the per locus DNA in the genomic DNA of several species of vertebrates. An unusual, tandemly repeated sequence forming a portion of the 4.5-kb per transcript is homologous to DNA in chicken, mouse and man. Cloned DNAs from the mouse and Drosophila are related by long, uninterrupted tandem repetitions of the sequence ACNGGN. At the per locus, these tandem repeats are predicted to code for poly(Thr-Gly) tracts up to 48 amino acids long. These repeated sequences are also transcribed in the mouse. Several long tracts of poly(Thr-Gly) appear to be encoded by DNA cloned from the mouse.

Amino Acid Sequence↗
PubMed1998

The P-selectin gene is highly polymorphic: reduced frequency of the Pro715 allele carriers in patients with myocardial infarction.

P-selectin is an adhesion molecule, expressed at the surface of activated cells, that mediates the interaction of activated endothelial cells or platelets with leukocytes. P-selectin expression is increased in atherosclerotic plaques, and high plasma levels of this molecule have been observed in patients with unstable angina. We investigated the P-selectin gene as a possible candidate for myocardial infarction (MI). The P-selectin gene is situated on chromosome 1q21-q24, spans >50 kb and contains 17 exons. The sequences of the 5'-flanking region and exons of 40 alleles from patients with MI were screened for polymorphisms using polymerase chain reaction/single-strand conformation polymorphism (PCR-SSCP) and sequencing. Thirteen polymorphisms were identified: five in the 5'-flanking and eight in the exonic sequences. Four polymorphisms (Ser290Asn, Asn562Asp, Leu599Val and Thr715Pro) predicted a change in the amino acid sequence of the P-selectin protein. All P-selectin polymorphisms as well as a common E-selectin polymorphism, Ser128Arg which has been reported as being associated with an increased risk of premature coronary heart disease (CHD), and is in tight linkage disequilibrium with several P-selectin polymorphisms, were investigated in 647 patients with MI and 758 control subjects from four regions of France and Northern Ireland (the ECTIM study). The entire set of P-selectin polymorphisms provided a heterozygosity of 91%. The polymorphisms were tightly associated with one another and displayed patterns of linkage disequilibrium suggesting the existence of highly conserved ancestral haplotypes. The five polymorphisms in the 5'-flanking region of the gene were unrelated to MI or any relevant phenotype measured in the ECTIM study. We inferred that the four missense variants identified in the coding region predicted eight common forms of the P-selectin protein. The Pro715 allele which characterizes one of these forms was less frequent in France than in Northern Ireland ( P < 0.002) and in cases than in controls ( P < 0.002; P < 0.02 after correction for the number of tests). We conclude that the P-selectin gene is highly polymorphic and hypothesize that the Pro715 variant may be protective for MI. Whether this variant affects the properties of the P-selectin protein in a way which is compatible with this hypothesis needs to be checked experimentally.

Adult↗
PubMed1993

Molecular cloning and primary structure of Man9-mannosidase from human kidney.

Man9-mannosidase, a processing enzyme found in the endoplasmic reticulum (ER), catalyses the removal of three distinct mannose residues from peptide-bound Man9-GlcNAc2 oligosaccharides producing a single Man6 isomer [Bause, E., Breuer, W., Schweden, J., Roesser, R. & Geyer, R. (1992) Eur. J. Biochem. 208, 451-457]. We have isolated four Man9-mannosidase-specific clones from a human kidney cDNA library and used these to construct a full-length cDNA of 3250 base pairs. A single open reading frame of 1875 nucleotides encodes a protein of approximately 71 kDa, consistent with data from immunological studies. Analysis of the coding sequence predicts that Man9-mannosidase is a type II transmembrane protein consisting of a short cytoplasmic polypeptide tail, a single transmembrane domain acting as a non-cleavable signal sequence and a large luminal catalytic domain. This domain architecture closely resembles that of other ER and Golgi-located processing enzymes, pointing to common structural motifs involved in membrane insertion and topology. The protein sequence of the Man9-mannosidase contains three potential N-glycosylation sites of which only one site is used. The amino acid sequence of several peptide regions, including a calcium-binding consensus sequence, bears striking similarities to an ER alpha-1,2-mannosidase from yeast, whereas, by contrast, no sequence similarity was detectable with rat liver ER alpha-mannosidase and Golgi alpha-mannosidase II. This finding may indicate that the mammalian alpha-mannosidases, which differ significantly in their substrate specificity, are coded for by evolutionarily unrelated genes, providing an attractive means of regulation and fine-tuning oligosaccharide processing, not only at the enzymic but also at the transcriptional level.

Amino Acid Sequence↗
PubMed1998

Identification of recurrent and novel mutations in the LDL receptor gene in Spanish patients with familial hypercholesterolemia. Mutations in brief no. 135. Online.

We used the single strand conformation polymorphism (SSCP) method to investigate 13 apparently unrelated Spanish patients with familial hypercholesterolemia (FH) for mutations in the promoter region and the 18 exons and their flanking intron sequences of the low density lipoprotein (LDL) receptor gene. We found 16 aberrant SSCP patterns, and the underlying mutations were characterized by DNA sequencing. Five novel missense mutations, Q71E, C74G, C95R, C281Y and D679E, and one nonsense mutation, Q133X, were identified. We also found six missense mutations, S156L, D200Y, D200G, E256K, T413K and C646Y, and one stop codon mutation, W(-18)X, that were previously described in patients from other populations. A new frameshift mutation, 2085del19, was found in one patient. We also identified three splicing mutations; two of them are novel mutations, 1706-10G->A and 2390-1G->A, and the other one has been reported recently, 313+1G->C. Four patients were found to carry two different mutations in the same allele: Q71E and 313+1G->C; C95R and D679E; W(-18)X and E256K, and C281Y and 1706-10G->A. Our results demonstrate that there is a broad spectrum of mutations in the LDL receptor gene in the Spanish population.

DNA Mutational Analysis↗
PubMed1988

Nucleotide sequence of cloned cDNAs encoding chicken preproparathyroid hormone.

In order to characterize an avian parathyroid hormone gene, a lambda gt10 cDNA library constructed from chicken parathyroid gland mRNA was screened with a human preproparathyroid hormone (preproPTH) cDNA probe. Nucleotide sequence analysis of three independent clones confirmed that they encoded chicken preproPTH. This analysis, complemented by primer extension and Northern blot analysis of mRNA, demonstrated a 5'-untranslated region for chicken preproPTH of 127 nucleotides, a coding region of 357 nucleotides, and a 3'-untranslated region of approximately 2500 nucleotides. The coding sequence predicts a mature chicken PTH of 88 amino acids in contrast to the 84 amino acids of the mammalian hormones. Comparison of the avian and the mammalian hormones shows striking homology in the region of amino acids 1-32. The middle and carboxyl-terminal portions of chicken PTH, however, differ considerably from the mammalian hormones and include deletions of sequences conserved in mammalian PTH and insertions of novel peptide sequences. Comparison of the avian and mammalian structures suggests potential alterations of the mammalian sequences that may lead to altered bioactivity and/or hormone metabolism.

Amino Acid Sequence↗
PubMed1995

Cloning and expression of the alpha subunit of succinyl-CoA synthetase from Dictyostelium discoideum.

We have isolated and characterized a genomic fragment and a cDNA clone for the alpha subunit of succinyl-CoA synthetase (SCS) from Dictyostelium discoideum. The coding region predicts a protein of 310 amino acids. Direct amino acid sequence data indicate that the first 16 amino acids encoded by the cDNA comprise a mitochondrial targeting sequence. The predicted molecular mass of the mature protein is 31 kDa on sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The deduced amino acid sequence of the alpha subunit from D. discoideum shows 75% identity to that from rat liver, which represents a GTP-utilizing form of SCS, and 62% identity to the Escherichia coli protein, which is an ATP-utilizing form. We have previously shown that the enzyme purified from growing D. discoideum is a GTP-utilizing enzyme. In D. discoideum, the alpha subunit is a single copy gene that is developmentally regulated. Highest levels of its mRNA are seen in growing cells, which is followed by a relatively dramatic decline at the time cells complete their aggregation program. In contrast, the level of the protein, as determined by Western blots, remains unchanged throughout development. This indicates that any developmental changes in SCS activity reflect changes in the availability of its substrates or effectors and not changes in the level of enzyme.

Amino Acid Sequence↗
PubMed1997

Molecular cloning of a bovine renal G-protein coupled receptor gene (bRGR): regulation of bRGR mRNA levels by amino acid availability.

A cDNA of 3.2 kb, encoding a putative G protein-coupled receptor and hence called bRGR1, has been isolated from a cDNA library generated from the bovine renal epithelial cell line NBL-1. This cDNA consisted of 41 base pairs of 5'-untranslated sequence, an open reading frame of 1083 base pairs, and a 2.07 kb fragment of 3'-untranslated sequence that includes a poly(dA) tail. The coding sequence predicts a protein of 361 residues. The ligand of the bRGR1 protein may be of low molecular weight, as deduced from the analysis of the predicted primary structure of the receptor protein and the comparison with other subtypes of the G protein-coupled receptor family. The amounts of bRGR1 mRNA significantly increase when NBL-1 cells are cultured in an amino acid-depleted medium. This effect can not be caused by a decrease in protein synthesis because cycloheximide did not mimic the increase in bRGR1 mRNA levels triggered by amino acid starvation. These data suggest that bRGR1 may be an amino acid-regulated gene.

Amino Acid Sequence↗
PubMed1998

Molecular cloning and expression of a cDNA encoding a human thioredoxin-like protein.

This report describes the cloning of a human cDNA that encodes a new protein (Txl, Thioredoxin-like) that belongs to the expanding family of thioredoxins based on sequence comparison of the deduced amino acid sequence. This cDNA, with a total length of 1,278 bp, consists of 205 bp of 5'-untranslated sequence (including an in frame stop codon), an open reading frame of 870 bp and a 203 bp fragment of 3'-untranslated sequence. The coding sequence predicts a protein of 289 amino acids with two distinct domains: an N-terminal domain of 105 residues homologous to the rest of mammalian thioredoxins containing the conserved active site (CGPC) and a C-terminal domain of 184 residues with no homology with any other protein in the database. Northern blot analysis indicates that the txl probe hybridizes to a 1.3 Kb mRNA and is ubiquitously expressed in human tissues with the highest expression in stomach, testis and bone marrow.

Amino Acid Sequence↗
PubMed1996

Gonadotropins beta-GtHI and beta-GtHII from the gilthead seabream, Sparus aurata.

Full-length cDNA sequences encoding the beta-subunits of the gonadotrophins GtHI and GtHII were isolated, cloned, and sequenced from a single gilthead seabream (Sparus aurata) pituitary using RACE PCR. Beta-GtHI and beta-GtHII degenerate PCR primers were designed according to regions of high amino acid sequence homology between the chum salmon and the bonito beta-GtHI or beta-GtHII. DNA sequence analysis of the cloned PCR products confirmed the presence of the predicted complete coding region as well as 5' and 3' untranslated sequences. The deduced amino acid sequences of beta-GtHI and beta-GtHII from the gilthead seabream were compared to GtH sequences from a number of teleosts. Seabream beta-GtHI shows the highest homology to the bonito beta-GtHI (76%) and the striped bass (74%), while seabream beta-GtHII is 98% homologous to the yellow fin porgy, 87% homologous to the bonito, and 93% homologous to the striped bass beta-GtHII. Northern blot analysis showed the transcripts of the gilthead seabream beta-GtHI and beta-GtHII to be about 700 and 740 bases, respectively. During the spawning season, beta-GtHI is expressed at higher levels in males than in females while beta-GtHII is expressed at similar levels in both sexes.

Amino Acid Sequence↗
PubMed1999

Duality of gonadotropin in a primitive teleost, Japanese eel (Anguilla japonica).

The duality of gonadotropin (GTH) is well-established in relatively modern teleosts. In primitive teleosts such as eel and catfish, however, only a single GTH (GTH-II) has been isolated and characterized. Therefore, the objective of this study was to clarify the duality of GTH, particularly the presence of GTH-I in primitive teleosts. We attempted to obtain a cDNA encoding the beta subunit of GTH-I from Japanese eel, Anguilla japonica, as a representative primitive teleost species. Rapid amplification of cDNA ends (RACE) polymerase chain reaction (PCR) was used to amplify GTH-Ibeta cDNA prepared from immature male Japanese eel pituitaries, and the obtained PCR products were subcloned and sequenced. A degenerate PCR primer was designed based on a highly conserved region between teleost GTH-Ibeta and mammalian FSHbeta. DNA sequence analysis of the cloned PCR products confirmed the presence of the predicted complete coding region as well as the 5' and 3' untranslated regions. The deduced amino acid sequence from these clones showed high homology to goldfish GTH-Ibeta (60%), whereas the identity between Japanese eel GTH-Ibeta and GTH-IIbeta was lower (42%). Phylogenetic analysis confirmed that Japanese eel GTH-Ibeta belonged to the teleost GTH-Ibeta group. These results provide a definitive proof of the presence of two types of GTHs (GTH-I and GTH-II) in Japanese eel, as has been shown in other teleosts. The duality of GTHs is applicable for teleosts in general. Northern blot analysis showed the transcripts of Japanese eel GTH-Ibeta and GTH-IIbeta to be 1200 and 750 bases, respectively. GTH-Ibeta gene was expressed in immature fish, while GTH-IIbeta gene was expressed in spermiating males and ovulated females, suggesting that two GTHs are differentially expressed at different sexual stages and may play separate roles in the reproductive process in Japanese eel.

Amino Acid Sequence↗
PubMed1996

Molecular cloning, tissue distribution, and chromosomal localization of human cationic amino acid transporter 2 (HCAT2).

Human cationic amino acid transporter 2 (HCAT2) was isolated from a human intestine cDNA library. The nucleotide sequence of the coding region predicts a 658-amino-acid protein with a calculated molecular weight of 71,669. As 91% of the residues are identical with those of the mouse cationic amino acid transporter 2 (MCAT2), HCAT2 seems to be a human counterpart of MCAT2. We found no isoform as was present in MCAT2. In Northern blot analysis, a single (9.0 kb) HCAT2 mRNA transcript was present in various human tissues. The highest level of expression was observed in skeletal muscle and the lowest level in the kidney. Hydropathy plots indicated that the translated protein is predicted to have 14 transmembrane domains with three potential N-glycosylation sites. Two patients with lysinuric protein intolerance (MIM No. 222700) were analyzed for HCAT2 cDNA but no mutation was detected. The HCAT2 gene was assigned to human chromosome 8p21.3-p22.

Amino Acid Metabolism, Inborn Errors↗
PubMed1998

Multiple transcriptional variants and RNA editing in C18orf1, a novel gene with LDLRA and transmembrane domains on 18p11.2.

C18orf1 is a novel brain-expressed transcript, mapping to 18p11.2. Upon further characterization, we found multiple and differentially expressed transcriptional variants. C18orf1 alpha 1, an 8.5-kb transcript, was predicted to code for a 306-amino-acid protein and a 7.1-kb 3'-untranslated region (UTR). This variant was encoded by at least six exons. Alternative transcripts included alpha 2, identical to alpha 1 but missing 18 residues, and N-terminal-truncated variants termed beta 1 and beta 2. A motif search suggested the presence of a transmembrane domain in both alpha and beta and a low-density lipoprotein receptor class A (LDLRA) domain in the alpha-specific N-terminal. In LDLR, LDLRA has been shown to be involved in binding Ca2+ and LDL, raising the possibility that C18orf1 might bind Ca2+ and an unknown ligand. We also present evidence of RNA editing in the 5'-UTR of beta 2, the first demonstration of this phenomenon in 5'-UTR.

Adult↗
PubMed1995

The DNA sequence of equine herpesvirus 2.

The complete DNA sequence of equine herpesvirus 2 (EHV-2) strain 86/67 was determined. The genome is 184,427 bp in size and has a base composition of 57.5% G + C. Unusually for a herpesvirus, about a third of the sequence distributed in several large blocks appears not to encode proteins. The 79 open reading frames that were identified as probably polypeptide-coding are predicted to encode 77 distinct proteins. Amino acid sequence comparisons confirmed that EHV-2 is a gamma-herpesvirus that is genetically collinear with herpesvirus saimiri (HVS; a gamma 2-herpesvirus) and Epstein-Barr virus (EBV; a gamma 1-herpesvirus), with a closer relationship to the former. Moreover, EHV-2 specifies eight proteins that have counterparts in HVS but not in EBV and only a single protein that has a homologue in EBV but not in HVS (EBV BCRF1, which encodes an interleukin 10-like protein). EHV-2 also encodes three potential G protein-coupled receptors, one with a counterpart in HVS that is specific for alpha chemokines, another with a counterpart in human cytomegalovirus (a beta-herpesvirus), which is specific for beta chemokines, and a third that is assigned more tentatively and lacks detectable counterparts in other herpesviruses.

Amino Acid Sequence↗
PubMed1998

The identification and characterization of microsatellites in the compact genome of the Japanese pufferfish, Fugu rubripes: perspectives in functional and comparative genomic analyses.

Fugu rubripes (Fugu) has one of the smallest recorded vertebrate genomes and is an economic tool for comparative DNA sequence analysis. Initial characterization of 128 kb of Fugu DNA attributed the compactness of this genome, in part, to a sparseness of repetitive DNA sequence compared with mammalian genomic sequences. This paper describes a new and comprehensive analysis in which 501 theoretically possible microsatellites with a repeat unit of one to six bases were used to query two orders of magnitude more Fugu DNA (i.e. 11.338 Mb). A total of 6042 microsatellites were identified and categorized. In decreasing order, the 20 most frequently occurring microsatellites are AC, A, C, AGG, AG, AGC, AAT, AAAT, ACAG, ACGC, ATCC, AAC, ATC, AGGG, AAAG, AAG, AAAC, AT, CCG and TTAGGG. The 20 most frequently occurring microsatellites represent 81.79% of all microsatellites identified. Our results indicate that one microsatellite occurs every 1.876 kb of DNA in Fugu, 11.55% of the microsatellites are detected in open reading frames that are predicted protein coding regions. With respect to the proportion of microsatellites present in open reading frames and the total abundance (bp) of all microsatellites, the genome of Fugu is similar to the genome of many other vertebrate species. Previous estimates performed indicate that approximately 1% of many vertebrate genomes are comprized of microsatellite sequences. However, many differences prevail in the abundance and frequency of the individual microsatellite classes. Many of the frequently occurring microsatellites in Fugu are known to code in other species for regions in proteins such as transcription factors, whilst others are associated with known functions, such as transcription factor binding sites and form part of promoter regions in DNA sequences of genes. Therefore, it is likely that such repeats in genomes have a role in the evolution of genes, regulation of gene expression and consequently the evolution of species.

Animals↗
PubMed1996

Identification, molecular cloning, and transcription analysis of the Choristoneura fumiferana nuclear polyhedrosis virus spindle-like protein gene.

The Choristoneura fumiferana nuclear polyhedrosis virus spindle-like protein (slp) gene has been identified and localized immediately downstream and in the same orientation as the CfMNPV DNA polymerase gene. The slp gene is 1101 bp long, predicted to code for a 366 amino acid (42.1 kDa) polypeptide. Transcriptional analysis revealed that the CfMNPV slp gene is expressed at late times postinfection, beginning at 24 hr postinfection and is most abundantly expressed after 36 hr. Transcription initiates within a single baculovirus consensus late start site sequence (GTAAG) at position -18 relative to the translation start codon. Based on amino acid comparisons, the CfMNPV gene is closely related to other similar baculovirus genes and distantly but recognizably related to the fusolin proteins of two entomopoxviruses. The conservation of amino acid sequence, glycosylation signals and specific domains throughout the protein suggest that this gene product may play an important role in insect DNA virus replication.

Amino Acid Sequence↗