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At least 595 records · Page 33Linked to original sources
PubMed1994

Extent of RNA editing of glutamate receptor subunit GluR5 in different brain regions of the rat.

1. The structure and function of glutamate receptor subunits GluR2, GluR5, and GluR6 are changed by RNA editing. This reaction produces a base transition in the second transmembrane spanning region. The triplet CAG (coding for glutamine) is changed to CGG (coding for arginine). This transition has a pronounced effect on calcium fluxes through the respective ion channels, because calcium currents decrease with the rate of editing. 2. In the present study the extent of RNA editing of the glutamate receptor subunit GluR5 was studied in different brain regions of control rats using a newly developed analysis system. This system is based on restriction analysis of the polymerase chain reaction (PCR) product, derived from reverse-transcribed mRNA as template, with the enzyme Bbv1. Bbv1 recognizes the sequence of the nonedited receptor subunit around the edited base (sequence GCAGC) but not that of the edited subunit (sequence GCGGC; A edited to G). 3. Total RNA was isolated from the cerebral cortex, striatum, hippocampus, thalamus, hypothalamus, cerebellum, pons/medulla oblongata, and white matter and reverse transcribed into cDNA. The region across the edited sequence was amplified by PCR using GluR5-specific primers and the cDNA as template. PCR products were cleaned by ethanol precipitation, incubated with Bbv1, and electrophoresed on an agarose gel together with standards. Gels were photographed and the extent of GluR5 mRNA editing was quantified using an image analysis system. A calibration curve was obtained using PCR products amplified from plasmids with edited and nonedited GluR5 as inserts. 4. In the brain of control rats the extent of RNA editing of the GluR5 subunit amounted to 62 +/- 6.0% of total (cortex), 43 +/- 5.3% (striatum), 52 +/- 5.3% (hippocampus), 91 +/- 6.3% (thalamus), 85 +/- 10.2% (hypothalamus), 82 +/- 6.5% (cerebellum), 88 +/- 6.8% (pons/medulla oblongata), and 41 +/- 2.7% (white matter). 5. The extent of RNA editing varied, thus, considerably in different brain regions, being lowest in the white matter and striatum and highest in the thalamus and pons/medulla oblongate. RNA editing of glutamate receptor subunits may play an important role in the control of calcium fluxes through non-N-methyl-D-aspartate receptor channels in different physiological and/or pathological states of the brain.

Animals↗
PubMed1985

Nucleic acid sequence database VI: Retroviral oncogenes and cellular proto-oncogenes.

The databases of the Protein Identification Resource at the National Biomedical Research Foundation (NBRF) contain nucleic acid and protein sequences from 18 retroviral oncogenes (v-onc) and 8 cellular proto-oncogenes (c-onc). Comparison of the sequences between the v-onc and c-onc genes reveals: (i) The c-src, c-abl, c-mos, c-fos, c-ras, c-myb, c-myc, and c-sis genes contain coding regions that are highly conserved in the respective v-onc genes with a small number of base changes. (ii) There are more transitions than transversions. (iii) Some of these base changes are silent mutations and others generate amino acid substitutions in the viral proteins. The causes of these base changes in the coding sequences and the significance to oncogenic transformation of the amino acid substitutions in the viral proteins remain to be determined.

Animals↗
PubMed1985

Chemical modifications and genetic engineering of food proteins.

Relationships of structure to function of proteins can be studied using chemical modifications of amino-acid side chains and, more recently, recombinant deoxyribonucleic acid techniques to alter primary sequences. A wide array of chemical modifications are available to the food chemist for manipulating the functionality of food proteins. The esterification of side-chain carboxyl groups in proteins to yield polycationic polymers is emphasized in this review as an example of changing the functionality of a protein via chemical derivatization. However, chemical modifications of proteins generally suffer from a lack of control in the extent of derivatization attainable, oftentimes yielding polydisperse products. Recent advances in recombinant deoxyribonucleic acid technology offer the opportunity to relate systematically well-defined alterations in the primary sequence to changes in protein functionality. Using oligonucleotide-directed mutagenesis, one can now use synthetic oligodeoxynucleotides to prepare semisynthetic genes coding for specific changes in the primary sequence of proteins. Incorporation of the altered genes into an appropriate host can lead to the production of the modified protein for structure-function relationship studies. These recombinant deoxyribonucleic acid techniques may eventually provide the means to engineer proteins and enzymes.

Circular Dichroism↗
PubMed1987

Increased rates of illness and death from asthma in Canada.

Recent rates of illness and death from asthma in Canada and rates of hospital admission/separation for asthma were examined by age group and region. The death rates were higher in 1982-84 than in 1970-72, especially among those aged 15 to 34 years. Increases were also noted in hospital admission/separation rates, especially among those less than 15 years of age. Hospital admission/separation rates were highest in the Maritime provinces and Saskatchewan, whereas death rates were highest in Alberta and Saskatchewan. Examination of death certificates for coding errors and recoding of certificates to a single (8th) revision of the International Classification of Diseases indicated that changes in disease coding and errors in coding did not account for the significant increase in rates of death from asthma for those aged 15 to 34 years. These increases in rates of illness and death from asthma are unexplained and warrant further investigation.

Adolescent↗
PubMed1980

Appearance of receptors for Macaca speciosa red blood cells on human fibroblasts transformed by simian virus 40.

Receptors for monkey red blood cells (MRBC) that are expressed on subpopulations of human lymphoid cells are coded by genes linked to the major histocompatibility complex (MHC) region. Since malignant transformation of cells is associated with changes in structures coded by the MHC region, 10 cultured human melanoma and sarcoma cells and autologous SV40-transformed fibroblasts were tested for expression of MRBC receptors and compared with normal autologous fibroblasts. Only 2 of the tumor cell lines and normal fibroblasts from the same individual formed rosettes with MRBC. On the other hand, SV40 transformation induced in all the fibroblasts expression of receptors for MRBC. MRBC receptors on SV40-transformed fibroblasts show properties similar to those on B lymphoid cells.

Animals↗
PubMedDate not supplied

[The mutation units of loci coding for lactate dehydrogenase and their directed changes in the phylogenetic progression of vertebrate animals].

Comparison of the electrophoretic mobility of various alleles of Ldh-A and B loci within and between species demonstrated a decreased range of variation from fish to anuran amphibians and from anurans to mammals. Fish and mammals feature incompatible ranges of this variation, usually having a mobility range above and below the first zone of Ldh-A and B loci heterodimers, respectively. Amphibians feature both types of variation. Such a quality difference in allelic variation may result from scaling down the amino acid changes from mutation of intragenic regions in fish to single amino acid substitutions in mammals.

Alleles↗
PubMed2005

The evaluation of parodontium in medical students of the Medical University of Białystok according to CPITN index.

PURPOSE: The aim of the study was the evaluation of parodontium according to Community Peridental Index of Treatment Needs (CPITN) index in 455 students of The Medical and Dentistry Department of The Medical University of Białystok. MATERIAL AND METHODS: After the examination, the students filled a survey according to their own project concerning hygienic habits as well as smoking, sweet intake. The results underwent statistical analysis. RESULTS: There were 1334 (48.86%) sextants observed with healthy parodontium in the studied population. Gingivorrhoea was stated in 440 sextants (16.12%), more often in men than in women. Calculus was reveled in 790 sextants (28.94%) of the population. The number of sextants with code 3 was 1.76%. Sextants with shallow pockets were more numerous in women (37 sextants) than in men (11 sextants). Advanced changes in parodontium (code 4) were observed in 9 sextants (0.33%). On the basis of the analysis of treatment needs in the group of 455 students, it can be stated that only 24.62% of the examined subjects did not need parodontium treatment. CONCLUSIONS: The diagnosis of parodontopathy and the factor that can have harmful influence on the parodontium tissues in young people is a superior criterion in the fight with irreversible parodontium changes in adults.

Adolescent↗
PubMedDate not supplied

The nucleotide sequence of the genes encoded in early region 2b of human adenovirus type 7.

The nucleotide sequence of a cloned DNA segment encoding the early region 2b from the group B human adenovirus Ad7 has been determined. When compared to Ad2, a group C adenovirus, these sequences were found to be approx. 80% homologous within the l-strand gene-coding regions. Most changes are transitions or transversions, although several deletions/insertions also occur within the N-terminal domain of one of the coding regions. The substantial nucleotide homology results in a high degree of amino acid conservation in the predicted polypeptides encoded by the early region 2b genes. Two major open reading frames, corresponding to the Mr 87000 and Mr 140000 polypeptides of Ad2, are found in the l strand of Ad7 between genome coordinates 28.5 to 23.1 and 13.8, respectively. The r strand of the DNA in this region encodes the three leader segments joined to the 5' end of the most late viral mRNAs, and also encodes the i-leader segment found between the second and third leaders on some mRNAs. The positions of the donor and acceptor splice sites of the three leaders are conserved and can be identified by homology to Ad2. Only two of the unidentified open reading frames (URF) in Ad2 (Gingeras et al., J. Biol. Chem., in press) can be found in Ad7. URF1, encoding an Mr 13500 polypeptide at genome coordinate 17, is predominantly conserved in nucleotide and amino acid sequence, but contains one half as many arginine amino acids as does URF1 of Ad2. URF2, encoding an Mr 13600 protein which lies within the i-leader region, is not well conserved in either nucleotide or amino acid sequence.

Adenoviruses, Human↗
PubMed1980

Sequence and heterogeneity in the 5S RNA gene cluster of Drosophila melanogaster.

The sequence of the entire 5S RNA gene of Drosophila melanogaster was determined by sequencing collectively 23 copies contained in a cloned fragment of Drosophila DNA and by sequencing individually four subcloned gene copies. A repetitive heptamer (GCTG CCT) present in variable numbers immediately following the coding sequence, is responsible for the length heterogeneity in the spacer region. Some of the gene copies contain a nucleotide change in the coding region which results in a new site for the restriction enzyme Mn1 I. The variant 5S RNA produced by these gene copies has not been detected in vivo. Two other single nucleotide variations were identified in the spacer region.

Animals↗
PubMed2005

ERCC1 codon 118 polymorphism is a predictive factor for the tumor response to oxaliplatin/5-fluorouracil combination chemotherapy in patients with advanced colorectal cancer.

PURPOSE: The aim of our study was to assess whether the polymorphism of the nucleotide excision repair enzyme, excision repair cross-complementing rodent repair deficiency, complementation group 1 (ERCC1), had an effect on the tumor response in patients treated with standard chemotherapy regimens for a metastatic colorectal cancer. We have studied the synonymous polymorphism that causes a single nucleotide change C to T at codon 118 converting a codon of common usage (AAC) to a less used codon (AAT), both coding asparagine. This change results in a decreased ERCC1 gene expression, which impairs repair activity. EXPERIMENTAL DESIGN: Ninety-one patients with a median age of 55.1 years treated for a metastatic colorectal cancer were included in our retrospective study. The ERCC1 polymorphism was analyzed in the normal tissue of all patients. RESULTS: Twenty (22%) were homozygous for AAC codon (C/C genotype), 30 were (33%) homozygous for AAT codon (T/T genotype), and 41 (45%) were heterozygous (C/T genotype). The objective response rate to oxaliplatin in combination with 5-fluorouracil (5-FU) was significantly higher in the T/T genotype group compared with the C/T and the C/C genotype groups (61.9%, 42.3%, and 21.4%, respectively; P = 0.018). By contrast, no significant difference was observed when patients were treated with either 5-FU alone (45%, 29.2%, and 33.3%, respectively; P = 0.407) or in combination with irinotecan (46.1%, 25.0%, and 27.3%, respectively; P = 0.305). CONCLUSIONS: Our observations allowed us to define the first useful predictive criterion for oxaliplatin/5-FU response in patients with metastatic colorectal cancer.

Antineoplastic Combined Chemotherapy Protocols↗
PubMed2005

Allopolyploidy--a shaping force in the evolution of wheat genomes.

Recent studies have shown that allopolyploidy accelerates genome evolution in wheat in two ways: (1) allopolyploidization triggers rapid genome changes (revolutionary changes) through the instantaneous generation of a variety of cardinal genetic and epigenetic alterations, and (2) the allopolyploid condition facilitates sporadic genomic changes during the life of the species (evolutionary changes) that are not attainable at the diploid level. The revolutionary changes comprise (1) non-random elimination of coding and non-coding DNA sequences, (2) epigenetic changes such as DNA methylation of coding and non-coding DNA leading, among others, to gene silencing, (3) activation of genes and retroelements which in turn alters the expression of adjacent genes. These highly reproducible changes occur in the F1 hybrids or in the first generation(s) of the nascent allopolyploids and were similar to those that occurred twice in nature: first in the formation of allotetraploid wheat (approximately 0.5 million years ago) and second in the formation of hexaploid wheat (approximately 10,000 years ago). Elimination of non-coding sequences from one of the two homoeologous pairs in tetraploids and from two homoeologous pairs in hexaploids, augments the differentiation of homoeologous chromosomes at the polyploid level, thus providing the physical basis for the diploid-like meiotic behavior of allopolyploid wheat. Regulation of gene expression may lead to improved inter-genomic interactions. Gene inactivation brings about rapid diploidization while activation of genes through demethylation or through transcriptional activation of retroelements altering the expression of adjacent genes, leads to novel expression patterns. The evolutionary changes comprise (1) horizontal inter-genomic transfer of chromosome segments between the constituent genomes, (2) production of recombinant genomes through hybridization and introgression between different allopolyploid species or, more seldom, between allopolyploids and diploids, and (3) mutations. These phenomena, emphasizing the plasticity of the genome with regards to both structure and function, might improve the adaptability of the newly formed allopolyploids and facilitate their rapid and successful establishment in nature.

Chromosomes, Plant↗
PubMed2003

The role of spectral change detectors in temporal order judgment of tones.

Human listeners can judge the temporal order of acoustic events quite accurately in certain conditions. We hypothesized that this accuracy is realized by coding temporal order as a single neural code of spectral change in the auditory system. To test this hypothesis, we examined whether adaptation to linear frequency glides affects subsequent temporal order judgment of brief tones. We found that the point of subjective simultaneity between two tones shifted depending on the direction of spectral change of the adaptor, as predicted by the hypothesis. The amount of aftereffect was significantly reduced when adaptor and test tones were presented in different frequency regions or to different ears, suggesting that the relevant neural units exist predominantly in a frequency-selective monaural pathway.

Acoustic Stimulation↗
PubMed1984

The implications of genetic variation in human pathology.

Each human cell contains enough DNA to code for several million proteins. As a result of the technical advances which are broadly described as 'genetic engineering', each of these sequences can be isolated and purified in large amounts, free from those surrounding it in the genome. The sequences are not identical from person to person, nor even for each of a pair of chromosomes for a single person, but contain many variations. These include single base changes in both coding and non-coding regions, deletions, insertions and rearrangements. Using these changes as markers, the molecular geneticist can compare the structure and expression of normal and mutated human gene sequences and follow their inheritance in families.

Cloning, Molecular↗
PubMed1980

Nomina dubia and available names.

The availability or non-availability of a name is a question of historical fact. A name once made available under the International Code of Zoological Nomenclature can be rendered unavailable only by use of the plenary powers of the Commission. The question whether a name is a nomen dubium or not is a matter of taxonomic judgement. The difficulty with the Sarcocystinae discussed by Frenkel et al. (1979) stems from the fact that, under the present provisions of the Code, it is not possible to designate for the species concerned types that will serve any useful function. The Commission is now considering changes to the Code proposed to remedy this defect in a general, legislative way. It will not, as a matter of general practice, entertain proposals for the suppression of names merely because they are considered to be nomina dubia. The application submitted by Professor Frenkel and his collegaues will nevertheless be published in the Bulletin of Zoological Nomenclature so that the Commission can, if necessary, deliver a ruling on it before the new edition of the Code has appeared.

Animals↗
PubMed2004

An isolate of Aspergillus flavus used to reduce aflatoxin contamination in cottonseed has a defective polyketide synthase gene.

Contamination of certain foods and feeds with the highly toxic and carcinogenic family of Aspergillus mycotoxins, the aflatoxins, can place a severe economic burden on farmers. As one strategy to reduce aflatoxin contamination, the non-aflatoxin-producing A. flavus isolate AF36 is currently being applied to agricultural fields to competitively exclude aflatoxin-producing Aspergillus species. We now show that the polyketide synthase gene (pksA) required for aflatoxin biosynthesis in AF36, and in other members of the same vegetative compatibility group, possesses a nucleotide polymorphism near the beginning of the coding sequence. This nucleotide change introduces a premature stop codon into the coding sequence, thereby preventing enzyme production and aflatoxin accumulation.

Aflatoxins↗
PubMed1989

Characterisation of the dihydrofolate reductase-thymidylate synthetase gene from human malaria parasites highly resistant to pyrimethamine.

To investigate the genetic basis of drug resistance in human malaria parasites, we have sequenced the entire dihydrofolate reductase thymidylate synthetase DHFR-TS bifunctional gene from the highly pyrimethamine-resistant K1 isolate of Plasmodium falciparum. The protein is predicted to consist of 607 amino acids (aa), (71,685 Da), with an N-terminal methionine encoded by the second start codon of the open reading frame. Compared to the sequence from drug-sensitive parasites, there are two nucleotide changes in the coding region which bring about a substitution of Arg for Cys at aa position 59 and Asn for Thr at aa position 108. Both changes occur in regions of the DHFR domain involved in inhibitor and cofactor binding and are hence strongly implicated in drug resistance. The gene is present as a single copy in both K1 and drug-sensitive FCR3 isolates, and is assigned to chromosome 4. Codon usage follows the pattern observed in that of malarial surface antigen genes, with the exception fo codons corresponding to Val and Pro. The Asn and Lys contents of the predicted protein are exceptionally high, these residues being particularly concentrated in the DHFR and junction domains.

Amino Acid Sequence↗
PubMed2001

Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis.

Comparative sequence analysis has facilitated the discovery of protein coding genes and important functional sequences within proteins, but has been less useful for identifying functional sequence elements in nonprotein-coding DNA because the relatively rapid rate of change of nonprotein-coding sequences and the relative simplicity of non-coding regulatory sequence elements necessitates the comparison of sequences of relatively closely related species. We tested the use of comparative DNA sequence analysis to aid identification of promoter regulatory elements, nonprotein-coding RNA genes, and small protein-coding genes by surveying random DNA sequences of several Saccharomyces yeast species, with the goal of learning which species are best suited for comparisons with S. cerevisiae. We also determined the DNA sequence of a few specific promoters and RNA genes of several Saccharomyces species to determine the degree of conservation of known functional elements within the genome. Our results lead us to conclude that comparative DNA sequence analysis will enable identification of functionally conserved elements within the yeast genome, and suggest a path for obtaining this information.

Base Sequence↗
PubMed1997

The composition of coding joints formed in V(D)J recombination is strongly affected by the nucleotide sequence of the coding ends and their relationship to the recombination signal sequences.

V(D)J recombination proceeds in two stages. Precise cleavage at the border of the conserved recombination signal sequences (RSSs) and the coding ends results in flush double-stranded signal ends and coding ends terminating in hairpins. In the second stage, the signal and coding ends are processed into signal and coding joints. Coding ends containing certain nucleotide homopolymers affect the efficiency of V(D)J recombination. In this study, we have tested the effect of small changes in coding-end nucleotide composition on the frequency of coding- and signal joint formation. Furthermore, we have determined the sequences of coding joints resulting from recombination of coding ends with different compositions. We found that the presence of two T nucleotides 5' of both RSSs, but not a single T, reduces the frequency of signal joint formation, i.e., interferes with the cleavage stage of V(D)J recombination. However, coding-joint processing is sensitive even to a single T. Both the sequence of the coding ends and the particular RSS (12-mer or 23-mer) with which the coding end is associated affect the final composition of the coding joints. Thus, the presence of P nucleotides, the conservation of one undeleted coding end, the formation of joints without any deletions, and the template-dependent insertion of nucleotides are strongly influenced by the coding-end nucleotide composition and/or RSS association. The implications of these results with respect to the processing of coding ends are discussed.

Animals↗