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PubMed1982

Variation of influenza A, B, and C viruses.

Influenza is caused by highly variable RNA viruses belonging to the orthomyxovirus group. These viruses are capable of constantly changing the genes coding for their surface proteins as well as for their nonsurface proteins. The mechanisms responsible for these changes in type A influenza viruses include recombination (reassortment) of genes among strains, deletions and insertions in genes, and, frequently, point mutations. In addition, old strains may reappear in the population. Influenza viruses of types B and C appear to vary to a lesser degree. The mechanisms responsible for changes in these viruses are not well characterized.

Genetic Variation↗
PubMed1994

The role of upstream U3 sequences in the pathogenesis of simian immunodeficiency virus-induced AIDS in rhesus monkeys.

The nef reading frame overlaps about 70% of the U3 region of the 3' long terminal repeat (LTR) in primate lentiviruses. We investigated the functional role of these overlapping U3 sequences by analyzing the properties of three mutant forms of the pathogenic SIVmac239 clone. In mutant UScon, 90 of 275 bp in the upstream sequences (US) of U3 were changed in a conservative fashion without changing the predicted nef coding sequence. In mutant USnon, 101 of 275 bp in this region were changed in a nonconservative fashion, again without changing the predicted nef coding sequence. In mutant delta US, 275 bp in this region were deleted. Full-size, immunoreactive nef protein was synthesized in cells infected with the UScon and USnon mutants. The USnon and delta US mutants replicated with similar kinetics and to similar extents as wild-type, parental SIVmac239 in primary rhesus monkey peripheral blood mononuclear cell (PBMC) cultures. The UScon mutant replicated with slightly delayed kinetics in rhesus monkey PBMC cultures. In the CEMx174 cell line, the delta US mutant replicated similarly to the wild type, but the UScon and USnon mutants replicated with significantly delayed kinetics. Analysis of LTR-driven chloramphenicol acetyltransferase (CAT) activity and the effects of 5-azacytidine on virus replication suggested that the growth defect of the point mutants in CEMx174 cells was due in whole or in part to the introduction of multiple CG methylation sites in proviral DNA. Rhesus monkeys were experimentally infected with the UScon and USnon mutants, and the characteristics of the infection were compared with those of the parental SIVmac239. Analysis of the levels of plasma antigenemia, virus load, and CD4+ cells in PBMC revealed no decreased virulence of the mutant viruses. Analysis of lymph node biopsies taken from animals that received mutant viruses revealed histologic changes and levels of virus expression indistinguishable from those of the wild type. Furthermore, the wild-type behavior of the mutant viruses in rhesus monkeys occurred without any specific reversional events through at least 20 weeks of infection. These results, and the recent results of Kirchhoff et al. (F. Kirchoff, H. W. Kestler III, and R. C. Desrosiers, J. Virol. 68:2031-2037, 1994), suggest that these upstream sequences in U3 are primarily or exclusively nef coding sequence.

Amino Acid Sequence↗
PubMed2001

Neurotransmitter coding of enteric neurones in the submucous plexus is changed in non-inflamed rectum of patients with Crohn's disease.

Knowledge of the neurochemical coding of submucosal neurones in the human gut is important to assess neuronal changes under pathological conditions. We therefore investigated transmitter colocalization patterns in rectal submucosal neurones in normal tissue (n=11) and in noninflamed tissue of Crohn's disease (CD) patients (n=17). Neurone-specific enolase (NSE), choline acetyltransferase (ChAT), vasoactive intestinal polypeptide (VIP), substance P (SP), nitric oxide synthase (NOS) and calcitonin gene-related peptide (CGRP) were detected immunohistochemically in whole-mount preparations from rectal biopsies. The neuronal marker NSE revealed no differences in the number of cells per ganglion (controls 5.0; CD 5.1). Four cell populations with distinct neurochemical codes were identified. The sizes of the populations ChAT/VIP (58% vs. 55%), ChAT/SP (8% vs. 8%), and ChAT/- (22% vs. 22%) were similar in control and CD. The population VIP/- was significantly increased in CD (12% vs. 2% in controls). Unlike in controls, all NOS neurones colocalized ChAT in CD. Thickened CGRP-fibres occurred in CD. We identified neurochemically distinct populations in the human submucous plexus. The increase in the VIP/- population, extensive colocalization of ChAT and NOS and hypertrophied CGRP fibres indicated adaptive changes in the enteric nervous system in noninflamed rectum of CD patients.

Adolescent↗
PubMed1998

A new pair of HLA-C alleles, Cw*12042 and Cw*1203, differing at the KIR-related dimorphism of codons 77-80.

A previously unknown HLA-C variant of the Cw*12 group was identified by PCR-SSP from genomic DNA of cell NDS-JD. Molecular cloning and nucleotide sequence analysis permitted the characterization of the complete coding region of this new allele, Cw*12042. The new variant differs from the recently reported Cw*12041 by two silent changes at exons 2 and 3, and from Cw*1203 by coding changes at codons 77 and 80. Cw*1203 (Ser-Asn) and Cw*12042 (Asn-Lys) constitute the second known example of HLA-C alleles only differing at the KIR-related dimorphism of residues 77-80. The new allele is associated in cell NDS-JD with the haplotype HLA-A*2403, Cw*12042, B*51, DRB1*1502, DRB5*0102, DQB1*0601, possibly related from the evolutionary aspect to the ancestral haplotype A*2402, Cw*1202, B*5201, DRB1*1502, DRB5*0102, DQB1*0601.

Alleles↗
PubMed2001

Identification of single nucleotide polymorphisms (SNPs) and other sequence changes and estimation of nucleotide diversity in coding and flanking regions of the NMDAR1 receptor gene in schizophrenic patients.

Glutamatergic dysregulation has been hypothesized to play a role in schizophrenia. The N-methyl-D-aspartate (NMDA) type of glutamate receptor especially is of interest because, in addition to binding sites for glutamate and glycine, a necessary co-agonist, this receptor also contains noncompetitive binding sites for the psychotomimetics phencyclidine (PCP), MK-801, and ketamine. PCP-induced psychosis has been a useful disease model in that both the positive as well as the negative symptomatologies seen in schizophrenia are observed. Recently, a mouse deficient in expression of the NR1 subunit gene (NMDAR1) of the heteromeric receptor has been developed and shown to display aberrant behaviors, with reduced social and sexual interactions as well as increased stereotypic motor activity. In an extensive examination of the NMDAR1 gene in our laboratory in approximately 100 chronic schizophrenic patients, 28 unique sequence changes were identified, including eight single nucleotide polymorphisms (SNPs) in the 5' untranslated region (5'UTR), six SNPs in coding regions (cSNPs), eleven intronic SNPs, two intronic deletions of 7 and 30 bp, and an intronic microinsertion/deletion. With the exception of one previously reported cSNP, all of the identified changes were novel. The frequency of polymorphisms differed significantly by ethnicity and several appeared to be in linkage disequilibrium. None of the changes appeared likely to be of functional significance, thus suggesting that changes in the genomic NMDAR1 are unlikely to contribute to the etiology of schizophrenia. Estimates of nucleotide diversity are comparable to those observed in studies of other genes.

Asian People↗
PubMed2004

Characterizing changes in MR images with color-coded Jacobians.

Image registration is the process of establishing spatial correspondence between two images or between two image volumes. Registration can be achieved by rigid, elastic, or a combination of rigid and elastic transforms that attempt to bring the two images into coincidence. A rigid transform accounts for differences in positioning and an elastic transform describes deformations due to differences in tissue properties, temporal changes due to growth or atrophy, or differences between individuals. Deformation-based morphometry uses the resulting deformation fields from these transforms to evaluate differences between the images being registered. Three methods of registration were evaluated: rigid (affine) transformation, elastic optical flow transformation, and elastic spline transformation. All three methods produce vector deformation fields that map each point in one image to a point in the other image. A 12-color map of the transformation Jacobian was used to represent local volume changes. Using the three registration methods, color-mapped Jacobians were determined using a simulated three-dimensional block with known translation, rotation, expansion, contraction, and intensity modulations. Color-coded Jacobians were also generated for experimentally measured magnetic resonance image volumes of water-filled balloons and 7-year-old twin boys. Color-coded Jacobians overlaid on anatomical images provide a convenient method to identify regional tissue expansion and contraction.

Algorithms↗
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↗