PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “coding change”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

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

At least 55 records · Page 3Linked to original sources
PubMed1992

Restricted use of fetal VH3 immunoglobulin genes by unselected B cells in the adult. Predominance of 56p1-like VH genes in common variable immunodeficiency.

The large VH3 family of human immunoglobulin genes is commonly used throughout B cell ontogeny. However, B cells of the fetus and certain autoantibody-producing clones are restricted to a recurrent subset of VH3 genes, and VH3 B cells are deficient in certain immunodeficiency diseases. In this study, we have sequenced a set of rearranged VH3 genes generated by genomic polymerase chain reaction (PCR) from normal adults and those with common variable immunodeficiency (CVI). In both groups, all cones were readily identifiable with the fetal VH3 subset, and were further distinguished by limited DH motifs and exclusive use of JH4. In CVI, the residual population of VH3 B cells were notable for predominant use of 56p1-like VH genes. All clones displayed sequence divergence (including somatic mutation) with evidence of strong selection against complementarity-determining region (CDR) coding change. A survey of other V gene families indicates that human V gene diversity may be restricted in general by germline mechanisms. These findings suggest that the expressed antibody repertoire in the human adult may be much smaller than anticipated, and selected by processes in part distinct from the paradigm of maximal antigen-binding diversity.

Antibody Diversity↗
PubMed1990

Exon 7 Ncol restriction site within CYP21B (steroid 21-hydroxylase) is a normal polymorphism.

A point mutation within exon 7 producing an amino acid coding change and a recognition site for the endonuclease Ncol has been reported in the HLA-Bw47-linked CYP21A pseudogene and some mutant CYP21B (steroid 21-hydroxylase) genes of patients with congenital adrenal hyperplasia (CAH). Whether this mutation is deleterious was not demonstrated. We analyzed DNA from various subjects for the presence of the exon 7 Ncol site: group 1, 10 normal subjects; group 2, 11 patients with salt-losing CAH; and group 3, 18 members of an Amish pedigree in which 10 expressed HLA-Bw47 not linked to CAH. Southern blots of Ncol-digested genomic DNA which were hybridized with CYP21 cDNA showed that four subjects of group 1 had a heterozygous Ncol pattern. In group 2, seven patients had the Ncol site; two of them were homozygous for the site and had deletions of both CYP21B genes. The other five were heterozygous for the Ncol site, which was linked to a CYP21B deletion and a HLA-Bw47 haplotype. In group 3, no one exhibited the exon 7 Ncol site. To map the Ncol sites to CYP21A or CYP21B in the normal subjects, DNA from the four Ncol heterozygous subjects was double digested with Ncol and Mbol and hybridized with CYP21 cDNA. Ncol-Mbol fragments unique to CYP21A were identified in all four, but the smaller CYP21B-specific fragments were not detected. Their genomic DNA in the region of exon 7 (bases +1167 to +2058) was then amplified, cloned, and sequenced.(ABSTRACT TRUNCATED AT 250 WORDS)

Adrenal Hyperplasia, Congenital↗
PubMed2025

Prioritization of causal genes from genome-wide association studies by Bayesian data integration across loci.

MOTIVATION: Genome-wide association studies (GWAS) have identified genetic variants, usually single-nucleotide polymorphisms (SNPs), associated with human traits, including disease and disease risk. These variants (or causal variants in linkage disequilibrium with them) usually affect the regulation or function of a nearby gene. A GWAS locus can span many genes, however, and prioritizing which gene or genes in a locus are most likely to be causal remains a challenge. Better prioritization and prediction of causal genes could reveal disease mechanisms and suggest interventions. RESULTS: We describe a new Bayesian method, termed SigNet for significance networks, that combines information both within and across loci to identify the most likely causal gene at each locus. The SigNet method builds on existing methods that focus on individual loci with evidence from gene distance and expression quantitative trait loci (eQTL) by sharing information across loci using protein-protein and gene regulatory interaction network data. In an application to cardiac electrophysiology with 226 GWAS loci, only 46 (20%) have within-locus evidence from Mendelian genes, protein-coding changes, or colocalization with eQTL signals. At the remaining 180 loci lacking functional information, SigNet selects 56 genes other than the minimum distance gene, equal to 31% of the information-poor loci and 25% of the GWAS loci overall. Assessment by pathway enrichment demonstrates improved performance by SigNet. Review of individual loci shows literature evidence for genes selected by SigNet, including PMP22 as a novel causal gene candidate.

Genome-Wide Association Study↗
PubMed2026

Codon bias variation in Staphylococcus aureus.

BACKGROUND: Staphylococcus aureus causes a multiplicity of human diseases acquired in community and healthcare settings alike around the globe. While most studies focus on coding changes to assess genome evolution and study genetic adaptation, interrogation of silent mutations in the form of synonymous codon usage bias is less well-studied. As such, understanding of patterns in codon bias at the gene and genome levels, and how codon bias impacts protein expression in S. aureus remains incomplete. METHODS: The codon bias of 2,565 protein encoding genes from NCTC 8325 was queried against all publicly available closed S. aureus genomes. Using public BioSample data, genomes were sorted by disease state, submitting institution, and collection site. Codon bias was assessed at the level of gene and genome using the codon adaptation index (CAI), calculated using 30S and 50S ribosomal genes. Gene set enrichment analysis was applied to determine associations between physiological functions, CAI gene scores, and interquartile ranges. CAI scores were also compared to an in vitro S. aureus proteomics database to correlate codon bias and protein expression. RESULTS: CAI scores varied within and between isolates at the gene and genome levels. Genes with ribosome-associated functions were most enriched among high CAI genes, and had low CAI interquartile ranges (IQR), suggesting selective pressure to maintain high expression of these genes across all S. aureus isolates. Genome sequences submitted by Aga Khan University Hospital, Nairobi, Kenya were most different from others. For the LAC USA 300 strain, CAI and protein expression were moderately positively correlated (cor&#x2009;=&#x2009;0.534, p&#x2009;<&#x2009;2.2e-16). CONCLUSIONS: Codon bias in S. aureus was shown to vary between gene, and to be a source of genetic variation between isolates; CAI and in vitro protein expression were positively correlated.

Staphylococcus aureus↗
PubMed1986

On the consistency of the MMPI in borderline personality disorder.

14 patients diagnosed as having Borderline Personality Disorder were examined on two separate occasions with the MMPI. Results strongly suggest that, as a group, borderline patients are quite consistent responders on the MMPI under test-retest conditions (1 to 58 mo.). The frequency distribution of scale elevations and code types was also examined which showed the often-noted heterogeneity of profile code types within this population. Thus, a note of caution is advised for those investigators who assume that a prototypical borderline MMPI profile exists. Specifically, considerable heterogeneity is seen among this sample of patients with respect to a two-point coding strategy, and individual codes change over time.

Adult↗
PubMed1987

Kepiński's information metabolism, Carnot's principle and information theory.

The generalized Carnot principle introduced by Brillouin provides a link between negentropy and information, but does not take into account the information stored in the brain, which is clearly excluded by the author. Further step in the generalization of Carnot's principle, which includes information turnover in the brain was accomplished by Kepiński in his theory of the metabolism of energy and information. According to Schrödinger, life processes require a supply of negentropy rather than energy stored in the food, more precisely, e.g., in glucose utilized by the brain, since energy is conserved, whereas negentropy is dissipated. The information (communication) channel transmits maximum information when the band width of the transmitted frequency is limited, and much less information when the restriction concerns the transmitted power, or energy. This can explain a considerable decrease in the information metabolism observed in depressive patients, whose life dynamics and, consequently, the amount of energy available for information metabolism is severly lowered. Thus, the fall in information metabolism is more pronounced in depression than in not too late phases of schizophrenia. As appears from Fonberg's studies the amygdaloid nucleus is responsible for the life dynamics. In different types of neuron code change is a significant parameter, which was so strongly stressed by Kepiński. Other problems discussed in the paper include: selection of information and its structural localization, localization of particular phases of information metabolism and their phylogenetic significance.

Brain↗
PubMed1988

Genetic variation among geographic isolates of Rift Valley fever virus.

The genetic variation of Rift Valley fever virus (RVFV) was estimated by sequencing a portion of the M segment RNA of 22 isolates from a variety of host species collected over 34 years in 6 African countries. The M segment RNA of the Egyptian isolate, ZH501, which has been molecularly cloned and sequenced, was used as a reference for these comparisons. Specific gene regions, responsible for antigenic determinants presumed to play a role in protection against disease, were emphasized in these investigations. Comparative sequence data revealed that most isolates were very similar to ZH501 at both the nucleic acid and deduced amino acid sequence levels. Nucleic acid sequence variation range was 0-4.5%. Amino acid sequence variation range was 0-2.4%. We identified specific amino acid coding changes which may be involved in virus neutralization and may contribute to the virulence characteristics of RVFV.

Amino Acid Sequence↗
PubMed1990

Molecular genetics of the glucose-6-phosphate dehydrogenase (G6PD) Mediterranean variant and description of a new G6PD mutant, G6PD Andalus1361A.

Glucose-6-phosphate dehydrogenase (G6PD; E.C.1.1.1.49) deficiency is the most common human enzymopathy; more than 300 different biochemical variants of the enzyme have been described. In many parts of the world the Mediterranean type of G6PD deficiency is prevalent. However, G6PD Mediterranean has come to be regarded as a generic term applied to similar G6PD mutations thought, however, to represent a somewhat heterogeneous group. A C----T mutation at nucleotide 563 of G6PD Mediterranean has been identified by Vulliamy et al., and the same mutation has been found by De Vita et al. in G6PD Mediterranean, G6PD Sassari, and G6PD Cagliari. The latter subjects had an additional mutation, at nucleotide 1311, that did not produce a coding change. We have examined genomic DNA of five patients--four of Spanish origin and one of Jewish origin--having enzymatically documented G6PD Mediterranean. All had both the mutation at nucleotide 563 and that at nucleotide 1311. A sixth sample, resembling G6PD Mediterranean kinetically but with a slightly rapid electrophoretic mobility, was designated G6PD Andalus and was found to have a different mutation, a G----A transition at nucleotide 1361, producing an arginine-to-histidine substitution. These studies suggest that G6PD Mediterranean is, after all, relatively homogeneous.

Base Sequence↗
PubMedDate not supplied

Trends in alcohol-related morbidity and mortality.

Two major trends regarding alcohol use and consequences of alcohol abuse in the United States are showing significant improvement. Continued declines are evident in age-adjusted rates of liver cirrhosis mortality, and per capita alcohol consumption is at its lowest level in 15 years. Two other trends, however, are less clear. After declining in 1982 and continuing through 1984, alcohol-related morbidity--as measured by principal diagnoses listed on short-stay, community hospital discharges--showed a slight increase in 1985. Similarly, after declining every year but one since 1981, alcohol-related motor vehicle fatalities showed a significant increase in 1986. The downward trends suggest that progress is being made in efforts to reduce alcohol-related deaths and morbidity, but there are no easy explanations for any of the trends. Reductions in liver cirrhosis death rates may reflect coding changes in liver disease categories, less chronic heavy drinking, or better medical care. Lower per capita alcohol consumption may indicate the public's increased awareness of drinking risks or the aging of the U.S. population. Ironically, the recent increase in alcohol-related motor vehicle fatalities may reflect stronger enforcement of drunk driving laws and increased BAC (blood alcohol content) testing.

Accidents, Traffic↗
PubMed1979

Some correlates of language deterioration in severely and profoundly retarded long-term institutionalized residents.

Progress or deterioration in language use was observed in two samples of retarded institutionalized residents. One sample was observed twice, and the other three times, at 5-year intervals. We coded change in language use as noncommunicating, regressed irregular, stable, or progressed. Change in language use was found to be related to two indicators of intellectual capacity. Central nervous system involvement may play a part in irregular or totally absent communication. Institutional policies regarding transfer of residents also affect the apparent language deficit in longer-term residents.

Age Factors↗
PubMed1990

Evolutionary changes in the genetic code.

The genetic code has been influenced by directional mutation pressure affecting the base composition of DNA, sometimes in the direction of increased GC content and at other times, in the direction of AT. Such pressure led to changes in species-specific usages of codons and tRNA anticodons, and also in amino acid assignments of codons in mitochondria and in several intact organisms. These code changes are probably recent evolutionary events. The genetic code is not 'frozen', but instead it is still evolving.

Base Sequence↗
PubMed1988

The consequences of reviewing serial changes in the Minnesota code for diagnosis of acute myocardial infarction.

We investigated the effect of reviewing serial electrocardiograms (ECGs) for significance of changes in the Minnesota code, and the influence of this effect on the MONICA diagnosis of myocardial infarction (MI). We used the data from 1340 consecutive admissions to the coronary care units of our MONICA centre and we developed ECG classifications and MONICA diagnoses that were based once on the unreviewed Minnesota code and once on the reviewed code. A comparison of the two ECG classifications showed that codes for evolution of Q-waves and injury currents were much more likely to change as a result of a review (46.8%) than codes for evolution of repolarization changes (12.8%). The review of serial Minnesota codes caused a change of the MONICA diagnosis primarily in the category definite MI (10%). In a blinded clinical assessment, the cases that changed diagnosis were judged to be different from those that remained constant. It is concluded that the use of ECG classification based on unreviewed Minnesota code changes introduces heterogeneity. The significance of this effect depends on the use of the results.

Coronary Care Units↗
PubMed1990

Changes in the coding sequence of the H-2Dk gene of metastatic cells that might account for immunogenic abnormality of its encoded antigen.

In previous studies we have demonstrated that metastatic cells, derived from T-10 fibrosarcoma, express an immunogenically abnormal H-2Dk glycoprotein which is involved in manifesting their metastatic phenotype. In the present study we show that these cells contain a remarkably high level of H-2Dk specific mRNA. Moreover, by cloning cDNA of this gene and analyzing its nucleotide sequence, we found 4 single nucleotide changes. Two of them did not change the encoded amino acids, whereas the others resulted in two amino acid substitutions in the alpha-2 domain of the protein product that might account for its immunogenic abnormality.

Amino Acid Sequence↗
PubMed1991

Stability of classification of filamentous fungi under changes in character coding strategy.

The characteristics of a number of filamentous fungal cultures were obtained from two previously published numerical taxonomic studies on Penicillium and Phoma. The coding strategies for some of the physiological and morphological properties employed in the original studies were re-examined and the data was re-coded by combining sets of characters into single ordered multistate characters. The different coding procedures were compared by generating average linkage (UPGMA) dendrograms which were in turn compared by calculating correlation coefficients between the final similarity matrices implied by these dendrograms. The character conversions had no significant effect on the final outcome of the clustering.

Mitosporic Fungi↗
PubMed1979

Coding of incremental changes in skin temperature by single warm fibers in the monkey.

1. Experiments were designed to answer the question: how well does a single warm fiber innervating the glabrous skin of the monkey's hand resolve incremental changes in the intensity of near-rectangular warming pulses applied to the fiber's receptive field? 2. In these experiments the measure of the warm fiber's capacity to resolve incremental changes in the intensity of successive warming pulses was termed the discriminable stimulus increment (DSI). The DSI is defined as that incremental difference in the intensity of a pair of warming pulses that could be resolved correctly, with a probability of 0.75, by comparing the fiber's responses to these two stimuli. In the specified conditions of the experiment, DSI = 0.67 sigma delta tau/(dR/dI) where sigma delta tau is the standard deviation of the difference in responses of the fiber to pairs of stimuli, and dr/dI is the fiber's sensitivity to incremental stimulus change. (dr/dI) was experimentally determined as the mean rate of change of the fiber's responses to incremental changes in the intensity of the warming pulse. 3. The DSI, as defined above, assumes that the basis for differentiating the stimuli in each pair was that the larger response in the fiber was in each instance generated by the more intense stimulus. A more general form of the DSI was also developed and used to examine the effects on intensity resolution of different discrimination rules that the brain might use. 4. In the experimental analysis the response measure of each warm fiber was the cumulative impulse count over successively longer segments of the stimulus period. With short integration intervals the DSI was high (i.e., intensity resolution was poor), but typically the DSI fell to a plateau level within 2.0--2.5 s of the onset of the warming stimulus. 5. The DSI was measured on 23 warm fibers in Macaca nemestrina for warming pulses with intensities of 0, 2, 4, 6, and 8 degrees C, at T-base levels of 29, 34 (near normal temperature of palmar skin), and 39 degrees C. For most observations the intensity resolution possible from the responses of single warm fibers, measured over this wide variety of stimulus conditions, was less than is achieved by the human observer trained to differentiate comparable warming pulses applied to the skin of the thenar eminence.

Adaptation, Physiological↗