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 343 records · Page 19Linked to original sources

PubMed1993

Chromatin structure of the yeast FBP1 gene: transcription-dependent changes in the regulatory and coding regions.

We have studied the chromatin structure of the Saccharomyces cerevisiae FBP1 gene, which codes for fructose-1,6-bisphosphatase. A strong, constitutive, DNase I, micrococcal nuclease and S1 nuclease hypersensitive site is present close to the 3' end of the coding region. In the repressed state, positioned nucleosomes exist around this site, and subtle changes occur in this nucleosomal organization upon derepression. A DNase I hypersensitive region is located within the promoter between positions -540 and -400 and its extends towards the gene in the derepressed state, leading to an alteration of nucleosomal positioning. Psoralen crosslinking of chromatin, which is used for the first time to study the mobility of restriction fragments from an RNA polymerase II gene, revealed that part of the promoter is nucleosome-free, in accordance with the results of DNase I digestion. A model is presented that, based on the chromatin structure, puts forward the hypothesis that the promoter UAS is located between -540 and -340. Finally, psoralen crosslinking, as well as digestions with micrococcal nuclease or restriction endonucleases suggests that most if not all of the copies of the active FBP1 gene are covered by nucleosomes.

Chromatin↗

PubMed1967

Frequency sensitivity of single auditory neurons in the gecko Coleonyx variegatus.

Although acoustic communication is not pronounced in reptiles, analysis of single auditory neurons in the medulla oblongata shows that the cochlea is a frequency analyser. Auditory neurons of the lizard Coleonyx variegatus respond to acoustic stimuli over a range of less than 0.1 to 17 kilohertz and are maximally responsive between 0.8 and 2.0 kilohertz. The frequencies to which they are most sensitive differ from neuron to neuron, ranging from 0.11 to 4 kilohertz. Some neurons have an inhibitory area which greatly overlaps the response area, so that inhibitory areas do not seem to sharply tune the response area at this level of the auditory tract. The inhibitory area is responsible for producing in some neurons a phasic response and nonmonotonic relation between sound intensity and number of impulses. The response pattern shows a tendency to change from tonic to phasic in more advanced auditory centers. This may serve to code rapid changes in the acoustic stimuli.

Animals↗

PubMed2006

Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change.

BACKGROUND: Non-coding RNAs (ncRNAs) have a multitude of roles in the cell, many of which remain to be discovered. However, it is difficult to detect novel ncRNAs in biochemical screens. To advance biological knowledge, computational methods that can accurately detect ncRNAs in sequenced genomes are therefore desirable. The increasing number of genomic sequences provides a rich dataset for computational comparative sequence analysis and detection of novel ncRNAs. RESULTS: Here, Dynalign, a program for predicting secondary structures common to two RNA sequences on the basis of minimizing folding free energy change, is utilized as a computational ncRNA detection tool. The Dynalign-computed optimal total free energy change, which scores the structural alignment and the free energy change of folding into a common structure for two RNA sequences, is shown to be an effective measure for distinguishing ncRNA from randomized sequences. To make the classification as a ncRNA, the total free energy change of an input sequence pair can either be compared with the total free energy changes of a set of control sequence pairs, or be used in combination with sequence length and nucleotide frequencies as input to a classification support vector machine. The latter method is much faster, but slightly less sensitive at a given specificity. Additionally, the classification support vector machine method is shown to be sensitive and specific on genomic ncRNA screens of two different Escherichia coli and Salmonella typhi genome alignments, in which many ncRNAs are known. The Dynalign computational experiments are also compared with two other ncRNA detection programs, RNAz and QRNA. CONCLUSION: The Dynalign-based support vector machine method is more sensitive for known ncRNAs in the test genomic screens than RNAz and QRNA. Additionally, both Dynalign-based methods are more sensitive than RNAz and QRNA at low sequence pair identities. Dynalign can be used as a comparable or more accurate tool than RNAz or QRNA in genomic screens, especially for low-identity regions. Dynalign provides a method for discovering ncRNAs in sequenced genomes that other methods may not identify. Significant improvements in Dynalign runtime have also been achieved.

Algorithms↗

PubMed2001

The Booroola (FecB) phenotype is associated with a mutation in the bone morphogenetic receptor type 1 B (BMPR1B) gene.

Genetic variations in ovulation rate which occur in different breeds of sheep provide useful models to explore the mechanisms regulating the development of antral follicles. The Booroola gene, an autosomal mutation that affects ovulation rate, has been known for over two decades and despite intensive research it has not yet been identified. Using resources from human genome mapping and known data about gene linkage and chromosome location in the sheep, we selected the gene encoding the Bone Morphogenetic Protein receptor (BMPR) type 1 B (ALK-6) as a candidate site for the mutation. The BMPR1B gene in the human is located at the region linked with the Booroola mutation, syntenic to chromosome 6 in the sheep. A fragment of the sheep BMPR1B gene was cloned from an ovarian cDNA and the deduced aminoacid (AA) sequence is over 98% homologous to the known mammalian sequences. cDNA and genomic DNA from 20 Booroola genotypes were screened and two point mutation were found in the kinase domain of the receptor, one at base 746 of the coding region (A in the ++ to a G in FF animals) which results in a change from a glutamine in the wild type to a arginine in the Booroola animals. Another point mutation was identified at position 1113, (C to A) but this mutation does not change the coding aminoacid. The first mutation was confirmed in genomic DNA from 10 ewes from an independent Brazilian flock which segregates the Booroola phenotype. In all instances homozygous FecB gene carrier (n=11) had only the 746 A to G mutation, non gene carriers (n=14) had only the wild type sequence and heterozygote gene carriers (n=5) had both sequences. This mutation in the subdomain 3 of the kinase domain could result in an alteration in the expression and/or phosphorylation of SMADs, resulting in the phenotype characteristic of the Booroola animals which is the 'precocious' development of a large number of small antral follicles resulting in increased ovulation rate.

Amino Acid Sequence↗

PubMed2004

[Germline mutations in the BRCA1 and BRCA2 genes from breast cancer families in China Han people].

OBJECTIVE: To detect BRCA1 and BRCA2 gene germline mutation in the Chinese breast cancer families. METHODS: Samples of peripheral blood were collected to prepare genomic DNA by conventional techniques from 15 inherited breast cancer patients from 14 breast cancer families, 76 sporadic breast cancer patients, and 100 healthy controls based on informed consent. Exons 4, 8, 11 and 18 - 20 of BRCA1, and exons 1 - 14, 17 - 24 and 27 of BRCA2, were analyzed using DNA direct sequencing. RESULTS: Six single nucleotide polymorphisms (SNPs) were found on the exon 11 of BRCA1, 2 being silent changes without change of amino acid coding, and 4 with change of amino acid coding among which 2 were polymorphic amino acid alterations and 2 were pathogenic SNPs, i.e. mutational sites. One novel BRCA1 mutation, C1196T (Pro 359 Leu), was identified in a family breast cancer patients, who was diagnosed at the age of 37. Another BRCA1 mutation, Trp 372 stop was found in a breast cancer patient who was diagnosed at the age 29. Eight SNPs were found on the exon3, 10 and 11 of BRCA2, among which 5 were silent changes and 3 were polymorphic amino acid alterations. A1093C (Asn289His) in exon 10 and A 3199G (Asn991Asp) in exon 11 being found simultaneously in the patients of 2 families but not appearing in pool DNA sample, and Asn 371 His appearing as A/C heterozygote in pool DNA sample. CONCLUSION: Two pathogenic SNPs have been found in BRCA1 and may be related to early-onset breast cancer. One of them may be a novel mutation characterized of familial breast cancer in China.

Base Sequence↗

PubMed1991

A quantitative measure of error minimization in the genetic code.

We have calculated the average effect of changing a codon by a single base for all possible single-base changes in the genetic code and for changes in the first, second, and third codon positions separately. Such values were calculated for an amino acid's polar requirement, hydropathy, molecular volume, and isoelectric point. For each attribute the average effect of single-base changes was also calculated for a large number of randomly generated codes that retained the same level of redundancy as the natural code. Amino acids whose codons differed by a single base in the first and third codon positions were very similar with respect to polar requirement and hydropathy. The major differences between amino acids were specified by the second codon position. Codons with U in the second position are hydrophobic, whereas most codons with A in the second position are hydrophilic. This accounts for the observation of complementary hydropathy. Single-base changes in the natural code had a smaller average effect on polar requirement than all but 0.02% of random codes. This result is most easily explained by selection to minimize deleterious effects of translation errors during the early evolution of the code.

Amino Acids↗

PubMed1996

Events associated with identity status change

This study examines events associated with identity status change between late adolescence and mid-adulthood. One hundred adults, aged 40-63 years, participated in a retrospective study of identity development. An adaptation of Marcia's (1966) Identity Status Interview was used to examine identity status movements within five identity domains. For each identity transition, the event judged to be primarily responsible for precipitating change was coded as follows: "age-graded," "history-graded," "critical," "family life cycle stage," "different milieu," "internal change," "influence of significant other," and "lack of opportunity". "Internal change" was associated with the greatest frequency of changes into achievement, moratorium, and diffusion statuses across most domains; "influence of a significant other" was most commonly associated with the transition to foreclosure in most domains. Few significant associations were found among identity status, event type, and demographic variables within each identity domain. Implications of these findings for our understanding of identity formation are briefly discussed.

Journal Article↗

PubMed2002

Fatal alcohol poisoning: medico-legal practices and mortality statistics.

Compilation of mortality statistics from death certificate data is based on international and national conventions which in certain situations result in the underlying cause-of-death other than that established and reported by the physician. The present study compares all fatal alcohol poisonings in 1997 as registered on forensic toxicological grounds at the accredited central laboratory and as presented in the national cause-of-death statistics, according to the underlying cause-of-death, by applying international statistical rules and principles in ICD-10. Four groups were formed, and case frequencies in each group were obtained from forensic toxicological data, group "T51" for acute poisonings due to alcohol alone, and group "Comb" for acute alcohol poisonings combined with some drug, medicament or other biological substance, and from cause-of-death statistics data, group "X45", for deaths from alcohol poisoning, and group "F102" for those medico-legal fatal alcohol poisoning deaths which at the statistics office were inferred to be due to alcoholism. The study shows that in Finland the officially compiled statistics on fatal alcohol poisonings, when compared with medico-legal statements based on forensic toxicological examinations, were underrepresented by 31.4% in 1997. About two-thirds of this underrepresentation is explained by preferring, as the underlying cause-of-death, alcoholism to acute alcohol poisoning, and about one-third by preferring, in cases of acute combined poisonings, the drug component to the alcohol. From 1998 onwards, more emphasis has been put on the alcohol component when coding medico-legally proven accidental deaths from simultaneous poisoning with alcohol and a medicinal agent. This change in coding practices presumably explains the subsequent decline in the annual underrepresentation rate of alcohol poisoning in mortality statistics to the level of 15-16%. It is concluded that the present ICD rules inevitably lead to underrepresentation of alcohol poisonings in the mortality statistics, and conceptual and practical proposals for future procedures are made.

2-Propanol↗

PubMed1996

Effect of hypoxia on abdominal motor unit activities in spontaneously breathing cats.

These experiments were designed to examine the behavior of external oblique motor units in spontaneously breathing cats during hypoxia and to estimate the contribution of recruitment and rate coding to changes in the integrated external oblique electromyogram (iEMG). Motor unit activities in the external oblique muscle were identified while the cats expired against a positive end-expiratory pressure (PEEP) of 1-2.5 cmH2O. After localization of unit activity, PEEP was removed, and recordings were made continuously for 3-4 min during hyperoxia, normoxia, and hypoxia. A total of 35 single motor unit activities were recorded from 10 cats. At each level of fractional concentration of end-tidal O2, the motor unit activity was characterized by an abrupt increase in mean discharge frequency, at approximately 30% of expiratory time, which then continued to increase gradually or remained constant before declining abruptly at the end of expiration. The transition from hyperoxia to normoxia and hypoxia was accompanied by an increase in the number of active motor units (16 of 35, 20 of 35, and 29 of 35, respectively) and by an increase in the mean discharge frequency of those units active during hyperoxia. The changes in motor unit activity recorded during hypoxia were accompanied by a significant increase in the average peak amplitude of the abdominal iEMG. Linear regression analysis revealed that motor unit rate coding was responsible for close to 60% of the increase in peak iEMG amplitude. The changes in abdominal motor unit activity and the external oblique iEMG that occurred during hypoxia were abolished if the arterial PCO2 was allowed to fall. We conclude that external oblique motor units are activated during the latter two-thirds of expiration and that rate coding and recruitment contribute almost equally to the increase in expiratory muscle activity that occurs with hypoxia. In addition, the excitation of abdominal motor units during hypoxia is critically dependent on changes in CO2 and/or tidal volume.

Abdominal Muscles↗

PubMed2001

Adaptation reveals a neural code for the visual location of orientation change.

We apply an adaptation technique to explore the neural code for the visual location of textures defined by modulation of orientation over space. In showing that adaptation to textures modulated around one orientation shifts the perceived location of textures modulated around a different orientation, we demonstrate the existence of a neural code for the location of orientation change that generalises across orientation content. Using competitive adaptation, we characterise the neural processes underlying this code as single-opponent for orientation, that is with concentric excitatory/inhibitory receptive areas tuned to a single orientation.

Adaptation, Physiological↗

PubMed1996

Methodology of serial ECG classification using an adaptation of the NOVACODE for Q wave myocardial infarction in the Bypass Angioplasty Revascularization Investigation (BARI).

Serial electrocardiographic (ECG) changes are a critical component of the diagnostic algorithm for classification of myocardial ischemic events in large-scale clinical trials. This study describes a computerized serial ECG classification program developed at the St. Louis University Core ECG Laboratory for use in the Bypass Angioplasty Revascularization Investigation (BARI) trial, in which patients with multivessel coronary artery disease were randomized to receive either coronary artery bypass grafting or percutaneous transluminal coronary angioplasty. The St. Louis University program detects and codes serial changes in Q, ST, and T wave items according to Minnesota code (MC) criteria using a modified NOVACODE hierarchical classification system. Measurements using a seven-power calibrated coding loupe are used to generate the MC from a customized software program. Significant minor or major changes are detected by the serial comparison program and referred to a physician coder for verification. Serial comparison coding rules are used to adjust for weaknesses in the standard MC classification system resulting from instability at decision boundaries. Of 4,244 BARI randomized and registry study participants with follow-up ECGs received at the Core ECG Laboratory as of March 1995, a grade 2 MC Q wave progression was noted in 568 participants (13.4%) using MC criteria alone, as compared with 367 (8.6%) after the St. Louis University coding rules were applied. The incidence of grade 1 MC Q wave progressions was 16.4% (697/4,244) versus 6.1% (259/4,244) when the St. Louis University program was applied. Intraobserver variability for grade 2 Q wave progression codes determined from a sample of 812 serial.

Algorithms↗

PubMed1987

Estimation of myocardial infarction mortality from routinely collected data in Western Australia.

The accuracy of routinely collected mortality data for ischemic heart disease (IHD) as indicators of death from acute myocardial infarction (AMI) was assessed in ages 25-64 years, according to the WHO criteria defined in 1983. Cases were identified from computer records (linked for individuals) of all death certificates and hospital discharges in Western Australia between 1971 and 1982. Where the official cause was IHD about 90% of deaths fulfilled the WHO criteria for definite or possible AMI. Up to 10% of fatal cases of definite or possible AMI were coded to other causes in the official death statistics, however it appeared that variations in this figure with changes in coding practices could cause appreciable bias in the estimation of secular trends in IHD mortality. This problem could largely be overcome by reviewing fatal events where the death certificate was coded to one of a limited number of other ICD rubrics.

Adult↗

PubMed1989

A new epidemiologic classification system for interim myocardial infarction from serial electrocardiographic changes.

Many clinical trials or population studies have used change in Minnesota Q code, ST-segment depression code or T-wave inversion code as evidence of new myocardial infarction or new coronary heart disease event. Direct electrocardiogram (ECG) waveform comparison is a new standardized procedure for diagnosing interim myocardial infarction from ECGs classified according to the Minnesota code (serial Q-wave pattern change). This procedure was investigated for its application in epidemiologic studies. Use of this procedure in the Multiple Risk Factor Intervention Trial resulted in a 50% increase in the positive predictive accuracy, improved agreement with clinically defined myocardial infarction and a strong independent prognostic association with total and coronary heart disease mortality. Among those with major Minnesota Q-code findings, there was substantial variation in mortality. The 5-year coronary heart disease death rates estimated by life table analysis were 8.5% for those with major serial Q-wave pattern change, 5.1% for those with minor serial Q-wave pattern change and 1.5 to 2.6% for those with major or minor Minnesota Q-code change not substantiated by direct waveform comparison, compared with 2.4% for those with no Minnesota Q-code findings. The coronary heart disease death rate for those with major serial Q-wave pattern change was greater than that for the other ECG groups (p less than 0.01). Adjustment for age and other risk factors did not qualitatively alter these findings. This new approach is eminently suitable for export to other investigators, for incorporation into computer analysis programs and for statistical analysis.

Actuarial Analysis↗

PubMed2003

Genetic diversity: frameshift mechanisms alter coding of a gene (Epstein-Barr virus LF3 gene) that contains multiple 102-base-pair direct sequence repeats.

Frameshift mutations provide recognized mechanisms for changing the coding potential of an organism. Here, multiple frameshifts are identified in repetitive sequences within an Epstein-Barr virus unspliced early gene, LF3, which is associated with the viral replicative cycle and also transcriptionally expressed in many virally associated tumors. On the DNA strand encoding LF3, there are three open reading frames, only one of which contains an initiation codon. Most (>95%) of the gene consists of numerous (>20, varying with cell source) GC-rich copies of a 102-bp direct repeat (called IR 4) flanked by small unique sequences. LF3 may express a protein if its initiation and termination codons reside in the same reading frame, but this is not always the case. Frameshifting events, occurring in short runs of pyrimidines (mainly C residues) in the repeats, give rise to mutations which may provide a mechanism for escape of an LF3 function from host surveillance. Sequence studies link these frameshifts to DNA replication errors. Notably, the number of sites in LF3 at which such mutations can occur permits a very large amount of diversity in this gene. Our data also suggest a second degeneracy mechanism within the protein itself, which influences its stability and may reflect a host defense mechanism. LF3 thus provides a potentially important model for studying the quest for supremacy between a virus and its host.

Amino Acid Sequence↗

PubMed2001

Human cancer: etiologic agents/dose responses/DNA repair/cellular and animal models.

The observation of cancer in an individual does not identify the causative agent(s). However, epidemiological data on populations do indicate that a large fraction of human cancers are associated with lifestyle/diet. Such studies may also help identify the etiologic agents but unless there are good dose-response data for humans and/or animal models, the probability of identifying the agent is not high. Cancers may result from endogenous reactions, such as oxidations or from exogenous agents, such as tobacco smoke (lung cancer), sunlight exposure (skin cancer), aflatoxin (liver cancer), and relatively high doses of ionizing radiations (many types of cancers). Many carcinogenic chemicals have been identified in the workplace but, they usually do not affect the overall population. Most cancer causing agents affect cellular DNA and change its coding specificity and act as cancer initiators. The repair of DNA damage ameliorates most of these endogenous and exogenous changes. The important role of DNA repair in controlling the induction of human cancer came from the observation that individuals with the skin cancer-susceptible, human disease xeroderma pigmentosum (XP) were defective in nucleotide excision repair. Endogenous DNA damages are usually damages to individual bases and are usually repaired by systems of glycosylases and endonucleases. It should be useful to investigate the rates of appearance of tumors in normal mice and in mice knocked out for specific repair enzymes because such mice could be used to test the roles of diet and caloric input in affecting particular types of endogenous damages.

Animals↗

PubMed1990

How the visual system detects changes in the direction of moving targets.

To determine how the visual system represents information about change in target direction, we studied the detection of such change under conditions of varying stimulus certainty. Target direction was either held constant over trials or was allowed to vary randomly. When target direction was constant the observer could be certain about that stimulus characteristic; randomizing the target direction rendered the observer uncertain. We measured response times (RTs) to changes in target direction following initial trajectories of varying time and distance. In different conditions, the observer was uncertain about either the direction of the initial trajectory, or the direction of change or both. With brief initial trajectories in random directions, uncertainty about initial direction elevated RTs by 50 ms or more. When the initial trajectories were at least 500 ms, this directional uncertainty ceased to affect RTs; then, only uncertainty about the direction of change affected RTs. We discuss the implications of these results for (i) schemes by which the visual system might code directional change; (ii) the visual integration time for directional information; and (iii) adaptational processes in motion perception.

Attention↗

PubMed2004

MAX meets ADAM: a dosimetric comparison between a voxel-based and a mathematical model for external exposure to photons.

The International Commission on Radiological Protection intends to revise the organ and tissue equivalent dose conversion coefficients published in various reports. For this purpose the mathematical human medical internal radiation dose (MIRD) phantoms, actually in use, have to be replaced by recently developed voxel-based phantoms. This study investigates the dosimetric consequences, especially with respect to the effective male dose, if not only a MIRD phantom is replaced by a voxel phantom, but also if the tissue compositions and the radiation transport codes are changed. This task will be resolved by systematically replacing in the mathematical ADAM/GSF exposure model, first the radiation transport code, then the tissue composition and finally the phantom anatomy, in order to arrive at the voxel-based MAX/EGS4 exposure model. The results show that the combined effect of these replacements can decrease the effective male dose by up to 25% for external exposures to photons for incident energies above 30 keV for different field geometries, mainly because of increased shielding by a heterogeneous skeleton and by the overlying adipose and muscle tissue, and also because of the positions internal organs have in a realistically designed human body compared to their positions in the mathematically constructed phantom.

Adult↗

PubMed1982

The ovalbumin gene family: complete sequence and structure of the Y gene.

The "ovalbumin Y" gene, one of three which constitute the ovalbumin gene family in chicken has been completely sequenced. The exact location of exons can be derived from the comparison with the ovalbumin gene sequence and from the map previously established by electron microscopy analysis. During evolution of the Y gene, selective pressure has operated to retain a sequence coding for an ovalbumin-like protein. The location of splice junctions, the length of protein coding exons and the reading phase are as in the ovalbumin gene. The overall homology between the Y and ovalbumin protein coding sequences is 72.6% (resulting in a 58% homology for the amino acid sequences). A significantly high number of base changes within coding sequences are present in clusters, which appear in several cases to be correlated with the occurrence of direct repeats. The 3' untranslated sequences of the Y and ovalbumin mRNAs have diverged much more, and the Y sequence contains a peculiar U(T) rich region. Corresponding introns of the ovalbumin and Y genes differ extensively both in sequence and in length. They share however characteristic biases in their base distribution.

Animals↗