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Results for “VARIATION”

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PubMed1999

Variation of clinical expression in patients with Stargardt dystrophy and sequence variations in the ABCR gene.

OBJECTIVE: To report the spectrum of ophthalmic findings in patients with Stargardt dystrophy or fundus flavimaculatus who have a specific sequence variation in the ABCR gene. PATIENTS: Twenty-nine patients with Stargardt dystrophy or fundus flavimaculatus from different pedigrees were identified with possible disease-causing sequence variations in the ABCR gene from a group of 66 patients who were screened for sequence variations in this gene. METHODS: Patients underwent a routine ocular examination, including slitlamp biomicroscopy and a dilated fundus examination. Fluorescein angiography was performed on 22 patients, and electroretinographic measurements were obtained on 24 of 29 patients. Kinetic visual fields were measured with a Goldmann perimeter in 26 patients. Single-strand conformation polymorphism analysis and DNA sequencing were used to identify variations in coding sequences of the ABCR gene. RESULTS: Three clinical phenotypes were observed among these 29 patients. In phenotype I, 9 of 12 patients had a sequence change in exon 42 of the ABCR gene in which the amino acid glutamic acid was substituted for glycine (Gly1961Glu). In only 4 of these 9 patients was a second possible disease-causing mutation found on the other ABCR allele. In addition to an atrophic-appearing macular lesion, phenotype I was characterized by localized perifoveal yellowish white flecks, the absence of a dark choroid, and normal electroretinographic amplitudes. Phenotype II consisted of 10 patients who showed a dark choroid and more diffuse yellowish white flecks in the fundus. None exhibited the Gly1961Glu change. Phenotype III consisted of 7 patients who showed extensive atrophic-appearing changes of the retinal pigment epithelium. Electroretinographic cone and rod amplitudes were reduced. One patient showed the Gly1961Glu change. CONCLUSIONS: A wide variation in clinical phenotype can occur in patients with sequence changes in the ABCR gene. In individual patients, a certain phenotype seems to be associated with the presence of a Gly1961Glu change in exon 42 of the ABCR gene. CLINICAL RELEVANCE: The identification of correlations between specific mutations in the ABCR gene and clinical phenotypes will better facilitate the counseling of patients on their visual prognosis. This information will also likely be important for future therapeutic trials in patients with Stargardt dystrophy.

ATP-Binding Cassette Transporters↗

PubMed1976

Variation in a natural population of Schizophyllum commune. Variation within the extreme isolates for growth rate.

Two extreme dikaryotic idolates chosen from a large sample of a localised population of Schizophyllum commune exhibited a considerable amount of genetical variation for growth rate at the near ambient temperature of 20 degrees C and at the higher temperature of 30 degrees C. The potential variation within these extreme isolates were greater than the variation observed in the whole sample. Regression analysis of the variation in growth rate of the dikaryotic progeny of the extreme isolates on that of their component monokaryons showed that the nature of gene action was not the same in these two stages of the life cycle. The simple additive-dominance model of gene action was adequate to explain the variation in growth rate in both of the extreme isolates at both of the temperatures. The small deviations from this model could be accounted for by unequal gene frequencies due to small sample size although a low incidence of non-allelic interactions could not be rule out. Directional dominance for growth rate was detected in both isolates at the more normal temperature and it was opposing in direction in the two isolates. In the slow growing isolate the dominance was for faster growth and in the fast growing isolate it was for slower growth. This is expected for a character which displays overall ambi-directional dominance if isolates with more extreme growth rates than those recovered in the population sample are eliminated by stabilising selection. The dominance is temperature dependent being ambi-directional in both isolates at the higher temperature. Environmental heterogeneity, the buffering effects of directional dominance and genotype-environment interactions and opposing selective forces operating on the monokaryotic and dikaryotic stages of the life cycle are possible contributory factors to the considerable free and potential variability displayed in this small, localised population.

Agaricales↗

PubMed1989

Genetic variation in an inbred plant: variation in tissue cultures of soybean [Glycine max (L.) Merrill].

Although soybean [Glycine max (L.) Merrill] grows as an inbreeding, generally homozygous, plant, the germplasm of the species contains large amounts of genetic variation. Analysis of soybean DNA has indicated that variation of RFLP (restriction fragment length polymorphism) markers within the species usually entails only two alleles at any one locus and that mixtures of such dimorphic loci account for virtually all of the restriction fragment variation seen in soybean (G. max), and in its ancestors, G. soja and G. gracilis. We report here that tissue cultures prepared from root tissue of individual soybean plants develop RFLP allelic differences at various loci. However, these newly generated alleles are almost always the same as ones previously found and characterized in other varieties of cultivated soybean (cultivars). This repeated generation of particular alleles suggests that much of the genetic variation seen in soybean could be the consequence of specific, relatively frequently employed, recombinational events. Such a mechanism would allow inbred cultivars to generate genetic variation (in the form of alternative alleles) in a controlled manner, perhaps in response to stress.

DNA Probes↗

PubMed2005

Does variation in interpretation of ultrasonograms account for the variation in incidence of germinal matrix/intraventricular haemorrhage between newborn intensive care units in New Zealand?

BACKGROUND: The incidence of germinal matrix/intraventricular haemorrhage (GM/IVH) reported to the Australian and New Zealand Neonatal Network (ANZNN) varies between neonatal intensive care units (NICUs). HYPOTHESIS: Differences in the capture, storage, and interpretation of the cerebral ultrasound scans may account for some of this variation. METHODS: A total of 255 infants with birth weight <1500 g and gestation <32 weeks born between 1997 and 2002 were randomly selected from the ANZNN database, 44 from each of the six NICUs in New Zealand. Twenty two infants from each NICU had cerebral ultrasound scans previously reported to ANZNN as normal; another 22 had scans reported as abnormal. The original scans were copied using digital photography and anonymised and independently read by a panel of three experts using a standardised method of reviewing and reporting. RESULTS: There was considerable variation between NICUs in methods of image capture and quality and completeness of the scans. However, there was little variation in the reporting of scans between the reviewers and the reports to ANZNN (weighted kappa 0.75-0.91). Grade 1 GM/IVH was generally over-reported and grade 4 under-reported to the ANZNN. CONCLUSION: For all NICUs, a high level of agreement was found between the reviewers' reports and the reports to the ANZNN. Thus the variation between NICUs in the incidence of GM/IVH reported to the ANZNN is unlikely to be due to differences in capture, storage, and interpretation of the cerebral ultrasound scans. Further investigation is warranted into the reasons for the variation in incidence of GM/IVH between NICUs.

Cerebral Hemorrhage↗

PubMed1992

A comprehensive study of genic variation in natural populations of Drosophila melanogaster. V. Structural-functional constraints on protein molecules and enzymes and the levels and patterns of variation among genes.

Ever since isozyme-allozyme polymorphisms were detected there has been an incessant effort to relate the amount of observed protein variation to various aspects of molecular structure and function. Structural-functional constraints can limit the amount of overall genic variation, and the observed variation can be due to neutral mutation and random genetic drift, mutation-selection balance, or balancing selection. The present analysis of structural-functional constraints on gene-enzyme variation in natural populations of Drosophila melanogaster shows that while both subunit size and substrate group show significant effects on number of alleles and mean heterozygosity, only substrate group affects population structure significantly. Subunit structure (monomer vs. multimer), IUB enzyme class (e.g., transferase, lyase), and tolerance of null alleles showed no significant effect on level or pattern of variation. While partly interdependent, these results suggest that efforts should be made to distinguish between constraints arising from molecular structure and physiological function.

Animals↗

PubMed2006

No variation and low synonymous substitution rates in coral mtDNA despite high nuclear variation.

BACKGROUND: The mitochondrial DNA (mtDNA) of most animals evolves more rapidly than nuclear DNA, and often shows higher levels of intraspecific polymorphism and population subdivision. The mtDNA of anthozoans (corals, sea fans, and their kin), by contrast, appears to evolve slowly. Slow mtDNA evolution has been reported for several anthozoans, however this slow pace has been difficult to put in phylogenetic context without parallel surveys of nuclear variation or calibrated rates of synonymous substitution that could permit quantitative rate comparisons across taxa. Here, I survey variation in the coding region of a mitochondrial gene from a coral species (Balanophyllia elegans) known to possess high levels of nuclear gene variation, and estimate synonymous rates of mtDNA substitution by comparison to another coral (Tubastrea coccinea). RESULTS: The mtDNA surveyed (630 bp of cytochrome oxidase subunit I) was invariant among individuals sampled from 18 populations spanning 3000 km of the range of B. elegans, despite high levels of variation and population subdivision for allozymes over these same populations. The synonymous substitution rate between B. elegans and T. coccinea (0.05%/site/106 years) is similar to that in most plants, but 50-100 times lower than rates typical for most animals. In addition, while substitutions to mtDNA in most animals exhibit a strong bias toward transitions, mtDNA from these corals does not. CONCLUSION: Slow rates of mitochondrial nucleotide substitution result in low levels of intraspecific mtDNA variation in corals, even when nuclear loci vary. Slow mtDNA evolution appears to be the basal condition among eukaryotes. mtDNA substitution rates switch from slow to fast abruptly and unidirectionally. This switch may stem from the loss of just one or a few mitochondrion-specific DNA repair or replication genes.

Animals↗

PubMed1998

Variation in the AU(AT)-rich element within the 3'-untranslated region of PPP1R3 is associated with variation in plasma glucose in aboriginal Canadians.

We are investigating associations between variations in candidate genes on chromosome 7q and diabetes-related phenotypes in Canadian Oji-Cree. One of these genes encodes the skeletal muscle regulatory G subunit of the glycogen-associated form of protein phosphatase 1 (PPPIR3), which may play a key role in muscle glycogen metabolism. There is a common 5-bp insertion-deletion polymorphism in a messenger ribonucleic acid-stabilizing AU(AT)-rich element within the 3'-untranslated region (UTR) of PPPIR3. The D allele had a frequency of 0.30 in the Oji-Cree. We found that this 3'-UTR variation of PPPIR3 was significantly associated with variation in 2-h postprandial glucose in adult Oji-Cree with type 2 diabetes or impaired glucose tolerance (IGT). Specifically, Oji-Cree with diabetes or IGT who were D/D homozygotes had significantly lower 2-h postprandial plasma glucose than subjects with the other genotypes. There was no association of the PPPIR3 genotype either with the presence of type 2 diabetes or IGT or with other quantitative traits in this sample. These findings suggest that common PPPIR3 3'-UTR variation that potentially affects messenger ribonucleic acid stability is associated with variation in glycemia in Oji-Cree subjects with type 2 diabetes.

3' Untranslated Regions↗

PubMed2003

Does advertisement call variation coincide with genetic variation in the genetically diverse frog taxon currently known as Leptodactylus fuscus (Amphibia: Leptodactylidae)?

The frog Leptodactylus fuscus is found throughout much of South America in open and disturbed habitats. Previous study of genetic differentiation in L. fuscus demonstrated that there was lack of genetic exchange among population units consistent with multiple species, rather than a single species. We examine advertisement vocalizations of L. fuscus to determine whether call variation coincides with genetic differentiation. Calls were analyzed for 32 individual frogs from 25 localities throughout the distributional range of L. fuscus. Although there is variation in calls among geographic samples, call variation is not concordant with genetic variation or geographic distance and the call variation observed is less than that typically found among other closely related species of Leptodactylus. This study is an example of the rare pattern of strong genetic differentiation unaccompanied by salient differences in advertisement calls. The relative infrequency of this pattern as currently understood may only reflect the lack of detailed analyses of genetic and acoustic differentiation within population systems currently understood as single species with substantial geographic distributions.

Animals↗

PubMed1992

Biological complexity and strategies for finding DNA variations responsible for inter-individual variation in risk of a common chronic disease, coronary artery disease.

Most common chronic diseases of humans aggregate, but do not segregate, in families. The segregation-linkage research paradigm has not provided great insights into their genetic etiology. In this paper, using coronary artery disease as an example, we discuss hierarchical organization, coherence, emergent properties and dynamism as features that characterize the complexity of genotype-phenotype relationships. We summarize a research strategy for evaluating the contribution of genetic and environmental factors to the prediction of inter-individual variation in risk of disease. We then review a statistical strategy that employs cladistic theory to identify individuals carrying mutant DNA sequences responsible for an observed association between marker variation in a gene and inter-individual variation in biological traits that determine risk of a common multifactorial disease. Finding these DNA sequences is a necessary step in our search for an understanding of the nature of the mapping of genetic variation into variation in risk of a disease like coronary artery disease.

Coronary Disease↗

PubMed2001

Frequency variations of discrete cranial traits in major human populations. I. Supernumerary ossicle variations.

Four supernumerary ossicle variations-the ossicle at the lambda, the parietal notch bone, the asterionic bone, and the occipitomastoid bone-were examined for laterality differences, intertrait correlations, sex differences, and between group variations in the samples from around the world. Significant laterality differences were not detected in almost all samples. In some pairs of traits, significant association of occurrence were found. Several geographic samples were sexually dimorphic with respect to the asterionic bone and to a lesser extent for the parietal notch bone. East/Northeast Asians including the Arctic populations in general had lower frequencies of the 4 accessory ossicles. Australians, Melanesians and the majority of the New World peoples, on the other hand, generally had high frequencies. In the western hemisphere of the Old World, Subsaharan Africans had relatively high frequencies. Except for the ossicle at the lambda, the distribution pattern in incidence showed clinal variation from south to north. Any identifiable adaptive value related to environmental or subsistence factors may be expressed in such clinal variation. This may allow us to hypothesise that not only mechanical factors but a founder effect, genetic drift, and population structure could have been the underlying causes for interregional variation and possible clines in the incidences of the accessory ossicles.

Female↗

PubMed2002

Inter-individual variation, seasonal variation and close correlation of OGG1 and ERCC1 mRNA levels in full blood from healthy volunteers.

The mRNA levels of the nucleotide excision DNA repair gene ERCC1 and the base excision DNA repair gene OGG1 were quantified in 43 healthy volunteers in a dietary intervention trial as markers for the DNA repair capacity. Nine samples were collected from each subject over a period of 52 days. Sampling took place from January to May. The mRNA levels of OGG1 and ERCC1 correlated closely (r = 0.86, P << 0.0001) after normalization to either 18S ribosomal RNA or to beta-actin mRNA. The levels of OGG1 and ERCC1 mRNA were relatively constant within an individual with intra-individual correlation (R(2) = 0.45-0.46) in a General Linear Model. The amounts of ERCC1 and OGG1 relative to 18S RNA were doubled in May compared with January. This coincided with an increase in the monthly influx of sunlight from 18 MJ/m(2) in January to 242 MJ/m(2) in May. The mRNA levels of both ERCC1 and OGG1 were positively correlated to the average daily influx of sunlight in the previous 30 and 5 days (r = 0.49; r = 0.37, respectively, P << 0.001). There were no significant effects of the dietary interventions. The inter-individual variation was 5-10-fold, which is more than the observed 2-3-fold seasonal variation. Thus, despite seasonal variation of the individual mRNA levels, the inter-person variation is still far larger than the intra-person variation, supporting the use as biomarkers.

Adult↗

PubMed1994

Why does geographic variation in health care practices matter? (And seven questions to ask in evaluating studies on geographic variation).

One of the most active fields in health services research is the study of "geographic variation," or disparities in rates of certain types of health care practices among large areas (such as countries or regions of a country) or small areas (such as countries or hospital market areas); "small area analysis" in particular has received much attention in journals and the popular press. Increasingly, data upon which to base studies of geographic variation are becoming available. This article poses questions to ask in applying studies on geographic variation to health care settings. Because findings from these studies may ultimately affect patient care, the questions are important for physicians as well as health services researchers. The questions are: 1) What events are to be analyzed? 2) What geographic units are to be analyzed? 3) How good are the data? 4) Are differences in rates due to chance alone? 5) Are high rates too high? 6) How is geographic variation to be explained? 7) What is the role of "presentation style" in explaining geographic variation?

Geography↗

PubMed1984

Interobserver variation in assessment of respiratory signs. Physicians' guesses as to interobserver variation.

Interobserver variation was studied for 11 respiratory signs and for the diagnostic conclusions made on the basis of these signs. Two physicians each, with and without knowledge of the patient's history, performed physical examination of the lungs in a total of 202 unselected patients from a department of internal medicine. The interobserver variation was calculated as the kappa coefficient, using a modified method that made it possible to calculate the interobserver variation for a pair of observers made up by varying physicians. No difference was demonstrated between the kappa coefficients obtained for examinations performed with and without knowledge of the history. The kappa values for the signs ranged from -0.04 to 0.58, and for the diagnoses from 0.15 to 0.68, i.e., expressed by kappa values, poor agreement. In a questionnaire study we asked a number of physicians from departments of internal medicine to guess the size of the interobserver variation for the 11 respiratory signs examined. A total of 47 physicians (90%) returned the questionnaire and the answers showed that the physicians markedly underestimated the interobserver variation.

Clinical Competence↗

PubMed1987

Flagellar variation in Serratia marcescens is associated with color variation.

The pigmented enterobacterium Serratia marcescens, an opportunistic pathogen, shows a striking variation of its red color. Different strains differ greatly both in color and in the frequency with which they produce color variants. Within a strain, the variations occur at constant rates and are reversible. During an investigation of this phenomenon we observed that variation of a 39-kilodalton protein in S. marcescens 274 is closely associated with color variation. Using antibodies to this protein we identified it as being a component of the bacterial flagella. Variation of surface proteins often provides an organism with alternate offense-defense strategies for survival in a challenging environment. The pigment, in association with flagella, may provide such a function for S. marcescens.

Antibodies↗

PubMed2006

Inter- and intra-individual variation in applied force when listening at a surface, and resulting variation in earprints.

We aimed to explore the level of inter- and intra-individual variation in applied force when listening at a surface, and assess the resulting variation in earprints. We further intended to identify possible sources of this variation. Forty subjects each listened twenty-four times at a surface while applied force was recorded. In between efforts the level and frequency of the target sound, and the level of ambient noise were varied. Each listening effort was characterized by two values: the mean of a series of force recordings ('functional force') and the highest force reading of the effort ('peak value'). A mixed model analysis of variance revealed that repetition during multiple efforts of listening and the level of the target sound significantly affected both values for applied force. The frequency of the target sound affected the peak value, but we assume this was due to confounding effects. The level of ambient noise did not affect applied force. To explore the correlation between values for applied force of various efforts by single ear, the intra-class correlation coefficient was calculated. For functional force it was 0.80; for the peak value it was 0.79. To study intra-individual variation in earprints, five prints from each ear were lifted and studied. Variation in prints is discussed.

Analysis of Variance↗

PubMed1992

Treatment-induced cyclic variations in serum lipids, lipoproteins, and apolipoproteins after 2 years of combined hormone replacement therapy: exaggerated cyclic variations in smokers.

OBJECTIVE: To study the long-term effect of cigarette smoking on cyclic variations in serum lipids, lipoproteins, and apolipoproteins following combined hormone replacement therapy. METHODS: One hundred eighteen healthy, early postmenopausal women were followed for 2 years in a randomized, placebo-controlled study. Four treatment groups received estradiol, either sequentially combined with levonorgestrel (75 micrograms), medroxyprogesterone acetate (10 mg), or desogestrel (150 micrograms), or continuously combined with cyproterone acetate (1 mg). Two groups received placebo. Serum lipids, lipoproteins, and apolipoproteins were measured at well-defined times. Information on smoking habits was elicited by questionnaire. RESULTS: We found statistically significant cyclic variations in apolipoprotein A1 in the levonorgestrel group (6.7%; 95% confidence interval [CI] 1.1-12.7%) and the desogestrel group (7.4%; 95% CI 2.9-12.1%). The cyclic variations in high-density lipoprotein (HDL) cholesterol were highly statistically significant in the levonorgestrel group (24.9%; 95% CI 10.2-39.2%). When women from sequential regimens were combined, further analysis showed that smokers had significantly larger cyclic variations in HDL cholesterol (P less than .01) and apolipoprotein A1 (P less than .05) than non-smokers. CONCLUSIONS: Sequentially combined hormone replacement therapy produces cyclic variations in HDL cholesterol and apolipoprotein A1 for at least 2 years. In addition, cigarette smoking is associated with an exaggeration of the cyclic effect of treatment on these indices.

Androgen Antagonists↗

PubMed1987

Antigenic variation and lentivirus persistence: variations in envelope gene sequences during EIAV infection resemble changes reported for sequential isolates of HIV.

The extent and nature of genomic variation among nine antigenically distinct EIAV isolates recovered during sequential clinical episodes from two experimentally infected ponies were examined by restriction fragment analysis and nucleotide sequencing. Only minor variations in restriction enzyme patterns were observed among the viral genomes. In contrast, env gene sequences of four isolates from one pony revealed numerous clustered base substitutions. Divergence in env gene nucleotide and deduced amino acid sequences between pairs of virus isolates ranged from 0.62 to 3.4% env gene mutation rates for isolates recovered during sequential febrile episodes were calculated to be greater than 10(-2) base substitutions per site per year. The degree and nature of env gene variation in EIAV is remarkably similar to the human immunodeficiency virus, suggesting common mechanisms for env gene variation among lentiviruses.

Amino Acid Sequence↗

PubMed1997

Partitioning of genetic variation between regulatory and coding gene segments: the predominance of software variation in genes encoding introvert proteins.

In considering genetic variation in eukaryotes, a fundamental distinction can be made between variation in regulatory (software) and coding (hardware) gene segments. For quantitative traits the bulk of variation, particularly that near the population mean, appears to reside in regulatory segments. The main exceptions to this rule concern proteins which handle extrinsic substances, here termed extrovert proteins. The immune system includes an unusually large proportion of this exceptional category, but even so its chief source of variation may well be polymorphism in regulatory gene segments. The main evidence for this view emerges from genome scanning for quantitative trait loci (QTL), which in the case of the immune system points to a major contribution of pro-inflammatory cytokine genes. Further support comes from sequencing of major histocompatibility complex (Mhc) class II promoters, where a high level of polymorphism has been detected. These Mhc promoters appear to act, in part at least, by gating the back-signal from T cells into antigen-presenting cells. Both these forms of polymorphism are likely to be sustained by the need for flexibility in the immune response. Future work on promoter polymorphism is likely to benefit from the input from genome informatics.

Animals↗