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Results for “Genetic Variation”

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PubMed2004

Molecular genetic variation in Chinese populations of three subspecies of Hippophae rhamnoides.

To provide a population-level genetic profile for investigation and conservation of genetic diversity of the sea buckthorn (Hippophae rhamnoides L.), 300 individuals of fifteen natural populations of sea buckthorn in China were analyzed by using ISSR (inter-simple sequence repeats) markers. On the basis of Shannon's index and Nei's genetic diversity, the mean genetic diversity detected in the natural populations of Hippophae rhamnoides ssp. yunnanensis, ssp. sinensis, and ssp. gyantsensis was 0.1944, 0.2169, and 0.1372, respectively. The coefficient of gene differentiation (Gst) of seven ssp. yunnanensis populations is 0.2790, and that of seven ssp. sinensis populations is 0.4184. This means that 28% of the total molecular variance of seven ssp. yunnanensis populations existed among populations, and 42% for seven ssp. sinensis populations, suggesting that the subspecies have different genetic structures. No significant correlation between genetic and geographic distances of the populations was found using ISSR markers.

China↗

PubMed1980

Genetic variation in the proteins of human nail.

In a survey of the proteins from human nail, genetic variation has been observed in both the low-sulfur and high-sulfur protein fractions. The low-sulfur proteins were examined by polyacrylamide gel electrophoresis at pH 7 in the presence of sodium dodecyl sulfate, whilst the high-sulfur proteins were characterized by gel electrophoresis at pH 2.6 in 3 M urea. Of 106 samples of apparently normal nail, 69% showed a characteristic pattern of 3 major low-sulfur and 5 major high-sulfur proteins. The remaining samples showed an additional high-sulfur band, and about half of these samples also manifested an additional major low-sulfur band. The proportion of nail samples containing the variant proteins was much higher in some families. Two-dimensional eletrophoresis of the low-sulfur proteins showed five major low-sulfur components in the normal nail with an additional component in the variant sample. Peptide maps of the proteins showed that the additional protein was sufficiently different in amino acid sequence to the other proteins to indicate that a mutation in a structural gene had not occurred. In the high-sulfur protein fractions, over 30 proteins were observed in the two-dimensional electrophoretic patterns and there were at least 3 additional components in the variant fraction.

Amino Acids↗

PubMed1993

Genetic variation in a Tanzanian population of Glossina swynnertoni (Diptera: Glossinidae).

Adult Glossina swynnertoni Austen that emerged from puparia collected during 1989 and 1991 near Makuyuni, Tanzania, were examined by polyacrylamide gel electrophoresis. Fourteen of 17 enzymes were monomorphic. Midgut alkaline phosphatase (ALKPH), phosphoglucomutase (PGM), and glucose-6-phosphate isomerase (PGI) from the head and thorax were polymorphic. Banding patterns indicated that the locus for PGM was on the X chromosome and loci for ALKPH and PGI were autosomal. For the 17 loci studied, the mean heterozygosity per locus was 6.1 +/- 3.7% in the 1989 sample and 5.7 +/- 3.7% in the 1991 sample. The effective number of alleles per locus was 1.11 and 1.10 in these samples. This level of genetic variation was low compared with other populations of tsetse flies and indicated that the sample may have been drawn from a small inbred population or one that recently had gone through a genetic bottleneck.

Alleles↗

PubMedDate not supplied

Genetic variation between susceptible and non-susceptible snails to Schistosoma infection using random amplified polymorphic DNA analysis (RAPDs).

Susceptibility of snails to infection by certain trematodes and their suitability as hosts for continued development has been a bewildering problem in host-parasite relationships. The present work emphasizes our interest in snail genetics to determine what genes or gene products are specifically responsible for susceptibility of snails to infection. High molecular weight DNA was extracted from both susceptible and non-susceptible snails within the same species Biomphalaria tenagophila. RAPD was undertaken to distinguish between the two types of snails. Random primers (10 mers) were used to amplify the extracted DNA by the polymerase chain reaction (PCR) followed by polyacrylamide gel electrophoresis (PAGE) and silver staining. The results suggest that RAPD represents an efficient means of genome comparison, since many molecular markers were detected as genetic variations between susceptible and non-susceptible snails.

Animals↗

PubMed2006

Genetic variation among different populations of Aster tripolium grown on naturally and anthropogenic salt-contaminated habitats: implications for conservation strategies.

The sea aster, Aster tripolium L., grows naturally in temperate regions, mainly in the salt meadows close to the coast. The species is also found in naturally and anthropogenically salt-contaminated inland habitats, such as potash mine dumps. The genetic relationships among populations from different habitats and correlations of the genotype with physiological and vegetational parameters were investigated. A. tripolium plants from five different sites close to the seashore on the North Sea island Baltrum, from five different potash mine dumps and, as an outgroup, from the seashore in Japan were probed. DNA was extracted from five plants from each of the 11 A. tripolium populations and analyzed for random amplified polymorphic DNA (RAPD). Altogether 35 polymorphic bands in 51 individuals and 45 different detectable genotypes could be identified. For evaluation of the genetic variation using RAPD bands, the neighbor-joining method, the principal coordinate analysis, and the analysis of molecular variance were applied, resulting in the classification into three genetic groups. A. tripolium plants from different ecological habitats on Baltrum were closely related while the plants growing at the deposit dumps showed a higher genetic diversity. The Japanese population was genetically very different from the German populations. Correlations between phytosociological and soil parameters and the respective genotype were not significant. The results argue for a conservation of anthropogenically salt-contaminated habitats to maintain genetic variability not only on the species level, but also within a species.

Adaptation, Physiological↗

PubMed1998

Identification of genetic variation in the human hormone-sensitive lipase gene and 5' sequences: homology of 5' sequences with mouse promoter and identification of potential regulatory elements.

Hormone-sensitive lipase (HSL) plays a crucial role in triglyceride hydrolysis in adipose tissue and exhibits cholesterol hydrolase activity in steroidogenic tissue and macrophages. Thus, common genetic variation in the HSL gene could affect both energy metabolism and atherogenesis. Using overlapping single-strand conformational polymorphism analysis (SSCP), a common single base change (T/C) in intron 4 [allele frequency 0.012 (95% CI 0.007-0. 018)] and a variable CA repeat in intron 6 with 9 alleles (heterozygosity index = 0.66) were identified. Sequence of 1.123 kb upstream from the reported 5'UTR (1) which includes intron B, exon B, and 159 bp of the promoter (2) was obtained and a single common nucleotide change, -60C/G [allele frequency 0.052 (95% CI 0.039-0. 064)], identified. Preliminary in vitro studies show that the -60G construct has 38.5% lower luciferase activity compared to the -60C construct (P = 0.035), suggesting a functional change affecting HSL gene expression. The 5' sequence shows 57-59% homology with the mouse promoter with higher homology at potential regulatory motifs. Thus, the 1.7 kb of 5' sequences is well conserved and may play a part in the regulation of HSL gene expression.

Adipocytes↗

PubMed1995

Genetic variation in VP7 gene of human rotavirus serotype 2 (G2 type) isolated in Japan, China, and Pakistan.

Sequence analysis of the gene encoding the major neutralization glycoprotein (VP7) was performed on sixteen human isolates of serotype 2 of rotavirus in Japan, China, and Pakistan and their genetic variations were examined. Comparative studies of their nucleotide and deduced amino acid sequences between the sixteen isolates and the HU5 strain revealed an overall homology of more than 94%. A higher degree of homology in nucleotides was observed among the sixteen isolates than between HU5 and the isolates. A total of thirteen amino acid residues frequently converted to another amino acid. Out of the thirteen, five amino acid residues belonging to the major neutralizing epitope regions (C, E, and F in this communication) converted frequently. From the amino acid sequences three subtypes, subtype 1, subtype 2, and intermediate, were suggested to be classified as previously reported for serotype 1 (Xin et al, Virology, 1993, 197: 813-816).

Amino Acid Sequence↗

PubMed1997

Genetic variation in the porcine myogenin gene locus.

The myogenin (MYOG) gene fulfills a key function in muscle differentiation by controlling the onset of myoblast fusion and the establishment of myofibers. In meat-producing animals like pigs and cattle, myofiber numbers have been related to growth capacity. We have characterized the porcine MYOG gene to detect genetic variation at this locus and to relate it to growth characteristics. MYOG gene fragments were isolated by PCR on genomic DNA and by screening a genomic library with a mixture of the four human MyoD cDNA fragments. Both the exons and promoter region were very similar to the human and mouse genes. Southern blot analysis of 105 unrelated pigs revealed three polymorphic MspI sites, located in the promoter region, the second intron, and at the 3' side of the gene. PCR-RFLP tests detecting four MYOG alleles were developed. PCR analysis of a panel of pig-rodent somatic cell hybrids confirmed the genetic localization of MYOG on pig Chromosome (Chr) 9. The PCR-RFLP tests and microsatellite markers on Chr 9 offer the possibility to genotype large numbers of pigs for studies of genetic linkage to meat deposition and growth characteristics.

Animals↗

PubMed1999

Quantitative genetic variation for oviposition preference with respect to phenylthiocarbamide in Drosophila melanogaster.

Seven isogenic strains of Drosophila melanogaster were assayed for oviposition preference on food with phenylthiocarbamide (PTC) versus plain food. There was significant variation among strains for the percentage of eggs oviposited on each medium, ranging from 70 +/- 4% (SE) preference for plain food to no significant preference. Reciprocal hybrid, backcross, and F2 generations derived from two extreme parent strains revealed significant additive and nonadditive genetic variation but no evidence of maternal, paternal, or sex-chromosome effects.

Animals↗

PubMed1993

Genetic variation in VP7 gene of human rotavirus serotype 1 (G1 type) isolated in Japan and China.

Sequence analysis of the gene encoding the major neutralization glycoprotein (VP7) was performed on 12 human isolates of serotype 1 of rotavirus in Japan and China. They were examined for genetic variations among serotype 1 isolates. Comparative studies of their nucleotide and deduced amino acid sequences between the 12 isolates and the Wa strain revealed an overall homology of more than 92 and 96%, respectively. Higher degrees of homologies were observed between Wa and 2 strains (K1 and K2) in Tokyo, 1979-1980, than between Wa and recent isolated strains in Tokyo and in China. In our isolates, a total of 16 amino acid residues frequently converted to another amino acid. Six amino acid residues belonging to the major neutralizing epitope regions (B, D, and E in this communication) frequently converted. From these data three subtypes (subtypes A, B, and intermediate) were suggested to be divided. Whether these differences are an important mechanism in the epidemiology of rotaviruses requires further investigation.

Amino Acid Sequence↗

PubMed2004

Genetic variation in carbon isotope discrimination in six European populations of Castanea sativa Mill. originating from contrasting localities.

The objective of this study was to evaluate the variability of physiological performances of Castanea sativa Mill. in relation to drought tolerance, among and within European populations coming from contrasting environmental conditions. Forty-eight open-pollinated families from a stratified sample (temperature/precipitation) of six naturalized populations from Spain, Italy and Greece were grown for one growth period under two temperature regimes (25 and 32 degrees C), in combination with two watering regimes in growth chambers. Complementary to growth traits analysed in a previous study, carbon isotope discrimination (Delta), a complex physiological trait involved in acclimation and adaptive processes, was studied. anova indicated significant Delta variability for C. sativa populations across Europe and, thereby, variation in adaptedness to drought. The European pattern of Delta variability matches the previously reported one for the centre of origin of C. sativa (Ponto-Caucasian region). This suggests that common mechanisms of drought adaptedness, involving both genetic and physiological determinants, give C. sativa the capacity to colonize a wide range of site conditions. The highest Delta values, indicating the lowest water-use efficiency (WUE), were found within each treatment for populations originating from Mediterranean drought-prone sites. These populations also had the highest phenotypic plasticity of Delta. Significant among-family genetic variation in Delta was found. The heritability based on the joint anova was estimated at 0.31 +/- 0.07. The estimates of the coefficients for the additive variance varied in the range 2.6-4.0%, suggesting possibilities for selection on WUE and adaptedness to drought. The genetic correlations between Delta and growth traits were generally strong and negative, especially in the two high temperature treatments.

Adaptation, Physiological↗

PubMed1984

The human glutathione S-transferases: studies on the tissue distribution and genetic variation of the GST1, GST2 and GST3 isozymes.

Three sets of isozymes of glutathione-S-transferase (GST) have been identified in human tissues. They differ in their tissue distribution, incidence of genetic variation, susceptibility to inactivation by N-ethylmaleimide and in their electrophoretic mobilities. The GST1 isozymes exhibit four phenotypes, including a common 'null' phenotype attributable to different combinations of three autosomal alleles GST1 1, GST1 2 and GST1 0 of frequency 0.13, 0.23 and 0.64, respectively, in the European population. The genetic polymorphism of GST1 is easily demonstrable in adult liver, kidney, adrenal and stomach but the isozymes are only weakly expressed in skeletal and cardiac muscle and not at all in fetal liver, fibroblasts, erythrocytes, lymphocytes and platelets. The GST2 isozymes also exhibit variant patterns but these are probably due to post-synthetic modification rather than allelic variation. The GST2 isozymes are not detectable in erythrocytes, platelets, cultured fibroblasts or lymphocytoid cells but are found in many other tissues, including fetal liver. GST3 isozymes were found as relatively strong components in every tissue examined except adult liver, with slight tissue to tissue variability in electrophoretic mobility.

Adrenal Glands↗

PubMed2003

Research on the genetic variations of a1-fucosytransferase (FUT1) gene in 26 pig breeds.

Enterotoxigenic Escherichia coli F18(ECF18) is a main pathogen that causes edema disease and post-weaning diarrhoea in piglets, and al-fucosytransferase (FUT1) gene has been identified as a candidate gene for controlling the expression of the receptor for ECF18 bacteria. The genetic variations at position 307 nucleotide in open reading frame of FUT1 gene in 26 pig breeds (total 1458 individuals) from 5 western commercial pig breeds and 21 Chinese native pig breeds were investigated by PCR-RFLP. The results showed that the genetic polymorphisms of the FUT1 locus were only detected in 5 western pig breeds and the Chinese Lingao pig breed, 5 western pig breeds possessed 3 different genotypes, and Lingao pig breed had two susceptible genotypes GG and AG, while all the other 20 Chinese native pig breeds only presented the susceptible genotype GG. The results indicated that if M307G-A point mutation in the coding region of FUT1 gene was the key factor determining the expression of the ECF18 receptor, most of Chinese native pig breeds were absent of the genetic background on the resistance to ECF18 bacteria. In this case, it was inferred that the resistance gene to ECF18 might be originated from western pig breeds. In addition, it is of great importance for the conservation of Lingao pig breed as it is the only found Chinese native pig breed possessing resistance M307A allele in FUT1 gene. Generally, compared with exotic pig breeds, Chinese native pig breeds have stronger resistance to edema disease and post-weaning diarrhoea in piglets. The results suggested that further study should be done to identify and characterize putative QTL (quantitative trait locus) or/and the functional gene responsible for the resistance to ECF18 in Chinese native pig breeds.

Alleles↗

PubMed2006

Assessment of the role of common genetic variation in the transient neonatal diabetes mellitus (TNDM) region in type 2 diabetes: a comparative genomic and tagging single nucleotide polymorphism approach.

Recent evidence supports the strong overlap between genes implicated in monogenic diabetes and susceptibility to type 2 diabetes. Transient neonatal diabetes mellitus (TNDM) is a rare disorder associated with overexpression of genes at a paternally expressed imprinted locus on chromosome 6q24. There are two overlapping genes in this region: the transcription factor zinc finger protein associated with cell cycle control and apoptosis (ZAC also known as PLAGL1) and HYMA1, which encodes an untranslated mRNA. Several type 2 diabetes linkage studies have reported linkage to chromosome 6q22-25. We hypothesized that common genetic variation at this TNDM region influences type 2 diabetes susceptibility. In addition to the coding regions, we used comparative genomic analysis to identify conserved noncoding regions, which were resequenced for single nucleotide polymorphism (SNP) discovery in 47 individuals. Twenty-six SNPs were identified. Fifteen tag SNPs (tSNPs) were successfully genotyped in a large case-control (n = 3,594) and family-based (n = 1,654) study. We did not find any evidence of association or overtransmission of any tSNP to affected offspring or of a parent-of-origin effect. Using a study sufficiently powered to detect odds ratios of <1.2, we conclude that common variation in the TNDM region does not play an important role in the genetic susceptibility to type 2 diabetes.

Alleles↗

PubMed1995

Application of DNA fingerprinting with digoxigenated oligonucleotide probe (CAC)5 to analysis of the genetic variation within Taenia taeniaeformis.

DNA from T. taeniaeformis digested with the restriction endonuclease was hybridized with digoxigenated oligonucleotide probe (CAC)5. Metacestode and adult showed same clear multibanding patterns, which were characteristic of multilocus DNA fingerprinting. The fingerprinting patterns were quite different from those of the rodent hosts. Genetic variations in 4 laboratory-reared isolates of T. taeniaeformis, including 3 isolates which have been reported to be indistinguishable by infectivity, morphology and protein composition of metacestode, were investigated using this technique. Each of the 4 isolates exhibited isolate-specific fingerprinting patterns and were easily distinguished from one another, thus it was considered that (CAC)5 was a highly resolvable and informative probe for cestodes. However, it was also indicated that (CAC)5 was so sensitive that applying fingerprinting with (CAC)5 to taxonomical or phylogenetic analysis was limited where habitat of the host was restricted to the small area. In comparison to fingerprinting with 32P-labeled (CAC)5, fingerprinting with digoxigenated (CAC)5 represented more and sharper bands. It was considered that a digoxigenated probe was more useful for genetic analysis of cestodes.

Animals↗

PubMed2005

Genetic variation in the HSD17B1 gene and risk of prostate cancer.

Steroid hormones are believed to play an important role in prostate carcinogenesis, but epidemiological evidence linking prostate cancer and steroid hormone genes has been inconclusive, in part due to small sample sizes or incomplete characterization of genetic variation at the locus of interest. Here we report on the results of a comprehensive study of the association between HSD17B1 and prostate cancer by the Breast and Prostate Cancer Cohort Consortium, a large collaborative study. HSD17B1 encodes 17beta-hydroxysteroid dehydrogenase 1, an enzyme that converts dihydroepiandrosterone to the testosterone precursor Delta5-androsterone-3beta,17beta-diol and converts estrone to estradiol. The Breast and Prostate Cancer Cohort Consortium researchers systematically characterized variation in HSD17B1 by targeted resequencing and dense genotyping; selected haplotype-tagging single nucleotide polymorphisms (htSNPs) that efficiently predict common variants in U.S. and European whites, Latinos, Japanese Americans, and Native Hawaiians; and genotyped these htSNPs in 8,290 prostate cancer cases and 9,367 study-, age-, and ethnicity-matched controls. We found no evidence that HSD17B1 htSNPs (including the nonsynonymous coding SNP S312G) or htSNP haplotypes were associated with risk of prostate cancer or tumor stage in the pooled multiethnic sample or in U.S. and European whites. Analyses stratified by age, body mass index, and family history of disease found no subgroup-specific associations between these HSD17B1 htSNPs and prostate cancer. We found significant evidence of heterogeneity in associations between HSD17B1 haplotypes and prostate cancer across ethnicity: one haplotype had a significant (p < 0.002) inverse association with risk of prostate cancer in Latinos and Japanese Americans but showed no evidence of association in African Americans, Native Hawaiians, or whites. However, the smaller numbers of Latinos and Japanese Americans in this study makes these subgroup analyses less reliable. These results suggest that the germline variants in HSD17B1 characterized by these htSNPs do not substantially influence the risk of prostate cancer in U.S. and European whites.

17-Hydroxysteroid Dehydrogenases↗

PubMedDate not supplied

Elephant seal genetic variation and the use of simulation models to investigate historical population bottlenecks.

Because the northern elephant seal (Mirounga angustirostrus) was heavily exploited during the 19th century, it experienced an extreme population bottleneck. Since then, under legislative protection in the United States and Mexico, northern elephant seals have recovered dramatically in number, although their genomic diversity was greatly reduced, apparently as a consequence of the bottleneck. In this study we investigated DNA sequence diversity in two mtDNA regions (the control region and 16S RNA) and found low genetic variation in the northern elephant seal: there were only two control region haplotypes (sequence difference = 1%), which was consistent with an extreme founder event in the recent history of the northern species. We also reaffirmed the lack of allozyme diversity in this species. In contrast, the southern elephant seal (M. leonina), which though similarly exploited never fell below 1,000 animals, had 23 control region mtDNA haplotypes (average sequence difference = 2.3%). To investigate the extent of the founder event in the northern elephant seal we devised a simulation model based on extensive demographic data. This allowed a statistical analysis of the likely outcome of bottlenecks of different size and duration. Given these historical data, our results indicate (within 95% confidence) a bottleneck of less than 30 seals and 20-year duration, or, if hunting was the primary pressure on the population, a single-year bottleneck of less than 20 seals.

Animals↗

PubMed2004

Systemic lupus erythematosus and genetic variation in the interleukin 1 gene cluster: a population based study in the southeastern United States.

BACKGROUND: Interleukin (IL)1alpha and IL1beta, and their endogenous receptor antagonist (IL1Ra), have been related to the pathology of systemic lupus erythematosus (SLE), but the role of IL1 polymorphisms in the aetiology of SLE is unknown. OBJECTIVE: To examine polymorphisms at IL1alpha -889(C-->T), IL1alpha +4845(C-->T), IL1beta -511(C-->T), IL1beta +3953(G-->T), and IL1Ra (86 bp VNTR) in a population based study of SLE in North Carolina and South Carolina. METHODS: Genotypes from 230 cases who met ACR classification criteria, and from 275 controls matched for age, sex, and state, were analysed separately for African Americans and whites. Odds ratios (ORs) were estimated by logistic regression models for each locus alone and also after adjusting for polymorphisms at adjacent loci. RESULTS: An increased risk of SLE for the IL1alpha -889C/C genotype compared with carriage of the -889T allele was found in both African Americans (OR = 3.1, p = 0.001) and whites (OR = 2.9, p = 0.005). In African Americans, carriage of the IL1beta -511T allele was associated with a higher risk of SLE than carriage of the -511C/C genotype (OR = 2.4, p = 0.017), independent of variation at IL1alpha -889. CONCLUSIONS: The observed associations support the hypothesis that genetic variation in IL1 is involved in the aetiology of SLE and merit further investigation.

Adolescent↗