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Results for “Genetic Variation”

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PubMed2004

Genetic variation of Cordyceps sinensis, a fruit-body-producing entomopathogenic species from different geographical regions in China.

Cordyceps sinensis is one of the most valuable medicinal fungi in the Orient. It is naturally distributed in the eastern extension area of the Qinghai-Tibet plateau, at an altitude over 4000 m high. In order to investigate genetic variation and evolutionary relationships of C. sinensis from different geographical regions, 17 isolates of C. sinensis were collected from different provinces and the complete sequences of rDNA ITS were determined. On the basis of 5.8S rDNA and ITS region analysis, it was clearly shown that the ITS sequences within C. sinensis are highly homologous regardless of geographical origin. The distance values between the sequences in this study were lower than 0.03. This implied that C. sinensis from different geographic regions are the same species; they are not different species or a species complex. The results also showed that distance values between C. sinensis and Hirsutella sinensis are of the same order as those within C. sinensis from different geographic regions. This confirmed our previous results that C. sinensis should only have H. sinensis as its asexual stage whatever the geographic region from which the samples were collected. An rDNA ITS clone library was established to obtain further evidence for the interpretation of the fungal community structure from C. sinensis and to confirm the accuracy of the taxonomic identities produced by directly sequencing the rDNA ITS region. The discrimination between intraspecies of C. sinensis might provide additional data for the authentication of medicinal material at the species or intraspecies level.

Animals↗

PubMed2001

Understanding human disease mutations through the use of interspecific genetic variation.

Data on replacement mutations in genes of disease patients exist in a variety of online resources. In addition, genome sequencing projects and individual gene sequencing efforts have led to the identification of disease gene homologs in diverse metazoan species. The availability of these two types of information provides unique opportunities to investigate factors that are important in the development of genetically based disease by contrasting long and short-term molecular evolutionary patterns. Therefore, we conducted an analysis of disease-associated human genetic variation for seven disease genes: the cystic fibrosis transmembrane conductance regulator, glucose-6-phosphate dehydrogenase, the neural cell adhesion molecule L1, phenylalanine hydroxylase, paired box 6, the X-linked retinoschisis gene and TSC2/tuberin. Our analyses indicate that disease mutations show definite patterns when examined from an evolutionary perspective. Human replacement mutations resulting in disease are overabundant at amino acid positions most conserved throughout the long-term history of metazoans. In contrast, human polymorphic replacement mutations and silent mutations are randomly distributed across sites with respect to the level of conservation of amino acid sites within genes. Furthermore, disease-causing amino acid changes are of types usually not observed among species. Using Grantham's chemical difference matrix, we find that amino acid changes observed in disease patients are far more radical than the variation found among species and in non-diseased humans. Overall, our results demonstrate the usefulness of evolutionary analyses for understanding patterns of human disease mutations and underscore the biomedical significance of sequence data currently being generated from various model organism genome sequencing projects.

Amino Acids↗

PubMed1975

Genetical variation for enzyme activity in a population of Drosophila melanogaster. II. Aspects of the inheritance of alcohol dehydrogenase activity in Adhs/s flies.

Two inbred lines of Drosophila melanogaster extracted from a laboratory cage population and homozygous for the AdhS allele of alcohol dehydrogenase (Adh) showed almost a twofold difference in specific activity. Analysis of generations derived from these lines showed that the genetic variation in ADH activity was controlled by additive gene action. There was no evidence of directional dominance or of non-allelic interactions. Although the Adh structural gene is on the second chromosome there was a significant effect of the X chromosome, indicating the action of modifying genes.

Alcohol Oxidoreductases↗

PubMed1989

Genetic variation and microevolution of dengue 2 virus in Southeast Asia.

Dengue 2 (DEN 2) virus strains collected from dengue hemorrhagic fever (DHF) patients and Aedes aegypti mosquitoes in Thailand, Burma, and Vietnam over a 25-year period have been analyzed by computer assisted T1-RNase-resistant oligonucleotide fingerprinting. Fifty-seven DEN 2 virus strains of the Thailand topotype were separated into four major clusters by phylogenetic analysis of 97 unique oligonucleotides identified in a common well-resolved region of the fingerprints. Similarities in the 57 fingerprints indicated that DEN 2 virus of a single, continually evolving genetic population has been involved in endemic transmission of the disease. Virus isolates from DHF cases and mosquitoes are genetically very similar, indicating that different genetic topotypes are not selectively the cause of severe DEN disease in Thailand. Microevolution of the DEN 2 virus genome from 1962-1986 was gradual with detectable changes in the pattern of oligonucleotides through time. Segregation of the DEN 2 virus fingerprints into the three decades (1960s, 1970s, and 1980s) revealed the rate of genetic change to be one consensus oligonucleotide per year. Based on average association coefficient (Sab) values between the consensus fingerprints for each decade, the similarity between the consensus fingerprints decreased by 1.4% per year. Genetic variation during each of the three decades was found to be essentially the same (0.866 +/- 0.053). Constancy in the microevolutionary rate and genetic variability suggests that a balance of genetic drift and natural selection acting on the viral population did not significantly change throughout the 25-year period.

Aedes↗

PubMedDate not supplied

Genetic variations of the porcine PRKAG3 gene in Chinese indigenous pig breeds.

Four missense substitutions (T30N, G52S, V199I and R200Q) in the porcine PRKAG3 gene were considered as the likely candidate loci affecting meat quality. In this study, the R200Q substitution was investigated in a sample of 62 individuals from Hampshire, Chinese Min and Erhualian pigs, and the genetic variations of T30N, G52S and V199I substitutions were detected in 1505 individuals from 21 Chinese indigenous breeds, 5 Western commercial pig breeds, and the wild pig. Allele 200R was fixed in Chinese Min and Erhualian pigs. Haplotypes II-QQ and IV-QQ were not observed in the Hampshire population, supporting the hypothesis that allele 200Q is tightly linked with allele 199V. Significant differences in allele frequencies of the three substitutions (T30N, G52S and V199I) between Chinese indigenous pigs and Western commercial pigs were observed. Obvious high frequencies of the "favorable" alleles 30T and 52G in terms of meat quality were detected in Chinese indigenous pigs, which are well known for high meat quality. However, the frequency of the "favorable" allele 199I, which was reported to have a greater effect on meat quality in comparison with 30T and 52G, was very low in all of the Chinese indigenous pigs except for the Min pig. The reasons accounting for this discrepancy remain to be addressed. The presence of the three substitutions in purebred Chinese Tibetan pigs indicates that the three substitutions were ancestral mutations. A novel A/G substitution at position 51 in exon 1 was identified. The results suggest that further studies are required to investigate the associations of these substitutions in the PRKAG3 gene with meat quality of Chinese indigenous pigs, and to uncover other polymorphisms in the PRKAG3 gene with potential effects on meat quality in Chinese indigenous pigs.

Adenine↗

PubMed1978

Genetic variation in activity of the enzymes of glycolysis and gluconeogenesis between inbred strains of mice.

Variation in the activity of 21 liver and 15 erythrocyte enzymes between seven inbred strains of mice has been studied in a single area of metabolism, glycolysis and gluconeogenesis. Most of the variation between the strains is genetic. From the variation within and between inbred strains heritabilities (H2) were determined. Out of 35, 26 showed significant values above 0.4. A comparison with previously published work suggests that enzyme activities have mainly dominance and interaction components of variance, and this is discussed in relation to the variation in quantitative characters such as growth. In nine of the pairwise comparisons of the strains, the activity of the enzyme varied more than two-fold. In these cases the genetics and biochemistry of the enzyme was studied; F2 progeny were produced and assessed for segregation, and the heat stability of the enzyme was determined. No unequivocal segregation was observed, although in one case we found a considerable difference in heat stability. The variations found were not considered to be great enough to be useful as models of human inborn errors of metabolism or to study metabolic control. If such variants are to be found, sources of variation other than inbred strains must be used.

Animals↗

PubMed2007

Genetic variations of the NR3A subunit of the NMDA receptor modulate prefrontal cerebral activity in humans.

INTRODUCTION: Recently, a novel N-methyl-D-aspartate (NMDA) receptor subunit, NR3A, has been discovered in the brain. This subunit decreases NMDA receptor activity by modulating the calcium permeability of the receptor channel and current density in cortical cells. Because the NR3A is expressed in the human prefrontal cortex, we hypothesized that genetic variations of the NR3A subunit modulate prefrontal activation. METHODS: Electromagnetic activity during selective attention (auditory oddball task with target processing) was measured in 281 healthy subjects. Genotyping of a missense variation (rs10989591, Val362Met) of the NR3A gene was performed. RESULTS: Individuals carrying Val/Val genotype showed significantly reduced frontal P300 amplitudes compared with Met/Met subjects. Subsequent low-resolution electromagnetic source analysis revealed that this group difference is likely caused by reduced activation in the inferior frontal gyrus. CONCLUSIONS: It was shown for the first time that the genetic constitution of the subunit composition of NMDA receptor regulation might be relevant for prefrontal information processing in humans. The results underline the pivotal role of glutamate in frontal lobe function and indicate that the NR3A subunit could be a plausible candidate gene for diseases with prefrontal dysfunctions.

Adult↗

PubMed1989

Murine natural suppressor cells in the newborn, in bone marrow, and after cyclophosphamide. Genetic variations and dependence on IFN-gamma.

Natural suppressor (NS) cells are potent, Ag nonspecific, MHC-unrestricted inhibitors of immune responses. Murine NS activity is found in several situations, including adult bone marrow (BM) and neonatal/newborn spleen, and spleen following total lymphoid irradiation, after BM transplantation and after cyclophosphamide (CY) treatment. Using three of these situations (adult BM, newborn spleen, and spleen after CY treatment), the strain distribution of NS cell activity was assessed. A wide variation in potency is seen in both naturally occurring (adult BM and newborn spleen) and induced (after CY treatment) NS cell activity. Up to 10-fold differences in NS activity are seen between high and low NS strains. This reflects an intrinsic genetic variation between mouse strains in both naturally occurring and CY-induced NS cell activity. Thus, a strain with high NS activity at birth, has high NS activity in its BM as an adult and in its spleen after CY treatment. Of the strains tested, B10.D2 has the highest NS cell activity while BALB/c has the lowest, and the F1 between these two strains is intermediate in NS activity. Finally, the NS cell activity from all strains tested required IFN-gamma for expression of its inhibitory activity.

Aging↗

PubMed2006

Genetic variations and haplotype structures of the ABCB1 gene in a Japanese population: an expanded haplotype block covering the distal promoter region, and associated ethnic differences.

As functional ABCB1 haplotypes were recently reported in the promoter region of the gene, we resequenced the ABCB1 distal promoter region, along with other regions (the enhancer and proximal promoter regions, and all 28 exons), in a total of 533 Japanese subjects. Linkage disequilibrium (LD) analysis based on 92 genetic variations revealed 4 LD blocks with the same make up as previously described (Blocks -1, 1, 2 and 3), except that Block 1 was expanded to include the distal promoter region, and that a new linkage between polymorphisms -1,789G>A in the distal promoter region and IVS5 + 123A>G in intron 5 was identified. We re-assigned Block 1 haplotypes, and added novel haplotypes to the other 3 blocks. The reported promoter haplotypes were further classified into several types according to tagging variations within Block 1 coding or intronic regions. Our current data reconfirm the haplotype profiles of the other three blocks, add more detailed information on functionally-important haplotypes in Block 1 and 2 in the Japanese population, and identified differences in haplotype profiles between ethnic groups. Our updated analysis of ABCB1 haplotype blocks will assist pharmacogenetic and disease-association studies carried out using Asian subjects.

ATP Binding Cassette Transporter, Subfamily B↗

PubMedDate not supplied

[Genetic variation of Azov and Black sea herring Alosa pontica (Eihwald, 1838), (Clupeiformes, Alosinae) in Danube river: analysis of biochemical gene markers].

Genetic variation and structure of Danube stock of Aloca pontica pontica were investigated during the spawning moving by means of biochemical genetic marking. The level of heterozygosity was Hobs = 0,009. It is essentially lower than the average level for populations of other Teleostei and Clupeidae representatives. Polymorphism was defined only for Es-D of 20 analyzed loci expressed in muscle tissues. The allele frequencies for this locus were reliably different in the early spawning and later spawning parts of the stock, as well as proportion of heterozygotes and genotype diversity which was higher at the beginning of spawning moving. These results are discussed from two points of view: genetic differences between subpopulations in the course of spawning moving and presence of two close species of herring which come for the spawning together and hybridize to each other.

Alleles↗

PubMed2002

Genetic variation in original and colonizing Drosophila buzzatii populations analysed by microsatellite loci isolated with a new PCR screening method.

A new polymerase chain reaction-based screening method for microsatellites is presented. Using this method, we isolated 12 microsatellite loci from Drosophila buzzatii, two of which were X-linked. We applied the other 10 microsatellite loci to the analysis of genetic variation in five natural populations of D. buzzatii. Two populations were from the species' original distribution in Argentina, whereas the other three were from Europe (two) and Australia that were colonized 200 and 65 years ago, respectively. Allelic variation was much larger in the original populations than in the colonizing ones and there was a tendency to decreased heterozygosity in the colonizing populations. We used three different statistical procedures for detecting population bottlenecks. All procedures suggested that the low variability in the populations in the Old World was not the result of the recent population decline, but was due to a founder effect followed by a population expansion. In fact, one procedure which detects population expansions and declines based on the genealogical history of microsatellite data suggested that an expansion had taken place in all the colonized populations.

Animals↗

PubMed2005

Genetic variations of the dihydrofolate reductase gene of Plasmodium vivax in Mandalay Division, Myanmar.

Dihydrofolate reductase (DHFR; EC1.5.1.3) is a known target enzyme for antifolate agents, which are used as alternative chemotherapeutics for chloroquine-resistant malaria. Mutations in the dhfr gene of Plasmodium vivax are thought to be associated with resistance to the antifolate drugs. In this study, we have analyzed genetic variations in the dhfr genes of clinical isolates of P. vivax (n=21) in Myanmar, to monitor antifolate resistance in this country. Sequence variations within the entire dhfr gene were highly restricted to codons from 57 to 117, and the GGDN tandem repeat region. Double (S58R and S117N/T) or quadruple mutations (F57L/I, S58R, T61M, and S117N/T), which may be closely related to the drug resistance, were recognized in most of the isolates (20/21 cases). Our results suggest that antifolate-resistant P. vivax is becoming widespread in Myanmar, as it also is in the neighboring countries in Southeast Asia. It appears that the drug resistance situation may be worsening in the country.

Amino Acid Sequence↗

PubMed2002

Intrastrain and interstrain genetic variation within a paralogous gene family in Chlamydia pneumoniae.

BACKGROUND: Chlamydia pneumoniae causes human respiratory diseases and has recently been associated with atherosclerosis. Analysis of the three recently published C. pneumoniae genomes has led to the identification of a new gene family (the Cpn 1054 family) that consists of 11 predicted genes and gene fragments. Each member encodes a polypeptide with a hydrophobic domain characteristic of proteins localized to the inclusion membrane. RESULTS: Comparative analysis of this gene family within the published genome sequences provided evidence that multiple levels of genetic variation are evident within this single collection of paralogous genes. Frameshift mutations are found that result in both truncated gene products and pseudogenes that vary among isolates. Several genes in this family contain polycytosine (polyC) tracts either upstream or within the terminal 5' end of the predicted coding sequence. The length of the polyC stretch varies between paralogous genes and within single genes in the three genomes. Sequence analysis of genomic DNA from a collection of 12 C. pneumoniae clinical isolates was used to determine the extent of the variation in the Cpn 1054 gene family. CONCLUSIONS: These studies demonstrate that sequence variability is present both among strains and within strains at several of the loci. In particular, changes in the length of the polyC tract associated with the different Cpn 1054 gene family members are common within each tested C. pneumoniae isolate. The variability identified within this newly described gene family may modulate either phase or antigenic variation and subsequent physiologic diversity within a C. pneumoniae population.

5' Flanking Region↗

PubMed1997

Genetic variation of 3 beta-hydroxysteroid dehydrogenase type II in three racial/ethnic groups: implications for prostate cancer risk.

BACKGROUND: Elevated prostatic dihydrotestosterone (DHT) has been suggested to increase the risk of prostate cancer. The HSD3B2 gene encodes the type II 3 beta-hydroxysteroid dehydrogenase: one of two enzymes that initiate the inactivation of DHT. Thus, the HSD3B2 gene is a candidate gene for predisposition to prostate cancer. METHODS: We have determine the distribution of a complex dinucleotide repeat in the HSD3B2 gene in high-risk African-Americans, intermediate-risk Euro-Americans, and low-risk Asians. Genomic DNA from 312 individuals was amplified by polymerase chain reaction (PCR) and analyzed by electrophoresis on denaturing polyacrylamide gels. RESULTS: We have found that certain alleles are either unique to or much more common in either African-Americans, Asians, or Euro-Americans. Our data also substantially expand the number of alleles reported for the complex dinucleotide repeat polymorphism in the HSD3B2 gene. CONCLUSIONS: Our report demonstrates substantial genetic variation in the HSD3B2 gene. We hypothesize that allelic variants of the HSD3B2 gene may play a role in predisposition to prostate cancer, and in explaining the substantial racial/ethnic variation in risk.

3-Hydroxysteroid Dehydrogenases↗

PubMed1979

Genetic variation in Hawaiian Drosophila. VIII. Heterozygosity and genic changes in isolated populations of D. engyochracea.

Drosophila engyochracea, an endemic Hawaiian fly found only in two, finite populations in Volcano National Park, has extensive electrophoretic heterozygosity on a par with that found in species with much wider distributions. A study of six polymorphic loci in both populations over an 18-month period revealed that the population in the more xeric environment is more dynamic genetically as well as more variable. In addition, genetic changes at one locus, Pgm, are correlaed to changes in an environmental moisture parameter. These findings confirm that migration is not necessary to maintain genetic variation in isolated population and demonstrate that D. engyochracea gene pools are susceptible to errors in Hardy-Weinberg equilibria during specific seasonal periods.

Animals↗

PubMed1994

Genetic variation in the humoral immune response in Atlantic salmon (Salmo salar) against Aeromonas salmonicida A-layer.

Antibody responses to Aeromonas salmonicida A-layer were analysed in family material of Atlantic salmon (Salmo salar), consisting of 791 fish belonging to 34 full-sib groups within 12 paternal half-sib groups. The fish were immunized twice and blood samples were collected three times. Significant increase in antibody titre from first to second, and from second to third sampling, was observed. Genetic variation in antibody titres was observed at the three samplings with estimated heritabilities ranging from 0.16 to 0.20, and a significant heritability estimate was recorded in the antibody response after the second immunization (h2 = 0.16). Moderate to high genetic (r = 0.5-0.72) and phenotypic (r = 0.29-0.57) correlations were found between the titre values at different samplings, and between selected titres and titre increases. Production parameters, such as mean slaughter weight and mean survival rate were obtained for fish which were reared commercially in the sea, and which belonged to the same full-sib groups as those analysed for A. salmonicida A-layer antibodies. No significant correlation between the mean antibody titre to A. salmonicida A-layer in this study and mean slaughter weight and survival rate in full-sib family material in the sea was observed.

Aeromonas↗

PubMed2005

Thlaspi caerulescens on nonmetalliferous soil in Luxembourg: ecological niche and genetic variation in mineral element composition.

Forty-seven populations of Thlaspi caerulescens in Luxembourg were characterised for population size, soil mineral element composition and other habitat characteristics. Foliar concentrations of eight elements were assessed in 15 populations in the field and in eight populations cultivated in zinc (Zn)-cadmium (Cd)-nickel (Ni)-enriched soil. T. caerulescens favoured stony soil developed on steep, south-facing Emsian shale outcrops. All soil samples were nonmetalliferous. Soil pH ranged from 4.2 to 6.9. Field-growing plants had very high concentrations of heavy metals in the leaves (Zn, 3000-13 000 mg kg(-1); Cd, 11-44 mg kg(-1); Ni, 38-473 mg kg(-1)). Positive soil-plant correlations existed for Zn and Mn. In cultivation, significant genetic variation was found for biomass and six of eight mineral elements. For Cd and Zn, variation range among 48 half-sib families was two-fold (Cd, 183-334 mg kg(-1); Zn, 8030-16 295 mg kg(-1)). Most of the variation occurred among populations, consistent with the selfing mating system of those populations. There was a tight Zn-Cd genetic correlation (r = +0.83, P < 0.0001). The significance of the results to the conservation of T. caerulescens in Luxembourg is briefly discussed.

Ecosystem↗

PubMed2003

Genetic variation among world populations: inferences from 100 Alu insertion polymorphisms.

We examine the distribution and structure of human genetic diversity for 710 individuals representing 31 populations from Africa, East Asia, Europe, and India using 100 Alu insertion polymorphisms from all 22 autosomes. Alu diversity is highest in Africans (0.349) and lowest in Europeans (0.297). Alu insertion frequency is lowest in Africans (0.463) and higher in Indians (0.544), E. Asians (0.557), and Europeans (0.559). Large genetic distances are observed among African populations and between African and non-African populations. The root of a neighbor-joining network is located closest to the African populations. These findings are consistent with an African origin of modern humans and with a bottleneck effect in the human populations that left Africa to colonize the rest of the world. Genetic distances among all pairs of populations show a significant product-moment correlation with geographic distances (r = 0.69, P < 0.00001). F(ST), the proportion of genetic diversity attributable to population subdivision is 0.141 for Africans/E. Asians/Europeans, 0.047 for E. Asians/Indians/Europeans, and 0.090 for all 31 populations. Resampling analyses show that approximately 50 Alu polymorphisms are sufficient to obtain accurate and reliable genetic distance estimates. These analyses also demonstrate that markers with higher F(ST) values have greater resolving power and produce more consistent genetic distance estimates.

Africa↗