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PubMed2006

Genetic variation among isolates of Sarcocystis neurona, the agent of protozoal myeloencephalitis, as revealed by amplified fragment length polymorphism markers.

Sarcocystis neurona causes serious neurological disease in horses and other vertebrates in the Americas. Based on epidemiological data, this parasite has recently emerged. Here, the genetic diversity of Sarcocystis neurona was evaluated using the amplified fragment length polymorphism (AFLP) method. Fifteen S. neurona taxa from different regions collected over the last 10 years were used; six isolates were from clinically diseased horses, eight isolates were from wild-caught opossums (Didelphis virginiana), and one isolate was from a cowbird (Molothrus ater). Additionally, four outgroup taxa were also fingerprinted. Nine primer pairs were used to generate AFLP patterns, with a total number of amplified fragments ranging from 30 to 60, depending on the isolate and primers tested. Based on the presence/absence of amplified AFLP fragments and pairwise similarity values, all the S. neurona isolates tested were clustered in one monophyletic group. No significant correlation could be found between genomic similarity and host origin of the S. neurona isolates. AFLP revealed significant intraspecific genetic variations, and S. neurona appeared as a highly variable species. Furthermore, linkage disequilibrium analysis suggested that S. neurona populations within Michigan have an intermediate type of population structure that includes characteristics of both clonal and panamictic population structures. AFLP is a reliable molecular technique that has provided one of the most informative approaches to ascertain phylogenetic relationships in S. neurona and its closest relatives, allowing them to be clustered by relative similarity using band matching and unweighted pair group method with arithmetic mean analysis, which may be applicable to other related protozoal species.

Animals↗

PubMed2004

Phylogenetic analysis of polyomavirus simian virus 40 from monkeys and humans reveals genetic variation.

A phylogenetic analysis of 14 complete simian virus 40 (SV40) genomes was conducted in order to determine strain relatedness and the extent of genetic variation. This analysis included infectious isolates recovered between 1960 and 1999 from primary cultures of monkey kidney cells, from contaminated poliovaccines and an adenovirus seed stock, from human malignancies, and from transformed human cells. Maximum-parsimony and distance methods revealed distinct SV40 clades. However, no clear patterns of association between genotype and viral source were apparent. One clade (clade A) is derived from strain 776, the reference strain of SV40. Clade B contains isolates from poliovaccines (strains 777 and Baylor), from monkeys (strains N128, Rh911, and K661), and from human tumors (strains SVCPC and SVMEN). Thus, adaptation is not essential for SV40 survival in humans. The C terminus of the T-antigen (T-ag-C) gene contains the highest proportion of variable sites in the SV40 genome. An analysis based on just the T-ag-C region was highly congruent with the whole-genome analysis; hence, sequencing of just this one region is useful in strain identification. Analysis of an additional 16 strains for which only the T-ag-C gene was sequenced indicated that further SV40 genetic diversity is likely, resulting in a provisional clade (clade C) that currently contains strains associated with human tumors and human strain PML-1. Four other polymorphic regions in the genome were also identified. If these regions were analyzed in conjunction with the T-ag-C region, most of the phylogenetic signal could be captured without complete genome sequencing. This report represents the first whole-genome approach to establishing phylogenetic relatedness among different strains of SV40. It will be important in the future to develop a more complete catalog of SV40 variation in its natural monkey host, to determine if SV40 strains from different clades vary in biological or pathogenic properties, and to identify which SV40 strains are transmissible among humans.

Animals↗

PubMed1995

The effect of adaptive mutagenesis on genetic variation at a linked, neutral locus.

Based on recent studies in single-celled organisms, it has been argued that a fitness benefit associated with a mutation will increase the probability of that mutation occurring. This increase is independent of mutation rates at other loci and is called adaptive mutagenesis. We modeled the effect of adaptive mutagenesis on populations of haploid organisms with adaptive mutation rates ranging from 0 to 1 x 10(-5). Allele frequencies at the selected locus and a neutral linked locus were tracked. We also observed the amount of linkage disequilibrium during the selective sweep and the final heterozygosity after the sweep. The presence of adaptive mutagenesis increases the number of genetic backgrounds carrying the new fitter allele, making the outcomes more representative of the population before the selection. Therefore, more neutral genetic variation is preserved in simulations with adaptive mutagenesis than in those without it due to hitchhiking. Since adaptive mutagenesis is time-dependent, it can generate mutants when other mechanisms of mutation cannot. In addition, adaptive mutagenesis has the potential to confound both phylogeny construction and the detection of natural selection from patterns of nucleotide variation.

Adaptation, Physiological↗

PubMedDate not supplied

Genetic variations in vascular endothelial growth factor and endothelial nitric oxide synthase and their contributions to human disease.

This review addresses a rapidly growing area of vascular biology, i.e. genomic variations in vascular genes that underlie different human phenotypes. Two of the most important molecular in vascular biology, endothelial nitric oxide synthase (eNOS) and vascular endothelial cell growth factor (VEGF)are discussed. Variations in the eNOS gene have been correlated with a number of human diseases including hypertension, coronary vasospasm, smoking dependent risk of coronary disease, myocardial infarction and placental disruption. Similarly, variations in the VEGF gene have been associated with increased risk of various cancers, DiGeorge syndrome, psoriasis, diabetic renal disease and amyotropic lateral sclerosis. Understanding the molecular basis of these genetic variations and how they contribute to the pathophysiology provides new and important insights into human disease.

Cardiovascular Diseases↗

PubMed2005

Genetic variation in UCP2 (uncoupling protein-2) is associated with energy metabolism in Pima Indians.

AIMS/HYPOTHESIS: Uncoupling protein-2 (UCP2) is thought to play a role in insulin secretion and the development of obesity. In this study, we investigated the effects of genetic variation in UCP2 on type 2 diabetes and obesity, as well as on metabolic phenotypes related to these diseases, in Pima Indians. METHODS: The coding and untranslated regions of UCP2, and approximately 1 kb of the 5' upstream region, were sequenced in DNA samples taken from 83 extremely obese Pima Indians who were not first-degree relatives. RESULTS: Five variants were identified: (1) a -866G/A in the 5' upstream region; (2) a G/A in exon 2; (3) a C/T resulting in an Ala55Val substitution in exon 4; and (4, 5) two insertion/deletions (ins/del; 45-bp and 3-bp) in the 3' untranslated region. Among the 83 subjects whose DNA was sequenced, the -866G/A was in complete genotypic concordance with the Ala55Val and the 3-bp ins/del polymorphism. The G/A polymorphism in exon 2 was extremely rare. To capture the common variation in this gene for association analyses, the -866G/A variant (as a representative of Ala55Val and the 3-bp ins/del polymorphism) and the 45-bp ins/del were also genotyped for 864 full-blooded Pima Indians. Neither of these variants was associated with type 2 diabetes or body mass index. However, in a subgroup of 185 subjects who had undergone detailed metabolic measurements, these variants were associated with 24-h energy expenditure as measured in a human metabolic chamber (p=0.007 for the 45-bp ins/del and p=0.03 for the -866G/A after adjusting for age, sex, family membership, fat-free mass and fat mass). CONCLUSIONS/INTERPRETATION: Our data indicate that variation in UCP2 may play a role in energy metabolism, but this gene does not contribute significantly to the aetiology of type 2 diabetes and/or obesity in Pima Indians.

3' Untranslated Regions↗

PubMed2003

Genetic variation among temporally and geographically distinct West Nile virus isolates, United States, 2001, 2002.

Analysis of partial nucleotide sequences of 22 West Nile virus (WNV) isolates collected during the summer and fall of 2001 and 2002 indicated genetic variation among strains circulating in geographically distinct regions of the United States and continued divergence from isolates collected in the northeastern United States during 1999 and 2000. Sequence analysis of a 2,004-nucleotide region showed that 14 isolates shared two nucleotide mutations and one amino acid substitution when they were compared with the prototype WN-NY99 strain, with 10 of these isolates sharing an additional nucleotide mutation. In comparison, isolates collected from coastal regions of southeast Texas shared the following differences from WN-NY99: five nucleotide mutations and one amino acid substitution. The maximum nucleotide divergence of the 22 isolates from WN-NY99 was 0.35% (mean = 0.18%). These results show the geographic clustering of genetically similar WNV isolates and the possible emergence of a dominant variant circulating across much of the United States during 2002.

Base Sequence↗

PubMed2004

Genetic variation coincides with geographic structure in the common bush-tanager (Chlorospingus ophthalmicus) complex from Mexico.

Cloud forests are distributed in the Neotropics, from northern Mexico to Argentina, under very specific ecological conditions, namely slopes with high humidity input from clouds and mist. Its distribution in Mesoamerica is highly fragmented, similar to an archipelago, and taxa are thus frequently represented as sets of isolated populations, each restricted to particular mountain ranges and often showing a high degree of divergence, both morphologically and genetically. The common bush-tanager (Chlorospingus ophthalmicus, Aves: Thraupidae) inhabits cloud forests from eastern and southern Mexico south to northwestern Argentina. Here we use 676bp of mtDNA (around the ATPase 8 gene) to explore the genetic variation and phylogeographic structure of the Mexican populations of C. ophthalmicus. Phylogenetic analyses of mtDNA sequences indicate deep genetic structure. Five major clades, which segregate according to geographic breaks, are identified (starting from the deepest one in the phylogeny): (1) Southern Chiapas and Northern Central America, (2) Tuxtlas massif, (3) Sierra Madre del Sur, (4) Eastern Oaxaca and Northern Chiapas, and (5) Sierra Madre Oriental. The long history of isolation undergone by each clade, as suggested by the phylogeny, implies that the species status of each of them should be revised.

Animals↗

PubMed2006

Genetic variation in fertility of heat-stressed male mice.

The damaging effects of heat stress on male fertility are evident in developing spermatozoa expressed in ejaculates 18-28 days post-stress in mice. Our objectives were to: (1) assess genetic variation in fertility of heat-stressed male mice and (2) determine response to selection for fertility after heat stress in male mice. Mature male mice were exposed to heat stress (35+/-1 degrees C; n=50) or control (21+/-1 degrees C; n=10) conditions for 24h (day 0) and then hemicastrated for tissue collection. Two periods of mating tests followed, period 1 (from days 3 to 11) when no reductions in fertility were anticipated, and period 2 (days 18-26) when variation in fertility was expected. Period 2 pregnant females were sacrificed in late gestation. Males were indexed by multiplying overall mean ovulation rate by pre-implantation survival and number of pregnant period 2 mates. The five highest and five lowest ranking males were identified as heat stress resistant and susceptible, respectively. Resistant males were 61.2units superior in the index, 57.5% greater in pregnancy rate, and 57.6 total fetuses greater than susceptible males. Progeny of resistant sires were superior to progeny of susceptible sires in estimated breeding value by 4.5units for the index, 4.1% for pregnancy rate, and 5.2 fetuses (P<0.0001). Heritability estimates for the index, pregnancy rate, and number of fetuses ranged from 0.09 to 0.13, suggesting male fertility following heat stress is heritable and responds to selection.

Animals↗

PubMed2004

[The genetic variation of two microsatellite markers of Escherichia coli F4(K88) receptor in different swine breeds].

The genetic variation of ETEC F4 receptor in Shaziling and Yorkshire breeds were studied using two micro-satellite markers(S0223 and S0068). The results showed that there were polymorphisms in the two markers, and there were great variations of the gene heterozygosity and Shannon information index in the two breeds. It was also reported that there were differences in K88ab and K88ac receptors in Chinese native breeds and foreign breeds, so the two markers might be the genetic markers of F4 receptor gene.

Alleles↗

PubMed2004

Genetic variation and heritability of the antibody response to Mycobacterium avium subspecies paratuberculosis in Danish Holstein cows.

The purpose of this study was to estimate the genetic variation and the heritability of the ability to establish an immune response by producing antibodies to Mycobacterium avium subsp. paratuberculosis. Antibody levels were determined using an ELISA and measuring optical density (OD) values from milk samples of 11,535 cows from 99 herds. The pedigree of the 11,535 cows and information about days in milk, parity, milk yield, and others were obtained from the Danish Cattle database. The statistical analyses were made using a bivariate mixed animal model. The bivariate model with daily milk yield and OD as dependent variables showed a significant heritability of the ability to produce Mycobacterium avium subsp. paratuberculosis antibodies of 0.102 (genetic variance=0.054) and a nonsignificant genetic correlation of -0.037 between daily milk yield and OD. When a sire model was used, the estimated heritability was 0.091. To evaluate whether intrauterine infection could be reflected in the OD, variation among 2715 dam-daughter or maternal sister groups was also estimated. Variation in this data was nonsignificant, possibly because only very few clinical cases or end-stage cows, i.e., heavy bacterial shedders may have been represented among the cows sampled. It does not appear that intrauterine transmission is of major importance in the transmission of paratuberculosis.

Analysis of Variance↗

PubMed1995

Genetic variation and aging.

Life span is subject to genetic modification in yeasts, nematodes, fruit flies, mice, humans, and other vertebrates and invertebrates. There are a few single-gene mutants known that extend life span in yeast and nematodes; in other experimental systems the character is treated quantitatively, and generally has a low to moderate heritability. Life span responds to artificial selection in Drosophila and Caenorhabditis. There are many candidate genes presently under investigation, including the anti-oxidizing enzymes and heat-shock proteins. The main evolutionary models of senescence are antagonistic pleiotropy and mutation accumulation, neither of which has substantial experimental support. The incorporation of analytical techniques from demography is playing an increasing role in research on aging.

Aging↗

PubMed2005

Patterns of genetic variation in humans and mice.

Positional cloning of genes underlying the heritability of autoimmune disease, as in many complex diseases, has largely been a frustrating exercise with few replicated positive findings despite enormous efforts at linkage and association mapping over the past ten years. Similar difficulties have been encountered by researchers attempting to identify such genes in murine models of autoimmunity. One reason is the lack of primary knowledge of genetic variation patterns that would enable the more efficient design and interpretation of comprehensive genetic association studies. We here describe progress towards haplotype maps of both the human and mouse genomes including their current application in the search for genes underlying autoimmune and inflammatory disorders.

Animals↗

PubMed1990

Genetic variation at the omp2 porin locus of the brucellae: species-specific markers.

The omp2 locus of Brucella abortus is composed of two closely related genes (omp2a and omp2b) that encode, and potentially both express, homologous porin proteins. Genetic variation at this locus is revealed in the form of restriction-fragment-length polymorphisms which can be used to distinguish the type strains of all six Brucella species. Five of the six species contain single copies of omp2a and omp2b, whereas Brucella ovis appears to have two copies of the omp2a gene. The implications of these results with regard to the physiological functions of the omp2a and the omp2b gene products, phylogeny of the genus, and species-specific adaptation are discussed.

Bacterial Outer Membrane Proteins↗

PubMed2001

Genetic variation in the transforming growth factor beta1 gene in multiple sclerosis.

Transforming growth factor beta1 (TGFbeta1) is a Th2 cytokine encoded on chromosome 19q13, a region possibly linked to multiple sclerosis (MS). TGFbeta1 exerts favorable effects on experimental allergic encephalomyelitis. We performed a comprehensive search for genetic variants in this gene in 122 population-based sporadic cases of MS. We detected six variants, including three missense variants. We tested for association of the variants with susceptibility and course of MS and for linkage and transmission disequilibrium in a family series consisting of 395 samples in 59 pedigrees. Genetic variation in TGFB1 does not appear to contribute in a major way to susceptibility to MS.

Adult↗

PubMed1998

Genetic variation and bill size dimorphism in a passerine bird, the reed bunting Emberiza schoeniclus.

In passerine birds morphological differentiation in bill size within species is not commonly observed. Bill size is usually associated with a trophic niche, and strong differences in it may reflect the process of genetic differentiation and, possibly, speciation. We used both mitochondrial DNA (mtDNA) and nuclear microsatellites to study genetic variation between two subspecies of reed bunting, Emberiza schoeniclus schoeniclus and E.s. intermedia, along their distributional boundary in western Europe. These two subspecies are characterized by a high dimorphism in bill size and, although breeding populations of the two subspecies are found very close to each other in northern Italy, apparently no interbreeding occurs. The observed morphological pattern between the two subspecies may be maintained by geographically varying selective forces or, alternatively, may be the result of a long geographical separation followed by a secondary contact. MtDNA sequences of cytochrome b and ND5 (515 bp) showed little variation and did not discriminate between the two subspecies, indicating a divergence time of less than 500 000 years. The analysis of four microsatellite loci suggested a clear, although weak, degree of genetic differentiation in the large- and small-billed populations, as indicated by FST and RST values and genetic distances. The correlation between bill size and genetic distance between populations remained significant after accounting for the geographical distances between sampling localities. Altogether, these results indicate a very recent genetic differentiation between the two bill morphs and suggest that a strong selection for large bills in the southern part of the breeding range is probably involved in maintaining the geographical differentiation of this species.

Alleles↗

PubMed2000

[Heavy heat shock induces genetic variation in a polygenic system of a quantitative trait in Drosophila].

Results of two experiments dealing with positive and negative selection on the quantitative trait radius incompletus in an isogenic line of Drosophila melanogaster after heavy heat shock (HHS) are presented. Selection was not effective in the control without HHS. In experiment 1, in which offspring of HHS-exposed males lacked transposition induction, selection also was ineffective. By contrast, selection was highly effective in offspring of males that responded to HHS exposure by transposition induction. Thus, HHS, which is not mutagenic, generates genetic variation in a polygenic system of a quantitative trait via transpositions and excisions of mobile genetic elements. In experiment 2, positive and negative selection was conducted in three replicates, which showed concerted dynamics of the selected trait. This means that the trait dynamics is mainly related to the nearly deterministic process of accumulation of active polygenic alleles rather than to genetic drift. The induced variation of polygenic systems promotes rapid selection of "champion" genotypes. This variation is probably associated with "soft" modification of polygene expression by adjacent MGE copies.

Animals↗

PubMed1986

On the maintenance of genetic variation: global analysis of Kimura's continuum-of-alleles model.

Methods of functional analysis are applied to provide an exact mathematical analysis of Kimura's continuum-of-alleles model. By an approximate analysis, Kimura obtained the result that the equilibrium distribution of allelic effects determining a quantitative character is Gaussian if fitness decreases quadratically from the optimum and if production of new mutants follows a Gaussian density. Lande extended this model considerably and proposed that high levels of genetic variation can be maintained by mutation even when there is strong stabilizing selection. This hypothesis has been questioned recently by Turelli, who published analyses and computer simulations of some multiallele models, approximating the continuum-of-alleles model, and reviewed relevant data. He found that the Kimura and Lande predictions overestimate the amount of equilibrium variance considerably if selection is not extremely weak or mutation rate not extremely high. The present analysis provides the first proof that in Kimura's model an equilibrium in fact exists and, moreover, that it is globally stable. Finally, using methods from quantum mechanics, estimates of the exact equilibrium variance are derived which are in best accordance with Turelli's results. This shows that continuum-of-alleles models may be excellent approximations to multiallele models, if analysed appropriately.

Alleles↗

PubMed1997

Genetic variation in the tumor necrosis factor alpha gene and the outcome of multiple sclerosis.

The objective of this study was to determine whether sequence variation in the tumor necrosis factor alpha (TNF alpha) gene is associated with MS course and severity in Olmsted County, MN. The severity and temporal course of MS are heterogeneous. Genetic factors may play a role in determining the course of MS. TNF alpha expression is temporally associated with exacerbations of MS and is increased in individuals with progressive disease. The entire TNF alpha gene was amplified by polymerase chain reaction in 78 MS patients and in 39 patients with schizophrenia. Denaturation finger-printing, a modification of direct sequencing that detects virtually all genetic polymorphisms, was performed for four regions spanning the functionally significant portions of the gene, including the promoter region. Polymorphisms were confirmed by complete sequencing. The severity and temporal course of MS were compared in those with wild-type versus variant alleles. Four sequence changes were detected, three of which occurred in MS patients. None occurred in a protein-encoding sequence. Neither of the two most common sequence variants were associated with disease severity or temporal course. Genetic variation of the TNF alpha gene is not associated with variation in the course or long-term outcome of MS in this population-based sample.

Alleles↗