SEARCH · PubMed Health

Results for “Single locus”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 829 records · Page 46Linked to original sources

PubMed1993

Ac-induced instability at the Xanthophyllic locus of tomato.

To detect genomic instability caused by Ac elements in transgenic tomatoes, we used the incompletely dominant mutation Xanthophyllic-1 (Xa-1) as a whole plant marker gene. Xa-1 is located on chromosome 10 and in the heterozygote state causes leaves to be yellow. Transgenic Ac-containing tomato plants which differed in the location and number of their Ac elements were crossed to Xa-1 tester lines and F1 progeny were scored for aberrant somatic sectoring. Of 800 test and control F1 progeny screened, only four plants had aberrantly high levels of somatic sectors. Three of the plants had twin sectors consisting of green tissue adjacent to white tissue, and the other had twin sectors comprised of green tissue adjacent to tissue more yellow than the heterozygote background. Sectoring was inherited and the two sectoring phenotypes mapped to opposite homologs of chromosome 10; the green/yellow sectoring phenotype mapped in coupling to Xa-1 while the green/white sectoring phenotype mapped in repulsion. The two sectoring phenotypes cosegregated with different single, non-rearranged Acs, and loss of these Acs from the genome corresponded to the loss of sectoring. Sectoring was still observed after transposition of the Ac to a new site which indicated that sectoring was not limited to a single locus. In both sectored lines, meiotic recombination of the sectoring Ac to the opposite homolog caused the phenotype to switch between the green/yellow and the green/white phenotypes. Thus the two different sectoring phenotypes arose from the same Ac-induced mechanism; the phenotype depended on which chromosome 10 homolog the Ac was on. We believe that the twin sectors resulted from chromosome breakage mediated by a single intact, transposition-competent Ac element.

Chromosome Mapping↗

PubMed2003

The population genetics of clonal and partially clonal diploids.

The consequences of variable rates of clonal reproduction on the population genetics of neutral markers are explored in diploid organisms within a subdivided population (island model). We use both analytical and stochastic simulation approaches. High rates of clonal reproduction will positively affect heterozygosity. As a consequence, nearly twice as many alleles per locus can be maintained and population differentiation estimated as F(ST) value is strongly decreased in purely clonal populations as compared to purely sexual ones. With increasing clonal reproduction, effective population size first slowly increases and then points toward extreme values when the reproductive system tends toward strict clonality. This reflects the fact that polymorphism is protected within individuals due to fixed heterozygosity. Contrarily, genotypic diversity smoothly decreases with increasing rates of clonal reproduction. Asexual populations thus maintain higher genetic diversity at each single locus but a lower number of different genotypes. Mixed clonal/sexual reproduction is nearly indistinguishable from strict sexual reproduction as long as the proportion of clonal reproduction is not strongly predominant for all quantities investigated, except for genotypic diversities (both at individual loci and over multiple loci).

Alleles↗

PubMed2026

Mitogenomic and phylogenomic analyses identify a cohesive Western Atlantic lineage within the Narcine complex (Torpediniformes: Narcinidae).

BACKGROUND: Accurate species delimitation within electric rays of the genus Narcine has been hindered by overlapping morphological characters and limited molecular resolution in previous single-locus studies. This study aims to evaluate phylogenetic relationships and species boundaries within the Narcine species complex across the Western Atlantic using complete mitochondrial genomes. METHODS AND RESULTS: Seven complete mitogenomes were newly assembled from individuals representing distinct morphotypes sampled across geographically widespread Western Atlantic localities and analyzed together with publicly available reference sequences. Mitochondrial protein-coding genes (PCGs) were examined using concatenated nucleotide and amino acid datasets under partitioned maximum-likelihood frameworks. Both approaches recovered highly congruent topologies, consistently supporting a single, well-defined western Atlantic mitochondrial lineage with low internal divergence (0.04-2.13%). Species delimitation analyses based on multiple methods yielded partially congruent results but consistently identified a dominant lineage encompassing all Atlantic samples. In contrast, two Colombian reference mitogenomes formed a separate and highly divergent lineage relative to the Atlantic group, despite showing moderate divergence between them. Comparative mitogenomic analyses revealed conserved genome organization, nucleotide composition bias, codon usage, and transfer RNA (tRNA) structures. All PCGs evolved under strong purifying selection, with Ka/Ks ratios well below unity. CONCLUSIONS: These results support mitochondrial genetic continuity across the Western Atlantic Narcine populations and do not provide mitochondrial evidence for multiple evolutionary lineages within the Western Atlantic. The marked mitochondrial divergence of Colombian reference mitogenomes highlights potential issues in sequence attribution and underscores the importance of data curation. Overall, complete mitochondrial genomes provide a robust framework for species delimitation and future integrative taxonomic assessments within Narcine.

Animals↗

PubMed1998

Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms.

Traditional and molecular typing schemes for the characterization of pathogenic microorganisms are poorly portable because they index variation that is difficult to compare among laboratories. To overcome these problems, we propose multilocus sequence typing (MLST), which exploits the unambiguous nature and electronic portability of nucleotide sequence data for the characterization of microorganisms. To evaluate MLST, we determined the sequences of approximately 470-bp fragments from 11 housekeeping genes in a reference set of 107 isolates of Neisseria meningitidis from invasive disease and healthy carriers. For each locus, alleles were assigned arbitrary numbers and dendrograms were constructed from the pairwise differences in multilocus allelic profiles by cluster analysis. The strain associations obtained were consistent with clonal groupings previously determined by multilocus enzyme electrophoresis. A subset of six gene fragments was chosen that retained the resolution and congruence achieved by using all 11 loci. Most isolates from hyper-virulent lineages of serogroups A, B, and C meningococci were identical for all loci or differed from the majority type at only a single locus. MLST using six loci therefore reliably identified the major meningococcal lineages associated with invasive disease. MLST can be applied to almost all bacterial species and other haploid organisms, including those that are difficult to cultivate. The overwhelming advantage of MLST over other molecular typing methods is that sequence data are truly portable between laboratories, permitting one expanding global database per species to be placed on a World-Wide Web site, thus enabling exchange of molecular typing data for global epidemiology via the Internet.

Bacterial Typing Techniques↗

PubMed1991

Dissecting the primary causes of genetic hypertension in rats.

Blood pressure has a genetic component influenced by several to many genetic loci in both humans and animals; that is, blood pressure is a polygenic trait. Ultimately, the primary causes of genetic hypertension can only be established with genetic techniques. The primary tools for this analysis in animals are inbred strains of rodents selectively bred for differences in blood pressure and the genetic analysis of these strains by cosegregation techniques. This analysis determines whether it is possible to separate specific alleles at a candidate genetic locus from a component of blood pressure in genetically segregating populations. If the candidate alleles cosegregate with a component of blood pressure, these alleles must be the cause of the blood pressure differences or be linked on the same chromosome to alleles at other loci that cause blood pressure differences. If, on the other hand, the candidate alleles do not cosegregate with blood pressure, they cannot be the cause of the blood pressure differences. This analysis is straightforward in the case of a single-locus Mendelian candidate trait but is less informative if a candidate trait is itself polygenic. In this case, genetic analysis yields either 1) results that are compatible with, but not definitive proof for, a genetic role of the trait in causing blood pressure differences or 2) results that eliminate the trait as a cause of genetic differences in blood pressure. A complete listing of all the traits that have undergone genetic cosegregation analysis in rodents is given.

Animals↗

PubMed1989

An extremely polymorphic locus on the short arm of the human X chromosome with homology to the long arm of the Y chromosome.

A genomic DNA clone named CRI-S232 reveals an array of highly polymorphic restriction fragments on the X chromosome as well as a set of non-polymorphic fragments on the Y chromosome. Every individual has multiple bands, highly variable in length, in every restriction enzyme digest tested. One set of bands is found in all males, and co-segregates with the Y chromosome in families. These sequences have been regionally localized by deletion mapping to the long arm of the Y chromosome. Segregation analysis in families shows that all of the remaining fragments co-segregate as a single locus on the X chromosome, each haplotype consisting of three or more polymorphic fragments. This locus (designated DXS278) is linked to several markers on Xp, the closest being dic56 (DXS143) at a distance of 2 cM. Although it is outside the pseudoautosomal region, the S232 X chromosome locus shows linkage to pseudoautosomal markers in female meiosis. In determining the X chromosome S232 haplotypes of 138 offspring among 19 families, we observed three non-parental haplotypes. Two were recombinant haplotypes, consistent with a cross-over among the S232-hybridizing fragments in maternal meiosis. The third was a mutant haplotype arising on a paternal X chromosome. The locus identified by CRI-S232 may therefore be a recombination and mutation hotspot.

Cell Line↗

PubMed1992

A fourth family of the Plasmodium falciparum S-antigen.

The S-antigen of Plasmodium falciparum is a highly diverse heat stable protein that is located in the parasitophorous vacuole of the mature asexual intraerythrocytic parasite. The gene for S-antigen exists within the parasite population as multiple alleles at a single locus. Its sequence contains a large central block of tandemly arranged peptides that are identical or very similar in one allele but differ widely in sequence, repeat length and number among different alleles, and consequently antigenic specificity. Thus, antibodies directed against the repeat region can be used to define the serotype of an S-antigen. Flanking this repeat block are 2 short regions of non-repetitive sequence which have been described as occurring in three different forms, each of which is used to define a single S-antigen family. We present the S-antigen sequence for the isolate 3D7 which defines not only a novel serotype but also a novel S-antigen family. The central repeat block is composed of 57 copies of an 8-residue peptide with consensus sequence ED(E/K)VSNG(R/G). Comparison of the four S-antigen families reveals that they differ considerably from each other with variation being most pronounced in the carboxy terminal-flanking region. This pattern of sequence variation differs considerably from that found for MSA-1 and MSA-2, the only other diverse proteins of P. falciparum for which sequence information is available.

Amino Acid Sequence↗

PubMed1999

Genetic variation and correlations between genotype and locomotor physiology in outbred laboratory house mice (Mus domesticus).

Laboratory strains of house mice (Mus domesticus) are increasingly used as model organisms in evolutionary physiology, so information on levels of genetic variation is important. For example, are levels of genetic variation comparable to those found in populations of wild house mice? We studied allozymes to estimate genetic variation in outbred Hsd:ICR mice, which have been used in several studies with evolutionary emphasis. The physiological significance of allozyme variation remains obscure. Several workers have reported relationships between multi-locus heterozygosity and metabolic traits, but endotherms have not been studied. Therefore, we also measured mice for basal metabolic rate (BMR), maximal oxygen consumption during forced treadmill exercise (VO2max), and 12 other traits related to locomotor physiology, before genotyping them for 10 allozyme loci. Four of these loci were polymorphic, all were in Hardy-Weinberg equilibrium, and inbreeding coefficients were not significantly different from zero. Average heterozygosities were 11%, similar to values reported for wild populations of house mice. Fourteen percent of the associations between single-locus genotype and physiological traits were statistically significant. Multi-locus heterozygosity was not significantly related to VO2max, but was positively correlated with BMR, a result opposite to the negative correlation between standard metabolic rate and heterozygosity reported in many ectotherms. Therefore, the proposed mechanisms for the effect of multi-locus heterozygosity on metabolic rate in ectotherms may not apply to endotherms.

Animals↗

PubMed1995

A genetic locus on Plasmodium falciparum chromosome 12 linked to a defect in mosquito-infectivity and male gametogenesis.

Infection of mosquitoes by Plasmodium spp. requires sexual differentiation of the malarial parasite in the vertebrate host and mating of the heterogametes in the vector midgut. A Plasmodium falciparum clone, Dd2, differentiates into normal-appearing gametocytes, yet poorly infects mosquitoes. The Dd2 clone, however, effectively cross-fertilized HB3, a Central American P. falciparum clone, and yielded several independent recombinant progeny. We have examined 11 HB3 x Dd2 progeny for their ability to infect mosquitoes and to differentiate into male gametes. Our analyses indicate that the poor mosquito-infectivity of the Dd2 clone results from a defect in male gametogenesis. This defect was inherited as a single locus in the independent recombinant progeny of HB3 x Dd2. Comparison with a restriction fragment length polymorphism map of the HB3 x Dd2 cross indicates that the defective phenotype of Dd2 maps to a locus on P. falciparum chromosome 12. This genetic locus may contain determinants that play a crucial role in male gametogenesis by P. falciparum.

Animals↗

PubMed2003

Cross-species amplification of mitochondrial DNA sequence-tagged-site markers in conifers: the nature of polymorphism and variation within and among species in Picea.

Primers previously developed to amplify specific non-coding regions of the mitochondrial genome in Angiosperms, and new primers for additional non-coding mtDNA regions, were tested for their ability to direct DNA amplification in 12 conifer taxa and to detect sequence-tagged-site (STS) polymorphisms within and among eight species in Picea. Out of 12 primer pairs, nine were successful at amplifying mtDNA in most of the taxa surveyed. In conifers, indels and substitutions were observed for several loci, allowing them to distinguish between families, genera and, in some cases, between species within genera. In Picea, interspecific polymorphism was detected for four loci, while intraspecific variation was observed for three of the mtDNA regions studied. One of these (SSU rRNA V1 region) exhibited indel polymorphisms, and the two others ( nad1 intron b/c and nad5 intron1) revealed restriction differences after digestion with Sau3AI (PCR-RFLP). A fourth locus, the nad4L- orf25 intergenic region, showed a multibanding pattern for most of the spruce species, suggesting a possible gene duplication. Maternal inheritance, expected for mtDNA in conifers, was observed for all polymorphic markers except the intergenic region nad4L- orf25. Pooling of the variation observed with the remaining three markers resulted in two to six different mtDNA haplotypes within the different species of Picea. Evidence for intra-genomic recombination was observed in at least two taxa. Thus, these mitotypes are likely to be more informative than single-locus haplotypes. They should be particularly useful for the study of biogeography and the dynamics of hybrid zones.

Base Sequence↗

PubMed2006

Plasminogen activator inhibitor-1 gene: selection of tagging single nucleotide polymorphisms and association with coronary heart disease.

OBJECTIVE: To explore the effect of plasminogen activator inhibitor-1 (PAI-1) gene variations on the risk of coronary heart disease (CHD) in Chinese Han population. METHODS AND RESULTS: We screened all exons and the promoter region of PAI-1 gene in 48 patients and identified 17 polymorphisms. Five tagging single nucleotide polymorphisms were selected and genotyped in 816 patients with CHD and 937 controls. In the total sample, no main effects of the loci or haplotypes reached statistical significance after adjusting environmental covariates. However, a strongly significant gene-smoking interaction was observed. Among nonsmokers, 2 polymorphisms located at promoter region (rs2227631 and rs1799889) showed significant association with CHD. The cases had higher frequency of rs2227631 A allele and rs1799889 4G allele than the controls (0.42 versus 0.33, P=0.001; 0.60 versus 0.52, P=0.002). Haplotype analyses confirmed the effects of the PAI-1 gene-smoking interaction on CHD risk. Compared with the most common haplotype G-5G-A-A-T (35.1%), the haplotype A-4G-A-A-C (32.7%) significantly increased the risk of CHD with adjusted odds ratio of 1.51 (95% CI, 1.12 to 2.05; P=0.008) in nonsmokers. CONCLUSIONS: This study identified a significant interaction between PAI-1 gene and smoking status. Both single locus and haplotype analyses indicated that rs2227631 A allele and rs1799889 4G allele increased the risk of CHD among nonsmokers in Chinese.

Adult↗

PubMed2007

Accumulating quantitative trait linkage evidence across multiple datasets using the posterior probability of linkage.

Genome scans for complex disorders are frequently inconclusive, prompting researchers to increase sample size in an effort to obtain stronger evidence. However, increasing sample size in the presence of locus heterogeneity may actually, on average, decrease the linkage signal at a true susceptibility gene. The posterior probability of linkage, or PPL, was specifically designed to address this issue in the context of categorical trait analysis, by appropriately accumulating evidence either for or against linkage as new data are added. We now formulate a quantitative trait (QT) analog, the QT-PPL, which directly measures the evidence that a QT is linked to a genetic marker or location. The new QT-PPL is based on a classical single-locus QT likelihood with the trait parameters (allele frequency, genotypic means and variances) integrated out. We show using simulations that the QT-PPL is robust to two key modeling violations (multiple trait loci and non-normality in the form of excess kurtosis), as well as being inherently ascertainment corrected, and illustrate the advantages of the QT-PPL for accumulating linkage evidence across multiple sets of data compared to other QT linkage methods.

Computer Simulation↗

PubMed1999

Population models of genomic imprinting. I. Differential viability in the sexes and the analogy with genetic dominance.

Many single-locus, two-allele selection models of genomic imprinting have been shown to reduce formally to one-locus Mendelian models with a modified parameter for genetic dominance. One exception is the model where selection at the imprinted locus affects the sexes differently. We present two models of maternal inactivation with differential viability in the sexes, one with complete inactivation, and the other with a partial penetrance for inactivation. We show that, provided dominance relations at the imprintable locus are the same in both sexes, a globally stable polymorphism exists for a range of viabilities that is independent of the penetrance of imprinting. The conditions for a polymorphism are the same as in previous models with differential viability in the sexes but without imprinting and in a model of the paternal X-inactivation system in marsupials. The model with incomplete inactivation is used to illustrate the analogy between imprinting and dominance by comparing equilibrium bifurcation plots for fixed values of dominance and penetrance. We also derive a single expression for the dominance parameter that leaves the frequency and stability of equilibria unchanged for all levels of inactivation. Although an imprinting model with sex differences does not formally reduce to a nonimprinting scheme, close theoretical parallels clearly exist.

Animals↗

PubMed1996

Estimation in an island model using simulation.

Estimation for an island model where mutation maintains a k-allele neutral polymorphism at a single locus on each island is considered. The likelihood of an observed sample type configuration is obtained by applying a computational algorithm analogous to Griffiths and Tavaré (Theor. Popul. Biol. 46 (1994), 131-159). This allows the computation of sampling distributions in an island model and investigation of their properties. Given a sample type configuration, the maximum likelihood estimate of the migration parameter is obtained by simulating independently the likelihood at a grid of points and, also, using a surface simulation method. The latter method generates the whole likelihood trajectory in a single application of the simulation program. An estimate of variance of the estimate of the migration parameter is obtained using the likelihood trajectory. A comparison of the maximum likelihood estimates of the gene flow between subpopulations is made with those obtained by using Wright's FST statistic.

Algorithms↗

PubMed1997

Quinacrine and ethidium bromide bind the same locus on the nicotinic acetylcholine receptor from Torpedo californica.

Quinacrine is a noncompetitive antagonist of the nicotinic acetylcholine receptor (AChR) which displays severalfold fluorescent enhancement upon binding to AChR-rich membranes from Torpedo californica electric organ. It is demonstrated that the fluorescence enhancement comprises two components: specific interaction at a high-affinity binding site on the AChR, and interaction with the lipid bilayer. The interaction with the lipid bilayer can be attenuated by other noncompetitive antagonists, but at concentrations substantially higher than those required for binding to the AChR. It is further shown that quinacrine can inhibit the binding of [3H]phencyclidine and [3H]ethidium in a manner fully consistent with simple competitive inhibition. The data support a model for high-affinity quinacrine binding to the same, single locus of the acetylcholine receptor as phencyclidine and ethidium. This site is likely within the lumen of the ion channel.

Animals↗

PubMed1996

The chromosomal distribution of mouse odorant receptor genes.

Odorant receptors (ORs) on nasal olfactory sensory neurons are encoded by a large multigene family. Each member of the family is expressed in a small percentage of neurons that are confined to one of several spatial zones in the nose but are randomly distributed throughout that zone. This pattern of expression suggests that when the sensory neuron selects which OR gene to express it may be confined to a particular zonal gene set of several hundred OR genes but select from among the members of that set via a stochastic mechanism. Both locus-dependent and locus-independent models of OR gene choice have been proposed. To investigate the feasibility of these models, we determined the chromosomal locations of 21 OR genes expressed in four different spatial zones. We found that OR genes are clustered within multiple loci that are broadly distributed in the genome. These loci lie within paralogous chromosomal regions that appear to have arisen by duplications of large chromosomal domains followed by extensive gene duplication and divergence. Our studies show that OR genes expressed in the same zone map to numerous loci; moreover, a single locus can contain genes expressed in different zones. These findings raise the possibility that OR gene choice may be locus-independent or involve consecutive stochastic choices.

Animals↗

PubMed1996

Microsatellite and chromosome evolution of parthenogenetic sitobion aphids in Australia.

Single-locus microsatellite variation correlated perfectly with chromosome number in Sitobion miscanthi aphids. The microsatellites were highly heterozygous, with up to 10 alleles per locus in this species. Despite this considerable allelic variation, only seven different S. miscanthi genotypes were discovered in 555 individuals collected from a wide range of locations, hosts and sampling periods. Relatedness between genotypes suggests only two successful colonizations of Australia. There was no evidence for genetic recombination in 555 S. miscanthi so the occurrence of recent sexual reproduction must be near zero. Thus diversification is by mutation and chromosomal rearrangement alone. Since the aphids showed no sexual recombination, microsatellites can mutate without meiosis. Five of seven microsatellite differences were a single repeat unit, and one larger jump is likely. The minimum numbers of changes between karyotypes corresponded roughly one-to-one with microsatellite allele changes, which suggests very rapid chromosomal evolution. A chromosomal fission occurred in a cultured line, and a previously unknown chromosomal race was detected. All 121 diverse S. near fragariae were heterozygous but revealed only one genotype. This species too must have a low rate of sexual reproduction and few colonizations of Australia.

Animals↗

PubMed1997

Increased excitability and inward rectification in layer V cortical pyramidal neurons in the epileptic mutant mouse Stargazer.

The excitability of layer V cortical pyramidal neurons was studied in vitro in the single-locus mutant mouse stargazer (stg), a genetic model of spike wave epilepsy. Field recordings in neocortical slices from mutant mice bathed in artificial cerebrospinal fluid revealed spontaneous synchronous network discharges that were never present in wild-type slices. Intracellular and whole cell recordings from stg/stg neurons in deep layers showed spontaneous giant depolarizing excitatory post-synaptic potentials generating bursts of action potentials, and a 78% reduction in the afterburst hyperpolarization. Whole cell recordings revealed gene-linked differences in active membrane properties in two types of regular spiking neurons. Single action potential rise and decay times were reduced, and the rheobase current was decreased by 68% in mutant cells. Plots of spike frequency-current relationships revealed that the gain of this relation was augmented by 29% in the mutant. Comparisons of visually identified pyramidal neurons firing properties in both genotypes revealed no difference in single action potential afterhyperpolarization. Voltage-clamp recordings showed an approximately threefold amplitude increase in a cesium-sensitive inward rectifier. No cell density or soma size differences were observed in the layer V pyramidal neuron population between the two genotypes. These results demonstrate an autonomous increase in cortical network excitability in a genetic epilepsy model. This defect could lower the threshold for aberrant thalamocortical spike wave oscillations in vivo, and may contribute to the mechanism of one form of inherited absence epilepsy.

Action Potentials↗