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PubMed2002

Polymorphisms in the methylenetetrahydrofolate reductase gene were associated with both the efficacy and the toxicity of methotrexate used for the treatment of rheumatoid arthritis, as evidenced by single locus and haplotype analyses.

5,10-Methylenetetrahydrofolate reductase (MTHFR), a key enzyme involved in folate metabolism, has two common polymorphisms that affect enzyme activity. The objective of this study was to examine whether there was a correlation between the genotype or haplotype of the MTHFR gene and the efficacy or toxicity of methotrexate (MTX) in the treatment of rheumatoid arthritis. MTX-treated rheumatoid arthritis patients (n = 106) were selected from outpatient clinics and used for a retrospective study to examine the correlation between genotypes or haplotypes concerning polymorphisms of the MTHFR gene, and the efficacy or toxicity of MTX. Estimation of the haplotype frequencies was performed by maximum likelihood estimation based on expectation maximization algorithm. Single locus analysis examining each locus separately showed that patients with 1298C were receiving significantly lower doses of MTX compared to patients without [P < 0.05, relative risk (RR) = 2.18, 95% confidence interval (CI) 1.17-4.06], while a higher rate of overall MTX toxicity was observed in patients with 677T than those without (P < 0.05, RR = 1.25, 95% CI 1.05-1.49). An estimation of haplotype frequencies showed that there was no 677T-1298C haplotype in the population. Posterior distribution of the diplotype configuration for each individual was concentrated on a single configuration. Patients with the 677C-1298C haplotype were receiving lower doses of MTX than those without (P < 0.05, RR = 2.14, 95% CI 1.13-4.07), while subjects with 677T-1298A had a higher frequency of side-effects from MTX (P < 0.05, RR = 1.42, 95% CI 1.11-1.82). Both single locus and haplotype analyses suggest that polymorphisms within the MTHFR gene are associated with both the efficacy and toxicity of MTX in rheumatoid arthritis patients. Pharmacokinetic studies are necessary to prove the association.

Antirheumatic Agents↗
PubMed2003

Single-locus heterotic effects and dominance by dominance interactions can adequately explain the genetic basis of heterosis in an elite rice hybrid.

The genetic basis of heterosis of an elite rice hybrid was investigated by using an "immortalized F(2)" population produced by randomly permutated intermating of 240 recombinant inbred lines from a cross between the parents of Shanyou 63, the most widely cultivated hybrid in China. Measurements of heterosis for crosses in the immortalized F(2) population were obtained from replicated field trials over 2 years by inter-planting the hybrids with the parental recombinant inbred lines. The analyses were conducted making use of a linkage map comprising 231 segregating molecular marker loci covering the entire rice genome. Heterotic effects were detected at 33 loci for the four traits with modified composite interval mapping. The heterotic loci showed little overlap with quantitative trait loci for trait performance, suggesting that heterosis and trait performance may be conditioned by different sets of loci. Large numbers of digenic interactions were resolved by using two-way ANOVA and confirmed by randomization tests. All kinds of genetic effects, including partial-, full-, and overdominance at single-locus level and all three forms of digenic interactions (additive by additive, additive by dominance, and dominance by dominance), contributed to heterosis in the immortalized F(2) population, indicating that these genetic components were not mutually exclusive in the genetic basis of heterosis. Heterotic effects at the single-locus level, in combination with the marginal advantages of double heterozygotes caused by dominance by dominance interaction at the two-locus level could adequately explain the genetic basis of heterosis in Shanyou 63. These results may help reconcile the century-long debate concerning the genetic basis of heterosis.

Analysis of Variance↗
PubMed2000

Age-dependent changes in axonal branching of single locus coeruleus neurons projecting to two different terminal fields.

Age-dependent changes in the axonal branching patterns of single locus coeruleus neurons, which innervate both the frontal cortex and hippocampus dentate gyrus, have been studied in male F344 rats. We used an electrophysiological approach involving antidromic activation to differentiate single from multi-threshold locus coeruleus neurons in each terminal field with age (7-27 mo of age). Most of these neurons have a single threshold in the young rats, whereas in the older brains, the neurons have multi-threshold responses. This implies an increased amount of axonal branching in the older brains. The time course of the increase differs in the two terminal fields, suggesting that the degree of plasticity or age-dependent increase in branching can differ across terminal fields.

Aging↗
PubMed1993

Genetic polymorphism of the single locus probes pL159-1 and pL355-8.

The genetic polymorphism of the single-locus probes pL159-1 (D18S17) and pL355-8 (D20S15) was investigated in 445 unrelated individuals using PstI as restriction enzyme. Fragment size calculations were obtained using the molecular weight size marker MW-SBH. The basic relationship between migration distance and molecular weight was transformed using an exponential function. Fragment size frequency data show 2 peaks for pL159-1 at 4.36kb (2.36%) and 4.67 kb (6.29%) and one peak for pL355-8 at 6.04 kb (5.73%). The rate of heterozygosity exceeded 70% for both probes.

Alleles↗
PubMed2004

Single-locus complementary sex determination in the inbreeding wasp Euodynerus foraminatus Saussure (Hymenoptera: Vespidae).

The Hymenoptera have arrhenotokous haplodiploidy in which males normally develop from unfertilized eggs and are haploid, while females develop from fertilized eggs and are diploid. Multiple sex determination systems are known to underlie haplodiploidy, and the best understood is single-locus complementary sex determination (sl-CSD) in which sex is determined at a single polymorphic locus. Individuals heterozygous at the sex locus develop as females; individuals that are hemizygous (haploid) or homozygous (diploid) at the sex locus develop as males. sl-CSD can be detected with inbreeding experiments that produce diploid males in predictable proportions as well as sex ratio shifts due to diploid male production. This sex determination system is considered incompatible with inbreeding because the ensuing increase in homozygosity increases the production of diploid males that are inviable or infertile, imposing a high cost on matings between close relatives. However, in the solitary hunting wasp Euodynerus foraminatus, a species suspected of having sl-CSD, inbreeding may be common due to a high incidence of sibling matings at natal nests. In laboratory crosses with E. foraminatus, we find that sex ratios and diploid male production (detected as microsatellite heterozygosity) are consistent with sl-CSD, but not with other sex determination systems. This is the first documented example of sl-CSD in a hymenopteran with an apparent natural history of inbreeding, and thus presents a paradox for our understanding of hymenopteran genetics.

Animals↗
PubMed1996

Protein and microsatellite single locus variability in Salmo salar L. (Atlantic salmon).

We describe genetic variation at three microsatellite single loci and six allozyme loci of seven natural Atlantic salmon populations from Ireland and Spain. A comparison of genetic variability detected at both types of loci is performed. Also, the relative value of microsatellite single locus variability with regard to the identification of individual salmon populations is assessed. Microsatellite loci are shown to display higher levels of variation than allozyme loci. Mean number of alleles (6 +/- 1.53) and heterozygosity (0.46 +/- 0.04) at microsatellite loci are greater than those found for allozymes (1.85 +/- 0.05 and 0.21 +/- 0.03, respectively), and some microsatellite alleles appear to be specific for a location or geographical area. Allozyme and microsatellite variation show the same pattern of differentiation between populations with Irish and Spanish populations grouped into different clusters. However, greater values of genetic distance were found among microsatellite (D = 0.0747 +/- 0.011) rather than among allozyme loci (D = 0.0449 +/- 0.008). These results provide evidence that microsatellite-based analysis of genetic variation will be useful in the identification of individual populations of Atlantic salmon.

Alleles↗
PubMed2005

[Dynamic regimes in a model of single-locus density-dependent selection].

A model of density-dependent selection in a Mendelian single-locus population was analyzed in the case where the fitnesses of genotypic forms are exponential functions of the population size. Analytical and numerical studies of the model were performed for a diallelic locus, and parametric regions were established for different dynamic behaviors of the model. The diallelic model of density-dependent selection was generalized to a multiallelic locus; the results of its analysis are described.

Models, Genetic↗
PubMed1991

Application of single-locus hypervariable region DNA probes to deficiency cases in paternity testing.

Seven DNA probes which recognize single-locus hypervariable region (HVR) were applied to a paternity test in which the putative father and his wife were deceased. Three legitimate children, an illegitimate child and her mother were available for analysis. The cumulative paternity index of the illegitimate child derived from 15 conventional blood group markers was 18.71 and from 7 DNA probes 92,572.08, that is, 4,948 times higher than the former. Thus the DNA analyses gave nearly conclusive evidence that the putative father was the biological father of the child. The application of highly discriminating polymorphisms of DNA which recognize single HVR loci is considered to be extremely informative in cases of disputed parentage.

Child↗
PubMed1997

Linkage analysis of complex traits using affected sibpairs: effects of single-locus approximations on estimates of the required sample size.

We investigated the power of the affected sibpair method for detecting a disease locus when the disease is inherited through two bi-allelic loci. The power was computed for all possible values of the gene frequencies and penetrances that lead to a given population prevalence and a given sibling relative risk. A method to generate rapidly all possible models that give a specific population prevalence and relative risk is provided. We applied it to the case of a two-locus disease with a prevalence of 10% and a low sibling relative risk of 1.5. For this particular example, regardless of the true underlying model, a sample size (N = 450 for alpha = 0.05, N = 1,500 for alpha = 0.0001) may be determined such that one would expect enough power (0.80) to detect at least one of the two disease genes. In addition to the general case, we examined a special class of models in which the marginal penetrances at each locus are either recessive or dominant. In this instance, the gene frequencies were excellent predictors of the power afforded by a particular sample size. These methods have been implemented in a C program called SIBPOWER which is freely available from the first author. With this program, investigators can perform their own power calculations for any two-locus model of their choice thus avoiding the need to use single-locus approximations that may grossly underestimate the necessary sample size.

Gene Frequency↗
PubMed1994

Plasmodium falciparum genetic diversity can be characterised using the polymorphic merozoite surface antigen 2 (MSA-2) gene as a single locus marker.

The genetic diversity of Solomon Island Plasmodium falciparum isolates was examined using MSA-2 as a single locus marker. Amplification of MSA-2 gene fragments showed size polymorphism and the presence of mixed infections. Sequence analysis indicated a global representation of MSA-2 alleles with representatives of 3D7/CAMP allelic subfamilies and the FCQ-27 allelic family being identified. A simplified method of characterisation, utilising PCR-RFLPs of MSA-2 gene fragments, was developed. The RFLPs allowed identification of allelic families and further distinction within the 3D7/CAMP family. The amplification of MSA-2 gene fragments from culture derived lines revealed a loss of diversity for a number of Solomon Island isolates. Genomic diversity was confirmed for Solomon Island lines, along with Papua New Guinean and Thai lines, by the generation of 7H8/6 fingerprints. All lines were distinct and band sharing frequencies and Wagner tree construction failed to identify any geographic clustering.

Amino Acid Sequence↗
PubMedDate not supplied

Report of a European collaborative exercise comparing DNA typing results using a single locus VNTR probe.

A collaborative exercise was carried out in 1989 among 12 European forensic laboratories using the single locus VNTR probe pYNH24, the restriction enzyme HinfI, the same set of human genomic DNA samples, and a standardized DNA size marker. The objectives of the exercise were: (1) to study the degree of variation within and between laboratories, (2) to obtain information on requirements for technical standardization allowing the exchange of typing results and (3) to compare different approaches for the identification of allelic DNA fragments of unknown size. Each laboratory carried out up to 10 independent typing experiments using the same DNA samples. The results were analysed independently by two laboratories using three different methods. The results of the exercise demonstrate the correlation of typing that can be achieved within and between laboratories under conditions of minimal standardization.

Alleles↗
PubMed1988

The maintenance of single-locus polymorphism. I. Numerical studies of a viability selection model.

The ability of viability selection to maintain single-locus polymorphism is investigated with two models in which the population is bombarded with a series of mutations with random fitnesses. In the first model, the population is allowed to reach equilibrium before mutation resumes; in the second the iterations and mutation occur simultaneously. Monte Carlo simulations of these models show that viability selection is easily able to maintain stable 6- or 7-allele polymorphisms and that monomorphisms and diallelic polymorphisms are uncommon. The question of how monomorphisms arise is also discussed.

Alleles↗
PubMed1991

Individual identification by VNTR analysis using minisatellite DNA probe to distinguish variable alleles at a single locus.

Variable number of tandem repeat analysis using a ministatellite DNA probe pYNH24 to distinguish variable alleles at a single locus was applied to forensic analysis of DNA extracted from a murder and body abandonment specimen. Two bands detected by pYNH24 correspond to identical DNA from both the upper and lower halves of a separated body, suggesting that these halves were from the same body.

DNA Probes↗
PubMedDate not supplied

A guide to interpreting single locus profiles of DNA mixtures in forensic cases.

Analysis of a mixed body fluid crime sample by means of a single locus DNA probe may give rise to several bands. If a suspect is found to have a profile which matches two of the bands, then the evaluation of the evidential strength requires careful analysis. This paper describes the analysis of two relatively simple case examples. It is intended that the principles of the interpretative process will provide a guide to caseworkers who may encounter similar cases. The extension of the treatment to more complex cases should be clear.

Body Fluids↗
PubMed1992

Restriction fragment length polymorphism analysis of zoo animals using HaeIII and four single-locus probes.

Using HaeIII as the restriction endonuclease, restriction fragment length polymorphism analysis of dried blood samples from various animals was conducted. Single-locus probes D2S44, D10S28, D1S7, and D4S139, as well as monomorphic probe D7Z2, were used to examine for banding patterns. If bands were present, the samples were further examined for heterogeneity (whether single or multiple bands were observed) and polymorphism (whether variation in band location was shown between the animals studied within a species). Blood samples from animals, including primates, were obtained from Miami Metrozoo, Miami, Florida. Some of the animals were non-related individuals while others were related. Banding patterns were observed in colobus' for D2S44, D1S7, and D4S139; owl monkeys for D2S44; gorillas for D2S44 and D4S139; gibbons for D2S44 and D4S139; siamangs for D2S44, talapoins for DiS7; cranes for D1S7; and otters for D1S7. Based upon these, all of the animals for which a conclusion could be drawn appeared to be homozygous and monomorphic (exhibited only an invariant single band) for the loci examined except colobus' for D4S139, gorillas for D4S139, cranes for D1S7, and otters for D1S7.

Animals↗
PubMed2001

The dangers of using single locus markers in parasite epidemiology: Ascaris as a case study.

Molecular markers are used widely to discriminate between closely related species of parasites, and in many cases a single locus is used for this purpose. This article aims to show how molecular data derived from a single genetic marker or linkage group - in this case mitochondrial DNA - can lead to ambiguous conclusions and to illustrate how a multilocus approach has enhanced our understanding of the epidemiology of two closely related parasites, the nematodes Ascaris suum, which infects pigs, and Ascaris lumbicoides, which infects humans.

Animals↗
PubMed1986

Tolerance to opioids in single locus coeruleus neurons of the rat.

Chronic treatment of rats with morphine caused tolerance to the membrane hyperpolarizing action of morphine in single locus coeruleus neurons in vitro. Tolerance was less pronounced for Try-D-Ala-Gly-MePhe-Gly-ol (DAGO) than for normorphine. No changes were found in affinity of naloxone for mu-receptors on these neurons, nor in the properties of the potassium conductance increase caused by mu-receptor activation. These results suggest that the mechanisms underlying tolerance involve either a reduction of the number of mu-receptors on each cell, or a reduced coupling of mu-receptors to potassium channels.

Animals↗