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PubMed1965

IMMUNOGLOBULIN ISOANTIGENS (ALLOTYPES) IN THE MOUSE. I. GENETICS AND CROSS-REACTIONS OF THE 7S GAMMA-2A-ISOANTIGENS CONTROLLED BY ALLELES AT THE IG-1 LOCUS.

Eight antigens of 7S gamma(2)-immunoglobulins controlled by alleles at a single locus Ig-1, have been identified in mice. This locus has previously been shown to determine antigenic specificities on the F fragments of 7S gamma(2a)-globulins. The reactions of these antigens with various isoantisera have shown that the antigens all cross react with one another. New methods for the analysis of antigenic specificities of soluble proteins are presented in detail. A sensitive method for detecting in the order of 0.01 microg of these isoantigens has been developed, based on the quantitative inhibition of precipitation of I(125)-labeled antigen. Cross-reactions of the antigens were analysed in inhibition assays and the data is compatible with the existence of a minimum of eight antigenic specificities. Each of the antigens is composed of different combinations of these specificities, with only one antigen having a specificity not present in any other. Sixty-eight mouse strains have been tested with specific isoantisera, and on the basis of the results, have been placed into the eight allele groups. Evidence for close genetic linkage of the Ig-1 locus and 11 chromosome markers has been sought and not found.

Alleles↗

PubMed2006

Effect of repeat copy number on variable-number tandem repeat mutations in Escherichia coli O157:H7.

Variable-number tandem repeat (VNTR) loci have shown a remarkable ability to discriminate among isolates of the recently emerged clonal pathogen Escherichia coli O157:H7, making them a very useful molecular epidemiological tool. However, little is known about the rates at which these sequences mutate, the factors that affect mutation rates, or the mechanisms by which mutations occur at these loci. Here, we measure mutation rates for 28 VNTR loci and investigate the effects of repeat copy number and mismatch repair on mutation rate using in vitro-generated populations for 10 E. coli O157:H7 strains. We find single-locus rates as high as 7.0 x 10(-4) mutations/generation and a combined 28-locus rate of 6.4 x 10(-4) mutations/generation. We observed single- and multirepeat mutations that were consistent with a slipped-strand mispairing mutation model, as well as a smaller number of large repeat copy number mutations that were consistent with recombination-mediated events. Repeat copy number within an array was strongly correlated with mutation rate both at the most mutable locus, O157-10 (r2= 0.565, P = 0.0196), and across all mutating loci. The combined locus model was significant whether locus O157-10 was included (r2= 0.833, P < 0.0001) or excluded (r2= 0.452, P < 0.0001) from the analysis. Deficient mismatch repair did not affect mutation rate at any of the 28 VNTRs with repeat unit sizes of >5 bp, although a poly(G) homomeric tract was destabilized in the mutS strain. Finally, we describe a general model for VNTR mutations that encompasses insertions and deletions, single- and multiple-repeat mutations, and their relative frequencies based upon our empirical mutation rate data.

Animals↗

PubMed1999

Glutamate-induced currents in acutely dissociated guinea pig locus coeruleus neurons.

To investigate the properties of L-glutamate (Glu) receptors in single locus coeruleus (LC) neurons at mature stage, we recorded the Glu-induced currents in the LC neurons acutely dissociated from adult guinea pigs, using the whole-cell patch-clamp technique. The concentration-current relationships show that Glu-induced currents in LC neurons might be predominantly mediated by non-NMDA receptors rather than NMDA receptors. The current-voltage relationship of NMDA or non-NMDA receptor-mediated currents indicated that both subtypes of the Glu-receptors operate non-selective cation channels, and that the NMDA receptor-operated channels but not the non-NMDA receptor-operated channels are permeable to Ca2+. These results suggest that in LC neurons, the normal excitatory neurotransmission may be mediated through non-NMDA receptors, and that NMDA receptors may be involved in intracellular signal transduction by their Ca2+ permeability.

Animals↗

PubMed1982

Isolation and characterization of a human locus homologous to the transforming gene (v-fes) of feline sarcoma virus.

A single locus (designated c-fes) in the human genome which exhibits homology to the transformation-specific onc gene (v-fes) of Snyder-Theilen feline sarcoma virus was identified by the Southern blot technique. Recombinant clones containing 16- to 18-kilobase inserts of human DNA including the c-fes locus were constructed. Restriction endonuclease mapping of these clones verified their identity with native human c-fes and demonstrated the presence of at least two sequences in human c-fes interrupting v-fes-homologous regions. The v-fes-homologous locus in the human genome spans about 4 kilobases. The 5'-3' orientation of the c-fes clones with respect to feline sarcoma virus proviral DNA was determined. The region of the human genome that is homologous to v-fes is proximal to the highly reiterated human Alu sequence but not to the highly reiterated human alphoid sequence.

Cell Transformation, Viral↗

PubMed1995

Epistasis and its contribution to genetic variance components.

We present a new parameterization of physiological epistasis that allows the measurement of epistasis separate from its effects on the interaction (epistatic) genetic variance component. Epistasis is the deviation of two-locus genotypic values from the sum of the contributing single-locus genotypic values. This parameterization leads to statistical tests for epistasis given estimates of two-locus genotypic values such as can be obtained from quantitative trait locus studies. The contributions of epistasis to the additive, dominance and interaction genetic variances are specified. Epistasis can make substantial contributions to each of these variance components. This parameterization of epistasis allows general consideration of the role of epistasis in evolution by defining its contribution to the additive genetic variance.

Animals↗

PubMed1993

Segregation of delta F508 and normal CFTR alleles in human sperm.

Single sperm typing provides an accurate method to order tightly linked loci by single cell DNA high resolution segregation analysis. We have used similar methods to type individual sperm from a known delta F508 cystic fibrosis heterozygote to determine the frequency of the mutation within his germ cell population, and to test possible explanations for the reported sex ratio distortion of the cystic fibrosis (CF) mutation to male offspring. Using a nested polymerase chain reaction we have been able to amplify a single locus sequence, cystic fibrosis transmembrane conductance regulator (CFTR), from a single target sperm haploid genome to detectable amounts without the use of radioactivity. The same sperm from a single male delta F508 carrier were simultaneously typed for the presence of the sex chromosomes to verify the ratio of X- to Y-bearing sperm and to determine the association, if any, between sex and delta F508 in male gametes. We have demonstrated that there is a significant difference in the proportions of 'normal' and 'delta F508' sperm (X2 = 7.36, p < 0.01), although when the same sperm are sexed the difference between delta F508/X and delta F508/Y sperm is not significant (X2 = 1.71, p = 0.192). Single sperm typing can address questions about segregation distortion in man, and it is unlikely that sex ratio distortion for CF carriers is due to events which occur pre-fertilisation. As these data are from one individual only, they should be confirmed for other male carriers, including those with different CF mutations.

Alleles↗

PubMed2006

Absence of significant associations between four AKT1 SNP markers and schizophrenia in the Taiwanese population.

AKT1 (V-akt murine thymoma viral oncogene homolog 1) is a protein kinase isoform of AKT. Five single-nucleotide polymorphisms, rs3803300, rs1130214, rs3730358, rs2498799 and rs2494732, at the genomic region of AKT1 have been reported to be significantly associated with schizophrenia. We tested for the presence of these five single-nucleotide polymorphisms in a Taiwanese population by genotyping 218 co-affected schizophrenia families. Both single locus and haplotypes analyses showed no association of these single-nucleotide polymorphisms with schizophrenia. These findings fail to support AKT1 as a susceptibility gene for schizophrenia in the Taiwanese population.

Genetic Markers↗

PubMed1980

The assignment of four new loci, including the coumarin sensitivity locus couA, to linkage group VII of Dictyostelium discoideum.

The assignment to linkage group VII of the coumarin sensitivity mutation couA351, which leads to a loss of colony-forming ability on agar containing coumarin, was established using the linkage group VII markers cobA1 and tsgK21. Complementation of the couA351 and bsgA5 mutations was an effective method of selecting heterozygous diploids at 21 +/- 1 degree C, i.e. without requiring a temperature sensitivity mutation. A morphological mutation, frtB353, which affects the distribution of fruiting bodies was also assigned to linkage group VII. Both the couA351 and frtB353 mutations were discovered in the tsgK21 strain NP187. Eight independently isolated, recessive mutations leading to resistance of 300 micrograms CoCl2 ml-1 were allelic with the cobA1 mutation. The partially dominant cob-353 mutation was shown to map in linkage group VII on the basis of its segregation relative to the couA351 and tsgK21 mutations and is almost certainly an allele of the cobA locus. These results are consistent with there being only a single locus at which mutations can lead to resistance to high concentrations of CoCl2. Two temperature sensitivity mutations tsgM357 and tsgG4 were also assigned to linkage group VII.

Chromosome Mapping↗

PubMed1989

Genetic modulation of the senescent phenotype in Homo sapiens.

While it is important to search for unifying mechanisms of aging among a variety of model systems, evolutionary arguments suggest that the pathophysiological details of senescence may be, to some extent, species specific. Moreover, in species that are characterized by extensive genetic heterogeneity, such as our own, one is likely to find kindreds with both "private" and "public" markers of aging. Crude estimates of the number of loci with the potential to modulate aspects of the senescent phenotype of man suggest that thousands of genes could be involved. No single locus appears to modulate all features. Some affect predominantly a single aspect ("unimodal progeroid syndromes"); familial Alzheimer's disease is discussed as a prototype. Linkage studies indicate genetic heterogeneity for autosomal dominant forms of the disease. Some loci affect multiple aspects of the phenotype ("segmental progeroid disorders"); the prototype is Werner's syndrome, an autosomal recessive. Cells from homozygotes behave like mutator strains and undergo accelerated senescence in vitro. Elucidation of the biochemical genetic basis of such abiotrophic disorders may shed light on specific aging processes in man.

Aging↗

PubMed1993

Two-locus models of disease: comparison of likelihood and nonparametric linkage methods.

The power to detect linkage for likelihood and nonparametric (Haseman-Elston, affected-sib-pair, and affected-pedigree-member) methods is compared for the case of a common, dichotomous trait resulting from the segregation of two loci. Pedigree data for several two-locus epistatic and heterogeneity models have been simulated, with one of the loci linked to a marker locus. Replicate samples of 20 three-generation pedigrees (16 individuals/pedigree) were simulated and then ascertained for having at least 6 affected individuals. The power of linkage detection calculated under the correct two-locus model is only slightly higher than that under a single locus model with reduced penetrance. As expected, the nonparametric linkage methods have somewhat lower power than does the lod-score method, the difference depending on the mode of transmission of the linked locus. Thus, for many pedigree linkage studies, the lod-score method will have the best power. However, this conclusion depends on how many times the lod score will be calculated for a given marker. The Haseman-Elston method would likely be preferable to calculating lod scores under a large number of genetic models (i.e., varying both the mode of transmission and the penetrances), since such an analysis requires an increase in the critical value of the lod criterion. The power of the affected-pedigree-member method is lower than the other methods, which can be shown to be largely due to the fact that marker genotypes for unaffected individuals are not used.

Chromosome Mapping↗

PubMed2006

Clustering of haplotypes based on phylogeny: how good a strategy for association testing?

Haplotypes are now widely used in association studies between markers and disease susceptibility locus. However, when a large number of markers are considered, the number of possible haplotypes increases leading to two problems: an increased number of degrees of freedom that may result in a lack of power and the existence of rare haplotypes that may be difficult to take into account in the statistical analysis. In a recent paper, Durrant et al proposed a method, CLADHC, to group haplotypes based on distance matrices and showed that this could considerably increase the power of the association test as compared to either single-locus analysis or haplotype analysis without prior grouping. Although the authors considered different one-disease-locus susceptibility models in their simulations, they did not study the impact of the linkage disequilibrium (LD) pattern and of the susceptibility allele frequency on their conclusions. Here, we show, using haplotype data from five regions of the genome of different lengths and with different LD patterns, that, when a single disease susceptibility locus is simulated, the prior grouping of haplotypes based on the algorithm of Durrant et al does not increase the power of association testing except in very particular situations of LD patterns and allele frequencies.

Computer Simulation↗

PubMed1987

Electrophysiological actions of cocaine on noradrenergic neurons in rat locus ceruleus.

Extracellular microelectrode experiments were conducted to study the effects of cocaine HCl on the activity of spontaneously firing single locus ceruleus (LC) noradrenergic neurons in vivo. The responses of single identified noradrenergic LC neurons to the systemic (i.v.) administration of cocaine were observed over a wide range of doses (0.0625-2.0 mg/kg). The spontaneous activity of all LC neurons receiving doses greater than the threshold dose (0.0625 mg/kg) was inhibited in a dose-dependent manner. The local anesthetics, procaine and mepivacaine, did not affect LC neuronal activity, action potential amplitude or slope. The inhibitory effects of cocaine on spontaneous LC neuron activity was reversed by the subsequent i.v. administration of the specific alpha-2 adrenoceptor antagonist, piperoxone, but not the opiate receptor antagonist, naloxone. Pretreatment with another alpha-2 adrenoceptor antagonist, yohimbine (5 mg/kg i.p.), attenuated significantly the inhibition of spontaneous LC activity elicited by i.v. cocaine. Intravenous cocaine produced a brief increase in mean arterial pressure which did not appear to be correlated with the more sustained inhibition of LC neurons. Reserpine pretreatment (10 mg/kg i.p.) attenuated significantly the inhibitory effects of cocaine on LC activity. These results suggest that the inhibition of spontaneous LC neuron activity by i.v. cocaine is most likely mediated by an augmented action of catecholamines at central alpha-2 adrenoceptors and not by the local anesthetic effects of cocaine.

Action Potentials↗

PubMed2006

Molecular genotyping of Candida parapsilosis group I clinical isolates by analysis of polymorphic microsatellite markers.

Candida parapsilosis, a pathogenic yeast, is composed of three newly designated genomic species that are physiologically and morphologically indistinguishable. Nosocomial infections caused by group I C. parapsilosis are often associated with the breakdown of infection control practices and the contamination of medical devices, solutions, and indwelling catheters. Due to the low levels of nucleotide sequence variation that are observed, an investigation of the size polymorphisms in loci harboring microsatellite repeat sequences was applied for the typing of C. parapsilosis group I isolates. PCR primer sets that flank the microsatellite repeats for seven loci were designed. Following amplification by PCR, the size of each amplification product was determined automatically by capillary electrophoresis. A total of 42 C. parapsilosis group I isolates were typed by microsatellite analysis, and their profiles were compared to the hybridization profiles obtained by use of the Cp3-13 DNA probe. A high degree of discrimination (discriminatory power = 0.971) was observed by microsatellite analysis. The number of different alleles per locus ranged from 14 for locus B to 5 for locus C. Microsatellite analysis detected 30 different microsatellite genotypes, with 24 genotypes represented by a single isolate. Comparison of the genotypes obtained by microsatellite analysis and those obtained by analysis of the Cp3-13 hybridization profiles showed that they were similar, and these methods were able to identify related and unrelated isolates. Some discrepancies were observed between the methods and may be due to higher mutation rates and/or homoplasy by microsatellite markers. Identical results were observed between microsatellite analysis and Cp3-13 DNA hybridization profile analysis for C. parapsilosis isolates obtained from two patients, demonstrating the reproducibilities of the methods in vivo. Identical microsatellite profiles were observed for isolates displaying different phenotypic switching morphologies. Indistinguishable Cp3-13 DNA hybridization profiles were observed for six epidemiologically related isolates; however, only three of six primary isolates had identical microsatellite profiles. Size variation at a single locus was observed for three of six isolates obtained either after the outbreak period or from a different body site, suggesting the potential of the method to detect microevolutionary events. Interestingly, for most loci a single allele per strain was observed; in contrast, two alleles per locus were observed for some strains, and consistent with the findings for natural isolates, some isolates may be aneuploid. Due to the potential for high throughput, reproducibility, and discrimination, microsatellite analysis may provide a robust and efficient method for the genotyping of large numbers of C. parapsilosis group I isolates.

Alleles↗

PubMed2004

Natural genetic variation in Arabidopsis identifies BREVIS RADIX, a novel regulator of cell proliferation and elongation in the root.

Mutant analysis has been tremendously successful in deciphering the genetics of plant development. However, less is known about the molecular basis of morphological variation within species, which is caused by naturally occurring alleles. In this study, we succeeded in isolating a novel regulator of root growth by exploiting natural genetic variation in the model plant Arabidopsis. Quantitative trait locus analysis of a cross between isogenized accessions revealed that a single locus is responsible for approximately 80% of the variance of the observed difference in root length. This gene, named BREVIS RADIX (BRX), controls the extent of cell proliferation and elongation in the growth zone of the root tip. We isolated BRX by positional cloning. BRX is a member of a small group of highly conserved genes, the BRX gene family, which is only found in multicellular plants. Analyses of Arabidopsis single and double mutants suggest that BRX is the only gene of this family with a role in root development. The BRX protein is nuclear localized and activates transcription in a heterologous yeast system, indicating that BRX family proteins represent a novel class of transcription factors. Thus, we have identified a novel regulatory factor controlling quantitative aspects of root growth.

Amino Acid Sequence↗

PubMed1993

A 5-hydroxytryptamine2 agonist augments gamma-aminobutyric acid and excitatory amino acid inputs to noradrenergic locus coeruleus neurons.

We examined the effects of the 5-hydroxytryptamine2 receptor agonist, (+-)1-(2,5-dimethoxy-4-iodophenyl)-2-aminopropane, on spontaneous and evoked discharge of locus coeruleus neurons in the rat. Extracellular recordings were obtained from single locus coeruleus neurons while (+-)1-(2,5-dimethoxy-4-iodophenyl)-2-aminopropane was injected systemically or locally into the locus coeruleus. Systemic, but not local, administration of (+-)1-(2,5-dimethoxy-4-iodophenyl)-2-aminopropane decreased spontaneous discharge of locus coeruleus neurons in a dose-dependent manner while simultaneously increasing responses evoked by somatosensory stimulation, consistent with previous studies using 5-hydroxytryptamine2 agonists. Increased responsiveness was observed after both low- and high-intensity stimulation and, in the latter, resulted from the addition of a second, longer latency response after (+-)1-(2,5-dimethoxy-4-iodophenyl)-2-aminopropane administration, when cells typically responded to each stimulation with two driven spikes instead of one. Both of these effects could be completely reversed by systemic administration of the 5-hydroxytryptamine2 receptor antagonist, ketanserin. Furthermore, we report that: (i) the (+/-)1-(2,5-dimethoxy-4-iodophenyl)-2-aminopropane-induced decrease in spontaneous firing was blocked by local infusion of the GABA antagonists bicuculline or picrotoxin into the locus coeruleus, but not by local infusion of the alpha-2 adrenoceptor antagonist, idazoxan; and (ii) the enhancement of locus coeruleus sensory responses after high-intensity stimulation was blocked by local application of the selective antagonist of N-methyl-D-aspartate receptors, 2-amino-5-phosphonopentanoic acid, but not by local infusion of the preferential antagonist of non-N-methyl-D-aspartate receptors, 6-cyano-7-nitroquinoxaline-2,3-dione. Together, these results lead us to propose that systemic 5-hydroxytryptamine2 agonists influence locus coeruleus indirectly, causing tonic activation of a GABAergic input to the locus coeruleus, and facilitating sensory inputs that act via excitatory amino acid receptors within locus coeruleus.

2-Amino-5-phosphonovalerate↗

PubMed1997

Linkage of multilocus components of variance to polymorphic markers.

Haseman & Elston (1972) introduced a sib pair method using classical regression analysis to detect linkage between a polymorphic marker locus and any quantitative trait locus. Most of the diseases mapped to date follow simple Mendelian, single locus transmission. But there are many familial diseases that do not follow simple Mendelian segregation, for example diabetes, several forms of cancer, etc. In this paper, we extend Haseman and Elston's sib pair method to two unlinked quantitative trait loci each linked to one of two unlinked polymorphic marker loci. For the two-locus epistatic model, we give a general formulation of the complete regression model and details of the regression coefficients in terms of variance components.

Analysis of Variance↗

PubMed1994

Lupus susceptibility loci in New Zealand mice.

Susceptibility to systemic lupus erythematosus has been unequivocally established to be an inherited trait, but the exact genes and how they confer susceptibility remain largely unknown. In this study of (NZB x NZW)F2 intercross mice, we used linkage analysis of markers covering > 90% of the autosomal genome and identified eight susceptibility loci (Lbw1 to -8, chromosomes 17, 4-7, 18, 1, 11, respectively) associated with antichromatin autoantibody production, glomerulonephritis, and/or mortality. Only one locus, the major histocompatibility complex, was linked to all three traits. Two other loci were associated with both glomerulonephritis and mortality, whereas the remaining loci were linked to one of the above traits. Two additional loci (Sbw1 and -2) that contributed to splenomegaly were also identified. The Sbw2 locus mapped to the identical region as Lbw2, a locus on chromosome 4 linked to glomerulonephritis and mortality, suggesting a single locus with pleiotropic effects. The results indicate that the immunopathologic features of lupus are affected by distinct, but additive, genetic contributions. Studies to determine the nature of the genes associated with these loci should help define the genetic mechanisms involved in this systemic autoimmune disease.

Animals↗

PubMed1996

Molecular dissection of a major gene effect on a quantitative trait: the level of alcohol dehydrogenase expression in Drosophila melanogaster.

A molecular mapping experiment shows that a major gene effect on a quantitative trait, the level of alcohol dehydrogenase expression in Drosophila melanogaster, is due to multiple polymorphisms within the Adh gene. These polymorphisms are located in an intron, the coding sequence, and the 3' untranslated region. Because of nonrandom associations among polymorphisms at different sites, the individual effects combine (in some cases epistatically) to produce "superalleles" with large effect. These results have implications for the interpretation of major gene effects detected by quantitative trait locus mapping methods. They show that large effects due to a single locus may be due to multiple associated polymorphisms (or sequential fixations in isolated populations) rather than individual mutations of large effect.

Alcohol Dehydrogenase↗