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At least 1,711 records · Page 95Linked to original sources
PubMed2005

Computational genetics: from mouse to human?

In this article, we describe a novel computational-analysis method that rapidly identified the genetic basis for several trait differences among inbred mouse strains. This approach enables researchers to identify a causative genetic factor by correlating a pattern of observable physiological or pathological differences among selected inbred strains with a pattern of genetic variation. Compared with conventional methods used for mouse genetic analysis, which require many years to produce results, this haplotype-based computational analysis can be rapidly performed. We discuss the factors affecting the performance and precision of this computational method. Although it currently can analyze traits of limited genetic complexity in mouse, the potential application of this genetic-analysis method to other experimental organisms, and possibly humans, is evaluated.

Animals↗
PubMed2005

A major bristle QTL from a selected population of Drosophila uncovers the zinc-finger transcription factor poils-au-dos, a repressor of achaete-scute.

Traditional screens aiming at identifying genes regulating development have relied on mutagenesis. Here, we describe a new gene involved in bristle development, identified through the use of natural variation and selection. Drosophila melanogaster bears a pattern of 11 macrochaetes per heminotum. From a population initially sampled in Marrakech, a strain was selected for an increased number of thoracic macrochaetes. Using recombination and single nucleotide polymorphisms, the factor responsible was mapped to a single locus on the third chromosome, poils au dos, that encodes a zinc-finger-ZAD protein. The original, as well as new, presumed null, alleles of poils au dos, is associated with ectopic achaete-scute expression that results in the additional bristles. This suggests a possible role for Poils au dos as a repressor of achaete and scute. Ectopic expression appears to be independent of the activity of known cis-regulatory enhancer sequences at the achaete-scute complex that mediate activation at specific sites on the notum. The target sequences for Poils au dos activity were mapped to a 14 kb region around scute. In addition, we show that pad interacts synergistically with the repressor hairy and with Dpp signaling in posterior and anterior regions of the notum, respectively.

Alleles↗
PubMed2000

A new statistic for the analysis of association between trait and polymorphic marker loci.

Inference for detecting the existence of an association between a diallelic marker and a trait locus is based on the chi-squared statistic with one degree of freedom. For polymorphic markers with m alleles (2), three approaches are mainly used in practice. First, one may use Pearson's chi-squared statistic with m-1 degrees of freedom (d.f.) but this leads to a loss in test power. Second, one can select an allele to be the most associated and then collapse the other allele categories into a single class. This reduces in a biased way, the locus to a diallelic system. Third, one may use the Terwilliger [J.D. Terwilliger, Am. J. Hum. Genet. 56 (1995) 777] likelihood ratio statistic which has a non-standard unknown limiting probability distribution. In this paper, we propose a new statistic, L(D), based on the second testing approach. We derive the asymptotic probability distribution of L(D) in an easy way. Simulation studies show that L(D) is more powerful than Pearson's chi-squared statistic with m-1 d.f.

Alleles↗
PubMed1997

Echinococcosis.

Hydatids, the intermediate stages, or metacestodes, of the tapeworm genus, Echinococcus, present a major immunological problem; they survive, grow and metastasize in immunized hosts which are protected against reinfection and possess effector mechanisms capable of killing the parasite. Explanations for this state of concomitant immunity have been made from investigations of avoidance strategies, genetics and quantitative hydatid growth. The latter study suggests that the host-parasite relationship is sustained as a dynamic equilibrium between parasite growth and acquired immunity, the balance being subject to mutual regulation and including the possibility of spontaneous rejection of the parasite. Two immunoregulatory, or cytokine-like, factors have been detected in hydatids of Echinococcus spp. One appears to be a mediator of the previously reported mitogenic effects of hydatids. Recent evidence has linked these effects to generation of T-suppressor populations. The second factor interferes with the interaction of macrophages and T-cells, mimics the effect of metacestode infection in impairing the accessory action of macrophages in lymphoproliferative responses, and is suppressive for rosette-forming cell responses against third-party antigens. It is suggested that these factors form part of a primary homeostatic mechanism regulating hydatid growth and immunity.

Animals↗
PubMed2003

The genetics of gene expression and gene mapping.

A recent publication has shown that a significant portion of gene expression levels are under genetic control in different organisms, that there are hotspot regions in the genome that control the expression of many other genes, and how gene expression data can be used to localize genes that affect clinical traits.

Adipose Tissue↗
PubMed1999

From complex traits to complex alleles.

Several recent studies using natural populations of Drosophila show that one must be very careful when sorting among the large number of molecular polymorphisms found at most loci to identify the nucleotide changes responsible for phenotypic variation in complex traits. Indeed, several mutations within a single allele can interact to generate the overall observed effect. The results are instructive both for those interested in the genetics of evolutionary change and for those attempting to ferret out the genetic basis of complex human diseases.

Alleles↗
PubMed2002

P300 amplitude in adolescent twins discordant and concordant for alcohol use disorders.

The sons of alcoholics have repeatedly been found to have reduced P300 amplitude. Further, quantitative behavioral genetic and molecular genetic studies indicating a genetic influence on P300 amplitude have fueled speculation that this component may be a biological vulnerability marker for alcoholism. To further explore this possibility, we examined P300 in adolescent twin pairs from an epidemiological sample who were (a) discordant for alcohol abuse/dependence, (b) concordant for alcohol abuse/dependence, or (c) concordant for the absence of alcohol abuse/dependence and other relevant disorders. For discordant pairs, the alcohol abusing/dependent twins' amplitude did not differ from that of non-alcoholic co-twins. Pairs free of psychopathology had greater amplitudes than both alcoholism discordant and concordant pairs. P300 amplitude was more similar in monozygotic than dizygotic discordant pairs, suggesting a genetic influence on P300 amplitude in this group. The findings are consistent with P300 amplitude being a marker of vulnerability to alcohol use disorders.

Adolescent↗
PubMed2004

Aging as an evolved characteristic - Weismann's theory reconsidered.

Theories of aging have become significantly more important because of discoveries which indicate that aging is not universal or inevitable and which therefore indicate that major medical intervention in aging is possible. Directions of anti-aging research could be significantly influenced by basic theories of aging. Weismann proposed in 1882 that aging was an evolved genetically programmed adaptation that had a species benefit. Since then this idea has been largely replaced by various theories in which aging is not an adaptation but results from accumulated adverse mutations or is an adverse side effect of some essential process. Arguments are presented to the effect that aging is an evolved beneficial characteristic and is therefore likely to result from a more complex and structured mechanism than if it resulted from more random processes such as mutation accumulation. Further, aging appears to be one of a number of related and interactive life-cycle characteristics including age-at-puberty suggesting that it might be controlled by similar biological mechanisms.

Adaptation, Biological↗
PubMed2006

Correlation analysis of economic traits in Liaoning new breed of cashmere goats using microsatellite DNA markers.

The economic traits of Liaoning new breed of cashmere goats, a special Chinese genetic resource, were analyzed in 150 animals by typing 11 microsatellite loci. The association between three economic traits (body weight, cashmere yield and fineness) in this new breed of goats and the marker genotypes were analyzed. The results show that: AA and BC at LSCV13, DE at IDVGA64 and BB at BMS2782 were favorable genotypes for body weight. AB at LSCV13, AD and BE at CSSM11, BD and CC at IDVGA64, BC and DE at BMS2782 were favorable genotypes for cashmere yield. AA at CSSM11, BC and DE at IDVGA64, CD at BMS2782 were favorable genotypes for cashmere fineness.

Animals↗
PubMed2006

Comparison of different foreground and background selection methods in marker-assisted introgression.

Three different methods for foreground selection and four different methods for background selection were compared in terms of the efficiency of marker-assisted introgression of a QTL allele from a donor line into a recipient line and also in terms of the recovery of the recipient genetic background. The results showed that for the introgression of a donor QTL allele, a direct selection on the QTL itself (when the QTL genotype can be directly identified) would ensure that the allele is successfully introgressed and rapidly fixed. However, when a direct selection on the QTL is not feasible, an indirect selection using two closely linked flanking markers can be used, which also shows similar results. For the recovery of the recipient genetic background, if the goal is to recover the whole genetic background of the recipient, genomic similarity selection or marker index selection would be the best choice: Only three generations of backcrosses were required to recover over 98% of the recipient genome. Whereas if the goal is to recover certain background traits of the recipient, MBLUP selection would give the best results, which achieved not only over 99% recovery of the recipient QTL alleles for the background traits after three generations of backcrosses, but also showed the best genetic improvement of these traits.

Breeding↗
PubMedDate not supplied

Offspring sex ratio is not associated with parental GSTT1 and GSTM1 null genotypes.

The present study evaluated the association between offspring sex ratio and parental inherited variations of xenobiotic metabolism by glutathione S-transferase (GST) T1 and GSTM1. Polymorphisms of GSTT1 and GSTM1 were investigated in 235 Iranian Muslims (153 males, 82 females) using polymerase chain reaction-based method. Statistical analysis of 890 offspring in the study families revealed that there was no association between GSTM1 null genotype of either the fathers (OR=1.28; 95% CI=0.88-1.85; P=0.17) or mothers (OR=0.77; 95% CI=0.49-1.19; P=0.22) and offspring sex ratio. There was no association between paternal GSTT1 null genotype and sex ratio in offspring (OR=1.04; 95% CI=0.71-1.54; P=0.84), whereas there was a weak association between maternal GSTT1 null genotype and offspring sex ratio (OR=1.54; 95% CI=1.0-2.38; P=0.05). Combination of parental GSTT1 and GSTM1 genotypes showed no association with offspring sex ratio.

Female↗
PubMed2000

Adaptation of the extended transmission/disequilibrium test to distinguish disease associations of multiple loci: the Conditional Extended Transmission/Disequilibrium Test.

Linkage and association studies in complex diseases are used to identify and fine map disease loci. The process of identifying the aetiological polymorphism, the molecular variant responsible for the linkage and association of the chromosome region with disease, is complicated by the low penetrance of the disease variant, the linkage disequilibrium between physically-linked polymorphic markers flanking the disease variant, and the possibility that more than one polymorphism in the most associated region is aetiological. It is important to be able to detect additional disease determinants in a region containing a cluster of genes, such as the major histocompatibility complex (MHC) region on chromosome 6p21. Some methods have been developed for detection of additional variants, such as the Haplotype Method, Marker Association Segregation Chi-squares (MASC) Method, and the Homozygous Parent Test. Here, the Extended Transmission/Disequilibrium Test is adapted to test for association conditional on a previously associated locus. This test is referred to as the Conditional Extended TDT (CETDT). We discuss the advantages of the CETDT compared to existing methods and, using simulated data, investigate the effect of polymorphism, inheritance, and linkage disequilibrium on the CETDT.

Genetic Diseases, Inborn↗
PubMed2001

A powerful and rapid approach to human genome scanning using small quantities of genomic DNA.

Dense maps of short-tandem-repeat polymorphisms (STRPs) have allowed genome-wide searches for genes involved in a great variety of diseases with genetic influences, including common complex diseases. Generally for this purpose, marker sets with a 10 cM spacing are genotyped in hundreds of individuals. We have performed power simulations to estimate the maximum possible intermarker distance that still allows for sufficient power. In this paper we further report on modifications of previously published protocols, resulting in a powerful screening set containing 229 STRPs with an average spacing of 18.3 cM. A complete genome scan using our protocol requires only 80 multiplex PCR reactions which are all carried out using one set of conditions and which do not contain overlapping marker allele sizes. The multiplex PCR reactions are grouped by sets of chromosomes, which enables on-line statistical analysis of a set of chromosomes, as sets of chromosomes are being genotyped. A genome scan following this modified protocol can be performed using a maximum amount of 2.5 micrograms of genomic DNA per individual, isolated from either blood or from mouth swabs.

Alleles↗
PubMed2006

Natural history of Ashkenazi intelligence.

This paper elaborates the hypothesis that the unique demography and sociology of Ashkenazim in medieval Europe selected for intelligence. Ashkenazi literacy, economic specialization, and closure to inward gene flow led to a social environment in which there was high fitness payoff to intelligence, specifically verbal and mathematical intelligence but not spatial ability. As with any regime of strong directional selection on a quantitative trait, genetic variants that were otherwise fitness reducing rose in frequency. In particular we propose that the well-known clusters of Ashkenazi genetic diseases, the sphingolipid cluster and the DNA repair cluster in particular, increase intelligence in heterozygotes. Other Ashkenazi disorders are known to increase intelligence. Although these disorders have been attributed to a bottleneck in Ashkenazi history and consequent genetic drift, there is no evidence of any bottleneck. Gene frequencies at a large number of autosomal loci show that if there was a bottleneck then subsequent gene flow from Europeans must have been very large, obliterating the effects of any bottleneck. The clustering of the disorders in only a few pathways and the presence at elevated frequency of more than one deleterious allele at many of them could not have been produced by drift. Instead these are signatures of strong and recent natural selection.

Brain↗
PubMed2005

Synthesis and screening of anilides having olefinic and alkyl moiety in the side chain as chemical hybridizing agents for wheat (Triticum aestivum L.).

Induction of male sterility by deployment of chemical hybridizing agents (CHAs) holds immense potential in heterosis breeding of wheat. A total of 21 anilides having different aromatic substitutions and side-chain variation were synthesized and screened as CHAs on three genotypes of wheat viz., PBW 343, HW 2046, and HD 2733, at winter season. Various anilides having vinyl moiety in the acyl side chain were synthesized by condensation between substituted anilines with different esters or acid chlorides. Another lead in the form of N-alkyl anilines also became evident. The percent male sterility data caused by CHAs revealed the significant contribution of anilides containing vinyl double bond incorporated in the form of closed ring structure viz., furyl moiety as the side chain. 4'-Fluoro-furyl anilide (1) and 4'-bromo-furyl anilide (2) are found to be promising lead CHAs for the design of highly active molecules. QSAR analysis revealed a direct relationship of field effect exemplified by the Swain-Lupton constant F(p) for the aromatic substitution but an inverse relationship of molar refractivity MR for the side chain. The negative influences of parachor for the acyl domain have been underlined. The real guiding principle for selectivity of CHA action was found to be the pi value. The CHAs act by mimicking UDP-glucose, the key substrate in the synthesis of callose, or lead to an imbalance in acid-base equilibrium in pollen mother cells resulting in dissolution of callose wall by premature callase secretion.

Anilides↗
PubMed2000

AFLP fingerprinting for assessing intraspecific variation and genome mapping in mites.

Molecular genetic techniques have come a long way in the last decade. With the advent of PCR, genetic markers are now accessible for all organisms, including mites. However, there is usually a trade-off between the accuracy of the molecular technique or genetic marker and expediency. In mites, many molecular techniques are not applicable due to their small size. Here we describe a relatively new molecular fingerprinting technique, amplified fragment length polymorphism (AFLP), which is currently used widely in plant genomic research. We outline the AFLP procedure adapted for mites, show results using this technique from our own research and discuss the benefits and limitations of AFLPs for assessing genetic variation and for genome mapping. It is our intention to highlight the possible use of AFLPs as genetic markers with a broad application in acarological research.

Animals↗
PubMed2001

Identifying genetic influences on sleep: an approach to discovering the mechanisms of sleep regulation.

Comparisons of sleep patterns of various inbred strains of mice have revealed differences in daily amounts of slow-wave sleep and rapid-eye movement sleep, in circadian patterns of sleep, and in some parameters of the electroencephalograms both in healthy mice and in mice undergoing microbial infections. Technical considerations will probably be an important variable in achieving consensus between different independent studies that use a genetic approach to identify sleep-regulatory genes or mechanisms. However, despite such differences, current data suggest that both normal sleep and various sleep disorders either have a genetic basis or are influenced by genetically determined physiologic or environmental predispositions. Excessive sleepiness, abnormal sleep patterns, nonrestorative sleep, and fatigue are becoming increasingly pervasive in modern society. Identifying genes that influence vigilance may ultimately contribute to a better understanding of the processes that control normal sleep and contribute to sleep disorders and may eventually promote the development of interventions to prevent or alleviate these disabling medical conditions.

Animals↗
PubMed2002

Estimation of sib-pair IBD sharing and multipoint polymorphism information content by linear regression.

A simple method of estimating IBD sharing (pi) of sibling pairs from multipoint genotype data based on linear regression is presented. The new method is an extension of that developed by Fulker, Cherny, and Cardon (1995) and involves a measure of sib-pair specific information, W, defined as the difference between the unconditional variance of pi and the conditional variance of pi given the marker genotype data. When markers are not fully informative, the W method provides estimates closer to those obtained from the exact hidden Markov method (HMM) than the original Fulker method. Using W, we also derive a generalisation for the polymorphism information content (PIC) for multiple markers. This multipoint polymorphism information content (MPIC) can be evaluated at any location along a marker map and is proportional to the noncentrality parameter for linkage. We illustrate MPIC by assessing the relative information content of single nucleotide polymorphism (SNP) and microsatellite markers.

Alleles↗