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At least 1,603 records · Page 89Linked to original sources
PubMed2006

Distribution of genetic variation within and among local populations of Arabidopsis thaliana over its species range.

A detailed description of local population structure in Arabidopsis thaliana is presented, including an assessment of the genetic relatedness of individuals collected from the same field. A hierarchical sample of four individuals from 37 local populations, including North America, England, Eastern and Western Europe, and Asia, and a selection of ecotypes, were analysed for variation in Adh, ChiA, FAH1, F3H, Rpm1, Rps5, and five microsatellite loci. Twenty-eight of the 37 population samples contained individuals with identical multilocus haplotypes, 12 of which were fixed for a single haplotype. These monomorphic populations were evenly distributed over the species range. Only in North America did we find a single multilocus haplotype shared among different populations, perhaps indicating a continental founder event. Despite the occurrence of local inbreeding, a considerable amount of genetic variation was found segregating within and among local populations. A novel analysis of haplotype differences reveals that genetic differentiation occurs at every geographic scale in A. thaliana, where we find a surprising under-representation of recent migrants between local populations. This leads us to hypothesize that most dispersal between A. thaliana populations is by pollen rather than seed. Based on the structure of A. thaliana populations, it appears that regional groups of local populations may provide the most appropriate genetic material for linkage disequilibrium mapping of adaptive traits.

Arabidopsis↗
PubMed2006

Identification of QTL controlling root growth response to phosphate starvation in Arabidopsis thaliana.

One of the responses of plants to low sources of external phosphorus (P) is to modify root architecture. In Arabidopsis thaliana plantlets grown on low P, the primary root length (PRL) is reduced whereas lateral root growth is promoted. By using the Bay-0 x Shahdara recombinant inbred line (RIL) population, we have mapped three quantitative trait loci (QTL) involved in the root growth response to low P. The Shahdara alleles at these three QTL promote the response of the primary root to low P (i.e., root length reduction). One of these QTL, LPR1, located in a 2.8 Mb region at the top of chromosome 1, explains 52% of the variance of the PRL. We also detected a single QTL associated with primary root cell elongation in response to low P which colocalizes with LPR1. LPR1 does not seem to be involved in other typical P-starvation responses such as growth and density of root hairs, excretion of acid phosphatases, anthocyanin accumulation or the transcriptional induction of the P transporter Phtl;4. LPR1 might highlight new aspects of root growth that are revealed specifically under low P conditions.

Alleles↗
PubMed1983

Genetics of natural resistance to Sendai virus infection in mice.

The genetics of resistance to a naturally occurring respiratory infection caused by Sendai virus was examined in F1, F2, and backcross progeny of resistant C57BL/6J and susceptible DBA/2J mice and in 25 recombinant inbred strains. An intranasal inoculum of 0.1 50% tissue culture infective dose (low dose) of Sendai virus caused 0% mortality in C57BL/6J and F1 mice and 73% mortality in DBA/2J mice. An inoculum of 1.0 50% tissue culture infective dose (high dose) caused 3, 0, and 89% mortality in C57BL/6J, F1, and DBA/2J mice, respectively. Low-dose infection caused 36% mortality in F1 X DBA/2J hybrids and 0% mortality in F2 hybrids. High-dose infection caused 29 and 32% mortality in F1 X DBA/2J and F2 hybrids, respectively. Resistance was not linked to H-2 haplotype, coat color, or sex. High-dose infection caused deaths in 12 recombinant inbred strains, and the strain distribution pattern was concordant with that of a chromosome 1 marker, Sas-1, in 20 of 25 strains (P less than 0.01). Resistance therefore behaved as a simple Mendelian dominant trait which presumptively mapped to chromosome 1.

Animals↗
PubMed2004

Defensive behavior of honey bees: organization, genetics, and comparisons with other bees.

One key advantage of eusociality is shared defense of the nest, brood, and stored food; nest defense plays an important role in the biology of eusocial bees. Recent studies on honey bees, Apis mellifera, have focused on the placement of defensive activity in the overall scheme of division of labor, showing that guard bees play a unique and important role in colony defense. Alarm pheromones function in integrating defensive responses; honey bee alarm pheromone is an excellent example of a multicomponent pheromonal blend. The genetic regulation of defensive behavior is now better understood from the mapping of quantitative trait loci (QTLs) associated with variation in defensiveness. Colony defense in other eusocial bees is less well understood, but enough information is available to provide interesting comparisons between A. mellifera and other species of Apis, as well as with allodapine, halictine, bombine, and meliponine bees. These comparative studies illustrate the wide variety of evolutionary solutions to problems in colony defense in the Apoidea.

Agonistic Behavior↗
PubMed2006

Relationship patterns in alexithymia: a study using the core conflictual relationship theme method.

BACKGROUND: Alexithymia is a disturbance in regulating affective states. Clinical observations suggest that alexithymic patients relate to others in a specific way. This paper explores whether specific relationship or transference patterns are typical of alexithymia. SAMPLING AND METHODS: Relationship patterns were assessed by means of the Core Conflictual Relationship Theme method, standard categories version. This method examines transference patterns and was applied to clinical interview data collected from a sample (n = 31) of mental health outpatients. Alexithymia was assessed by means of a score on the 20-item Toronto Alexithymia Scale corrected for the degree of depression (measured by the Beck Depression Inventory-II). Data were analysed by means of the leaps and bounds regression algorithm for selecting optimal subsets of indicators and by bootstrapping to determine 95% confidence intervals. RESULTS: First, we observed that alexithymia can be meaningfully explained by typical wishes, typical subjective perceptions of how others respond and one's own typical responses to others. This result indicates that the more marked a patient's alexithymic traits are, the more probable it is that specific transference themes come to the fore. Second, a set of three core indicators of trait alexithymia was mapped: little concern about being good to others, a strong perception of others as cooperative, and weak levels of reacting to others and to conflict by means of somatic symptoms. CONCLUSION: Alexithymia is related to a double interpersonal indifference: not much is expected from others, nor is there a personal urge to fulfill the expectations of others. Moreover, in alexithymia somatic symptoms proved to be non-reactive to interpersonal situations. Implications for diagnosis and treatment are highlighted. Limitations of our study are that alexithymia was only assessed with a self-report measure and that conclusions are based only upon data from a heterogeneous mental health sample.

Adjustment Disorders↗
PubMed1998

Abnormal nonshivering thermogenesis in mice with inherited defects of fatty acid oxidation.

When placed in the cold (4 degreesC), BALB/cByJ mice of both genders rapidly lose body temperature as compared with the control strain, C57BL/6J. This sensitivity to cold resembles that previously described for mice with a defect in nonshivering thermogenesis due to the targeted inactivation of the brown adipocyte-specific mitochondrial uncoupling protein gene, Ucp1. Genetic mapping of the trait placed the gene on chromosome 5 near Acads, a gene encoding the short chain acyl CoA dehydrogenase, which is mutated in BALB/cByJ mice. The analysis of candidate genes in the region indicated a defect only in the expression of Acads. Confirmation of the importance of fatty acid oxidation to thermogenesis came from our finding that mice carrying the targeted inactivation of the long chain acyl CoA dehydrogenase gene (Acadl) are also sensitive to the cold. Both of these mutations attenuate the induction of genes normally responsive to adrenergic signaling in brown adipocytes. These results suggest that the action of fatty acids as regulators of gene expression has been perturbed in the mutant mice. From a clinical perspective, it is important to determine whether defects in thermogenesis may be a phenotype in human neonates with inherited deficiencies in fatty acid beta-oxidation.

Acyl-CoA Dehydrogenase↗
PubMed2005

Haseman-Elston weighted by marker informativity.

In the Haseman-Elston approach the squared phenotypic difference is regressed on the proportion of alleles shared identical by descent (IBD) to map a quantitative trait to a genetic marker. In applications the IBD distribution is estimated and usually cannot be determined uniquely owing to incomplete marker information. At Genetic Analysis Workshop (GAW) 13, Jacobs et al. [BMC Genet 2003, 4(Suppl 1):S82] proposed to improve the power of the Haseman-Elston algorithm by weighting for information available from marker genotypes. The authors did not show, however, the validity of the employed asymptotic distribution. In this paper, we use the simulated data provided for GAW 14 and show that weighting Haseman-Elston by marker information results in increased type I error rates. Specifically, we demonstrate that the number of significant findings throughout the chromosome is significantly increased with weighting schemes. Furthermore, we show that the classical Haseman-Elston method keeps its nominal significance level when applied to the same data. We therefore recommend to use Haseman-Elston with marker informativity weights only in conjunction with empirical p-values. Whether this approach in fact yields an increase in power needs to be investigated further.

Chromosomes, Human, Pair 4↗
PubMed1994

Chromosomal localization of the parathyroid hormone/parathyroid hormone-related protein receptor gene to human chromosome 3p21.1-p24.2.

The human PTH/PTH-related peptide (PTH/PTHrP) receptor could be involved in hereditary disorders of PTH or PTHrP action. Knowledge of the gene's chromosomal location would allow studies linking it to specific disease traits. Therefore, we mapped the human PTH/PTHrP receptor gene by polymerase chain reaction of human/rodent somatic cell hybrid panels using oligonucleotide primers designed to amplify a portion of the gene from genomic DNA. The PTH/PTHrP gene was unambiguously assigned to the short arm of human chromosome 3, in the region designated 3p21.1-p24.2. Analysis of a second chromosome 3-specific mapping panel suggests that the gene is located near the 3p21.2-p21.3 boundary. The availability of highly polymorphic markers located in this region will permit exploration of the PTH/PTHrP receptor locus in genetic linkage searches for the causes of bone, calcium, and other potential disorders.

Animals↗
PubMed2002

Chromosome 3 linked frontotemporal dementia (FTD-3).

BACKGROUND: The authors have identified and studied a large kindred in which frontotemporal dementia (FTD) is inherited as an autosomal dominant trait. The trait has been mapped to the pericentromeric region of chromosome 3. METHODS: The authors report on the clinical, neuroimaging, neuropsychological, and pathologic features in this unique pedigree collected during 17 years of study. RESULTS: Twenty-two individuals in three generations have been affected; the age at onset varies between 46 and 65 years. The disease presents with a predominantly frontal lobe syndrome but there is also evidence for temporal and dominant parietal lobe dysfunction. Late in the illness individuals develop a florid motor syndrome with pyramidal and extrapyramidal features. Structural imaging reveals generalized cerebral atrophy; H2 15 O-PET scanning in two individuals relatively early and late in the disease shows a striking global reduction in cerebral blood flow affecting all lobes. On macroscopic pathologic examination, there is generalized cerebral atrophy affecting the frontal lobes preferentially. Microscopically, there is neuronal loss and gliosis without specific histopathologic features. CONCLUSIONS: FTD-3 shares clinical and pathologic features with other forms of FTD and fulfills international consensus criteria for FTD. There is involvement of the parietal lobes clinically, radiologically, and pathologically in FTD-3 in contrast to some forms of FTD. This more diffuse involvement of the cerebral cortex leads to a distinctive, global pattern of reduced blood flow on PET scanning.

Autopsy↗
PubMed2006

A statistical framework for genetic association studies of power curves in bird flight.

How the power required for bird flight varies as a function of forward speed can be used to predict the flight style and behavioral strategy of a bird for feeding and migration. A U-shaped curve was observed between the power and flight velocity in many birds, which is consistent to the theoretical prediction by aerodynamic models. In this article, we present a general genetic model for fine mapping of quantitative trait loci (QTL) responsible for power curves in a sample of birds drawn from a natural population. This model is developed within the maximum likelihood context, implemented with the EM algorithm for estimating the population genetic parameters of QTL and the simplex algorithm for estimating the QTL genotype-specific parameters of power curves. Using Monte Carlo simulation derived from empirical observations of power curves in the European starling (Sturnus vulgaris), we demonstrate how the underlying QTL for power curves can be detected from molecular markers and how the QTL detected affect the most appropriate flight speeds used to design an optimal migration strategy. The results from our model can be directly integrated into a conceptual framework for understanding flight origin and evolution.

Journal Article↗
PubMed2026

Co-regulation of HIV control and cytomegalovirus pp65-specific IL-1β and TNF-α responses by genetic variants in the MHC region.

The spontaneous control of HIV infection in the absence of antiretroviral therapy, termed HIV control, is associated with genetic variation in the Major Histocompatibility Complex (MHC) locus. These variants are known to influence the immune response to HIV itself. However, people living with HIV are often co-infected with other pathogens that can also elicit immune responses, which might also be regulated by these variants. Here, we assessed whether genetic variants associated with HIV control influence cytokine responses to various co-pathogens. HIV-control-associated single nucleotide polymorphisms (SNPs) were enriched among variants regulating TNF-α and IL-1β production upon CMV pp65 peptide pool stimulation. The top enriched SNPs, rs1128175-A and rs2853971-A, were linked to lower odds of HIV control and increased cytokine responses to CMV. These SNPs were in linkage disequilibrium (LD) with classical HLA alleles HLA-B*07:02 and HLA-C*07:02. Intracellular cytokine staining showed CMV serostatus-dependent production of TNF-α by monocytes and CD8 T cells. The rs1128175-A/rs2853971-A/HLA-B*07:02/HLA-C*07:02 haplotype was associated with increased IFN-γ production by CD8 T cells upon CMV pp65 peptide pool stimulation, indicating an effect on memory responses. Quantitative trait locus (QTL) mapping showed that rs1128175 and rs2853971 influence HLA-B and HLA-C expression, DNA methylation levels and cell-type-specific cis-effects on chromatin accessibility, as well as CD8 T cell subset abundance. These QTL associations suggest that variants associated with poor HIV control are linked to heightened pro-inflammatory responses to CMV pp65 through effects on antigen presentation, epigenetic modifications, gene expression and immune cell repertoire, potentially negatively affecting HIV control status.

Humans↗
PubMed2005

Combining the meiosis Gibbs sampler with the random walk approach for linkage and association studies with a general complex pedigree and multimarker loci.

A linkage analysis for finding inheritance states and haplotype configurations is an essential process for linkage and association mapping. The linkage analysis is routinely based upon observed pedigree information and marker genotypes for individuals in the pedigree. It is not feasible for exact methods to use all such information for a large complex pedigree especially when there are many missing genotypic data. Proposed Markov chain Monte Carlo approaches such as a single-site Gibbs sampler or the meiosis Gibbs sampler are able to handle a complex pedigree with sparse genotypic data; however, they often have reducibility problems, causing biased estimates. We present a combined method, applying the random walk approach to the reducible sites in the meiosis sampler. Therefore, one can efficiently obtain reliable estimates such as identity-by-descent coefficients between individuals based on inheritance states or haplotype configurations, and a wider range of data can be used for mapping of quantitative trait loci within a reasonable time.

Computer Simulation↗
PubMed2006

Genetic dissection of vasculitis, myeloperoxidase-specific antineutrophil cytoplasmic autoantibody production, and related traits in spontaneous crescentic glomerulonephritis-forming/Kinjoh mice.

The spontaneous crescentic glomerulonephritis-forming/Kinjoh (SCG/Kj) mouse is a model of human crescentic glomerulonephritis and vasculitis associated with the production of the myeloperoxidase (MPO)-specific antineutrophil cytoplasmic autoantibody (MPO-ANCA). Although the disease is mediated initially by mutation of the Fas gene (lpr), SCG/Kj mice also have non-Fas predisposing genetic factors. To define these factors, genome-wide quantitative trait locus (QTL) mapping was performed on female (B(6)x SCG/Kj) F(2) intercross mice. Fourteen non-Fas QTLs were identified. QTLs of glomerulonephritis were located on chromosomes 1, 10, 13, 16, and 17, vasculitis on chromosomes 1 and 17, splenomegaly on chromosome 1, hypergammaglobulinemia on chromosomes 1, 2, 4, 6, 7, 11, 13, and 17, antinuclear Ab on chromosomes 1, 8, 10, and 12, and MPO-ANCA production on chromosomes 1 and 10. Significant QTLs derived from SCG/Kj on chromosomes 1, 2, 7, and 13 were designated Scg-1 to Scg-5, respectively, and those derived from B(6) on chromosomes 4, 6, 17, and 10 were designated Sxb-1 to Sxb-4, respectively. Two loci linked to MPO-ANCA production on chromosomes 1 and 10 were designated Man-1 and Man-2 (for MPO-ANCA), respectively. Although both Scg-1 and Scg-2 were on chromosome 1 and shared several functions, it was of interest that aberrant MPO-ANCA production was exclusively controlled by Man-1, the centromeric half region of the Scg-2 chromosomal segment. We also examined the epistatic effects between the lpr mutation and non-Fas susceptibility genes. QTLs are discussed in relation to previously described loci, with emphasis on their candidate genes.

Animals↗
PubMed1999

Dynamic changes in mouse hematopoietic stem cell numbers during aging.

To address the fundamental question of whether or not stem cell populations age, we performed quantitative measurements of the cycling status and frequency of hematopoietic stem cells in long-lived C57BL/6 (B6) and short-lived DBA/2 (DBA) mice at different developmental and aging stages. The frequency of cobblestone area-forming cells (CAFC) day-35 in DBA fetal liver was twofold to threefold higher than in B6 mice, and by late gestation, the total stem cell number was nearly as large as that of young DBA adults. Following a further approximately 50% increase in stem cells between 6 weeks and 1 year of age, numbers in old DBA mice dropped precipitously between 12 and 20 months of age. In marked contrast, this stem cell population in B6 mice increased at a constant rate from late gestation to 20 months of age with no signs of abatement. Throughout development an inverse correlation was observed between stem cell numbers and the percentage of cells in S-phase. Because a strong genetic component contributed to the changes in stem cell numbers during aging, we quantified stem cells of 20-month old BXD recombinant inbred (RI) mice, derived from B6 and DBA progenitor strains, thus permitting detailed interstrain genetic analysis. For each BXD strain we calculated the stem cell increase or decrease as mice aged from 2 to 20 months. Net changes in CAFC-day 35 numbers among BXD strains ranged from an approximately 10-fold decrease to an approximately 10-fold increase. A genome-wide search for loci associated with this quantitative trait was performed. Several loci contribute to the trait-putative loci map to chromosomes X, 2, and 14. We conclude that stem cell numbers fluctuate widely during aging and that this has a strong genetic basis.

Aging↗
PubMed2004

[Novel molecular marker systems--SRAP and TRAP and their application].

SRAP and TRAP are two kinds of newly developed molecular marker systems with the advantages of simplicity, high throughput, numerous co-dominant makers, highly reproducibility and ready to sequence, especially preferential targeting ORFs. The principle and protocol of SRAP and TRAP, which were developed in Brassica and Helianthus crops firstly, are introduced in the paper. Primer design is a key step for SRAP and TRAP, and some F-and R-primers were developed. Unlike SRAP technique, the TRAP requires cDNA or EST sequence information for fixed primer development. The annealing temperature is 35 degrees in the first 5 cycles and 50 degrees in the subsequent 30~35 cycles. The amplicons can be separated by polyacrylamide or agarose gel, and detected by autoradiography, silver or EB staining. SRAP and TRAP are applied in germplasm genetic diversity analysis, genetic map including transcriptome map construction, important trait gene tagging and gene cloning in many crops.

Acid Phosphatase↗
PubMed2002

[Microsatellite markers and applications in the barley genome].

Microsatellites, also called simple sequence repeats (SSR), are simple, tandemly repeated DNA sequences with a repeat length of a few base pairs,and are very ideally used as molecular markers because of their abundance, high level of polymorphism, co-dominance and ease of assay with the polymerase chain reaction (PCR) by selecting primers as the conserved DNA sequences flanking the SSRs,as well as better stability. The experiments showed that SSRs are randomly distributed throughout the barley genome,and there are 3-18 alleles at a single SSR locus,up to 37 alleles/locus. SSR markers have being widely applied in the construction of molecular genetic map, the study of genetic diversity,the identification of germplasm, gene mapping for important traits and molecular marker-assisted selection. Meanwhile,most of markers are strongly clustered around the centromeric regions of all seven linkage groups. As a result of the clustering,genome coverage with SSRs remains incomplete with an obvious lack of markers on the long arms of chromosomes 1H and 5H and short arm of chromosome 6H. Therefore,it is very potential and necessary to further develop SSR markers in barley.

English Abstract↗
PubMed1995

The applications of the polymerase chain reaction in the life sciences.

The polymerase chain reaction (PCR) allows the in vitro amplification of DNA fragments starting with tiny amounts of biological sample and oligonucleotide primers derived from sequence data. Since the technique is fast and easy, PCR has taken the DNA-technology to the routine laboratoria. We present a survey of the following applications of PCR: 1) The amplification of gene fragments as fast alternative of cloning. 2) The modification of DNA fragments. 3) The sensitive detection of pathogenic microorganisms, if desired followed by an accurate genotyping. 4) DNA analysis of arachaeological specimens. 5) The detection of mutations relevant for inherited diseases, malignant transformation or tissue typing. 6) The analysis of genetic markers for forensic applications, for paternity testing and for the mapping of hereditary traits. 7) The species-specific amplification of DNA segments between interspersed-repeat elements. 8) The study of gene expression.

Animals↗
PubMed1993

Recent developments in alcoholism:genetic transmission.

This chapter is an overview of developments in the study of genetic factors in vulnerability in alcoholism. The focus is on recent developments, including heritability studies in twins and transmission studies in families, both of which have continued to reveal evidence for a substantial role for genetic factors but also for etiologic complexity and variation in vulnerability across generations and across cultures. Studies are discussed which utilized psychophysiological and neurochemical markers for alcoholism for analysis of genetic association, transmission, and linkage. These markers include the low P300 event-related potential, sensitivity to ethanol's intoxicating and euphoric effects, platelet adenylate cyclase, and neurotransmitter metabolite concentrations. Although it is highly likely that many alcoholism-associated physiologic phenotypes are secondary traits, these approaches have increased the specificity of genetic analyses and genetic analyses are clarifying their relationship to alcoholism. For example, early efforts to study, in families, the co-occurrence of the P300 marker and alcoholism have yielded results indicating that the P300 abnormality precedes significant exposure to alcohol and that relatives of alcoholics are more likely to have this trait. In the area of animal models, two nonhuman primate species, the vervet monkey and the rhesus macaque, were shown to willingly consume alcohol to intoxicating blood levels. Also, linkage studies using the quantitative trait locus (QTL) mapping strategy were attempted for phenotypes relevant for alcoholism. The QTL strategy is theoretically capable of identifying determinant genes which contribute only a small portion of the variance. In human linkage studies, a genetic association was found to the DRD2 dopamine receptor. The DRD2 finding generated controversy, as a number of other groups failed to replicate it, and also focused attention on the advantages and pitfalls of the population association approach for detecting genes influencing behavior. The relationship of the alcohol metabolic gene variants to alcoholism was clarified by the finding that functional variants of alcohol and aldehyde dehydrogenases can act additively to determine vulnerability to alcoholism.

Alcoholism↗