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At least 667 records · Page 37Linked to original sources
PubMed2001

Cortical change in Alzheimer's disease detected with a disease-specific population-based brain atlas.

We report the first detailed population-based maps of cortical gray matter loss in Alzheimer's disease (AD), revealing prominent features of early structural change. New computational approaches were used to: (i) distinguish variations in gray matter distribution from variations in gyral patterns; (ii) encode these variations in a brain atlas (n = 46); (iii) create detailed maps localizing gray matter differences across groups. High resolution 3D magnetic resonance imaging (MRI) volumes were acquired from 26 subjects with mild to moderate AD (age 75.8+/-1.7 years, MMSE score 20.0+/-0.9) and 20 normal elderly controls (72.4+/-1.3 years) matched for age, sex, handedness and educational level. Image data were aligned into a standardized coordinate space specifically developed for an elderly population. Eighty-four anatomical models per brain, based on parametric surface meshes, were created for all 46 subjects. Structures modeled included: cortical surfaces, all major superficial and deep cortical sulci, callosal and hippocampal surfaces, 14 ventricular regions and 36 gyral boundaries. An elastic warping approach, driven by anatomical features, was then used to measure gyral pattern variations. Measures of gray matter distribution were made in corresponding regions of cortex across all 46 subjects. Statistical variations in cortical patterning, asymmetry, gray matter distribution and average gray matter loss were then encoded locally across the cortex. Maps of group differences were generated. Average maps revealed complex profiles of gray matter loss in disease. Greatest deficits (20-30% loss, P<0.001-0.0001) were mapped in the temporo-parietal cortices. The sensorimotor and occipital cortices were comparatively spared (0-5% loss, P>0.05). Gray matter loss was greater in the left hemisphere, with different patterns in the heteromodal and idiotypic cortex. Gyral pattern variability also differed in cortical regions appearing at different embryonic phases. 3D mapping revealed profiles of structural deficits consistent with the cognitive, metabolic and histological changes in early AD. These deficits can therefore be (i) charted in a living population and (ii) compared across individuals and groups, facilitating longitudinal, genetic and interventional studies of dementia.

Aged↗
PubMed2004

Landscape features and spatial distribution of adult northern corn rootworm (Coleoptera: Chrysomelidae) in the South Dakota areawide management site.

The northern corn rootworm, Diabrotica barberi Smith & Lawrence (Coleoptera: Chrysomelidae), creates economic and environmental concerns in the Corn Belt. To supplement the population control tactics of the Areawide Pest Management Program in Brookings, SD, geographic information systems were used from 1997 to 2001 to examine the spatial relationships between D. barberi population dynamics and habitat structure, soil texture, and elevation. Using the inverse distance weighted interpolation technique, D. barberi population density maps were created from georeferenced emergence and postemergence traps placed in maize, Zea mays L., fields. For each year, these maps were overlaid with vegetation, soil, and elevation maps to search for quantitative relationships between pest numbers and landscape structure. Through visual interpretation and correlation analysis, shifts in landscape structure, such as size, number, and arrangement of patches were shown to associate with D. barberi population abundance and distribution in varying degrees. D. barberi were found in greater proportions than expected on loam and silty clay loam soils and on elevations between 500 and 509 m. An understanding of the interactions between D. barberi population dynamics and landscape variables provides information to pest managers, which can be used to identify patterns in the landscape that promote high insect population density patches to improve pest management strategies.

Animals↗
PubMed2004

Multiple-interval mapping for quantitative trait loci controlling endosperm traits.

Endosperm traits are trisomic inheritant and are of great economic importance because they are usually directly related to grain quality. Mapping for quantitative trait loci (QTL) underlying endosperm traits can provide an efficient way to genetically improve grain quality. As the traditional QTL mapping methods (diploid methods) are usually designed for traits under diploid control, they are not the ideal approaches to map endosperm traits because they ignore the triploid nature of endosperm. In this article, a statistical method considering the triploid nature of endosperm (triploid method) is developed on the basis of multiple-interval mapping (MIM) to map for the underlying QTL. The proposed triploid MIM method is derived to broadly use the marker information either from only the maternal plants or from both the maternal plants and their embryos in the backcross and F2 populations for mapping endosperm traits. Due to the use of multiple intervals simultaneously to take multiple QTL into account, the triploid MIM method can provide better detection power and estimation precision, and as shown in this article it is capable of analyzing and searching for epistatic QTL directly as compared to the traditional diploid methods and current triploid methods using only one (or two) interval(s). Several important issues in endosperm trait mapping, such as the relation and differences between the diploid and triploid methods, variance components of genetic variation, and the problems if effects are present and ignored, are also addressed. Simulations are performed to further explore these issues, to investigate the relative efficiency of different experimental designs, and to evaluate the performance of the proposed and current methods in mapping endosperm traits. The MIM-based triploid method can provide a powerful tool to estimate the genetic architecture of endosperm traits and to assist the marker-assisted selection for the improvement of grain quality in crop science. The triploid MIM FORTRAN program for mapping endosperm traits is available on the worldwide web (http://www.stat.sinica.edu.tw/chkao/).

Chromosome Mapping↗
PubMed2000

Molecular studies of beta-thalassemia heterozygotes with raised Hb F levels.

Hb F levels in beta-thalassemia heterozygotes are usually less than 2%, but amongst 1,059 patients studied, 73 (7%) had Hb F levels above 2.5% (2.6-14.0%). To investigate factors that may influence the increase of Hb F levels in these heterozygotes, we characterized the beta-thalassemia mutations and their chromosomal background, gamma-globin gene promoter variations, and alpha-globin genotypes. All 73 beta-thalassemia heterozygotes carried beta-thalassemia point mutations previously observed in the Greek population; gene mapping excluded b gene cluster deletions; only two cases had an additional gamma-globin gene (gammagammagamma/gammagamma). Five alpha-globin genes (alphaalphaalpha/alphaalpha) were detected in 17/73 cases (23%) as compared to a carrier rate of 1.76% in the general population. Molecular, hematological, and biosynthetic findings in these compound heterozygotes indicated that the raised Hb F levels were caused by cell selection due to ineffective erythropoiesis. In the remaining 56 simple beta-thalassemia heterozygotes, 11 beta-thalassemia mutations were observed, each on the expected haplotype(s), and analysis of the gamma gene promoters revealed three known polymorphisms (in linkage disequilibrium), with minimal influence on gamma-globin levels. However, the overall distribution of beta-thalassemia mutations in the 56 simple beta-thalassemia heterozygotes was significantly different (P<0.0002) compared to that in 986 simple beta-thalassemia heterozygotes with <2.5% Hb F, implicating an association between beta-thalassemia mutations and moderately increased Hb F levels, most notably codon 39 (C-->T), IVS-II-1 (G-->A), codon 6 (-A), and codon 8 (-AA), which accounted for 41/56 (73%) cases with >2.5% Hb F. In the remaining 15/56 (27%) cases, no common underlying globin genotypes could explain the raised Hb F levels. Overall, this study indicates that the control of Hb F levels in beta-thalassemia heterozygotes is heterogeneous and multi-factorial.

Chromosome Mapping↗
PubMedDate not supplied

Expanding the genetic map of maize with the intermated B73 x Mo17 (IBM) population.

The effects of intermating on recombination and the development of linkage maps were assessed in maize. Progeny derived from a common population (B73 x Mo17) before and after five generations of intermating were genotyped at the same set of 190 RFLP loci. Intermating resulted in nearly a four-fold increase in the genetic map distance and increased the potential for improved genetic resolution in 91% of the intervals evaluated. This mapping population and related information should connect research involving dense genetic maps, physical mapping, gene isolation, comparative genomics, analysis of quantitative trait loci and investigations of heterosis.

Chromosome Mapping↗
PubMed2005

Targeted mapping of ESTs linked to the adult plant resistance gene Lr46 in wheat using synteny with rice.

The gene Lr46 has provided slow-rusting resistance to leaf rust caused by Puccinia triticina in wheat (Triticum aestivum), which has remained durable for almost 30 years. Using linked markers and wheat deletion stocks, we located Lr46 in the deletion bin 1BL (0.84-0.89) comprising 5% of the 1BL arm. The distal part of chromosome 1BL of wheat is syntenic to chromosome 5L of rice. Wheat expressed sequence tags (ESTs) mapping in the terminal 15% of chromosome 1BL with significant homology to sequences from the terminal region of chromosome 5L of rice were chosen for sequence-tagged site (STS) primer design and were mapped physically and genetically. In addition, sequences from two rice bacterial artificial chromosome clones covering the targeted syntenic region were used to identify additional linked wheat ESTs. Fourteen new markers potentially linked to Lr46 were developed; eight were mapped in a segregating population. Markers flanking (2.2 cM proximal and 2.2 cM distal) and cosegregating with Lr46 were identified. The physical location of Lr46 was narrowed to a submicroscopic region between the breakpoints of deletion lines 1BL-13 [fraction length (FL)=0.89-1] and 1BL-10 (FL=0.89-3). We are now developing a high-resolution mapping population for the positional cloning of Lr46.

Basidiomycota↗
PubMedDate not supplied

RFLP mapping of expressed sequence tags in the chicken.

Chicken cDNA probes were used to map 10 loci by restriction fragment length polymorphism (RFLP) analysis in progeny of the Jungle Fowl x White Leghorn chicken backcross gene mapping reference population. The cDNA probes were from a subset of a T-cell library whose sequence tags showed significant homology to other avian or mammalian sequences in the EMBL database. Placement of loci generated by Compton cDNA clones on the East Lansing linkage map contributes to development of a consensus from the two linkage maps and will help provide a framework to evaluate the phenotypic effects of these genes.

Animals↗
PubMed2006

A microsatellite-based genetic linkage map of the waterflea, Daphnia pulex: On the prospect of crustacean genomics.

We describe the first genetic linkage map for Daphnia pulex using 185 microsatellite markers, including 115 new markers reported in this study. Our approach was to study the segregation of polymorphisms in 129 F2 progeny of one F1 hybrid obtained by crossing two genetically divergent lineages of Daphnia isolated from two Oregon populations. The map spanned 1206 Kosambi cM and had an average intermarker distance of 7 cM. Linkage groups ranged in size from 7 to 185 cM and contained 4 to 27 markers. The map revealed 12 linkage groups corresponding to the expected number of chromosomes and covers approximately 87% of the genome. Tests for random segregation of alleles at individual loci revealed that 21% of the markers showed significant transmission ratio distortion (primarily homozygote deficiency) likely due to markers being linked to deleterious recessive alleles. This map will become the anchor for the physical map of the Daphnia genome and will serve as a starting point for mapping single and quantitative trait loci affecting ecologically important phenotypes. By mapping 342 tentative orthologous gene pairs (Daphnia/Drosophila) into the Daphnia linkage map, we facilitate future comparative projects.

Animals↗
PubMed1997

Additional thyroid dose factor from transportation sources in Russia after the Chernobyl disaster.

Beginning approximately 4 years after the Chernobyl nuclear accident a steady increase in the incidence of thyroid cancer was observed in children and adolescents of the Bryansk Oblast, which received the highest level of radionuclide contaminants in Russia. We examined the spatial relationship between the residence location of patients with identified thyroid cancer (0-18 years old at the time of the accident) and a number of geographic parameters to better account for the etiology of thyroid cancer spatial distribution. Geographic parameters analyzed included spatial distribution of 137Cs and 131I in soil, population demographics, measurements and reconstructions. of absorbed thyroid 131I doses in the population, and maps of major transportation arteries. An interesting finding is the lack of a consistent correlation between the spatial distribution of radionuclides in the soil and thyroid cancer incidence. Instead, most of the thyroid cancer cases were diagnosed in settlements situated on major railways and roads. Correlating population with thyroid cancer cases and transportation arteries reveals a much higher cancer rate on or near major roads and railways than at a distance from them, again independent of radionuclide soil concentration. There are other important factors, of course, that must be considered in future evaluations of this phenomenon. These include the influence of iodine endemic zones, genetic predisposition to thyroid cancer, and duration of residence time in contaminated areas. The feasibility of radionuclide transport on railways and roads is discussed, together with the vectors for transfer of the contaminants to the human population. Developing a model to reconstruct the radiation dose to the thyroid over time in this geographic region is proposed in light of the impact of transportation arteries. Specific studies are outlined to provide the data necessary to develop this model as well as to better characterize the feasibility and scientific validity of the contribution to human health effects of this transport factor. Transport factor refers to the transport of radionuclides on transportation arteries and the transfer of these agents to the human population residing in the vicinity of these arteries. If the impact on thyroid cancer of the transport of radionuclides on major railways and roads is indeed significant, a major reappraisal of the risk of large-scale radioactive release into the environment is necessary.

Adolescent↗
PubMed1997

Physical localization and characterization of the BglI element in the genomes of Atlantic salmon (Salmo salar L.) and brown trout (S. trutta L.).

This work describes chromosomal localization, fine physical mapping, and population variation of the BglI element in the genome of Atlantic salmon (Salmo salar L.) and a similar sequence in the genome of brown trout (S. trutta L.). Results from a variety of complementary approaches, clearly demonstrate that the BglI element does not occur as a satellite-like repetitive DNA in these species but is part of the rDNA cistron as suggested by Goodier and Davidson (1993). Coincident hybridization of BglI clones with rDNA loci in both single and double-probe fluorescence in situ hybridization (FISH) experiments demonstrated physical linkage between the BglI element and rDNA loci. Fine physical mapping by Southern analysis and PCR amplification showed the BglI element to be located approximately 1.6 kb upstream of the 18S gene. The BglI element was used to screen for population-specific markers by Southern analysis. Population-specific banding patterns were only observed in brown trout, allowing identification of individual populations of this species. Sequence comparisons revealed sequences similar to the BglI element present in the rDNA cistron of other salmonids. This result suggests the presence of this sequence in the genome of the salmonid tetraploid ancestor.

Animals↗
PubMed2006

A core linkage map of the bumblebee Bombus terrestris.

The bumblebee Bombus terrestris is an economically important pollinator and an emerging model species in quantitative and population genetics. We generated genetic linkage maps for 3 independent mapping populations of B. terrestris. The linkage map with the highest resolution had 21 linkage groups, which adequately represents the haploid chromosome number of B. terrestris (n = 18). This map can be considered saturated, with an average marker distance of 10.3 cM and an estimated genome coverage of 81%. Using flow cytometry, we have estimated the genome size of this species to be 625 Mb. With an estimated total recombination genome length of 2760 cM, this results in a ratio of 226 kb/cM between the physical and genetic genome sizes. A recurring set of microsatellites and amplified fragment length polymorphism (AFLP) markers allowed the alignment of 14 linkage groups between the 3 maps. We propose to adopt this core map as a reference tool for future genetic and molecular work in B. terrestris.

Animals↗
PubMed1996

[Geography of effective size in the rural population of northern Eurasia: effective size and the intensity of random genetic drift].

On the basis of 655 direct and indirect estimations of effective size (Ne) of rural populations, a map of the geographic distribution of Ne in northern Eurasia was constructed. A geographic cline of Ne was found, with its value decreasing by three orders of magnitude from the direction of southwest (the western Caucasus and Central Asia) to northeast (the coasts of the Sea of Okhotsk and the Bering Sea). The area of highest distribution density of mean Ne values was situated meridionally between the Ob and Yenisei rivers from the Arctic coast of Taimyr Peninsula to the eastern Sayany and the south Baikal regions. Another similar area covered the south Baltic region, Belarus, and northwestern Ukraine. The average effective population size in northern Eurasia was Ne = 211.6, the geometrical mean G = 176, the harmonic mean H = 147, and the modal value Mo = 102. These characteristics of effective population size indicate a considerable contribution of stochastic gene drift to the differentiation of the northern Eurasian gene pool and the geographic cline of the rate of gene drift in the subcontinent. By means of transformation of the Ne map, a map for the rate of stochastic gene drift (1/4Ne) in northern Eurasia was obtained.

Asia↗
PubMed1987

Characterization of a new alpha zero thalassaemia defect in the South African population.

A new alpha thalassemia defect has been detected in the South African population. Restriction mapping of the alpha globin gene cluster in affected individuals has established that the defect is associated with the removal of 22.8-23.7 kb of DNA, including the psi zeta 1, psi alpha 1, psi alpha 2, alpha 2 and alpha 1 globin genes. The 5' endpoint of the deletion has been localized between the zeta 2 and psi zeta 1 globin genes, and the 3' endpoint lies 4-5 kb 3' to the alpha 1 globin gene. We have called the deletion - -SA in order to distinguish it from alpha zero thalassaemia defects described in other populations.

Chromosome Deletion↗
PubMed2004

[Maximum likelihood analysis for mapping dynamic trait QTL in outbred population II. Simulation].

Based on the maximum likelihood analysis principle for dynamic trait QTL mapping, selecting three orders Legendre polynomial as sub-model,the effects of the individual number, the frequency of test day,the marker density and heritability on detecting power are investigated by Monte-Carlo simulation. Each factor is divided into three levels such as the high,middle and low,the combinations of which are arranged by using orthologal design. The simulating result shows that the high heritability needs less number of individuals and frequency of test day than the low one, but the number of individuals of more than 300 and the frequency of test day of 5% above can guarantee sufficient detecting power no matter what the heritability is like. The number of individuals has almost the same effect as the frequency of test day in dynamic traits QTL mapping and the number of individuals and the frequency of test day compensate each other under the same size of samples. As to the QTL detection for a dynamic point,simulation indicates that the presented dynamic trait QTL mapping method that focuses on the whole dynamic process is significantly superior to the classical mapping methods on each individual dynamic point.

Humans↗
PubMed1997

True and false positive peaks in genomewide scans: applications of length-biased sampling to linkage mapping.

Disease-susceptibility loci are now being mapped via genomewide scans in which a linkage statistic is computed at each of a large number of markers. Such disease-susceptibility loci may be identified via a peak in the test statistic when the latter is plotted against the genetic map. In this paper we establish, by appealing to renewal theory, that true positive peaks are expected to be longer than false positive peaks. These results are verified by a realistic simulation of a genomewide linkage study based on the affected-sib-pair design. Since longer peaks are more likely to contain a gene of interest than are shorter peaks, these differences may aid in linkage mapping, justifying assignment of lower priority to shorter peaks. However, since these differences are generally small, statistics based on both peak length and height may not be much more powerful than those based on height alone. The results presented here also provide a theoretical framework for methods that use the length of shared haplotypes in populations to map disease genes.

Chromosome Mapping↗
PubMed2025

Integrative omics of the genetic basis for wheat WUE and drought resilience reveal the function of TaMYB7-A1.

Improving wheat&#xa0;drought resilience and water use efficiency (WUE) is critical for sustaining productivity under increasing water scarcity. Here, we integrate genome-wide association&#xa0;study (GWAS), expression quantitative trait locus (eQTL) mapping, population-transcriptome analysis, and summary-data-based mendelian randomization (SMR), followed by functional validation using indexed EMS mutants and transgenic lines, to systematically identify key WUE regulators. GWAS across water conditions in 228 accessions identifies 73 quantitative trait loci (QTLs) for WUE-traits. Transcriptome profiling of 110 diverse accessions reveals 28 drought-responsive modules. eQTL mapping uncovers 146,966 regulatory variants, including condition-specific hotspots associated with key drought-related pathways. Integrative analysis underscores 85 high-confidence candidate genes, notably TaMYB7-A1. Overexpression of TaMYB7-A1 enhances photosynthesis, WUE, root development, and grain yield under drought condition by activating TaPIP2;2-B1 (water transport), TaRD20-D1 (stomatal regulation), and TaABCB4-B1 (root growth), reflecting reduced water loss and improved physiological resilience. Our study presents a comprehensive regulatory map and robust targets for wheat drought adaptation and resilient cultivar breeding.

Triticum↗
PubMed1990

Estimation of recombination frequencies and construction of RFLP linkage maps in plants from crosses between heterozygous parents.

The construction of a restriction fragment length polymorphism (RFLP) linkage map is based on the estimation of recombination frequencies between genetic loci and on the determination of the linear order of loci in linkage groups. RFLP loci can be identified as segregations of singular or allelic DNA-restriction fragments. From crosses between heterozygous individuals several allele (fragment) configurations are possible, and this leads to a set of formulas for the evaluation of p, the recombination frequency between two loci. Tables and figures are presented illustrating a general outline of gene mapping using heterozygous populations. The method encompasses as special cases the mapping of loci from segregating populations of pure lines. Formulas for deriving the recombination frequencies and information functions are given for different fragment configurations. Information functions derived for relevant configurations are also compared. A procedure for map construction is presented, as it has been applied to RFLP mapping in an allogamous crop.

Alleles↗
PubMed1986

Mapping of an olfactory receptor population that projects to a specific region in the rat olfactory bulb.

An anatomically distinct group of glomeruli, termed the modified glomerular complex (MGC), is present in the posterior dorsomedial portion of the main olfactory bulb. This region has been strongly implicated as part of the pathway that processes odor cues for suckling in neonatal rat pups. We studied the distribution pattern of olfactory receptor neurons that project to the MGC region after ionophoretic injections of WGA-HRP into the olfactory bulbs of 12-day-old rat pups. HRP label was confined to an identifiable localized region in the MGC of the main olfactory bulb. Label extended over 2-7% of the glomerular sheet of the main olfactory bulb, including the MGC. Olfactory receptor neurons within the olfactory epithelium of the nasal cavity were labeled with HRP ipsilateral to the injected side. Maps constructed of the olfactory epithelium revealed that the labeled neurons occurred within topographically defined regions. Anteriorly, labeled olfactory neurons were confined to a narrow strip medial to the dorsal recess, and, more posteriorly, this strip widened medially along the septal wall and laterally onto a limited area on the nasal turbinates. Only a portion of the receptor population within a region was labeled. The boundaries between labeled and unlabeled regions were sharp. These findings support the concept that the olfactory epithelium is an anatomical mosaic in which receptors with different glomerular projections sites are intermingled. In conjunction with previous evidence on the functional specificity of the MGC, and staining of receptor neuron subgroups with monoclonal antibodies, these findings further suggest that olfactory receptor neurons form a functional mosaic within the olfactory epithelium.

Animals↗