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PubMed1988

Transformations of maps to investigate clusters of disease.

An approach is presented to display and analyze epidemiologic data using population density equalized maps (cartograms). The algorithm for generating these maps is discussed. A specific method for statistically analyzing plotted data is given, followed by an application of maps and analysis to 73 sets of age-, race-, sex-, and site-specific cancer incidence data. The data were obtained from the Surveillance, Epidemiology and End Results project for San Francisco City/County (1978-1981) and combined with 1980 U.S. Census data.

Adult↗
PubMedDate not supplied

Genetic determinants of osteoporosis susceptibility in a female Ashkenazi Jewish population.

PURPOSE: To determine the heritability of low bone mineral density (BMD) at the hip in Ashkenazi Jewish families. METHODS: BMD at hip was accessed by dual x-ray absorptiometry (DEXA) in 166 female subjects from 61 families. Variance component analysis was used to estimate genetic contributions. RESULTS: We observed significant genetic contributions to age-adjusted BMD at the femoral neck as measured by heritability 0.67 (P < 0.0001). CONCLUSION: There is significant genetic determination in decreased BMD at the femoral neck in an Ashkenazi Jewish female population. These results warrant further gene mapping studies in this population to identify osteoporosis susceptibility loci.

Adult↗
PubMedDate not supplied

Gene mapping and marker clustering using Shannon's mutual information.

Finding the causal genetic regions underlying complex traits is one of the main aims in human genetics. In the context of complex diseases, which are believed to be controlled by multiple contributing loci of largely unknown effect and position, it is especially important to develop general yet sensitive methods for gene mapping. We discuss the use of Shannon's information theory for population-based gene mapping of discrete and quantitative traits and for marker clustering. Various measures of mutual information were employed in order to develop a comprehensive framework for gene mapping analyses. An algorithm aimed at finding so-called relevance chains of causal markers is proposed. Moreover, entropy measures are used in conjunction with multidimensional scaling to visualize clusters of genetic markers. The relevance chain algorithm successfully detected the two causal regions in a simulated scenario. The approach has also been applied to a published clinical study on autoimmune (Graves') disease. Results were consistent with those of standard statistical methods, but identified an additional locus of interest in the promotor region of the associated gene CTLA4. The developed software is freely available at http://www.Int.ei.tum.de/download/InfoGeneMap/.

Algorithms↗
PubMed2005

Fermionic superfluidity with imbalanced spin populations.

We established superfluidity in a two-state mixture of ultracold fermionic atoms with imbalanced state populations. This study relates to the long-standing debate about the nature of the superfluid state in Fermi systems. Indicators for superfluidity were condensates of fermion pairs and vortices in rotating clouds. For strong interactions, near a Feshbach resonance, superfluidity was observed for a broad range of population imbalances. We mapped out the superfluid regime as a function of interaction strength and population imbalance and characterized the quantum phase transition to the normal state, known as the Pauli limit of superfluidity.

Journal Article↗
PubMed2002

Genetic and physical mapping of Lrk10-like receptor kinase sequences in hexaploid oat (Avena sativa L.).

Oat receptor-like kinase gene sequences, homologous to the Lrk10 gene from wheat (Triticum aestivum L.), were mapped in oat (Avena sativa L.). PCR primers designed from the wheat Lrk10 were used to produce ALrk10 from oat. Two DNA sequences, ALrk1A1 and ALrk4A5, were produced from primers designed from coding and noncoding regions of ALrk10. Their use as RFLP probes indicated that the kinase genes mapped to four loci on different hexaploid oat 'Kanota' x 'Ogle' linkage groups (4_12, 5, 6, and 13) and to a fifth locus unlinked to other markers. Three of these linkage groups contain a region homologous to the short arm of chromosome I of wheat and the fourth contains a region homologous to chromosome 3 of wheat. Analysis with several nullisomics of oat indicated that two of the map locations are on satellite chromosomes. RFLP mapping in a 'Dumont' x 'OT328' population indicated that one map location is closely linked to Pg9, a resistance gene to oat stem rust (Puccinia graminis subsp. avenae). Comparative mapping indicates this to be the region of a presumed cluster of crown rust (Puccinia coronata subsp. avenae) and stem rust resistance genes (Pg3, Pg9, Pc44, Pc46, Pc50, Pc68, Pc95, and PcX). The map position of several RGAs located on KO6 and KO3_38 with respect to Lrk10 and storage protein genes are also reported.

Avena↗
PubMed2004

A genetic map of candidate genes and QTLs involved in tomato fruit size and composition.

In order to screen for putative candidate genes linked to tomato fruit weight and to sugar or acid content, genes and QTLs involved in fruit size and composition were mapped. Genes were selected among EST clones in the TIGR tomato EST database (http://www.tigr.org/tdb/tgi/lgi/) or corresponded to genes preferentially expressed in the early stages of fruit development. These clones were located on the tomato map using a population of introgression lines (ILs) having one segment of Lycopersicon pennellii (LA716) in a L. esculentum (M82) background. The 75 ILs allowed the genome to be segmented into 107 bins. Sixty-three genes involved in carbon metabolism revealed 79 loci. They represented enzymes involved in the Calvin cycle, glycolysis, the TCA cycle, sugar and starch metabolism, transport, and a few other functions. In addition, seven cell-cycle-specific genes mapped into nine loci. Fourteen genes, primarily expressed during the cell division stage, and 23 genes primarily expressed during the cell expansion stage, revealed 24 and 26 loci, respectively. The fruit weight, sugars, and organic acids content of each IL was measured and several QTLs controlling these traits were mapped. Comparison between map location of QTLs and candidate gene loci indicated a few candidate genes that may influence the variation of sugar or acid contents. Furthermore, the gene/QTL locations could be compared with the loci mapped in other tomato populations.

Chromosome Mapping↗
PubMed2005

QTLs mapping for fruit size and shape in chromosomes 2 and 4 in pepper and a comparison of the pepper QTL map with that of tomato.

Quantitative trait locus (QTL) mapping for fruit weight and shape in pepper (Capsicum spp.) was performed using C. chinense and C. frutescens introgression lines of chromosomes 2 and 4. In chromosome 2, a single major fruit-weight QTL, fw2.1, was detected in both populations that explained 62% of the trait variation. This QTL, as well as a fruit-shape QTL, fs2.1, which had a more minor effect, were localized to the tomato fruit-shape gene ovate. The cloned tomato fruit-weight QTL, fw2.2, did not play a major role in controlling fruit size variations in pepper. In chromosome 4, two fruit-weight QTLs, fw4.1 and fw4.2, were detected in the same genomic regions in both mapping populations. In addition, a single fruit-shape QTL was detected in each of the mapping populations that co-localized with one of the fruit-weight QTLs, suggesting pleiotropy or close linkage of the genes controlling size and shape. fw2.1 and fw4.2 represent major fruit-weight QTLs that are conserved in the three Capsicum species analyzed to date for fruit-size variations. Co-localization of the pepper QTLs with QTLs identified for similar traits in tomato suggests that the pepper and tomato QTLs are orthologous. Compared to fruit-shape QTLs, fruit-weight QTLs were more often conserved between pepper and tomato. This implies that different modes of selection were employed for these traits during domestication of the two Solanaceae species.

Capsicum↗
PubMed2006

Real time computation: zooming in on population codes.

Information processing in nervous systems intricately combines computation at the neuronal and network levels. Many computations may be envisioned as sequences of signal processing steps along some pathway. How can information encoded by single cells be mapped onto network population codes, and how do different modules or layers in the computation synchronize their communication and computation? These fundamental questions are particularly severe when dealing with real time streams of inputs. Here we study this problem within the context of a minimal signal perception task. In particular, we encode neuronal information by externally applying a space- and time-localized stimulus to individual neurons within a network. We show that a pulse-coupled recurrent neural network can successfully handle this task in real time, and obeys three key requirements: (i) stimulus dependence, (ii) initial-conditions independence, and (iii) accessibility by a readout mechanism. In particular, we suggest that the network's overall level of activity can be used as a temporal cue for a robust readout mechanism. Within this framework, the network can rapidly map a local stimulus onto a population code that can then be reliably read out during some narrow but well defined window of time.

Computer Simulation↗
PubMed2003

[A porcine linkage map of microsatellite markers using a commercial population as a reference].

A commercial population created with 19 hybrid boars [Piétrain x (Piétrain x Hampshire)], 52 hybrid sows [Leicoma x (Large White x Landrace)] and their 332 offspring was used to construct a whole genome porcine linkage map. The genetic markers used in this study include 172 microsatellite markers and 3 type- I markers (RYR1, PIT1 and PRKAG3). All microsatellite markers were genotyped using multiplex PCR reactions and visualized on ABI 377 sequencer. Three type I markers were assayed using PCR-RFLP technique. CRIMAP (2.4) analysis revealed a total length of the sex-averaged map for SSC1-SSC18 by 2449.2 cM and the length of SSCX by 143.1 cM. The average interval distance accounts to 16.3 cM. The heterozygosity of the parents at the microsatellite loci averaged 0.70. This map will play an important role in screening of QTL for growth, carcass and meat quality and reproduction in commercial populations.

Animals↗
PubMed2003

Conversion of an amplified fragment length polymorphism marker into a co-dominant marker in the mapping of the Rph15 gene conferring resistance to barley leaf rust, Puccinia hordei Otth.

Leaf rust, caused by Puccinia hordei, is an important disease afflicting barley ( Hordeum vulgare) in many production regions of the world. The leaf rust resistance gene Rph15 was identified in an accession of wild barley ( Hordeum vulgare subsp. spontaneum) and is one of the most broadly effective resistance genes known. Using amplified fragment length polymorphism (AFLP) and simple sequence repeat markers, Rph15 was mapped to chromosome 2HS in an F(2) population derived from a cross between Bowman ( Rph15), a Bowman backcross-derived line carrying Rph15, and the susceptible cultivar Bowman. AFLP marker P13M40 co-segregated with Rph15 in this mapping population and two others involving Bowman ( Rph15) and cultivars Proctor and Nudinka. The dominant AFLP marker P13M40 was converted to a co-dominant PCR-based marker that may be useful in breeding programs employing marker-assisted selection. The allelic relationship between Rph15 and the gene Rph16, also mapping to chromosome 2HS, was studied. The lack of segregation in F(2) progeny derived from the two resistance sources indicates that Rph15 and Rph16 are alleles of the same locus.

Base Sequence↗
PubMed2001

A linkage map of hexaploid oat based on grass anchor DNA clones and its relationship to other oat maps.

A cultivated oat linkage map was developed using a recombinant inbred population of 136 F6:7 lines from the cross 'Ogle' x 'TAM O-301'. A total of 441 marker loci, including 355 restriction fragment length polymorphism (RFLP) markers, 40 amplified fragment length polymorphisms (AFLPs), 22 random amplified polymorphic DNAs (RAPDs), 7 sequence-tagged sites (STSs), 1 simple sequence repeat (SSR), 12 isozyme loci, and 4 discrete morphological traits, was mapped. Fifteen loci remained unlinked, and 426 loci produced 34 linkage groups (with 2-43 loci each) spanning 2049 cM of the oat genome (from 4.2 to 174.0 cM per group). Comparisons with other Avena maps revealed 35 genome regions syntenic between hexaploid maps and 16-34 regions conserved between diploid and hexaploid maps. Those portions of hexaploid oat maps that could be compared were completely conserved. Considerable conservation of diploid genome regions on the hexaploid map also was observed (89-95%); however, at the whole-chromosome level, colinearity was much lower. Comparisons among linkage groups, both within and among Avena mapping populations, revealed several putative homoeologous linkage group sets as well as some linkage groups composed of segments from different homoeologous groups. The relationships between many Avena linkage groups remain uncertain, however, due to incomplete coverage by comparative markers and to complications introduced by genomic duplications and rearrangements.

Avena↗
PubMed1991

Fine mapping of a human chromosome 6 ferritin heavy chain pseudogene: relevance to haemochromatosis.

We have used a somatic cell hybrid regional mapping panel for the short arm of chromosome 6, linkage analysis and a population study to map in detail a previously described ferritin heavy chain pseudogene sequence on chromosome 6. Our results show that this sequence maps to the short arm of chromosome 6 centromeric to the glyoxylase locus. The ferritin pseudogene locus is thus distant from the locus for the iron storage disease haemochromatosis, confirming previous evidence that this sequence is not a candidate for the haemochromatosis gene.

Chromosome Mapping↗
PubMedDate not supplied

Mapping genes conferring resistance to Phytophthora root rot of soybean, Rps1a and Rps7.

A linkage map was constructed for two Phytophthora sojae Kauf. +Gerd. root rot resistance genes, Rps1a and Rps7, in soybean (Glycine max (L.) Merr.) using microsatellite or simple sequence repeat (SSR) markers. An F2 population consisting of 81 individuals derived from a cross between OX281, which carries Rps7, and Mukden, which carries Rps1a, was used as the mapping population. A linkage map consisting of 10 SSR markers was first constructed using the computer software MapMaker/EXP 3.0. Rps1a and Rps7 were then placed at two different loci in the same linkage group with LOD scores of 2.88 and 9.16, respectively. Rps1a and Rps7 were linked at a distance of 13.8 cM. Rps1a was flanked by Satt159 (0.7 cM) and Satt009 (3.2 cM). Rps7 was flanked by Satt009 (10.6 cM) and Satt125 (29.1 cM).

Chromosome Mapping↗
PubMed1990

Changes in the population of larger cities of the USSR, 1979-1989.

"An overview of the dynamics of Soviet cities of over 100,000 population for the period 1979-1989 is presented, based largely on maps and tables depicting five key 'subsets' or city groupings: (a) cities increasing by over 100,000 inhabitants; (b) the fastest growing cities in percentage terms; (c) their comparison with fastest growing cities, 1959-1979; (d) the slowest growing cities in percentage terms; and (e) their comparison with slowest growing cities, 1959-1979. The paper, by focusing on these parameters and utilizing extensively graphic and cartographic methods of data presentation, provides...insights into city growth trends...."

Demography↗
PubMed2024

QTL mapping for seed vigor-related traits under artificial aging in common wheat in two introgression line (IL) populations.

BACKGROUND: Seed vigor recognized as a quantitative trait is of particular importance for agricultural production. However, limited knowledge is available for understanding genetic basis of wheat seed vigor. METHODS: The aim of this study was to identify quantitative trait loci (QTL) responsible for 10 seed vigor-related traits representing multiple aspects of seed-vigor dynamics during artificial aging with 6 different treatment times (0, 24, 36, 48, 60, and 72 h) under controlled conditions (48&#xa0;&#xb0;C, 95% humidity, and dark). The mapping populations were two wheat introgression lines (IL-1 and IL-2) derived from recipient parent (Lumai 14) and donor parent (Shaanhan 8675 or Jing 411). RESULTS: A total of 26 additive QTLs and 72 pairs of epistatic QTLs were detected for wheat seed-vigor traits. Importantly, chromosomes 1B and 7B contained several co-located QTLs, and chromosome 2A had a QTL-rich region near the marker Xwmc667, indicating that these QTLs may affect wheat seed vigor with pleiotropic effects. Furthermore, several possible consistent QTLs (hot-spot regions) were examined by comparison analysis of QTLs detected in this study and reported previously. Finally, a set of candidate genes for wheat seed vigor were predicted to be involved in transcription regulation, carbohydrate and lipid metabolism. CONCLUSION: The present findings lay new insights into the mechanism underlying wheat seed vigor, providing valuable information for wheat genetic improvement especially marker-assisted breeding to increase seed vigor and consequently achieve high grain yield despite of further investigation required.

Triticum↗
PubMed1999

Mapping glutamatergic drive in the vertebrate retina with a channel-permeant organic cation.

Patterns of neuronal excitation in complex populations can be mapped anatomically by activating ionotropic glutamate receptors in the presence of 1-amino-4-guanidobutane (AGB), a channel-permeant guanidinium analogue. Intracellular AGB signals were trapped with conventional glutaraldehyde fixation and were detected by probing registered serial thin sections with anti-AGB and anti-amino acid immunoglobulins, revealing both the accumulated AGB and the characteristic neurochemical signatures of individual cells. In isolated rabbit retina, both glutamate and the ionotropic glutamate receptor agonists alpha-amino-3-hydroxyl-5-methylisoxazole-4-propionic acid (AMPA), kainic acid (KA), and N-methyl-D-aspartic acid (NMDA) activated permeation of AGB into retinal neurons in dose-dependent and pharmacologically specific modes. Horizontal cells and bipolar cells were dominated by AMPA/KA receptor activation with little or no evidence of NMDA receptor involvement. Strong NMDA activation of AGB permeation was restricted to subsets of the amacrine and ganglion cell populations. Threshold agonist doses for the most responsive cell groups (AMPA, 300 nm; KA, 2 microM; NMDA, 63 microm; glutamate, 1 mM) were similar to values obtained from electrophysiological and neurotransmitter release measures. The threshold for activation of AGB permeation by exogenous glutamate was shifted to <200 microM in the presence of the glutamate transporter antagonist dihydrokainate, indicating substantial spatial buffering of extracellular glutamate levels in vitro. Agonist-activated permeation of AGB into neurons persisted under blockades of Na+ -dependent transporters, voltage-activated Ca2+ and Na+ channels, and ionotropic gamma-aminobutyric acid and glycine receptors. Cholinergic agonists evoked no permeation.

Agmatine↗
PubMed2006

Exploring dynamics of protein structure determination and homology-based prediction to estimate the number of superfamilies and folds.

BACKGROUND: As tertiary structure is currently available only for a fraction of known protein families, it is important to assess what parts of sequence space have been structurally characterized. We consider protein domains whose structure can be predicted by sequence similarity to proteins with solved structure and address the following questions. Do these domains represent an unbiased random sample of all sequence families? Do targets solved by structural genomic initiatives (SGI) provide such a sample? What are approximate total numbers of structure-based superfamilies and folds among soluble globular domains? RESULTS: To make these assessments, we combine two approaches: (i) sequence analysis and homology-based structure prediction for proteins from complete genomes; and (ii) monitoring dynamics of the assigned structure set in time, with the accumulation of experimentally solved structures. In the Clusters of Orthologous Groups (COG) database, we map the growing population of structurally characterized domain families onto the network of sequence-based connections between domains. This mapping reveals a systematic bias suggesting that target families for structure determination tend to be located in highly populated areas of sequence space. In contrast, the subset of domains whose structure is initially inferred by SGI is similar to a random sample from the whole population. To accommodate for the observed bias, we propose a new non-parametric approach to the estimation of the total numbers of structural superfamilies and folds, which does not rely on a specific model of the sampling process. Based on dynamics of robust distribution-based parameters in the growing set of structure predictions, we estimate the total numbers of superfamilies and folds among soluble globular proteins in the COG database. CONCLUSION: The set of currently solved protein structures allows for structure prediction in approximately a third of sequence-based domain families. The choice of targets for structure determination is biased towards domains with many sequence-based homologs. The growing SGI output in the future should further contribute to the reduction of this bias. The total number of structural superfamilies and folds in the COG database are estimated as approximately 4000 and approximately 1700. These numbers are respectively four and three times higher than the numbers of superfamilies and folds that can currently be assigned to COG proteins.

Data Interpretation, Statistical↗