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Sample records for multiple marker mapping

  1. Multiple marker abundance profiling

    Hooper, Cornelia M.; Stevens, Tim J.; Saukkonen, Anna

    2017-01-01

    proteins and the scoring accuracy of lower-abundance proteins in Arabidopsis. NPAS was combined with subcellular protein localization data, facilitating quantitative estimations of organelle abundance during routine experimental procedures. A suite of targeted proteomics markers for subcellular compartment...

  2. A molecular marker map for roses

    Debener, T.; Mattiesch, L.; Vosman, B.

    2001-01-01

    n addition to an existing core map for diploid roses which comprised 305 molecular markers 60 additional markers were mapped to extend the map. As a first application of the information contained in the map, the map position of a resistance gene from roses, Rdr1, was determined by identifying

  3. Markers and mapping revisited: finding your gene.

    Jones, Neil; Ougham, Helen; Thomas, Howard; Pasakinskiene, Izolda

    2009-01-01

    This paper is an update of our earlier review (Jones et al., 1997, Markers and mapping: we are all geneticists now. New Phytologist 137: 165-177), which dealt with the genetics of mapping, in terms of recombination as the basis of the procedure, and covered some of the first generation of markers, including restriction fragment length polymorphisms (RFLPs), random amplified polymorphic DNA (RAPDs), simple sequence repeats (SSRs) and quantitative trait loci (QTLs). In the intervening decade there have been numerous developments in marker science with many new systems becoming available, which are herein described: cleavage amplification polymorphism (CAP), sequence-specific amplification polymorphism (S-SAP), inter-simple sequence repeat (ISSR), sequence tagged site (STS), sequence characterized amplification region (SCAR), selective amplification of microsatellite polymorphic loci (SAMPL), single nucleotide polymorphism (SNP), expressed sequence tag (EST), sequence-related amplified polymorphism (SRAP), target region amplification polymorphism (TRAP), microarrays, diversity arrays technology (DArT), single-strand conformation polymorphism (SSCP), denaturing gradient gel electrophoresis (DGGE), temperature gradient gel electrophoresis (TGGE) and methylation-sensitive PCR. In addition there has been an explosion of knowledge and databases in the area of genomics and bioinformatics. The number of flowering plant ESTs is c. 19 million and counting, with all the opportunity that this provides for gene-hunting, while the survey of bioinformatics and computer resources points to a rapid growth point for future activities in unravelling and applying the burst of new information on plant genomes. A case study is presented on tracking down a specific gene (stay-green (SGR), a post-transcriptional senescence regulator) using the full suite of mapping tools and comparative mapping resources. We end with a brief speculation on how genome analysis may progress into the future of

  4. Incorporation of conventional genetic markers and RAPD markers into an RFLP based map in maize

    Coe, E.H. Jr.; McMullen, M.D.; Polacco, M.; Davis, G.L.; Chao, S.

    1998-01-01

    Integration of classical genetic markers, in particular mutants, onto the maize Restriction Fragment Length Polymorphism (RFLP) map will provide the tools necessary to further our understanding of plant development and of complex traits. Initially integration was accomplished by visual alignment of common markers and sometimes involved the use of information from several different molecular maps to determine the relative placement of a single mutant. The maize core marker set was designed to provide a common set of markers which could be used for integration of map data. We have completed the mapping, of 56 mutants on chromosome one relative to the core marker set. Phenotypes included whole plant, seedling, and kernel effects and represented a variety of biological processes. Since these mutants were previously located to chromosome arm, mapping required the use of only seven markers per mutant to define the correct bin location. Two mistakes in marker order relative to the classical map were identified, as well as, six groups of mutants which require allelism testing. Placement of mutants and cDNAs into bins using, the core markers provides a necessary resource for identification of gene function in maize. (author)

  5. Single Nucleotide Polymorphism Markers for Genetic Mapping in Drosophila melanogaster

    Hoskins, Roger A.; Phan, Alexander C.; Naeemuddin, Mohammed; Mapa, Felipa A.; Ruddy, David A.; Ryan, Jessica J.; Young, Lynn M.; Wells, Trent; Kopczynski, Casey; Ellis, Michael C.

    2001-01-01

    For nearly a century, genetic analysis in Drosophila melanogaster has been a powerful tool for analyzing gene function, yet Drosophila lacks the molecular genetic mapping tools that recently have revolutionized human, mouse, and plant genetics. Here, we describe the systematic characterization of a dense set of molecular markers in Drosophila by using a sequence tagged site-based physical map of the genome. We identify 474 biallelic markers in standard laboratory strains of Drosophila that sp...

  6. [Studies of marker screening efficiency and corresponding influencing factors in QTL composite interval mapping].

    Gao, Yong-Ming; Wan, Ping

    2002-06-01

    Screening markers efficiently is the foundation of mapping QTLs by composite interval mapping. Main and interaction markers distinguished, besides using background control for genetic variation, could also be used to construct intervals of two-way searching for mapping QTLs with epistasis, which can save a lot of calculation time. Therefore, the efficiency of marker screening would affect power and precision of QTL mapping. A doubled haploid population with 200 individuals and 5 chromosomes was constructed, with 50 markers evenly distributed at 10 cM space. Among a total of 6 QTLs, one was placed on chromosome I, two linked on chromosome II, and the other three linked on chromosome IV. QTL setting included additive effects and epistatic effects of additive x additive, the corresponding QTL interaction effects were set if data were collected under multiple environments. The heritability was assumed to be 0.5 if no special declaration. The power of marker screening by stepwise regression, forward regression, and three methods for random effect prediction, e.g. best linear unbiased prediction (BLUP), linear unbiased prediction (LUP) and adjusted unbiased prediction (AUP), was studied and compared through 100 Monte Carlo simulations. The results indicated that the marker screening power by stepwise regression at 0.1, 0.05 and 0.01 significant level changed from 2% to 68%, the power changed from 2% to 72% by forward regression. The larger the QTL effects, the higher the marker screening power. While the power of marker screening by three random effect prediction was very low, the maximum was only 13%. That suggested that regression methods were much better than those by using the approaches of random effect prediction to identify efficient markers flanking QTLs, and forward selection method was more simple and efficient. The results of simulation study on heritability showed that heightening of both general heritability and interaction heritability of genotype x

  7. Lod scores for gene mapping in the presence of marker map uncertainty.

    Stringham, H M; Boehnke, M

    2001-07-01

    Multipoint lod scores are typically calculated for a grid of locus positions, moving the putative disease locus across a fixed map of genetic markers. Changing the order of a set of markers and/or the distances between the markers can make a substantial difference in the resulting lod score curve and the location and height of its maximum. The typical approach of using the best maximum likelihood marker map is not easily justified if other marker orders are nearly as likely and give substantially different lod score curves. To deal with this problem, we propose three weighted multipoint lod score statistics that make use of information from all plausible marker orders. In each of these statistics, the information conditional on a particular marker order is included in a weighted sum, with weight equal to the posterior probability of that order. We evaluate the type 1 error rate and power of these three statistics on the basis of results from simulated data, and compare these results to those obtained using the best maximum likelihood map and the map with the true marker order. We find that the lod score based on a weighted sum of maximum likelihoods improves on using only the best maximum likelihood map, having a type 1 error rate and power closest to that of using the true marker order in the simulation scenarios we considered. Copyright 2001 Wiley-Liss, Inc.

  8. Evaluation of algorithms used to order markers on genetic maps.

    Mollinari, M; Margarido, G R A; Vencovsky, R; Garcia, A A F

    2009-12-01

    When building genetic maps, it is necessary to choose from several marker ordering algorithms and criteria, and the choice is not always simple. In this study, we evaluate the efficiency of algorithms try (TRY), seriation (SER), rapid chain delineation (RCD), recombination counting and ordering (RECORD) and unidirectional growth (UG), as well as the criteria PARF (product of adjacent recombination fractions), SARF (sum of adjacent recombination fractions), SALOD (sum of adjacent LOD scores) and LHMC (likelihood through hidden Markov chains), used with the RIPPLE algorithm for error verification, in the construction of genetic linkage maps. A linkage map of a hypothetical diploid and monoecious plant species was simulated containing one linkage group and 21 markers with fixed distance of 3 cM between them. In all, 700 F(2) populations were randomly simulated with 100 and 400 individuals with different combinations of dominant and co-dominant markers, as well as 10 and 20% of missing data. The simulations showed that, in the presence of co-dominant markers only, any combination of algorithm and criteria may be used, even for a reduced population size. In the case of a smaller proportion of dominant markers, any of the algorithms and criteria (except SALOD) investigated may be used. In the presence of high proportions of dominant markers and smaller samples (around 100), the probability of repulsion linkage increases between them and, in this case, use of the algorithms TRY and SER associated to RIPPLE with criterion LHMC would provide better results.

  9. SLAMM: Visual monocular SLAM with continuous mapping using multiple maps.

    Hayyan Afeef Daoud

    Full Text Available This paper presents the concept of Simultaneous Localization and Multi-Mapping (SLAMM. It is a system that ensures continuous mapping and information preservation despite failures in tracking due to corrupted frames or sensor's malfunction; making it suitable for real-world applications. It works with single or multiple robots. In a single robot scenario the algorithm generates a new map at the time of tracking failure, and later it merges maps at the event of loop closure. Similarly, maps generated from multiple robots are merged without prior knowledge of their relative poses; which makes this algorithm flexible. The system works in real time at frame-rate speed. The proposed approach was tested on the KITTI and TUM RGB-D public datasets and it showed superior results compared to the state-of-the-arts in calibrated visual monocular keyframe-based SLAM. The mean tracking time is around 22 milliseconds. The initialization is twice as fast as it is in ORB-SLAM, and the retrieved map can reach up to 90 percent more in terms of information preservation depending on tracking loss and loop closure events. For the benefit of the community, the source code along with a framework to be run with Bebop drone are made available at https://github.com/hdaoud/ORBSLAMM.

  10. Simple sequence repeat marker development and genetic mapping ...

    polymorphic SSR (simple sequence repeats) markers from libraries enriched for GA, CAA and AAT repeats, as well as 6 ... ers for quinoa was the development of a genetic linkage map ...... Weber J. L. 1990 Informativeness of human (dC-dA)n.

  11. Development and mapping of DArT markers within the Festuca - Lolium complex

    Kopecký, David; Bartoš, Jan; Lukaszewski, Adam J; Baird, James H; Černoch, Vladimír; Kölliker, Roland; Rognli, Odd Arne; Blois, Helene; Caig, Vanessa; Lübberstedt, Thomas; Studer, Bruno; Shaw, Paul; Doležel, Jaroslav; Kilian, Andrzej

    2009-01-01

    Background Grasses are among the most important and widely cultivated plants on Earth. They provide high quality fodder for livestock, are used for turf and amenity purposes, and play a fundamental role in environment protection. Among cultivated grasses, species within the Festuca-Lolium complex predominate, especially in temperate regions. To facilitate high-throughput genome profiling and genetic mapping within the complex, we have developed a Diversity Arrays Technology (DArT) array for five grass species: F. pratensis, F. arundinacea, F. glaucescens, L. perenne and L. multiflorum. Results The DArTFest array contains 7680 probes derived from methyl-filtered genomic representations. In a first marker discovery experiment performed on 40 genotypes from each species (with the exception of F. glaucescens for which only 7 genotypes were used), we identified 3884 polymorphic markers. The number of DArT markers identified in every single genotype varied from 821 to 1852. To test the usefulness of DArTFest array for physical mapping, DArT markers were assigned to each of the seven chromosomes of F. pratensis using single chromosome substitution lines while recombinants of F. pratensis chromosome 3 were used to allocate the markers to seven chromosome bins. Conclusion The resources developed in this project will facilitate the development of genetic maps in Festuca and Lolium, the analysis on genetic diversity, and the monitoring of the genomic constitution of the Festuca × Lolium hybrids. They will also enable marker-assisted selection for multiple traits or for specific genome regions. PMID:19832973

  12. EST-derived SSR markers used as anchor loci for the construction of a consensus linkage map in ryegrass (Lolium spp.

    Studer Bruno

    2010-08-01

    Full Text Available Abstract Background Genetic markers and linkage mapping are basic prerequisites for marker-assisted selection and map-based cloning. In the case of the key grassland species Lolium spp., numerous mapping populations have been developed and characterised for various traits. Although some genetic linkage maps of these populations have been aligned with each other using publicly available DNA markers, the number of common markers among genetic maps is still low, limiting the ability to compare candidate gene and QTL locations across germplasm. Results A set of 204 expressed sequence tag (EST-derived simple sequence repeat (SSR markers has been assigned to map positions using eight different ryegrass mapping populations. Marker properties of a subset of 64 EST-SSRs were assessed in six to eight individuals of each mapping population and revealed 83% of the markers to be polymorphic in at least one population and an average number of alleles of 4.88. EST-SSR markers polymorphic in multiple populations served as anchor markers and allowed the construction of the first comprehensive consensus map for ryegrass. The integrated map was complemented with 97 SSRs from previously published linkage maps and finally contained 284 EST-derived and genomic SSR markers. The total map length was 742 centiMorgan (cM, ranging for individual chromosomes from 70 cM of linkage group (LG 6 to 171 cM of LG 2. Conclusions The consensus linkage map for ryegrass based on eight mapping populations and constructed using a large set of publicly available Lolium EST-SSRs mapped for the first time together with previously mapped SSR markers will allow for consolidating existing mapping and QTL information in ryegrass. Map and markers presented here will prove to be an asset in the development for both molecular breeding of ryegrass as well as comparative genetics and genomics within grass species.

  13. Development and mapping of DArT markers within the Festuca - Lolium complex

    Studer Bruno

    2009-10-01

    Full Text Available Abstract Background Grasses are among the most important and widely cultivated plants on Earth. They provide high quality fodder for livestock, are used for turf and amenity purposes, and play a fundamental role in environment protection. Among cultivated grasses, species within the Festuca-Lolium complex predominate, especially in temperate regions. To facilitate high-throughput genome profiling and genetic mapping within the complex, we have developed a Diversity Arrays Technology (DArT array for five grass species: F. pratensis, F. arundinacea, F. glaucescens, L. perenne and L. multiflorum. Results The DArTFest array contains 7680 probes derived from methyl-filtered genomic representations. In a first marker discovery experiment performed on 40 genotypes from each species (with the exception of F. glaucescens for which only 7 genotypes were used, we identified 3884 polymorphic markers. The number of DArT markers identified in every single genotype varied from 821 to 1852. To test the usefulness of DArTFest array for physical mapping, DArT markers were assigned to each of the seven chromosomes of F. pratensis using single chromosome substitution lines while recombinants of F. pratensis chromosome 3 were used to allocate the markers to seven chromosome bins. Conclusion The resources developed in this project will facilitate the development of genetic maps in Festuca and Lolium, the analysis on genetic diversity, and the monitoring of the genomic constitution of the Festuca × Lolium hybrids. They will also enable marker-assisted selection for multiple traits or for specific genome regions.

  14. Case studies: Soil mapping using multiple methods

    Petersen, Hauke; Wunderlich, Tina; Hagrey, Said A. Al; Rabbel, Wolfgang; Stümpel, Harald

    2010-05-01

    Soil is a non-renewable resource with fundamental functions like filtering (e.g. water), storing (e.g. carbon), transforming (e.g. nutrients) and buffering (e.g. contamination). Degradation of soils is meanwhile not only to scientists a well known fact, also decision makers in politics have accepted this as a serious problem for several environmental aspects. National and international authorities have already worked out preservation and restoration strategies for soil degradation, though it is still work of active research how to put these strategies into real practice. But common to all strategies the description of soil state and dynamics is required as a base step. This includes collecting information from soils with methods ranging from direct soil sampling to remote applications. In an intermediate scale mobile geophysical methods are applied with the advantage of fast working progress but disadvantage of site specific calibration and interpretation issues. In the framework of the iSOIL project we present here some case studies for soil mapping performed using multiple geophysical methods. We will present examples of combined field measurements with EMI-, GPR-, magnetic and gammaspectrometric techniques carried out with the mobile multi-sensor-system of Kiel University (GER). Depending on soil type and actual environmental conditions, different methods show a different quality of information. With application of diverse methods we want to figure out, which methods or combination of methods will give the most reliable information concerning soil state and properties. To investigate the influence of varying material we performed mapping campaigns on field sites with sandy, loamy and loessy soils. Classification of measured or derived attributes show not only the lateral variability but also gives hints to a variation in the vertical distribution of soil material. For all soils of course soil water content can be a critical factor concerning a succesful

  15. Construction of a genetic linkage map in Lilium using a RIL mapping population based on SRAP marker

    Chen Li-Jing

    2015-01-01

    Full Text Available A genetic linkage map of lily was constructed using RILs (recombinant inbred lines population of 180 individuals. This mapping population was developed by crossing Raizan No.1 (Formolongo and Gelria (Longiflomm cultivars through single-seed descent (SSD. SRAPs were generated by using restriction enzymes EcoRI in combination with either MseI. The resulting products were separated by electrophoresis on 6% denaturing polyacrylamide gel and visualized by silver staining. The segregation of each marker and linkage analysis was done using the program Mapmaker3.0. With 50 primer pairs, a total of 189 parental polymorphic bands were detected and 78 were used for mapping. The total map length was 2,135.5 cM consisted of 16 linkage groups. The number of markers in the linkage groups varied from 1 to 12. The length of linkage groups was range from 11.2 cM to 425.9 cM and mean marker interval distance range from 9.4 cM to 345.4 cM individually. The mean marker interval distance between markers was 27.4 cM. The map developed in the present study was the first sequence-related amplified polymorphism markers map of lily constructed with recombinant inbred lines, it could be used for genetic mapping and molecular marker assisted breeding and quantitative trait locus mapping of Lilium.

  16. Pheno2Geno - High-throughput generation of genetic markers and maps from molecular phenotypes for crosses between inbred strains.

    Zych, Konrad; Li, Yang; van der Velde, Joeri K; Joosen, Ronny V L; Ligterink, Wilco; Jansen, Ritsert C; Arends, Danny

    2015-02-19

    Genetic markers and maps are instrumental in quantitative trait locus (QTL) mapping in segregating populations. The resolution of QTL localization depends on the number of informative recombinations in the population and how well they are tagged by markers. Larger populations and denser marker maps are better for detecting and locating QTLs. Marker maps that are initially too sparse can be saturated or derived de novo from high-throughput omics data, (e.g. gene expression, protein or metabolite abundance). If these molecular phenotypes are affected by genetic variation due to a major QTL they will show a clear multimodal distribution. Using this information, phenotypes can be converted into genetic markers. The Pheno2Geno tool uses mixture modeling to select phenotypes and transform them into genetic markers suitable for construction and/or saturation of a genetic map. Pheno2Geno excludes candidate genetic markers that show evidence for multiple possibly epistatically interacting QTL and/or interaction with the environment, in order to provide a set of robust markers for follow-up QTL mapping. We demonstrate the use of Pheno2Geno on gene expression data of 370,000 probes in 148 A. thaliana recombinant inbred lines. Pheno2Geno is able to saturate the existing genetic map, decreasing the average distance between markers from 7.1 cM to 0.89 cM, close to the theoretical limit of 0.68 cM (with 148 individuals we expect a recombination every 100/148=0.68 cM); this pinpointed almost all of the informative recombinations in the population. The Pheno2Geno package makes use of genome-wide molecular profiling and provides a tool for high-throughput de novo map construction and saturation of existing genetic maps. Processing of the showcase dataset takes less than 30 minutes on an average desktop PC. Pheno2Geno improves QTL mapping results at no additional laboratory cost and with minimum computational effort. Its results are formatted for direct use in R/qtl, the leading R

  17. Development and mapping of a public reference set of SSR markers in Lolium perenne L.

    Bach, J.L.; Muylle, H.; Arens, P.F.P.; Andersen, C.H.; Bach Holm, P.; Ghesquiere, M.; Julier, B.; Lubberstedt, T.; Nielsen, K.K.; Riek, de J.; Roldán-Ruiz, I.; Roulund, N.; Taylor, C.; Vosman, B.J.; Barre, P.

    2005-01-01

    We report on the characterization and mapping of 76 simple sequence repeat (SSR) markers for Lolium perenne. These markers are publicly available or obtained either from genomic libraries enriched for SSR motifs or L. perenne expressed sequence tag (EST) clones. Four L. perenne mapping populations

  18. Genotyping by Sequencing in Almond: SNP Discovery, Linkage Mapping, and Marker Design

    Shashi N. Goonetilleke

    2018-01-01

    Full Text Available In crop plant genetics, linkage maps provide the basis for the mapping of loci that affect important traits and for the selection of markers to be applied in crop improvement. In outcrossing species such as almond (Prunus dulcis Mill. D. A. Webb, application of a double pseudotestcross mapping approach to the F1 progeny of a biparental cross leads to the construction of a linkage map for each parent. Here, we report on the application of genotyping by sequencing to discover and map single nucleotide polymorphisms in the almond cultivars “Nonpareil” and “Lauranne.” Allele-specific marker assays were developed for 309 tag pairs. Application of these assays to 231 Nonpareil × Lauranne F1 progeny provided robust linkage maps for each parent. Analysis of phenotypic data for shell hardness demonstrated the utility of these maps for quantitative trait locus mapping. Comparison of these maps to the peach genome assembly confirmed high synteny and collinearity between the peach and almond genomes. The marker assays were applied to progeny from several other Nonpareil crosses, providing the basis for a composite linkage map of Nonpareil. Applications of the assays to a panel of almond clones and a panel of rootstocks used for almond production demonstrated the broad applicability of the markers and provide subsets of markers that could be used to discriminate among accessions. The sequence-based linkage maps and single nucleotide polymorphism assays presented here could be useful resources for the genetic analysis and genetic improvement of almond.

  19. A DArT marker genetic map of perennial ryegrass (Lolium perenne L.) integrated with detailed comparative mapping information; comparison with existing DArT marker genetic maps of Lolium perenne, L. multiflorum and Festuca pratensis.

    King, Julie; Thomas, Ann; James, Caron; King, Ian; Armstead, Ian

    2013-07-03

    Ryegrasses and fescues (genera, Lolium and Festuca) are species of forage and turf grasses which are used widely in agricultural and amenity situations. They are classified within the sub-family Pooideae and so are closely related to Brachypodium distachyon, wheat, barley, rye and oats. Recently, a DArT array has been developed which can be used in generating marker and mapping information for ryegrasses and fescues. This represents a potential common marker set for ryegrass and fescue researchers which can be linked through to comparative genomic information for the grasses. A F2 perennial ryegrass genetic map was developed consisting of 7 linkage groups defined by 1316 markers and deriving a total map length of 683 cM. The marker set included 866 DArT and 315 gene sequence-based markers. Comparison with previous DArT mapping studies in perennial and Italian ryegrass (L. multiflorum) identified 87 and 105 DArT markers in common, respectively, of which 94% and 87% mapped to homoeologous linkage groups. A similar comparison with meadow fescue (F. pratensis) identified only 28 DArT markers in common, of which c. 50% mapped to non-homoelogous linkage groups. In L. perenne, the genetic distance spanned by the DArT markers encompassed the majority of the regions that could be described in terms of comparative genomic relationships with rice, Brachypodium distachyon, and Sorghum bicolor. DArT markers are likely to be a useful common marker resource for ryegrasses and fescues, though the success in aligning different populations through the mapping of common markers will be influenced by degrees of population interrelatedness. The detailed mapping of DArT and gene-based markers in this study potentially allows comparative relationships to be derived in future mapping populations characterised using solely DArT markers.

  20. A consensus linkage map of lentil based on DArT markers from three RIL mapping populations.

    Duygu Ates

    Full Text Available Lentil (Lens culinaris ssp. culinaris Medikus is a diploid (2n = 2x = 14, self-pollinating grain legume with a haploid genome size of about 4 Gbp and is grown throughout the world with current annual production of 4.9 million tonnes.A consensus map of lentil (Lens culinaris ssp. culinaris Medikus was constructed using three different lentils recombinant inbred line (RIL populations, including "CDC Redberry" x "ILL7502" (LR8, "ILL8006" x "CDC Milestone" (LR11 and "PI320937" x "Eston" (LR39.The lentil consensus map was composed of 9,793 DArT markers, covered a total of 977.47 cM with an average distance of 0.10 cM between adjacent markers and constructed 7 linkage groups representing 7 chromosomes of the lentil genome. The consensus map had no gap larger than 12.67 cM and only 5 gaps were found to be between 12.67 cM and 6.0 cM (on LG3 and LG4. The localization of the SNP markers on the lentil consensus map were in general consistent with their localization on the three individual genetic linkage maps and the lentil consensus map has longer map length, higher marker density and shorter average distance between the adjacent markers compared to the component linkage maps.This high-density consensus map could provide insight into the lentil genome. The consensus map could also help to construct a physical map using a Bacterial Artificial Chromosome library and map based cloning studies. Sequence information of DArT may help localization of orientation scaffolds from Next Generation Sequencing data.

  1. A consensus linkage map of lentil based on DArT markers from three RIL mapping populations.

    Ates, Duygu; Aldemir, Secil; Alsaleh, Ahmad; Erdogmus, Semih; Nemli, Seda; Kahriman, Abdullah; Ozkan, Hakan; Vandenberg, Albert; Tanyolac, Bahattin

    2018-01-01

    Lentil (Lens culinaris ssp. culinaris Medikus) is a diploid (2n = 2x = 14), self-pollinating grain legume with a haploid genome size of about 4 Gbp and is grown throughout the world with current annual production of 4.9 million tonnes. A consensus map of lentil (Lens culinaris ssp. culinaris Medikus) was constructed using three different lentils recombinant inbred line (RIL) populations, including "CDC Redberry" x "ILL7502" (LR8), "ILL8006" x "CDC Milestone" (LR11) and "PI320937" x "Eston" (LR39). The lentil consensus map was composed of 9,793 DArT markers, covered a total of 977.47 cM with an average distance of 0.10 cM between adjacent markers and constructed 7 linkage groups representing 7 chromosomes of the lentil genome. The consensus map had no gap larger than 12.67 cM and only 5 gaps were found to be between 12.67 cM and 6.0 cM (on LG3 and LG4). The localization of the SNP markers on the lentil consensus map were in general consistent with their localization on the three individual genetic linkage maps and the lentil consensus map has longer map length, higher marker density and shorter average distance between the adjacent markers compared to the component linkage maps. This high-density consensus map could provide insight into the lentil genome. The consensus map could also help to construct a physical map using a Bacterial Artificial Chromosome library and map based cloning studies. Sequence information of DArT may help localization of orientation scaffolds from Next Generation Sequencing data.

  2. An annotated genetic map of loblolly pine based on microsatellite and cDNA markers

    Wimalanathan Kokulapalan

    2011-01-01

    Full Text Available Abstract Background Previous loblolly pine (Pinus taeda L. genetic linkage maps have been based on a variety of DNA polymorphisms, such as AFLPs, RAPDs, RFLPs, and ESTPs, but only a few SSRs (simple sequence repeats, also known as simple tandem repeats or microsatellites, have been mapped in P. taeda. The objective of this study was to integrate a large set of SSR markers from a variety of sources and published cDNA markers into a composite P. taeda genetic map constructed from two reference mapping pedigrees. A dense genetic map that incorporates SSR loci will benefit complete pine genome sequencing, pine population genetics studies, and pine breeding programs. Careful marker annotation using a variety of references further enhances the utility of the integrated SSR map. Results The updated P. taeda genetic map, with an estimated genome coverage of 1,515 cM(Kosambi across 12 linkage groups, incorporated 170 new SSR markers and 290 previously reported SSR, RFLP, and ESTP markers. The average marker interval was 3.1 cM. Of 233 mapped SSR loci, 84 were from cDNA-derived sequences (EST-SSRs and 149 were from non-transcribed genomic sequences (genomic-SSRs. Of all 311 mapped cDNA-derived markers, 77% were associated with NCBI Pta UniGene clusters, 67% with RefSeq proteins, and 62% with functional Gene Ontology (GO terms. Duplicate (i.e., redundant accessory and paralogous markers were tentatively identified by evaluating marker sequences by their UniGene cluster IDs, clone IDs, and relative map positions. The average gene diversity, He, among polymorphic SSR loci, including those that were not mapped, was 0.43 for 94 EST-SSRs and 0.72 for 83 genomic-SSRs. The genetic map can be viewed and queried at http://www.conifergdb.org/pinemap. Conclusions Many polymorphic and genetically mapped SSR markers are now available for use in P. taeda population genetics, studies of adaptive traits, and various germplasm management applications. Annotating mapped

  3. Transcriptome-enabled marker discovery and mapping of plastochron-related genes in Petunia spp.

    Guo, Yufang; Wiegert-Rininger, Krystle E; Vallejo, Veronica A; Barry, Cornelius S; Warner, Ryan M

    2015-09-24

    Petunia (Petunia × hybrida), derived from a hybrid between P. axillaris and P. integrifolia, is one of the most economically important bedding plant crops and Petunia spp. serve as model systems for investigating the mechanisms underlying diverse mating systems and pollination syndromes. In addition, we have previously described genetic variation and quantitative trait loci (QTL) related to petunia development rate and morphology, which represent important breeding targets for the floriculture industry to improve crop production and performance. Despite the importance of petunia as a crop, the floriculture industry has been slow to adopt marker assisted selection to facilitate breeding strategies and there remains a limited availability of sequences and molecular markers from the genus compared to other economically important members of the Solanaceae family such as tomato, potato and pepper. Here we report the de novo assembly, annotation and characterization of transcriptomes from P. axillaris, P. exserta and P. integrifolia. Each transcriptome assembly was derived from five tissue libraries (callus, 3-week old seedlings, shoot apices, flowers of mixed developmental stages, and trichomes). A total of 74,573, 54,913, and 104,739 assembled transcripts were recovered from P. axillaris, P. exserta and P. integrifolia, respectively and following removal of multiple isoforms, 32,994 P. axillaris, 30,225 P. exserta, and 33,540 P. integrifolia high quality representative transcripts were extracted for annotation and expression analysis. The transcriptome data was mined for single nucleotide polymorphisms (SNP) and simple sequence repeat (SSR) markers, yielding 89,007 high quality SNPs and 2949 SSRs, respectively. 15,701 SNPs were computationally converted into user-friendly cleaved amplified polymorphic sequence (CAPS) markers and a subset of SNP and CAPS markers were experimentally verified. CAPS markers developed from plastochron-related homologous transcripts

  4. Identification of milling and baking quality QTL in multiple soft wheat mapping populations.

    Cabrera, Antonio; Guttieri, Mary; Smith, Nathan; Souza, Edward; Sturbaum, Anne; Hua, Duc; Griffey, Carl; Barnett, Marla; Murphy, Paul; Ohm, Herb; Uphaus, Jim; Sorrells, Mark; Heffner, Elliot; Brown-Guedira, Gina; Van Sanford, David; Sneller, Clay

    2015-11-01

    Two mapping approaches were use to identify and validate milling and baking quality QTL in soft wheat. Two LG were consistently found important for multiple traits and we recommend the use marker-assisted selection on specific markers reported here. Wheat-derived food products require a range of characteristics. Identification and understanding of the genetic components controlling end-use quality of wheat is important for crop improvement. We assessed the underlying genetics controlling specific milling and baking quality parameters of soft wheat including flour yield, softness equivalent, flour protein, sucrose, sodium carbonate, water absorption and lactic acid, solvent retention capacities in a diversity panel and five bi-parental mapping populations. The populations were genotyped with SSR and DArT markers, with markers specific for the 1BL.1RS translocation and sucrose synthase gene. Association analysis and composite interval mapping were performed to identify quantitative trait loci (QTL). High heritability was observed for each of the traits evaluated, trait correlations were consistent over populations, and transgressive segregants were common in all bi-parental populations. A total of 26 regions were identified as potential QTL in the diversity panel and 74 QTL were identified across all five bi-parental mapping populations. Collinearity of QTL from chromosomes 1B and 2B was observed across mapping populations and was consistent with results from the association analysis in the diversity panel. Multiple regression analysis showed the importance of the two 1B and 2B regions and marker-assisted selection for the favorable alleles at these regions should improve quality.

  5. Development and genetic mapping of SSR markers in foxtail millet [Setaria italica (L.) P. Beauv.].

    Jia, Xiaoping; Zhang, Zhongbao; Liu, Yinghui; Zhang, Chengwei; Shi, Yunsu; Song, Yanchun; Wang, Tianyu; Li, Yu

    2009-02-01

    SSR markers are desirable markers in analysis of genetic diversity, quantitative trait loci mapping and gene locating. In this study, SSR markers were developed from two genomic libraries enriched for (GA)n and (CA)n of foxtail millet [Setaria italica (L.) P. Beauv.], a crop of historical importance in China. A total of 100 SSR markers among the 193 primer pairs detected polymorphism between two mapping parents of an F(2) population, i.e. "B100" of cultivated S. italica and "A10" of wild S. viridis. Excluding 14 markers with unclear amplifications, and five markers unlinked with any linkage group, a foxtail millet SSR linkage map was constructed by integrating 81 new developed SSR markers with 20 RFLP anchored markers. The 81 SSRs covered nine chromosomes of foxtail millet. The length of the map was 1,654 cM, with an average interval distance between markers of 16.4 cM. The 81 SSR markers were not evenly distributed throughout the nine chromosomes, with Ch.8 harbouring the least (3 markers) and Ch.9 harbouring the most (18 markers). To verify the usefulness of the SSR markers developed, 37 SSR markers were randomly chosen to analyze genetic diversity of 40 foxtail millet accessions. Totally 228 alleles were detected, with an average 6.16 alleles per locus. Polymorphism information content (PIC) value for each locus ranged from 0.413 to 0.847, with an average of 0.697. A positive correlation between PIC and number of alleles and between PIC and number of repeat unit were found [0.802 and 0.429, respectively (P < 0.01)]. UPGMA analysis revealed that the 40 foxtail millet cultivars could be grouped into five clusters in which the landraces' grouping was largely consistent with ecotypes while the breeding varieties from different provinces in China tended to be grouped together.

  6. Preliminary genetic linkage map of Miscanthus sinensis with RAPD markers

    Atienza, S.G.; Satovic, Z.; Petersen, K.K.; Dolstra, O.; Martin, A.

    2002-01-01

    We have used an "offspring cross" mapping strategy in combination with the random amplified polymorphic DNA (RAPD) assay to construct the first genetic map of the species Miscanthus sinensis (2n = 2x = 38). This map is based on an outbred population of 89 individuals resulting from the cross between

  7. M3: Matrix Multiplication on MapReduce

    Silvestri, Francesco; Ceccarello, Matteo

    2015-01-01

    M3 is an Hadoop library for performing dense and sparse matrix multiplication in MapReduce. The library is based on multi-round algorithms exploiting the 3D decomposition of the problem.......M3 is an Hadoop library for performing dense and sparse matrix multiplication in MapReduce. The library is based on multi-round algorithms exploiting the 3D decomposition of the problem....

  8. Multiple Autonomous Vehicles for Minefield Reconnaissance and Mapping

    1997-12-01

    NPS-ME-97-008 NAVAL POSTGRADUATE SCHOOL Monterey, California ItC A D- 19980421 131 =C QUALTY Ui Ji.CTEJ) THESIS MULTIPLE AUTONOMOUS VEHICLES FOR...MULTIPLE AUTONOMOUS VEHICLES FOR MINEFIELD 5. FUNDING NUMBERS RECONNAISSANCE AND MAPPING N0001497WX30039 6. AUTHOR(S) Jack A. Starr 7. PERFORMING... AUTONOMOUS VEHICLES FOR MINEFIELD RECONNAISSANCE AND MAPPING Jack A. Starr Lieutenant, United States Navy B.S., Oregon State University, 1991 Submitted in

  9. Elimination of ghost markers during dual sensor-based infrared tracking of multiple individual reflective markers

    Stroian, G.; Falco, T.; Seuntjens, J.P.

    2004-01-01

    The accuracy of dose delivery in radiotherapy is affected by the uncertainty in tumor localization. Motion of internal anatomy due to physiological processes such as respiration may lead to significant displacements which compromise tumor coverage and generate irradiation of healthy tissue. Real-time tracking with infrared-based systems is often used for tracking thoracic motion in radiation therapy. We studied the origin of ghost markers ('crosstalk') which may appear during dual sensor-based infrared tracking of independent reflective markers. Ghost markers occur when two or more reflective markers are coplanar with each other and with the sensors of the two camera-based infrared tracking system. Analysis shows that sensors are not points but they have a finite extent and this extent determines for each marker a 'ghost volume'. If one reflective marker enters the ghost volume of another marker, ghost markers will be reported by the tracking system; if the reflective markers belong to a surface their 'ghost volume' is reduced to a 'ghost surface' (ghost zone). Appearance of ghost markers is predicted for markers taped on the torso of an anthropomorphic phantom. This study illustrates the dependence of the shape, extent, and location of the ghost zones on the shape of the anthropomorphic phantom, the angle of view of the tracking system, and the distance between the tracking system and the anthropomorphic phantom. It is concluded that the appearance of ghost markers can be avoided by positioning the markers outside the ghost zones of the other markers. However, if this is not possible and the initial marker configuration is ghost marker-free, ghost markers can be eliminated during real-time tracking by virtue of the fact that they appear in the coordinate data sequence only temporarily

  10. A genetic linkage map of hexaploid naked oat constructed with SSR markers

    Gaoyuan Song

    2015-08-01

    Full Text Available Naked oat is a unique health food crop in China. Using 202 F2 individuals derived from a hybrid between the variety 578 and the landrace Sanfensan, we constructed a genetic linkage map consisting of 22 linkage groups covering 2070.50 cM and including 208 simple sequence repeat (SSR markers. The minimum distance between adjacent markers was 0.01 cM and the average was 9.95 cM. Each linkage group contained 2–22 markers. The largest linkage group covered 174.40 cM and the shortest one covered 36.80 cM, with an average of 94.11 cM. Thirty-six markers (17.3% showing distorted segregation were distributed across linkage groups LG5 to LG22. This map complements published oat genetic maps and is applicable for quantitative trait locus analysis, gene cloning and molecular marker-assisted selection.

  11. High-density Integrated Linkage Map Based on SSR Markers in Soybean

    Hwang, Tae-Young; Sayama, Takashi; Takahashi, Masakazu; Takada, Yoshitake; Nakamoto, Yumi; Funatsuki, Hideyuki; Hisano, Hiroshi; Sasamoto, Shigemi; Sato, Shusei; Tabata, Satoshi; Kono, Izumi; Hoshi, Masako; Hanawa, Masayoshi; Yano, Chizuru; Xia, Zhengjun; Harada, Kyuya; Kitamura, Keisuke; Ishimoto, Masao

    2009-01-01

    A well-saturated molecular linkage map is a prerequisite for modern plant breeding. Several genetic maps have been developed for soybean with various types of molecular markers. Simple sequence repeats (SSRs) are single-locus markers with high allelic variation and are widely applicable to different genotypes. We have now mapped 1810 SSR or sequence-tagged site markers in one or more of three recombinant inbred populations of soybean (the US cultivar ‘Jack’ × the Japanese cultivar ‘Fukuyutaka’, the Chinese cultivar ‘Peking’ × the Japanese cultivar ‘Akita’, and the Japanese cultivar ‘Misuzudaizu’ × the Chinese breeding line ‘Moshidou Gong 503’) and have aligned these markers with the 20 consensus linkage groups (LGs). The total length of the integrated linkage map was 2442.9 cM, and the average number of molecular markers was 90.5 (range of 70–114) for the 20 LGs. We examined allelic diversity for 1238 of the SSR markers among 23 soybean cultivars or lines and a wild accession. The number of alleles per locus ranged from 2 to 7, with an average of 2.8. Our high-density linkage map should facilitate ongoing and future genomic research such as analysis of quantitative trait loci and positional cloning in addition to marker-assisted selection in soybean breeding. PMID:19531560

  12. Reconstruction of multiple line source attenuation maps

    Celler, A.; Sitek, A.; Harrop, R.

    1996-01-01

    A simple configuration for a transmission source for the single photon emission computed tomography (SPECT) was proposed, which utilizes a series of collimated line sources parallel to the axis of rotation of a camera. The detector is equipped with a standard parallel hole collimator. We have demonstrated that this type of source configuration can be used to generate sufficient data for the reconstruction of the attenuation map when using 8-10 line sources spaced by 3.5-4.5 cm for a 30 x 40cm detector at 65cm distance from the sources. Transmission data for a nonuniform thorax phantom was simulated, then binned and reconstructed using filtered backprojection (FBP) and iterative methods. The optimum maps are obtained with data binned into 2-3 bins and FBP reconstruction. The activity in the source was investigated for uniform and exponential activity distributions, as well as the effect of gaps and overlaps of the neighboring fan beams. A prototype of the line source has been built and the experimental verification of the technique has started

  13. A detailed linkage map of lettuce based on SSAP, AFLP and NBS markers

    Syed, H.; Sorensen, A.P.; Antonise, R.; van de Wiel, C.; van der Linden, C.G.; van 't Westende, W.; Hooftman, D.A.P.; den Nijs, J.C.M.; Flavell, A.J.

    2006-01-01

    Abstract Molecular markers based upon a novel lettuce LTR retrotransposon and the nucleotide binding site-leucine-rich repeat (NBS-LRR) family of disease resistance-associated genes have been combined with AFLP markers to generate a 458 locus genetic linkage map for lettuce. A total of 187

  14. Association Mapping for Important Agronomic Traits in Safflower (Carthamus tinctorius L.) Core Collection Using Microsatellite Markers

    Heena Ambreen; Shivendra Kumar; Amar Kumar; Manu Agarwal; Arun Jagannath; Shailendra Goel

    2018-01-01

    Carthamus tinctorius L. (safflower) is an important oilseed crop producing seed oil rich in unsaturated fatty acids. Scarcity of identified marker-trait associations is a major limitation toward development of successful marker-assisted breeding programs in safflower. In the present study, a safflower panel (CartAP) comprising 124 accessions derived from two core collections was assayed for its suitability for association mapping. Genotyping of CartAP using microsatellite markers revealed sig...

  15. On Supra-Additive and Supra-Multiplicative Maps

    Jin Xi Chen; Zi Li Chen

    2013-01-01

    Let A and B be ordered algebras over ℝ, where A has a generating positive cone and B satisfies the property that b2>0 if 0≠b∈B. We give some conditions for a map T:A→B which is supra-additive and supra-multiplicative for all positive and negative elements to be linear and multiplicative; that is, T is a homomorphism of algebras. Our results generalize some known results on supra-additive and supra-multiplicative maps between spaces of real functions.

  16. Sequence based polymorphic (SBP marker technology for targeted genomic regions: its application in generating a molecular map of the Arabidopsis thaliana genome

    Sahu Binod B

    2012-01-01

    Full Text Available Abstract Background Molecular markers facilitate both genotype identification, essential for modern animal and plant breeding, and the isolation of genes based on their map positions. Advancements in sequencing technology have made possible the identification of single nucleotide polymorphisms (SNPs for any genomic regions. Here a sequence based polymorphic (SBP marker technology for generating molecular markers for targeted genomic regions in Arabidopsis is described. Results A ~3X genome coverage sequence of the Arabidopsis thaliana ecotype, Niederzenz (Nd-0 was obtained by applying Illumina's sequencing by synthesis (Solexa technology. Comparison of the Nd-0 genome sequence with the assembled Columbia-0 (Col-0 genome sequence identified putative single nucleotide polymorphisms (SNPs throughout the entire genome. Multiple 75 base pair Nd-0 sequence reads containing SNPs and originating from individual genomic DNA molecules were the basis for developing co-dominant SBP markers. SNPs containing Col-0 sequences, supported by transcript sequences or sequences from multiple BAC clones, were compared to the respective Nd-0 sequences to identify possible restriction endonuclease enzyme site variations. Small amplicons, PCR amplified from both ecotypes, were digested with suitable restriction enzymes and resolved on a gel to reveal the sequence based polymorphisms. By applying this technology, 21 SBP markers for the marker poor regions of the Arabidopsis map representing polymorphisms between Col-0 and Nd-0 ecotypes were generated. Conclusions The SBP marker technology described here allowed the development of molecular markers for targeted genomic regions of Arabidopsis. It should facilitate isolation of co-dominant molecular markers for targeted genomic regions of any animal or plant species, whose genomic sequences have been assembled. This technology will particularly facilitate the development of high density molecular marker maps, essential for

  17. Admixture mapping of end stage kidney disease genetic susceptibility using estimated mutual information ancestry informative markers

    Geiger Dan

    2010-10-01

    Full Text Available Abstract Background The question of a genetic contribution to the higher prevalence and incidence of end stage kidney disease (ESKD among African Americans (AA remained unresolved, until recent findings using admixture mapping pointed to the association of a genomic locus on chromosome 22 with this disease phenotype. In the current study we utilize this example to demonstrate the utility of applying a multi-step admixture mapping approach. Methods A multi-step case only admixture mapping study, consisted of the following steps was designed: 1 Assembly of the sample dataset (ESKD AA; 2 Design of the estimated mutual information ancestry informative markers (n = 2016 screening panel 3; Genotyping the sample set whose size was determined by a power analysis (n = 576 appropriate for the initial screening panel; 4 Inference of local ancestry for each individual and identification of regions with increased AA ancestry using two different ancestry inference statistical approaches; 5 Enrichment of the initial screening panel; 6 Power analysis of the enriched panel 7 Genotyping of additional samples. 8 Re-analysis of the genotyping results to identify a genetic risk locus. Results The initial screening phase yielded a significant peak using the ADMIXMAP ancestry inference program applying case only statistics. Subgroup analysis of 299 ESKD patients with no history of diabetes yielded peaks using both the ANCESTRYMAP and ADMIXMAP ancestry inference programs. The significant peak was found on chromosome 22. Genotyping of additional ancestry informative markers on chromosome 22 that took into account linkage disequilibrium in the ancestral populations, and the addition of samples increased the statistical significance of the finding. Conclusions A multi-step admixture mapping analysis of AA ESKD patients replicated the finding of a candidate risk locus on chromosome 22, contributing to the heightened susceptibility of African Americans to develop non

  18. Body fluid markers to monitor multiple sclerosis: The assays and the challenges

    Laman, J.D.; Thompson, E.J.; Kappos, L.

    1998-01-01

    The need for reliable markers of disease activity in multiple sclerosis (MS) to better guide basic research, diagnosis, treatment, and monitoring of therapy is well-recognized. A recent European Charcot Foundation Symposium (Body fluid markers for course and activity of disease in multiple sclerosis

  19. Genetic linkage mapping in an F2 perennial ryegrass population using DArT markers

    Tomaszewski, Céline; Byrne, Stephen; Foito, Alexandra

    2012-01-01

    Perennial ryegrass is the principal forage grass species used in temperate agriculture. In recent years, significant efforts have been made to develop molecular marker strategies to allow cost-effective characterization of a large number of loci simultaneously. One such strategy involves using DAr......T markers, and a DArT array has recently been developed for the Lolium-Festuca complex. In this study, we report the first use of the DArTFest array to generate a genetic linkage map based on 326 markers in a Lolium perenne F2 population, consisting of 325 genotypes. For proof of concept, the map was used...

  20. An annotated genetic map of loblolly pine based on microsatellite and cDNA markers

    Craig S. Echt; Surya Saha; Konstantin V. Krutovsky; Kokulapalan Wimalanathan; John E. Erpelding; Chun Liang; C Dana Nelson

    2011-01-01

    Previous loblolly pine (Pinus taeda L.) genetic linkage maps have been based on a variety of DNA polymorphisms, such as AFLPs, RAPDs, RFLPs, and ESTPs, but only a few SSRs (simple sequence repeats), also known as simple tandem repeats or microsatellites, have been mapped in P. taeda. The objective of this study was to integrate a large set of SSR markers from a variety...

  1. Development of genomic SSR markers for fingerprinting lettuce (Lactuca sativa L.) cultivars and mapping genes.

    Rauscher, Gilda; Simko, Ivan

    2013-01-22

    Lettuce (Lactuca sativa L.) is the major crop from the group of leafy vegetables. Several types of molecular markers were developed that are effectively used in lettuce breeding and genetic studies. However only a very limited number of microsattelite-based markers are publicly available. We have employed the method of enriched microsatellite libraries to develop 97 genomic SSR markers. Testing of newly developed markers on a set of 36 Lactuca accession (33 L. sativa, and one of each L. serriola L., L. saligna L., and L. virosa L.) revealed that both the genetic heterozygosity (UHe = 0.56) and the number of loci per SSR (Na = 5.50) are significantly higher for genomic SSR markers than for previously developed EST-based SSR markers (UHe = 0.32, Na = 3.56). Fifty-four genomic SSR markers were placed on the molecular linkage map of lettuce. Distribution of markers in the genome appeared to be random, with the exception of possible cluster on linkage group 6. Any combination of 32 genomic SSRs was able to distinguish genotypes of all 36 accessions. Fourteen of newly developed SSR markers originate from fragments with high sequence similarity to resistance gene candidates (RGCs) and RGC pseudogenes. Analysis of molecular variance (AMOVA) of L. sativa accessions showed that approximately 3% of genetic diversity was within accessions, 79% among accessions, and 18% among horticultural types. The newly developed genomic SSR markers were added to the pool of previously developed EST-SSRs markers. These two types of SSR-based markers provide useful tools for lettuce cultivar fingerprinting, development of integrated molecular linkage maps, and mapping of genes.

  2. Towards the Development of a Molecular Map in Switchgrass: I. Microsatellite Marker Development; ANNUAL

    Gunter, L.E.

    2001-01-01

    The long-term goal of the switchgrass breeding program is to improve regionally adapted varieties and increase biomass yield and feedstock quality. Although, to some extent, biomass yields are dependent on environmental constraints, increased yield can be achieved through the development of genotypes with improved seasonal adaptation, tolerance to unfavorable environmental conditions, and improved resistance to pest and disease. To date, improvement in switchgrass has relied on recurrent breeding strategies based on phenotypic or genotypic selection. Yield improvements have been modest by this method. If we expect to make significant increase in yields, we need tools that will allow us to map complex traits and uncover the genes that influence them. A genetic linkage map could be a powerful tool for accelerating switchgrass development through marker-assisted selection, breeding and recombination. This type of mapping requires the development of markers that can be associated with phenotypic traits in a population of known pedigree. The most commonly used markers for mapping include restriction fragment length polymorphisms (RFLP) and simple sequence repeats (SSR). At ORNL, we have been concentrating on the development of SSR markers, while our colleagues at the University of Georgia are developing RFLP markers in order to select parents to produce a mapping population and from there to create a framework map from(approx)100 F1 progeny

  3. Gene-based single nucleotide polymorphism markers for genetic and association mapping in common bean.

    Galeano, Carlos H; Cortés, Andrés J; Fernández, Andrea C; Soler, Álvaro; Franco-Herrera, Natalia; Makunde, Godwill; Vanderleyden, Jos; Blair, Matthew W

    2012-06-26

    In common bean, expressed sequence tags (ESTs) are an underestimated source of gene-based markers such as insertion-deletions (Indels) or single-nucleotide polymorphisms (SNPs). However, due to the nature of these conserved sequences, detection of markers is difficult and portrays low levels of polymorphism. Therefore, development of intron-spanning EST-SNP markers can be a valuable resource for genetic experiments such as genetic mapping and association studies. In this study, a total of 313 new gene-based markers were developed at target genes. Intronic variation was deeply explored in order to capture more polymorphism. Introns were putatively identified after comparing the common bean ESTs with the soybean genome, and the primers were designed over intron-flanking regions. The intronic regions were evaluated for parental polymorphisms using the single strand conformational polymorphism (SSCP) technique and Sequenom MassARRAY system. A total of 53 new marker loci were placed on an integrated molecular map in the DOR364 × G19833 recombinant inbred line (RIL) population. The new linkage map was used to build a consensus map, merging the linkage maps of the BAT93 × JALO EEP558 and DOR364 × BAT477 populations. A total of 1,060 markers were mapped, with a total map length of 2,041 cM across 11 linkage groups. As a second application of the generated resource, a diversity panel with 93 genotypes was evaluated with 173 SNP markers using the MassARRAY-platform and KASPar technology. These results were coupled with previous SSR evaluations and drought tolerance assays carried out on the same individuals. This agglomerative dataset was examined, in order to discover marker-trait associations, using general linear model (GLM) and mixed linear model (MLM). Some significant associations with yield components were identified, and were consistent with previous findings. In short, this study illustrates the power of intron-based markers for linkage and association mapping in

  4. Effect of Co-segregating Markers on High-Density Genetic Maps and Prediction of Map Expansion Using Machine Learning Algorithms.

    N'Diaye, Amidou; Haile, Jemanesh K; Fowler, D Brian; Ammar, Karim; Pozniak, Curtis J

    2017-01-01

    Advances in sequencing and genotyping methods have enable cost-effective production of high throughput single nucleotide polymorphism (SNP) markers, making them the choice for linkage mapping. As a result, many laboratories have developed high-throughput SNP assays and built high-density genetic maps. However, the number of markers may, by orders of magnitude, exceed the resolution of recombination for a given population size so that only a minority of markers can accurately be ordered. Another issue attached to the so-called 'large p, small n' problem is that high-density genetic maps inevitably result in many markers clustering at the same position (co-segregating markers). While there are a number of related papers, none have addressed the impact of co-segregating markers on genetic maps. In the present study, we investigated the effects of co-segregating markers on high-density genetic map length and marker order using empirical data from two populations of wheat, Mohawk × Cocorit (durum wheat) and Norstar × Cappelle Desprez (bread wheat). The maps of both populations consisted of 85% co-segregating markers. Our study clearly showed that excess of co-segregating markers can lead to map expansion, but has little effect on markers order. To estimate the inflation factor (IF), we generated a total of 24,473 linkage maps (8,203 maps for Mohawk × Cocorit and 16,270 maps for Norstar × Cappelle Desprez). Using seven machine learning algorithms, we were able to predict with an accuracy of 0.7 the map expansion due to the proportion of co-segregating markers. For example in Mohawk × Cocorit, with 10 and 80% co-segregating markers the length of the map inflated by 4.5 and 16.6%, respectively. Similarly, the map of Norstar × Cappelle Desprez expanded by 3.8 and 11.7% with 10 and 80% co-segregating markers. With the increasing number of markers on SNP-chips, the proportion of co-segregating markers in high-density maps will continue to increase making map expansion

  5. Effect of Co-segregating Markers on High-Density Genetic Maps and Prediction of Map Expansion Using Machine Learning Algorithms

    Amidou N’Diaye

    2017-08-01

    Full Text Available Advances in sequencing and genotyping methods have enable cost-effective production of high throughput single nucleotide polymorphism (SNP markers, making them the choice for linkage mapping. As a result, many laboratories have developed high-throughput SNP assays and built high-density genetic maps. However, the number of markers may, by orders of magnitude, exceed the resolution of recombination for a given population size so that only a minority of markers can accurately be ordered. Another issue attached to the so-called ‘large p, small n’ problem is that high-density genetic maps inevitably result in many markers clustering at the same position (co-segregating markers. While there are a number of related papers, none have addressed the impact of co-segregating markers on genetic maps. In the present study, we investigated the effects of co-segregating markers on high-density genetic map length and marker order using empirical data from two populations of wheat, Mohawk × Cocorit (durum wheat and Norstar × Cappelle Desprez (bread wheat. The maps of both populations consisted of 85% co-segregating markers. Our study clearly showed that excess of co-segregating markers can lead to map expansion, but has little effect on markers order. To estimate the inflation factor (IF, we generated a total of 24,473 linkage maps (8,203 maps for Mohawk × Cocorit and 16,270 maps for Norstar × Cappelle Desprez. Using seven machine learning algorithms, we were able to predict with an accuracy of 0.7 the map expansion due to the proportion of co-segregating markers. For example in Mohawk × Cocorit, with 10 and 80% co-segregating markers the length of the map inflated by 4.5 and 16.6%, respectively. Similarly, the map of Norstar × Cappelle Desprez expanded by 3.8 and 11.7% with 10 and 80% co-segregating markers. With the increasing number of markers on SNP-chips, the proportion of co-segregating markers in high-density maps will continue to increase

  6. Multiple Brain Markers are Linked to Age-Related Variation in Cognition

    Hedden, Trey; Schultz, Aaron P.; Rieckmann, Anna; Mormino, Elizabeth C.; Johnson, Keith A.; Sperling, Reisa A.; Buckner, Randy L.

    2016-01-01

    Age-related alterations in brain structure and function have been challenging to link to cognition due to potential overlapping influences of multiple neurobiological cascades. We examined multiple brain markers associated with age-related variation in cognition. Clinically normal older humans aged 65–90 from the Harvard Aging Brain Study (N = 186) were characterized on a priori magnetic resonance imaging markers of gray matter thickness and volume, white matter hyperintensities, fractional anisotropy (FA), resting-state functional connectivity, positron emission tomography markers of glucose metabolism and amyloid burden, and cognitive factors of processing speed, executive function, and episodic memory. Partial correlation and mediation analyses estimated age-related variance in cognition shared with individual brain markers and unique to each marker. The largest relationships linked FA and striatum volume to processing speed and executive function, and hippocampal volume to episodic memory. Of the age-related variance in cognition, 70–80% was accounted for by combining all brain markers (but only ∼20% of total variance). Age had significant indirect effects on cognition via brain markers, with significant markers varying across cognitive domains. These results suggest that most age-related variation in cognition is shared among multiple brain markers, but potential specificity between some brain markers and cognitive domains motivates additional study of age-related markers of neural health. PMID:25316342

  7. MAP17 and SGLT1 protein expression levels as prognostic markers for cervical tumor patient survival.

    Marco Perez

    Full Text Available MAP17 is a membrane-associated protein that is overexpressed in human tumors. Because the expression of MAP17 increases reactive oxygen species (ROS generation through SGLT1 in cancer cells, in the present work, we investigated whether MAP17 and/or SGLT1 might be markers for the activity of treatments involving oxidative stress, such as cisplatin or radiotherapy. First, we confirmed transcriptional alterations in genes involved in the oxidative stress induced by MAP17 expression in HeLa cervical tumor cells and found that Hela cells expressing MAP17 were more sensitive to therapies that induce ROS than were parental cells. Furthermore, MAP17 increased glucose uptake through SGLT receptors. We then analyzed MAP17 and SGLT1 expression levels in cervical tumors treated with cisplatin plus radiotherapy and correlated the expression levels with patient survival. MAP17 and SGLT1 were expressed in approximately 70% and 50% of cervical tumors of different types, respectively, but they were not expressed in adenoma tumors. Furthermore, there was a significant correlation between MAP17 and SGLT1 expression levels. High levels of either MAP17 or SGLT1 correlated with improved patient survival after treatment. However, the patients with high levels of both MAP17 and SGLT1 survived through the end of this study. Therefore, the combination of high MAP17 and SGLT1 levels is a marker for good prognosis in patients with cervical tumors after cisplatin plus radiotherapy treatment. These results also suggest that the use of MAP17 and SGLT1 markers may identify patients who are likely to exhibit a better response to treatments that boost oxidative stress in other cancer types.

  8. Use of a human chromosome 11 radiation hybrid panel to map markers at 11q13

    Withers, D.; Richard, C. III; Meeker, T.C.; Maurer, S.; Evans, G.; Myers, R.M.; Cox, D.R.

    1990-01-01

    A human/hamster hybrid cell line containing human chromosome 11 was X-irradiated and 102-independent derivative lines were recovered. These 'radiation hybrids' contain random fragments of human chromosome 11. This radiation hybrid panel was used to score the retention of markers at band 11q13. Statistical analysis of marker co-retention patterns in the radiation hybrid panel permits a preliminary ordering and mapping of the markers used. The best order for six scored markers is: proximal - CD5 - CD20 - PGA - HST - BCL1 - SEA - distal. Additional markers are currently being scored. The six 11q13 markers above are spread over approximately 10-12 mB of DNA. The mapping data has implications for the identification of the bcl-1 gene. bcl-1 is the site of chromosome breakage in translocations associated with B lymphocytic malignancy. bcl-1 markers map at least 4 Mb away from any of four genes previously hypothesized to be activated by such translocations, thereby making them unlikely candidates for activation

  9. A novel linkage map of sugarcane with evidence for clustering of retrotransposon-based markers

    Palhares Alessandra C

    2012-06-01

    Full Text Available Abstract Background The development of sugarcane as a sustainable crop has unlimited applications. The crop is one of the most economically viable for renewable energy production, and CO2 balance. Linkage maps are valuable tools for understanding genetic and genomic organization, particularly in sugarcane due to its complex polyploid genome of multispecific origins. The overall objective of our study was to construct a novel sugarcane linkage map, compiling AFLP and EST-SSR markers, and to generate data on the distribution of markers anchored to sequences of scIvana_1, a complete sugarcane transposable element, and member of the Copia superfamily. Results The mapping population parents (‘IAC66-6’ and ‘TUC71-7’ contributed equally to polymorphisms, independent of marker type, and generated markers that were distributed into nearly the same number of co-segregation groups (or CGs. Bi-parentally inherited alleles provided the integration of 19 CGs. The marker number per CG ranged from two to 39. The total map length was 4,843.19 cM, with a marker density of 8.87 cM. Markers were assembled into 92 CGs that ranged in length from 1.14 to 404.72 cM, with an estimated average length of 52.64 cM. The greatest distance between two adjacent markers was 48.25 cM. The scIvana_1-based markers (56 were positioned on 21 CGs, but were not regularly distributed. Interestingly, the distance between adjacent scIvana_1-based markers was less than 5 cM, and was observed on five CGs, suggesting a clustered organization. Conclusions Results indicated the use of a NBS-profiling technique was efficient to develop retrotransposon-based markers in sugarcane. The simultaneous maximum-likelihood estimates of linkage and linkage phase based strategies confirmed the suitability of its approach to estimate linkage, and construct the linkage map. Interestingly, using our genetic data it was possible to calculate the number of retrotransposon scIvana_1 (~60

  10. Use of multiple genetic markers in prediction of breeding values.

    Arendonk, van J.A.M.; Tier, B.; Kinghorn, B.P.

    1994-01-01

    Genotypes at a marker locus give information on transmission of genes from parents to offspring and that information can be used in predicting the individuals' additive genetic value at a linked quantitative trait locus (MQTL). In this paper a recursive method is presented to build the gametic

  11. Short Communication: Genetic linkage map of Cucurbita maxima with molecular and morphological markers.

    Ge, Y; Li, X; Yang, X X; Cui, C S; Qu, S P

    2015-05-22

    Cucurbita maxima is one of the most widely cultivated vegetables in China and exhibits distinct morphological characteristics. In this study, genetic linkage analysis with 57 simple-sequence repeats, 21 amplified fragment length polymorphisms, 3 random-amplified polymorphic DNA, and one morphological marker revealed 20 genetic linkage groups of C. maxima covering a genetic distance of 991.5 cM with an average of 12.1 cM between adjacent markers. Genetic linkage analysis identified the simple-sequence repeat marker 'PU078072' 5.9 cM away from the locus 'Rc', which controls rind color. The genetic map in the present study will be useful for better mapping, tagging, and cloning of quantitative trait loci/gene(s) affecting economically important traits and for breeding new varieties of C. maxima through marker-assisted selection.

  12. The Multiplication Map for Global Sections of Line Bundles and ...

    Let be an integral projective curve and ∈ Pic(), ∈ Pic() with ℎ1(, ) = ℎ1(, ) = 0 and , general. Here we study the rank of the multiplication map ,:0(, ) ⊗ 0(, ) → 0(, ⊗ ). We also study the same problem when and are rank 1 torsion free sheaves on . Most of our results are for  ...

  13. A simple method for combining genetic mapping data from multiple crosses and experimental designs.

    Jeremy L Peirce

    Full Text Available BACKGROUND: Over the past decade many linkage studies have defined chromosomal intervals containing polymorphisms that modulate a variety of traits. Many phenotypes are now associated with enough mapping data that meta-analysis could help refine locations of known QTLs and detect many novel QTLs. METHODOLOGY/PRINCIPAL FINDINGS: We describe a simple approach to combining QTL mapping results for multiple studies and demonstrate its utility using two hippocampus weight loci. Using data taken from two populations, a recombinant inbred strain set and an advanced intercross population we demonstrate considerable improvements in significance and resolution for both loci. 1-LOD support intervals were improved 51% for Hipp1a and 37% for Hipp9a. We first generate locus-wise permuted P-values for association with the phenotype from multiple maps, which can be done using a permutation method appropriate to each population. These results are then assigned to defined physical positions by interpolation between markers with known physical and genetic positions. We then use Fisher's combination test to combine position-by-position probabilities among experiments. Finally, we calculate genome-wide combined P-values by generating locus-specific P-values for each permuted map for each experiment. These permuted maps are then sampled with replacement and combined. The distribution of best locus-specific P-values for each combined map is the null distribution of genome-wide adjusted P-values. CONCLUSIONS/SIGNIFICANCE: Our approach is applicable to a wide variety of segregating and non-segregating mapping populations, facilitates rapid refinement of physical QTL position, is complementary to other QTL fine mapping methods, and provides an appropriate genome-wide criterion of significance for combined mapping results.

  14. Diversity arrays technology (DArT) markers in apple for genetic linkage maps

    Schouten, H.J.; Weg, van de, W.E.; Carling, J.; Khan, S.A.; McKay, S.J.; Kaauwen, van, M.P.W.

    2012-01-01

    Diversity Arrays Technology (DArT) provides a high-throughput whole-genome genotyping platform for the detection and scoring of hundreds of polymorphic loci without any need for prior sequence information. The work presented here details the development and performance of a DArT genotyping array for apple. This is the first paper on DArT in horticultural trees. Genetic mapping of DArT markers in two mapping populations and their integration with other marker types showed that DArT is a powerf...

  15. Diversity arrays technology (DArT) markers in apple for genetic linkage maps

    Schouten, Henk J.; van de Weg, W. Eric; Carling, Jason; Khan, Sabaz Ali; McKay, Steven J.; van Kaauwen, Martijn P. W.; Wittenberg, Alexander H. J.; Koehorst-van Putten, Herma J. J.; Noordijk, Yolanda; Gao, Zhongshan; Rees, D. Jasper G.; Van Dyk, Maria M.; Jaccoud, Damian; Considine, Michael J.; Kilian, Andrzej

    2011-01-01

    Diversity Arrays Technology (DArT) provides a high-throughput whole-genome genotyping platform for the detection and scoring of hundreds of polymorphic loci without any need for prior sequence information. The work presented here details the development and performance of a DArT genotyping array for apple. This is the first paper on DArT in horticultural trees. Genetic mapping of DArT markers in two mapping populations and their integration with other marker types showed that DArT is a powerf...

  16. Cerebrospinal fluid CXCL13 in multiple sclerosis: a suggestive prognostic marker for the disease course

    Khademi, Mohsen; Kockum, Ingrid; Andersson, Magnus L

    2011-01-01

    Levels of CXCL13, a potent B-cell chemoattractant, are elevated in the cerebrospinal fluid (CSF) during multiple sclerosis (MS) and are associated with markers of MS activity. Levels decrease upon effective treatments.......Levels of CXCL13, a potent B-cell chemoattractant, are elevated in the cerebrospinal fluid (CSF) during multiple sclerosis (MS) and are associated with markers of MS activity. Levels decrease upon effective treatments....

  17. Diversity arrays technology (DArT) markers in apple for genetic linkage maps.

    Schouten, Henk J; van de Weg, W Eric; Carling, Jason; Khan, Sabaz Ali; McKay, Steven J; van Kaauwen, Martijn P W; Wittenberg, Alexander H J; Koehorst-van Putten, Herma J J; Noordijk, Yolanda; Gao, Zhongshan; Rees, D Jasper G; Van Dyk, Maria M; Jaccoud, Damian; Considine, Michael J; Kilian, Andrzej

    2012-03-01

    Diversity Arrays Technology (DArT) provides a high-throughput whole-genome genotyping platform for the detection and scoring of hundreds of polymorphic loci without any need for prior sequence information. The work presented here details the development and performance of a DArT genotyping array for apple. This is the first paper on DArT in horticultural trees. Genetic mapping of DArT markers in two mapping populations and their integration with other marker types showed that DArT is a powerful high-throughput method for obtaining accurate and reproducible marker data, despite the low cost per data point. This method appears to be suitable for aligning the genetic maps of different segregating populations. The standard complexity reduction method, based on the methylation-sensitive PstI restriction enzyme, resulted in a high frequency of markers, although there was 52-54% redundancy due to the repeated sampling of highly similar sequences. Sequencing of the marker clones showed that they are significantly enriched for low-copy, genic regions. The genome coverage using the standard method was 55-76%. For improved genome coverage, an alternative complexity reduction method was examined, which resulted in less redundancy and additional segregating markers. The DArT markers proved to be of high quality and were very suitable for genetic mapping at low cost for the apple, providing moderate genome coverage. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11032-011-9579-5) contains supplementary material, which is available to authorized users.

  18. Development and mapping of SSR markers linked to resistance-gene homologue clusters in common bean

    Luz; Nayibe; Garzon; Matthew; Wohlgemuth; Blair

    2014-01-01

    Common bean is an important but often a disease-susceptible legume crop of temperate,subtropical and tropical regions worldwide. The crop is affected by bacterial, fungal and viral pathogens. The strategy of resistance-gene homologue(RGH) cloning has proven to be an efficient tool for identifying markers and R(resistance) genes associated with resistances to diseases. Microsatellite or SSR markers can be identified by physical association with RGH clones on large-insert DNA clones such as bacterial artificial chromosomes(BACs). Our objectives in this work were to identify RGH-SSR in a BAC library from the Andean genotype G19833 and to test and map any polymorphic markers to identify associations with known positions of disease resistance genes. We developed a set of specific probes designed for clades of common bean RGH genes and then identified positive BAC clones and developed microsatellites from BACs having SSR loci in their end sequences. A total of 629 new RGH-SSRs were identified and named BMr(bean microsatellite RGH-associated markers). A subset of these markers was screened for detecting polymorphism in the genetic mapping population DOR364 × G19833. A genetic map was constructed with a total of 264 markers,among which were 80 RGH loci anchored to single-copy RFLP and SSR markers. Clusters of RGH-SSRs were observed on most of the linkage groups of common bean and in positions associated with R-genes and QTL. The use of these new markers to select for disease resistance is discussed.

  19. The development and mapping of functional markers in Fragaria and their transferability and potential for mapping in other genera.

    Sargent, D J; Rys, A; Nier, S; Simpson, D W; Tobutt, K R

    2007-01-01

    We have developed 46 primer pairs from exon sequences flanking polymorphic introns of 23 Fragaria gene sequences and one Malus sequence deposited in the EMBL database. Sequencing of a set of the PCR products amplified with the novel primer pairs in diploid Fragaria showed the products to be homologous to the sequences from which the primers were originally designed. By scoring the segregation of the 24 genes in two diploid Fragaria progenies FV x FN (F. vesca x F. nubicola F(2)) and 815 x 903BC (F. vesca x F. viridis BC(1)) 29 genetic loci at discrete positions on the seven linkage groups previously characterised could be mapped, bringing to 35 the total number of known function genes mapped in Fragaria. Twenty primer pairs, representing 14 genes, amplified a product of the expected size in both Malus and Prunus. To demonstrate the applicability of these gene-specific loci to comparative mapping in Rosaceae, five markers that displayed clear polymorphism between the parents of a Malus and a Prunus mapping population were selected. The markers were then scored and mapped in at least one of the two additional progenies.

  20. Clinical values of detection of multiple tumor markers in pleural fluid for diagnosis malignancy

    Xiao Chuangqing; Jiang Li; Zhou Guanghua; He Yunnan

    2005-01-01

    Objective: To improve the diagnostic accuracy for the differentiation of malignant from tuberculous pleural effusion with determination of multiple tumor markers in pleural fluid. Methods: With a multiple tumor markers combined protein chip diagnostic system, contents of twelve common tumor markers were detected in the chest fluid from 60 patients with malignant pleural effusion and 30 patients with tuberculous pleural effusion. Results: For pulmonary carcinoma related pleural effusion, the contents of four common tumor markers (CEA, NSE, SF, CA125) in chest fluid were significantly higher those in tuberculous related chest fluid. The diagnostic positive rate of combined test of these four marker for malignancy could be as high as 96.7%. Conclusion: Combined determination of chest fluid CEA, NSE, SF, CA125 contents was very sensitive and accurate for differentiation of malignant from tuberculous pleural effusion. (authors)

  1. [Application of Multiple Genetic Markers in a Case of Determination of Half Sibling].

    Yang, Xue; Shi, Mei-sen; Yuan, Li; Lu, Di

    2016-02-01

    A case of half sibling was determined with multiple genetic markers, which could be potentially applied for determination of half sibling relationship from same father. Half sibling relationship was detected by 39 autosomal STR genetic markers, 23 Y-chromosomal STR genetic markers and 12 X -chromosomal STR genetic markers among ZHAO -1, ZHAO -2, ZHAO -3, ZHAO -4, and ZHAO-5. According to autosomal STR, Y-STR and X-STR genotyping results, it was determined that ZHAO-4 (alleged half sibling) was unrelated with ZHAO-1 and ZHAO-2; however, ZHAO-3 (alleged half sibling), ZHAO-5 (alleged half sibling) shared same genetic profile with ZHAO-1, and ZHAO-2 from same father. It is reliable to use multiple genetic markers and family gene reconstruction to determine half sibling relationship from same father, but it is difficult to determination by calculating half sibling index with ITO and discriminant functions.

  2. A general mixture model for mapping quantitative trait loci by using molecular markers

    Jansen, R.C.

    1992-01-01

    In a segregating population a quantitative trait may be considered to follow a mixture of (normal) distributions, the mixing proportions being based on Mendelian segregation rules. A general and flexible mixture model is proposed for mapping quantitative trait loci (QTLs) by using molecular markers.

  3. Mapping Late Leaf Spot Resistance in Peanut (Arachis hypogaea Using QTL-seq Reveals Markers for Marker-Assisted Selection

    Josh Clevenger

    2018-02-01

    Full Text Available Late leaf spot (LLS; Cercosporidium personatum is a major fungal disease of cultivated peanut (Arachis hypogaea. A recombinant inbred line population segregating for quantitative field resistance was used to identify quantitative trait loci (QTL using QTL-seq. High rates of false positive SNP calls using established methods in this allotetraploid crop obscured significant QTLs. To resolve this problem, robust parental SNPs were first identified using polyploid-specific SNP identification pipelines, leading to discovery of significant QTLs for LLS resistance. These QTLs were confirmed over 4 years of field data. Selection with markers linked to these QTLs resulted in a significant increase in resistance, showing that these markers can be immediately applied in breeding programs. This study demonstrates that QTL-seq can be used to rapidly identify QTLs controlling highly quantitative traits in polyploid crops with complex genomes. Markers identified can then be deployed in breeding programs, increasing the efficiency of selection using molecular tools.Key Message: Field resistance to late leaf spot is a quantitative trait controlled by many QTLs. Using polyploid-specific methods, QTL-seq is faster and more cost effective than QTL mapping.

  4. Genic Microsatellite Markers in Brassica rapa: Development, Characterization, Mapping, and Their Utility in Other Cultivated and Wild Brassica Relatives

    Ramchiary, Nirala; Nguyen, Van Dan; Li, Xiaonan; Hong, Chang Pyo; Dhandapani, Vignesh; Choi, Su Ryun; Yu, Ge; Piao, Zhong Yun; Lim, Yong Pyo

    2011-01-01

    Genic microsatellite markers, also known as functional markers, are preferred over anonymous markers as they reveal the variation in transcribed genes among individuals. In this study, we developed a total of 707 expressed sequence tag-derived simple sequence repeat markers (EST-SSRs) and used for development of a high-density integrated map using four individual mapping populations of B. rapa. This map contains a total of 1426 markers, consisting of 306 EST-SSRs, 153 intron polymorphic markers, 395 bacterial artificial chromosome-derived SSRs (BAC-SSRs), and 572 public SSRs and other markers covering a total distance of 1245.9 cM of the B. rapa genome. Analysis of allelic diversity in 24 B. rapa germplasm using 234 mapped EST-SSR markers showed amplification of 2 alleles by majority of EST-SSRs, although amplification of alleles ranging from 2 to 8 was found. Transferability analysis of 167 EST-SSRs in 35 species belonging to cultivated and wild brassica relatives showed 42.51% (Sysimprium leteum) to 100% (B. carinata, B. juncea, and B. napus) amplification. Our newly developed EST-SSRs and high-density linkage map based on highly transferable genic markers would facilitate the molecular mapping of quantitative trait loci and the positional cloning of specific genes, in addition to marker-assisted selection and comparative genomic studies of B. rapa with other related species. PMID:21768136

  5. Development and Integration of Genome-Wide Polymorphic Microsatellite Markers onto a Reference Linkage Map for Constructing a High-Density Genetic Map of Chickpea.

    Yash Paul Khajuria

    Full Text Available The identification of informative in silico polymorphic genomic and genic microsatellite markers by comparing the genome and transcriptome sequences of crop genotypes is a rapid, cost-effective and non-laborious approach for large-scale marker validation and genotyping applications, including construction of high-density genetic maps. We designed 1494 markers, including 1016 genomic and 478 transcript-derived microsatellite markers showing in-silico fragment length polymorphism between two parental genotypes (Cicer arietinum ICC4958 and C. reticulatum PI489777 of an inter-specific reference mapping population. High amplification efficiency (87%, experimental validation success rate (81% and polymorphic potential (55% of these microsatellite markers suggest their effective use in various applications of chickpea genetics and breeding. Intra-specific polymorphic potential (48% detected by microsatellite markers in 22 desi and kabuli chickpea genotypes was lower than inter-specific polymorphic potential (59%. An advanced, high-density, integrated and inter-specific chickpea genetic map (ICC4958 x PI489777 having 1697 map positions spanning 1061.16 cM with an average inter-marker distance of 0.625 cM was constructed by assigning 634 novel informative transcript-derived and genomic microsatellite markers on eight linkage groups (LGs of our prior documented, 1063 marker-based genetic map. The constructed genome map identified 88, including four major (7-23 cM longest high-resolution genomic regions on LGs 3, 5 and 8, where the maximum number of novel genomic and genic microsatellite markers were specifically clustered within 1 cM genetic distance. It was for the first time in chickpea that in silico FLP analysis at genome-wide level was carried out and such a large number of microsatellite markers were identified, experimentally validated and further used in genetic mapping. To best of our knowledge, in the presently constructed genetic map, we mapped

  6. A General Method for QTL Mapping in Multiple Related Populations Derived from Multiple Parents

    Yan AO

    2009-03-01

    Full Text Available It's well known that incorporating some existing populations derived from multiple parents may improve QTL mapping and QTL-based breeding programs. However, no general maximum likelihood method has been available for this strategy. Based on the QTL mapping in multiple related populations derived from two parents, a maximum likelihood estimation method was proposed, which can incorporate several populations derived from three or more parents and also can be used to handle different mating designs. Taking a circle design as an example, we conducted simulation studies to study the effect of QTL heritability and sample size upon the proposed method. The results showed that under the same heritability, enhanced power of QTL detection and more precise and accurate estimation of parameters could be obtained when three F2 populations were jointly analyzed, compared with the joint analysis of any two F2 populations. Higher heritability, especially with larger sample sizes, would increase the ability of QTL detection and improve the estimation of parameters. Potential advantages of the method are as follows: firstly, the existing results of QTL mapping in single population can be compared and integrated with each other with the proposed method, therefore the ability of QTL detection and precision of QTL mapping can be improved. Secondly, owing to multiple alleles in multiple parents, the method can exploit gene resource more adequately, which will lay an important genetic groundwork for plant improvement.

  7. Development and bin mapping of a Rosaceae Conserved Ortholog Set (COS) of markers.

    Cabrera, Antonio; Kozik, Alex; Howad, Werner; Arus, Pere; Iezzoni, Amy F; van der Knaap, Esther

    2009-11-29

    Detailed comparative genome analyses within the economically important Rosaceae family have not been conducted. This is largely due to the lack of conserved gene-based molecular markers that are transferable among the important crop genera within the family [e.g. Malus (apple), Fragaria (strawberry), and Prunus (peach, cherry, apricot and almond)]. The lack of molecular markers and comparative whole genome sequence analysis for this family severely hampers crop improvement efforts as well as QTL confirmation and validation studies. We identified a set of 3,818 rosaceaous unigenes comprised of two or more ESTs that correspond to single copy Arabidopsis genes. From this Rosaceae Conserved Orthologous Set (RosCOS), 1039 were selected from which 857 were used for the development of intron-flanking primers and allele amplification. This led to successful amplification and subsequent mapping of 613 RosCOS onto the Prunus TxE reference map resulting in a genome-wide coverage of 0.67 to 1.06 gene-based markers per cM per linkage group. Furthermore, the RosCOS primers showed amplification success rates from 23 to 100% across the family indicating that a substantial part of the RosCOS primers can be directly employed in other less studied rosaceaous crops. Comparisons of the genetic map positions of the RosCOS with the physical locations of the orthologs in the Populus trichocarpa genome identified regions of colinearity between the genomes of Prunus-Rosaceae and Populus-Salicaceae. Conserved orthologous genes are extremely useful for the analysis of genome evolution among closely and distantly related species. The results presented in this study demonstrate the considerable potential of the mapped Prunus RosCOS for genome-wide marker employment and comparative whole genome studies within the Rosaceae family. Moreover, these markers will also function as useful anchor points for the genome sequencing efforts currently ongoing in this family as well as for comparative QTL

  8. [Utility of Multiple Increased Lung Cancer Tumor Markers in Treatment of Patients with Advanced Lung Adenocarcinoma].

    Peng, Yan; Wang, Yan; Hao, Xuezhi; Li, Junling; Liu, Yutao; Wang, Hongyu

    2017-10-20

    Among frequently-used tumor markers in lung cancer, carcinoembryonic antigen (CEA) and carbohydrate antigen 125 (CA125), cytokeratin 19 (CYFRA21-1) and squamous carcinoma antigen (SCC), neuron specific enolase (NSE) and pro-gastrin-releasing peptide (ProGRP) are respectively expressed highly in lung adenocarcinoma, lung squamous carcinoma and small cell lung cancer. By comparing patients with multiple increased tumor markers (group A) and patients with increase of CEA and/or CA125 (group B), this study aims to investigate the utility of multiple increased tumor markers in therapeutic evaluation and prediction of disease relapsing in patients with advanced lung adenocarcinoma. Patients with stage IV lung adenocarcinoma who receiving the first line chemotherapy in Cancer Hospital, Chinese Academy of Medical Sciences were enrolled and retrospectively analyzed. Clinical characteristic, serum tumor markers before chemotherapy, efficacy evaluation, progression-free survival (PFS) were analyzed. Except CEA and CA125, the highest ratio of increased tumor markersin group A was CYFRA21-1 (93%), then was NSE (36%), SCC (13%) and ProGRP (12%). Patients with multiple increased tumor markers tend to have more distant metastasis (Ptumor markers have high risk of relapse, and maintenance therapy can reduce relapse risk.

  9. Multiple-clone infections of Plasmodium vivax: definition of a panel of markers for molecular epidemiology.

    de Souza, Aracele M; de Araújo, Flávia C F; Fontes, Cor J F; Carvalho, Luzia H; de Brito, Cristiana F A; de Sousa, Taís N

    2015-08-25

    Plasmodium vivax infections commonly contain multiple genetically distinct parasite clones. The detection of multiple-clone infections depends on several factors, such as the accuracy of the genotyping method, and the type and number of the molecular markers analysed. Characterizing the multiplicity of infection has broad implications that range from population genetic studies of the parasite to malaria treatment and control. This study compared and evaluated the efficiency of neutral and non-neutral markers that are widely used in studies of molecular epidemiology to detect the multiplicity of P. vivax infection. The performance of six markers was evaluated using 11 mixtures of DNA with well-defined proportions of two different parasite genotypes for each marker. These mixtures were generated by mixing cloned PCR products or patient-derived genomic DNA. In addition, 51 samples of natural infections from the Brazil were genotyped for all markers. The PCR-capillary electrophoresis-based method was used to permit direct comparisons among the markers. The criteria for differentiating minor peaks from artifacts were also evaluated. The analysis of DNA mixtures showed that the tandem repeat MN21 and the polymorphic blocks 2 (msp1B2) and 10 (msp1B10) of merozoite surface protein-1 allowed for the estimation of the expected ratio of both alleles in the majority of preparations. Nevertheless, msp1B2 was not able to detect the majority of multiple-clone infections in field samples; it identified only 6 % of these infections. The merozoite surface protein-3 alpha and microsatellites (PvMS6 and PvMS7) did not accurately estimate the relative clonal proportions in artificial mixtures, but the microsatellites performed well in detecting natural multiple-clone infections. Notably, the use of a less stringent criterion to score rare alleles significantly increased the sensitivity of the detection of multi-clonal infections. Depending on the type of marker used, a considerable

  10. Fast empirical Bayesian LASSO for multiple quantitative trait locus mapping

    Xu Shizhong

    2011-05-01

    Full Text Available Abstract Background The Bayesian shrinkage technique has been applied to multiple quantitative trait loci (QTLs mapping to estimate the genetic effects of QTLs on quantitative traits from a very large set of possible effects including the main and epistatic effects of QTLs. Although the recently developed empirical Bayes (EB method significantly reduced computation comparing with the fully Bayesian approach, its speed and accuracy are limited by the fact that numerical optimization is required to estimate the variance components in the QTL model. Results We developed a fast empirical Bayesian LASSO (EBLASSO method for multiple QTL mapping. The fact that the EBLASSO can estimate the variance components in a closed form along with other algorithmic techniques render the EBLASSO method more efficient and accurate. Comparing with the EB method, our simulation study demonstrated that the EBLASSO method could substantially improve the computational speed and detect more QTL effects without increasing the false positive rate. Particularly, the EBLASSO algorithm running on a personal computer could easily handle a linear QTL model with more than 100,000 variables in our simulation study. Real data analysis also demonstrated that the EBLASSO method detected more reasonable effects than the EB method. Comparing with the LASSO, our simulation showed that the current version of the EBLASSO implemented in Matlab had similar speed as the LASSO implemented in Fortran, and that the EBLASSO detected the same number of true effects as the LASSO but a much smaller number of false positive effects. Conclusions The EBLASSO method can handle a large number of effects possibly including both the main and epistatic QTL effects, environmental effects and the effects of gene-environment interactions. It will be a very useful tool for multiple QTL mapping.

  11. THE METHOD OF MULTIPLE SPATIAL PLANNING BASIC MAP

    C. Zhang

    2018-04-01

    Full Text Available The “Provincial Space Plan Pilot Program” issued in December 2016 pointed out that the existing space management and control information management platforms of various departments were integrated, and a spatial planning information management platform was established to integrate basic data, target indicators, space coordinates, and technical specifications. The planning and preparation will provide supportive decision support, digital monitoring and evaluation of the implementation of the plan, implementation of various types of investment projects and space management and control departments involved in military construction projects in parallel to approve and approve, and improve the efficiency of administrative approval. The space planning system should be set up to delimit the control limits for the development of production, life and ecological space, and the control of use is implemented. On the one hand, it is necessary to clarify the functional orientation between various kinds of planning space. On the other hand, it is necessary to achieve “multi-compliance” of various space planning. Multiple spatial planning intergration need unified and standard basic map(geographic database and technical specificaton to division of urban, agricultural, ecological three types of space and provide technical support for the refinement of the space control zoning for the relevant planning. The article analysis the main space datum, the land use classification standards, base map planning, planning basic platform main technical problems. Based on the geographic conditions, the results of the census preparation of spatial planning map, and Heilongjiang, Hainan many rules combined with a pilot application.

  12. The Method of Multiple Spatial Planning Basic Map

    Zhang, C.; Fang, C.

    2018-04-01

    The "Provincial Space Plan Pilot Program" issued in December 2016 pointed out that the existing space management and control information management platforms of various departments were integrated, and a spatial planning information management platform was established to integrate basic data, target indicators, space coordinates, and technical specifications. The planning and preparation will provide supportive decision support, digital monitoring and evaluation of the implementation of the plan, implementation of various types of investment projects and space management and control departments involved in military construction projects in parallel to approve and approve, and improve the efficiency of administrative approval. The space planning system should be set up to delimit the control limits for the development of production, life and ecological space, and the control of use is implemented. On the one hand, it is necessary to clarify the functional orientation between various kinds of planning space. On the other hand, it is necessary to achieve "multi-compliance" of various space planning. Multiple spatial planning intergration need unified and standard basic map(geographic database and technical specificaton) to division of urban, agricultural, ecological three types of space and provide technical support for the refinement of the space control zoning for the relevant planning. The article analysis the main space datum, the land use classification standards, base map planning, planning basic platform main technical problems. Based on the geographic conditions, the results of the census preparation of spatial planning map, and Heilongjiang, Hainan many rules combined with a pilot application.

  13. Annotated genetic linkage maps of Pinus pinaster Ait. from a Central Spain population using microsatellite and gene based markers.

    de Miguel, Marina; de Maria, Nuria; Guevara, M Angeles; Diaz, Luis; Sáez-Laguna, Enrique; Sánchez-Gómez, David; Chancerel, Emilie; Aranda, Ismael; Collada, Carmen; Plomion, Christophe; Cabezas, José-Antonio; Cervera, María-Teresa

    2012-10-04

    Pinus pinaster Ait. is a major resin producing species in Spain. Genetic linkage mapping can facilitate marker-assisted selection (MAS) through the identification of Quantitative Trait Loci and selection of allelic variants of interest in breeding populations. In this study, we report annotated genetic linkage maps for two individuals (C14 and C15) belonging to a breeding program aiming to increase resin production. We use different types of DNA markers, including last-generation molecular markers. We obtained 13 and 14 linkage groups for C14 and C15 maps, respectively. A total of 211 and 215 markers were positioned on each map and estimated genome length was between 1,870 and 2,166 cM respectively, which represents near 65% of genome coverage. Comparative mapping with previously developed genetic linkage maps for P. pinaster based on about 60 common markers enabled aligning linkage groups to this reference map. The comparison of our annotated linkage maps and linkage maps reporting QTL information revealed 11 annotated SNPs in candidate genes that co-localized with previously reported QTLs for wood properties and water use efficiency. This study provides genetic linkage maps from a Spanish population that shows high levels of genetic divergence with French populations from which segregating progenies have been previously mapped. These genetic maps will be of interest to construct a reliable consensus linkage map for the species. The importance of developing functional genetic linkage maps is highlighted, especially when working with breeding populations for its future application in MAS for traits of interest.

  14. Annotated genetic linkage maps of Pinus pinaster Ait. from a Central Spain population using microsatellite and gene based markers

    de Miguel Marina

    2012-10-01

    Full Text Available Abstract Background Pinus pinaster Ait. is a major resin producing species in Spain. Genetic linkage mapping can facilitate marker-assisted selection (MAS through the identification of Quantitative Trait Loci and selection of allelic variants of interest in breeding populations. In this study, we report annotated genetic linkage maps for two individuals (C14 and C15 belonging to a breeding program aiming to increase resin production. We use different types of DNA markers, including last-generation molecular markers. Results We obtained 13 and 14 linkage groups for C14 and C15 maps, respectively. A total of 211 and 215 markers were positioned on each map and estimated genome length was between 1,870 and 2,166 cM respectively, which represents near 65% of genome coverage. Comparative mapping with previously developed genetic linkage maps for P. pinaster based on about 60 common markers enabled aligning linkage groups to this reference map. The comparison of our annotated linkage maps and linkage maps reporting QTL information revealed 11 annotated SNPs in candidate genes that co-localized with previously reported QTLs for wood properties and water use efficiency. Conclusions This study provides genetic linkage maps from a Spanish population that shows high levels of genetic divergence with French populations from which segregating progenies have been previously mapped. These genetic maps will be of interest to construct a reliable consensus linkage map for the species. The importance of developing functional genetic linkage maps is highlighted, especially when working with breeding populations for its future application in MAS for traits of interest.

  15. A novel data mining system points out hidden relationships between immunological markers in multiple sclerosis

    Gironi Maira

    2013-01-01

    Full Text Available Abstract Background Multiple Sclerosis (MS is a multi-factorial disease, where a single biomarker unlikely can provide comprehensive information. Moreover, due to the non-linearity of biomarkers, traditional statistic is both unsuitable and underpowered to dissect their relationship. Patients affected with primary (PP=14, secondary (SP=33, benign (BB=26, relapsing-remitting (RR=30 MS, and 42 sex and age matched healthy controls were studied. We performed a depth immune-phenotypic and functional analysis of peripheral blood mononuclear cell (PBMCs by flow-cytometry. Semantic connectivity maps (AutoCM were applied to find the natural associations among immunological markers. AutoCM is a special kind of Artificial Neural Network able to find consistent trends and associations among variables. The matrix of connections, visualized through minimum spanning tree, keeps non linear associations among variables and captures connection schemes among clusters. Results Complex immunological relationships were shown to be related to different disease courses. Low CD4IL25+ cells level was strongly related (link strength, ls=0.81 to SP MS. This phenotype was also associated to high CD4ROR+ cells levels (ls=0.56. BB MS was related to high CD4+IL13 cell levels (ls=0.90, as well as to high CD14+IL6 cells percentage (ls=0.80. RR MS was strongly (ls=0.87 related to CD4+IL25 high cell levels, as well indirectly to high percentages of CD4+IL13 cells. In this latter strong (ls=0.92 association could be confirmed the induction activity of the former cells (CD4+IL25 on the latter (CD4+IL13. Another interesting topographic data was the isolation of Th9 cells (CD4IL9 from the main part of the immunological network related to MS, suggesting a possible secondary role of this new described cell phenotype in MS disease. Conclusions This novel application of non-linear mathematical techniques suggests peculiar immunological signatures for different MS phenotypes. Notably, the

  16. Markers

    Healthy Schools Network, Inc., 2011

    2011-01-01

    Dry erase whiteboards come with toxic dry erase markers and toxic cleaning products. Dry erase markers labeled "nontoxic" are not free of toxic chemicals and can cause health problems. Children are especially vulnerable to environmental health hazards; moreover, schools commonly have problems with indoor air pollution, as they are more densely…

  17. Identification and reproducibility of diagnostic DNA markers for tuber starch and yield optimization in a novel association mapping population of potato (Solanum tuberosum L.).

    Schönhals, E M; Ortega, F; Barandalla, L; Aragones, A; Ruiz de Galarreta, J I; Liao, J-C; Sanetomo, R; Walkemeier, B; Tacke, E; Ritter, E; Gebhardt, C

    2016-04-01

    SNPs in candidate genes Pain - 1, InvCD141 (invertases), SSIV (starch synthase), StCDF1 (transcription factor), LapN (leucine aminopeptidase), and cytoplasm type are associated with potato tuber yield, starch content and/or starch yield. Tuber yield (TY), starch content (TSC), and starch yield (TSY) are complex characters of high importance for the potato crop in general and for industrial starch production in particular. DNA markers associated with superior alleles of genes that control the natural variation of TY, TSC, and TSY could increase precision and speed of breeding new cultivars optimized for potato starch production. Diagnostic DNA markers are identified by association mapping in populations of tetraploid potato varieties and advanced breeding clones. A novel association mapping population of 282 genotypes including varieties, breeding clones and Andean landraces was assembled and field evaluated in Northern Spain for TY, TSC, TSY, tuber number (TN) and tuber weight (TW). The landraces had lower mean values of TY, TW, TN, and TSY. The population was genotyped for 183 microsatellite alleles, 221 single nucleotide polymorphisms (SNPs) in fourteen candidate genes and eight known diagnostic markers for TSC and TSY. Association test statistics including kinship and population structure reproduced five known marker-trait associations of candidate genes and discovered new ones, particularly for tuber yield and starch yield. The inclusion of landraces increased the number of detected marker-trait associations. Integration of the present association mapping results with previous QTL linkage mapping studies for TY, TSC, TSY, TW, TN, and tuberization revealed some hot spots of QTL for these traits in the potato genome. The genomic positions of markers linked or associated with QTL for complex tuber traits suggest high multiplicity and genome wide distribution of the underlying genes.

  18. Development and bin mapping of a Rosaceae Conserved Ortholog Set (COS of markers

    Kozik Alex

    2009-01-01

    Full Text Available Abstract Background Detailed comparative genome analyses within the economically important Rosaceae family have not been conducted. This is largely due to the lack of conserved gene-based molecular markers that are transferable among the important crop genera within the family [e.g. Malus (apple, Fragaria (strawberry, and Prunus (peach, cherry, apricot and almond]. The lack of molecular markers and comparative whole genome sequence analysis for this family severely hampers crop improvement efforts as well as QTL confirmation and validation studies. Results We identified a set of 3,818 rosaceaous unigenes comprised of two or more ESTs that correspond to single copy Arabidopsis genes. From this Rosaceae Conserved Orthologous Set (RosCOS, 1039 were selected from which 857 were used for the development of intron-flanking primers and allele amplification. This led to successful amplification and subsequent mapping of 613 RosCOS onto the Prunus TxE reference map resulting in a genome-wide coverage of 0.67 to 1.06 gene-based markers per cM per linkage group. Furthermore, the RosCOS primers showed amplification success rates from 23 to 100% across the family indicating that a substantial part of the RosCOS primers can be directly employed in other less studied rosaceaous crops. Comparisons of the genetic map positions of the RosCOS with the physical locations of the orthologs in the Populus trichocarpa genome identified regions of colinearity between the genomes of Prunus-Rosaceae and Populus-Salicaceae. Conclusion Conserved orthologous genes are extremely useful for the analysis of genome evolution among closely and distantly related species. The results presented in this study demonstrate the considerable potential of the mapped Prunus RosCOS for genome-wide marker employment and comparative whole genome studies within the Rosaceae family. Moreover, these markers will also function as useful anchor points for the genome sequencing efforts currently

  19. Association Mapping for Important Agronomic Traits in Safflower (Carthamus tinctorius L. Core Collection Using Microsatellite Markers

    Heena Ambreen

    2018-03-01

    Full Text Available Carthamus tinctorius L. (safflower is an important oilseed crop producing seed oil rich in unsaturated fatty acids. Scarcity of identified marker-trait associations is a major limitation toward development of successful marker-assisted breeding programs in safflower. In the present study, a safflower panel (CartAP comprising 124 accessions derived from two core collections was assayed for its suitability for association mapping. Genotyping of CartAP using microsatellite markers revealed significant genetic diversity indicated by Shannon information index (H = 0.7537 and Nei's expected heterozygosity (I = 0.4432. In Principal Coordinate Analysis, the CartAP accessions were distributed homogeneously in all quadrants indicating their diverse nature. Distance-based Neighbor Joining analysis did not delineate the CartAP accessions in consonance with their geographical origin. Bayesian analysis of population structure of CartAP demonstrated the unstructured nature of the association panel. Kinship analysis at population (Gij and individual level (Fij revealed absence of or weak relatedness between the CartAP accessions. The above parameters established the suitability of CartAP for association mapping. We performed association mapping using phenotypic data for eight traits of agronomic value (viz., seed oil content, oleic acid, linoleic acid, plant height, number of primary branches, number of capitula per plant, 100-seed weight and days to 50% flowering available for two growing seasons (2011–2012 and 2012–2013 through General Linear Model and Mixed Linear Model. Our study identified ninety-six significant marker-trait associations (MTAs; P < 0.05 of which, several MTAs with correlation coefficient (R2 > 10% were consistently represented in both models and in both seasons for traits viz., oil content, oleic acid content, linoleic acid content and number of primary branches. Several MTAs with high R2-values were detected either in a majority or in

  20. Association Mapping for Important Agronomic Traits in Safflower (Carthamus tinctorius L.) Core Collection Using Microsatellite Markers.

    Ambreen, Heena; Kumar, Shivendra; Kumar, Amar; Agarwal, Manu; Jagannath, Arun; Goel, Shailendra

    2018-01-01

    Carthamus tinctorius L. (safflower) is an important oilseed crop producing seed oil rich in unsaturated fatty acids. Scarcity of identified marker-trait associations is a major limitation toward development of successful marker-assisted breeding programs in safflower. In the present study, a safflower panel (CartAP) comprising 124 accessions derived from two core collections was assayed for its suitability for association mapping. Genotyping of CartAP using microsatellite markers revealed significant genetic diversity indicated by Shannon information index ( H = 0.7537) and Nei's expected heterozygosity ( I = 0.4432). In Principal Coordinate Analysis, the CartAP accessions were distributed homogeneously in all quadrants indicating their diverse nature. Distance-based Neighbor Joining analysis did not delineate the CartAP accessions in consonance with their geographical origin. Bayesian analysis of population structure of CartAP demonstrated the unstructured nature of the association panel. Kinship analysis at population ( G ij ) and individual level ( F ij ) revealed absence of or weak relatedness between the CartAP accessions. The above parameters established the suitability of CartAP for association mapping. We performed association mapping using phenotypic data for eight traits of agronomic value ( viz ., seed oil content, oleic acid, linoleic acid, plant height, number of primary branches, number of capitula per plant, 100-seed weight and days to 50% flowering) available for two growing seasons (2011-2012 and 2012-2013) through General Linear Model and Mixed Linear Model. Our study identified ninety-six significant marker-trait associations (MTAs; P 10% were consistently represented in both models and in both seasons for traits viz ., oil content, oleic acid content, linoleic acid content and number of primary branches. Several MTAs with high R 2 -values were detected either in a majority or in some environments (models and/or seasons). Many MTAs were also

  1. An Improved Consensus Linkage Map of Barley Based on Flow-Sorted Chromosomes and Single Nucleotide Polymorphism Markers

    María Muñoz-Amatriaín

    2011-11-01

    Full Text Available Recent advances in high-throughput genotyping have made it easier to combine information from different mapping populations into consensus genetic maps, which provide increased marker density and genome coverage compared to individual maps. Previously, a single nucleotide polymorphism (SNP-based genotyping platform was developed and used to genotype 373 individuals in four barley ( L. mapping populations. This led to a 2943 SNP consensus genetic map with 975 unique positions. In this work, we add data from six additional populations and more individuals from one of the original populations to develop an improved consensus map from 1133 individuals. A stringent and systematic analysis of each of the 10 populations was performed to achieve uniformity. This involved reexamination of the four populations included in the previous map. As a consequence, we present a robust consensus genetic map that contains 2994 SNP loci mapped to 1163 unique positions. The map spans 1137.3 cM with an average density of one marker bin per 0.99 cM. A novel application of the genotyping platform for gene detection allowed the assignment of 2930 genes to flow-sorted chromosomes or arms, confirmed the position of 2545 SNP-mapped loci, added chromosome or arm allocations to an additional 370 SNP loci, and delineated pericentromeric regions for chromosomes 2H to 7H. Marker order has been improved and map resolution has been increased by almost 20%. These increased precision outcomes enable more optimized SNP selection for marker-assisted breeding and support association genetic analysis and map-based cloning. It will also improve the anchoring of DNA sequence scaffolds and the barley physical map to the genetic map.

  2. Construction of an SSR and RAD-Marker Based Molecular Linkage Map of Vigna vexillata (L.) A. Rich.

    Marubodee, Rusama; Ogiso-Tanaka, Eri; Isemura, Takehisa; Chankaew, Sompong; Kaga, Akito; Naito, Ken; Ehara, Hiroshi; Tomooka, Norihiko

    2015-01-01

    Vigna vexillata (L.) A. Rich. (tuber cowpea) is an underutilized crop for consuming its tuber and mature seeds. Wild form of V. vexillata is a pan-tropical perennial herbaceous plant which has been used by local people as a food. Wild V. vexillata has also been considered as useful gene(s) source for V. unguiculata (cowpea), since it was reported to have various resistance gene(s) for insects and diseases of cowpea. To exploit the potential of V. vexillata, an SSR-based linkage map of V. vexillata was developed. A total of 874 SSR markers successfully amplified single DNA fragment in V. vexillata among 1,336 SSR markers developed from Vigna angularis (azuki bean), V. unguiculata and Phaseolus vulgaris (common bean). An F2 population of 300 plants derived from a cross between salt resistant (V1) and susceptible (V5) accessions was used for mapping. A genetic linkage map was constructed using 82 polymorphic SSR markers loci, which could be assigned to 11 linkage groups spanning 511.5 cM in length with a mean distance of 7.2 cM between adjacent markers. To develop higher density molecular linkage map and to confirm SSR markers position in a linkage map, RAD markers were developed and a combined SSR and RAD markers linkage map of V. vexillata was constructed. A total of 559 (84 SSR and 475 RAD) markers loci could be assigned to 11 linkage groups spanning 973.9 cM in length with a mean distance of 1.8 cM between adjacent markers. Linkage and genetic position of all SSR markers in an SSR linkage map were confirmed. When an SSR genetic linkage map of V. vexillata was compared with those of V. radiata and V. unguiculata, it was suggested that the structure of V. vexillata chromosome was considerably differentiated. This map is the first SSR and RAD marker-based V. vexillata linkage map which can be used for the mapping of useful traits.

  3. Optimized multiple linear mappings for single image super-resolution

    Zhang, Kaibing; Li, Jie; Xiong, Zenggang; Liu, Xiuping; Gao, Xinbo

    2017-12-01

    Learning piecewise linear regression has been recognized as an effective way for example learning-based single image super-resolution (SR) in literature. In this paper, we employ an expectation-maximization (EM) algorithm to further improve the SR performance of our previous multiple linear mappings (MLM) based SR method. In the training stage, the proposed method starts with a set of linear regressors obtained by the MLM-based method, and then jointly optimizes the clustering results and the low- and high-resolution subdictionary pairs for regression functions by using the metric of the reconstruction errors. In the test stage, we select the optimal regressor for SR reconstruction by accumulating the reconstruction errors of m-nearest neighbors in the training set. Thorough experimental results carried on six publicly available datasets demonstrate that the proposed SR method can yield high-quality images with finer details and sharper edges in terms of both quantitative and perceptual image quality assessments.

  4. On coding genotypes for genetic markers with multiple alleles in genetic association study of quantitative traits

    Wang Tao

    2011-09-01

    Full Text Available Abstract Background In genetic association study of quantitative traits using F∞ models, how to code the marker genotypes and interpret the model parameters appropriately is important for constructing hypothesis tests and making statistical inferences. Currently, the coding of marker genotypes in building F∞ models has mainly focused on the biallelic case. A thorough work on the coding of marker genotypes and interpretation of model parameters for F∞ models is needed especially for genetic markers with multiple alleles. Results In this study, we will formulate F∞ genetic models under various regression model frameworks and introduce three genotype coding schemes for genetic markers with multiple alleles. Starting from an allele-based modeling strategy, we first describe a regression framework to model the expected genotypic values at given markers. Then, as extension from the biallelic case, we introduce three coding schemes for constructing fully parameterized one-locus F∞ models and discuss the relationships between the model parameters and the expected genotypic values. Next, under a simplified modeling framework for the expected genotypic values, we consider several reduced one-locus F∞ models from the three coding schemes on the estimability and interpretation of their model parameters. Finally, we explore some extensions of the one-locus F∞ models to two loci. Several fully parameterized as well as reduced two-locus F∞ models are addressed. Conclusions The genotype coding schemes provide different ways to construct F∞ models for association testing of multi-allele genetic markers with quantitative traits. Which coding scheme should be applied depends on how convenient it can provide the statistical inferences on the parameters of our research interests. Based on these F∞ models, the standard regression model fitting tools can be used to estimate and test for various genetic effects through statistical contrasts with the

  5. EST-derived SSR markers used as anchor loci for the construction of a consensus linkage map in ryegrass (Lolium spp.)

    Studer, Bruno; Kölliker, Roland; Muylle, Hilde

    2010-01-01

    Background Genetic markers and linkage mapping are basic prerequisites for marker-assisted selection and map-based cloning. In the case of the key grassland species Lolium spp., numerous mapping populations have been developed and characterised for various traits. Although some genetic linkage maps...

  6. EST-derived SSR markers used as anchor loci for the construction of a consensus linkage map in ryegrass (Lolium spp.)

    Studer, B.; Kolliker, R.; Muylle, H.; Asp, T.; Frei, U.; Roldan-Ruiz, I.; Barre, P.; Tomaszewski, C.; Meally, H.; Barth, S.; Skot, L.; Armstead, I.P.; Dolstra, O.; Lubberstedt, T.

    2010-01-01

    Background: Genetic markers and linkage mapping are basic prerequisites for marker-assisted selection and map-based cloning. In the case of the key grassland species Lolium spp., numerous mapping populations have been developed and characterised for various traits. Although some genetic linkage maps

  7. A sequence-based genetic map of Medicago truncatula and comparison of marker colinearity with M. sativa

    Choi, H.K.; Kim, D.; Uhm, T.; Limpens, E.H.M.; Lim, H.; Mun, J.H.; Kalo, P.; Penmetsa, R.V.; Seres, A.; Kulikova, O.; Roe, B.A.; Bisseling, T.; Kiss, G.B.; Cook, D.R.

    2004-01-01

    A core genetic map of the legume Medicago truncatula has been established by analyzing the segregation of 288 sequence-characterized genetic markers in an E, population composed of 93 individuals. These molecular markers correspond to 141 ESTs, 80 BAC end sequence tags, and 67 resistance gene

  8. Effects of the number of markers per haplotype and clustering of haplotypes on the accuracy of QTL mapping and prediction of genomic breeding values

    Schrooten Chris

    2009-01-01

    Full Text Available Abstract The aim of this paper was to compare the effect of haplotype definition on the precision of QTL-mapping and on the accuracy of predicted genomic breeding values. In a multiple QTL model using identity-by-descent (IBD probabilities between haplotypes, various haplotype definitions were tested i.e. including 2, 6, 12 or 20 marker alleles and clustering base haplotypes related with an IBD probability of > 0.55, 0.75 or 0.95. Simulated data contained 1100 animals with known genotypes and phenotypes and 1000 animals with known genotypes and unknown phenotypes. Genomes comprising 3 Morgan were simulated and contained 74 polymorphic QTL and 383 polymorphic SNP markers with an average r2 value of 0.14 between adjacent markers. The total number of haplotypes decreased up to 50% when the window size was increased from two to 20 markers and decreased by at least 50% when haplotypes related with an IBD probability of > 0.55 instead of > 0.95 were clustered. An intermediate window size led to more precise QTL mapping. Window size and clustering had a limited effect on the accuracy of predicted total breeding values, ranging from 0.79 to 0.81. Our conclusion is that different optimal window sizes should be used in QTL-mapping versus genome-wide breeding value prediction.

  9. Identification of QTLs Associated with Callogenesis and Embryogenesis in Oil Palm Using Genetic Linkage Maps Improved with SSR Markers

    Ting, Ngoot-Chin; Jansen, Johannes; Nagappan, Jayanthi; Ishak, Zamzuri; Chin, Cheuk-Weng; Tan, Soon-Guan; Cheah, Suan-Choo; Singh, Rajinder

    2013-01-01

    Clonal reproduction of oil palm by means of tissue culture is a very inefficient process. Tissue culturability is known to be genotype dependent with some genotypes being more amenable to tissue culture than others. In this study, genetic linkage maps enriched with simple sequence repeat (SSR) markers were developed for dura (ENL48) and pisifera (ML161), the two fruit forms of oil palm, Elaeis guineensis. The SSR markers were mapped onto earlier reported parental maps based on amplified fragment length polymorphism (AFLP) and restriction fragment length polymorphism (RFLP) markers. The new linkage map of ENL48 contains 148 markers (33 AFLPs, 38 RFLPs and 77 SSRs) in 23 linkage groups (LGs), covering a total map length of 798.0 cM. The ML161 map contains 240 markers (50 AFLPs, 71 RFLPs and 119 SSRs) in 24 LGs covering a total of 1,328.1 cM. Using the improved maps, two quantitative trait loci (QTLs) associated with tissue culturability were identified each for callusing rate and embryogenesis rate. A QTL for callogenesis was identified in LGD4b of ENL48 and explained 17.5% of the phenotypic variation. For embryogenesis rate, a QTL was detected on LGP16b in ML161 and explained 20.1% of the variation. This study is the first attempt to identify QTL associated with tissue culture amenity in oil palm which is an important step towards understanding the molecular processes underlying clonal regeneration of oil palm. PMID:23382832

  10. Identification of QTLs associated with callogenesis and embryogenesis in oil palm using genetic linkage maps improved with SSR markers.

    Ngoot-Chin Ting

    Full Text Available Clonal reproduction of oil palm by means of tissue culture is a very inefficient process. Tissue culturability is known to be genotype dependent with some genotypes being more amenable to tissue culture than others. In this study, genetic linkage maps enriched with simple sequence repeat (SSR markers were developed for dura (ENL48 and pisifera (ML161, the two fruit forms of oil palm, Elaeis guineensis. The SSR markers were mapped onto earlier reported parental maps based on amplified fragment length polymorphism (AFLP and restriction fragment length polymorphism (RFLP markers. The new linkage map of ENL48 contains 148 markers (33 AFLPs, 38 RFLPs and 77 SSRs in 23 linkage groups (LGs, covering a total map length of 798.0 cM. The ML161 map contains 240 markers (50 AFLPs, 71 RFLPs and 119 SSRs in 24 LGs covering a total of 1,328.1 cM. Using the improved maps, two quantitative trait loci (QTLs associated with tissue culturability were identified each for callusing rate and embryogenesis rate. A QTL for callogenesis was identified in LGD4b of ENL48 and explained 17.5% of the phenotypic variation. For embryogenesis rate, a QTL was detected on LGP16b in ML161 and explained 20.1% of the variation. This study is the first attempt to identify QTL associated with tissue culture amenity in oil palm which is an important step towards understanding the molecular processes underlying clonal regeneration of oil palm.

  11. A multifaceted comparison of ArcGIS and MapMarker for automated geocoding

    Sanjaya Kumar

    2012-11-01

    Full Text Available Geocoding is increasingly being used for public health surveillance and spatial epidemiology studies. Public health departments in the United States of America (USA often use this approach to investigate disease outbreaks and clusters or assign health records to appropriate geographic units. We evaluated two commonly used geocoding software packages, ArcGIS and MapMarker, for automated geocoding of a large number of residential addresses from health administrative data in New York State, USA to better understand their features, performance and limitations. The comparison was based on three metrics of evaluation: completeness (or match rate, geocode similarity and positional accuracy. Of the 551,798 input addresses, 318,302 (57.7% were geocoded by MapMarker and 420,813 (76.3% by the ArcGIS composite address locator. High similarity between the geocodes assigned by the two methods was found, especially in suburban and urban areas. Among addresses with a distance of greater than 100 m between the geocodes assigned by the two packages, the point assigned by ArcGIS was closer to the associated parcel centroid (“true” location compared with that assigned by MapMarker. In addition, the composite address locator in ArcGIS allows users to fully utilise available reference data, which consequently results in better geocoding results. However, the positional differences found were minimal, and a large majority of addresses were placed on the same locations by both geocoding packages. Using both methods and combining the results can maximise match rates and save the time needed for manual geocoding.

  12. A multifaceted comparison of ArcGIS and MapMarker for automated geocoding.

    Kumar, Sanjaya; Liu, Ming; Hwang, Syni-An

    2012-11-01

    Geocoding is increasingly being used for public health surveillance and spatial epidemiology studies. Public health departments in the United States of America (USA) often use this approach to investigate disease outbreaks and clusters or assign health records to appropriate geographic units. We evaluated two commonly used geocoding software packages, ArcGIS and MapMarker, for automated geocoding of a large number of residential addresses from health administrative data in New York State, USA to better understand their features, performance and limitations. The comparison was based on three metrics of evaluation: completeness (or match rate), geocode similarity and positional accuracy. Of the 551,798 input addresses, 318,302 (57.7%) were geocoded by MapMarker and 420,813 (76.3%) by the ArcGIS composite address locator. High similarity between the geocodes assigned by the two methods was found, especially in suburban and urban areas. Among addresses with a distance of greater than 100 m between the geocodes assigned by the two packages, the point assigned by ArcGIS was closer to the associated parcel centroid ("true" location) compared with that assigned by MapMarker. In addition, the composite address locator in ArcGIS allows users to fully utilise available reference data, which consequently results in better geocoding results. However, the positional differences found were minimal, and a large majority of addresses were placed on the same locations by both geocoding packages. Using both methods and combining the results can maximise match rates and save the time needed for manual geocoding.

  13. Fine mapping of the rice bacterial blight resistance gene Xa-4 and its co-segregation marker

    2000-01-01

    An F2 population developed from the Xa-4 near isogenic lines,IR24 and IRBB4,was used for fine mapping of the rice bacterial blight resistance gene,Xa-4.Some restriction fragment length polymorphism (RFLP) markers on the high-density map constructed by Harushima et al.and the amplified DNA fragments homologous to the conserved domains of plant disease resistance (R) genes were used to construct the genetic linkage map around the gene Xa-4 by scoring susceptible individuals in the population.Xa-4 was mapped between the RFLP marker G181 and the polymerase chain reaction (PCR) marker M55.The R gene homologous fragment marker RS13 was found co-segregating with Xa-4 by analyzing all the plants in the population.This result opened an approach to map-based cloning of this gene,and marker RS13 can be applied to molecular marker-assisted selection of Xa-4 in rice breeding programs.

  14. Large-scale development of SSR markers in tobacco and construction of a linkage map in flue-cured tobacco.

    Tong, Zhijun; Xiao, Bingguang; Jiao, Fangchan; Fang, Dunhuang; Zeng, Jianmin; Wu, Xingfu; Chen, Xuejun; Yang, Jiankang; Li, Yongping

    2016-06-01

    Tobacco (Nicotiana tabacum L.), particularly flue-cured tobacco, is one of the most economically important nonfood crops and is also an important model system in plant biotechnology. Despite its importance, only limited molecular marker resources are available for genome analysis, genetic mapping, and breeding. Simple sequence repeats (SSR) are one of the most widely-used molecular markers, having significant advantages including that they are generally co-dominant, easy to use, abundant in eukaryotic organisms, and produce highly reproducible results. In this study, based on the genome sequence data of flue-cured tobacco (K326), we developed a total of 13,645 mostly novel SSR markers, which were working in a set of eighteen tobacco varieties of four different types. A mapping population of 213 backcross (BC1) individuals, which were derived from an intra-type cross between two flue-cured tobacco varieties, Y3 and K326, was selected for mapping. Based on the newly developed SSR markers as well as published SSR markers, we constructed a genetic map consisting of 626 SSR loci distributed across 24 linkage groups and covering a total length of 1120.45 cM with an average distance of 1.79 cM between adjacent markers, which is the highest density map of flue-cured tobacco till date.

  15. Precise localization of multiple epiphyseal dysplasia and pseudoachondroplasia mutations by genetic and physical mapping of chromosome 19

    Knowlton, R.G.; Cekleniak, J.A. [Jefferson Medical College, Philadelphia, PA (United States); Cohn, D.H. [Cedars-Sinai Medical Center, Los Angeles, CA (United States)] [and others

    1994-09-01

    Multiple epiphyseal dysplasia (EDM1), a dominantly inherited chondrodysplasia resulting in peripheral joint deformities and premature osteoarthritis, and pseudoachondroplasia (PSACH), a more severe disorder associated with short-limbed dwarfism, have recently been mapped to the pericentromeric region of chromosome 19. Chondrocytes from some PSACH patients accumulate lamellar deposits in the endoplasmic reticulum that are immunologically cross-reactive with aggrecan. However, neither aggrecan nor any known candidate gene maps to the EDM1/PSACH region of chromosome 19. Genetic linkage mapping in two lage families had placed the disease locus between D19S215 (19p12) and D19S212 (19p13.1), an interval of about 3.5 Mb. With at least five potentially informative cross-overs within this interval, recombination mapping at greater resolution was undertaken. From cosmids assigned to the region by fluorescence in situ hybridization and contig assembly, dinucleotide repeat tracts were identified for use as polymorphic genetic markers. Linkage data from three new dinucleotide repeat markers from cosmids mapped between D19S212 and D19S215 limit the EDM1/PSACH locus to an interval spanning approximately 2 Mb.

  16. Detection of multiple tumor markers using ultra-long carbon nanotube devices

    So, Hye-Mi; Park, Dong-Won; Kim, Beom Soo; Kong, Ki-Jeong; Buh, Gyoung-Ho; Chang, Hyunju; Lee, Jeong-O.; Kong, Jing

    2008-03-01

    For the simultaneous detection of multiple tumor markers, we have fabricated ultra-long carbon nanotube sensors that can detect carcinoembryonic antigen (CEA) and prostate specific antigen (PSA), simultaneously. Ultra-long carbon nanotubes, several millimeters long, were grown by ethanol CVD, and fabricated as FET sensors by using conventional photolithography. To functionalize each segment of a single ultra-long nanotube device with multiple-tumor markers, we first functionalize the entire device with CDI-Tween 20 linking molecules, and then immobilized CEA and PSA antibodies using the microfluidic channel. The electrical conductance from CEA-antibody functionalized and PSA-antibody functionalized segment of a ultra-long carbon nanotube device was monitored simultaneously with Ag/AgCl reference electrode as a liquid gate. We will discuss the advantages of long-nanotube device in detail.

  17. Cerebrospinal fluid inflammatory markers in patients with multiple sclerosis: a pilot study.

    Matejčíková, Z; Mareš, J; Přikrylová Vranová, H; Klosová, J; Sládková, V; Doláková, J; Zapletalová, J; Kaňovský, P

    2015-02-01

    Multiple sclerosis (MS) is an inflammatory demyelinating disease of the central nervous system. Autoimmune inflammation is common in the early stages of MS. This stage is followed by the neurodegenerative process. The result of these changes is axon and myelin breakdown. Although MS is according to McDonald's revised diagnostic criteria primarily a clinical diagnosis, paraclinical investigation methods are an important part in the diagnosis of MS. In common practice, magnetic resonance imaging of the brain and spinal cord, examination of cerebrospinal fluid (CSF) and examination of visual evoked potentials are used. There are an increasing number of studies dealing with biomarkers in CSF and their role in the diagnosis and treatment of MS. We hypothesized that the levels of some markers could be changed in MS in comparison with controls. We studied five inflammatory markers [interleukin-6 (IL-6), interleukin-8, interleukin-10 (IL-10), beta-2-microglobulin, orosomucoid]. CSF and serum levels of inflammatory markers were assessed in 38 patients with newly diagnosed MS meeting McDonald's revised diagnostic criteria and in 28 subjects as a control group (CG). Levels of beta-2-microglobulin and interleukin-8 in CSF were found to be significantly higher in MS patients in comparison to CG (p < 0.001 resp. p = 0.007). No differences in other CSF markers (IL-6, IL-10 and orosomucoid) and serum levels of all markers between both groups were found. The levels of two studied inflammatory markers were found to be increased at the time of first clinical symptoms of MS. Research on the role of inflammatory and neurodegenerative markers in MS should continue.

  18. Integrating Multiple Data Sources for Combinatorial Marker Discovery: A Study in Tumorigenesis.

    Bandyopadhyay, Sanghamitra; Mallik, Saurav

    2018-01-01

    Identification of combinatorial markers from multiple data sources is a challenging task in bioinformatics. Here, we propose a novel computational framework for identifying significant combinatorial markers ( s) using both gene expression and methylation data. The gene expression and methylation data are integrated into a single continuous data as well as a (post-discretized) boolean data based on their intrinsic (i.e., inverse) relationship. A novel combined score of methylation and expression data (viz., ) is introduced which is computed on the integrated continuous data for identifying initial non-redundant set of genes. Thereafter, (maximal) frequent closed homogeneous genesets are identified using a well-known biclustering algorithm applied on the integrated boolean data of the determined non-redundant set of genes. A novel sample-based weighted support ( ) is then proposed that is consecutively calculated on the integrated boolean data of the determined non-redundant set of genes in order to identify the non-redundant significant genesets. The top few resulting genesets are identified as potential s. Since our proposed method generates a smaller number of significant non-redundant genesets than those by other popular methods, the method is much faster than the others. Application of the proposed technique on an expression and a methylation data for Uterine tumor or Prostate Carcinoma produces a set of significant combination of markers. We expect that such a combination of markers will produce lower false positives than individual markers.

  19. Photo guided sentinel node mapping in breast cancer using marker free photo gamma fusion lymphoscintigraphy

    Lee, Eun Seong; Chun, In Kook; Ha, Seungn Gyun; Yoon, Hai Jeon; Jung, So Youn; Lee, See Youn; Kim, Seok Won; Lee, Eun Sook; Kim, Tae Yoon; Kim, Kwang Gi; Kim, Tae Sung; Kim, Seok Ki; Lee, Byung Il

    2012-01-01

    Photo gamma fusion lymphoscintigraphy (PGFLS) was developed by overlying a conventional planar gamma image on a photograph for the guidance of sentinel node biopsy. The feasibility and accuracy of PGFLS was assessed in breast cancer patients. A digital camera and a gamma camera were coordinated to obtain photograph and gamma images from the same angle. Using the distance to the object and calibration acquisition with a flat phantom and radioactive markers, PGFLS was performed both in phantom and in patients without fiducial markers. Marker free PGFLS was verified using flat phantom, anthropomorphic phantom with markers simulating sentinel nodes and breast cancer patients. In addition, the depth of the radioactive marker or sentinel node was calculated using two gamma images taken at right angles. The feasibility and accuracy of PGFLS were assessed in terms of mismatch errors of co registration and depth with reference to the data from SPECT/CT. The mismatch error was less than 6mm in the flat phantom image at a distance from 50 to 62cm without misalignment. In the anthropomorphic phantom study, co registration error was 0.42±0.29cm; depth error was 0.51±0.37cm, which was well correlated with the reference value on SPECT/CT (x scale: R'2'=0.99, p<0.01; y scale: R'2'=0.09, p<0.01; depth: R'2'=0.99, p<0.01). In ten patients with breast cancer referred for lympho SPECT/CT, PGFSL enabled photo guided sentinel lymph node mapping with acceptable accuracy (co-registration error, 0.47±0.24cm; depth error, 1.20±0.41cm). The results from PGFSL showed close correlation with those from SPECT/CT (x scale: R'2'=0.99, p<0.01; y scale: R'2'=0.98, p<0/01; depth: R'2'=0.77, p<0.01). The novel and convenient PGFLS technique is clinically feasible, showing acceptable accuracy and providing additional visual and quantitative information for sentinel lymph node mapping. This approach will facilitate photo guided sentinel lymph node dissection in breast cancer

  20. Is impaired cerebral vasoreactivity an early marker of cognitive decline in multiple sclerosis patients?

    Metzger, Aude; Le Bars, Emmanuelle; Deverdun, Jeremy; Molino, François; Maréchal, Bénédicte; Picot, Marie-Christine; Ayrignac, Xavier; Carra, Clarisse; Bauchet, Luc; Krainik, Alexandre; Labauge, Pierre; Menjot de Champfleur, Nicolas

    2018-03-01

    The link between cerebral vasoreactivity and cognitive status in multiple sclerosis remains unclear. The aim of the present study was to investigate a potential decrease of cerebral vasoreactivity in multiple sclerosis patients and correlate it with cognitive status. Thirty-three patients with multiple sclerosis (nine progressive and 24 remitting forms, median age: 39 years, 12 males) and 22 controls underwent MRI with a hypercapnic challenge to assess cerebral vasoreactivity and a neuropsychological assessment. Cerebral vasoreactivity, measured as the cerebral blood flow percent increase normalised by end-tidal carbon dioxide variation, was assessed globally and by regions of interest using the blood oxygen level-dependent technique. Non-parametric statistics tests were used to assess differences between groups, and associations were estimated using linear models. Cerebral vasoreactivity was lower in patients with cognitive impairment than in cognitively normal patients (p=0.004) and was associated with education level in patients (R 2 = 0.35; p = 0.047). There was no decrease in cerebral vasoreactivity between patients and controls. Cognitive impairment in multiple sclerosis may be mediated through decreased cerebral vasoreactivity. Cerebral vasoreactivity could therefore be considered as a marker of cognitive decline in multiple sclerosis. • Cerebral vasoreactivity does not differ between multiple sclerosis patients and controls. • Cerebral vasoreactivity measure is linked to cognitive impairment in multiple sclerosis. • Cerebral vasoreactivity is linked to level of education in multiple sclerosis.

  1. Mapping habitat for multiple species in the Desert Southwest

    Inman, Richard D.; Nussear, Kenneth E.; Esque, Todd C.; Vandergast, Amy G.; Hathaway, Stacie A.; Wood, Dustin A.; Barr, Kelly R.; Fisher, Robert N.

    2014-01-01

    Many utility scale renewable energy projects are currently proposed across the Mojave Ecoregion. Agencies that manage biological resources throughout this region need to understand the potential impacts of these renewable energy projects and their associated infrastructure (for example, transmission corridors, substations, access roads, etc.) on species movement, genetic exchange among populations, and species’ abilities to adapt to changing environmental conditions. Understanding these factors will help managers’ select appropriate project sites and possibly mitigate for anticipated effects of management activities. We used species distribution models to map habitat for 15 species across the Mojave Ecoregion to aid regional land-use management planning. Models were developed using a common 1 × 1 kilometer resolution with maximum entropy and generalized additive models. Occurrence data were compiled from multiple sources, including VertNet (http://vertnet.org/), HerpNET (http://www.herpnet.org), and MaNIS (http://manisnet.org), as well as from internal U.S. Geological Survey databases and other biologists. Background data included 20 environmental covariates representing terrain, vegetation, and climate covariates. This report summarizes these environmental covariates and species distribution models used to predict habitat for the 15 species across the Mojave Ecoregion.

  2. Complete physical mapping of IL6 reveals a new marker associated with chronic periodontitis.

    Farhat, S B; de Souza, C M; Braosi, A P R; Kim, S H; Tramontina, V A; Papalexiou, V; Olandoski, M; Mira, M T; Luczyszyn, S M; Trevilatto, P C

    2017-04-01

    Interleukin-6 (IL-6) is a powerful stimulator of osteoclast differentiation and bone resorption. Production of IL-6 is modulated by polymorphisms, and higher levels of this cytokine are found locally in patients with chronic periodontitis. In this study we performed a modern approach - Complete physical mapping of the IL6 gene - to identify the polymorphisms associated with chronic periodontitis in a southern Brazilian population sample. One-hundred and nine individuals of both genders (mean age: 41.5 ± 8.5 years) were divided into a study group (56 participants with periodontitis) and a control group (53 individuals without periodontitis). After collection and purification of DNA, nine tag single nucleotide polymorphisms (SNPs; rs1524107, rs2069835, rs2069837, rs2069838, rs2069840, rs2069842, rs2069843, rs2069845 and rs2069849) covering the entire gene were selected according to the information available on the International HapMap Project website and evaluated using real-time PCR. Differences in the distribution of the following parameters were statistically significant between study and control groups: number of teeth (p = 0.030); probing depth (p chronic periodontitis in a Brazilian population in the presence of clinical variables, such as visible plaque, dentist visit frequency and dental floss use, and was suggested for the first time as a marker of susceptibility to chronic periodontitis. Complete physical mapping of IL6 (using tag SNPs) was carried out for the first time, unveiling allele G of polymorphism rs2069837 (located in the second intron of IL6) as a suggestive marker of protection against chronic periodontitis in a Brazilian population. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  3. Fine mapping of multiple QTL using combined linkage and linkage disequilibrium mapping – A comparison of single QTL and multi QTL methods

    Meuwissen Theo HE

    2007-04-01

    Full Text Available Abstract Two previously described QTL mapping methods, which combine linkage analysis (LA and linkage disequilibrium analysis (LD, were compared for their ability to detect and map multiple QTL. The methods were tested on five different simulated data sets in which the exact QTL positions were known. Every simulated data set contained two QTL, but the distances between these QTL were varied from 15 to 150 cM. The results show that the single QTL mapping method (LDLA gave good results as long as the distance between the QTL was large (> 90 cM. When the distance between the QTL was reduced, the single QTL method had problems positioning the two QTL and tended to position only one QTL, i.e. a "ghost" QTL, in between the two real QTL positions. The multi QTL mapping method (MP-LDLA gave good results for all evaluated distances between the QTL. For the large distances between the QTL (> 90 cM the single QTL method more often positioned the QTL in the correct marker bracket, but considering the broader likelihood peaks of the single point method it could be argued that the multi QTL method was more precise. Since the distances were reduced the multi QTL method was clearly more accurate than the single QTL method. The two methods combine well, and together provide a good tool to position single or multiple QTL in practical situations, where the number of QTL and their positions are unknown.

  4. Enriching an intraspecific genetic map and identifying QTL for fiber quality and yield component traits across multiple environments in Upland cotton (Gossypium hirsutum L.).

    Liu, Xueying; Teng, Zhonghua; Wang, Jinxia; Wu, Tiantian; Zhang, Zhiqin; Deng, Xianping; Fang, Xiaomei; Tan, Zhaoyun; Ali, Iftikhar; Liu, Dexin; Zhang, Jian; Liu, Dajun; Liu, Fang; Zhang, Zhengsheng

    2017-12-01

    Cotton is a significant commercial crop that plays an indispensable role in many domains. Constructing high-density genetic maps and identifying stable quantitative trait locus (QTL) controlling agronomic traits are necessary prerequisites for marker-assisted selection (MAS). A total of 14,899 SSR primer pairs designed from the genome sequence of G. raimondii were screened for polymorphic markers between mapping parents CCRI 35 and Yumian 1, and 712 SSR markers showing polymorphism were used to genotype 180 lines from a (CCRI 35 × Yumian 1) recombinant inbred line (RIL) population. Genetic linkage analysis was conducted on 726 loci obtained from the 712 polymorphic SSR markers, along with 1379 SSR loci obtained in our previous study, and a high-density genetic map with 2051 loci was constructed, which spanned 3508.29 cM with an average distance of 1.71 cM between adjacent markers. Marker orders on the linkage map are highly consistent with the corresponding physical orders on a G. hirsutum genome sequence. Based on fiber quality and yield component trait data collected from six environments, 113 QTLs were identified through two analytical methods. Among these 113 QTLs, 50 were considered stable (detected in multiple environments or for which phenotypic variance explained by additive effect was greater than environment effect), and 18 of these 50 were identified with stability by both methods. These 18 QTLs, including eleven for fiber quality and seven for yield component traits, could be priorities for MAS.

  5. Transferability of molecular markers from major legumes to Lathyrus spp. for their application in mapping and diversity studies.

    Almeida, Nuno Felipe; Trindade Leitão, Susana; Caminero, Constantino; Torres, Ana Maria; Rubiales, Diego; Vaz Patto, Maria Carlota

    2014-01-01

    Lathyrus cicera L. (chickling pea) and L. sativus L. (grass pea) have great potential among grain legumes due to their adaptability to inauspicious environments, high protein content and resistance to serious diseases. Nevertheless, due to its past underused, further activities are required to exploit this potential and to capitalise on the advances in molecular biology that enable improved Lathyrus spp. breeding programmes. In this study we evaluated the transferability of molecular markers developed for closely related legume species to Lathyrus spp. (Medicago truncatula, pea, lentil, faba bean and lupin) and tested the application of those new molecular tools on Lathyrus mapping and diversity studies. Genomic and expressed sequence tag microsatellite, intron-targeted amplified polymorphic, resistance gene analogue and defence-related gene markers were tested. In total 128 (27.7 %) and 132 (28.6 %) molecular markers were successfully cross-amplified, respectively in L. cicera and L. sativus. In total, the efficiency of transferability from genomic microsatellites was 5 %, and from gene-based markers, 55 %. For L. cicera, three cleaved amplified polymorphic sequence markers and one derived cleaved amplified polymorphic sequence marker based on the cross-amplified markers were also developed. Nine of those molecular markers were suitable for mapping in a L. cicera recombinant inbred line population. From the 17 molecular markers tested for diversity analysis, six (35 %) in L. cicera and seven (41 %) in L. sativus were polymorphic and discriminate well all the L. sativus accessions. Additionally, L. cicera accessions were clearly distinguished from L. sativus accessions. This work revealed a high number of transferable molecular markers to be used in current genomic studies in Lathyrus spp. Although their usefulness was higher on diversity studies, they represent the first steps for future comparative mapping involving these species.

  6. Identification and Mapping of Simple Sequence Repeat Markers from Common Bean (Phaseolus vulgaris L. Bacterial Artificial Chromosome End Sequences for Genome Characterization and Genetic–Physical Map Integration

    Juana M. Córdoba

    2010-11-01

    Full Text Available Microsatellite markers or simple sequence repeat (SSR loci are useful for diversity characterization and genetic–physical mapping. Different in silico microsatellite search methods have been developed for mining bacterial artificial chromosome (BAC end sequences for SSRs. The overall goal of this study was genome characterization based on SSRs in 89,017 BAC end sequences (BESs from the G19833 common bean ( L. library. Another objective was to identify new SSR taking into account three tandem motif identification programs (Automated Microsatellite Marker Development [AMMD], Tandem Repeats Finder [TRF], and SSRLocator [SSRL]. Among the microsatellite search engines, SSRL identified the highest number of SSRs; however, when primer design was attempted, the number dropped due to poor primer design regions. Automated Microsatellite Marker Development software identified many SSRs with valuable AT/TA or AG/TC motifs, while TRF found fewer SSRs and produced no primers. A subgroup of 323 AT-rich, di-, and trinucleotide SSRs were selected from the AMMD results and used in a parental survey with DOR364 and G19833, of which 75 could be mapped in the corresponding population; these represented 4052 BAC clones. Together with 92 previously mapped BES- and 114 non-BES-derived markers, a total of 280 SSRs were included in the polymerase chain reaction (PCR-based map, integrating a total of 8232 BAC clones in 162 contigs from the physical map.

  7. Novel fluorescent sequence-related amplified polymorphism(FSRAP markers for the construction of a genetic linkage map of wheat(Triticum aestivum L.

    Zhao Lingbo

    2017-01-01

    Full Text Available Novel fluorescent sequence-related amplified polymorphism (FSRAP markers were developed based on the SRAP molecular marker. Then, the FSRAP markers were used to construct the genetic map of a wheat (Triticum aestivumL. recombinant inbred line population derived from a Chuanmai 42×Chuannong 16 cross. Reproducibility and polymorphism tests indicated that the FSRAP markers have repeatability and better reflect the polymorphism of wheat varieties compared with SRAP markers. A total of 430 polymorphic loci between Chuanmai 42 and Chuannong 16 were detected with 189 FSRAP primer combinations. A total of 281 FSARP markers and 39 SSR markers re classified into 20 linkage groups. The maps spanned a total length of 2499.3cM with an average distance of 7.81cM between markers. A total of 201 markers were mapped on the B genome and covered a distance of 1013cM. On the A genome, 84 markers were mapped and covered a distance of 849.6cM. On the D genome, however, only 35 markers were mapped and covered a distance of 636.7cM. No FSRAP markers were distributed on the 7D chromosome. The results of the present study revealed that the novel FSRAP markers can be used to generate dense, uniform genetic maps of wheat.

  8. Diagnostic significance of combined detention of multiple tumour markers in lung cancer

    Chen Yanming; Qiu Jianming

    2003-01-01

    Objective: To explore the diagnostic value of combined detection of multiple markers in the determination of lung cancer. Methods: Using enzyme-linked immunosorbent assay (ELISA), the serum CEA, CA19-9, CA125, CA15-3 was determined in eighty-six lung cancer patients, thirty benign lung disease patients and thirty healthy persons. Results; Serum concentrations of CEA, CA19-9, CA125 and CA15-3 were significantly higher in patents with lung cancer than that in the patients with benign lung disease patients and healthy persons. The single test sensitivity of CEA, CA19-9, CA125 and CA15-3 for diagnosis of lung cancer is 41.9%, 37.2%, 48.9%, 36% respectively; the combined test sensitivity is 94.2%. Conclusions: Assessing several tumour markers can help differentiating various histological type of lung cancer and increase the sensitivity

  9. Sequential analysis of biochemical markers of bone resorption and bone densitometry in multiple myeloma

    Abildgaard, Niels; Brixen, K; Eriksen, E.F

    2004-01-01

    BACKGROUND AND OBJECTIVES: Bone lesions often occur in multiple myeloma (MM), but no tests have proven useful in identifying patients with increased risk. Bone marker assays and bone densitometry are non-invasive methods that can be used repeatedly at low cost. This study was performed to evaluate...... 6 weeks, DEXA-scans performed every 3 months, and skeletal radiographs were done every 6 months as well as when indicated. RESULTS: Serum ICTP and urinary NTx were predictive of progressive bone events. Markers of bone formation, bone mineral density assessments, and M component measurements were...... changes, and our data do not support routine use of sequential DEXA-scans. However, lumbar DEXA-scans at diagnosis can identify patients with increased risk of early vertebral collapses. Sequential analyses of serum ICTP and urinary NTx are useful for monitoring bone damage....

  10. Reconstructions of human history by mapping dental markers in living Eurasian populations

    Kashibadze, Vera F.; Nasonova, Olga G.; Nasonov, Dmitry S.

    2013-01-01

    Using advances in gene geography and anthropophenetics, the phenogeographical method for anthropological research was initiated and developed using dental data. Statistical and cartographical analyses are provided for 498 living Eurasian populations. Mapping principal components supplied evidence for the phene pool structure in Eurasian populations, and for reconstructions of Homo sapiens history on the continent. Longitudinal variability seems to be the most important regularity revealed by principal components analysis (PCA) and mapping, indicating the division of the whole area into western and eastern main provinces. So, the most ancient scenario in the history of Eurasian populations developed from two perspective different groups: a western group related to ancient populations of West Asia and an eastern one rooted in ancestry in South and/or East Asia. In spite of the enormous territory and the revealed divergence, the populations of the continent have undergone wide scale and intensive timeespace interaction. Many details in the revealed landscapes are background to different historical events. Migrations and assimilation are two essential phenomena in Eurasian history: the widespread of the western combination through the whole continent to the Pacific coastline and the movement of the paradoxical combinations of eastern and western markers from South or Central Asia to the east and west. Taking into account that no additional eastern combinations in the total variation in Asian groups have been found, but that mixed or western markers' sets and that eastern dental characteristics are traced in Asia since Homo erectus, the assumption is made in favour of the hetero-level assimilation in the eastern province and of net-like evolution of H. sapiens.

  11. Development of Insertion and Deletion Markers based on Biparental Resequencing for Fine Mapping Seed Weight in Soybean

    Ying-hui Li

    2014-11-01

    Full Text Available As a complement to single nucleotide polymorphisms (SNPs and simple sequence repeats (SSRs, biallelic insertions and deletions (InDels represent powerful molecular markers with desirable features for filling the gap in current genetic linkage maps. In this study, 28,908 small InDel polymorphisms (1–5 base pair, bp distributed genome-wide were identified and annotated by comparison of a whole-genome resequencing data set from two soybean [ (L. Merr.] genotypes, cultivar Zhonghunag13 (ZH and line Zhongpin03-5373 (ZP. The physical distribution of InDel polymorphisms in soybean genome was uneven, and matched closely with the distribution of previously annotated genes. The average density of InDel in the arm region was significantly higher than that in the pericentromeric region. The genomic regions that were fixed between the two elites were elucidated. With this information, five InDel markers within a putative quantitative trait locus (QTL for seed weight (SW, , were developed and used to genotype 254 recombinant inbred lines (RILs derived from the cross of ZP × ZH. Adding these five InDel markers to previously used SNP and SSR markers facilitated the discovery of further recombination events allowing fine-mapping the QTL to a 0.5 Mbp region. Our study clearly underlines the high value of InDel markers for map-based cloning and marker-assisted selection in soybean.

  12. Allele-specific marker generation and linkage mapping on the Xiphophorus sex chromosomes.

    Woolcock, B; Kazianis, S; Lucito, R; Walter, R B; Kallman, K D; Morizot, D C; Vielkind, J R

    2006-01-01

    There is great interest in the sex chromosomes of Xiphophorus fishes because both WY/YY and XX/XY sex-determining mechanisms function in these species, with at least one taxon possessing all three types of sex chromosomes, and because in certain interspecific hybrids melanoma arises as a consequence of inheritance of the sex-linked macromelanophore determining locus (MDL). Representational difference analysis (RDA) has been used to clone two sequences from the sex-determining region of X. maculatus, including a cholinergic receptor, nicotinic, delta polypeptide (CHRND) orthologue. Allele-specific assays for these sequences, as well as for the sex-linked XMRK1 and XMRK2 genes, were developed to distinguish W, X, and Y chromosomes derived from a X. maculatus (XX/XY) strain and a X. helleri (WY/YY) strain. Linkage mapping localized these markers to linkage group (LG) 24. No recombinants were observed between XMRK2 and MDL, confirming a role for XMRK2 in macromelanophore development. Although the master sex-determining (SD) locus certainly resides on Xiphophorus LG 24, autosomal loci are probably involved in sex determination as well, as indicated by the abnormal sex ratios in the backcross hybrids that contrast theoretical predictions based on LG 24 genotyping. Marker development and allelic discrimination on the Xiphophorus sex chromosomes should prove highly useful for studies that utilize this genus as an animal model.

  13. QTL mapping of soybean oil content for marker-assisted selection in plant breeding program.

    Leite, D C; Pinheiro, J B; Campos, J B; Di Mauro, A O; Unêda-Trevisoli, S H

    2016-03-18

    The present study was undertaken to detect and map the quantitative trait loci (QTL) related to soybean oil content. We used 244 progenies derived from a bi-parental cross of the Lineage 69 (from Universidade Estadual Paulista "Júlio de Mesquita Filho"/Faculdade de Ciências Agrárias e Veterinárias - Breeding Program) and Tucunaré cultivar. A total of 358 simple sequence repeat (SSR; microsatellite) markers were used to investigate the polymorphism between the parental lines, and for the polymorphic lines all the F2 individuals were tested. Evaluation of the oil content and phenotype was performed with the aid of a Tango equipment by near infra-red reflectance spectroscopy, using single F2 seeds and F2:3 progenies, in triplicate. The data were analyzed by QTL Cartographer program for 56 SSR polymorphic markers. Two oil-content related QTLs were detected on K and H linkage groups. The total phenotypic variation explained by QTLs ranged from 7.8 to 46.75% for oil content. New QTLs were identified for the oil content in addition to those previously identified in other studies. The results reported in this study show that regions different from those already known could be involved in the genetic control of soybean oil content.

  14. First genetic linkage map of Taraxacum koksaghyz Rodin based on AFLP, SSR, COS and EST-SSR markers.

    Arias, Marina; Hernandez, Monica; Remondegui, Naroa; Huvenaars, Koen; van Dijk, Peter; Ritter, Enrique

    2016-08-04

    Taraxacum koksaghyz Rodin (TKS) has been studied in many occasions as a possible alternative source for natural rubber production of good quality and for inulin production. Some tire companies are already testing TKS tire prototypes. There are also many investigations on the production of bio-fuels from inulin and inulin applications for health improvement and in the food industry. A limited amount of genomic resources exist for TKS and particularly no genetic linkage map is available in this species. We have constructed the first TKS genetic linkage map based on AFLP, COS, SSR and EST-SSR markers. The integrated linkage map with eight linkage groups (LG), representing the eight chromosomes of Russian dandelion, has 185 individual AFLP markers from parent 1, 188 individual AFLP markers from parent 2, 75 common AFLP markers and 6 COS, 1 SSR and 63 EST-SSR loci. Blasting the EST-SSR sequences against known sequences from lettuce allowed a partial alignment of our TKS map with a lettuce map. Blast searches against plant gene databases revealed some homologies with useful genes for downstream applications in the future.

  15. Fine mapping of the rice Bph1 gene, which confers resistance to the brown planthopper (Nilaparvata lugens stal), and development of STS markers for marker-assisted selection.

    Cha, Young-Soon; Ji, Hyeonso; Yun, Doh-Won; Ahn, Byoung-Ohg; Lee, Myung Chul; Suh, Seok-Cheol; Lee, Chun Seok; Ahn, Eok Keun; Jeon, Yong-Hee; Jin, Il-Doo; Sohn, Jae-Keun; Koh, Hee-Jong; Eun, Moo-Young

    2008-08-31

    The brown planthopper (BPH) is a major insect pest in rice, and damages these plants by sucking phloem-sap and transmitting viral diseases. Many BPH resistance genes have been identified in indica varieties and wild rice accessions, but none has yet been cloned. In the present study we report fine mapping of the region containing the Bph1 locus, which enabled us to perform marker-aided selection (MAS). We used 273 F8 recombinant inbred lines (RILs) derived from a cross between Cheongcheongbyeo, an indica type variety harboring Bph1 from Mudgo, and Hwayeongbyeo, a BPH susceptible japonica variety. By random amplification of polymorphic DNA (RAPD) analysis using 656 random 10-mer primers, three RAPD markers (OPH09, OPA10 and OPA15) linked to Bph1 were identified and converted to SCAR (sequence characterized amplified region) markers. These markers were found to be contained in two BAC clones derived from chromosome 12: OPH09 on OSJNBa0011B18, and both OPA10 and OPA15 on OSJNBa0040E10. By sequence analysis of ten additional BAC clones evenly distributed between OSJNBa0011B18 and OSJNBa0040E10, we developed 15 STS markers. Of these, pBPH4 and pBPH14 flanked Bph1 at distances of 0.2 cM and 0.8 cM, respectively. The STS markers pBPH9, pBPH19, pBPH20, and pBPH21 co-segregated with Bph1. These markers were shown to be very useful for marker-assisted selection (MAS) in breeding populations of 32 F6 RILs from a cross between Andabyeo and IR71190, and 32 F5 RILs from a cross between Andabyeo and Suwon452.

  16. Prosomeric map of the lamprey forebrain based on calretinin immunocytochemistry, Nissl stain, and ancillary markers.

    Pombal, M A; Puelles, L

    1999-11-22

    The structural organization of the lamprey extratelencephalic forebrain is re-examined from the perspective of the prosomeric segmental paradigm. The question asked was whether the prosomeric forebrain model used for gnathostomes is of material advantage for interpreting subdivisions in the lamprey forebrain. To this aim, the main longitudinal and transverse landmarks recognized by the prosomeric model in other vertebrates were identified in Nissl-stained lamprey material. Lines of cytoarchitectural discontinuity and contours of migrated neuronal groups were mapped in a two-dimensional sagittal representation and were also classified according to their radial position. Immunocytochemical mapping of calretinin expression in adjacent sections served to define particular structural units better, in particular, the dorsal thalamus. These data were complemented by numerous other chemoarchitectonic observations obtained with ancillary markers, which identified additional specific formations, subdivisions, or boundaries. Emphasis was placed on studying whether such chemically defined neuronal groups showed boundaries aligned with the postulated inter- or intraprosomeric boundaries. The course of diverse axonal tracts was studied also with regard to their prosomeric topography. This analysis showed that the full prosomeric model applies straightforwardly to the lamprey forebrain. This finding implies that a common segmental and longitudinal organization of the neural tube may be primitive for all vertebrates. Interesting novel aspects appear in the interpretation of the lamprey pretectum, the dorsal and ventral thalami, and the hypothalamus. The topologic continuity of the prosomeric forebrain regions with evaginated or non-evaginated portions of the telencephalon was also examined. Copyright 1999 Wiley-Liss, Inc.

  17. A consensus linkage map for molecular markers and Quantitative Trait Loci associated with economically important traits in melon (Cucumis melo L.)

    2011-01-01

    Background A number of molecular marker linkage maps have been developed for melon (Cucumis melo L.) over the last two decades. However, these maps were constructed using different marker sets, thus, making comparative analysis among maps difficult. In order to solve this problem, a consensus genetic map in melon was constructed using primarily highly transferable anchor markers that have broad potential use for mapping, synteny, and comparative quantitative trait loci (QTL) analysis, increasing breeding effectiveness and efficiency via marker-assisted selection (MAS). Results Under the framework of the International Cucurbit Genomics Initiative (ICuGI, http://www.icugi.org), an integrated genetic map has been constructed by merging data from eight independent mapping experiments using a genetically diverse array of parental lines. The consensus map spans 1150 cM across the 12 melon linkage groups and is composed of 1592 markers (640 SSRs, 330 SNPs, 252 AFLPs, 239 RFLPs, 89 RAPDs, 15 IMAs, 16 indels and 11 morphological traits) with a mean marker density of 0.72 cM/marker. One hundred and ninety-six of these markers (157 SSRs, 32 SNPs, 6 indels and 1 RAPD) were newly developed, mapped or provided by industry representatives as released markers, including 27 SNPs and 5 indels from genes involved in the organic acid metabolism and transport, and 58 EST-SSRs. Additionally, 85 of 822 SSR markers contributed by Syngenta Seeds were included in the integrated map. In addition, 370 QTL controlling 62 traits from 18 previously reported mapping experiments using genetically diverse parental genotypes were also integrated into the consensus map. Some QTL associated with economically important traits detected in separate studies mapped to similar genomic positions. For example, independently identified QTL controlling fruit shape were mapped on similar genomic positions, suggesting that such QTL are possibly responsible for the phenotypic variability observed for this trait in

  18. A consensus linkage map for molecular markers and Quantitative Trait Loci associated with economically important traits in melon (Cucumis melo L.

    Schaffer Arthur

    2011-07-01

    Full Text Available Abstract Background A number of molecular marker linkage maps have been developed for melon (Cucumis melo L. over the last two decades. However, these maps were constructed using different marker sets, thus, making comparative analysis among maps difficult. In order to solve this problem, a consensus genetic map in melon was constructed using primarily highly transferable anchor markers that have broad potential use for mapping, synteny, and comparative quantitative trait loci (QTL analysis, increasing breeding effectiveness and efficiency via marker-assisted selection (MAS. Results Under the framework of the International Cucurbit Genomics Initiative (ICuGI, http://www.icugi.org, an integrated genetic map has been constructed by merging data from eight independent mapping experiments using a genetically diverse array of parental lines. The consensus map spans 1150 cM across the 12 melon linkage groups and is composed of 1592 markers (640 SSRs, 330 SNPs, 252 AFLPs, 239 RFLPs, 89 RAPDs, 15 IMAs, 16 indels and 11 morphological traits with a mean marker density of 0.72 cM/marker. One hundred and ninety-six of these markers (157 SSRs, 32 SNPs, 6 indels and 1 RAPD were newly developed, mapped or provided by industry representatives as released markers, including 27 SNPs and 5 indels from genes involved in the organic acid metabolism and transport, and 58 EST-SSRs. Additionally, 85 of 822 SSR markers contributed by Syngenta Seeds were included in the integrated map. In addition, 370 QTL controlling 62 traits from 18 previously reported mapping experiments using genetically diverse parental genotypes were also integrated into the consensus map. Some QTL associated with economically important traits detected in separate studies mapped to similar genomic positions. For example, independently identified QTL controlling fruit shape were mapped on similar genomic positions, suggesting that such QTL are possibly responsible for the phenotypic variability

  19. Is impaired cerebral vasoreactivity an early marker of cognitive decline in multiple sclerosis patients?

    Metzger, Aude; Le Bars, Emmanuelle; Deverdun, Jeremy; Molino, Francois; Marechal, Benedicte; Picot, Marie-Christine; Ayrignac, Xavier; Carra, Clarisse; Labauge, Pierre; Bauchet, Luc; Krainik, Alexandre; Menjot de Champfleur, Nicolas

    2018-01-01

    The link between cerebral vasoreactivity and cognitive status in multiple sclerosis remains unclear. The aim of the present study was to investigate a potential decrease of cerebral vasoreactivity in multiple sclerosis patients and correlate it with cognitive status. Thirty-three patients with multiple sclerosis (nine progressive and 24 remitting forms, median age: 39 years, 12 males) and 22 controls underwent MRI with a hypercapnic challenge to assess cerebral vasoreactivity and a neuropsychological assessment. Cerebral vasoreactivity, measured as the cerebral blood flow percent increase normalised by end-tidal carbon dioxide variation, was assessed globally and by regions of interest using the blood oxygen level-dependent technique. Non-parametric statistics tests were used to assess differences between groups, and associations were estimated using linear models. Cerebral vasoreactivity was lower in patients with cognitive impairment than in cognitively normal patients (p=0.004) and was associated with education level in patients (R 2 = 0.35; p = 0.047). There was no decrease in cerebral vasoreactivity between patients and controls. Cognitive impairment in multiple sclerosis may be mediated through decreased cerebral vasoreactivity. Cerebral vasoreactivity could therefore be considered as a marker of cognitive decline in multiple sclerosis. (orig.)

  20. Is impaired cerebral vasoreactivity an early marker of cognitive decline in multiple sclerosis patients?

    Metzger, Aude [University Hospital Center, Department of Neurology, Montpellier (France); University Hospital Center, Department of Neurology, Memory Ressource and Research Center, Montpellier (France); Le Bars, Emmanuelle; Deverdun, Jeremy [Centre Hospitalier Regional Universitaire de Montpellier, Departement de Neuroradiologie, Hopital Gui de Chauliac, Montpellier (France); Centre Hospitalier Regional Universitaire de Montpellier, Institut d' Imagerie Fonctionnelle Humaine (I2FH), Hopital Gui de Chauliac, Montpellier (France); Universite de Montpellier, Laboratoire Charles Coulomb, CNRS UMR 5221, Montpellier (France); Molino, Francois [Universite de Montpellier, Laboratoire Charles Coulomb, CNRS UMR 5221, Montpellier (France); Universite de Montpellier, Institut de Genomique Fonctionnelle, CNRS UMR 5203, INSERM U661, Montpellier (France); Marechal, Benedicte [Siemens Healthcare, Advanced Clinical Imaging Technology, Lausanne (Switzerland); CHUV, Department of Radiology, Lausanne (Switzerland); LTS5, EPFL, Lausanne (Switzerland); Picot, Marie-Christine [Centre Hospitalier Regional Universitaire de Montpellier, Departement de Biostatistiques, Montpellier (France); Ayrignac, Xavier; Carra, Clarisse; Labauge, Pierre [University Hospital Center, Department of Neurology, Montpellier (France); Bauchet, Luc [Centre Hospitalier Regional Universitaire de Montpellier, Departement de Neurochirurgie, Hopital Gui de Chauliac, Montpellier (France); Hopital Saint Eloi, Institut de Neurosciences de Montpellier, INSERM U1051, Montpellier (France); Krainik, Alexandre [University Hospital of Grenoble, MR Unit CS 10217, Grenoble (France); Menjot de Champfleur, Nicolas [Centre Hospitalier Regional Universitaire de Montpellier, Departement de Neuroradiologie, Hopital Gui de Chauliac, Montpellier (France); Centre Hospitalier Regional Universitaire de Montpellier, Institut d' Imagerie Fonctionnelle Humaine (I2FH), Hopital Gui de Chauliac, Montpellier (France); Universite de Montpellier, Laboratoire Charles Coulomb, CNRS UMR 5221, Montpellier (France); Centre Hospitalier Universitaire Caremeau, Departement d' Imagerie Medicale, Nimes (France)

    2018-03-15

    The link between cerebral vasoreactivity and cognitive status in multiple sclerosis remains unclear. The aim of the present study was to investigate a potential decrease of cerebral vasoreactivity in multiple sclerosis patients and correlate it with cognitive status. Thirty-three patients with multiple sclerosis (nine progressive and 24 remitting forms, median age: 39 years, 12 males) and 22 controls underwent MRI with a hypercapnic challenge to assess cerebral vasoreactivity and a neuropsychological assessment. Cerebral vasoreactivity, measured as the cerebral blood flow percent increase normalised by end-tidal carbon dioxide variation, was assessed globally and by regions of interest using the blood oxygen level-dependent technique. Non-parametric statistics tests were used to assess differences between groups, and associations were estimated using linear models. Cerebral vasoreactivity was lower in patients with cognitive impairment than in cognitively normal patients (p=0.004) and was associated with education level in patients (R{sup 2} = 0.35; p = 0.047). There was no decrease in cerebral vasoreactivity between patients and controls. Cognitive impairment in multiple sclerosis may be mediated through decreased cerebral vasoreactivity. Cerebral vasoreactivity could therefore be considered as a marker of cognitive decline in multiple sclerosis. (orig.)

  1. Regularity of optimal transport maps on multiple products of spheres

    Figalli, Alessio; Kim, Young-Heon; McCann, Robert J.

    2010-01-01

    This article addresses regularity of optimal transport maps for cost="squared distance" on Riemannian manifolds that are products of arbitrarily many round spheres with arbitrary sizes and dimensions. Such manifolds are known to be non-negatively cross-curved [KM2]. Under boundedness and non-vanishing assumptions on the transfered source and target densities we show that optimal maps stay away from the cut-locus (where the cost exhibits singularity), and obtain injectivity and continuity of o...

  2. A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study

    Cherubini Marcello

    2010-10-01

    Full Text Available Abstract Background Expressed Sequence Tags (ESTs are a source of simple sequence repeats (SSRs that can be used to develop molecular markers for genetic studies. The availability of ESTs for Quercus robur and Quercus petraea provided a unique opportunity to develop microsatellite markers to accelerate research aimed at studying adaptation of these long-lived species to their environment. As a first step toward the construction of a SSR-based linkage map of oak for quantitative trait locus (QTL mapping, we describe the mining and survey of EST-SSRs as well as a fast and cost-effective approach (bin mapping to assign these markers to an approximate map position. We also compared the level of polymorphism between genomic and EST-derived SSRs and address the transferability of EST-SSRs in Castanea sativa (chestnut. Results A catalogue of 103,000 Sanger ESTs was assembled into 28,024 unigenes from which 18.6% presented one or more SSR motifs. More than 42% of these SSRs corresponded to trinucleotides. Primer pairs were designed for 748 putative unigenes. Overall 37.7% (283 were found to amplify a single polymorphic locus in a reference full-sib pedigree of Quercus robur. The usefulness of these loci for establishing a genetic map was assessed using a bin mapping approach. Bin maps were constructed for the male and female parental tree for which framework linkage maps based on AFLP markers were available. The bin set consisting of 14 highly informative offspring selected based on the number and position of crossover sites. The female and male maps comprised 44 and 37 bins, with an average bin length of 16.5 cM and 20.99 cM, respectively. A total of 256 EST-SSRs were assigned to bins and their map position was further validated by linkage mapping. EST-SSRs were found to be less polymorphic than genomic SSRs, but their transferability rate to chestnut, a phylogenetically related species to oak, was higher. Conclusion We have generated a bin map for oak

  3. Real-time segmentation of multiple implanted cylindrical liver markers in kilovoltage and megavoltage x-ray images

    Fledelius, W; Worm, E; Høyer, M; Grau, C; Poulsen, P R

    2014-01-01

    Gold markers implanted in or near a tumor can be used as x-ray visible landmarks for image based tumor localization. The aim of this study was to develop and demonstrate fast and reliable real-time segmentation of multiple liver tumor markers in intra-treatment kV and MV images and in cone-beam CT (CBCT) projections, for real-time motion management. Thirteen patients treated with conformal stereotactic body radiation therapy in three fractions had 2–3 cylindrical gold markers implanted in the liver prior to treatment. At each fraction, the projection images of a pre-treatment CBCT scan were used for automatic generation of a 3D marker model that consisted of the size, orientation, and estimated 3D trajectory of each marker during the CBCT scan. The 3D marker model was used for real-time template based segmentation in subsequent x-ray images by projecting each marker's 3D shape and likely 3D motion range onto the imager plane. The segmentation was performed in intra-treatment kV images (526 marker traces, 92 097 marker projections) and MV images (88 marker traces, 22 382 marker projections), and in post-treatment CBCT projections (42 CBCT scans, 71 381 marker projections). 227 kV marker traces with low mean contrast-to-noise ratio were excluded as markers were not visible due to MV scatter. Online segmentation times measured for a limited dataset were used for estimating real-time segmentation times for all images. The percentage of detected markers was 94.8% (kV), 96.1% (MV), and 98.6% (CBCT). For the detected markers, the real-time segmentation was erroneous in 0.2–0.31% of the cases. The mean segmentation time per marker was 5.6 ms [2.1–12 ms] (kV), 5.5 ms [1.6–13 ms] (MV), and 6.5 ms [1.8–15 ms] (CBCT). Fast and reliable real-time segmentation of multiple liver tumor markers in intra-treatment kV and MV images and in CBCT projections was demonstrated for a large dataset. (paper)

  4. Association mapping to discover significant marker-trait associations for resistance against fusarium wilt variant 2 in pigeonpea [Cajanus cajan (L.) Millspaugh] using SSR markers.

    Patil, Prakash G; Dubey, Jyotirmay; Bohra, Abhishek; Mishra, R K; Saabale, P R; Das, Alok; Rathore, Meenal; Singh, N P

    2017-08-01

    Pigeonpea production is severely constrained by wilt disease caused by Fusarium udum. In the current study, we discover the putative genomic regions that control resistance response to variant 2 of fusarium wilt using association mapping approach. The association panel comprised of 89 diverse pigeonpea genotypes including seven varieties, three landraces and 79 germplasm lines. The panel was screened rigorously for 3 consecutive years (2013-14, 2014-15 and 2015-2016) against variant 2 in a wilt-sick field. A total of 65 pigeonpea specific hypervariable SSR markers (HASSRs) were screened representing seven linkage groups and 29 scaffolds of the pigeonpea genome. A total of 181 alleles were detected, with average values of gene diversity and polymorphism information content (PIC) of 0.55 and 0.47, respectively. Further analysis using model based (STRUCTURE) and distance based (clustering) approaches separated the entire pigeonpea collection into two distinct subgroups (K = 2). The marker trait associations (MTAs) were established based on three-year wilt incidence data and SSR dataset using a unified mixed linear model. Consequently, six SSR markers were identified, which were significantly associated with wilt resistance and explained up to 6% phenotypic variance (PV) across the years. Among these SSRs, HASSR18 was found to be the most stable and significant, accounting for 5-6% PV across the years. To the best of our knowledge, this is the first report of identification of favourable alleles for resistance to variant 2 of Fusarium udum in pigeonpea using association mapping. The SSR markers identified here will greatly facilitate marker assisted resistance breeding against fusarium wilt in pigeonpea.

  5. Towards barcode markers in Fungi: an intron map of Ascomycota mitochondria.

    Santamaria, Monica; Vicario, Saverio; Pappadà, Graziano; Scioscia, Gaetano; Scazzocchio, Claudio; Saccone, Cecilia

    2009-06-16

    A standardized and cost-effective molecular identification system is now an urgent need for Fungi owing to their wide involvement in human life quality. In particular the potential use of mitochondrial DNA species markers has been taken in account. Unfortunately, a serious difficulty in the PCR and bioinformatic surveys is due to the presence of mobile introns in almost all the fungal mitochondrial genes. The aim of this work is to verify the incidence of this phenomenon in Ascomycota, testing, at the same time, a new bioinformatic tool for extracting and managing sequence databases annotations, in order to identify the mitochondrial gene regions where introns are missing so as to propose them as species markers. The general trend towards a large occurrence of introns in the mitochondrial genome of Fungi has been confirmed in Ascomycota by an extensive bioinformatic analysis, performed on all the entries concerning 11 mitochondrial protein coding genes and 2 mitochondrial rRNA (ribosomal RNA) specifying genes, belonging to this phylum, available in public nucleotide sequence databases. A new query approach has been developed to retrieve effectively introns information included in these entries. After comparing the new query-based approach with a blast-based procedure, with the aim of designing a faithful Ascomycota mitochondrial intron map, the first method appeared clearly the most accurate. Within this map, despite the large pervasiveness of introns, it is possible to distinguish specific regions comprised in several genes, including the full NADH dehydrogenase subunit 6 (ND6) gene, which could be considered as barcode candidates for Ascomycota due to their paucity of introns and to their length, above 400 bp, comparable to the lower end size of the length range of barcodes successfully used in animals. The development of the new query system described here would answer the pressing requirement to improve drastically the bioinformatics support to the DNA Barcode

  6. A minimally invasive multiple marker approach allows highly efficient detection of meningioma tumors

    Meese Eckart

    2006-12-01

    Full Text Available Abstract Background The development of effective frameworks that permit an accurate diagnosis of tumors, especially in their early stages, remains a grand challenge in the field of bioinformatics. Our approach uses statistical learning techniques applied to multiple antigen tumor antigen markers utilizing the immune system as a very sensitive marker of molecular pathological processes. For validation purposes we choose the intracranial meningioma tumors as model system since they occur very frequently, are mostly benign, and are genetically stable. Results A total of 183 blood samples from 93 meningioma patients (WHO stages I-III and 90 healthy controls were screened for seroreactivity with a set of 57 meningioma-associated antigens. We tested several established statistical learning methods on the resulting reactivity patterns using 10-fold cross validation. The best performance was achieved by Naïve Bayes Classifiers. With this classification method, our framework, called Minimally Invasive Multiple Marker (MIMM approach, yielded a specificity of 96.2%, a sensitivity of 84.5%, and an accuracy of 90.3%, the respective area under the ROC curve was 0.957. Detailed analysis revealed that prediction performs particularly well on low-grade (WHO I tumors, consistent with our goal of early stage tumor detection. For these tumors the best classification result with a specificity of 97.5%, a sensitivity of 91.3%, an accuracy of 95.6%, and an area under the ROC curve of 0.971 was achieved using a set of 12 antigen markers only. This antigen set was detected by a subset selection method based on Mutual Information. Remarkably, our study proves that the inclusion of non-specific antigens, detected not only in tumor but also in normal sera, increases the performance significantly, since non-specific antigens contribute additional diagnostic information. Conclusion Our approach offers the possibility to screen members of risk groups as a matter of routine

  7. Multiple Concurrent Visual-Motor Mappings: Implications for Models of Adaptation

    Cunningham, H. A.; Welch, Robert B.

    1994-01-01

    Previous research on adaptation to visual-motor rearrangement suggests that the central nervous system represents accurately only 1 visual-motor mapping at a time. This idea was examined in 3 experiments where subjects tracked a moving target under repeated alternations between 2 initially interfering mappings (the 'normal' mapping characteristic of computer input devices and a 108' rotation of the normal mapping). Alternation between the 2 mappings led to significant reduction in error under the rotated mapping and significant reduction in the adaptation aftereffect ordinarily caused by switching between mappings. Color as a discriminative cue, interference versus decay in adaptation aftereffect, and intermanual transfer were also examined. The results reveal a capacity for multiple concurrent visual-motor mappings, possibly controlled by a parametric process near the motor output stage of processing.

  8. Construction of a genetic map using EST-SSR markers and QTL analysis of major agronomic characters in hexaploid sweet potato (Ipomoea batatas (L.) Lam).

    Kim, Jin-Hee; Chung, Il Kyung; Kim, Kyung-Min

    2017-01-01

    The Sweet potato, Ipomoea batatas (L.) Lam, is difficult to study in genetics and genomics because it is a hexaploid. The sweet potato study not have been performed domestically or internationally. In this study was performed to construct genetic map and quantitative trait loci (QTL) analysis. A total of 245 EST-SSR markers were developed, and the map was constructed by using 210 of those markers. The total map length was 1508.1 cM, and the mean distance between markers was 7.2 cM. Fifteen characteristics were investigated for QTLs analysis. According to those, the Four QTLs were identified, and The LOD score was 3.0. Further studies need to develop molecular markers in terms of EST-SSR markers for doing to be capable of efficient breeding. The genetic map created here using EST-SSR markers will facilitate planned breeding of sweet potato cultivars with various desirable traits.

  9. High Resolution of Quantitative Traits Into Multiple Loci via Interval Mapping

    Jansen, Ritsert C.; Stam, Piet

    1994-01-01

    A very general method is described for multiple linear regression of a quantitative phenotype on genotype [putative quantitative trait loci (QTLs) and markers] in segregating generations obtained from line crosses. The method exploits two features, (a) the use of additional parental and F1 data, which fixes the joint QTL effects and the environmental error, and (b) the use of markers as cofactors, which reduces the genetic background noise. As a result, a significant increase of QTL detection...

  10. In silico polymorphism analysis for the development of simple sequence repeat and transposon markers and construction of linkage map in cultivated peanut

    Shirasawa Kenta

    2012-06-01

    Full Text Available Abstract Background Peanut (Arachis hypogaea is an autogamous allotetraploid legume (2n = 4x = 40 that is widely cultivated as a food and oil crop. More than 6,000 DNA markers have been developed in Arachis spp., but high-density linkage maps useful for genetics, genomics, and breeding have not been constructed due to extremely low genetic diversity. Polymorphic marker loci are useful for the construction of such high-density linkage maps. The present study used in silico analysis to develop simple sequence repeat-based and transposon-based markers. Results The use of in silico analysis increased the efficiency of polymorphic marker development by more than 3-fold. In total, 926 (34.2% of 2,702 markers showed polymorphisms between parental lines of the mapping population. Linkage analysis of the 926 markers along with 253 polymorphic markers selected from 4,449 published markers generated 21 linkage groups covering 2,166.4 cM with 1,114 loci. Based on the map thus produced, 23 quantitative trait loci (QTLs for 15 agronomical traits were detected. Another linkage map with 326 loci was also constructed and revealed a relationship between the genotypes of the FAD2 genes and the ratio of oleic/linoleic acid in peanut seed. Conclusions In silico analysis of polymorphisms increased the efficiency of polymorphic marker development, and contributed to the construction of high-density linkage maps in cultivated peanut. The resultant maps were applicable to QTL analysis. Marker subsets and linkage maps developed in this study should be useful for genetics, genomics, and breeding in Arachis. The data are available at the Kazusa DNA Marker Database (http://marker.kazusa.or.jp.

  11. The neutrophil-to-lymphocyte ratio as disease actvity marker in multiple sclerosis and optic neuritis

    Bisgaard, A K; Pihl-Jensen, G; Frederiksen, J L

    2017-01-01

    BACKGROUND: Multiple sclerosis (MS) is a chronic inflammatory disease of the central nervous system (CNS). The neutrophil-to-lymphocyte ratio (NLR) has been identified as a disease activity marker in several diseases. We aim to evaluate the significance of the NLR in the different subtypes of MS......, optic neuritis (ON) and in relation to disease activity and Expanded Disability Status Scale (EDSS). METHODS: We included 378 patients and 813 healthy controls (HC) from The Nordic Reference Interval Project 2000 (NORIP). Complete blood count, demographic and clinical data from patients were evaluated...... between NLR and time of blood sampling. Logistic regression models were constructed for EDSS ≥ 4.0 as outcome. RESULTS: The NLR was significantly higher (p higher NLR (p

  12. T regulatory cells are markers of disease activity in multiple sclerosis patients.

    Dacia Dalla Libera

    Full Text Available FoxP3⁺ Treg cells are believed to play a role in the occurrence of autoimmunity and in the determination of clinical recurrences. Contradictory reports are, however, available describing frequency and function of Treg cells during autoimmune diseases. We examined, by both polychromatic flow cytometry, and real-time RT-PCR, several Treg markers in peripheral blood mononuclear cells from patients with multiple sclerosis (MS, an autoimmune disease affecting the central nervous system. We found that Tregs, as defined by CD25, CD39, FoxP3, CTLA4, and GITR expression, were significantly decreased in stable MS patients as compared to healthy donors, but, surprisingly, restored to normal levels during an acute clinical attack. We conclude that Treg cells are not involved in causing clinical relapses, but rather react to inflammation in the attempt to restore homeostasis.

  13. Linkage study of nonsyndromic cleft lip with or without cleft palate using candidate genes and mapped polymorphic markers

    Stein, J.D.; Nelson, L.D.; Conner, B.J. [Univ. of Texas, Houston (United States)] [and others

    1994-09-01

    Nonsyndromic cleft lip with or without cleft palate (CL(P)) involves fusion or growth failure of facial primordia during development. Complex segregation analysis of clefting populations suggest that an autosomal dominant gene may play a role in this common craniofacial disorder. We have ascertained 16 multigenerational families with CL(P) and tested linkage to 29 candidate genes and 139 mapped short tandem repeat markers. The candidate genes were selected based on their expression in craniofacial development or were identified through murine models. These include: TGF{alpha}, TGF{beta}1, TGF{beta}2, TGF{beta}3, EGF, EGFR, GRAS, cMyc, FGFR, Jun, JunB, PDFG{alpha}, PDGF{beta}, IGF2R, GCR Hox7, Hox8, Hox2B, twirler, 5 collagen and 3 extracellular matrix genes. Linkage was tested assuming an autosomal dominant model with sex-specific decreased penetrance. Linkage to all of the candidate loci was excluded in 11 families. RARA was tested and was not informative. However, haplotype analysis of markers flanking RARA on 17q allowed exclusion of this candidate locus. We have previously excluded linkage to 61 STR markers in 11 families. Seventy-eight mapped short tandem repeat markers have recently been tested in 16 families and 30 have been excluded. The remaining are being analyzed and an exclusion map is being developed based on the entire study results.

  14. New Hypervariable SSR Markers for Diversity Analysis, Hybrid Purity Testing and Trait Mapping in Pigeonpea [Cajanus cajan (L.) Millspaugh].

    Bohra, Abhishek; Jha, Rintu; Pandey, Gaurav; Patil, Prakash G; Saxena, Rachit K; Singh, Indra P; Singh, D; Mishra, R K; Mishra, Ankita; Singh, F; Varshney, Rajeev K; Singh, N P

    2017-01-01

    Draft genome sequence in pigeonpea offers unprecedented opportunities for genomics assisted crop improvement via enabling access to genome-wide genetic markers. In the present study, 421 hypervariable simple sequence repeat (SSR) markers from the pigeonpea genome were screened on a panel of eight pigeonpea genotypes yielding marker validation and polymorphism percentages of 95.24 and 54.11%, respectively. The SSR marker assay uncovered a total of 570 alleles with three as an average number of alleles per marker. Similarly, the mean values for gene diversity and PIC were 0.44 and 0.37, respectively. The number of polymorphic markers ranged from 39 to 89 for different parental combinations. Further, 60 of these SSRs were assayed on 94 genotypes, and model based clustering using STRUCTURE resulted in the identification of the two subpopulations ( K = 2). This remained in close agreement with the clustering patterns inferred from genetic distance (GD)-based approaches i.e., dendrogram, factorial and principal coordinate analysis (PCoA). The AMOVA accounted majority of the genetic variation within groups (89%) in comparison to the variation existing between the groups (11%). A subset of these markers was implicated for hybrid purity testing. We also demonstrated utility of these SSR markers in trait mapping through association and bi-parental linkage analyses. The general linear (GLM) and mixed linear (MLM) models both detected a single SSR marker (CcGM03681) with R 2 = 16.4 as associated with the resistance to Fusarium wilt variant 2. Similarly, by using SSR data in a segregating backcross population, the corresponding restorer-of-fertility ( Rf ) locus was putatively mapped at 39 cM with the marker CcGM08896. However, The marker-trait associations (MTAs) detected here represent a very preliminary type and hence demand deeper investigations for conclusive evidence. Given their ability to reveal polymorphism in simple agarose gels, the hypervariable SSRs are valuable

  15. Common Fixed Points of Generalized Rational Type Cocyclic Mappings in Multiplicative Metric Spaces

    Mujahid Abbas

    2015-01-01

    Full Text Available The aim of this paper is to present fixed point result of mappings satisfying a generalized rational contractive condition in the setup of multiplicative metric spaces. As an application, we obtain a common fixed point of a pair of weakly compatible mappings. Some common fixed point results of pair of rational contractive types mappings involved in cocyclic representation of a nonempty subset of a multiplicative metric space are also obtained. Some examples are presented to support the results proved herein. Our results generalize and extend various results in the existing literature.

  16. Physical mapping of chromosome 8p22 markers and their homozygous deletion in a metastatic prostate cancer

    Bova, G.S.; Pin, S.S.; Isaacs, W.B. [Johns Hopkins Univ. School of Medicine, Baltimore, MD (United States)]|[Brady Urological Institute, Baltimore, MD (United States)] [and others

    1996-07-01

    Numerous studies have implicated the short arm of chromosome 8 as the site of one or more tumor suppressor genes inactivated in carcinogenesis of the prostate, colon, lung, and liver. Previously, we identified a homozygous deletion on chromosome 8p22 in a metastatic prostate cancer. To map this homozygous deletion physically, long-range restriction mapping was performed using yeast artificial chromosomes (YACs) spanning approximately 2 Mb of chromosome band 8p22. Subcloned genomic DNA and cDNA probes isolated by hybrid capture from these YACs were mapped in relation to one another, reinforcing map integrity. Mapped single-copy probes from the region were then applied to DNA isolated from a metastatic prostate cancer containing a chromosome 8p22 homozygous deletion and indicated that its deletion spans 730-970 kb. Candidate genes PRLTS (PDGF-receptor {beta}-like tumor suppressor) and CTSB (cathepsin B) are located outside the region of homozygous deletion. Genethon marker D8S549 is located approximately at the center of this region of homozygous deletion. Two new microsatellite polymorphisms, D8S1991 and D8S1992, also located within the region of homozygous deletion on chromosome 8p22, are described. Physical mapping places cosmid CI8-2644 telomeric to MSR (macrophage scavenger receptor), the reverse of a previously published map, altering the interpretation of published deletion studies. This work should prove helpful in the identification of candidate tumor suppressor genes in this region. 47 refs., 5 figs., 1 tab.

  17. Tagging and mapping of SSR marker for rust resistance gene in lentil (Lens culinaris Medikus subsp. culinaris).

    Dikshit, H K; Singh, Akanksha; Singh, D; Aski, M; Jain, Neelu; Hegde, V S; Basandrai, A K; Basandrai, D; Sharma, T R

    2016-06-01

    Lentil, as an economical source of protein, minerals and vitamins, plays important role in nutritional security of the common man. Grown mainly in West Asia, North Africa (WANA) region and South Asia, it suffers from several biotic stresses such as wilt, rust, blight and broomrape. Lentil rust caused by autoecious fungus Uromyces viciae fabae (Pers.) Schroet is a serious lentil disease in Algeria, Bangladesh, Ethiopia, India, Italy, Morocco, Pakistan and Nepal. The disease symptoms are observed during flowering and early podding stages. Rust causes severe yield losses in lentil. It can only be effectively controlled by identifying the resistant source, understanding its inheritance and breeding for host resistance. The obligate parasitic nature of pathogen makes it difficult to maintain the pathogen in culture and to apply it to screen segregating progenies under controlled growth conditions. Hence, the use of molecular markers will compliment in identification of resistant types in different breeding programs. Here, we studied the inheritance of resistance to rust in lentil using F₁, F₂ and F₂:₃ from cross PL 8 (susceptible) x L 4149 (resistant) varieties. The phenotyping of lentil population was carried out at Sirmour, India. The result of genetic analysis revealed that a single dominant gene controls rust resistance in lentil genotype L 4149. The F2 population from this cross was used to tag and map the rust resistance gene using SSR and SRAP markers. Markers such as 270 SRAP and 162 SSR were studied for polymorphism and 101 SRAP and 33 SSRs were found to be polymorphic between the parents. Two SRAP and two SSR markers differentiated the resistant and susceptible bulks. SSR marker Gllc 527 was estimated to be linked to rust resistant locus at a distance of 5.9 cM. The Gllc 527 marker can be used for marker assisted selection for rust resistance; however, additional markers closer to rust resistant locus are required. The markers linked to the rust

  18. AUTOMATIC 3D MAPPING USING MULTIPLE UNCALIBRATED CLOSE RANGE IMAGES

    M. Rafiei

    2013-09-01

    Full Text Available Automatic three-dimensions modeling of the real world is an important research topic in the geomatics and computer vision fields for many years. By development of commercial digital cameras and modern image processing techniques, close range photogrammetry is vastly utilized in many fields such as structure measurements, topographic surveying, architectural and archeological surveying, etc. A non-contact photogrammetry provides methods to determine 3D locations of objects from two-dimensional (2D images. Problem of estimating the locations of 3D points from multiple images, often involves simultaneously estimating both 3D geometry (structure and camera pose (motion, it is commonly known as structure from motion (SfM. In this research a step by step approach to generate the 3D point cloud of a scene is considered. After taking images with a camera, we should detect corresponding points in each two views. Here an efficient SIFT method is used for image matching for large baselines. After that, we must retrieve the camera motion and 3D position of the matched feature points up to a projective transformation (projective reconstruction. Lacking additional information on the camera or the scene makes the parallel lines to be unparalleled. The results of SfM computation are much more useful if a metric reconstruction is obtained. Therefor multiple views Euclidean reconstruction applied and discussed. To refine and achieve the precise 3D points we use more general and useful approach, namely bundle adjustment. At the end two real cases have been considered to reconstruct (an excavation and a tower.

  19. Linkage Map Construction and QTL Analysis of Fruit Traits in Melon (Cucumis melo L.) Based on CAPS Markers

    Baloch, A. M.; Liu, S.; Wang, X.; Luan, F.; Baloch, A. W.; Baloch, M. J.

    2016-01-01

    In the current experiment, the quantitative trait loci (QTL) analysis was done by composite interval mapping method to detect QTLs in edge, central parts and fruit shape of melon. In this context, 235 F/sub 2/ populations along with their parents were evaluated for fruit size, shape and color under replicated trail at Horticulture Experimental Station of Northeast Agricultural University, Harbin, China, during the growing year 2014. Moreover, 96 pairs of CAPS markers were used to construct a linkage map using F/sub 2/ population that was derived from the cross between two contrasting parents (MR-1 and Topmark). The total length of linkage map was found to be 4984.1cM with an average of 51.9177 cM between the markers. In a total, we detected ten QTLs, in which one was major, while others were minor. Five QTLs were detected in the edge part of melon fruit and three QTLs were detected in central parts of melon and all were considered as Brix content. Two QTLs were related with fruit shape. Our present genetic and QTLs mapping would be proved useful in plant breeding programs for the improvement of economically important horticultural traits. (author)

  20. Mapping of a major QTL for salt tolerance of mature field-grown maize plants based on SNP markers.

    Luo, Meijie; Zhao, Yanxin; Zhang, Ruyang; Xing, Jinfeng; Duan, Minxiao; Li, Jingna; Wang, Naishun; Wang, Wenguang; Zhang, Shasha; Chen, Zhihui; Zhang, Huasheng; Shi, Zi; Song, Wei; Zhao, Jiuran

    2017-08-15

    Salt stress significantly restricts plant growth and production. Maize is an important food and economic crop but is also a salt sensitive crop. Identification of the genetic architecture controlling salt tolerance facilitates breeders to select salt tolerant lines. However, the critical quantitative trait loci (QTLs) responsible for the salt tolerance of field-grown maize plants are still unknown. To map the main genetic factors contributing to salt tolerance in mature maize, a double haploid population (240 individuals) and 1317 single nucleotide polymorphism (SNP) markers were employed to produce a genetic linkage map covering 1462.05 cM. Plant height of mature maize cultivated in the saline field (SPH) and plant height-based salt tolerance index (ratio of plant height between saline and control fields, PHI) were used to evaluate salt tolerance of mature maize plants. A major QTL for SPH was detected on Chromosome 1 with the LOD score of 22.4, which explained 31.2% of the phenotypic variation. In addition, the major QTL conditioning PHI was also mapped at the same position on Chromosome 1, and two candidate genes involving in ion homeostasis were identified within the confidence interval of this QTL. The detection of the major QTL in adult maize plant establishes the basis for the map-based cloning of genes associated with salt tolerance and provides a potential target for marker assisted selection in developing maize varieties with salt tolerance.

  1. Analysis of the results of serum tumor markers in patients with multiple abnormal concentrations in bone imagines

    Wu Xingyong; Jiang Min; Geng Jun; Hu Desheng; He Jian; Fan Xiandong

    2008-01-01

    To study the serum tumor markers in patients with multiple abnormal concentration of radiopharmaceuticals in whole body bone imagine, 73 patients with malignancy were under a whole body bone scan. The serum tumor markers levels of AFP, CEA, CA125, CA15-3 and CA19-9 were measured in 73 patients and 37 normal people. The results showed that there was significant difference only on serum CEA level (P<0.005), and no significant difference on CA125, CA15-3 and CA19-9 levels (P<0.05) between 36 patients with multiple abnormal concentration and the others with normal bone imagine. The serum levels of CEA, CA125 and CA19-9 in patients were significant higher than that of normal controls (P<0.005). Combined the whole body bone scan and detection of serum tumor markers might be regarded as clinical significance for the diagnosis of bone metastases. (authors)

  2. Low accuracy of tumor markers for diagnosing pancreatic neuroendocrine tumors in multiple endocrine neoplasia type 1 patients

    de Laat, Joanne M.; Pieterman, Carolina R. C.; Weijmans, Maaike; Hermus, Ad R.; Dekkers, Olaf M.; de Herder, Wouter W.; van der Horst-Schrivers, Anouk N. A.; Drent, Madeleine L.; Bisschop, Peter H.; Havekes, Bas; Vriens, Menno R.; Valk, Gerlof D.

    2013-01-01

    Context: The assessment of tumor markers for diagnosing pancreatic neuroendocrine tumors (pNET) in multiple endocrine neoplasia type 1 (MEN1) patients is advised in the current guidelines but has never been validated for this purpose. Objective: The objective of the study was to assess the

  3. Low Accuracy of Tumor Markers for Diagnosing Pancreatic Neuroendocrine Tumors in Multiple Endocrine Neoplasia Type 1 Patients

    de Laat, Joanne M.; Pieterman, Carolina R. C.; Weijmans, Maaike; Hermus, Ad R.; Dekkers, Olaf M.; de Herder, Wouter W.; van der Horst-Schrivers, Anouk N. A.; Drent, Madeleine L.; Bisschop, Peter H.; Havekes, Bas; Vriens, Menno R.; Valk, Gerlof D.

    2013-01-01

    Context: The assessment of tumor markers for diagnosing pancreatic neuroendocrine tumors (pNET) in multiple endocrine neoplasia type 1 (MEN1) patients is advised in the current guidelines but has never been validated for this purpose. Objective: The objective of the study was to assess the

  4. Applied immuno-epidemiological research: an approach for integrating existing knowledge into the statistical analysis of multiple immune markers.

    Genser, Bernd; Fischer, Joachim E; Figueiredo, Camila A; Alcântara-Neves, Neuza; Barreto, Mauricio L; Cooper, Philip J; Amorim, Leila D; Saemann, Marcus D; Weichhart, Thomas; Rodrigues, Laura C

    2016-05-20

    Immunologists often measure several correlated immunological markers, such as concentrations of different cytokines produced by different immune cells and/or measured under different conditions, to draw insights from complex immunological mechanisms. Although there have been recent methodological efforts to improve the statistical analysis of immunological data, a framework is still needed for the simultaneous analysis of multiple, often correlated, immune markers. This framework would allow the immunologists' hypotheses about the underlying biological mechanisms to be integrated. We present an analytical approach for statistical analysis of correlated immune markers, such as those commonly collected in modern immuno-epidemiological studies. We demonstrate i) how to deal with interdependencies among multiple measurements of the same immune marker, ii) how to analyse association patterns among different markers, iii) how to aggregate different measures and/or markers to immunological summary scores, iv) how to model the inter-relationships among these scores, and v) how to use these scores in epidemiological association analyses. We illustrate the application of our approach to multiple cytokine measurements from 818 children enrolled in a large immuno-epidemiological study (SCAALA Salvador), which aimed to quantify the major immunological mechanisms underlying atopic diseases or asthma. We demonstrate how to aggregate systematically the information captured in multiple cytokine measurements to immunological summary scores aimed at reflecting the presumed underlying immunological mechanisms (Th1/Th2 balance and immune regulatory network). We show how these aggregated immune scores can be used as predictors in regression models with outcomes of immunological studies (e.g. specific IgE) and compare the results to those obtained by a traditional multivariate regression approach. The proposed analytical approach may be especially useful to quantify complex immune

  5. Membrane-based oligonucleotide array developed from multiple markers for the detection of many Phytophthora species.

    Chen, Wen; Djama, Zeinab Robleh; Coffey, Michael D; Martin, Frank N; Bilodeau, Guillaume J; Radmer, Lorien; Denton, Geoff; Lévesque, C André

    2013-01-01

    Most Phytophthora spp. are destructive plant pathogens; therefore, effective monitoring and accurate early detection are important means of preventing potential epidemics and outbreaks of diseases. In the current study, a membrane-based oligonucleotide array was developed that can detect Phytophthora spp. reliably using three DNA regions; namely, the internal transcribed spacer (ITS), the 5' end of cytochrome c oxidase 1 gene (cox1), and the intergenic region between cytochrome c oxidase 2 gene (cox2) and cox1 (cox2-1 spacer). Each sequence data set contained ≈250 sequences representing 98 described and 15 undescribed species of Phytophthora. The array was validated with 143 pure cultures and 35 field samples. Together, nonrejected oligonucleotides from all three markers have the ability to reliably detect 82 described and 8 undescribed Phytophthora spp., including several quarantine or regulated pathogens such as Phytophthora ramorum. Our results showed that a DNA array containing signature oligonucleotides designed from multiple genomic regions provided robustness and redundancy for the detection and differentiation of closely related taxon groups. This array has the potential to be used as a routine diagnostic tool for Phytophthora spp. from complex environmental samples without the need for extensive growth of cultures.

  6. Phylogeography and postglacial recolonization of Europe by Rhinolophus hipposideros: evidence from multiple genetic markers.

    Dool, Serena E; Puechmaille, Sébastien J; Dietz, Christian; Juste, Javier; Ibáñez, Carlos; Hulva, Pavel; Roué, Stéphane G; Petit, Eric J; Jones, Gareth; Russo, Danilo; Toffoli, Roberto; Viglino, Andrea; Martinoli, Adriano; Rossiter, Stephen J; Teeling, Emma C

    2013-08-01

    The demographic history of Rhinolophus hipposideros (lesser horseshoe bat) was reconstructed across its European, North African and Middle-Eastern distribution prior to, during and following the most recent glaciations by generating and analysing a multimarker data set. This data set consisted of an X-linked nuclear intron (Bgn; 543 bp), mitochondrial DNA (cytb-tRNA-control region; 1630 bp) and eight variable microsatellite loci for up to 373 individuals from 86 localities. Using this data set of diverse markers, it was possible to determine the species' demography at three temporal stages. Nuclear intron data revealed early colonization into Europe from the east, which pre-dates the Quaternary glaciations. The mtDNA data supported multiple glacial refugia across the Mediterranean, the largest of which were found in the Ibero-Maghreb region and an eastern location (Anatolia/Middle East)-that were used by R. hipposideros during the most recent glacial cycles. Finally, microsatellites provided the most recent information on these species' movements since the Last Glacial Maximum and suggested that lineages that had diverged into glacial refugia, such as in the Ibero-Maghreb region, have remained isolated. These findings should be used to inform future conservation management strategies for R. hipposideros and show the power of using a multimarker data set for phylogeographic studies. © 2013 John Wiley & Sons Ltd.

  7. Electrocardiographic markers of ischemia during mental stress testing in postinfarction patients. Role of body surface mapping

    Bosimini, E.; Galli, M.; Guagliumi, G.; Giubbini, R.; Tavazzi, L.

    1991-01-01

    In patients with coronary artery disease, radionuclide investigations have documented a high incidence of mental stress-induced myocardial ischemia in the absence of significant electrocardiographic changes and/or angina. To investigate the causes of the low electrocardiographic sensitivity, we recorded body surface maps during mental arithmetic in 22 normal volunteers and 37 postinfarction patients with residual exercise ischemia. Myocardial perfusion was studied with thallium-201 or technetium-99 (SESTAMIBI) planar scans. In 14 patients, body surface maps were also recorded during atrial pacing at the heart rate values achieved during mental stress. While taking the body surface maps, the area from J point to 80 msec after this point (ST-80) was analyzed by integral maps, difference maps, and departure maps. The body surface mapping criteria for ischemia were a new negative area on the integral maps, a negative potential of more than 2 SD from mean normal values on the difference maps, and a negative departure index of more than 2. Scintigraphy showed asymptomatic myocardial hypoperfusion in 33 patients. Eight patients had significant ST segment depression. The ST-80 integral and difference maps identified 17 ischemic patients. Twenty-four patients presented abnormal departure maps. One patient presented ST depression and abnormal body surface maps without reversible tracer defect. In 14 of 14 patients, atrial pacing did not reproduce the body surface map abnormalities. The analyses of the other electrocardiographic variables showed that in patients with mental stress-induced perfusion defects, only changes of T apex-T offset (aT-eT) interval in Frank leads and changes of maximum negative potential value of aT-eT integral maps significantly differed from those of normal subjects

  8. Molecular mapping of the Pinus monticola Cr2 gene using AFLP and SCAR markers

    A.K.M. Ekramoddoullah

    2013-12-01

    Full Text Available White pine blister rust (WPBR, caused by Cronartium ribicola, is a devastating disease in five-needle pines. Genetic resistance is an important component of integrated strategies to control WPBR. The major resistance gene Cr2, discovered by Kinloch etal.(1999, is also effective against British Columbia (BC isolates of WPBR (Hunt et al. 2004. Pyramiding Cr2 gene with other resistancegenes is being pursued as a strategy in BC white pine breeding. To facilitate this strategy, we have recently identified a few RAPD markerslinked to Cr2 at one side (Liu et al. 2006. The objective of the present study was to identify amplified fragment length polymorphism(AFLP markers linked to both sides of Cr2 for its more precise apping. Use of the AFLP technique combined with bulked segregant analysis (BSA and haploid segregation analysis allowed the identification of five AFLP markers. Of these five AFLP markers in the Cr2 linkage, markers EacccMccgat-365, EactgMcccac- 290, and EacagEacag-750 werelinked in coupling and EacagMcccag-160r and EacccMccgat-180r in repulsion. Following cloning and sequencing of the AFLP andRAPD markers, specific PCR primers were designed and used in the amplification of sequence characterized amplified region(SCAR markers at both sides of Cr2. EacccMccgat- 365 and RAPD marker U570-843 reported previously were converted into SCARmarkers. These two SCARs segregated in a 1:1 (presence:absence ratio and the scoring cosegregated with their respective AFLP orRAPD marker. The SCAR marker EacccMccgat- 365-scar was positioned at 3.1 Kosambi cM from one side of Cr2 and U570-843-scarlocalized at 1.4 Kosambi cM from other side. Both SCAR markers can be useful in breeding programs with marker-assisted selection procedureto screen for resistance. This study represents the first report of the development of PCR-based sequence-specific markers linkedto blister rust resistance in five-needle pines. These findings may

  9. Application of dissociation curve analysis to radiation hybrid panel marker scoring: generation of a map of river buffalo (B. bubalis chromosome 20

    Schäffer Alejandro A

    2008-11-01

    Full Text Available Abstract Background Fluorescence of dyes bound to double-stranded PCR products has been utilized extensively in various real-time quantitative PCR applications, including post-amplification dissociation curve analysis, or differentiation of amplicon length or sequence composition. Despite the current era of whole-genome sequencing, mapping tools such as radiation hybrid DNA panels remain useful aids for sequence assembly, focused resequencing efforts, and for building physical maps of species that have not yet been sequenced. For placement of specific, individual genes or markers on a map, low-throughput methods remain commonplace. Typically, PCR amplification of DNA from each panel cell line is followed by gel electrophoresis and scoring of each clone for the presence or absence of PCR product. To improve sensitivity and efficiency of radiation hybrid panel analysis in comparison to gel-based methods, we adapted fluorescence-based real-time PCR and dissociation curve analysis for use as a novel scoring method. Results As proof of principle for this dissociation curve method, we generated new maps of river buffalo (Bubalus bubalis chromosome 20 by both dissociation curve analysis and conventional marker scoring. We also obtained sequence data to augment dissociation curve results. Few genes have been previously mapped to buffalo chromosome 20, and sequence detail is limited, so 65 markers were screened from the orthologous chromosome of domestic cattle. Thirty bovine markers (46% were suitable as cross-species markers for dissociation curve analysis in the buffalo radiation hybrid panel under a standard protocol, compared to 25 markers suitable for conventional typing. Computational analysis placed 27 markers on a chromosome map generated by the new method, while the gel-based approach produced only 20 mapped markers. Among 19 markers common to both maps, the marker order on the map was maintained perfectly. Conclusion Dissociation curve

  10. Genetic mapping, marker assisted selection and allelic relationships for the Pu 6 gene conferring rust resistance in sunflower.

    Bulos, Mariano; Vergani, Pablo Nicolas; Altieri, Emiliano

    2014-09-01

    Rust resistance in the sunflower line P386 is controlled by Pu 6 , a gene which was reported to segregate independently from other rust resistant genes, such as R 4 . The objectives of this work were to map Pu 6 , to provide and validate molecular tools for its identification, and to determine the linkage relationship of Pu 6 and R 4 . Genetic mapping of Pu 6 with six markers covered 24.8 cM of genetic distance on the lower end of linkage Group 13 of the sunflower consensus map. The marker most closely linked to Pu 6 was ORS316 at 2.5 cM in the distal position. ORS316 presented five alleles when was assayed with a representative set of resistant and susceptible lines. Allelism test between Pu 6 and R 4 indicated that both genes are linked at a genetic distance of 6.25 cM. This is the first confirmation based on an allelism test that at least two members of the R adv /R 4 /R 11 / R 13a /R 13b /Pu 6 cluster of genes are at different loci. A fine elucidation of the architecture of this complex locus will allow designing and constructing completely new genomic regions combining genes from different resistant sources and the elimination of the linkage drag around each resistant gene.

  11. Application of multiple geochemical markers to investigate organic pollution in a dynamic coastal zone.

    Liu, Liang-Ying; Wang, Ji-Zhong; Wong, Charles S; Qiu, Jian-Wen; Zeng, Eddy Y

    2013-02-01

    Multiple geochemical markers, including aliphatic hydrocarbons (n-alkanes), linear alkylbenzenes (LABs), and polycyclic aromatic hydrocarbons (PAHs), were employed to relate sediment organic chemical pollution in the coastal zone off South China to socioeconomic development there. Concentrations of Σn-C(15-35) (n-alkanes with 15-35 carbon atoms), ΣLAB (sum of C(10) to C(13) LABs), and Σ(26) PAH (sum of 26 PAH compounds) ranged from 110 to 3,160, 11 to 160, and 26 to 600 ng/g, with medians of 730, 40, and 230 ng/g, respectively. Natural hydrocarbons were mainly derived from terrestrial higher plant waxes, and in minor amounts from aquatic plankton and bacteria. Compositions of LABs indicated that considerable amounts of poorly treated wastewater had been directly discharged or transported to the eastern and western coastal areas of Guangdong Province. In addition, anthropogenic hydrocarbons were derived largely from vehicular emissions and combustion of domestic coal and biomass and to a lesser extent from oil spills. Eastern and western coastal sediments contained higher levels of LABs but lower levels of PAHs than those of the Pearl River Estuary, a coastal area of the Pearl River Delta. This spatial pattern of organic pollution was consistent with chemical use patterns. The eastern and western regions of Guangdong Province are economically less developed than the Pearl River Delta region, where more domestic wastewater treatment plants have been built. However, greater amounts of energy are consumed in the latter region to produce more combustion-derived PAH contamination. Copyright © 2012 SETAC.

  12. The "butterfly diagram": A gait marker for neurological and cerebellar impairment in people with multiple sclerosis.

    Kalron, Alon; Frid, Lior

    2015-11-15

    People with multiple sclerosis (PwMS) frequently experience walking and balance impairments. In our previous report, we demonstrated that spatio-temporal gait parameters, collected by the Zebris FDM-T instrumented treadmill (Zebris Medical GmbH, Germany), serve as valid markers of neurological impairment in the MS population. In the current study, we focused on a unique outcome statistic of the instrumented treadmill, the "butterfly" diagram which reflects the variability of the center of pressure trajectory during walking. Therefore, the aim of the study was to examine the relationship between parameters related to the gait butterfly diagram and the level of neurological impairment in PwMS. Specifically we examined whether the gait butterfly parameters can differentiate between MS patients with normal cerebellar function and those suffering from ataxia. Demographic, neurological and gait parameters were collected from 341 PwMS, 213 women, aged 42.3 (S.D.=13.8). MS participants with ataxia demonstrated higher scores relating to the butterfly gait variability parameters compared to PwMS with normal or slightly abnormal cerebellar function. According to the results of the binary regression analysis, gait variability in the ant-post direction was found to explain 18.1% of the variance related to cerebellar function; R(2)=0.181, χ(2)(1)=67.852, P<0.001. Measurements derived from the butterfly diagram are proper estimators for important neurological functions in PwMS and should be considered in order to improve diagnosis and assessment of the MS population. Copyright © 2015 Elsevier B.V. All rights reserved.

  13. Construction of an integrated genetic linkage map for the A genome of Brassica napus using SSR markers derived from sequenced BACs in B. rapa

    King Graham J

    2010-10-01

    Full Text Available Abstract Background The Multinational Brassica rapa Genome Sequencing Project (BrGSP has developed valuable genomic resources, including BAC libraries, BAC-end sequences, genetic and physical maps, and seed BAC sequences for Brassica rapa. An integrated linkage map between the amphidiploid B. napus and diploid B. rapa will facilitate the rapid transfer of these valuable resources from B. rapa to B. napus (Oilseed rape, Canola. Results In this study, we identified over 23,000 simple sequence repeats (SSRs from 536 sequenced BACs. 890 SSR markers (designated as BrGMS were developed and used for the construction of an integrated linkage map for the A genome in B. rapa and B. napus. Two hundred and nineteen BrGMS markers were integrated to an existing B. napus linkage map (BnaNZDH. Among these mapped BrGMS markers, 168 were only distributed on the A genome linkage groups (LGs, 18 distrubuted both on the A and C genome LGs, and 33 only distributed on the C genome LGs. Most of the A genome LGs in B. napus were collinear with the homoeologous LGs in B. rapa, although minor inversions or rearrangements occurred on A2 and A9. The mapping of these BAC-specific SSR markers enabled assignment of 161 sequenced B. rapa BACs, as well as the associated BAC contigs to the A genome LGs of B. napus. Conclusion The genetic mapping of SSR markers derived from sequenced BACs in B. rapa enabled direct links to be established between the B. napus linkage map and a B. rapa physical map, and thus the assignment of B. rapa BACs and the associated BAC contigs to the B. napus linkage map. This integrated genetic linkage map will facilitate exploitation of the B. rapa annotated genomic resources for gene tagging and map-based cloning in B. napus, and for comparative analysis of the A genome within Brassica species.

  14. An annotated genetic map of loblolly pine based on microsatellite and cDNA markers

    Previous loblolly pine (Pinus taeda L.) genetic linkage maps have been based on a variety of DNA polymorphisms, such as AFLPs, RAPDs, RFLPs, and ESTPs, but only a few SSRs (simple sequence repeats), also known as simple tandem repeats or microsatellites, have been mapped in P. taeda. The objective o...

  15. Improving Students' Creative Thinking and Achievement through the Implementation of Multiple Intelligence Approach with Mind Mapping

    Widiana, I. Wayan; Jampel, I. Nyoman

    2016-01-01

    This classroom action research aimed to improve the students' creative thinking and achievement in learning science. It conducted through the implementation of multiple intelligences with mind mapping approach and describing the students' responses. The subjects of this research were the fifth grade students of SD 8 Tianyar Barat, Kubu, and…

  16. Mapping the future: U.S. exposure to multiple landscape stressors

    Marie Oliver; Becky Kerns; John Kim; Jeff. Kline

    2017-01-01

    Landscape exposure to multiple stressors can pose risks to human health, biodiversity, and ecosystem services. Attempts to study, control, or mitigate these stressors can strain public and private budgets. An interdisciplinary team of Pacific Northwest Research Station and Oregon State University scientists created maps of the conterminous United States that indicate...

  17. Distinctive mitochondrial genome of Calanoid copepod Calanus sinicus with multiple large non-coding regions and reshuffled gene order: Useful molecular markers for phylogenetic and population studies

    2011-01-01

    Background Copepods are highly diverse and abundant, resulting in extensive ecological radiation in marine ecosystems. Calanus sinicus dominates continental shelf waters in the northwest Pacific Ocean and plays an important role in the local ecosystem by linking primary production to higher trophic levels. A lack of effective molecular markers has hindered phylogenetic and population genetic studies concerning copepods. As they are genome-level informative, mitochondrial DNA sequences can be used as markers for population genetic studies and phylogenetic studies. Results The mitochondrial genome of C. sinicus is distinct from other arthropods owing to the concurrence of multiple non-coding regions and a reshuffled gene arrangement. Further particularities in the mitogenome of C. sinicus include low A + T-content, symmetrical nucleotide composition between strands, abbreviated stop codons for several PCGs and extended lengths of the genes atp6 and atp8 relative to other copepods. The monophyletic Copepoda should be placed within the Vericrustacea. The close affinity between Cyclopoida and Poecilostomatoida suggests reassigning the latter as subordinate to the former. Monophyly of Maxillopoda is rejected. Within the alignment of 11 C. sinicus mitogenomes, there are 397 variable sites harbouring three 'hotspot' variable sites and three microsatellite loci. Conclusion The occurrence of the circular subgenomic fragment during laboratory assays suggests that special caution should be taken when sequencing mitogenomes using long PCR. Such a phenomenon may provide additional evidence of mitochondrial DNA recombination, which appears to have been a prerequisite for shaping the present mitochondrial profile of C. sinicus during its evolution. The lack of synapomorphic gene arrangements among copepods has cast doubt on the utility of gene order as a useful molecular marker for deep phylogenetic analysis. However, mitochondrial genomic sequences have been valuable markers for

  18. A genetic linkage map of willow (Salix viminalis) based on AFLP and microsatelite markers

    Hanley, S.; Barker, J.H.A.; Ooijen, van J.W.; Aldam, C.; Harris, S.L.; Ahman, I.; Larsson, S.; Karp, A.

    2002-01-01

    The genus Salix (willow) contains a number of species of great value as biomass crops. Efforts to breed varieties with improved biomass yields and resistances to pests and diseases are limited by the lack of knowledge on the genetic basis of the traits. We have used AFLP and microsatellite markers

  19. Development of SSR markers and construction of a linkage map in jute

    We recently initiated a programme to develop simple sequence repeat markers and reported a set of 2469 SSR that were developed using four SSR-enriched libraries (Mir et al. 2009). In this communication, we report an additional set of 607 novel SSR in 393 SSR containing sequences. However, primers could be ...

  20. Analysing the effect of multiple sclerosis on vitamin D related biochemical markers of bone remodelling.

    McKenna, Malachi J; Murray, Barbara; Lonergan, Roisin; Segurado, Ricardo; Tubridy, Niall; Kilbane, Mark T

    2018-03-01

    The Irish population is at risk of vitamin D deficiency during the winter months, but the secular trend over the past 40 years is for marked improvement. Multiple sclerosis (MS) is common in Ireland with a latitudinal pattern favouring highest incidence in northern regions; MS is linked strongly with vitamin D status as a causal factor. We sought firstly to study the relationship between vitamin D status and vitamin D-related bone biochemistry, and secondly to evaluate if MS had an independent effect on vitamin D related markers of bone remodelling. Using a case-control design of 165 pairs (MS patient and matched control) residing in three different geographic regions during winter months, we measured serum 25-hydroxyvitamin D (25OHD), parathyroid hormone (PTH), C-terminal telopeptide of type I collagen (CTX) and total procollagen type I amino-terminal propeptide (PINP). Given the paired case-control design, associations were explored using mixed-effects linear regression analysis with the patient-control pair as a random effect and after log transformation of 25OHD. A two-way interaction effect was tested for vitamin D status (25OHD <30nmol/L) and the presence of MS on PTH, CTX, and PINP. In the total group, just over one-third (34.5%) had 25OHD <30nmol/L. PTH was elevated in 7.6%. CTX was not elevated in any case, and PINP was elevated in 4.5%. On mixed-effects linear regression analysis after adjusting for confounders (age, sex, renal function, and serum albumin), we demonstrated the principal determinant of 25OHD was geographical location (p<0.001), of PTH was 25OHD (p<0.001), of CTX was PTH (p<0.001), and of PINP was PTH (p<0.001). MS did not have an independent effect on PTH (p=0.921), CTX (p=0.912), or PINP (p=0.495). As regards an interaction effect, the presence of MS and 25OHD <30nmol/L was not significant but tended towards having lower PTH (p=0.207). In conclusion, in Ireland in winter only a minority had any abnormality in the secondary indices of

  1. Dense genetic linkage maps of three Populus species (Populus deltoides, P. nigra and P. trichocarpa) based on AFLP and microsatellite markers.

    Cervera, M T; Storme, V; Ivens, B; Gusmão, J; Liu, B H; Hostyn, V; Van Slycken, J; Van Montagu, M; Boerjan, W

    2001-06-01

    Populus deltoides, P. nigra, and P. trichocarpa are the most important species for poplar breeding programs worldwide. In addition, Populus has become a model for fundamental research on trees. Linkage maps were constructed for these three species by analyzing progeny of two controlled crosses sharing the same female parent, Populus deltoides cv. S9-2 x P. nigra cv. Ghoy and P. deltoides cv. S9-2 x P. trichocarpa cv. V24. The two-way pseudotestcross mapping strategy was used to construct the maps. Amplified fragment length polymorphism (AFLP) markers that segregated 1:1 were used to form the four parental maps. Microsatellites and sequence-tagged sites were used to align homoeologous groups between the maps and to merge linkage groups within the individual maps. Linkage analysis and alignment of the homoeologous groups resulted in 566 markers distributed over 19 groups for P. deltoides covering 86% of the genome, 339 markers distributed over 19 groups for P. trichocarpa covering 73%, and 369 markers distributed over 28 groups for P. nigra covering 61%. Several tests for randomness showed that the AFLP markers were randomly distributed over the genome.

  2. Online unsupervised formation of cell assemblies for the encoding of multiple cognitive maps.

    Salihoglu, Utku; Bersini, Hugues; Yamaguchi, Yoko; Molter, Colin

    2009-01-01

    Since their introduction sixty years ago, cell assemblies have proved to be a powerful paradigm for brain information processing. After their introduction in artificial intelligence, cell assemblies became commonly used in computational neuroscience as a neural substrate for content addressable memories. However, the mechanisms underlying their formation are poorly understood and, so far, there is no biologically plausible algorithms which can explain how external stimuli can be online stored in cell assemblies. We addressed this question in a previous paper [Salihoglu, U., Bersini, H., Yamaguchi, Y., Molter, C., (2009). A model for the cognitive map formation: Application of the retroaxonal theory. In Proc. IEEE international joint conference on neural networks], were, based on biologically plausible mechanisms, a novel unsupervised algorithm for online cell assemblies' creation was developed. The procedure involved simultaneously, a fast Hebbian/anti-Hebbian learning of the network's recurrent connections for the creation of new cell assemblies, and a slower feedback signal which stabilized the cell assemblies by learning the feedforward input connections. Here, we first quantify the role played by the retroaxonal feedback mechanism. Then, we show how multiple cognitive maps, composed by a set of orthogonal input stimuli, can be encoded in the network. As a result, when facing a previously learned input, the system is able to retrieve the cognitive map it belongs to. As a consequence, ambiguous inputs which could belong to multiple cognitive maps can be disambiguated by the knowledge of the context, i.e. the cognitive map.

  3. Population structure and genetic diversity characterization of a sunflower association mapping population using SSR and SNP markers.

    Filippi, Carla V; Aguirre, Natalia; Rivas, Juan G; Zubrzycki, Jeremias; Puebla, Andrea; Cordes, Diego; Moreno, Maria V; Fusari, Corina M; Alvarez, Daniel; Heinz, Ruth A; Hopp, Horacio E; Paniego, Norma B; Lia, Veronica V

    2015-02-13

    Argentina has a long tradition of sunflower breeding, and its germplasm is a valuable genetic resource worldwide. However, knowledge of the genetic constitution and variability levels of the Argentinean germplasm is still scarce, rendering the global map of cultivated sunflower diversity incomplete. In this study, 42 microsatellite loci and 384 single nucleotide polymorphisms (SNPs) were used to characterize the first association mapping population used for quantitative trait loci mapping in sunflower, along with a selection of allied open-pollinated and composite populations from the germplasm bank of the National Institute of Agricultural Technology of Argentina. The ability of different kinds of markers to assess genetic diversity and population structure was also evaluated. The analysis of polymorphism in the set of sunflower accessions studied here showed that both the microsatellites and SNP markers were informative for germplasm characterization, although to different extents. In general, the estimates of genetic variability were moderate. The average genetic diversity, as quantified by the expected heterozygosity, was 0.52 for SSR loci and 0.29 for SNPs. Within SSR markers, those derived from non-coding regions were able to capture higher levels of diversity than EST-SSR. A significant correlation was found between SSR and SNP- based genetic distances among accessions. Bayesian and multivariate methods were used to infer population structure. Evidence for the existence of three different genetic groups was found consistently across data sets (i.e., SSR, SNP and SSR + SNP), with the maintainer/restorer status being the most prevalent characteristic associated with group delimitation. The present study constitutes the first report comparing the performance of SSR and SNP markers for population genetics analysis in cultivated sunflower. We show that the SSR and SNP panels examined here, either used separately or in conjunction, allowed consistent

  4. Design of an image encryption scheme based on a multiple chaotic map

    Tong, Xiao-Jun

    2013-07-01

    In order to solve the problem that chaos is degenerated in limited computer precision and Cat map is the small key space, this paper presents a chaotic map based on topological conjugacy and the chaotic characteristics are proved by Devaney definition. In order to produce a large key space, a Cat map named block Cat map is also designed for permutation process based on multiple-dimensional chaotic maps. The image encryption algorithm is based on permutation-substitution, and each key is controlled by different chaotic maps. The entropy analysis, differential analysis, weak-keys analysis, statistical analysis, cipher random analysis, and cipher sensibility analysis depending on key and plaintext are introduced to test the security of the new image encryption scheme. Through the comparison to the proposed scheme with AES, DES and Logistic encryption methods, we come to the conclusion that the image encryption method solves the problem of low precision of one dimensional chaotic function and has higher speed and higher security.

  5. A Genetic Linkage Map of Mycosphaerella Fijiensis, using SSR and DArT Markers

    Mycosphaerella fijiensis is the causal agent of black leaf streak or Black Sigatoka disease in bananas. This pathogen threatens global banana production as the main export Cavendish cultivars are highly susceptible. Previously a genetic linkage map was generated predominantly using anonymous AFLP ma...

  6. Genetic linkage mapping in an F2 perennial ryegrass population using DArT markers

    Tomaszewski, C.; Byrne, S. L.; Foito, A.; Kildea, S.; Kopecký, David; Doležel, Jaroslav; Heslop-Harrison, J. S.; Stewart, D.; Barth, S.

    2012-01-01

    Roč. 131, č. 2 (2012), s. 345-349 ISSN 0179-9541 Institutional research plan: CEZ:AV0Z50380511 Keywords : Lolium perenne * perennial ryegrass * genetic map Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.175, year: 2012

  7. An integrated physical map of 210 markers assigned to the short arm of human chromosome 11

    Redeker, E.; Hoovers, J. M.; Alders, M.; van Moorsel, C. J.; Ivens, A. C.; Gregory, S.; Kalikin, L.; Bliek, J.; de Galan, L.; van den Bogaard, R.; Visser, J.; van der Voort, R.; Feinberg, A. P.; Little, P. F. R.; Westerveld, A.; Mannens, M.

    1994-01-01

    Using a panel of patient cell lines with chromosomal breakpoints, we constructed a physical map for the short arm of human chromosome 11. We focused on 11p15, a chromosome band harboring at least 25 known genes and associated with the Beckwith-Wiedemann syndrome, several childhood tumors, and

  8. Multiple large solar lentigos on the upper back as clinical markers of past severe sunburn: a case-control study.

    Derancourt, C; Bourdon-Lanoy, E; Grob, J-J; Guillaume, J-C; Bernard, P; Bastuji-Garin, S

    2007-01-01

    Multiple solar lentigos commonly seen on the upper back and shoulders of adults are classically considered as a sign of photodamage, although epidemiological studies are scarce. To assess whether these lesions are clinical markers of past severe sunburn. A case-control study in two outpatient dermatology clinics in French university hospitals. Past episodes of moderate and severe sunburn were compared between 145 adult patients with multiple solar lentigos on the upper back and 145 matched controls. In multivariate analysis adjusted for potential confounders, recalled episodes of sunburn during childhood, adolescence and adulthood were independently associated with the presence of multiple solar lentigos (adjusted odds ratios, 95% confidence intervals: 2.3 (1.1-5.2) and 28.1 (10.4-75.6) for moderate and severe sunburn, respectively). Multiple solar lentigos on the upper back and shoulders of adults are potential clinical markers of past severe sunburn which may thus be used to identify a population at higher risk of developing cutaneous malignant melanoma.

  9. Construction of High Density Sweet Cherry (Prunus avium L. Linkage Maps Using Microsatellite Markers and SNPs Detected by Genotyping-by-Sequencing (GBS.

    Verónica Guajardo

    Full Text Available Linkage maps are valuable tools in genetic and genomic studies. For sweet cherry, linkage maps have been constructed using mainly microsatellite markers (SSRs and, recently, using single nucleotide polymorphism markers (SNPs from a cherry 6K SNP array. Genotyping-by-sequencing (GBS, a new methodology based on high-throughput sequencing, holds great promise for identification of high number of SNPs and construction of high density linkage maps. In this study, GBS was used to identify SNPs from an intra-specific sweet cherry cross. A total of 8,476 high quality SNPs were selected for mapping. The physical position for each SNP was determined using the peach genome, Peach v1.0, as reference, and a homogeneous distribution of markers along the eight peach scaffolds was obtained. On average, 65.6% of the SNPs were present in genic regions and 49.8% were located in exonic regions. In addition to the SNPs, a group of SSRs was also used for construction of linkage maps. Parental and consensus high density maps were constructed by genotyping 166 siblings from a 'Rainier' x 'Rivedel' (Ra x Ri cross. Using Ra x Ri population, 462, 489 and 985 markers were mapped into eight linkage groups in 'Rainier', 'Rivedel' and the Ra x Ri map, respectively, with 80% of mapped SNPs located in genic regions. Obtained maps spanned 549.5, 582.6 and 731.3 cM for 'Rainier', 'Rivedel' and consensus maps, respectively, with an average distance of 1.2 cM between adjacent markers for both 'Rainier' and 'Rivedel' maps and of 0.7 cM for Ra x Ri map. High synteny and co-linearity was observed between obtained maps and with Peach v1.0. These new high density linkage maps provide valuable information on the sweet cherry genome, and serve as the basis for identification of QTLs and genes relevant for the breeding of the species.

  10. Corpus callosum atrophy as a marker of clinically meaningful cognitive decline in secondary progressive multiple sclerosis. Impact on employment status.

    Papathanasiou, Athanasios; Messinis, Lambros; Zampakis, Petros; Papathanasopoulos, Panagiotis

    2017-09-01

    Cognitive impairment in Multiple Sclerosis (MS) is more frequent and pronounced in secondary progressive MS (SPMS). Cognitive decline is an important predictor of employment status in patients with MS. Magnetic Resonance Imaging (MRI) markers have been used to associate tissue damage with cognitive dysfunction. The aim of the study was to designate the MRI marker that predicts cognitive decline in SPMS and explore its effect on employment status. 30 SPMS patients and 30 healthy participants underwent neuropsychological assessment using the Trail Making Test (TMT) parts A and B, semantic and phonological verbal fluency task and a computerized cognitive screening battery (Central Nervous System Vital Signs). Employment status was obtained as a quality of life measure. Brain MRI was performed in all participants. We measured total lesion volume, third ventricle width, thalamic and corpus callosum atrophy. The frequency of cognitive decline for our SPMS patients was 80%. SPMS patients differed significantly from controls in all neuropsychological measures. Corpus callosum area was correlated with cognitive flexibility, processing speed, composite memory, executive functions, psychomotor speed, reaction time and phonological verbal fluency task. Processing speed and composite memory were the most sensitive markers for predicting employment status. Corpus callosum area was the most sensitive MRI marker for memory and processing speed. Corpus callosum atrophy predicts a clinically meaningful cognitive decline, affecting employment status in our SPMS patients. Copyright © 2017 Elsevier Ltd. All rights reserved.

  11. QTL mapping in multiple populations and development stages reveals dynamic quantitative trait loci for fruit size in cucumbers of different market classes.

    Weng, Yiqun; Colle, Marivi; Wang, Yuhui; Yang, Luming; Rubinstein, Mor; Sherman, Amir; Ophir, Ron; Grumet, Rebecca

    2015-09-01

    QTL analysis in multi-development stages with different QTL models identified 12 consensus QTLs underlying fruit elongation and radial growth presenting a dynamic view of genetic control of cucumber fruit development. Fruit size is an important quality trait in cucumber (Cucumis sativus L.) of different market classes. However, the genetic and molecular basis of fruit size variations in cucumber is not well understood. In this study, we conducted QTL mapping of fruit size in cucumber using F2, F2-derived F3 families and recombinant inbred lines (RILs) from a cross between two inbred lines Gy14 (North American picking cucumber) and 9930 (North China fresh market cucumber). Phenotypic data of fruit length and diameter were collected at three development stages (anthesis, immature and mature fruits) in six environments over 4 years. QTL analysis was performed with three QTL models including composite interval mapping (CIM), Bayesian interval mapping (BIM), and multiple QTL mapping (MQM). Twenty-nine consistent and distinct QTLs were detected for nine traits from multiple mapping populations and QTL models. Synthesis of information from available fruit size QTLs allowed establishment of 12 consensus QTLs underlying fruit elongation and radial growth, which presented a dynamic view of genetic control of cucumber fruit development. Results from this study highlighted the benefits of QTL analysis with multiple QTL models and different mapping populations in improving the power of QTL detection. Discussion was presented in the context of domestication and diversifying selection of fruit length and diameter, marker-assisted selection of fruit size, as well as identification of candidate genes for fruit size QTLs in cucumber.

  12. On the Application of Joint-Domain Dictionary Mapping for Multiple Power Disturbance Assessment

    Delong Cai

    2018-02-01

    Full Text Available This paper proposes a joint-domain dictionary mapping method to obtain high assessment accuracy of multiple power disturbances. Firstly, in order to achieve resolutions in both the time and frequency domains, a joint-domain dictionary is proposed which consists of a discrete Hartley base and an identity matrix. Due to the low correlation between the discrete Hartley base and the identity matrix, the joint-domain dictionary mapping can separately capture the approximations of the sinusoidal components and transients. Since the mapping coefficients contain the physical quantities, the eigenvalues of each component can be effectively estimated. A quantified eigenvalue classifier was designed for identifying power disturbances using the estimated eigenvalues. The proposed method was compared with several advanced methods through simulated power disturbances under different noise conditions, and actual data from the Institute of Electrical and Electronics Engineers Power and Energy Society database. The results reveal that the joint-domain dictionary mapping technique shows good performance on parameter estimation and recognition precision, even dealing with complicated multiple power disturbances.

  13. Diagnostic value of multiple tumor markers for patients with esophageal carcinoma.

    Zhang, Jun; Zhu, Zhenli; Liu, Yan; Jin, Xueyuan; Xu, Zhiwei; Yu, Qiuyan; Li, Ke

    2015-01-01

    Various studies assessing the diagnostic value of serum tumor markers in patients with esophageal cancer remain controversial. This study aims to comprehensively and quantitatively summarize the potential diagnostic value of 5 serum tumour markers in esophageal cancer. We systematically searched PubMed, Embase, Chinese National Knowledge Infrastructure (CNKI) and Chinese Biomedical Database (CBM), through February 28, 2013, without language restriction. Studies were assessed for quality using QUADAS (quality assessment of studies of diagnostic accuracy). The positive likelihood ratio (PLR) and negative likelihood ratio (NLR) were pooled separately and compared with overall accuracy measures using diagnostic odds ratios (DORs) and symmetric summary receiver operating characteristic (SROC) curves. Of 4391 studies initially identified, 44 eligible studies including five tumor markers met the inclusion criteria for the meta-analysis, while meta-analysis could not be conducted for 12 other tumor markers. Approximately 79.55% (35/44) of the included studies were of relatively high quality (QUADAS score≥7). The summary estimates of the positive likelihood ratio (PLR), negative likelihood ratio (NLR) and diagnostic odds ratio (DOR) for diagnosing EC were as follows: CEA, 5.94/0.76/9.26; Cyfra21-1, 12.110.59/22.27; p53 antibody, 6.71/0.75/9.60; SCC-Ag, 7.66/0.68/12.41; and VEGF-C, 0.74/0.37/8.12. The estimated summary receiver operating characteristic curves showed that the performance of all five tumor markers was reasonable. The current evidence suggests that CEA, Cyfra21-1, p53, SCC-Ag and VEGF-C have a potential diagnostic value for esophageal carcinoma.

  14. Association mapping of agro-morphological characters among the global collection of finger millet genotypes using genomic SSR markers.

    Kalyana Babu, B; Agrawal, P K; Pandey, Dinesh; Jaiswal, J P; Kumar, Anil

    2014-08-01

    Identification of alleles responsible for various agro-morphological characters is a major concern to further improve the finger millet germplasm. Forty-six genomic SSRs were used for genetic analysis and population structure analysis of a global collection of 190 finger millet genotypes and fifteen agro-morphological characters were evaluated. The overall results showed that Asian genotypes were smaller in height, smaller flag leaf length, less basal tiller number, early flowering and early maturity nature, small ear head length, and smaller in length of longest finger. The 46 SSRs yielded 90 scorable alleles and the polymorphism information content values varied from 0.292 to 0.703 at an average of 0.442. The gene diversity was in the range of 0.355 to 0.750 with an average value of 0.528. The 46 genomic SSR loci grouped the 190 finger millet genotypes into two major clusters based on their geographical origin by the both phylogenetic clustering and population structure analysis by STRUCTURE software. Association mapping of QTLs for 15 agro-morphological characters with 46 genomic SSRs resulted in identification of five markers were linked to QTLs of four traits at a significant threshold (P) level of ≤ 0.01 and ≤ 0.001. The QTL for basal tiller number was strongly associated with the locus UGEP81 at a P value of 0.001 by explaining the phenotypic variance (R (2)) of 10.8%. The QTL for days to 50% flowering was linked by two SSR loci UGEP77 and UGEP90, explained 10 and 8.7% of R (2) respectively at a P value of 0.01. The SSR marker, FM9 found to have strong association to two agro-morphological traits, flag leaf width (P-0.001, R(2)-14.1 %) and plant height (P-0.001, R(2)-11.2%). The markers linked to the QTLs for above agro-morphological characters found in the present study can be further used for cloning of the full length gene, fine mapping and their further use in the marker assisted breeding programmes for introgression of alleles into locally well

  15. A first linkage map of globe artichoke (Cynara cardunculus var. scolymus L.) based on AFLP, S-SAP, M-AFLP and microsatellite markers.

    Lanteri, S; Acquadro, A; Comino, C; Mauro, R; Mauromicale, G; Portis, E

    2006-05-01

    We present the first genetic maps of globe artichoke (Cynara cardunculus var. scolymus L. 2n=2x=34), constructed with a two-way pseudo-testcross strategy. A F1 mapping population of 94 individuals was generated between a late-maturing, non-spiny type and an early-maturing spiny type. The 30 AFLP, 13 M-AFLP and 9 S-SAP primer combinations chosen identified, respectively, 352, 38 and 41 polymorphic markers. Of 32 microsatellite primer pairs tested, 12 identified heterozygous loci in one or other parent, and 7 were fully informative as they segregated in both parents. The female parent map comprised 204 loci, spread over 18 linkage groups and spanned 1330.5 cM with a mean marker density of 6.5 cM. The equivalent figures for the male parent map were 180 loci, 17 linkage groups, 1239.4 and 6.9 cM. About 3% of the AFLP and AFLP-derived markers displayed segregation distortion with a P value below 0.01, and were not used for map construction. All the SSR loci were included in the linkage analysis, although one locus did show some segregation distortion. The presence of 78 markers in common to both maps allowed the alignment of 16 linkage groups. The maps generated provide a firm basis for the mapping of agriculturally relevant traits, which will then open the way for the application of a marker-assisted selection breeding strategy in this species.

  16. Development and mapping of DArT markers within the Festuca-Lolium complex

    Kopecký, David; Bartoš, Jan; Lukaszewski, A.; Baird, J. H.; Černoch, V.; Koelliker, R.; Rognli, O. A.; Blois, H.; Caig, V.; Luebberstedt, T.; Studer, B.; Shaw, P.; Doležel, Jaroslav; Kilian, A.

    2009-01-01

    Roč. 10, Art_No_473 (2009), s. 1-11 ISSN 1471-2164 R&D Projects: GA MZe QH71267; GA ČR GP521/07/P479 Institutional research plan: CEZ:AV0Z50380511 Keywords : DIVERSITY ARRAYS TECHNOLOGY * GENETIC-LINKAGE MAP * PERENNIAL RYEGRASS Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.759, year: 2009

  17. Selection of discrimination marker from various propolis for mapping and identify anti Candida albicans activity

    Mahadewi, Alfiani Guntari; Christina, Daisy; Hermansyah, Heri; Wijanarko, Anondho; Farida, Siti; Adawiyah, Robiatul; Rohmatin, Etin; Sahlan, Muhamad

    2018-02-01

    The increase in fungal resistance against antifungal drugs available in the market will reduce the effectiveness of treatment for Candidiasis. Propolis contains various compounds with antifungal properties Candida albicans, but the content of each type is very diverse. The sample used was Sulawesi propolis type smooth (taken from inside the nest), rough (taken from outside the hive) and mix (a combination of both). Anti-C. albicans molecule marker is a marker compound for selecting propolis with the ability to overcome Candidiasis. The initial step was to test the levels of flavonoids and phenolic by using UV-Vis spectrometry method. It was founded that each sample was not always superior to any substance, so propolis cannot be directly selected. In Phenolic content, mix propolis has the highest value than other 5.109%. In Flavonoid content, propolis smooth has the highest value than other, 16.38%. Furthermore, propolis selected by antifungal activity test with good diffusion method at the concentration propolis 5% either 7%, the inhibitory diameter zone propolis smooth and rough has same value 10 mm. Propolis mix has an advantage while propolis smooth and rough have the same capability range 12 mm and 13 mm. In this study, the phenolic content plays a major role in antifungal cases.

  18. Analysis of non-TIR NBS-LRR resistance gene analogs in Musa acuminata Colla: Isolation, RFLP marker development, and physical mapping

    Souza Manoel T

    2008-01-01

    Full Text Available Abstract Background Many commercial banana varieties lack sources of resistance to pests and diseases, as a consequence of sterility and narrow genetic background. Fertile wild relatives, by contrast, possess greater variability and represent potential sources of disease resistance genes (R-genes. The largest known family of plant R-genes encode proteins with nucleotide-binding site (NBS and C-terminal leucine-rich repeat (LRR domains. Conserved motifs in such genes in diverse plant species offer a means for isolation of candidate genes in banana which may be involved in plant defence. Results A computational strategy was developed for unbiased conserved motif discovery in NBS and LRR domains in R-genes and homologues in monocotyledonous plant species. Degenerate PCR primers targeting conserved motifs were tested on the wild cultivar Musa acuminata subsp. burmannicoides, var. Calcutta 4, which is resistant to a number of fungal pathogens and nematodes. One hundred and seventy four resistance gene analogs (RGAs were amplified and assembled into 52 contiguous sequences. Motifs present were typical of the non-TIR NBS-LRR RGA subfamily. A phylogenetic analysis of deduced amino-acid sequences for 33 RGAs with contiguous open reading frames (ORFs, together with RGAs from Arabidopsis thaliana and Oryza sativa, grouped most Musa RGAs within monocotyledon-specific clades. RFLP-RGA markers were developed, with 12 displaying distinct polymorphisms in parentals and F1 progeny of a diploid M. acuminata mapping population. Eighty eight BAC clones were identified in M. acuminata Calcutta 4, M. acuminata Grande Naine, and M. balbisiana Pisang Klutuk Wulung BAC libraries when hybridized to two RGA probes. Multiple copy RGAs were common within BAC clones, potentially representing variation reservoirs for evolution of new R-gene specificities. Conclusion This is the first large scale analysis of NBS-LRR RGAs in M. acuminata Calcutta 4. Contig sequences were

  19. Simultaneous quantitative detection of multiple tumor markers with a rapid and sensitive multicolor quantum dots based immunochromatographic test strip.

    Wang, Chunying; Hou, Fei; Ma, Yicai

    2015-06-15

    A novel multicolor quantum dots (QDs) based immunochromatographic test strip (ICTS) was developed for simultaneous quantitative detection of multiple tumor markers, by utilizing alpha fetoprotein (AFP) and carcinoembryonic antigen (CEA) as models. The immunosensor could realize simultaneous quantitative detection of tumor markers with only one test line and one control line on the nitrocellulose membrane (NC membrane) due to the introduction of multicolor QDs. In this method, a mixture of mouse anti-AFP McAb and mouse anti-CEA McAb was coated on NC membrane as test line and goat anti-mouse IgG antibody was coated as control line. Anti-AFP McAb-QDs546 conjugates and anti-CEA McAb-QDs620 conjugates were mixed and applied to the conjugate pad. Simultaneous quantitative detection of multiple tumor markers was achieved by detecting the fluorescence intensity of captured QDs labels on test line and control line using a test strip reader. Under the optimum conditions, AFP and CEA could be detected as low as 3 ng/mL and 2 ng/mL in 15 min with a sample volume of 80 μL, and no obvious cross-reactivity was observed. The immunosensor was validated with 130 clinical samples and in which it exhibited high sensitivity (93% for AFP and 87% for CEA) and specificity (94% for AFP and 97% for CEA). The immunosensor also demonstrated high recoveries (87.5-113% for AFP and 90-97.3% for CEA) and low relative standard deviations (RSDs) (2.8-6.2% for AFP and 4.9-9.6% for CEA) when testing spiked human serum. This novel multicolor QDs based ICTS provides an easy and rapid, simultaneous quantitative detecting strategy for point-of-care testing of tumor markers. Copyright © 2014 Elsevier B.V. All rights reserved.

  20. Admixture analysis of stocked brown trout populations using mapped microsatellite DNA markers: indigenous trout persist in introgressed populations

    Hansen, Michael Møller; Mensberg, Karen-Lise Dons

    2009-01-01

    , but resolution is low if genetic differentiation is weak. Here, we analyse stocked brown trout populations represented by historical (1943-1956) and contemporary (2000s) samples, where genetic differentiation between wild populations and stocked trout is weak (pair-wise F-ST of 0.047 and 0.053). By analysing...... a high number of microsatellite DNA markers (50) and making use of linkage map information, we achieve clear identification of admixed and non-admixed trout. Moreover, despite strong population-level admixture by hatchery strain trout in one of the populations (70.8%), non-admixed individuals...... nevertheless persist (7 out of 53 individuals). These remnants of the indigenous population are characterized by later spawning time than the majority of the admixed individuals. We hypothesize that isolation by time mediated by spawning time differences between wild and hatchery strain trout is a major factor...

  1. Simultaneous measurement of 25 inflammatory markers and neurotrophins in neonatal dried blood spots by immunoassay with xMAP technology

    Skogstrand, Kristin; Thorsen, Poul; Nørgaard-Pedersen, Bent

    2005-01-01

    BACKGROUND: Inflammatory reactions and other events in early life may be part of the etiology of late-onset diseases, including cerebral palsy, autism, and type 1 diabetes. Most neonatal screening programs for congenital disorders are based on analysis of dried blood spot samples (DBSS), and stored...... on flowmetric Luminex xMAP technology to measure inflammatory markers and neutrophins in DBSS. RESULTS: The high-capacity 25-plex multianalyte method measured 23 inflammatory and trophic cytokines, triggering receptor expressed on myeloid cells-1 (TREM-1), and C-reactive protein in two 3.2-mm punches from DBSS...... potential for high-capacity analysis of DBSS in epidemiologic case-control studies and, with further refinements, in neonatal screening....

  2. Diagnostic value of stool DNA testing for multiple markers of colorectal cancer and advanced adenoma: a meta-analysis.

    Yang, Hua; Xia, Bing-Qing; Jiang, Bo; Wang, Guozhen; Yang, Yi-Peng; Chen, Hao; Li, Bing-Sheng; Xu, An-Gao; Huang, Yun-Bo; Wang, Xin-Ying

    2013-08-01

    The diagnostic value of stool DNA (sDNA) testing for colorectal neoplasms remains controversial. To compensate for the lack of large-scale unbiased population studies, a meta-analysis was performed to evaluate the diagnostic value of sDNA testing for multiple markers of colorectal cancer (CRC) and advanced adenoma. The PubMed, Science Direct, Biosis Review, Cochrane Library and Embase databases were systematically searched in January 2012 without time restriction. Meta-analysis was performed using a random-effects model using sensitivity, specificity, diagnostic OR (DOR), summary ROC curves, area under the curve (AUC), and 95% CIs as effect measures. Heterogeneity was measured using the χ(2) test and Q statistic; subgroup analysis was also conducted. A total of 20 studies comprising 5876 individuals were eligible. There was no heterogeneity for CRC, but adenoma and advanced adenoma harboured considerable heterogeneity influenced by risk classification and various detection markers. Stratification analysis according to risk classification showed that multiple markers had a high DOR for the high-risk subgroups of both CRC (sensitivity 0.759 [95% CI 0.711 to 0.804]; specificity 0.883 [95% CI 0.846 to 0.913]; AUC 0.906) and advanced adenoma (sensitivity 0.683 [95% CI 0.584 to 0.771]; specificity 0.918 [95% CI 0.866 to 0.954]; AUC 0.946) but not for the average-risk subgroups of either. In the methylation subgroup, sDNA testing had significantly higher DOR for CRC (sensitivity 0.753 [95% CI 0.685 to 0.812]; specificity 0.913 [95% CI 0.860 to 0.950]; AUC 0.918) and advanced adenoma (sensitivity 0.623 [95% CI 0.527 to 0.712]; specificity 0.926 [95% CI 0.882 to 0.958]; AUC 0.910) compared with the mutation subgroup. There was no significant heterogeneity among studies for subgroup analysis. sDNA testing for multiple markers had strong diagnostic significance for CRC and advanced adenoma in high-risk subjects. Methylation makers had more diagnostic value than mutation

  3. Increased osteopontin plasma levels in multiple sclerosis patients correlate with bone-specific markers

    Vogt, M.H.J.; ten Kate, J.; Drent, R.J.M.; Polman, C.H.; Hupperts, R.

    2010-01-01

    The pro-inflammatory cytokine osteopontin has been found to be highly expressed in multiple sclerosis lesions and plasma levels are increased during relapses in relapse-onset multiple sclerosis patients. The objective was to determine the relationship between osteopontin plasma and cerebrospinal

  4. A genetic linkage map with 178 SSR and 1 901 SNP markers constructed using a RIL population in wheat (Triticum aestivum L.)

    ZHAI Hui-jie; FENG Zhi-yu; LIU Xin-ye; CHENG Xue-jiao; PENG Hui-ru; YAO Ying-yin; SUN Qi-xin; NI Zhong-fu

    2015-01-01

    The construction of high density genetic linkage map provides a powerful tool to detect and map quantitative trait loci (QTLs) controlling agronomically important traits. In this study, simple sequence repeat (SSR) markers and Illumina 9K iSelect single nucleotide polymorphism (SNP) genechip were employed to construct one genetic linkage map of common wheat (Triticum aestivum L.) using 191 recombinant inbred lines (RILs) derived from cross Yu 8679xJing 411. This map included 1 901 SNP loci and 178 SSR loci, covering 1 659.9 cM and 1 000 marker bins, with an average interval distance of 1.66 cM. A, B and D genomes covered 719.1,703.5 and 237.3 cM, with an average interval distance of 1.66, 1.45 and 2.9 cM, respectively. Notably, the genetic linkage map covered 20 chromosomes, with the exception of chromosome 5D. Bioinformatics analysis revealed that 1 754 (92.27%) of 1 901 mapped SNP loci could be aligned to 1 215 distinct wheat unigenes, among which 1 184 (97.4%) were located on one single chromosome, and the rest 31 (2.6%) were located on 2 to 3 chromosomes. By performing in silico comparison, 214 chromosome deletion bin-mapped expressed sequence tags (ESTs), 1 043 Brachypodium genes and 1 033 rice genes were further added onto the genetic linkage map. This map not only integrated genetic and physical maps, SSR and SNP loci, respectively, but also provided the information of Brachypodium and rice genes corresponding to 1 754 SNP loci. Therefore, it will be a useful tool for comparative genomics analysis, fine mapping of QTL/gene controlling agronomically important traits and marker-assisted selection breeding in wheat.

  5. Simplified fringe order correction for absolute phase maps recovered with multiple-spatial-frequency fringe projections

    Ding, Yi; Peng, Kai; Lu, Lei; Zhong, Kai; Zhu, Ziqi

    2017-01-01

    Various kinds of fringe order errors may occur in the absolute phase maps recovered with multi-spatial-frequency fringe projections. In existing methods, multiple successive pixels corrupted by fringe order errors are detected and corrected pixel-by-pixel with repeating searches, which is inefficient for applications. To improve the efficiency of multiple successive fringe order corrections, in this paper we propose a method to simplify the error detection and correction by the stepwise increasing property of fringe order. In the proposed method, the numbers of pixels in each step are estimated to find the possible true fringe order values, repeating the search in detecting multiple successive errors can be avoided for efficient error correction. The effectiveness of our proposed method is validated by experimental results. (paper)

  6. Gene Expression Profiling Soybean Stem Tissue Early Response to Sclerotinia sclerotiorum and In Silico Mapping in Relation to Resistance Markers

    Bernarda Calla

    2009-07-01

    Full Text Available White mold, caused by (Lib. de Bary, can be a serious disease of crops grown under cool, moist environments. In many plants, such as soybean [ (L. Merr.], complete genetic resistance does not exist. To identify possible genes involved in defense against this pathogen, and to determine possible physiological changes that occur during infection, a microarray screen was conducted using stem tissue to evaluate changes in gene expression between partially resistant and susceptible soybean genotypes at 8 and 14 hours post inoculation. RNA from 15 day-old inoculated plants was labeled and hybridized to soybean cDNA microarrays. ANOVA identified 1270 significant genes from the comparison between time points and 105 genes from the comparison between genotypes. Selected genes were classified into functional categories. The analyses identified changes in cell-wall composition and signaling pathways, as well as suggesting a role for anthocyanin and anthocyanidin synthesis in the defense against . In-silico mapping of both the differentially expressed transcripts and of public markers associated with partial resistance to white mold, provided evidence of several differentially expressed genes being closely positioned to white mold resistance markers, with the two most promising genes encoding a PR-5 and anthocyanidin synthase.

  7. Examination of X chromosome markers in Rett syndrome: Exclusion mapping with a novel variation on multilocus linkage analysis

    Ellison, K.A.; Fill, C.P. (Baylor College of Medicine, Houston, TX (United States)); Terwililger, J.; Percy, A.K.; Zobhbi, H. (Columbia University, NY (United States)); DeGennaro, L.J.; Ott, J. (University of Massachusetts Medical School, Worcester (United States)); Anvret, M.; Martin-Gallardo, A. (National Institutes of Health, Bethesda, MD (United States))

    1992-02-01

    Rett syndrome is a neurologic disorder characterized by early normal development followed by regression, acquired deceleration of head growth, autism, ataxia, and sterotypic hand movements. The exclusive occurrence of the syndrome in females and the occurrence of a few familial cases with inheritance through maternal lines suggest that this disorder is most likely secondary to a mutation on the X chromosome. To address this hypothesis and to identify candidate regions for the Rett syndrome gene locus, genotypic analysis was performed in two families with maternally related affected half-sisters by using 63 DNA markers from the X chromosome. Nineteen of the loci studied were chosen for multipoint linkage analysis because they have been previously genetically mapped using a large number of meioses from reference families. Using the exclusion criterion of a lod score less than [minus]2, the authors were able to exclude the region between the Duchenne muscular dystrophy locus and the DXS456 locus. This region extends from Xp21.2 to Xq21-q23. The use of the multipoint linkage analysis approach outlined in this study should allow the exclusion of additional regions of the X chromosome as new markers are analyzed.

  8. Construction of a high-density genetic map using specific length amplified fragment markers and identification of a quantitative trait locus for anthracnose resistance in walnut (Juglans regia L.).

    Zhu, Yufeng; Yin, Yanfei; Yang, Keqiang; Li, Jihong; Sang, Yalin; Huang, Long; Fan, Shu

    2015-08-18

    Walnut (Juglans regia, 2n = 32, approximately 606 Mb per 1C genome) is an economically important tree crop. Resistance to anthracnose, caused by Colletotrichum gloeosporioides, is a major objective of walnut genetic improvement in China. The recently developed specific length amplified fragment sequencing (SLAF-seq) is an efficient strategy that can obtain large numbers of markers with sufficient sequence information to construct high-density genetic maps and permits detection of quantitative trait loci (QTLs) for molecular breeding. SLAF-seq generated 161.64 M paired-end reads. 153,820 SLAF markers were obtained, of which 49,174 were polymorphic. 13,635 polymorphic markers were sorted into five segregation types and 2,577 markers of them were used to construct genetic linkage maps: 2,395 of these fell into 16 linkage groups (LGs) for the female map, 448 markers for the male map, and 2,577 markers for the integrated map. Taking into account the size of all LGs, the marker coverage was 2,664.36 cM for the female map, 1,305.58 cM for the male map, and 2,457.82 cM for the integrated map. The average intervals between two adjacent mapped markers were 1.11 cM, 2.91 cM and 0.95 cM for three maps, respectively. 'SNP_only' markers accounted for 89.25% of the markers on the integrated map. Mapping markers contained 5,043 single nucleotide polymorphisms (SNPs) loci, which corresponded to two SNP loci per SLAF marker. According to the integrated map, we used interval mapping (Logarithm of odds, LOD > 3.0) to detect our quantitative trait. One QTL was detected for anthracnose resistance. The interval of this QTL ranged from 165.51 cM to 176.33 cM on LG14, and ten markers in this interval that were above the threshold value were considered to be linked markers to the anthracnose resistance trait. The phenotypic variance explained by each marker ranged from 16.2 to 19.9%, and their LOD scores varied from 3.22 to 4.04. High-density genetic maps for walnut containing 16

  9. Single Image Super-Resolution Using Global Regression Based on Multiple Local Linear Mappings.

    Choi, Jae-Seok; Kim, Munchurl

    2017-03-01

    Super-resolution (SR) has become more vital, because of its capability to generate high-quality ultra-high definition (UHD) high-resolution (HR) images from low-resolution (LR) input images. Conventional SR methods entail high computational complexity, which makes them difficult to be implemented for up-scaling of full-high-definition input images into UHD-resolution images. Nevertheless, our previous super-interpolation (SI) method showed a good compromise between Peak-Signal-to-Noise Ratio (PSNR) performances and computational complexity. However, since SI only utilizes simple linear mappings, it may fail to precisely reconstruct HR patches with complex texture. In this paper, we present a novel SR method, which inherits the large-to-small patch conversion scheme from SI but uses global regression based on local linear mappings (GLM). Thus, our new SR method is called GLM-SI. In GLM-SI, each LR input patch is divided into 25 overlapped subpatches. Next, based on the local properties of these subpatches, 25 different local linear mappings are applied to the current LR input patch to generate 25 HR patch candidates, which are then regressed into one final HR patch using a global regressor. The local linear mappings are learned cluster-wise in our off-line training phase. The main contribution of this paper is as follows: Previously, linear-mapping-based conventional SR methods, including SI only used one simple yet coarse linear mapping to each patch to reconstruct its HR version. On the contrary, for each LR input patch, our GLM-SI is the first to apply a combination of multiple local linear mappings, where each local linear mapping is found according to local properties of the current LR patch. Therefore, it can better approximate nonlinear LR-to-HR mappings for HR patches with complex texture. Experiment results show that the proposed GLM-SI method outperforms most of the state-of-the-art methods, and shows comparable PSNR performance with much lower

  10. Dissecting Genetic Network of Fruit Branch Traits in Upland Cotton by Association Mapping Using SSR Markers.

    Yongjun Mei

    Full Text Available Genetic architecture of branch traits has large influences on the morphological structure, photosynthetic capacity, planting density, and yield of Upland cotton (Gossypium hirsutum L.. This research aims to reveal the genetic effects of six branch traits, including bottom fruit branch node number (BFBNN, bottom fruit branch length (BFBL, middle fruit branch node number (MFBNN, middle fruit branch length (MFBL, upper fruit branch node number (UFBNN, and upper fruit branch length (UFBL. Association mapping was conducted for these traits of 39 lines and their 178 F1 hybrids in three environments. There were 20 highly significant Quantitative Trait SSRs (QTSs detected by mixed linear model approach analyzing a full genetic model with genetic effects of additive, dominance, epistasis and their environment interaction. The phenotypic variation explained by genetic effects ranged from 32.64 ~ 91.61%, suggesting these branch traits largely influenced by genetic factors.

  11. Multiple Description Coding Based on Optimized Redundancy Removal for 3D Depth Map

    Sen Han

    2016-06-01

    Full Text Available Multiple description (MD coding is a promising alternative for the robust transmission of information over error-prone channels. In 3D image technology, the depth map represents the distance between the camera and objects in the scene. Using the depth map combined with the existing multiview image, it can be efficient to synthesize images of any virtual viewpoint position, which can display more realistic 3D scenes. Differently from the conventional 2D texture image, the depth map contains a lot of spatial redundancy information, which is not necessary for view synthesis, but may result in the waste of compressed bits, especially when using MD coding for robust transmission. In this paper, we focus on the redundancy removal of MD coding based on the DCT (discrete cosine transform domain. In view of the characteristics of DCT coefficients, at the encoder, a Lagrange optimization approach is designed to determine the amounts of high frequency coefficients in the DCT domain to be removed. It is noted considering the low computing complexity that the entropy is adopted to estimate the bit rate in the optimization. Furthermore, at the decoder, adaptive zero-padding is applied to reconstruct the depth map when some information is lost. The experimental results have shown that compared to the corresponding scheme, the proposed method demonstrates better rate central and side distortion performance.

  12. An Efficient Strategy Combining SSR Markers- and Advanced QTL-seq-driven QTL Mapping Unravels Candidate Genes Regulating Grain Weight in Rice.

    Daware, Anurag; Das, Sweta; Srivastava, Rishi; Badoni, Saurabh; Singh, Ashok K; Agarwal, Pinky; Parida, Swarup K; Tyagi, Akhilesh K

    2016-01-01

    Development and use of genome-wide informative simple sequence repeat (SSR) markers and novel integrated genomic strategies are vital to drive genomics-assisted breeding applications and for efficient dissection of quantitative trait loci (QTLs) underlying complex traits in rice. The present study developed 6244 genome-wide informative SSR markers exhibiting in silico fragment length polymorphism based on repeat-unit variations among genomic sequences of 11 indica, japonica, aus , and wild rice accessions. These markers were mapped on diverse coding and non-coding sequence components of known cloned/candidate genes annotated from 12 chromosomes and revealed a much higher amplification (97%) and polymorphic potential (88%) along with wider genetic/functional diversity level (16-74% with a mean 53%) especially among accessions belonging to indica cultivar group, suggesting their utility in large-scale genomics-assisted breeding applications in rice. A high-density 3791 SSR markers-anchored genetic linkage map (IR 64 × Sonasal) spanning 2060 cM total map-length with an average inter-marker distance of 0.54 cM was generated. This reference genetic map identified six major genomic regions harboring robust QTLs (31% combined phenotypic variation explained with a 5.7-8.7 LOD) governing grain weight on six rice chromosomes. One strong grain weight major QTL region ( OsqGW5.1 ) was narrowed-down by integrating traditional QTL mapping with high-resolution QTL region-specific integrated SSR and single nucleotide polymorphism markers-based QTL-seq analysis and differential expression profiling. This led us to delineate two natural allelic variants in two known cis -regulatory elements (RAV1AAT and CARGCW8GAT) of glycosyl hydrolase and serine carboxypeptidase genes exhibiting pronounced seed-specific differential regulation in low (Sonasal) and high (IR 64) grain weight mapping parental accessions. Our genome-wide SSR marker resource (polymorphic within/between diverse

  13. Single strand conformation polymorphism based SNP and Indel markers for genetic mapping and synteny analysis of common bean (Phaseolus vulgaris L.

    Gómez Marcela

    2009-12-01

    Full Text Available Abstract Background Expressed sequence tags (ESTs are an important source of gene-based markers such as those based on insertion-deletions (Indels or single-nucleotide polymorphisms (SNPs. Several gel based methods have been reported for the detection of sequence variants, however they have not been widely exploited in common bean, an important legume crop of the developing world. The objectives of this project were to develop and map EST based markers using analysis of single strand conformation polymorphisms (SSCPs, to create a transcript map for common bean and to compare synteny of the common bean map with sequenced chromosomes of other legumes. Results A set of 418 EST based amplicons were evaluated for parental polymorphisms using the SSCP technique and 26% of these presented a clear conformational or size polymorphism between Andean and Mesoamerican genotypes. The amplicon based markers were then used for genetic mapping with segregation analysis performed in the DOR364 × G19833 recombinant inbred line (RIL population. A total of 118 new marker loci were placed into an integrated molecular map for common bean consisting of 288 markers. Of these, 218 were used for synteny analysis and 186 presented homology with segments of the soybean genome with an e-value lower than 7 × 10-12. The synteny analysis with soybean showed a mosaic pattern of syntenic blocks with most segments of any one common bean linkage group associated with two soybean chromosomes. The analysis with Medicago truncatula and Lotus japonicus presented fewer syntenic regions consistent with the more distant phylogenetic relationship between the galegoid and phaseoloid legumes. Conclusion The SSCP technique is a useful and inexpensive alternative to other SNP or Indel detection techniques for saturating the common bean genetic map with functional markers that may be useful in marker assisted selection. In addition, the genetic markers based on ESTs allowed the construction

  14. Single strand conformation polymorphism based SNP and Indel markers for genetic mapping and synteny analysis of common bean (Phaseolus vulgaris L.).

    Galeano, Carlos H; Fernández, Andrea C; Gómez, Marcela; Blair, Matthew W

    2009-12-23

    Expressed sequence tags (ESTs) are an important source of gene-based markers such as those based on insertion-deletions (Indels) or single-nucleotide polymorphisms (SNPs). Several gel based methods have been reported for the detection of sequence variants, however they have not been widely exploited in common bean, an important legume crop of the developing world. The objectives of this project were to develop and map EST based markers using analysis of single strand conformation polymorphisms (SSCPs), to create a transcript map for common bean and to compare synteny of the common bean map with sequenced chromosomes of other legumes. A set of 418 EST based amplicons were evaluated for parental polymorphisms using the SSCP technique and 26% of these presented a clear conformational or size polymorphism between Andean and Mesoamerican genotypes. The amplicon based markers were then used for genetic mapping with segregation analysis performed in the DOR364 x G19833 recombinant inbred line (RIL) population. A total of 118 new marker loci were placed into an integrated molecular map for common bean consisting of 288 markers. Of these, 218 were used for synteny analysis and 186 presented homology with segments of the soybean genome with an e-value lower than 7 x 10-12. The synteny analysis with soybean showed a mosaic pattern of syntenic blocks with most segments of any one common bean linkage group associated with two soybean chromosomes. The analysis with Medicago truncatula and Lotus japonicus presented fewer syntenic regions consistent with the more distant phylogenetic relationship between the galegoid and phaseoloid legumes. The SSCP technique is a useful and inexpensive alternative to other SNP or Indel detection techniques for saturating the common bean genetic map with functional markers that may be useful in marker assisted selection. In addition, the genetic markers based on ESTs allowed the construction of a transcript map and given their high conservation

  15. Genomic Characterization of DArT Markers Based on High-Density Linkage Analysis and Physical Mapping to the Eucalyptus Genome

    Petroli, César D.; Sansaloni, Carolina P.; Carling, Jason; Steane, Dorothy A.; Vaillancourt, René E.; Myburg, Alexander A.; da Silva, Orzenil Bonfim; Pappas, Georgios Joannis; Kilian, Andrzej; Grattapaglia, Dario

    2012-01-01

    Diversity Arrays Technology (DArT) provides a robust, high throughput, cost-effective method to query thousands of sequence polymorphisms in a single assay. Despite the extensive use of this genotyping platform for numerous plant species, little is known regarding the sequence attributes and genome-wide distribution of DArT markers. We investigated the genomic properties of the 7,680 DArT marker probes of a Eucalyptus array, by sequencing them, constructing a high density linkage map and carrying out detailed physical mapping analyses to the Eucalyptus grandis reference genome. A consensus linkage map with 2,274 DArT markers anchored to 210 microsatellites and a framework map, with improved support for ordering, displayed extensive collinearity with the genome sequence. Only 1.4 Mbp of the 75 Mbp of still unplaced scaffold sequence was captured by 45 linkage mapped but physically unaligned markers to the 11 main Eucalyptus pseudochromosomes, providing compelling evidence for the quality and completeness of the current Eucalyptus genome assembly. A highly significant correspondence was found between the locations of DArT markers and predicted gene models, while most of the 89 DArT probes unaligned to the genome correspond to sequences likely absent in E. grandis, consistent with the pan-genomic feature of this multi-Eucalyptus species DArT array. These comprehensive linkage-to-physical mapping analyses provide novel data regarding the genomic attributes of DArT markers in plant genomes in general and for Eucalyptus in particular. DArT markers preferentially target the gene space and display a largely homogeneous distribution across the genome, thereby providing superb coverage for mapping and genome-wide applications in breeding and diversity studies. Data reported on these ubiquitous properties of DArT markers will be particularly valuable to researchers working on less-studied crop species who already count on DArT genotyping arrays but for which no reference

  16. Genomic characterization of DArT markers based on high-density linkage analysis and physical mapping to the Eucalyptus genome.

    César D Petroli

    Full Text Available Diversity Arrays Technology (DArT provides a robust, high throughput, cost-effective method to query thousands of sequence polymorphisms in a single assay. Despite the extensive use of this genotyping platform for numerous plant species, little is known regarding the sequence attributes and genome-wide distribution of DArT markers. We investigated the genomic properties of the 7,680 DArT marker probes of a Eucalyptus array, by sequencing them, constructing a high density linkage map and carrying out detailed physical mapping analyses to the Eucalyptus grandis reference genome. A consensus linkage map with 2,274 DArT markers anchored to 210 microsatellites and a framework map, with improved support for ordering, displayed extensive collinearity with the genome sequence. Only 1.4 Mbp of the 75 Mbp of still unplaced scaffold sequence was captured by 45 linkage mapped but physically unaligned markers to the 11 main Eucalyptus pseudochromosomes, providing compelling evidence for the quality and completeness of the current Eucalyptus genome assembly. A highly significant correspondence was found between the locations of DArT markers and predicted gene models, while most of the 89 DArT probes unaligned to the genome correspond to sequences likely absent in E. grandis, consistent with the pan-genomic feature of this multi-Eucalyptus species DArT array. These comprehensive linkage-to-physical mapping analyses provide novel data regarding the genomic attributes of DArT markers in plant genomes in general and for Eucalyptus in particular. DArT markers preferentially target the gene space and display a largely homogeneous distribution across the genome, thereby providing superb coverage for mapping and genome-wide applications in breeding and diversity studies. Data reported on these ubiquitous properties of DArT markers will be particularly valuable to researchers working on less-studied crop species who already count on DArT genotyping arrays but for

  17. Symbolic dynamics and synchronization of coupled map networks with multiple delays

    Atay, Fatihcan M.; Jalan, Sarika; Jost, Juergen

    2010-01-01

    We use symbolic dynamics to study discrete-time dynamical systems with multiple time delays. We exploit the concept of avoiding sets, which arise from specific non-generating partitions of the phase space and restrict the occurrence of certain symbol sequences related to the characteristics of the dynamics. In particular, we show that the resulting forbidden sequences are closely related to the time delays in the system. We present two applications to coupled map lattices, namely (1) detecting synchronization and (2) determining unknown values of the transmission delays in networks with possibly directed and weighted connections and measurement noise. The method is applicable to multi-dimensional as well as set-valued maps, and to networks with time-varying delays and connection structure.

  18. Multiple reaction monitoring targeted LC-MS analysis of potential cell death marker proteins for increased bioprocess control.

    Albrecht, Simone; Kaisermayer, Christian; Reinhart, David; Ambrose, Monica; Kunert, Renate; Lindeberg, Anna; Bones, Jonathan

    2018-05-01

    The monitoring of protein biomarkers for the early prediction of cell stress and death is a valuable tool for process characterization and efficient biomanufacturing control. A representative set of six proteins, namely GPDH, PRDX1, LGALS1, CFL1, TAGLN2 and MDH, which were identified in a previous CHO-K1 cell death model using discovery LC-MS E was translated into a targeted liquid chromatography multiple reaction monitoring mass spectrometry (LC-MRM-MS) platform and verified. The universality of the markers was confirmed in a cell growth model for which three Chinese hamster ovary host cell lines (CHO-K1, CHO-S, CHO-DG44) were grown in batch culture in two different types of basal media. LC-MRM-MS was also applied to spent media (n = 39) from four perfusion biomanufacturing series. Stable isotope-labelled peptide analogues and a stable isotope-labelled monoclonal antibody were used for improved protein quantitation and simultaneous monitoring of the workflow reproducibility. Significant increases in protein concentrations were observed for all viability marker proteins upon increased dead cell numbers and allowed for discrimination of spent media with dead cell densities below and above 1 × 10 6  dead cells/mL which highlights the potential of the selected viability marker proteins in bioprocess control. Graphical abstract Overview of the LC-MRM-MS workflow for the determination of proteomic markers in conditioned media from the bioreactor that correlate with CHO cell death.

  19. Inhibition of DEPDC1A, a bad prognostic marker in multiple myeloma, delays growth and induces mature plasma cell markers in malignant plasma cells.

    Alboukadel Kassambara

    Full Text Available High throughput DNA microarray has made it possible to outline genes whose expression in malignant plasma cells is associated with short overall survival of patients with Multiple Myeloma (MM. A further step is to elucidate the mechanisms encoded by these genes yielding to drug resistance and/or patients' short survival. We focus here on the biological role of the DEP (for Disheveled, EGL-10, Pleckstrin domain contained protein 1A (DEPDC1A, a poorly known protein encoded by DEPDC1A gene, whose high expression in malignant plasma cells is associated with short survival of patients. Using conditional lentiviral vector delivery of DEPDC1A shRNA, we report that DEPDC1A knockdown delayed the growth of human myeloma cell lines (HMCLs, with a block in G2 phase of the cell cycle, p53 phosphorylation and stabilization, and p21(Cip1 accumulation. DEPDC1A knockdown also resulted in increased expression of mature plasma cell markers, including CXCR4, IL6-R and CD38. Thus DEPDC1A could contribute to the plasmablast features of MMCs found in some patients with adverse prognosis, blocking the differentiation of malignant plasma cells and promoting cell cycle.

  20. A temporal study on #betta#2-microglobulin as marker for diagnosis and monitoring of multiple myeloma

    Neri, B.

    1982-01-01

    The most important objective carried on, in the field of oncology has been the finding of new means to improve diagnosis and monitoring of neoplastic diseases. So we have chronobiologically studied the behaviour of #betta# 2 -microglobulin, in three groups of patients: Group A: 11 healthy subjects; Group B: 11 untreated patients with multiple myeloma and Group C: 11 multiple myeloma patients, after treatment with polychemoterapy. #betta# 2 -microglobulin, was assayed in serum obtained at six consecutive 4-hourly intervals, by radioimmunoassay, the levels and the various rhythm parameters were analyzed by ''Group mean cosinor'' test. The data suggest, that a circadian rhythm for #betta# 2 -microglobulin in the three groups is not detectable; but ''mesor test'' establishes significant differences (p 2 -microglobulin, in diagnosis and monitoring of multiple myeloma, is suggested

  1. Mapping vulnerability to multiple stressors: climate change and globalization in India

    O' Brien, Karen; Aandahl, Guro; Tompkins, Heather [CICERO, Oslo (NO)] (and others)

    2004-12-01

    There is growing recognition in the human dimensions research community that climate change impact studies must take into account the effects of other ongoing global changes. Yet there has been no systematic methodology to study climate change vulnerability in the context of multiple stressors. Using the example of Indian agriculture, this paper presents a methodology for investigating regional vulnerability to climate change in combination with other global stressors. This method, which relies on both vulnerability mapping and local- level case studies, may be used to assess differential vulnerability for any particular sector within a nation or region, and it can serve as a basis for targeting policy interventions. (Author)

  2. Clustering Multiple Sclerosis Subgroups with Multifractal Methods and Self-Organizing Map Algorithm

    Karaca, Yeliz; Cattani, Carlo

    Magnetic resonance imaging (MRI) is the most sensitive method to detect chronic nervous system diseases such as multiple sclerosis (MS). In this paper, Brownian motion Hölder regularity functions (polynomial, periodic (sine), exponential) for 2D image, such as multifractal methods were applied to MR brain images, aiming to easily identify distressed regions, in MS patients. With these regions, we have proposed an MS classification based on the multifractal method by using the Self-Organizing Map (SOM) algorithm. Thus, we obtained a cluster analysis by identifying pixels from distressed regions in MR images through multifractal methods and by diagnosing subgroups of MS patients through artificial neural networks.

  3. Verification of the utility of molecular markers linked to the multiple ...

    GREGORY

    2010-08-30

    Aug 30, 2010 ... Feng Hui*, Wang Lili, Wei Peng, Liu Zhiyong, Li Chengyu, Wang Yugang, Ji Ruiqin and Zhang. Huaqing ..... Chin. Agric. Sci. Bull. 22: 377-379. Li CY, Feng H, Wei P, Wang LL, Zhang J, Yang HN, Jiang N (2009). Directional transfer of the genic multiple allele inherited male sterile line in Chinese cabbage.

  4. Biochemical markers of bone metabolism reflect osteoclastic and osteoblastic activity in multiple myeloma

    Abildgaard, N; Glerup, H; Rungby, Jørgen

    2000-01-01

    In order to evaluate the use of recently developed assays of bone metabolism in multiple myeloma we performed a histomorphometric study of bone biopsies in 16 myeloma patients. Furthermore, we measured the levels of interleukin-6 (IL-6), soluble IL-6 receptor (IL-6sR), IL-1beta, tumour necrosis f...

  5. A novel Multiple-Marker Method for the Early Diagnosis of Oral Squamous Cell Carcinoma

    Jutta Ries

    2009-01-01

    Full Text Available Objective: Melanoma associated antigens-A (MAGE-A expression is highly specific to cancer cells. Thus, they can be the most suitable targets for the diagnosis of malignancy. The aim of this study was to evaluate the sensitivity of multiple MAGE-A expression analysis for the diagnosis of oral squamous cell carcinoma (OSCC.

  6. Linkage Map of a Gene Controlling Zero Tannins (zt-1 in Faba Bean (Vicia faba L. with SSR and ISSR Markers

    Wanwei Hou

    2018-05-01

    Full Text Available Faba bean (Vicia faba L., a partially allogamous species, is rich in protein. Condensed tannins limit the use of faba beans as food and feed. Two recessive genes, zt-1 and zt-2, control the zero tannin content in faba bean and promote a white flower phenotype. To determine the inheritance and develop a linkage map for the zt-1 gene in the faba bean germplasm M3290, F2 and F3 progenies were derived from the purple flower and high tannin content genotypes Qinghai12 and zt-1 line M3290, respectively. Genetic analysis verified a single recessive gene for zero tannin content and flower colour. In total, 596 SSR markers and 100 ISSR markers were used to test the polymorphisms between the parents and bulks for the contrasting flower colour via Bulked Segregant Analysis (BSA. Subsequently, six SSR markers and seven ISSR markers were used to genotype the entire 413 F2 population. Linkage analysis showed that the zt-1 gene was closely linked to the SSR markers SSR84 and M78, with genetic distances of 2.9 and 5.8 cM, respectively. The two flanked SSR markers were used to test 34 faba bean genotypes with different flower colours. The closely linked SSR marker SSR84 predicted the zt-1 genotypes with absolute accuracy. The results from the marker-assisted selection (MAS from this study could provide a solid foundation for further faba bean breeding programmes.

  7. Movement disorders in multiple sclerosis and neuromyelitis optica: A clinical marker of neurological disability.

    Candeias da Silva, Carolina; Bichuetti, Denis Bernardi; Azevedo Silva, Sonia Maria Cesar de; Ferraz, Henrique Ballalai; Oliveira, Enedina Maria Lobato de; Borges, Vanderci

    2018-03-03

    Movement disorders are not rare in demyelinating diseases but there are few studies comparing their frequency between multiple sclerosis and neuromyelitis optica spectrum disorder. Our aim was to determine the frequency and the related features of movement disorders in a cohort of patients with multiple sclerosis and neuromyelitis optica spectrum disorder. It is a cross-sectional study of patients with multiple sclerosis and neuromyelitis optica spectrum disorder. Patients were evaluated by a movement disorder specialist. Data from a personal interview and neurological examination were collected. Fahn-Tolosa-Marin tremor rating scale was used for tremor evaluation. Health-related quality of life was assessed using EuroQol instrument. Two hundred fifty-three patients were included (mean [SD] age, 40 [12] years; 74.3% female; median [IQR] EDSS score 2.5 [1.0-6.0]); 26% presented with movement disorders. Paroxysmal dystonia (n = 32) and tremor (n = 27) were the most common movement disorders. Patients with multiple sclerosis and low Expanded Disability Status Scale score (below 4.0) have fewer movement disorders than patients with neuromyelitis optica spectrum disorder. The diagnosis of neuromyelitis optica spectrum disorder was strongly associated with paroxysmal dystonia (OR = 22.07, 95% CI = 2.56-189.78; p = 0.005). Patients with multiple sclerosis and patients without movement disorders have a slightly better quality of life. Paroxysmal dystonia was the most common movement disorder in demyelinating diseases and strongly associated with neuromyelitis optica spectrum disorder. Copyright © 2018 Elsevier Ltd. All rights reserved.

  8. Experimental Evaluation of Multi-Round Matrix Multiplication on MapReduce

    Ceccarello, Matteo; Silvestri, Francesco

    2015-01-01

    required by reduce functions. Then, we present an extensive study of this library on an in-house cluster and on Amazon Web Services aiming at showing its performance and at comparing monolithic and multi-round approaches. The experiments show that, even without a low level optimization, it is possible...... not be the best approach in cloud systems. Indeed, multi-round algorithms may exploit some features of cloud platforms by suitably setting the round number according to the execution context. In this paper we carry out an experimental study of multi-round MapReduce algorithms aiming at investigating...... the performance of the multi-round approach. We use matrix multiplication as a case study. We first propose a scalable Hadoop library, named M3, for matrix multiplication in the dense and sparse cases which allows to tradeoff round number with the amount of data shuffled in each round and the amount of memory...

  9. The first genetic map of a synthesized allohexaploid Brassica with A, B and C genomes based on simple sequence repeat markers.

    Yang, S; Chen, S; Geng, X X; Yan, G; Li, Z Y; Meng, J L; Cowling, W A; Zhou, W J

    2016-04-01

    We present the first genetic map of an allohexaploid Brassica species, based on segregating microsatellite markers in a doubled haploid mapping population generated from a hybrid between two hexaploid parents. This study reports the first genetic map of trigenomic Brassica. A doubled haploid mapping population consisting of 189 lines was obtained via microspore culture from a hybrid H16-1 derived from a cross between two allohexaploid Brassica lines (7H170-1 and Y54-2). Simple sequence repeat primer pairs specific to the A genome (107), B genome (44) and C genome (109) were used to construct a genetic linkage map of the population. Twenty-seven linkage groups were resolved from 274 polymorphic loci on the A genome (109), B genome (49) and C genome (116) covering a total genetic distance of 3178.8 cM with an average distance between markers of 11.60 cM. This is the first genetic framework map for the artificially synthesized Brassica allohexaploids. The linkage groups represent the expected complement of chromosomes in the A, B and C genomes from the original diploid and tetraploid parents. This framework linkage map will be valuable for QTL analysis and future genetic improvement of a new allohexaploid Brassica species, and in improving our understanding of the genetic control of meiosis in new polyploids.

  10. Differential intrathecal inflammatory markers in acute optic neuritis and later conversion to multiple sclerosis

    Olesen, Mads Nikolaj; Soelberg, Kerstin; Nilsson, Anna Christine

    Background: Optic neuritis (ON) is often an early inflammatory, demyelinating event of multiple sclerosis (MS). We proffer that cytokine and chemokine profiles may (a) differ between patients with MS-related ON and those with non-MS-related ON and (b) predict conversion to MS in patients presenting......-up compared to those who had not. These findings are of potential relevance to our understanding of the pathogenesis of MS and may predict conversion of ON to MS....

  11. Genome-wide linkage mapping of yield-related traits in three Chinese bread wheat populations using high-density SNP markers.

    Li, Faji; Wen, Weie; He, Zhonghu; Liu, Jindong; Jin, Hui; Cao, Shuanghe; Geng, Hongwei; Yan, Jun; Zhang, Pingzhi; Wan, Yingxiu; Xia, Xianchun

    2018-06-01

    We identified 21 new and stable QTL, and 11 QTL clusters for yield-related traits in three bread wheat populations using the wheat 90 K SNP assay. Identification of quantitative trait loci (QTL) for yield-related traits and closely linked molecular markers is important in order to identify gene/QTL for marker-assisted selection (MAS) in wheat breeding. The objectives of the present study were to identify QTL for yield-related traits and dissect the relationships among different traits in three wheat recombinant inbred line (RIL) populations derived from crosses Doumai × Shi 4185 (D × S), Gaocheng 8901 × Zhoumai 16 (G × Z) and Linmai 2 × Zhong 892 (L × Z). Using the available high-density linkage maps previously constructed with the wheat 90 K iSelect single nucleotide polymorphism (SNP) array, 65, 46 and 53 QTL for 12 traits were identified in the three RIL populations, respectively. Among them, 34, 23 and 27 were likely to be new QTL. Eighteen common QTL were detected across two or three populations. Eleven QTL clusters harboring multiple QTL were detected in different populations, and the interval 15.5-32.3 cM around the Rht-B1 locus on chromosome 4BS harboring 20 QTL is an important region determining grain yield (GY). Thousand-kernel weight (TKW) is significantly affected by kernel width and plant height (PH), whereas flag leaf width can be used to select lines with large kernel number per spike. Eleven candidate genes were identified, including eight cloned genes for kernel, heading date (HD) and PH-related traits as well as predicted genes for TKW, spike length and HD. The closest SNP markers of stable QTL or QTL clusters can be used for MAS in wheat breeding using kompetitive allele-specific PCR or semi-thermal asymmetric reverse PCR assays for improvement of GY.

  12. Fine mapping of breast cancer genome-wide association studies loci in women of African ancestry identifies novel susceptibility markers.

    Zheng, Yonglan; Ogundiran, Temidayo O; Falusi, Adeyinka G; Nathanson, Katherine L; John, Esther M; Hennis, Anselm J M; Ambs, Stefan; Domchek, Susan M; Rebbeck, Timothy R; Simon, Michael S; Nemesure, Barbara; Wu, Suh-Yuh; Leske, Maria Cristina; Odetunde, Abayomi; Niu, Qun; Zhang, Jing; Afolabi, Chibuzor; Gamazon, Eric R; Cox, Nancy J; Olopade, Christopher O; Olopade, Olufunmilayo I; Huo, Dezheng

    2013-07-01

    Numerous single nucleotide polymorphisms (SNPs) associated with breast cancer susceptibility have been identified by genome-wide association studies (GWAS). However, these SNPs were primarily discovered and validated in women of European and Asian ancestry. Because linkage disequilibrium is ancestry-dependent and heterogeneous among racial/ethnic populations, we evaluated common genetic variants at 22 GWAS-identified breast cancer susceptibility loci in a pooled sample of 1502 breast cancer cases and 1378 controls of African ancestry. None of the 22 GWAS index SNPs could be validated, challenging the direct generalizability of breast cancer risk variants identified in Caucasians or Asians to other populations. Novel breast cancer risk variants for women of African ancestry were identified in regions including 5p12 (odds ratio [OR] = 1.40, 95% confidence interval [CI] = 1.11-1.76; P = 0.004), 5q11.2 (OR = 1.22, 95% CI = 1.09-1.36; P = 0.00053) and 10p15.1 (OR = 1.22, 95% CI = 1.08-1.38; P = 0.0015). We also found positive association signals in three regions (6q25.1, 10q26.13 and 16q12.1-q12.2) previously confirmed by fine mapping in women of African ancestry. In addition, polygenic model indicated that eight best markers in this study, compared with 22 GWAS-identified SNPs, could better predict breast cancer risk in women of African ancestry (per-allele OR = 1.21, 95% CI = 1.16-1.27; P = 9.7 × 10(-16)). Our results demonstrate that fine mapping is a powerful approach to better characterize the breast cancer risk alleles in diverse populations. Future studies and new GWAS in women of African ancestry hold promise to discover additional variants for breast cancer susceptibility with clinical implications throughout the African diaspora.

  13. The application of GBS markers for extending the dense genetic map of rye (Secale cereale L.) and the localization of the Rfc1 gene restoring male fertility in plants with the C source of sterility-inducing cytoplasm.

    Milczarski, Paweł; Hanek, Monika; Tyrka, Mirosław; Stojałowski, Stefan

    2016-11-01

    Genotyping by sequencing (GBS) is an efficient method of genotyping in numerous plant species. One of the crucial steps toward the application of GBS markers in crop improvement is anchoring them on particular chromosomes. In rye (Secale cereale L.), chromosomal localization of GBS markers has not yet been reported. In this paper, the application of GBS markers generated by the DArTseq platform for extending the high-density map of rye is presented. Additionally, their application is used for the localization of the Rfc1 gene that restores male fertility in plants with the C source of sterility-inducing cytoplasm. The total number of markers anchored on the current version of the map is 19,081, of which 18,132 were obtained from the DArTseq platform. Numerous markers co-segregated within the studied mapping population, so, finally, only 3397 unique positions were located on the map of all seven rye chromosomes. The total length of the map is 1593 cM and the average distance between markers is 0.47 cM. In spite of the resolution of the map being not very high, it should be a useful tool for further studies of the Secale cereale genome because of the presence on this map of numerous GBS markers anchored for the first time on rye chromosomes. The Rfc1 gene was located on high-density maps of the long arm of the 4R chromosome obtained for two mapping populations. Genetic maps were composed of DArT, DArTseq, and PCR-based markers. Consistent mapping results were obtained and DArTs tightly linked to the Rfc1 gene were successfully applied for the development of six new PCR-based markers useful in marker-assisted selection.

  14. Real-time segmentation of multiple implanted cylindrical liver markers in kilovoltage and megavoltage x-ray images

    Fledelius, Walther; Worm, Esben Schjødt; Høyer, Morten

    2014-01-01

    (CBCT) projections, for real-time motion management. Thirteen patients treated with conformal stereotactic body radiation therapy in three fractions had 2-3 cylindrical gold markers implanted in the liver prior to treatment. At each fraction, the projection images of a pre-treatment CBCT scan were used...... for automatic generation of a 3D marker model that consisted of the size, orientation, and estimated 3D trajectory of each marker during the CBCT scan. The 3D marker model was used for real-time template based segmentation in subsequent x-ray images by projecting each marker's 3D shape and likely 3D motion...... range onto the imager plane. The segmentation was performed in intra-treatment kV images (526 marker traces, 92 097 marker projections) and MV images (88 marker traces, 22 382 marker projections), and in post-treatment CBCT projections (42 CBCT scans, 71 381 marker projections). 227 kV marker traces...

  15. Mapping of multiple criteria for priority setting of health interventions: an aid for decision makers

    Tromp Noor

    2012-12-01

    Full Text Available Abstract Background In rationing decisions in health, many criteria like costs, effectiveness, equity and feasibility concerns play a role. These criteria stem from different disciplines that all aim to inform health care rationing decisions, but a single underlying concept that incorporates all criteria does not yet exist. Therefore, we aim to develop a conceptual mapping of criteria, based on the World Health Organization’s Health Systems Performance and Health Systems Building Blocks frameworks. This map can be an aid to decision makers to identify the relevant criteria for priority setting in their specific context. Methods We made an inventory of all possible criteria for priority setting on the basis of literature review. We categorized the criteria according to both health system frameworks that spell out a country’s health system goals and input. We reason that the criteria that decision makers use in priority setting exercises are a direct manifestation of this. Results Our map includes thirty-one criteria that are distributed among five categories that reflect the goals of a health system (i.e. to improve level of health, fair distribution of health, responsiveness, social & financial risk protection and efficiency and leadership/governance one category that reflects feasibiliy based on the health system building blocks (i.e. service delivery, health care workforce , information, medical products, vaccines & technologies, financing and. Conclusions This conceptual mapping of criteria, based on well-established health system frameworks, will further develop the field of priority setting by assisting decision makers in the identification of multiple criteria for selection of health interventions.

  16. Quantifying Uncertainty in Flood Inundation Mapping Using Streamflow Ensembles and Multiple Hydraulic Modeling Techniques

    Hosseiny, S. M. H.; Zarzar, C.; Gomez, M.; Siddique, R.; Smith, V.; Mejia, A.; Demir, I.

    2016-12-01

    The National Water Model (NWM) provides a platform for operationalize nationwide flood inundation forecasting and mapping. The ability to model flood inundation on a national scale will provide invaluable information to decision makers and local emergency officials. Often, forecast products use deterministic model output to provide a visual representation of a single inundation scenario, which is subject to uncertainty from various sources. While this provides a straightforward representation of the potential inundation, the inherent uncertainty associated with the model output should be considered to optimize this tool for decision making support. The goal of this study is to produce ensembles of future flood inundation conditions (i.e. extent, depth, and velocity) to spatially quantify and visually assess uncertainties associated with the predicted flood inundation maps. The setting for this study is located in a highly urbanized watershed along the Darby Creek in Pennsylvania. A forecasting framework coupling the NWM with multiple hydraulic models was developed to produce a suite ensembles of future flood inundation predictions. Time lagged ensembles from the NWM short range forecasts were used to account for uncertainty associated with the hydrologic forecasts. The forecasts from the NWM were input to iRIC and HEC-RAS two-dimensional software packages, from which water extent, depth, and flow velocity were output. Quantifying the agreement between output ensembles for each forecast grid provided the uncertainty metrics for predicted flood water inundation extent, depth, and flow velocity. For visualization, a series of flood maps that display flood extent, water depth, and flow velocity along with the underlying uncertainty associated with each of the forecasted variables were produced. The results from this study demonstrate the potential to incorporate and visualize model uncertainties in flood inundation maps in order to identify the high flood risk zones.

  17. The involvement of multiple thrombogenic and atherogenic markers in premature coronary artery disease

    Antonio P. Mansur

    2013-12-01

    Full Text Available OBJECTIVE: To examine the association of atherogenic and thrombogenic markers and lymphotoxin-alfa gene mutations with the risk of premature coronary disease. METHODS: This cross-sectional, case-control, age-adjusted study was conducted in 336 patients with premature coronary disease (50% luminal reduction or a previous myocardial infarction. The laboratory data evaluated included thrombogenic factors (fibrinogen, protein C, protein S, and antithrombin III, atherogenic factors (glucose and lipid profiles, lipoprotein(a, and apolipoproteins AI and B, and lymphotoxin-alfa mutations. Genetic variability of lymphotoxin-alfa was determined by polymerase chain reaction analysis. RESULTS: Coronary disease patients exhibited lower concentrations of HDL-cholesterol and higher levels of glucose, lipoprotein(a, and protein S. The frequencies of AA, AG, and GG lymphotoxin-alfa mutation genotypes were 55.0%, 37.6%, and 7.4% for controls and 42.7%, 46.0%, and 11.3% for coronary disease patients (p = 0.02, respectively. Smoking, dyslipidemia, family history, and lipoprotein(a and lymphotoxin-alfa mutations in men were independent variables associated with coronary disease. The area under the curve (C-statistic increased from 0.779 to 0.802 (p<0.05 with the inclusion of lipoprotein(a and lymphotoxin-alfa mutations in the set of conventional risk factors. CONCLUSIONS: The inclusion of lipoprotein(a and lymphotoxin-alfa mutations in the set of conventional risk factors showed an additive but small increase in the risk prediction of premature coronary disease.

  18. Is serum neopterin level a marker of responsiveness to interferon beta-1a therapy in multiple sclerosis?

    Casoni, F; Merelli, E; Bedin, R; Sola, P; Bertolotto, A; Faglioni, P

    2004-01-01

    Interferon beta (INFbeta) may induce the expression of several proteins, including neopterin, considered a biological marker of INFbeta activity. The aim of this study was to determine the serum neopterin concentration at the beginning of, and during, IFNbeta-1a therapy in relapsing-remitting multiple sclerosis (r-r MS) patients, and to look for a possible correlation between protein synthesis and the clinical course of the disease. Thirteen r-r MS patients were treated with INFbeta-1a (i.m. 6 MIU/week) for 2 years. Blood samples for neopterin determinations were taken daily over a period of 1 week at the end of each 6 months of therapy, and tested for neutralizing antibodies (NABs). Neopterin levels peaked 24-48 h post-injection and returned to baseline after 120 h. After 1 year of therapy, four patients dropped out of the study because of progression of the disease: in these subjects a significant decrement of neopterin was observed. Neopterin baseline values were not found to decrease over the 2 years of therapy, and neopterin may be considered to be a useful marker of responsiveness to IFNbeta.

  19. Mapping and marker-assisted selection of a brown planthopper resistance gene bph2 in rice (Oryza sativa L.).

    Sun, Li-Hong; Wang, Chun-Ming; Su, Chang-Chao; Liu, Yu-Qiang; Zhai, Hu-Qu; Wan, Jian-Min

    2006-08-01

    Nilaparvata lugens Stål (brown planthopper, BPH), is one of the major insect pests of rice (Oryza sativa L.) in the temperate rice-growing region. In this study, ASD7 harboring a BPH resistance gene bph2 was crossed to a susceptible cultivar C418, a japonica restorer line. BPH resistance was evaluated using 134 F2:3 lines derived from the cross between "ASD7" and "C418". SSR assay and linkage analysis were carried out to detect bph2. As a result, the resistant gene bph2 in ASD7 was successfully mapped between RM7102 and RM463 on the long arm of chromosome 12, with distances of 7.6 cM and 7.2 cM, respectively. Meanwhile, both phenotypic selection and marker-assisted selection (MAS) were conducted in the BC1F1 and BC2F1 populations. Selection efficiencies of RM7102 and RM463 were determined to be 89.9% and 91.2%, respectively. It would be very beneficial for BPH resistance improvement by using MAS of this gene.

  20. Turning is an important marker of balance confidence and walking limitation in persons with multiple sclerosis.

    Gautam Adusumilli

    Full Text Available The standard functional tool for gait assessment in multiple sclerosis (MS clinical trials has been the 25-Foot Timed Walk Test, a measure of gait speed. Straight-line gait assessment may not reflect adequately upon balance and coordination. Walking tests with turns may add additional information towards understanding gait and balance status, and be more reflective of ambulation in the community. Understanding the impact of turn parameters on patient-reported outcomes of balance and walking would help MS clinicians better formulate treatment plans for persons with gait limitations. In this study, ninety-one persons with MS (Expanded Disability Status Score; EDSS, range: 0-6.5 were enrolled in an initial cross-sectional study. Twenty-four subjects (EDSS, range:1.0-6.0 completed a follow-up visit an average of 12 months later. Spatiotemporal gait analysis was collected at both visits using APDM Opal wireless body-worn sensors while performing the Timed-Up-and-Go (TUG and 6-Minute Walk Test (6MWT. For both cross-sectional and longitudinal data, regression analyses determined the impact on the addition of turning parameters to stride velocity (SV, in the prediction of self-reported balance confidence (Activities-Specific Balance Confidence Scale (ABC and walking limitation (12-item Multiple Sclerosis Walking Scale (MSWS-12. The addition of 6MWT peak turn velocity (PTV to 6MWT SV increased the predictive power of the 6MWT for the ABC from 20% to 33%, and increased the predictive power from 28% to 41% for the MSWS-12. TUG PTV added to TUG SV also strengthened the relationship of the TUG for the ABC from 19% to 28%, and 27% to 36% for the MSWS-12. For those with 1 year follow-up, percent change in turn number of steps (TNS%Δ during the 6MWT added to 6MWT SV%Δ improved the modeling of ABC%Δ from 24% to 33%. 6MWT PTV%Δ added to 6MWT SV%Δ increased the predictive power of MSWS-12%Δ from 8% to 27%. Conclusively, turn parameters improved modeling of

  1. Development, genetic mapping and QTL association of cotton PHYA, PHYB, and HY5-specific CAPS and dCAPS markers

    Among SNP markers that become increasingly valuable in molecular breeding of crop plants are the CAP and dCAP markers derived from the genes of interest. To date, the number of such gene-based markers is small in polyploid crop plants such as tetraploid cotton that has A and D subgenomes. The obje...

  2. TRAM (Transcriptome Mapper: database-driven creation and analysis of transcriptome maps from multiple sources

    Danieli Gian

    2011-02-01

    clusters with differential expression during the differentiation toward megakaryocyte were identified. Conclusions TRAM is designed to create, and statistically analyze, quantitative transcriptome maps, based on gene expression data from multiple sources. The release includes FileMaker Pro database management runtime application and it is freely available at http://apollo11.isto.unibo.it/software/, along with preconfigured implementations for mapping of human, mouse and zebrafish transcriptomes.

  3. Exhaled Breath Markers for Nonimaging and Noninvasive Measures for Detection of Multiple Sclerosis.

    Broza, Yoav Y; Har-Shai, Lior; Jeries, Raneen; Cancilla, John C; Glass-Marmor, Lea; Lejbkowicz, Izabella; Torrecilla, José S; Yao, Xuelin; Feng, Xinliang; Narita, Akimitsu; Müllen, Klaus; Miller, Ariel; Haick, Hossam

    2017-11-15

    Multiple sclerosis (MS) is the most common chronic neurological disease affecting young adults. MS diagnosis is based on clinical characteristics and confirmed by examination of the cerebrospinal fluids (CSF) or by magnetic resonance imaging (MRI) of the brain or spinal cord or both. However, neither of the current diagnostic procedures are adequate as a routine tool to determine disease state. Thus, diagnostic biomarkers are needed. In the current study, a novel approach that could meet these expectations is presented. The approach is based on noninvasive analysis of volatile organic compounds (VOCs) in breath. Exhaled breath was collected from 204 participants, 146 MS and 58 healthy control individuals. Analysis was performed by gas-chromatography mass-spectrometry (GC-MS) and nanomaterial-based sensor array. Predictive models were derived from the sensors, using artificial neural networks (ANNs). GC-MS analysis revealed significant differences in VOC abundance between MS patients and controls. Sensor data analysis on training sets was able to discriminate in binary comparisons between MS patients and controls with accuracies up to 90%. Blinded sets showed 95% positive predictive value (PPV) between MS-remission and control, 100% sensitivity with 100% negative predictive value (NPV) between MS not-treated (NT) and control, and 86% NPV between relapse and control. Possible links between VOC biomarkers and the MS pathogenesis were established. Preliminary results suggest the applicability of a new nanotechnology-based method for MS diagnostics.

  4. Through-container, extremely low concentration detection of multiple chemical markers of counterfeit alcohol using a handheld SORS device.

    Ellis, David I; Eccles, Rebecca; Xu, Yun; Griffen, Julia; Muhamadali, Howbeer; Matousek, Pavel; Goodall, Ian; Goodacre, Royston

    2017-09-21

    Major food adulteration incidents occur with alarming frequency and are episodic, with the latest incident, involving the adulteration of meat from 21 producers in Brazil supplied to 60 other countries, reinforcing this view. Food fraud and counterfeiting involves all types of foods, feed, beverages, and packaging, with the potential for serious health, as well as significant economic and social impacts. In the spirit drinks sector, counterfeiters often 'recycle' used genuine packaging, or employ good quality simulants. To prove that suspect products are non-authentic ideally requires accurate, sensitive, analysis of the complex chemical composition while still in its packaging. This has yet to be achieved. Here, we have developed handheld spatially offset Raman spectroscopy (SORS) for the first time in a food or beverage product, and demonstrate the potential for rapid in situ through-container analysis; achieving unequivocal detection of multiple chemical markers known for their use in the adulteration and counterfeiting of Scotch whisky, and other spirit drinks. We demonstrate that it is possible to detect a total of 10 denaturants/additives in extremely low concentrations without any contact with the sample; discriminate between and within multiple well-known Scotch whisky brands, and detect methanol concentrations well below the maximum human tolerable level.

  5. Semiparametric Allelic Tests for Mapping Multiple Phenotypes: Binomial Regression and Mahalanobis Distance.

    Majumdar, Arunabha; Witte, John S; Ghosh, Saurabh

    2015-12-01

    Binary phenotypes commonly arise due to multiple underlying quantitative precursors and genetic variants may impact multiple traits in a pleiotropic manner. Hence, simultaneously analyzing such correlated traits may be more powerful than analyzing individual traits. Various genotype-level methods, e.g., MultiPhen (O'Reilly et al. []), have been developed to identify genetic factors underlying a multivariate phenotype. For univariate phenotypes, the usefulness and applicability of allele-level tests have been investigated. The test of allele frequency difference among cases and controls is commonly used for mapping case-control association. However, allelic methods for multivariate association mapping have not been studied much. In this article, we explore two allelic tests of multivariate association: one using a Binomial regression model based on inverted regression of genotype on phenotype (Binomial regression-based Association of Multivariate Phenotypes [BAMP]), and the other employing the Mahalanobis distance between two sample means of the multivariate phenotype vector for two alleles at a single-nucleotide polymorphism (Distance-based Association of Multivariate Phenotypes [DAMP]). These methods can incorporate both discrete and continuous phenotypes. Some theoretical properties for BAMP are studied. Using simulations, the power of the methods for detecting multivariate association is compared with the genotype-level test MultiPhen's. The allelic tests yield marginally higher power than MultiPhen for multivariate phenotypes. For one/two binary traits under recessive mode of inheritance, allelic tests are found to be substantially more powerful. All three tests are applied to two different real data and the results offer some support for the simulation study. We propose a hybrid approach for testing multivariate association that implements MultiPhen when Hardy-Weinberg Equilibrium (HWE) is violated and BAMP otherwise, because the allelic approaches assume HWE

  6. Evaluation of Multiple Kernel Learning Algorithms for Crop Mapping Using Satellite Image Time-Series Data

    Niazmardi, S.; Safari, A.; Homayouni, S.

    2017-09-01

    Crop mapping through classification of Satellite Image Time-Series (SITS) data can provide very valuable information for several agricultural applications, such as crop monitoring, yield estimation, and crop inventory. However, the SITS data classification is not straightforward. Because different images of a SITS data have different levels of information regarding the classification problems. Moreover, the SITS data is a four-dimensional data that cannot be classified using the conventional classification algorithms. To address these issues in this paper, we presented a classification strategy based on Multiple Kernel Learning (MKL) algorithms for SITS data classification. In this strategy, initially different kernels are constructed from different images of the SITS data and then they are combined into a composite kernel using the MKL algorithms. The composite kernel, once constructed, can be used for the classification of the data using the kernel-based classification algorithms. We compared the computational time and the classification performances of the proposed classification strategy using different MKL algorithms for the purpose of crop mapping. The considered MKL algorithms are: MKL-Sum, SimpleMKL, LPMKL and Group-Lasso MKL algorithms. The experimental tests of the proposed strategy on two SITS data sets, acquired by SPOT satellite sensors, showed that this strategy was able to provide better performances when compared to the standard classification algorithm. The results also showed that the optimization method of the used MKL algorithms affects both the computational time and classification accuracy of this strategy.

  7. An Approach for Predicting Essential Genes Using Multiple Homology Mapping and Machine Learning Algorithms.

    Hua, Hong-Li; Zhang, Fa-Zhan; Labena, Abraham Alemayehu; Dong, Chuan; Jin, Yan-Ting; Guo, Feng-Biao

    Investigation of essential genes is significant to comprehend the minimal gene sets of cell and discover potential drug targets. In this study, a novel approach based on multiple homology mapping and machine learning method was introduced to predict essential genes. We focused on 25 bacteria which have characterized essential genes. The predictions yielded the highest area under receiver operating characteristic (ROC) curve (AUC) of 0.9716 through tenfold cross-validation test. Proper features were utilized to construct models to make predictions in distantly related bacteria. The accuracy of predictions was evaluated via the consistency of predictions and known essential genes of target species. The highest AUC of 0.9552 and average AUC of 0.8314 were achieved when making predictions across organisms. An independent dataset from Synechococcus elongatus , which was released recently, was obtained for further assessment of the performance of our model. The AUC score of predictions is 0.7855, which is higher than other methods. This research presents that features obtained by homology mapping uniquely can achieve quite great or even better results than those integrated features. Meanwhile, the work indicates that machine learning-based method can assign more efficient weight coefficients than using empirical formula based on biological knowledge.

  8. Gains in QTL detection using an ultra-high density SNP map based on population sequencing relative to traditional RFLP/SSR markers.

    Huihui Yu

    Full Text Available Huge efforts have been invested in the last two decades to dissect the genetic bases of complex traits including yields of many crop plants, through quantitative trait locus (QTL analyses. However, almost all the studies were based on linkage maps constructed using low-throughput molecular markers, e.g. restriction fragment length polymorphisms (RFLPs and simple sequence repeats (SSRs, thus are mostly of low density and not able to provide precise and complete information about the numbers and locations of the genes or QTLs controlling the traits. In this study, we constructed an ultra-high density genetic map based on high quality single nucleotide polymorphisms (SNPs from low-coverage sequences of a recombinant inbred line (RIL population of rice, generated using new sequencing technology. The quality of the map was assessed by validating the positions of several cloned genes including GS3 and GW5/qSW5, two major QTLs for grain length and grain width respectively, and OsC1, a qualitative trait locus for pigmentation. In all the cases the loci could be precisely resolved to the bins where the genes are located, indicating high quality and accuracy of the map. The SNP map was used to perform QTL analysis for yield and three yield-component traits, number of tillers per plant, number of grains per panicle and grain weight, using data from field trials conducted over years, in comparison to QTL mapping based on RFLPs/SSRs. The SNP map detected more QTLs especially for grain weight, with precise map locations, demonstrating advantages in detecting power and resolution relative to the RFLP/SSR map. Thus this study provided an example for ultra-high density map construction using sequencing technology. Moreover, the results obtained are helpful for understanding the genetic bases of the yield traits and for fine mapping and cloning of QTLs.

  9. Pigmentary Markers in Danes--Associations with Quantitative Skin Colour, Nevi Count, Familial Atypical Multiple-Mole, and Melanoma Syndrome.

    Peter Johansen

    Full Text Available To investigate whether pigmentation genes involved in the melanogenic pathway (melanogenesis contributed to melanoma predisposition, we compared pigmentary genetics with quantitative skin pigmentation measurements, the number of atypical nevi, the total nevus count, and the familial atypical multiple mole and melanoma (FAMMM syndrome. We typed 32 pigmentary SNP markers and sequenced MC1R in 246 healthy individuals and 116 individuals attending periodic control for malignant melanoma development, 50 of which were diagnosed with FAMMM. It was observed that individuals with any two grouped MC1R variants (missense, NM_002386:c. 456C > A (p.TYR152*, or NM_002386:c.83_84insA (p.Asn29Glnfs*14 had significantly (p<0.001 lighter skin pigmentation of the upper-inner arm than those with none or one MC1R variant. We did not observe any significant association of the MC1R variants with constitutive pigmentation measured on the buttock area. We hypothesize that the effect of MC1R variants on arm pigmentation is primarily reflecting the inability to tan when subjected to UVR. A gender specific effect on skin pigmentation was also observed, and it was found that the skin pigmentation of females on average were darker than that of males (p<0.01. We conclude that MC1R variants are associated with quantitative skin colour in a lightly pigmented Danish population. We did not observe any association between any pigmentary marker and the FAMMM syndrome. We suggest that the genetics of FAMMM is not related to the genetics of the pigmentary pathway.

  10. Development and Characterization of Simple Sequence Repeat (SSR) Markers Based on RNA-Sequencing of Medicago sativa and In silico Mapping onto the M. truncatula Genome

    Wang, Zan; Yu, Guohui; Shi, Binbin; Wang, Xuemin; Qiang, Haiping; Gao, Hongwen

    2014-01-01

    Sufficient codominant genetic markers are needed for various genetic investigations in alfalfa since the species is an outcrossing autotetraploid. With the newly developed next generation sequencing technology, a large amount of transcribed sequences of alfalfa have been generated and are available for identifying SSR markers by data mining. A total of 54,278 alfalfa non-redundant unigenes were assembled through the Illumina HiSeqTM 2000 sequencing technology. Based on 3,903 unigene sequences, 4,493 SSRs were identified. Tri-nucleotide repeats (56.71%) were the most abundant motif class while AG/CT (21.7%), AGG/CCT (19.8%), AAC/GTT (10.3%), ATC/ATG (8.8%), and ACC/GGT (6.3%) were the subsequent top five nucleotide repeat motifs. Eight hundred and thirty- seven EST-SSR primer pairs were successfully designed. Of these, 527 (63%) primer pairs yielded clear and scored PCR products and 372 (70.6%) exhibited polymorphisms. High transferability was observed for ssp falcata at 99.2% (523) and 71.7% (378) in M. truncatula. In addition, 313 of 527 SSR marker sequences were in silico mapped onto the eight M. truncatula chromosomes. Thirty-six polymorphic SSR primer pairs were used in the genetic relatedness analysis of 30 Chinese alfalfa cultivated accessions generating a total of 199 scored alleles. The mean observed heterozygosity and polymorphic information content were 0.767 and 0.635, respectively. The codominant markers not only enriched the current resources of molecular markers in alfalfa, but also would facilitate targeted investigations in marker-trait association, QTL mapping, and genetic diversity analysis in alfalfa. PMID:24642969

  11. Senescence marker protein 30 (SMP30 expression in eukaryotic cells: existence of multiple species and membrane localization.

    Peethambaran Arun

    Full Text Available Senescence marker protein (SMP30, also known as regucalcin, is a 34 kDa cytosolic marker protein of aging which plays an important role in intracellular Ca(2+ homeostasis, ascorbic acid biosynthesis, oxidative stress, and detoxification of chemical warfare nerve agents. In our goal to investigate the activity of SMP30 for the detoxification of nerve agents, we have produced a recombinant adenovirus expressing human SMP30 as a fusion protein with a hemaglutinin tag (Ad-SMP30-HA. Ad-SMP30-HA transduced the expression of SMP30-HA and two additional forms of SMP30 with molecular sizes ∼28 kDa and 24 kDa in HEK-293A and C3A liver cells in a dose and time-dependent manner. Intravenous administration of Ad-SMP30-HA in mice results in the expression of all the three forms of SMP30 in the liver and diaphragm. LC-MS/MS results confirmed that the lower molecular weight 28 kDa and 24 kDa proteins are related to the 34 kDa SMP30. The 28 kDa and 24 kDa SMP30 forms were also detected in normal rat liver and mice injected with Ad-SMP30-HA suggesting that SMP30 does exist in multiple forms under physiological conditions. Time course experiments in both cell lines suggest that the 28 kDa and 24 kDa SMP30 forms are likely generated from the 34 kDa SMP30. Interestingly, the 28 kDa and 24 kDa SMP30 forms appeared initially in the cytosol and shifted to the particulate fraction. Studies using small molecule inhibitors of proteolytic pathways revealed the potential involvement of β and γ-secretases but not calpains, lysosomal proteases, proteasome and caspases. This is the first report describing the existence of multiple forms of SMP30, their preferential distribution to membranes and their generation through proteolysis possibly mediated by secretase enzymes.

  12. Development and amplification of multiple co-dominant genetic markers from single spores of arbuscular mycorrhizal fungi by nested multiplex PCR

    Holtgrewe-Stukenbrock, Eva; Rosendahl, Søren

    2005-01-01

    Multiple co-dominant genetic markers from single spores of the arbuscular mycorrhizal (AM) fungi Glomus mosseae, Glomus caledonium, and Glomus geosporum were amplified by nested multiplex PCR using a combination of primers for simultaneous amplification of five loci in one PCR. Subsequently, each...... marker was amplified separately in nested PCR using specific primers. Polymorphic loci within the three putative single copy genes GmFOX2, GmTOR2, and GmGIN1 were characterized by sequencing and single strand conformation polymorphisms (SSCP). Primers specific for the LSU rDNA D2 region were included...... are homokaryotic. All isolates of G. mosseae had unique genotypes. The amplification of multiple co-dominant genetic markers from single spores by the nested multiplex PCR approach provides an important tool for future studies of AM fungi population genetics and evolution....

  13. Integration of gene-based markers in a pearl millet genetic map for identification of candidate genes underlying drought tolerance quantitative trait loci

    Sehgal Deepmala

    2012-01-01

    Full Text Available Abstract Background Identification of genes underlying drought tolerance (DT quantitative trait loci (QTLs will facilitate understanding of molecular mechanisms of drought tolerance, and also will accelerate genetic improvement of pearl millet through marker-assisted selection. We report a map based on genes with assigned functional roles in plant adaptation to drought and other abiotic stresses and demonstrate its use in identifying candidate genes underlying a major DT-QTL. Results Seventy five single nucleotide polymorphism (SNP and conserved intron spanning primer (CISP markers were developed from available expressed sequence tags (ESTs using four genotypes, H 77/833-2, PRLT 2/89-33, ICMR 01029 and ICMR 01004, representing parents of two mapping populations. A total of 228 SNPs were obtained from 30.5 kb sequenced region resulting in a SNP frequency of 1/134 bp. The positions of major pearl millet linkage group (LG 2 DT-QTLs (reported from crosses H 77/833-2 × PRLT 2/89-33 and 841B × 863B were added to the present consensus function map which identified 18 genes, coding for PSI reaction center subunit III, PHYC, actin, alanine glyoxylate aminotransferase, uridylate kinase, acyl-CoA oxidase, dipeptidyl peptidase IV, MADS-box, serine/threonine protein kinase, ubiquitin conjugating enzyme, zinc finger C- × 8-C × 5-C × 3-H type, Hd3, acetyl CoA carboxylase, chlorophyll a/b binding protein, photolyase, protein phosphatase1 regulatory subunit SDS22 and two hypothetical proteins, co-mapping in this DT-QTL interval. Many of these candidate genes were found to have significant association with QTLs of grain yield, flowering time and leaf rolling under drought stress conditions. Conclusions We have exploited available pearl millet EST sequences to generate a mapped resource of seventy five new gene-based markers for pearl millet and demonstrated its use in identifying candidate genes underlying a major DT-QTL in this species. The reported gene

  14. Identification of markers that functionally define a quiescent multiple myeloma cell sub-population surviving bortezomib treatment

    Adomako, Alfred; Calvo, Veronica; Biran, Noa; Osman, Keren; Chari, Ajai; Paton, James C; Paton, Adrienne W; Moore, Kateri; Schewe, Denis M; Aguirre-Ghiso, Julio A

    2015-01-01

    The mechanisms allowing residual multiple myeloma (MM) cells to persist after bortezomib (Bz) treatment remain unclear. We hypothesized that studying the biology of bortezomib-surviving cells may reveal markers to identify these cells and survival signals to target and kill residual MM cells. We used H2B-GFP label retention, biochemical tools and in vitro and in vivo experiments to characterize growth arrest and the unfolded protein responses in quiescent Bz-surviving cells. We also tested the effect of a demethylating agent, 5-Azacytidine, on Bz-induced quiescence and whether inhibiting the chaperone GRP78/BiP (henceforth GRP78) with a specific toxin induced apoptosis in Bz-surviving cells. Finally, we used MM patient samples to test whether GRP78 levels might associate with disease progression. Statistical analysis employed t-test and Mann-Whitney tests at a 95% confidence. We report that Bz-surviving MM cells in vitro and in vivo enter quiescence characterized by p21 CIP1 upregulation. Bz-surviving MM cells also downregulated CDK6, Ki67 and P-Rb. H2B-GFP label retention showed that Bz-surviving MM cells are either slow-cycling or deeply quiescent. The Bz-induced quiescence was stabilized by low dose (500nM) of 5-azacytidine (Aza) pre-treatment, which also potentiated the initial Bz-induced apoptosis. We also found that expression of GRP78, an unfolded protein response (UPR) survival factor, persisted in MM quiescent cells. Importantly, GRP78 downregulation using a specific SubAB bacterial toxin killed Bz-surviving MM cells. Finally, quantification of Grp78 high /CD138+ MM cells from patients suggested that high levels correlated with progressive disease. We conclude that Bz-surviving MM cells display a GRP78 HIGH /p21 HIGH /CDK6 LOW /P-Rb LOW profile, and these markers may identify quiescent MM cells capable of fueling recurrences. We further conclude that Aza + Bz treatment of MM may represent a novel strategy to delay recurrences by enhancing Bz

  15. Comparative mapping of DNA markers from the familial Alzheimer disease and Down syndrome regions of human chromosome 21 to mouse chromosomes 16 and 17

    Cheng, S.V.; Nadeau, J.H.; Tanzi, R.E.; Watkins, P.C.; Jagadesh, J.; Taylor, B.A.; Haines, J.L.; Sacchi, N.; Gusella, J.F. (Harvard Medical School, Boston, MA (USA))

    1988-08-01

    Mouse trisomy 16 has been proposed as an animal model of Down syndrome (DS), since this chromosome contains homologues of several loci from the q22 band of human chromosome 21. The recent mapping of the defect causing familial Alzheimer disease (FAD) and the locus encoding the Alzheimer amyloid {beta} precursor protein (APP) to human chromosome 21 has prompted a more detailed examination of the extent of conservation of this linkage group between the two species. Using anonymous DNA probes and cloned genes from human chromosome 21 in a combination of recombinant inbred and interspecific mouse backcross analyses, the authors have established that the linkage group shared by mouse chromosome 16 includes not only the critical DS region of human chromosome 21 but also the APP gene and FAD-linked markers. Extending from the anonymous DNA locus D21S52 to ETS2, the linkage map of six loci spans 39% recombination in man but only 6.4% recombination in the mouse. A break in synteny occurs distal to ETS2, with the homologue of the human marker D21S56 mapping to mouse chromosome 17. Conservation of the linkage relationships of markers in the FAD region suggests that the murine homologue of the FAD locus probably maps to chromosome 16 and that detailed comparison of the corresponding region in both species could facilitate identification of the primary defect in this disorder. The break in synteny between the terminal portion of human chromosome 21 and mouse chromosome 16 indicates, however, that mouse trisomy 16 may not represent a complete model of DS.

  16. Comparative mapping of DNA markers from the familial Alzheimer disease and Down syndrome regions of human chromosome 21 to mouse chromosomes 16 and 17

    Cheng, S.V.; Nadeau, J.H.; Tanzi, R.E.; Watkins, P.C.; Jagadesh, J.; Taylor, B.A.; Haines, J.L.; Sacchi, N.; Gusella, J.F.

    1988-01-01

    Mouse trisomy 16 has been proposed as an animal model of Down syndrome (DS), since this chromosome contains homologues of several loci from the q22 band of human chromosome 21. The recent mapping of the defect causing familial Alzheimer disease (FAD) and the locus encoding the Alzheimer amyloid β precursor protein (APP) to human chromosome 21 has prompted a more detailed examination of the extent of conservation of this linkage group between the two species. Using anonymous DNA probes and cloned genes from human chromosome 21 in a combination of recombinant inbred and interspecific mouse backcross analyses, the authors have established that the linkage group shared by mouse chromosome 16 includes not only the critical DS region of human chromosome 21 but also the APP gene and FAD-linked markers. Extending from the anonymous DNA locus D21S52 to ETS2, the linkage map of six loci spans 39% recombination in man but only 6.4% recombination in the mouse. A break in synteny occurs distal to ETS2, with the homologue of the human marker D21S56 mapping to mouse chromosome 17. Conservation of the linkage relationships of markers in the FAD region suggests that the murine homologue of the FAD locus probably maps to chromosome 16 and that detailed comparison of the corresponding region in both species could facilitate identification of the primary defect in this disorder. The break in synteny between the terminal portion of human chromosome 21 and mouse chromosome 16 indicates, however, that mouse trisomy 16 may not represent a complete model of DS

  17. Gene prediction using the Self-Organizing Map: automatic generation of multiple gene models.

    Mahony, Shaun; McInerney, James O; Smith, Terry J; Golden, Aaron

    2004-03-05

    Many current gene prediction methods use only one model to represent protein-coding regions in a genome, and so are less likely to predict the location of genes that have an atypical sequence composition. It is likely that future improvements in gene finding will involve the development of methods that can adequately deal with intra-genomic compositional variation. This work explores a new approach to gene-prediction, based on the Self-Organizing Map, which has the ability to automatically identify multiple gene models within a genome. The current implementation, named RescueNet, uses relative synonymous codon usage as the indicator of protein-coding potential. While its raw accuracy rate can be less than other methods, RescueNet consistently identifies some genes that other methods do not, and should therefore be of interest to gene-prediction software developers and genome annotation teams alike. RescueNet is recommended for use in conjunction with, or as a complement to, other gene prediction methods.

  18. Social Identity Mapping: A procedure for visual representation and assessment of subjective multiple group memberships.

    Cruwys, Tegan; Steffens, Niklas K; Haslam, S Alexander; Haslam, Catherine; Jetten, Jolanda; Dingle, Genevieve A

    2016-12-01

    In this research, we introduce Social Identity Mapping (SIM) as a method for visually representing and assessing a person's subjective network of group memberships. To provide evidence of its utility, we report validating data from three studies (two longitudinal), involving student, community, and clinical samples, together comprising over 400 participants. Results indicate that SIM is easy to use, internally consistent, with good convergent and discriminant validity. Each study also illustrates the ways that SIM can be used to address a range of novel research questions. Study 1 shows that multiple positive group memberships are a particularly powerful predictor of well-being. Study 2 shows that social support is primarily given and received within social groups and that only in-group support is beneficial for well-being. Study 3 shows that improved mental health following a social group intervention is attributable to an increase in group compatibility. In this way, the studies demonstrate the capacity for SIM to make a contribution both to the development of social-psychological theory and to its practical application. © 2016 The British Psychological Society.

  19. MAPPING AND ASSESSING MULTIPLE ECOSYSTEM SERVICES IN AN ALPINE REGION: A STUDY IN TRENTINO, ITALY

    M. Ferrari

    2014-04-01

    Full Text Available This research aims to identify ecosystem services relevant for Trentino (a region in the Italian Alps, and to assess them through spatial indicators. 51 experts were involved in the identification of relevant ecosystem services and appropriate indicators to represent them. Indicators were computed using the database available at administrative level. Indicators represent the actual or the potential supply of ecosystem services, expressed in terms of either stock or flow. Moreover, indicators may refer to biophysical, economic or socio-cultural values. In total, the experts selected 25 ecosystem services and 57 assessment indicators. Accordingly, the selected indicators were mapped over different spatial units of ecosystem services representation, including land use and forest types. This research was the first attempt to assess a multiple set of ecosystem services for Trentino. The results provide new information that can be used to achieve the objectives of the EU Biodiversity Strategy by 2014. The proposed approach can be reasonably extended to other Alpine areas with similar morphology, land cover and land use.

  20. 'Hybrid' multiple mapping conditioning on passive and reactive scalars

    Cleary, M.J.; Kronenburg, A. [Department of Mechanical Engineering, Imperial College London, London SW7 2AZ (United Kingdom)

    2007-12-15

    A two-dimensional, hybridized multiple mapping conditioning (MMC) model is used to model local extinction and reignition phenomena in homogeneous, isotropic decaying turbulence. The equations are solved in a prescribed, jointly Gaussian reference space with stochastic reference variables emulating the fluctuations of the mixture fraction and normalized sensible enthalpy conditioning variables. In ''pure'' MMC the joint PDF of the conditioning scalars is a solved quantity. Here we use a hybrid method where the time evolution of the marginal PDF for mixture fraction is solved and a presumed {beta}-PDF is used for the conditional distribution of the normalized sensible enthalpy. Model results are compared with DNS in three flame cases with varying levels of local extinction, up to global extinction. Results for principal chemical species are in very good agreement with DNS and those for intermediate species are also satisfactory. The doubly conditioned MMC yields results which are considerably more accurate than those by modeling with conditioning on mixture fraction alone. A transformation of the Gaussian reference space casts the MMC model in the same form as conditional moment closure (CMC). The great advantage is that the MMC model contains the doubly conditioned scalar dissipation terms in closed form and these are generally found to be in good agreement with the DNS data. (author)

  1. Inverse identification of intensity distributions from multiple flux maps in concentrating solar applications

    Erickson, Ben; Petrasch, Jörg

    2012-01-01

    Radiative flux measurements at the focal plane of solar concentrators are typically performed using digital cameras in conjunction with Lambertian targets. To accurately predict flux distributions on arbitrary receiver geometries directional information about the radiation is required. Currently, the directional characteristics of solar concentrating systems are predicted via ray tracing simulations. No direct experimental technique to determine intensities of concentrating solar systems is available. In the current paper, multiple parallel flux measurements at varying distances from the focal plane together with a linear inverse method and Tikhonov regularization are used to identify the directional and spatial intensity distribution at the solution plane. The directional binning feature of an in-house Monte Carlo ray tracing program is used to provide a reference solution. The method has been successfully applied to two-dimensional concentrators, namely parabolic troughs and elliptical troughs using forward Monte Carlo ray tracing simulations that provide the flux maps as well as consistent, associated intensity distribution for validation. In the two-dimensional case, intensity distributions obtained from the inverse method approach the Monte Carlo forward solution. In contrast, the method has not been successful for three dimensional and circular symmetric concentrator geometries.

  2. Right parietal cortex and calculation processing: intraoperative functional mapping of multiplication and addition in patients affected by a brain tumor.

    Della Puppa, Alessandro; De Pellegrin, Serena; d'Avella, Elena; Gioffrè, Giorgio; Munari, Marina; Saladini, Marina; Salillas, Elena; Scienza, Renato; Semenza, Carlo

    2013-11-01

    The role of parietal areas in number processing is well known. The significance of intraoperative functional mapping of these areas has been only partially explored, however, and only a few discordant data are available in the surgical literature with regard to the right parietal lobe. The purpose of this study was to evaluate the clinical impact of simple calculation in cortical electrostimulation of right-handed patients affected by a right parietal brain tumor. Calculation mapping in awake surgery was performed in 3 right-handed patients affected by high-grade gliomas located in the right parietal lobe. Preoperatively, none of the patients presented with calculation deficits. In all 3 cases, after sensorimotor and language mapping, cortical and intraparietal sulcus areas involved in single-digit multiplication and addition calculations were mapped using bipolar electrostimulation. In all patients, different sites of the right parietal cortex, mainly in the inferior lobule, were detected as being specifically related to calculation (multiplication or addition). In 2 patients the intraparietal sulcus was functionally specific for multiplication. No functional sites for language were detected. All sites functional for calculation were spared during tumor resection, which was complete in all cases without postoperative neurological deficits. These findings provide intraoperative data in support of an anatomofunctional organization for multiplication and addition within the right parietal area. Furthermore, the study shows the potential clinical relevance of intraoperative mapping of calculation in patients undergoing surgery in the right parietal area. Further and larger studies are needed to confirm these data and assess whether mapped areas are effectively essential for function.

  3. Values mapping with Latino forest users: Contributing to the dialogue on multiple land use conflict management

    Kelly Biedenweg; Lee Cerveny; Rebecca J. McLain

    2014-01-01

    Participatory mapping of landscape values is gaining ground as a method for engaging communities and stakeholders in natural resource management. Socio-spatial mapping allows the public to identify places of economic, social, cultural, or personal importance. In addition to providing data for planning and land management, the mapping process can open dialogue about...

  4. Effects of the number of markers per haplotype and clustering of haplotypes on the accuracy of QTL mapping and prediction of genomic breeding values

    Calus, M.P.L.; Meuwissen, T.H.E.; Windig, J.J.; Knol, E.F.; Schrooten, C.; Vereijken, A.L.J.; Veerkamp, R.F.

    2009-01-01

    The aim of this paper was to compare the effect of haplotype definition on the precision of QTL-mapping and on the accuracy of predicted genomic breeding values. In a multiple QTL model using identity-by-descent (IBD) probabilities between haplotypes, various haplotype definitions were tested i.e.

  5. Clinical value of assays of multiple serum tumor markers in conjunction with 18F-FDG SPECT for discriminating malignant from benign lung disorders

    Zhang Chunyan; Wang Linglong; Tu Liping; Yu Yuefang; Zhu Weijie; Cai Ao; Gao Shuxing

    2006-01-01

    Objective: To evaluate the clinical value of assays of multiple tumor markers in conjunction with 18 F-FDG SPECT for discriminating malignant from benign lung disorders. Methods: A total of 62 patients with malignant and benign lung diseases un- derwent 18 F-FDG SPECT examination and tests for serum tumor markers CEA, CA50, CA199 and CA242, alone or combined. The sensitivity, specificity, accuracy of these tests were examined. Results: The sensitivity, specificity accuracy of 18 F-FDG SPECT for the diagnosis of malignant lung tumors were 85.7 (30/35), 59.3 (16/27) and 74.2(46/62) respectively, those of each of serum CEA, CA199, CA50, CA242 levels in diagnosing malignant lung tumors were 22.9(8/35), 92.6(25/27), 59.7(33/62), 14.3(5/35), 100(27/27), 51.6 (32/62), 34.3 (12/35), 85.2 (23/27), 56.5 (35/62), 28.6 (10/35), 85.2 (23/27) and 53.2 (33/62) respectively, those of assays of multiple serum tumor markers for diagnosis of malignant lung tumors were 85.7 (30/35), 85.2 (23/27) and 85.5 (53/62) respectively, those of assays of multiple tumor markers in conjunction with 18 F-FDG SPECT for discriminating malignant from benign lung nodules were 88.6(31/35), 85.2(23/27) and 87.1 (54/62) respectively. Conclusion: Assays of multiple serum tumor markers in conjunction with 18 F-FDG SPECT for discriminating malignant from benign lung disorders can yield higher sensitivity, specialty and accuracy, making a significant contribution to clinical application. (authors)

  6. The use of biochemical markers of bone remodeling in multiple myeloma: a report of the International Myeloma Working Group

    Terpos, E; Dimopoulos, M A; Sezer, O

    2010-01-01

    progression and overall survival. Bone markers have also been used for the early diagnosis of bone lesions. This International Myeloma Working Group report summarizes the existing data for the role of bone markers in assessing the extent of MM bone disease and in monitoring bone turnover during anti...

  7. Repetitive, Marker-Free, Site-Specific Integration as a Novel Tool for Multiple Chromosomal Integration of DNA

    Petersen, Kia Vest; Martinussen, Jan; Jensen, Peter Ruhdal

    2013-01-01

    of a minimal bacterial attachment site (attBmin), two mutated loxP sequences (lox66 and lox71) allowing for removal of undesirable vector elements (antibiotic resistance marker), and a counterselection marker (oroP) for selection of loxP recombination on the pKV6 vector. When transformed into L. lactis...

  8. Clinically isolated syndrome. Prognostic markers for conversion to multiple sclerosis and initiation of disease-modifying therapy

    Kohriyama, Tatsuo

    2011-01-01

    Eighty-five percent of patients with multiple sclerosis (MS) initially present with a single demyelinating event, referred to as a clinically isolated syndrome (CIS) of the optic nerves, brainstem, or spinal cord. Following the onset of CIS, 38 to 68% of patients develop clinically definite MS (CDMS). Clinically silent brain lesions are seen on MRI in 50 to 80% of patients with CIS at first clinical presentation and 56 to 88% of CIS patients with abnormal MRI are at high risk of conversion to CDMS. Axonal damage, that is considered to underlie the development of persistent disability in MS, occurs in the CIS stage. Treatment with disease-modifying therapies (DMTs), that might prevent axonal damage and result in slowing the progression of disability, should be initiated early during the disease course. Clinical trials demonstrated that early treatment of CIS patients with the standard dose of interferon beta (IFNβ) significantly reduced the risk of progression to CDMS by 44 to 50%. After 5 years of follow-up, the results of the IFNβ treatment extension studies confirmed that the risk of conversion to CDMS was significantly reduced by 35 to 37% in patients receiving early treatment compared to that in those receiving delayed treatment. However, not every patient with CIS will progress to CDMS; the IFNβ treatment is appropriately indicated for CIS patients who are diagnosed with MS by McDonald diagnostic criteria based on MRI findings of dissemination in space and time and are at high risk for conversion to CDMS. Development of more reliable prognostic markers will enable DMTs to be targeted for those who are most likely to benefit. (author)

  9. Mapping of A1 conferring resistance to the aphid Amphorophora idaei and dw (dwarfing habit in red raspberry (Rubus idaeus L. using AFLP and microsatellite markers

    Knight Victoria H

    2007-03-01

    Full Text Available Abstract Background Raspberry breeding programmes worldwide aim to produce improved cultivars to satisfy market demands and within these programmes there are many targets, including increased fruit quality, yield and season, and improved pest and disease resistance and plant habit. The large raspberry aphid, Amphorophora idaei, transmits four viruses and vector resistance is an objective in raspberry breeding. The development of molecular tools that discriminate between aphid resistance genes from different sources will allow the pyramiding of such genes and the development of raspberry varieties with superior pest resistance. We have raised a red raspberry (Rubus idaeus F1 progeny from the cross 'Malling Jewel' × 'Malling Orion' (MJ × MO, which segregates for resistance to biotype 1 of the aphid Amphorophora idaei and for a second phenotypic trait, dwarf habit. These traits are controlled by single genes, denoted (A1 and (dw respectively. Results The progeny of 94 seedlings was scored for the segregation of 95 AFLP and 22 SSR markers and a linkage map was constructed that covers a total genetic distance of 505 cM over seven linkage groups. The average linkage group length was 72.2 cM and there was an average of 17 markers per linkage group, of which at least two were codominant SSRs, allowing comparisons with previously published maps of raspberry. The two phenotypic traits, A1 and dw, mapped to linkage groups 3 and 6 respectively. Conclusion The mapping of A1 will facilitate the discrimination of resistance genes from different sources and the pyramiding of aphid resistance genes in new raspberry cultivars; the mapping of dw will allow further investigations into the genetics of dwarfing habit in Rubus.

  10. Mapping compound cosmic telescopes containing multiple projected cluster-scale halos

    Ammons, S. Mark [Lawrence Livermore National Laboratory, Physics Division L-210, 7000 East Ave., Livermore, CA 94550 (United States); Wong, Kenneth C. [EACOA Fellow, Institute of Astronomy and Astrophysics, Academia Sinica (ASIAA), Taipei 10641, Taiwan (China); Zabludoff, Ann I. [Steward Observatory, University of Arizona, 933 Cherry Ave., Tucson, AZ 85721 (United States); Keeton, Charles R., E-mail: ammons1@llnl.gov, E-mail: kwong@as.arizona.edu, E-mail: aiz@email.arizona.edu, E-mail: keeton@physics.rutgers.edu [Department of Physics and Astronomy, Rutgers University, 136 Frelinghuysen Road, Piscataway, NJ 08854 (United States)

    2014-01-20

    Lines of sight with multiple projected cluster-scale gravitational lenses have high total masses and complex lens plane interactions that can boost the area of magnification, or étendue, making detection of faint background sources more likely than elsewhere. To identify these new 'compound' cosmic telescopes, we have found directions in the sky with the highest integrated mass densities, as traced by the projected concentrations of luminous red galaxies (LRGs). We use new galaxy spectroscopy to derive preliminary magnification maps for two such lines of sight with total mass exceeding ∼3 × 10{sup 15} M {sub ☉}. From 1151 MMT Hectospec spectra of galaxies down to i {sub AB} = 21.2, we identify two to three group- and cluster-scale halos in each beam. These are well traced by LRGs. The majority of the mass in beam J085007.6+360428 (0850) is contributed by Zwicky 1953, a massive cluster at z = 0.3774, whereas beam J130657.5+463219 (1306) is composed of three halos with virial masses of 6 × 10{sup 14}-2 × 10{sup 15} M {sub ☉}, one of which is A1682. The magnification maps derived from our mass models based on spectroscopy and Sloan Digital Sky Survey photometry alone display substantial étendue: the 68% confidence bands on the lens plane area with magnification exceeding 10 for a source plane of z{sub s} = 10 are [1.2, 3.8] arcmin{sup 2} for 0850 and [2.3, 6.7] arcmin{sup 2} for 1306. In deep Subaru Suprime-Cam imaging of beam 0850, we serendipitously discover a candidate multiply imaged V-dropout source at z {sub phot} = 5.03. The location of the candidate multiply imaged arcs is consistent with the critical curves for a source plane of z = 5.03 predicted by our mass model. Incorporating the position of the candidate multiply imaged galaxy as a constraint on the critical curve location in 0850 narrows the 68% confidence band on the lens plane area with μ > 10 and z{sub s} = 10 to [1.8, 4.2] arcmin{sup 2}, an étendue range comparable to that of

  11. Multiple Origins of Mutations in the mdr1 Gene--A Putative Marker of Chloroquine Resistance in P. vivax.

    Mette L Schousboe

    2015-11-01

    Full Text Available Chloroquine combined with primaquine has been the recommended antimalarial treatment of Plasmodium vivax malaria infections for six decades but the efficacy of this treatment regimen is threatened by chloroquine resistance (CQR. Single nucleotide polymorphisms (SNPs in the multidrug resistance gene, Pvmdr1 are putative determinants of CQR but the extent of their emergence at population level remains to be explored.In this study we describe the prevalence of SNPs in the Pvmdr1 among samples collected in seven P. vivax endemic countries and we looked for molecular evidence of drug selection by characterising polymorphism at microsatellite (MS loci flanking the Pvmdr1 gene.We examined the prevalence of SNPs in the Pvmdr1 gene among 267 samples collected from Pakistan, Afghanistan, Sri Lanka, Nepal, Sudan, São Tomé and Ecuador. We measured and diversity in four microsatellite (MS markers flanking the Pvmdr1 gene to look evidence of selection on mutant alleles.SNP polymorphism in the Pvmdr1 gene was largely confined to codons T958M, Y976F and F1076L. Only 2.4% of samples were wildtype at all three codons (TYF, n = 5, 13.3% (n = 28 of the samples were single mutant MYF, 63.0% of samples (n = 133 were double mutant MYL, and 21.3% (n = 45 were triple mutant MFL. Clear geographic differences in the prevalence of these Pvmdr mutation combinations were observed. Significant linkage disequilibrium (LD between Pvmdr1 and MS alleles was found in populations sampled in Ecuador, Nepal and Sri Lanka, while significant LD between Pvmdr1 and the combined 4 MS locus haplotype was only seen in Ecuador and Sri Lanka. When combining the 5 loci, high level diversity, measured as expected heterozygosity (He, was seen in the complete sample set (He = 0.99, while He estimates for individual loci ranged from 0.00-0.93. Although Pvmdr1 haplotypes were not consistently associated with specific flanking MS alleles, there was significant differentiation between geographic

  12. Logarithmic r-θ mapping for hybrid optical neural network filter for multiple objects recognition within cluttered scenes

    Kypraios, Ioannis; Young, Rupert C. D.; Chatwin, Chris R.; Birch, Phil M.

    2009-04-01

    θThe window unit in the design of the complex logarithmic r-θ mapping for hybrid optical neural network filter can allow multiple objects of the same class to be detected within the input image. Additionally, the architecture of the neural network unit of the complex logarithmic r-θ mapping for hybrid optical neural network filter becomes attractive for accommodating the recognition of multiple objects of different classes within the input image by modifying the output layer of the unit. We test the overall filter for multiple objects of the same and of different classes' recognition within cluttered input images and video sequences of cluttered scenes. Logarithmic r-θ mapping for hybrid optical neural network filter is shown to exhibit with a single pass over the input data simultaneously in-plane rotation, out-of-plane rotation, scale, log r-θ map translation and shift invariance, and good clutter tolerance by recognizing correctly the different objects within the cluttered scenes. We record in our results additional extracted information from the cluttered scenes about the objects' relative position, scale and in-plane rotation.

  13. A high-density SNP genetic linkage map for the silver-lipped pearl oyster, Pinctada maxima: a valuable resource for gene localisation and marker-assisted selection.

    Jones, David B; Jerry, Dean R; Khatkar, Mehar S; Raadsma, Herman W; Zenger, Kyall R

    2013-11-20

    The silver-lipped pearl oyster, Pinctada maxima, is an important tropical aquaculture species extensively farmed for the highly sought "South Sea" pearls. Traditional breeding programs have been initiated for this species in order to select for improved pearl quality, but many economic traits under selection are complex, polygenic and confounded with environmental factors, limiting the accuracy of selection. The incorporation of a marker-assisted selection (MAS) breeding approach would greatly benefit pearl breeding programs by allowing the direct selection of genes responsible for pearl quality. However, before MAS can be incorporated, substantial genomic resources such as genetic linkage maps need to be generated. The construction of a high-density genetic linkage map for P. maxima is not only essential for unravelling the genomic architecture of complex pearl quality traits, but also provides indispensable information on the genome structure of pearl oysters. A total of 1,189 informative genome-wide single nucleotide polymorphisms (SNPs) were incorporated into linkage map construction. The final linkage map consisted of 887 SNPs in 14 linkage groups, spans a total genetic distance of 831.7 centimorgans (cM), and covers an estimated 96% of the P. maxima genome. Assessment of sex-specific recombination across all linkage groups revealed limited overall heterochiasmy between the sexes (i.e. 1.15:1 F/M map length ratio). However, there were pronounced localised differences throughout the linkage groups, whereby male recombination was suppressed near the centromeres compared to female recombination, but inflated towards telomeric regions. Mean values of LD for adjacent SNP pairs suggest that a higher density of markers will be required for powerful genome-wide association studies. Finally, numerous nacre biomineralization genes were localised providing novel positional information for these genes. This high-density SNP genetic map is the first comprehensive linkage

  14. Mapping of government land encroachment in Cameron Highlands using multiple remote sensing datasets

    Zin, M H M; Ahmad, B

    2014-01-01

    The cold and refreshing highland weather is one of the factors that give impact to socio-economic growth in Cameron Highlands. This unique weather of the highland surrounded by tropical rain forest can only be found in a few places in Malaysia. It makes this place a famous tourism attraction and also provides a very suitable temperature for agriculture activities. Thus it makes agriculture such as tea plantation, vegetable, fruits and flowers one of the biggest economic activities in Cameron Highlands. However unauthorized agriculture activities are rampant. The government land, mostly forest area have been encroached by farmers, in many cases indiscriminately cutting down trees and hill slopes. This study is meant to detect and assess this encroachment using multiple remote sensing datasets. The datasets were used together with cadastral parcel data where survey lines describe property boundary, pieces of land are subdivided into lots of government and private. The general maximum likelihood classification method was used on remote sensing image to classify the land-cover in the study area. Ground truth data from field observation were used to assess the accuracy of the classification. Cadastral parcel data was overlaid on the classification map in order to detect the encroachment area. The result of this study shows that there is a land cover change of 93.535 ha in the government land of the study area between years 2001 to 2010, nevertheless almost no encroachment took place in the studied forest reserve area. The result of this study will be useful for the authority in monitoring and managing the forest

  15. Mapping of government land encroachment in Cameron Highlands using multiple remote sensing datasets

    Zin, M. H. M.; Ahmad, B.

    2014-02-01

    The cold and refreshing highland weather is one of the factors that give impact to socio-economic growth in Cameron Highlands. This unique weather of the highland surrounded by tropical rain forest can only be found in a few places in Malaysia. It makes this place a famous tourism attraction and also provides a very suitable temperature for agriculture activities. Thus it makes agriculture such as tea plantation, vegetable, fruits and flowers one of the biggest economic activities in Cameron Highlands. However unauthorized agriculture activities are rampant. The government land, mostly forest area have been encroached by farmers, in many cases indiscriminately cutting down trees and hill slopes. This study is meant to detect and assess this encroachment using multiple remote sensing datasets. The datasets were used together with cadastral parcel data where survey lines describe property boundary, pieces of land are subdivided into lots of government and private. The general maximum likelihood classification method was used on remote sensing image to classify the land-cover in the study area. Ground truth data from field observation were used to assess the accuracy of the classification. Cadastral parcel data was overlaid on the classification map in order to detect the encroachment area. The result of this study shows that there is a land cover change of 93.535 ha in the government land of the study area between years 2001 to 2010, nevertheless almost no encroachment took place in the studied forest reserve area. The result of this study will be useful for the authority in monitoring and managing the forest.

  16. High-density genetic mapping of a major QTL for resistance to multiple races of loose smut in a tetraploid wheat cross

    Kumar, Sachin; Knox, Ron E.; Singh, Asheesh K.; DePauw, Ron M.; Campbell, Heather L.; Isidro-Sanchez, Julio; Clarke, Fran R.; Pozniak, Curtis J.; N’Daye, Amidou; Meyer, Brad; Sharpe, Andrew; Ruan, Yuefeng; Cuthbert, Richard D.; Somers, Daryl; Fedak, George

    2018-01-01

    Loose smut, caused by Ustilago tritici (Pers.) Rostr., is a systemic disease of tetraploid durum wheat (Triticum turgidum L.). Loose smut can be economically controlled by growing resistant varieties, making it important to find and deploy new sources of resistance. Blackbird, a variety of T. turgidum L. subsp. carthlicum (Nevski) A. Love & D. Love, carries a high level of resistance to loose smut. Blackbird was crossed with the loose smut susceptible durum cultivar Strongfield to produce a doubled haploid (DH) mapping population. The parents and progenies were inoculated with U. tritici races T26, T32 and T33 individually and as a mixture at Swift Current, Canada in 2011 and 2012 and loose smut incidence (LSI) was assessed. Genotyping of the DH population and parents using an Infinium iSelect 90K single nucleotide polymorphism (SNP) array identified 12,952 polymorphic SNPs. The SNPs and 426 SSRs (previously genotyped in the same population) were mapped to 16 linkage groups spanning 3008.4 cM at an average inter-marker space of 0.2 cM in a high-density genetic map. Composite interval mapping analysis revealed three significant quantitative trait loci (QTL) for loose smut resistance on chromosomes 3A, 6B and 7A. The loose smut resistance QTL on 6B (QUt.spa-6B.2) and 7A (QUt.spa-7A.2) were derived from Blackbird. Strongfield contributed the minor QTL on 3A (QUt.spa-3A.2). The resistance on 6B was a stable major QTL effective against all individual races and the mixture of the three races; it explained up to 74% of the phenotypic variation. This study is the first attempt in durum wheat to identify and map loose smut resistance QTL using a high-density genetic map. The QTL QUt.spa-6B.2 would be an effective source for breeding resistance to multiple races of the loose smut pathogen because it provides near-complete broad resistance to the predominant virulence on the Canadian prairies. PMID:29485999

  17. High-density genetic mapping of a major QTL for resistance to multiple races of loose smut in a tetraploid wheat cross.

    Sachin Kumar

    Full Text Available Loose smut, caused by Ustilago tritici (Pers. Rostr., is a systemic disease of tetraploid durum wheat (Triticum turgidum L.. Loose smut can be economically controlled by growing resistant varieties, making it important to find and deploy new sources of resistance. Blackbird, a variety of T. turgidum L. subsp. carthlicum (Nevski A. Love & D. Love, carries a high level of resistance to loose smut. Blackbird was crossed with the loose smut susceptible durum cultivar Strongfield to produce a doubled haploid (DH mapping population. The parents and progenies were inoculated with U. tritici races T26, T32 and T33 individually and as a mixture at Swift Current, Canada in 2011 and 2012 and loose smut incidence (LSI was assessed. Genotyping of the DH population and parents using an Infinium iSelect 90K single nucleotide polymorphism (SNP array identified 12,952 polymorphic SNPs. The SNPs and 426 SSRs (previously genotyped in the same population were mapped to 16 linkage groups spanning 3008.4 cM at an average inter-marker space of 0.2 cM in a high-density genetic map. Composite interval mapping analysis revealed three significant quantitative trait loci (QTL for loose smut resistance on chromosomes 3A, 6B and 7A. The loose smut resistance QTL on 6B (QUt.spa-6B.2 and 7A (QUt.spa-7A.2 were derived from Blackbird. Strongfield contributed the minor QTL on 3A (QUt.spa-3A.2. The resistance on 6B was a stable major QTL effective against all individual races and the mixture of the three races; it explained up to 74% of the phenotypic variation. This study is the first attempt in durum wheat to identify and map loose smut resistance QTL using a high-density genetic map. The QTL QUt.spa-6B.2 would be an effective source for breeding resistance to multiple races of the loose smut pathogen because it provides near-complete broad resistance to the predominant virulence on the Canadian prairies.

  18. An integrated pan-tropical biomass map using multiple reference datasets.

    Avitabile, Valerio; Herold, Martin; Heuvelink, Gerard B M; Lewis, Simon L; Phillips, Oliver L; Asner, Gregory P; Armston, John; Ashton, Peter S; Banin, Lindsay; Bayol, Nicolas; Berry, Nicholas J; Boeckx, Pascal; de Jong, Bernardus H J; DeVries, Ben; Girardin, Cecile A J; Kearsley, Elizabeth; Lindsell, Jeremy A; Lopez-Gonzalez, Gabriela; Lucas, Richard; Malhi, Yadvinder; Morel, Alexandra; Mitchard, Edward T A; Nagy, Laszlo; Qie, Lan; Quinones, Marcela J; Ryan, Casey M; Ferry, Slik J W; Sunderland, Terry; Laurin, Gaia Vaglio; Gatti, Roberto Cazzolla; Valentini, Riccardo; Verbeeck, Hans; Wijaya, Arief; Willcock, Simon

    2016-04-01

    We combined two existing datasets of vegetation aboveground biomass (AGB) (Proceedings of the National Academy of Sciences of the United States of America, 108, 2011, 9899; Nature Climate Change, 2, 2012, 182) into a pan-tropical AGB map at 1-km resolution using an independent reference dataset of field observations and locally calibrated high-resolution biomass maps, harmonized and upscaled to 14 477 1-km AGB estimates. Our data fusion approach uses bias removal and weighted linear averaging that incorporates and spatializes the biomass patterns indicated by the reference data. The method was applied independently in areas (strata) with homogeneous error patterns of the input (Saatchi and Baccini) maps, which were estimated from the reference data and additional covariates. Based on the fused map, we estimated AGB stock for the tropics (23.4 N-23.4 S) of 375 Pg dry mass, 9-18% lower than the Saatchi and Baccini estimates. The fused map also showed differing spatial patterns of AGB over large areas, with higher AGB density in the dense forest areas in the Congo basin, Eastern Amazon and South-East Asia, and lower values in Central America and in most dry vegetation areas of Africa than either of the input maps. The validation exercise, based on 2118 estimates from the reference dataset not used in the fusion process, showed that the fused map had a RMSE 15-21% lower than that of the input maps and, most importantly, nearly unbiased estimates (mean bias 5 Mg dry mass ha(-1) vs. 21 and 28 Mg ha(-1) for the input maps). The fusion method can be applied at any scale including the policy-relevant national level, where it can provide improved biomass estimates by integrating existing regional biomass maps as input maps and additional, country-specific reference datasets. © 2015 John Wiley & Sons Ltd.

  19. Multiple SNP markers reveal fine-scale population and deep phylogeographic structure in European anchovy (Engraulis encrasicolus L.).

    Zarraonaindia, Iratxe; Iriondo, Mikel; Albaina, Aitor; Pardo, Miguel Angel; Manzano, Carmen; Grant, W Stewart; Irigoien, Xabier; Estonba, Andone

    2012-01-01

    DNA SNPs define two deep phylogroups that reflect ancient dispersals and colonizations. These markers define two ecological groups. One major group of Iberian-Atlantic populations is associated with upwelling areas on narrow continental shelves and includes

  20. Multitemporal burnt area mapping using Landsat 8: merging multiple burnt area indices to highlight burnt areas

    Vhengani, L

    2015-07-01

    Full Text Available gases. These, makes the study of wildfires important. The study of fires is in three phases. Firstly it is forecasting, which uses Fire Danger Index (FDI), secondly it is the mapping of active fires and thirdly, the mapping of burnt areas to access...

  1. Mapping groundwater dynamics using multiple sources of exhaustive high resolution data

    Finke, P.A.; Brus, D.J.; Bierkens, M.F.P.; Hoogland, T.; Knotters, M.; Vries, de F.

    2004-01-01

    Existing groundwater table (GWT) class maps, available at full coverage for the Netherlands at 1:50,000 scale, no longer satisfy user demands. Groundwater levels have changed due to strong human impact, so the maps are partially outdated. Furthermore, a more dynamic description of groundwater table

  2. Gaussian Multiple Instance Learning Approach for Mapping the Slums of the World Using Very High Resolution Imagery

    Vatsavai, Raju [ORNL

    2013-01-01

    In this paper, we present a computationally efficient algo- rithm based on multiple instance learning for mapping infor- mal settlements (slums) using very high-resolution remote sensing imagery. From remote sensing perspective, infor- mal settlements share unique spatial characteristics that dis- tinguish them from other urban structures like industrial, commercial, and formal residential settlements. However, regular pattern recognition and machine learning methods, which are predominantly single-instance or per-pixel classi- fiers, often fail to accurately map the informal settlements as they do not capture the complex spatial patterns. To overcome these limitations we employed a multiple instance based machine learning approach, where groups of contigu- ous pixels (image patches) are modeled as generated by a Gaussian distribution. We have conducted several experi- ments on very high-resolution satellite imagery, represent- ing four unique geographic regions across the world. Our method showed consistent improvement in accurately iden- tifying informal settlements.

  3. Candidate Gene Identification with SNP Marker-Based Fine Mapping of Anthracnose Resistance Gene Co-4 in Common Bean.

    Burt, Andrew J; William, H Manilal; Perry, Gregory; Khanal, Raja; Pauls, K Peter; Kelly, James D; Navabi, Alireza

    2015-01-01

    Anthracnose, caused by Colletotrichum lindemuthianum, is an important fungal disease of common bean (Phaseolus vulgaris). Alleles at the Co-4 locus confer resistance to a number of races of C. lindemuthianum. A population of 94 F4:5 recombinant inbred lines of a cross between resistant black bean genotype B09197 and susceptible navy bean cultivar Nautica was used to identify markers associated with resistance in bean chromosome 8 (Pv08) where Co-4 is localized. Three SCAR markers with known linkage to Co-4 and a panel of single nucleotide markers were used for genotyping. A refined physical region on Pv08 with significant association with anthracnose resistance identified by markers was used in BLAST searches with the genomic sequence of common bean accession G19833. Thirty two unique annotated candidate genes were identified that spanned a physical region of 936.46 kb. A majority of the annotated genes identified had functional similarity to leucine rich repeats/receptor like kinase domains. Three annotated genes had similarity to 1, 3-β-glucanase domains. There were sequence similarities between some of the annotated genes found in the study and the genes associated with phosphoinositide-specific phosphilipases C associated with Co-x and the COK-4 loci found in previous studies. It is possible that the Co-4 locus is structured as a group of genes with functional domains dominated by protein tyrosine kinase along with leucine rich repeats/nucleotide binding site, phosphilipases C as well as β-glucanases.

  4. SNP discovery and development of genetic markers for mapping immune response genes in common carp (Cyprinus carpio)

    Single nucleotide polymorphisms (SNPs) in immune response genes have been reported as markers for susceptibility to infectious diseases in human and livestock. A disease caused by cyprinid herpesvirus 3 (CyHV-3) is highly contagious and virulent in common carp (Cyprinus carpio). With the aim to de...

  5. Development of single nucleotide polymorphism (SNP) markers from the mango (Mangiferaindica) transcriptome for mapping and estimation of genetic diversity

    The development of resources for genomic studies in Mangifera indica (mango) will allow marker-assisted selection and identification of genetically diverse germplasm, greatly aiding mango breeding programs. We report here a first step in developing such resources, our identification of thousands una...

  6. Rapid Generation of Multiple Loci-Engineered Marker-free Poxvirus and Characterization of a Clinical-Grade Oncolytic Vaccinia Virus

    Zong Sheng Guo

    2017-12-01

    Full Text Available Recombinant poxviruses, utilized as vaccine vectors and oncolytic viruses, often require manipulation at multiple genetic loci in the viral genome. It is essential for viral vectors to possess no adventitious mutations and no (antibiotic selection marker in the final product for human patients in order to comply with the guidance from the regulatory agencies. Rintoul et al. have previously developed a selectable and excisable marker (SEM system for the rapid generation of recombinant vaccinia virus. In the current study, we describe an improved methodology for rapid creation and selection of recombinant poxviruses with multiple genetic manipulations solely based on expression of a fluorescent protein and with no requirement for drug selection that can lead to cellular stress and the risk of adventitious mutations throughout the viral genome. Using this improved procedure combined with the SEM system, we have constructed multiple marker-free oncolytic poxviruses expressing different cytokines and other therapeutic genes. The high fidelity of inserted DNA sequences validates the utility of this improved procedure for generation of therapeutic viruses for human patients. We have created an oncolytic poxvirus expressing human chemokine CCL5, designated as vvDD-A34R-hCCL5, with manipulations at two genetic loci in a single virus. Finally, we have produced and purified this virus in clinical grade for its use in a phase I clinical trial and presented data on initial in vitro characterization of the virus.

  7. Sewage pollution in urban stormwater runoff as evident from the widespread presence of multiple microbial and chemical source tracking markers.

    Sidhu, J P S; Ahmed, W; Gernjak, W; Aryal, R; McCarthy, D; Palmer, A; Kolotelo, P; Toze, S

    2013-10-01

    The concurrence of human sewage contamination in urban stormwater runoff (n=23) from six urban catchments across Australia was assessed by using both microbial source tracking (MST) and chemical source tracking (CST) markers. Out of 23 stormwater samples human adenovirus (HAv), human polyomavirus (HPv) and the sewage-associated markers; Methanobrevibacter smithii nifH and Bacteroides HF183 were detected in 91%, 56%, 43% and 96% of samples, respectively. Similarly, CST markers paracetamol (87%), salicylic acid (78%) acesulfame (96%) and caffeine (91%) were frequently detected. Twenty one samples (91%) were positive for six to eight sewage related MST and CST markers and remaining two samples were positive for five and four markers, respectively. A very good consensus (>91%) observed between the concurrence of the HF183, HAv, acesulfame and caffeine suggests good predictability of the presence of HAv in samples positive for one of the three markers. High prevalence of HAv (91%) also suggests that other enteric viruses may also be present in the stormwater samples which may pose significant health risks. This study underscores the benefits of employing a set of MST and CST markers which could include monitoring for HF183, adenovirus, caffeine and paracetamol to accurately detect human sewage contamination along with credible information on the presence of human enteric viruses, which could be used for more reliable public health risk assessments. Based on the results obtained in this study, it is recommended that some degree of treatment of captured stormwater would be required if it were to be used for non-potable purposes. Crown Copyright © 2013. Published by Elsevier B.V. All rights reserved.

  8. A proposed cell model for multiple-occurrence regional landslide events: Implications for landslide susceptibility mapping

    Crozier, M. J.

    2017-10-01

    Multiple-occurrence regional landslide events (MORLEs) consist of hundreds to thousands of shallow landslides occurring more or less simultaneously within defined areas, ranging from tens to thousands of square kilometres. While MORLEs can be triggered by rainstorms and earthquakes, this paper is confined to those landslide events triggered by rainstorms. Globally, MORLEs occur in a range of geological settings in areas of moderate to steep slopes subject to intense rainstorms. Individual landslides in rainstorm-triggered events are dominantly small, shallow debris and earth flows, and debris and earth slides involving regolith or weathered bedrock. The model used to characterise these events assumes that energy distribution within the event area is represented on the land surface by a cell structure; with maximum energy expenditure within an identifiable core and rapid dissipation concentrically away from the centre. The version of the model presented here has been developed for rainfall-triggered landslide events. It proposes that rainfall intensity can be used to determine different critical landslide response zones within the cell (referred to as core, middle, and periphery zones). These zones are most readily distinguished by two conditions: the proportion of the slope that fails and the particular type of the slope stability factor that assumes dominance in determining specific sites of landslide occurrence. The latter condition means that the power of any slope stability factor to distinguish between stable and unstable sites varies throughout the affected area in accordance with the landslide response zones within the cell; certain factors critical for determining the location of landslide sites in one part of the event area have little influence in other parts of the event area. The implication is that landslide susceptibility maps (and subsequently derived mitigation measures) based on conventional slope stability factors may have only limited validity

  9. Homozygosity mapping in albinism patients using a novel panel of 13 STR markers inside the nonsyndromic OCA genes: introducing 5 novel mutations.

    Khordadpoor-Deilamani, Faravareh; Akbari, Mohammad Taghi; Karimipoor, Morteza; Javadi, Gholam Reza

    2016-05-01

    Albinism is a heterogeneous genetic disorder of melanin synthesis that results in hypopigmented hair, skin and eyes. It is associated with decreased visual acuity, nystagmus, strabismus and photophobia. Six genes are known to be involved in nonsyndromic oculocutaneous albinism (OCA). In this study, we aimed to find the disease causing mutations in albinism patients using homozygosity mapping. Twenty three unrelated patients with nonsyndromic OCA or autosomal recessive ocular albinism were recruited in this study. All of the patients' parents had consanguineous marriage and all were screened for TYR mutations previously. At first, we performed homozygosity mapping using fluorescently labeled primers to amplify a novel panel of 13 STR markers inside the OCA genes and then the screened loci in each family were studied using PCR and cycle sequencing methods. We found five mutations including three mutations in OCA2, one mutation in SLC45A2 and one mutation in C10ORF11 genes, all of which were novel. In cases where the disease causing mutations are identical by descent due to a common ancestor, these STR markers can enable us to screen for the responsible genes.

  10. Studies of HVC Plasticity in Adult Canaries Reveal Social Effects and Sex Differences as Well as Limitations of Multiple Markers Available to Assess Adult Neurogenesis.

    Shevchouk, Olesya T; Ball, Gregory F; Cornil, Charlotte A; Balthazart, Jacques

    2017-01-01

    In songbirds, neurogenesis in the song control nucleus HVC is sensitive to the hormonal and social environment but the dynamics of this process is difficult to assess with a single exogenous marker of new neurons. We simultaneously used three independent markers to investigate HVC neurogenesis in male and female canaries. Males were castrated, implanted with testosterone and housed either alone (M), with a female (M-F) or with another male (M-M) while females were implanted with 17β-estradiol and housed with a male (F-M). All subjects received injections of the two thymidine analogues, BrdU and of EdU, respectively 21 and 10 days before brain collection. Cells containing BrdU or EdU or expressing doublecortin (DCX), which labels newborn neurons, were quantified. Social context and sex differentially affected total BrdU+, EdU+, BrdU+EdU- and DCX+ populations. M-M males had a higher density of BrdU+ cells in the ventricular zone adjacent to HVC and of EdU+ in HVC than M-F males. M birds had a higher ratio of BrdU+EdU- to EdU+ cells than M-F subjects suggesting higher survival of newer neurons in the former group. Total number of HVC DCX+ cells was lower in M-F than in M-M males. Sex differences were also dependent of the type of marker used. Several technical limitations associated with the use of these multiple markers were also identified. These results indicate that proliferation, recruitment and survival of new neurons can be independently affected by environmental conditions and effects can only be fully discerned through the use of multiple neurogenesis markers.

  11. Studies of HVC Plasticity in Adult Canaries Reveal Social Effects and Sex Differences as Well as Limitations of Multiple Markers Available to Assess Adult Neurogenesis.

    Olesya T Shevchouk

    Full Text Available In songbirds, neurogenesis in the song control nucleus HVC is sensitive to the hormonal and social environment but the dynamics of this process is difficult to assess with a single exogenous marker of new neurons. We simultaneously used three independent markers to investigate HVC neurogenesis in male and female canaries. Males were castrated, implanted with testosterone and housed either alone (M, with a female (M-F or with another male (M-M while females were implanted with 17β-estradiol and housed with a male (F-M. All subjects received injections of the two thymidine analogues, BrdU and of EdU, respectively 21 and 10 days before brain collection. Cells containing BrdU or EdU or expressing doublecortin (DCX, which labels newborn neurons, were quantified. Social context and sex differentially affected total BrdU+, EdU+, BrdU+EdU- and DCX+ populations. M-M males had a higher density of BrdU+ cells in the ventricular zone adjacent to HVC and of EdU+ in HVC than M-F males. M birds had a higher ratio of BrdU+EdU- to EdU+ cells than M-F subjects suggesting higher survival of newer neurons in the former group. Total number of HVC DCX+ cells was lower in M-F than in M-M males. Sex differences were also dependent of the type of marker used. Several technical limitations associated with the use of these multiple markers were also identified. These results indicate that proliferation, recruitment and survival of new neurons can be independently affected by environmental conditions and effects can only be fully discerned through the use of multiple neurogenesis markers.

  12. A National Approach for Mapping and Quantifying Habitat-based Biodiversity Metrics Across Multiple Spatial Scales

    Ecosystem services, i.e., "services provided to humans from natural systems," have become a key issue of this century in resource management, conservation planning, and environmental decision analysis. Mapping and quantifying ecosystem services have become strategic national inte...

  13. Genetic mapping and development of co-segregating markers of RpsQ, which provides resistance to Phytophthora sojae in soybean.

    Li, Yinping; Sun, Suli; Zhong, Chao; Wang, Xiaoming; Wu, Xiaofei; Zhu, Zhendong

    2017-06-01

    The RpsQ Phytophthora resistance locus was finely mapped to a 118-kb region on soybean chromosome 3. A best candidate gene was predicted and three co-segregating gene markers were developed. Phytophthora root rot (PRR), caused by Phytophthora sojae, is a major threat to sustainable soybean production. The use of genetically resistant cultivars is considered the most effective way to control this disease. The Chinese soybean cultivar Qichadou 1 exhibited a broad spectrum resistance, with a distinct resistance phenotype, following inoculation with 36 Chinese P. sojae isolates. Genetic analyses indicated that the disease resistance in Qichadou 1 is controlled by a single dominant gene. This gene locus was designated as RpsQ and mapped to a 118-kb region between BARCSOYSSR_03_0165 and InDel281 on soybean chromosome 3, and co-segregated with Insert11, Insert144 and SNP276. Within this region, there was only one gene Glyma.03g27200 encoding a protein with a typical serine/threonine protein kinase structure, and the expression pattern analysis showed that this gene induced by P. sojae infection, which was suggested as a best candidate gene of RpsQ. Candidate gene specific marker Insert144 was used to distinguish RpsQ from the other known Rps genes on chromosome 3. Identical polymerase chain reaction amplification products were produced for cultivars Qichadou 1 (RpsQ) and Ludou 4 (Rps9). All other cultivars carrying Rps genes on chromosome 3 produced different PCR products, which all lacked a 144-bp fragment present in Qichadou 1 and Ludou 4. The phenotypes of the analyzed cultivars combined with the physical position of the PRR resistance locus, candidate gene analyses, and the candidate gene marker test revealed RpsQ and Rps9 are likely the same gene, and confer resistance to P. sojae.

  14. QTL Mapping of Adult-Plant Resistance to Leaf Rust in the Wheat Cross Zhou 8425B/Chinese Spring Using High-Density SNP Markers

    Peipei Zhang

    2017-05-01

    Full Text Available Wheat leaf rust is an important disease worldwide. Growing resistant cultivars is an effective means to control the disease. In the present study, 244 recombinant inbred lines from Zhou 8425B/Chinese Spring cross were phenotyped for leaf rust severities during the 2011–2012, 2012–2013, 2013–2014, and 2014–2015 cropping seasons at Baoding, Hebei province, and 2012–2013 and 2013–2014 cropping seasons in Zhoukou, Henan province. The population was genotyped using the high-density Illumina iSelect 90K SNP assay and SSR markers. Inclusive composite interval mapping identified eight QTL, designated as QLr.hebau-2AL, QLr.hebau-2BS, QLr.hebau-3A, QLr.hebau-3BS, QLr.hebau-4AL, QLr.hebau-4B, QLr.hebau-5BL, and QLr.hebau-7DS, respectively. QLr.hebau-2BS, QLr.hebau-3A, QLr.hebau-3BS, and QLr.hebau-5BL were derived from Zhou 8425B, whereas the other four were from Chinese Spring. Three stable QTL on chromosomes 2BS, 4B and 7DS explained 7.5–10.6%, 5.5–24.4%, and 11.2–20.9% of the phenotypic variance, respectively. QLr.hebau-2BS in Zhou 8425B might be the same as LrZH22 in Zhoumai 22; QLr.hebau-4B might be the residual resistance of Lr12, and QLr.hebau-7DS is Lr34. QLr.hebau-2AL, QLr.hebau-3BS, QLr.hebau-4AL, and QLr.hebau-5BL are likely to be novel QTL for leaf rust. These QTL and their closely linked SNP and SSR markers can be used for fine mapping, candidate gene discovery, and marker-assisted selection in wheat breeding.

  15. Mapping recessive ophthalmic diseases: linkage of the locus for Usher syndrome type II to a DNA marker on chromosome 1q.

    Lewis, R A; Otterud, B; Stauffer, D; Lalouel, J M; Leppert, M

    1990-06-01

    Usher syndrome is a heterogeneous group of autosomal recessive disorders that combines variably severe congenital neurosensory hearing impairment with progressive night-blindness and visual loss similar to that in retinitis pigmentosa. Usher syndrome type I is distinguished by profound congenital (preverbal) deafness and retinal disease with onset in the first decade of life. Usher syndrome type II is characterized by partial hearing impairment and retinal dystrophy that occurs in late adolescence or early adulthood. The chromosomal assignment and the regional localization of the genetic mutation(s) causing the Usher syndromes are unknown. We analyzed a panel of polymorphic genomic markers for linkage to the disease gene among six families with Usher syndrome type I and 22 families with Usher syndrome type II. Significant linkage was established between Usher syndrome type II and the DNA marker locus THH33 (D1S81), which maps to chromosome 1q. The most likely location of the disease gene is at a map distance of 9 cM from THH33 (lod score 6.5). The same marker failed to show linkage in families segregating an allele for Usher syndrome type I. These data confirm the provisional assignment of the locus for Usher syndrome type II to the distal end of chromosome 1q and demonstrate that the clinical heterogeneity between Usher types I and II is caused by mutational events at different genetic loci. Regional localization has the potential to improve carrier detection and to provide antenatal diagnosis in families at risk for the disease.

  16. An integrated pan-tropical biomass map using multiple reference datasets

    Avitabile, V.; Herold, M.; Heuvelink, G. B. M.; Lewis, S. L.; Phillips, O. L.; Asner, G. P.; Armston, J.; Ashton, P. S.; Banin, L.; Bayol, N.; Berry, N. J.; Boeckx, P.; de Jong, B. H. J.; DeVries, B.; Girardin, C. A. J.

    2016-01-01

    We combined two existing datasets of vegetation aboveground biomass (AGB) (Proceedings of the National Academy of Sciences of the United States of America, 108, 2011, 9899; Nature Climate Change, 2, 2012, 182) into a pan-tropical AGB map at 1-km resolution using an independent reference dataset of field observations and locally calibrated high-resolution biomass maps, harmonized and upscaled to 14 477 1-km AGB estimates. Our data fusion approach uses bias removal and weighted linear averaging...

  17. Candidate Gene Identification with SNP Marker-Based Fine Mapping of Anthracnose Resistance Gene Co-4 in Common Bean.

    Andrew J Burt

    Full Text Available Anthracnose, caused by Colletotrichum lindemuthianum, is an important fungal disease of common bean (Phaseolus vulgaris. Alleles at the Co-4 locus confer resistance to a number of races of C. lindemuthianum. A population of 94 F4:5 recombinant inbred lines of a cross between resistant black bean genotype B09197 and susceptible navy bean cultivar Nautica was used to identify markers associated with resistance in bean chromosome 8 (Pv08 where Co-4 is localized. Three SCAR markers with known linkage to Co-4 and a panel of single nucleotide markers were used for genotyping. A refined physical region on Pv08 with significant association with anthracnose resistance identified by markers was used in BLAST searches with the genomic sequence of common bean accession G19833. Thirty two unique annotated candidate genes were identified that spanned a physical region of 936.46 kb. A majority of the annotated genes identified had functional similarity to leucine rich repeats/receptor like kinase domains. Three annotated genes had similarity to 1, 3-β-glucanase domains. There were sequence similarities between some of the annotated genes found in the study and the genes associated with phosphoinositide-specific phosphilipases C associated with Co-x and the COK-4 loci found in previous studies. It is possible that the Co-4 locus is structured as a group of genes with functional domains dominated by protein tyrosine kinase along with leucine rich repeats/nucleotide binding site, phosphilipases C as well as β-glucanases.

  18. A method for genotyping elite breeding stocks of leaf chicory (Cichorium intybus L.) by assaying mapped microsatellite marker loci.

    Ghedina, Andrea; Galla, Giulio; Cadalen, Thierry; Hilbert, Jean-Louis; Caenazzo, Silvano Tiozzo; Barcaccia, Gianni

    2015-12-30

    Leaf chicory (Cichorium intybus subsp. intybus var. foliosum L.) is a diploid plant species (2n = 18) of the Asteraceae family. The term "chicory" specifies at least two types of cultivated plants: a leafy vegetable, which is highly differentiated with respect to several cultural types, and a root crop, whose current industrial utilization primarily addresses the extraction of inulin or the production of a coffee substitute. The populations grown are generally represented by local varieties (i.e., landraces) with high variation and adaptation to the natural and anthropological environment where they originated, and have been yearly selected and multiplied by farmers. Currently, molecular genetics and biotechnology are widely utilized in marker-assisted breeding programs in this species. In particular, molecular markers are becoming essential tools for developing parental lines with traits of interest and for assessing the specific combining ability of these lines to breed F1 hybrids. The present research deals with the implementation of an efficient method for genotyping elite breeding stocks developed from old landraces of leaf chicory, Radicchio of Chioggia, which are locally dominant in the Veneto region, using 27 microsatellite (SSR) marker loci scattered throughout the linkage groups. Information on the genetic diversity across molecular markers and plant accessions was successfully assessed along with descriptive statistics over all marker loci and inbred lines. Our overall data support an efficient method for assessing a multi-locus genotype of plant individuals and lineages that is useful for the selection of new varieties and the certification of local products derived from Radicchio of Chioggia. This method proved to be useful for assessing the observed degree of homozygosity of the inbred lines as a measure of their genetic stability; plus it allowed an estimate of the specific combining ability (SCA) between maternal and paternal inbred lines on the

  19. Identification of RFLP and NBS/PK profiling markers for disease resistance loci in genetic maps of oats

    Sanz, M.J.; Loarce, Y.; Fominaya, A.; Vossen, J.H.; Ferrer, E.

    2013-01-01

    Two of the domains most widely shared among R genes are the nucleotide binding site (NBS) and protein kinase (PK) domains. The present study describes and maps a number of new oat resistance gene analogues (RGAs) with two purposes in mind: (1) to identify genetic regions that contain R genes and (2)

  20. Identification of QTLs Associated with Callogenesis and Embryogenesis in Oil Palm Using Genetic Linkage Maps Improved with SSR Markers.

    Ting, N.C.; Jansen, J.; Nagappan, J.; Ishak, Z.; Chin, C.W.; Tan, S.G.; Cheah, S.C.; Singh, R.

    2013-01-01

    Clonal reproduction of oil palm by means of tissue culture is a very inefficient process. Tissue culturability is known to be genotype dependent with some genotypes being more amenable to tissue culture than others. In this study, genetic linkage maps enriched with simple sequence repeat (SSR)

  1. Simultaneous 3D localization of multiple MR-visible markers in fully reconstructed MR images: proof-of-concept for subsecond position tracking.

    Thörmer, Gregor; Garnov, Nikita; Moche, Michael; Haase, Jürgen; Kahn, Thomas; Busse, Harald

    2012-04-01

    To determine whether a greatly reduced spatial resolution of fully reconstructed projection MR images can be used for the simultaneous 3D localization of multiple MR-visible markers and to assess the feasibility of a subsecond position tracking for clinical purposes. Miniature, inductively coupled RF coils were imaged in three orthogonal planes with a balanced steady-state free precession (SSFP) sequence and automatically localized using a two-dimensional template fitting and a subsequent three-dimensional (3D) matching of the coordinates. Precision, accuracy, speed and robustness of 3D localization were assessed for decreasing in-plane resolutions (0.6-4.7 mm). The feasibility of marker tracking was evaluated at the lowest resolution by following a robotically driven needle on a complex 3D trajectory. Average 3D precision and accuracy, sensitivity and specificity of localization ranged between 0.1 and 0.4 mm, 0.5 and 1.0 mm, 100% and 95%, and 100% and 96%, respectively. At the lowest resolution, imaging and localization took ≈350 ms and provided an accuracy of ≈1.0 mm. In the tracking experiment, the needle was clearly depicted on the oblique scan planes defined by the markers. Image-based marker localization at a greatly reduced spatial resolution is considered a feasible approach to monitor reference points or rigid instruments at subsecond update rates. Copyright © 2012 Elsevier Inc. All rights reserved.

  2. THE DIFFERENCE OF MAP1LC3 LEVEL AS MACROPHAGE AUTOPHAGY MARKER BETWEEN RESISTANT AND SENSITIVE TUBERCULOSIS PATIENTS ON RIFAMPICIN

    Dian novita W

    2018-04-01

    Full Text Available Mycobacterium tuberculosis (MTB is an intracelular bacteria that live in the host macrophage cells. Several organs can be affected by tuberculosis but most major illnesses are lung diseases. Immediately after infection, MTB will be phagocytosed by the alveolar macrophage cells and can survive in the phagosome. The macrophage plays a role in innate immunity towards an infection using autophagy by removing the microbe directly via phagocytosis. When bacteria phagocytosized, vacuole membrane formed double membranes called autophagosome, and followed by degradation by lysosome, which known as autolysosome. Induction of autophagy can be observed on the formation of microtubule-associated proteins 1B lightchain 3B (MAP1LC3B/LC3. MAP1LC3B is protein that have role at autophagic way for selection autophagy substrate and biogenesis. In this study we are used serum from patients TB with rifampicin resistant and rifampicin sensitive as control. Samples were divided using gene expert to differentiate between resistant and sensitive rifampicin.This research aims to compare MAP1LC3B levels in resistant and sensitive rifampicin to study macrophages respond in autophagic way in tuberculosis patients, and give information for define therapy plan to improve therapy for MDR-TB patients. Type of this research is a case control study design with cross sectional research with each groups sample is 19 from age 18-65 years old. Result, MAP1LC3B serum levels on the rifampicin resistant group are lower compared to rifampicin sensitive group. This occur because MTB is able to hide and evade innate immune defense mechanisms. MTB can maintain intracellular growth inside the phagosome by inhibiting phagolysosome formation in autophagy process especially inhibit MAP1LC3B formation by PDIM.

  3. Development of cleaved amplified polymorphic sequence markers and a CAPS-based genetic linkage map in watermelon (Citrullus lanatus [Thunb.] Matsum. and Nakai) constructed using whole-genome re-sequencing data.

    Liu, Shi; Gao, Peng; Zhu, Qianglong; Luan, Feishi; Davis, Angela R; Wang, Xiaolu

    2016-03-01

    Cleaved amplified polymorphic sequence (CAPS) markers are useful tools for detecting single nucleotide polymorphisms (SNPs). This study detected and converted SNP sites into CAPS markers based on high-throughput re-sequencing data in watermelon, for linkage map construction and quantitative trait locus (QTL) analysis. Two inbred lines, Cream of Saskatchewan (COS) and LSW-177 had been re-sequenced and analyzed by Perl self-compiled script for CAPS marker development. 88.7% and 78.5% of the assembled sequences of the two parental materials could map to the reference watermelon genome, respectively. Comparative assembled genome data analysis provided 225,693 and 19,268 SNPs and indels between the two materials. 532 pairs of CAPS markers were designed with 16 restriction enzymes, among which 271 pairs of primers gave distinct bands of the expected length and polymorphic bands, via PCR and enzyme digestion, with a polymorphic rate of 50.94%. Using the new CAPS markers, an initial CAPS-based genetic linkage map was constructed with the F2 population, spanning 1836.51 cM with 11 linkage groups and 301 markers. 12 QTLs were detected related to fruit flesh color, length, width, shape index, and brix content. These newly CAPS markers will be a valuable resource for breeding programs and genetic studies of watermelon.

  4. Cartography of memory in Chris Marker and W.G. Sebald: Notes about History, memory and maps

    Álvaro Brito

    2017-01-01

    Full Text Available This paper aims to approach the artists Chris Marker and W.G. Sebald, trying to determine and develop pervasive questions in their works: the construction of a historiographic discourse, the ambiguities of memory, the erratic movement of their characters and essayistic thinking. We have tried to draft some starting points to make possible the writing of a memory as a cartography, created through walking on the world and also through the collection of images and of stories that tell about lives that went astray in the mis-paths of History.

  5. THE USE OF MULTIPLE DATA SOURCES IN THE PROCESS OF TOPOGRAPHIC MAPS UPDATING

    A. Cantemir

    2016-06-01

    Full Text Available The methods used in the process of updating maps have evolved and become more complex, especially upon the development of the digital technology. At the same time, the development of technology has led to an abundance of available data that can be used in the updating process. The data sources came in a great variety of forms and formats from different acquisition sensors. Satellite images provided by certain satellite missions are now available on space agencies portals. Images stored in archives of satellite missions such us Sentinel, Landsat and other can be downloaded free of charge.The main advantages are represented by the large coverage area and rather good spatial resolution that enables the use of these images for the map updating at an appropriate scale. In our study we focused our research of these images on 1: 50.000 scale map. DEM that are globally available could represent an appropriate input for watershed delineation and stream network generation, that can be used as support for hydrography thematic layer update. If, in addition to remote sensing aerial photogrametry and LiDAR data are ussed, the accuracy of data sources is enhanced. Ortophotoimages and Digital Terrain Models are the main products that can be used for feature extraction and update. On the other side, the use of georeferenced analogical basemaps represent a significant addition to the process. Concerning the thematic maps, the classic representation of the terrain by contour lines derived from DTM, remains the best method of surfacing the earth on a map, nevertheless the correlation with other layers such as Hidrography are mandatory. In the context of the current national coverage of the Digital Terrain Model, one of the main concerns of the National Center of Cartography, through the Cartography and Photogrammetry Department, is represented by the exploitation of the available data in order to update the layers of the Topographic Reference Map 1:5000, known as

  6. PK11195 binding to the peripheral benzodiazepine receptor as a marker of microglia activation in multiple sclerosis and experimental autoimmune encephalomyelitis

    Vowinckel, E; Reutens, D; Becher, B

    1997-01-01

    Activated glial cells are implicated in regulating and effecting the immune response that occurs within the CNS as part of multiple sclerosis (MS) and its animal model experimental autoimmune encephalomyelitis (EAE). The peripheral benzodiazepine receptor (PBR) is expressed in glial cells. We...... examined the utility of using in vitro and in vivo ligand binding to the PBR as a measure of lesion activity in autoimmune CNS demyelinating diseases. Applying a combined autoradiography and immunohistochemical approach to spinal cord and brain tissues from mice with EAE, we found a correlation at sites...... of inflammatory lesions between [3H]-PK11195 binding and immunoreactivity for the activated microglial/macrophage marker Mac-1/CD11b. In MS tissues, [3H]-PK11195 binding correlated with sites of immunoreactivity for the microglial/macrophage marker CD68, at the edges of chronic active plaques. Positron emission...

  7. An integrated pan-tropical biomass map using multiple reference datasets

    Avitabile, V.; Herold, M.; Heuvelink, G.B.M.; Lewis, S.L.; Phillips, O.L.; Asner, G.P.; Armston, J.; Asthon, P.; Banin, L.F.; Bayol, N.; Berry, N.; Boeckx, P.; Jong, De B.; Devries, B.; Girardin, C.; Kearsley, E.; Lindsell, J.A.; Lopez-gonzalez, G.; Lucas, R.; Malhi, Y.; Morel, A.; Mitchard, E.; Nagy, L.; Qie, L.; Quinones, M.; Ryan, C.M.; Slik, F.; Sunderland, T.; Vaglio Laurin, G.; Valentini, R.; Verbeeck, H.; Wijaya, A.; Willcock, S.

    2016-01-01

    We combined two existing datasets of vegetation aboveground biomass (AGB) (Proceedings of the National Academy of Sciences of the United States of America, 108, 2011, 9899; Nature Climate Change, 2, 2012, 182) into a pan-tropical AGB map at 1-km resolution using an independent reference dataset of

  8. American cities, global networks: mapping the multiple geographies of globalization in the Americas

    Toly, N.J.; Bouteligier, S.; Smith, G.; Gibson, B.

    2012-01-01

    The mapping of advanced producer and financial service firms across global cities began to increase understanding of the role of cities in global governance, the presence and influence of cities in the shifting architecture of global political economy, and the role of globalization in shaping the

  9. Impact of multiple glacial surges - a geomorphological map from Brúarjökull, East Iceland

    Kjær, Kurt H.; Korsgaard, Niels Jákup; Schomacker, Anders

    2008-01-01

    of individual landforms. We mapped subglacial lineations such as flutes and drumlins on till plains, pitted outwash, eskers, minor meandering ridges, crevasse fill ridges, ice-free dead-ice moraine and concertina ridges, outwash fans and lake sediment plains. In addition, erosional drainage channels, ice...

  10. On generic obstructions to recovering correct statistics from climate simulations: Homogenization for deterministic maps and multiplicative noise

    Gottwald, Georg; Melbourne, Ian

    2013-04-01

    Whereas diffusion limits of stochastic multi-scale systems have a long and successful history, the case of constructing stochastic parametrizations of chaotic deterministic systems has been much less studied. We present rigorous results of convergence of a chaotic slow-fast system to a stochastic differential equation with multiplicative noise. Furthermore we present rigorous results for chaotic slow-fast maps, occurring as numerical discretizations of continuous time systems. This raises the issue of how to interpret certain stochastic integrals; surprisingly the resulting integrals of the stochastic limit system are generically neither of Stratonovich nor of Ito type in the case of maps. It is shown that the limit system of a numerical discretisation is different to the associated continuous time system. This has important consequences when interpreting the statistics of long time simulations of multi-scale systems - they may be very different to the one of the original continuous time system which we set out to study.

  11. Concept and simulation study of a novel localization method for robotic endoscopic capsules using multiple positron emission markers.

    Than, Trung Duc; Alici, Gursel; Harvey, Steven; Zhou, Hao; Li, Weihua

    2014-07-01

    Over the last decade, wireless capsule endoscope has been the tool of choice for noninvasive inspection of the gastrointestinal tract, especially in the small intestine. However, the latest clinical products have not been equipped with a sufficiently accurate localization system which makes it difficult to determine the location of intestinal abnormalities, and to apply follow-up interventions such as biopsy or drug delivery. In this paper, the authors present a novel localization method based on tracking three positron emission markers embedded inside an endoscopic capsule. Three spherical(22)Na markers with diameters of less than 1 mm are embedded in the cover of the capsule. Gamma ray detectors are arranged around a patient body to detect coincidence gamma rays emitted from the three markers. The position of each marker can then be estimated using the collected data by the authors' tracking algorithm which consists of four consecutive steps: a method to remove corrupted data, an initialization method, a clustering method based on the Fuzzy C-means clustering algorithm, and a failure prediction method. The tracking algorithm has been implemented inMATLAB utilizing simulation data generated from the Geant4 Application for Emission Tomography toolkit. The results show that this localization method can achieve real-time tracking with an average position error of less than 0.4 mm and an average orientation error of less than 2°. The authors conclude that this study has proven the feasibility and potential of the proposed technique in effectively determining the position and orientation of a robotic endoscopic capsule.

  12. Concept and simulation study of a novel localization method for robotic endoscopic capsules using multiple positron emission markers

    Than, Trung Duc; Alici, Gursel; Zhou, Hao; Li, Weihua; Harvey, Steven

    2014-01-01

    Purpose: Over the last decade, wireless capsule endoscope has been the tool of choice for noninvasive inspection of the gastrointestinal tract, especially in the small intestine. However, the latest clinical products have not been equipped with a sufficiently accurate localization system which makes it difficult to determine the location of intestinal abnormalities, and to apply follow-up interventions such as biopsy or drug delivery. In this paper, the authors present a novel localization method based on tracking three positron emission markers embedded inside an endoscopic capsule. Methods: Three spherical 22 Na markers with diameters of less than 1 mm are embedded in the cover of the capsule. Gamma ray detectors are arranged around a patient body to detect coincidence gamma rays emitted from the three markers. The position of each marker can then be estimated using the collected data by the authors’ tracking algorithm which consists of four consecutive steps: a method to remove corrupted data, an initialization method, a clustering method based on the Fuzzy C-means clustering algorithm, and a failure prediction method. Results: The tracking algorithm has been implemented inMATLAB utilizing simulation data generated from the Geant4 Application for Emission Tomography toolkit. The results show that this localization method can achieve real-time tracking with an average position error of less than 0.4 mm and an average orientation error of less than 2°. Conclusions: The authors conclude that this study has proven the feasibility and potential of the proposed technique in effectively determining the position and orientation of a robotic endoscopic capsule

  13. A Hierarchical Approach for Measuring the Consistency of Water Areas between Multiple Representations of Tile Maps with Different Scales

    Yilang Shen

    2017-08-01

    Full Text Available In geographic information systems, the reliability of querying, analysing, or reasoning results depends on the data quality. One central criterion of data quality is consistency, and identifying inconsistencies is crucial for maintaining the integrity of spatial data from multiple sources or at multiple resolutions. In traditional methods of consistency assessment, vector data are used as the primary experimental data. In this manuscript, we describe the use of a new type of raster data, tile maps, to access the consistency of information from multiscale representations of the water bodies that make up drainage systems. We describe a hierarchical methodology to determine the spatial consistency of tile-map datasets that display water areas in a raster format. Three characteristic indices, the degree of global feature consistency, the degree of local feature consistency, and the degree of overlap, are proposed to measure the consistency of multiscale representations of water areas. The perceptual hash algorithm and the scale-invariant feature transform (SIFT descriptor are applied to extract and measure the global and local features of water areas. By performing combined calculations using these three characteristic indices, the degrees of consistency of multiscale representations of water areas can be divided into five grades: exactly consistent, highly consistent, moderately consistent, less consistent, and inconsistent. For evaluation purposes, the proposed method is applied to several test areas from the Tiandi map of China. In addition, we identify key technologies that are related to the process of extracting water areas from a tile map. The accuracy of the consistency assessment method is evaluated, and our experimental results confirm that the proposed methodology is efficient and accurate.

  14. Analysis of recombination QTLs, segregation distortion, and epistasis for fitness in maize multiple populations using ultra-high-density markers

    Understanding the maize genomic features would be useful for the study of genetic diversity and evolution and for maize breeding. Here, we used two maize nested association mapping (NAM) populations separately derived in China (CN-NAM) and the US (US-NAM) to explore the maize genomic features. The t...

  15. Development and mapping of DArT markers within the Festuca - Lolium complex

    Kopecký, David; Bartos, Jan; Lukaszewski, Adam J

    2009-01-01

    Background Grasses are among the most important and widely cultivated plants on Earth. They provide high quality fodder for livestock, are used for turf and amenity purposes, and play a fundamental role in environment protection. Among cultivated grasses, species within the Festuca-Lolium complex...... predominate, especially in temperate regions. To facilitate high-throughput genome profiling and genetic mapping within the complex, we have developed a Diversity Arrays Technology (DArT) array for five grass species: F. pratensis, F. arundinacea, F. glaucescens, L. perenne and L. multiflorum. Results The DAr...

  16. A Spatial Framework to Map Heat Health Risks at Multiple Scales.

    Ho, Hung Chak; Knudby, Anders; Huang, Wei

    2015-12-18

    In the last few decades extreme heat events have led to substantial excess mortality, most dramatically in Central Europe in 2003, in Russia in 2010, and even in typically cool locations such as Vancouver, Canada, in 2009. Heat-related morbidity and mortality is expected to increase over the coming centuries as the result of climate-driven global increases in the severity and frequency of extreme heat events. Spatial information on heat exposure and population vulnerability may be combined to map the areas of highest risk and focus mitigation efforts there. However, a mismatch in spatial resolution between heat exposure and vulnerability data can cause spatial scale issues such as the Modifiable Areal Unit Problem (MAUP). We used a raster-based model to integrate heat exposure and vulnerability data in a multi-criteria decision analysis, and compared it to the traditional vector-based model. We then used the Getis-Ord G(i) index to generate spatially smoothed heat risk hotspot maps from fine to coarse spatial scales. The raster-based model allowed production of maps at spatial resolution, more description of local-scale heat risk variability, and identification of heat-risk areas not identified with the vector-based approach. Spatial smoothing with the Getis-Ord G(i) index produced heat risk hotspots from local to regional spatial scale. The approach is a framework for reducing spatial scale issues in future heat risk mapping, and for identifying heat risk hotspots at spatial scales ranging from the block-level to the municipality level.

  17. Exercise body surface potential mapping in single and multiple coronary artery disease

    Montague, T.J.; Witkowski, F.X.; Miller, R.M.; Johnstone, D.E.; MacKenzie, R.B.; Spencer, C.A.; Horacek, B.M.

    1990-01-01

    Body surface ST integral maps were recorded in 36 coronary artery disease (CAD) patients at: rest; peak, angina-limited exercise; and, 1 and 5 min of recovery. They were compared to maps of 15 CAD patients who exercised to fatigue, without angina, and eight normal subjects. Peak exercise heart rates were similar (NS) in all groups. With exercise angina, patients with two and three vessel CAD had significantly (p less than 0.05) greater decrease in the body surface sum of ST integral values than patients with single vessel CAD. CAD patients with exercise fatigue, in the absence of angina, had decreased ST integrals similar (NS) to patients with single vessel CAD who manifested angina and the normal control subjects. There was, however, considerable overlap among individuals; some patients with single vessel CAD had as much exercise ST integral decrease as patients with three vessel CAD. All CAD patients had persistent ST integral decreases at 5 min of recovery and there was a direct correlation of the recovery and peak exercise ST changes. Exercise ST changes correlated, as well, with quantitative CAD angiographic scores, but not with thallium perfusion scores. These data suggest exercise ST integral body surface mapping allows quantitation of myocardium at ischemic risk in patients with CAD, irrespective of the presence or absence of ischemic symptoms during exercise. A major potential application of this technique is selection of CAD therapy guided by quantitative assessment of ischemic myocardial risk

  18. A Synergy Cropland of China by Fusing Multiple Existing Maps and Statistics.

    Lu, Miao; Wu, Wenbin; You, Liangzhi; Chen, Di; Zhang, Li; Yang, Peng; Tang, Huajun

    2017-07-12

    Accurate information on cropland extent is critical for scientific research and resource management. Several cropland products from remotely sensed datasets are available. Nevertheless, significant inconsistency exists among these products and the cropland areas estimated from these products differ considerably from statistics. In this study, we propose a hierarchical optimization synergy approach (HOSA) to develop a hybrid cropland map of China, circa 2010, by fusing five existing cropland products, i.e., GlobeLand30, Climate Change Initiative Land Cover (CCI-LC), GlobCover 2009, MODIS Collection 5 (MODIS C5), and MODIS Cropland, and sub-national statistics of cropland area. HOSA simplifies the widely used method of score assignment into two steps, including determination of optimal agreement level and identification of the best product combination. The accuracy assessment indicates that the synergy map has higher accuracy of spatial locations and better consistency with statistics than the five existing datasets individually. This suggests that the synergy approach can improve the accuracy of cropland mapping and enhance consistency with statistics.

  19. Quantitative evaluation of cerebral white matter in patients with multiple sclerosis using multicomponent T2 mapping.

    Baranovicova, Eva; Mlynarik, Vladimir; Kantorova, Ema; Hnilicova, Petra; Dobrota, Dusan

    2016-05-01

    A standard magnetic resonance imaging (MRI) investigation of white matter (WM) areas with visible or expected pathology does not explain satisfactorily the relation between pathology and clinical outcome. Therefore, we focused on multicomponent T2 mapping of WM with the intention to characterize the WM, including normal-appearing white matter that has normal and prolonged T2 and lesions, including degenerated tissue. Twenty-nine patients with clinically diagnosed MS and 27 healthy controls underwent MRI examination. T2 mapping of the WM across the two whole MRI slices was carried out. The relative abundance of biologically relevant T2 regions was correlated with age and the expanded disability status scale (EDSS). The relative abundance of the T2 values of water trapped in myelin increased with age in both healthy subjects (p T2 assigned to intra- and extracellular water decreased with age in both groups (p T2 above 110 ms were not related to age, but strongly increased with EDSS (p T2 mapping of the WM can be a useful parameter for monitoring the progression of MS in patients.

  20. On optical detection of densely labeled synapses in neuropil and mapping connectivity with combinatorially multiplexed fluorescent synaptic markers.

    Yuriy Mishchenko

    Full Text Available We propose a new method for mapping neural connectivity optically, by utilizing Cre/Lox system Brainbow to tag synapses of different neurons with random mixtures of different fluorophores, such as GFP, YFP, etc., and then detecting patterns of fluorophores at different synapses using light microscopy (LM. Such patterns will immediately report the pre- and post-synaptic cells at each synaptic connection, without tracing neural projections from individual synapses to corresponding cell bodies. We simulate fluorescence from a population of densely labeled synapses in a block of hippocampal neuropil, completely reconstructed from electron microscopy data, and show that high-end LM is able to detect such patterns with over 95% accuracy. We conclude, therefore, that with the described approach neural connectivity in macroscopically large neural circuits can be mapped with great accuracy, in scalable manner, using fast optical tools, and straightforward image processing. Relying on an electron microscopy dataset, we also derive and explicitly enumerate the conditions that should be met to allow synaptic connectivity studies with high-resolution optical tools.

  1. Multiple SNP markers reveal fine-scale population and deep phylogeographic structure in European anchovy (Engraulis encrasicolus L.).

    Zarraonaindia, Iratxe

    2012-07-30

    Geographic surveys of allozymes, microsatellites, nuclear DNA (nDNA) and mitochondrial DNA (mtDNA) have detected several genetic subdivisions among European anchovy populations. However, these studies have been limited in their power to detect some aspects of population structure by the use of a single or a few molecular markers, or by limited geographic sampling. We use a multi-marker approach, 47 nDNA and 15 mtDNA single nucleotide polymorphisms (SNPs), to analyze 626 European anchovies from the whole range of the species to resolve shallow and deep levels of population structure. Nuclear SNPs define 10 genetic entities within two larger genetically distinctive groups associated with oceanic variables and different life-history traits. MtDNA SNPs define two deep phylogroups that reflect ancient dispersals and colonizations. These markers define two ecological groups. One major group of Iberian-Atlantic populations is associated with upwelling areas on narrow continental shelves and includes populations spawning and overwintering in coastal areas. A second major group includes northern populations in the North East (NE) Atlantic (including the Bay of Biscay) and the Mediterranean and is associated with wide continental shelves with local larval retention currents. This group tends to spawn and overwinter in oceanic areas. These two groups encompass ten populations that differ from previously defined management stocks in the Alboran Sea, Iberian-Atlantic and Bay of Biscay regions. In addition, a new North Sea-English Channel stock is defined. SNPs indicate that some populations in the Bay of Biscay are genetically closer to North Western (NW) Mediterranean populations than to other populations in the NE Atlantic, likely due to colonizations of the Bay of Biscay and NW Mediterranean by migrants from a common ancestral population. Northern NE Atlantic populations were subsequently established by migrants from the Bay of Biscay. Populations along the Iberian

  2. The renal protective effect of angiotensin receptor blockers depends on intra-individual response variation in multiple risk markers

    Schievink, Bauke; de Zeeuw, Dick; Parving, Hans-Henrik

    2015-01-01

    , haemoglobin, cholesterol and uric acid after 6 months of losartan treatment were assessed in the RENAAL database. Improvement in predictive performance of renal outcomes (ESRD or doubling serum creatinine) for each individual using ARB-induced changes in all risk markers was assessed by the relative...... integrative discrimination index (RIDI). RESULTS: SBP response showed high variability (mean -5.7 mmHg, 5(th) to 95(th) percentile -36.5 to +24.0 mmHg) between individuals. Changes in off-target parameters also showed high variability between individuals. No congruency was observed between responses...

  3. Mapping of the Pim-1 oncogene in mouse t-haplotypes and its use to define the relative map positions of the tcl loci t0(t6) and tw12 and the marker tf (tufted).

    Ark, B; Gummere, G; Bennett, D; Artzt, K

    1991-06-01

    Pim-1 is an oncogene activated in mouse T-cell lymphomas induced by Moloney and AKR mink cell focus (MCF) viruses. Pim-1 was previously mapped to chromosome 17 by somatic cell hybrids, and subsequently to the region between the hemoglobin alpha-chain pseudogene 4 (Hba-4ps) and the alpha-crystalline gene (Crya-1) by Southern blot analysis of DNA obtained from panels of recombinant inbred strains. We have now mapped Pim-1 more accurately in t-haplotypes by analysis of recombinant t-chromosomes. The recombinants were derived from Tts6tf/t12 parents backcrossed to + tf/ + tf, and scored for recombination between the loci of T and tf. For simplicity all t-complex lethal genes properly named tcl-tx are shortened to tx. The Pim-1 gene was localized 0.6 cM proximal to the tw12 lethal gene, thus placing the Pim-1 gene 5.2 cM distal to the H-2 region in t-haplotypes. Once mapped, the Pim-1 gene was used as a marker for further genetic analysis of t-haplotypes. tw12 is so close to tf that even with a large number of recombinants it was not possible to determine whether it is proximal or distal to tf. Southern blot analysis of DNA from T-tf recombinants with a separation of tw12 and tf indicated that tw12 is proximal to tf. The mapping of two allelic t-lethals, t0 and t6 with respect to tw12 and tf has also been a problem.(ABSTRACT TRUNCATED AT 250 WORDS)

  4. A Pilot Study of Multiple Password Interference Between Text and Map-Based Passwords

    Meng, Weizhi; Li, Wenjuan; Lee, Wang

    2017-01-01

    Today’s computer users have to remember several passwords for each of their accounts. It is easily noticed that people may have difficulty in remembering multiple passwords, which result in a weak password selection. Previous studies have shown that recall success rates are not statistically...

  5. Using AVIRIS data and multiple-masking techniques to map urban forest trees species

    Q. Xiao; S.L. Ustin; E.G. McPherson

    2004-01-01

    Tree type and species information are critical parameters for urban forest management, benefit cost analysis and urban planning. However, traditionally, these parameters have been derived based on limited field samples in urban forest management practice. In this study we used high-resolution Airborne Visible Infrared Imaging Spectrometer (AVIRIS) data and multiple-...

  6. a Pseudo-Random Number Generator Employing Multiple RÉNYI Maps

    Lui, Oi-Yan; Yuen, Ching-Hung; Wong, Kwok-Wo

    2013-11-01

    The increasing risk along with the drastic development of multimedia data transmission has raised a big concern on data security. A good pseudo-random number generator is an essential tool in cryptography. In this paper, we propose a novel pseudo-random number generator based on the controlled combination of the outputs of several digitized chaotic Rényi maps. The generated pseudo-random sequences have passed both the NIST 800-22 Revision 1a and the DIEHARD tests. Moreover, simulation results show that the proposed pseudo-random number generator requires less operation time than existing generators and is highly sensitive to the seed.

  7. Comparative mapping of Brassica juncea and Arabidopsis thaliana using Intron Polymorphism (IP markers: homoeologous relationships, diversification and evolution of the A, B and C Brassica genomes

    Gupta Vibha

    2008-03-01

    Full Text Available Abstract Background Extensive mapping efforts are currently underway for the establishment of comparative genomics between the model plant, Arabidopsis thaliana and various Brassica species. Most of these studies have deployed RFLP markers, the use of which is a laborious and time-consuming process. We therefore tested the efficacy of PCR-based Intron Polymorphism (IP markers to analyze genome-wide synteny between the oilseed crop, Brassica juncea (AABB genome and A. thaliana and analyzed the arrangement of 24 (previously described genomic block segments in the A, B and C Brassica genomes to study the evolutionary events contributing to karyotype variations in the three diploid Brassica genomes. Results IP markers were highly efficient and generated easily discernable polymorphisms on agarose gels. Comparative analysis of the segmental organization of the A and B genomes of B. juncea (present study with the A and B genomes of B. napus and B. nigra respectively (described earlier, revealed a high degree of colinearity suggesting minimal macro-level changes after polyploidization. The ancestral block arrangements that remained unaltered during evolution and the karyotype rearrangements that originated in the Oleracea lineage after its divergence from Rapa lineage were identified. Genomic rearrangements leading to the gain or loss of one chromosome each between the A-B and A-C lineages were deciphered. Complete homoeology in terms of block organization was found between three linkage groups (LG each for the A-B and A-C genomes. Based on the homoeology shared between the A, B and C genomes, a new nomenclature for the B genome LGs was assigned to establish uniformity in the international Brassica LG nomenclature code. Conclusion IP markers were highly effective in generating comparative relationships between Arabidopsis and various Brassica species. Comparative genomics between the three Brassica lineages established the major rearrangements

  8. Saccharomyces cerevisiae single-copy plasmids for auxotrophy compensation, multiple marker selection, and for designing metabolically cooperating communities [version 1; referees: 2 approved

    Michael Mülleder

    2016-09-01

    Full Text Available Auxotrophic markers are useful tools in cloning and genome editing, enable a large spectrum of genetic techniques, as well as facilitate the study of metabolite exchange interactions in microbial communities. If unused background auxotrophies are left uncomplemented however, yeast cells need to be grown in nutrient supplemented or rich growth media compositions, which precludes the analysis of biosynthetic metabolism, and which leads to a profound impact on physiology and gene expression. Here we present a series of 23 centromeric plasmids designed to restore prototrophy in typical Saccharomyces cerevisiae laboratory strains. The 23 single-copy plasmids complement for deficiencies in HIS3, LEU2, URA3, MET17 or LYS2 genes and in their combinations, to match the auxotrophic background of the popular functional-genomic yeast libraries that are based on the S288c strain. The plasmids are further suitable for designing self-establishing metabolically cooperating (SeMeCo communities, and possess a uniform multiple cloning site to exploit multiple parallel selection markers in protein expression experiments.

  9. A Preliminary Study on the Multiple Mapping Structure of Classification Systems for Heterogeneous Databases

    Seok-Hyoung Lee

    2012-06-01

    Full Text Available While science and technology information service portals and heterogeneous databases produced in Korea and other countries are integrated, methods of connecting the unique classification systems applied to each database have been studied. Results of technologists' research, such as, journal articles, patent specifications, and research reports, are organically related to each other. In this case, if the most basic and meaningful classification systems are not connected, it is difficult to achieve interoperability of the information and thus not easy to implement meaningful science technology information services through information convergence. This study aims to address the aforementioned issue by analyzing mapping systems between classification systems in order to design a structure to connect a variety of classification systems used in the academic information database of the Korea Institute of Science and Technology Information, which provides science and technology information portal service. This study also aims to design a mapping system for the classification systems to be applied to actual science and technology information services and information management systems.

  10. Propagation of error from parameter constraints in quantitative MRI: Example application of multiple spin echo T2 mapping.

    Lankford, Christopher L; Does, Mark D

    2018-02-01

    Quantitative MRI may require correcting for nuisance parameters which can or must be constrained to independently measured or assumed values. The noise and/or bias in these constraints propagate to fitted parameters. For example, the case of refocusing pulse flip angle constraint in multiple spin echo T 2 mapping is explored. An analytical expression for the mean-squared error of a parameter of interest was derived as a function of the accuracy and precision of an independent estimate of a nuisance parameter. The expression was validated by simulations and then used to evaluate the effects of flip angle (θ) constraint on the accuracy and precision of T⁁2 for a variety of multi-echo T 2 mapping protocols. Constraining θ improved T⁁2 precision when the θ-map signal-to-noise ratio was greater than approximately one-half that of the first spin echo image. For many practical scenarios, constrained fitting was calculated to reduce not just the variance but the full mean-squared error of T⁁2, for bias in θ⁁≲6%. The analytical expression derived in this work can be applied to inform experimental design in quantitative MRI. The example application to T 2 mapping provided specific cases, depending on θ⁁ accuracy and precision, in which θ⁁ measurement and constraint would be beneficial to T⁁2 variance or mean-squared error. Magn Reson Med 79:673-682, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

  11. Genome-Wide Association Mapping Reveals Multiple QTLs Governing Tolerance Response for Seedling Stage Chilling Stress in Indica Rice

    Sharat K. Pradhan

    2017-04-01

    Full Text Available Rice crop is sensitive to cold stress at seedling stage. A panel of population representing 304 shortlisted germplasm lines was studied for seedling stage chilling tolerance in indica rice. Six phenotypic classes were exposed to six low temperature stress regimes under control phenotyping facility to investigate response pattern. A panel of 66 genotypes representing all phenotypic classes was used for ensuring genetic diversity, population structure and association mapping for the trait using 58 simple sequence repeat (SSR and 2 direct trait linked markers. A moderate level of genetic diversity was detected in the panel population for the trait. Deviation of Hardy-Weinberg's expectation was detected in the studied population using Wright's F statistic. The panel showed 30% variation among population and 70% among individuals. The entire population was categorized into three sub-populations through STRUCTURE analysis. This revealed tolerance for the trait had a common primary ancestor for each sub-population with few admix individuals. The panel population showed the presence of many QTLs for cold stress tolerance in the individuals representing like genome-wide expression of the trait. Nineteen SSR markers were significantly associated at chilling stress of 8°C to 4°C for 7–21 days duration. Thus, the primers linked to the seedling stage cold tolerance QTLs namely qCTS9, qCTS-2, qCTS6.1, qSCT2, qSCT11, qSCT1a, qCTS-3.1, qCTS11.1, qCTS12.1, qCTS-1b, and CTB2 need to be pyramided for development of strongly chilling tolerant variety.

  12. MAPPING THE SHORES OF THE BROWN DWARF DESERT. II. MULTIPLE STAR FORMATION IN TAURUS-AURIGA

    Kraus, Adam L.; Ireland, Michael J.; Martinache, Frantz; Hillenbrand, Lynne A.

    2011-01-01

    We have conducted a high-resolution imaging study of the Taurus-Auriga star-forming region in order to characterize the primordial outcome of multiple star formation and the extent of the brown dwarf desert. Our survey identified 16 new binary companions to primary stars with masses of 0.25-2.5 M sun , raising the total number of binary pairs (including components of high-order multiples) with separations of 3-5000 AU to 90. We find that ∼2/3-3/4 of all Taurus members are multiple systems of two or more stars, while the other ∼1/4-1/3 appear to have formed as single stars; the distribution of high-order multiplicity suggests that fragmentation into a wide binary has no impact on the subsequent probability that either component will fragment again. The separation distribution for solar-type stars (0.7-2.5 M sun ) is nearly log-flat over separations of 3-5000 AU, but lower-mass stars (0.25-0.7 M sun ) show a paucity of binary companions with separations of ∼>200 AU. Across this full mass range, companion masses are well described with a linear-flat function; all system mass ratios (q = M B /M A ) are equally probable, apparently including substellar companions. Our results are broadly consistent with the two expected modes of binary formation (free-fall fragmentation on large scales and disk fragmentation on small scales), but the distributions provide some clues as to the epochs at which the companions are likely to form.

  13. Target intervention against multiple-risk markers to reduce cardiovascular disease in patients with type 2 diabetes

    Gaede, Peter; Pedersen, Oluf

    2004-01-01

    The risk of cardiovascular disease is markedly increased in patients with type 2 diabetes with a prevalence twice as high compared to the background population. With the recognition of multiple concomitant risk factors for both microvascular as well as cardiovascular disease in type 2 diabetic pa...

  14. Band width and multiple-angle valence-state mapping of diamond

    Jimenez, I.; Terminello, L.J.; Sutherland, D.G.J. [Lawrence Berkeley National Lab., CA (United States)] [and others

    1997-04-01

    The band width may be considered the single most important parameter characterizing the electronic structure of a solid. The ratio of band width and Coulomb repulsion determines how correlated or delocalized an electron system is. Some of the most interesting solids straddle the boundary between localized and delocalized, e.g. the high-temperature superconductors. The bulk of the band calculations available today is based on local density functional (DF) theory. Even though the Kohn-Sham eigenvalues from that theory do not represent the outcome of a band-mapping experiment, they are remarkably similar to the bands mapped via photoemission. Strictly speaking, one should use an excited state calculation that takes the solid`s many-body screening response to the hole created in photoemission into account. Diamond is a useful prototype semiconductor because of its low atomic number and large band width, which has made it a long-time favorite for testing band theory. Yet, the two experimental values of the band width of diamond have error bars of {+-}1 eV and differ by 3.2 eV. To obtain an accurate valence band width for diamond, the authors use a band-mapping method that collects momentum distributions instead of the usual energy distributions. This method has undergone extensive experimental and theoretical tests in determining the band width of lithium fluoride. An efficient, imaging photoelectron spectrometer is coupled with a state-of-the-art undulator beam line at the Advanced Light Source to allow collection of a large number of data sets. Since it takes only a few seconds to take a picture of the photoelectrons emitted into a 84{degrees} cone, the authors can use photon energies as high as 350 eV where the cross section for photoemission from the valence band is already quite low, but the emitted photoelectrons behave free-electron-like. This make its much easier to locate the origin of the inter-band transitions in momentum space.

  15. Band width and multiple-angle valence-state mapping of diamond

    Jimenez, I.; Terminello, L.J.; Sutherland, D.G.J.

    1997-01-01

    The band width may be considered the single most important parameter characterizing the electronic structure of a solid. The ratio of band width and Coulomb repulsion determines how correlated or delocalized an electron system is. Some of the most interesting solids straddle the boundary between localized and delocalized, e.g. the high-temperature superconductors. The bulk of the band calculations available today is based on local density functional (DF) theory. Even though the Kohn-Sham eigenvalues from that theory do not represent the outcome of a band-mapping experiment, they are remarkably similar to the bands mapped via photoemission. Strictly speaking, one should use an excited state calculation that takes the solid's many-body screening response to the hole created in photoemission into account. Diamond is a useful prototype semiconductor because of its low atomic number and large band width, which has made it a long-time favorite for testing band theory. Yet, the two experimental values of the band width of diamond have error bars of ±1 eV and differ by 3.2 eV. To obtain an accurate valence band width for diamond, the authors use a band-mapping method that collects momentum distributions instead of the usual energy distributions. This method has undergone extensive experimental and theoretical tests in determining the band width of lithium fluoride. An efficient, imaging photoelectron spectrometer is coupled with a state-of-the-art undulator beam line at the Advanced Light Source to allow collection of a large number of data sets. Since it takes only a few seconds to take a picture of the photoelectrons emitted into a 84 degrees cone, the authors can use photon energies as high as 350 eV where the cross section for photoemission from the valence band is already quite low, but the emitted photoelectrons behave free-electron-like. This make its much easier to locate the origin of the inter-band transitions in momentum space

  16. Interim Report on Multiple Sequence Alignments and TaqMan Signature Mapping to Phylogenetic Trees

    Gardner, S; Jaing, C

    2012-03-27

    The goal of this project is to develop forensic genotyping assays for select agent viruses, addressing a significant capability gap for the viral bioforensics and law enforcement community. We used a multipronged approach combining bioinformatics analysis, PCR-enriched samples, microarrays and TaqMan assays to develop high resolution and cost effective genotyping methods for strain level forensic discrimination of viruses. We have leveraged substantial experience and efficiency gained through year 1 on software development, SNP discovery, TaqMan signature design and phylogenetic signature mapping to scale up the development of forensics signatures in year 2. In this report, we have summarized the Taqman signature development for South American hemorrhagic fever viruses, tick-borne encephalitis viruses and henipaviruses, Old World Arenaviruses, filoviruses, Crimean-Congo hemorrhagic fever virus, Rift Valley fever virus and Japanese encephalitis virus.

  17. Multiple Linkage Disequilibrium Mapping Methods to Validate Additive Quantitative Trait Loci in Korean Native Cattle (Hanwoo

    Yi Li

    2015-07-01

    Full Text Available The efficiency of genome-wide association analysis (GWAS depends on power of detection for quantitative trait loci (QTL and precision for QTL mapping. In this study, three different strategies for GWAS were applied to detect QTL for carcass quality traits in the Korean cattle, Hanwoo; a linkage disequilibrium single locus regression method (LDRM, a combined linkage and linkage disequilibrium analysis (LDLA and a BayesCπ approach. The phenotypes of 486 steers were collected for weaning weight (WWT, yearling weight (YWT, carcass weight (CWT, backfat thickness (BFT, longissimus dorsi muscle area, and marbling score (Marb. Also the genotype data for the steers and their sires were scored with the Illumina bovine 50K single nucleotide polymorphism (SNP chips. For the two former GWAS methods, threshold values were set at false discovery rate <0.01 on a chromosome-wide level, while a cut-off threshold value was set in the latter model, such that the top five windows, each of which comprised 10 adjacent SNPs, were chosen with significant variation for the phenotype. Four major additive QTL from these three methods had high concordance found in 64.1 to 64.9Mb for Bos taurus autosome (BTA 7 for WWT, 24.3 to 25.4Mb for BTA14 for CWT, 0.5 to 1.5Mb for BTA6 for BFT and 26.3 to 33.4Mb for BTA29 for BFT. Several candidate genes (i.e. glutamate receptor, ionotropic, ampa 1 [GRIA1], family with sequence similarity 110, member B [FAM110B], and thymocyte selection-associated high mobility group box [TOX] may be identified close to these QTL. Our result suggests that the use of different linkage disequilibrium mapping approaches can provide more reliable chromosome regions to further pinpoint DNA makers or causative genes in these regions.

  18. The ROCK inhibitor Y-27632 improves recovery of human embryonic stem cells after fluorescence-activated cell sorting with multiple cell surface markers.

    Nil Emre

    Full Text Available BACKGROUND: Due to the inherent sensitivity of human embryonic stem cells (hESCs to manipulations, the recovery and survival of hESCs after fluorescence-activated cell sorting (FACS can be low. Additionally, a well characterized and robust methodology for performing FACS on hESCs using multiple-cell surface markers has not been described. The p160-Rho-associated coiled kinase (ROCK inhibitor, Y-27632, previously has been identified as enhancing survival of hESCs upon single-cell dissociation, as well as enhancing recovery from cryopreservation. Here we examined the application of Y-27632 to hESCs after FACS to improve survival in both feeder-dependent and feeder-independent growth conditions. METHODOLOGY/PRINCIPAL FINDINGS: HESCs were sorted using markers for SSEA-3, TRA-1-81, and SSEA-1. Cells were plated after sorting for 24 hours in either the presence or the absence of Y-27632. In both feeder-dependent and feeder-independent conditions, cell survival was greater when Y-27632 was applied to the hESCs after sort. Specifically, treatment of cells with Y-27632 improved post-sort recovery up to four fold. To determine the long-term effects of sorting with and without the application of Y-27632, hESCs were further analyzed. Specifically, hESCs sorted with and without the addition of Y-27632 retained normal morphology, expressed hESC-specific markers as measured by immunocytochemistry and flow cytometry, and maintained a stable karyotype. In addition, the hESCs could differentiate into three germ layers in vitro and in vivo in both feeder-dependent and feeder-independent growth conditions. CONCLUSIONS/SIGNIFICANCE: The application of Y-27632 to hESCs after cell sorting improves cell recovery with no observed effect on pluripotency, and enables the consistent recovery of hESCs by FACS using multiple surface markers. This improved methodology for cell sorting of hESCs will aid many applications such as removal of hESCs from secondary cell types

  19. Development of eSSR-Markers in Setaria italica and Their Applicability in Studying Genetic Diversity, Cross-Transferability and Comparative Mapping in Millet and Non-Millet Species.

    Kajal Kumari

    Full Text Available Foxtail millet (Setariaitalica L. is a tractable experimental model crop for studying functional genomics of millets and bioenergy grasses. But the limited availability of genomic resources, particularly expressed sequence-based genic markers is significantly impeding its genetic improvement. Considering this, we attempted to develop EST-derived-SSR (eSSR markers and utilize them in germplasm characterization, cross-genera transferability and in silico comparative mapping. From 66,027 foxtail millet EST sequences 24,828 non-redundant ESTs were deduced, representing ~16 Mb, which revealed 534 (~2% eSSRs in 495 SSR containing ESTs at a frequency of 1/30 kb. A total of 447 pp were successfully designed, of which 327 were mapped physically onto nine chromosomes. About 106 selected primer pairs representing the foxtail millet genome showed high-level of cross-genera amplification at an average of ~88% in eight millets and four non-millet species. Broad range of genetic diversity (0.02-0.65 obtained in constructed phylogenetic tree using 40 eSSR markers demonstrated its utility in germplasm characterizations and phylogenetics. Comparative mapping of physically mapped eSSR markers showed considerable proportion of sequence-based orthology and syntenic relationship between foxtail millet chromosomes and sorghum (~68%, maize (~61% and rice (~42% chromosomes. Synteny analysis of eSSRs of foxtail millet, rice, maize and sorghum suggested the nested chromosome fusion frequently observed in grass genomes. Thus, for the first time we had generated large-scale eSSR markers in foxtail millet and demonstrated their utility in germplasm characterization, transferability, phylogenetics and comparative mapping studies in millets and bioenergy grass species.

  20. Development of eSSR-Markers in Setaria italica and Their Applicability in Studying Genetic Diversity, Cross-Transferability and Comparative Mapping in Millet and Non-Millet Species.

    Kumari, Kajal; Muthamilarasan, Mehanathan; Misra, Gopal; Gupta, Sarika; Subramanian, Alagesan; Parida, Swarup Kumar; Chattopadhyay, Debasis; Prasad, Manoj

    2013-01-01

    Foxtail millet (Setariaitalica L.) is a tractable experimental model crop for studying functional genomics of millets and bioenergy grasses. But the limited availability of genomic resources, particularly expressed sequence-based genic markers is significantly impeding its genetic improvement. Considering this, we attempted to develop EST-derived-SSR (eSSR) markers and utilize them in germplasm characterization, cross-genera transferability and in silico comparative mapping. From 66,027 foxtail millet EST sequences 24,828 non-redundant ESTs were deduced, representing ~16 Mb, which revealed 534 (~2%) eSSRs in 495 SSR containing ESTs at a frequency of 1/30 kb. A total of 447 pp were successfully designed, of which 327 were mapped physically onto nine chromosomes. About 106 selected primer pairs representing the foxtail millet genome showed high-level of cross-genera amplification at an average of ~88% in eight millets and four non-millet species. Broad range of genetic diversity (0.02-0.65) obtained in constructed phylogenetic tree using 40 eSSR markers demonstrated its utility in germplasm characterizations and phylogenetics. Comparative mapping of physically mapped eSSR markers showed considerable proportion of sequence-based orthology and syntenic relationship between foxtail millet chromosomes and sorghum (~68%), maize (~61%) and rice (~42%) chromosomes. Synteny analysis of eSSRs of foxtail millet, rice, maize and sorghum suggested the nested chromosome fusion frequently observed in grass genomes. Thus, for the first time we had generated large-scale eSSR markers in foxtail millet and demonstrated their utility in germplasm characterization, transferability, phylogenetics and comparative mapping studies in millets and bioenergy grass species.

  1. What do you mean "drunk"? Convergent validation of multiple methods of mapping alcohol expectancy memory networks.

    Reich, Richard R; Ariel, Idan; Darkes, Jack; Goldman, Mark S

    2012-09-01

    The configuration and activation of memory networks have been theorized as mechanisms that underlie the often observed link between alcohol expectancies and drinking. A key component of this network is the expectancy "drunk." The memory network configuration of "drunk" was mapped by using cluster analysis of data gathered from the paired-similarities task (PST) and the Alcohol Expectancy Multi-Axial Assessment (AEMAX). A third task, the free associates task (FA), assessed participants' strongest alcohol expectancy associates and was used as a validity check for the cluster analyses. Six hundred forty-seven 18-19-year-olds completed these measures and a measure of alcohol consumption at baseline assessment for a 5-year longitudinal study. For both the PST and AEMAX, "drunk" clustered with mainly negative and sedating effects (e.g., "sick," "dizzy," "sleepy") in lighter drinkers and with more positive and arousing effects (e.g., "happy," "horny," "outgoing") in heavier drinkers, showing that the cognitive organization of expectancies reflected drinker type (and might influence the choice to drink). Consistent with the cluster analyses, in participants who gave "drunk" as an FA response, heavier drinkers rated the word as more positive and arousing than lighter drinkers. Additionally, gender did not account for the observed drinker-type differences. These results support the notion that for some emerging adults, drinking may be linked to what they mean by the word "drunk." PsycINFO Database Record (c) 2012 APA, all rights reserved.

  2. Mapping multiple components of malaria risk for improved targeting of elimination interventions.

    Cohen, Justin M; Le Menach, Arnaud; Pothin, Emilie; Eisele, Thomas P; Gething, Peter W; Eckhoff, Philip A; Moonen, Bruno; Schapira, Allan; Smith, David L

    2017-11-13

    There is a long history of considering the constituent components of malaria risk and the malaria transmission cycle via the use of mathematical models, yet strategic planning in endemic countries tends not to take full advantage of available disease intelligence to tailor interventions. National malaria programmes typically make operational decisions about where to implement vector control and surveillance activities based upon simple categorizations of annual parasite incidence. With technological advances, an enormous opportunity exists to better target specific malaria interventions to the places where they will have greatest impact by mapping and evaluating metrics related to a variety of risk components, each of which describes a different facet of the transmission cycle. Here, these components and their implications for operational decision-making are reviewed. For each component, related mappable malaria metrics are also described which may be measured and evaluated by malaria programmes seeking to better understand the determinants of malaria risk. Implementing tailored programmes based on knowledge of the heterogeneous distribution of the drivers of malaria transmission rather than only consideration of traditional metrics such as case incidence has the potential to result in substantial improvements in decision-making. As programmes improve their ability to prioritize their available tools to the places where evidence suggests they will be most effective, elimination aspirations may become increasingly feasible.

  3. Endovascular treatment of chronic cerebro spinal venous insufficiency in patients with multiple sclerosis modifies circulating markers of endothelial dysfunction and coagulation activation: a prospective study.

    Napolitano, Mariasanta; Bruno, Aldo; Mastrangelo, Diego; De Vizia, Marcella; Bernardo, Benedetto; Rosa, Buonagura; De Lucia, Domenico

    2014-10-01

    We performed a monocentric observational prospective study to evaluate coagulation activation and endothelial dysfunction parameters in patients with multiple sclerosis undergoing endovascular treatment for cerebro-spinal-venous insufficiency. Between February 2011 and July 2012, 144 endovascular procedures in 110 patients with multiple sclerosis and chronical cerebro-spinal venous insufficiency were performed and they were prospectively analyzed. Each patient was included in the study according to previously published criteria, assessed by the investigators before enrollment. Endothelial dysfunction and coagulation activation parameters were determined before the procedure and during follow-up at 1, 3, 6, 9, 12, 15 and 18 months after treatment, respectively. After the endovascular procedure, patients were treated with standard therapies, with the addition of mesoglycan. Fifty-five percent of patients experienced a favorable outcome of multiple sclerosis within 1 month after treatment, 25% regressed in the following 3 months, 24.9% did not experience any benefit. In only 0.1% patients, acute recurrence was observed and it was treated with high-dose immunosuppressive therapy. No major complications were observed. Coagulation activation and endothelial dysfunction parameters were shown to be reduced at 1 month and stable up to 12-month follow-up, and they were furthermore associated with a good clinical outcome. Endovascular procedures performed by a qualified staff are well tolerated; they can be associated with other currently adopted treatments. Correlations between inflammation, coagulation activation and neurodegenerative disorders are here supported by the observed variations in plasma levels of markers of coagulation activation and endothelial dysfunction.

  4. Complete analysis of MAP/G/1/N queue with single (multiple vacation(s under limited service discipline

    U. C. Gupta

    2005-01-01

    Full Text Available We consider a finite-buffer single-server queue with Markovian arrival process (MAP where the server serves a limited number of customers, and when the limit is reached it goes on vacation. Both single- and multiple-vacation policies are analyzed and the queue length distributions at various epochs, such as pre-arrival, arbitrary, departure, have been obtained. The effect of certain model parameters on some important performance measures, like probability of loss, mean queue lengths, mean waiting time, is discussed. The model can be applied in computer communication and networking, for example, performance analysis of token passing ring of LAN and SVC (switched virtual connection of ATM.

  5. The association between intra- and juxta-cortical pathology and cognitive impairment in multiple sclerosis by quantitative T2* mapping at 7 T MRI.

    Louapre, Céline; Govindarajan, Sindhuja T; Giannì, Costanza; Madigan, Nancy; Nielsen, A Scott; Sloane, Jacob A; Kinkel, Revere P; Mainero, Caterina

    2016-01-01

    Using quantitative T 2 * at 7 Tesla (T) magnetic resonance imaging, we investigated whether impairment in selective cognitive functions in multiple sclerosis (MS) can be explained by pathology in specific areas and/or layers of the cortex. Thirty-one MS patients underwent neuropsychological evaluation, acquisition of 7 T multi-echo T 2 * gradient-echo sequences, and 3 T anatomical images for cortical surfaces reconstruction. Seventeen age-matched healthy subjects served as controls. Cortical T 2 * maps were sampled at various depths throughout the cortex and juxtacortex. Relation between T 2 *, neuropsychological scores and a cognitive index (CI), calculated from a principal component analysis on the whole battery, was tested by a general linear model. Cognitive impairment correlated with T 2 * increase, independently from white matter lesions and cortical thickness, in cortical areas highly relevant for cognition belonging to the default-mode network (p < 0.05 corrected). Dysfunction in different cognitive functions correlated with longer T 2 * in selective cortical regions, most of which showed longer T 2 * relative to controls. For most tests, this association was strongest in deeper cortical layers. Executive dysfunction, however, was mainly related with pathology in juxtameningeal cortex. T 2 * explained up to 20% of the variance of the CI, independently of conventional imaging metrics (adjusted-R 2 : 52-67%, p < 5.10 - 4 ). Location of pathology across the cortical width and mantle showed selective correlation with impairment in differing cognitive domains. These findings may guide studies at lower field strength designed to develop surrogate markers of cognitive impairment in MS.

  6. Multivariate quantile mapping bias correction: an N-dimensional probability density function transform for climate model simulations of multiple variables

    Cannon, Alex J.

    2018-01-01

    Most bias correction algorithms used in climatology, for example quantile mapping, are applied to univariate time series. They neglect the dependence between different variables. Those that are multivariate often correct only limited measures of joint dependence, such as Pearson or Spearman rank correlation. Here, an image processing technique designed to transfer colour information from one image to another—the N-dimensional probability density function transform—is adapted for use as a multivariate bias correction algorithm (MBCn) for climate model projections/predictions of multiple climate variables. MBCn is a multivariate generalization of quantile mapping that transfers all aspects of an observed continuous multivariate distribution to the corresponding multivariate distribution of variables from a climate model. When applied to climate model projections, changes in quantiles of each variable between the historical and projection period are also preserved. The MBCn algorithm is demonstrated on three case studies. First, the method is applied to an image processing example with characteristics that mimic a climate projection problem. Second, MBCn is used to correct a suite of 3-hourly surface meteorological variables from the Canadian Centre for Climate Modelling and Analysis Regional Climate Model (CanRCM4) across a North American domain. Components of the Canadian Forest Fire Weather Index (FWI) System, a complicated set of multivariate indices that characterizes the risk of wildfire, are then calculated and verified against observed values. Third, MBCn is used to correct biases in the spatial dependence structure of CanRCM4 precipitation fields. Results are compared against a univariate quantile mapping algorithm, which neglects the dependence between variables, and two multivariate bias correction algorithms, each of which corrects a different form of inter-variable correlation structure. MBCn outperforms these alternatives, often by a large margin

  7. Gaia eclipsing binary and multiple systems. Supervised classification and self-organizing maps

    Süveges, M.; Barblan, F.; Lecoeur-Taïbi, I.; Prša, A.; Holl, B.; Eyer, L.; Kochoska, A.; Mowlavi, N.; Rimoldini, L.

    2017-07-01

    Context. Large surveys producing tera- and petabyte-scale databases require machine-learning and knowledge discovery methods to deal with the overwhelming quantity of data and the difficulties of extracting concise, meaningful information with reliable assessment of its uncertainty. This study investigates the potential of a few machine-learning methods for the automated analysis of eclipsing binaries in the data of such surveys. Aims: We aim to aid the extraction of samples of eclipsing binaries from such databases and to provide basic information about the objects. We intend to estimate class labels according to two different, well-known classification systems, one based on the light curve morphology (EA/EB/EW classes) and the other based on the physical characteristics of the binary system (system morphology classes; detached through overcontact systems). Furthermore, we explore low-dimensional surfaces along which the light curves of eclipsing binaries are concentrated, and consider their use in the characterization of the binary systems and in the exploration of biases of the full unknown Gaia data with respect to the training sets. Methods: We have explored the performance of principal component analysis (PCA), linear discriminant analysis (LDA), Random Forest classification and self-organizing maps (SOM) for the above aims. We pre-processed the photometric time series by combining a double Gaussian profile fit and a constrained smoothing spline, in order to de-noise and interpolate the observed light curves. We achieved further denoising, and selected the most important variability elements from the light curves using PCA. Supervised classification was performed using Random Forest and LDA based on the PC decomposition, while SOM gives a continuous 2-dimensional manifold of the light curves arranged by a few important features. We estimated the uncertainty of the supervised methods due to the specific finite training set using ensembles of models constructed

  8. MRD Testing in Multiple Myeloma: From a Surrogate Marker of Clinical Outcomes to an Every-Day Clinical Tool.

    Landgren, Ola

    2018-01-01

    Minimal residual disease (MRD) testing in multiple myeloma is here to stay. Studies show that MRD negativity is consistently associated with longer progression-free survival (PFS). It is just a matter of time until MRD negativity will become a regulatory endpoint for drug approval. Until that can happen, more analysis will be required to define the exact details of MRD in the regulatory setting. For example, for randomized studies there is need to define the amount of improvement in MRD negativity between the experimental arm and the control arm at a given time-point for a drug to obtain regulatory accelerated approval. Such efforts are underway. For the multiple myeloma field as a whole, important tasks for the (near) coming future are as follows: (1) to conduct or finalize the expanded analysis to define the exact details of MRD in the regulatory setting, (2) to develop new and better MRD assays-both more sensitive MRD assays for bone marrow aspirates and nonbone marrow aspirate-based assays (eg, blood-based and imaging-based MRD assays), and (3) to design novel clinical studies to formally assess the effect of MRD negativity in clinical decision making. The aim with this issue of the Journal is to provide a deep and comprehensive summary of the latest MRD knowledge in the field, and to outline future directions. Copyright © 2018 Elsevier Inc. All rights reserved.

  9. Non-invasive markers of bone turnover and plasma cytokines differ in osteoporotic patients with multiple myeloma and monoclonal gammopathies of undetermined significance

    Diamond, T.; Levy, S.; Smith, A.; Day, P.; Manoharan, A.

    2001-01-01

    Multiple myeloma (MM) is a common malignancy manifest by bone marrow infiltration with malignant plasma cells, the production of a paraprotein and lytic bone lesions. Monoclonal gammopathy of undetermined significance (MGUS) is assumed to be the precursor of clinically apparent myeloma, with one or more additional genetic events being required for progression to MM. Elderly patients presenting with osteoporosis and skeletal fractures are not infrequently found to have elevated serum paraprotein concentrations suggestive of either MM or MGUS. Differentiating between these two clinical disorders may prove challenging, despite bone marrow biopsy evidence of plasmacytosis. The underlying pathogenesis of bone loss in these conditions is complex and may be attributed to cytokine-induced osteoclastogenesis coupled with increased osteoclastic bone resorption. In the present study, various markers of bone turnover and plasma cytokines were measured in order to determine whether they may be of value in differentiating between these two disorders. It is concluded that the urinary deoxypyridinoline excretion rate is a sensitive marker of bone resorption and of underlying bone disease activity. It may also help to differentiate between MM and MGUS

  10. Increasing serum levels of vitamin A, D and E are associated with alterations of different inflammation markers in patients with multiple sclerosis.

    Røsjø, Egil; Myhr, Kjell-Morten; Løken-Amsrud, Kristin Ingeleiv; Bakke, Søren Jacob; Beiske, Antonie G; Bjerve, Kristian S; Hovdal, Harald; Lilleås, Finn; Midgard, Rune; Pedersen, Tom; Benth, Jūratė Saltytė; Torkildsen, Øivind; Wergeland, Stig; Michelsen, Annika E; Aukrust, Pål; Ueland, Thor; Holmøy, Trygve

    2014-06-15

    To explore the relationships between vitamin A, D and E and inflammation in relapsing remitting multiple sclerosis, we assessed their associations with 11 inflammation markers in 9 serial serum samples from 85 patients, before and during interferon-β1a treatment. A negative association was found between vitamin A and pentraxin 3 independent of interferon-β1a use, whereas positive associations between vitamin D and interleukin-1 receptor antagonist and secreted frizzled-related protein 3 were seen before, and between vitamin E and chemokine (C-X-C motif) ligand 16 during interferon-β1a treatment. These findings suggest associations with diverse inflammatory pathways, which may be differentially influenced by interferon-β1a treatment. Copyright © 2014 Elsevier B.V. All rights reserved.

  11. Phylogenetic reconstruction and DNA barcoding for closely related pine moth species (Dendrolimus) in China with multiple gene markers.

    Dai, Qing-Yan; Gao, Qiang; Wu, Chun-Sheng; Chesters, Douglas; Zhu, Chao-Dong; Zhang, Ai-Bing

    2012-01-01

    Unlike distinct species, closely related species offer a great challenge for phylogeny reconstruction and species identification with DNA barcoding due to their often overlapping genetic variation. We tested a sibling species group of pine moth pests in China with a standard cytochrome c oxidase subunit I (COI) gene and two alternative internal transcribed spacer (ITS) genes (ITS1 and ITS2). Five different phylogenetic/DNA barcoding analysis methods (Maximum likelihood (ML)/Neighbor-joining (NJ), "best close match" (BCM), Minimum distance (MD), and BP-based method (BP)), representing commonly used methodology (tree-based and non-tree based) in the field, were applied to both single-gene and multiple-gene analyses. Our results demonstrated clear reciprocal species monophyly for three relatively distant related species, Dendrolimus superans, D. houi, D. kikuchii, as recovered by both single and multiple genes while the phylogenetic relationship of three closely related species, D. punctatus, D. tabulaeformis, D. spectabilis, could not be resolved with the traditional tree-building methods. Additionally, we find the standard COI barcode outperforms two nuclear ITS genes, whatever the methods used. On average, the COI barcode achieved a success rate of 94.10-97.40%, while ITS1 and ITS2 obtained a success rate of 64.70-81.60%, indicating ITS genes are less suitable for species identification in this case. We propose the use of an overall success rate of species identification that takes both sequencing success and assignation success into account, since species identification success rates with multiple-gene barcoding system were generally overestimated, especially by tree-based methods, where only successfully sequenced DNA sequences were used to construct a phylogenetic tree. Non-tree based methods, such as MD, BCM, and BP approaches, presented advantages over tree-based methods by reporting the overall success rates with statistical significance. In addition, our

  12. Phylogenetic reconstruction and DNA barcoding for closely related pine moth species (Dendrolimus in China with multiple gene markers.

    Qing-Yan Dai

    Full Text Available Unlike distinct species, closely related species offer a great challenge for phylogeny reconstruction and species identification with DNA barcoding due to their often overlapping genetic variation. We tested a sibling species group of pine moth pests in China with a standard cytochrome c oxidase subunit I (COI gene and two alternative internal transcribed spacer (ITS genes (ITS1 and ITS2. Five different phylogenetic/DNA barcoding analysis methods (Maximum likelihood (ML/Neighbor-joining (NJ, "best close match" (BCM, Minimum distance (MD, and BP-based method (BP, representing commonly used methodology (tree-based and non-tree based in the field, were applied to both single-gene and multiple-gene analyses. Our results demonstrated clear reciprocal species monophyly for three relatively distant related species, Dendrolimus superans, D. houi, D. kikuchii, as recovered by both single and multiple genes while the phylogenetic relationship of three closely related species, D. punctatus, D. tabulaeformis, D. spectabilis, could not be resolved with the traditional tree-building methods. Additionally, we find the standard COI barcode outperforms two nuclear ITS genes, whatever the methods used. On average, the COI barcode achieved a success rate of 94.10-97.40%, while ITS1 and ITS2 obtained a success rate of 64.70-81.60%, indicating ITS genes are less suitable for species identification in this case. We propose the use of an overall success rate of species identification that takes both sequencing success and assignation success into account, since species identification success rates with multiple-gene barcoding system were generally overestimated, especially by tree-based methods, where only successfully sequenced DNA sequences were used to construct a phylogenetic tree. Non-tree based methods, such as MD, BCM, and BP approaches, presented advantages over tree-based methods by reporting the overall success rates with statistical significance. In

  13. IgV peptide mapping of native Ro60 autoantibody proteomes in primary Sjögren's syndrome reveals molecular markers of Ro/La diversification.

    Wang, Jing J; Al Kindi, Mahmood A; Colella, Alex D; Dykes, Lukah; Jackson, Michael W; Chataway, Tim K; Reed, Joanne H; Gordon, Tom P

    2016-12-01

    We have used high-resolution mass spectrometry to sequence precipitating anti-Ro60 proteomes from sera of patients with primary Sjögren's syndrome and compare immunoglobulin variable-region (IgV) peptide signatures in Ro/La autoantibody subsets. Anti-Ro60 were purified by elution from native Ro60-coated ELISA plates and subjected to combined de novo amino acid sequencing and database matching. Monospecific anti-Ro60 Igs comprised dominant public and minor private sets of IgG1 kappa and lambda restricted heavy and light chains. Specific IgV amino acid substitutions stratified anti-Ro60 from anti-Ro60/La responses, providing a molecular fingerprint of Ro60/La determinant spreading and suggesting that different forms of Ro60 antigen drive these responses. Sequencing of linked anti-Ro52 proteomes from individual patients and comparison with their anti-Ro60 partners revealed sharing of a dominant IGHV3-23/IGKV3-20 paired clonotype but with divergent IgV mutational signatures. In summary, anti-Ro60 IgV peptide mapping provides insights into Ro/La autoantibody diversification and reveals serum-based molecular markers of humoral Ro60 autoimmunity. Copyright © 2016 Elsevier Inc. All rights reserved.

  14. Material wealth in 3D: Mapping multiple paths to prosperity in low- and middle- income countries.

    Hruschka, Daniel J; Hadley, Craig; Hackman, Joseph

    2017-01-01

    Material wealth is a key factor shaping human development and well-being. Every year, hundreds of studies in social science and policy fields assess material wealth in low- and middle-income countries assuming that there is a single dimension by which households can move from poverty to prosperity. However, a one-dimensional model may miss important kinds of prosperity, particularly in countries where traditional subsistence-based livelihoods coexist with modern cash economies. Using multiple correspondence analysis to analyze representative household data from six countries-Nepal, Bangladesh, Ethiopia, Kenya, Tanzania and Guatemala-across three world regions, we identify a number of independent dimension of wealth, each with a clear link to locally relevant pathways to success in cash and agricultural economies. In all cases, the first dimension identified by this approach replicates standard one-dimensional estimates and captures success in cash economies. The novel dimensions we identify reflect success in different agricultural sectors and are independently associated with key benchmarks of food security and human growth, such as adult body mass index and child height. The multidimensional models of wealth we describe here provide new opportunities for examining the causes and consequences of wealth inequality that go beyond success in cash economies, for tracing the emergence of hybrid pathways to prosperity, and for assessing how these different pathways to economic success carry different health risks and social opportunities.

  15. Material wealth in 3D: Mapping multiple paths to prosperity in low- and middle- income countries.

    Daniel J Hruschka

    Full Text Available Material wealth is a key factor shaping human development and well-being. Every year, hundreds of studies in social science and policy fields assess material wealth in low- and middle-income countries assuming that there is a single dimension by which households can move from poverty to prosperity. However, a one-dimensional model may miss important kinds of prosperity, particularly in countries where traditional subsistence-based livelihoods coexist with modern cash economies. Using multiple correspondence analysis to analyze representative household data from six countries-Nepal, Bangladesh, Ethiopia, Kenya, Tanzania and Guatemala-across three world regions, we identify a number of independent dimension of wealth, each with a clear link to locally relevant pathways to success in cash and agricultural economies. In all cases, the first dimension identified by this approach replicates standard one-dimensional estimates and captures success in cash economies. The novel dimensions we identify reflect success in different agricultural sectors and are independently associated with key benchmarks of food security and human growth, such as adult body mass index and child height. The multidimensional models of wealth we describe here provide new opportunities for examining the causes and consequences of wealth inequality that go beyond success in cash economies, for tracing the emergence of hybrid pathways to prosperity, and for assessing how these different pathways to economic success carry different health risks and social opportunities.

  16. GAP1, a novel selection and counter-selection marker for multiple gene disruptions in Saccharomyces cerevisiae

    Regenberg, Birgitte; Hansen, J.

    2000-01-01

    the GAP1 gene. This is caused by recombination between two Salmonella typuimurium hisG direct repeats embracing GAP1, and will result in a sub-population of gap1 cells. Such cells are selected on a medium containing D-histidine, and may subsequently be used for a second gene disruption. Hence, multiple...... flanked by short (60 bp) stretches of the gene in question. Through homologous recombination, the cassette will integrate into the target gene, which is thus replaced by GAP1, and mutants are selected for on minimal L-citrulline medium. When propagated under non-selective conditions, some cells will lose...... gene disruptions can be made fast, cheaply and easily in a gap1 strain, with two positive selection steps for each disruption. Copyright (C) 2000 John Wiley & Sons, Ltd....

  17. MARCADORES RAPD PARA MAPEAMENTO GENÉTICO E SELEÇÃO DE HÍBRIDOS DE CITROS RAPD MARKERS TO GENETIC MAPPING AND SELECTION OF CITRUS HYBRIDS

    ROBERTO PEDROSO DE OLIVEIRA

    2001-12-01

    Full Text Available Os marcadores moleculares apresentam várias aplicações no melhoramento de plantas, permitindo uma série de análises genéticas. Este trabalho foi realizado com o objetivo de estabelecer marcadores RAPD para serem utilizados em estudos de mapeamento genético e na seleção de híbridos entre tangerina-'Cravo' (Citrus reticulata Blanco e laranja-'Pêra' (C. sinensis (L. Osbeck. Extraiu-se DNA de folhas dos parentais e de seis híbridos F1. As reações de amplificação foram preparadas em 13 uL de solução, constituída por tampão 1x GIBCO BRL; soluções 1,54 mM de MgCl2 e 0,2 mM de cada dNTP; 15 ng de cada 'primer'; 1,5 unidade de 'Taq DNA Polymerase' e 15 ng de DNA genômico. As reações foram realizadas em termocicladores programados para 36 ciclos de 1 min a 92ºC, 1 min a 36ºC, 2 min a 72ºC e 10 min de extensão a 72ºC. Foram testados 'primers' decâmeros arbitrários dos 'kits' A, AB, AT, AV, B, C, D, E, G, H, M, N, P, Q, R e U da Operon, sendo selecionados 113 por apresentarem polimorfismo, com número de marcadores variando de 1 a 6 por 'primer'. Esses 'primers' amplificaram 201 (23,13% bandas polimórficas, aplicáveis no mapeamento genético e seleção de híbridos. A freqüência de 'primers' com 1; 2; 3; 4; 5 e 6 bandas polimórficas foi de 49,5%, 33,6%, 9,7%, 4,4%, 1,8% e 1,0%, respectivamente.Molecular markers have many applications in plant breeding, enabling some types of genetic analyses. The aim of this work was to establish RAPD markers to be used to genetic mapping studies and selection of hybrids between 'Cravo' tangerine (Citrus reticulata Blanco and 'Pêra' orange (C. sinensis (L. Osbeck. DNA of the parents and six hybrids F1 was isolated from the leaves. The amplification reactions were performed in volumes of 13 µL, composed by GIBCO BRL 1x buffer, 1,54 mM MgCl2, 0,2 mM of each dNTP, 15 ng of each primer, 1,5 unit of Taq DNA Polymerase and 15 ng of genomic DNA. These reactions were carried out in

  18. A Partial Least Square Approach for Modeling Gene-gene and Gene-environment Interactions When Multiple Markers Are Genotyped

    Wang, Tao; Ho, Gloria; Ye, Kenny; Strickler, Howard; Elston, Robert C.

    2008-01-01

    Genetic association studies achieve an unprecedented level of resolution in mapping disease genes by genotyping dense SNPs in a gene region. Meanwhile, these studies require new powerful statistical tools that can optimally handle a large amount of information provided by genotype data. A question that arises is how to model interactions between two genes. Simply modeling all possible interactions between the SNPs in two gene regions is not desirable because a greatly increased number of degrees of freedom can be involved in the test statistic. We introduce an approach to reduce the genotype dimension in modeling interactions. The genotype compression of this approach is built upon the information on both the trait and the cross-locus gametic disequilibrium between SNPs in two interacting genes, in such a way as to parsimoniously model the interactions without loss of useful information in the process of dimension reduction. As a result, it improves power to detect association in the presence of gene-gene interactions. This approach can be similarly applied for modeling gene-environment interactions. We compare this method with other approaches: the corresponding test without modeling any interaction, that based on a saturated interaction model, that based on principal component analysis, and that based on Tukey’s 1-df model. Our simulations suggest that this new approach has superior power to that of the other methods. In an application to endometrial cancer case-control data from the Women’s Health Initiative (WHI), this approach detected AKT1 and AKT2 as being significantly associated with endometrial cancer susceptibility by taking into account their interactions with BMI. PMID:18615621

  19. Fine-mapping identifies multiple prostate cancer risk loci at 5p15, one of which associates with TERT expression

    Kote-Jarai, Zsofia; Saunders, Edward J.; Leongamornlert, Daniel A.; Tymrakiewicz, Malgorzata; Dadaev, Tokhir; Jugurnauth-Little, Sarah; Ross-Adams, Helen; Al Olama, Ali Amin; Benlloch, Sara; Halim, Silvia; Russel, Roslin; Dunning, Alison M.; Luccarini, Craig; Dennis, Joe; Neal, David E.; Hamdy, Freddie C.; Donovan, Jenny L.; Muir, Ken; Giles, Graham G.; Severi, Gianluca; Wiklund, Fredrik; Gronberg, Henrik; Haiman, Christopher A.; Schumacher, Fredrick; Henderson, Brian E.; Le Marchand, Loic; Lindstrom, Sara; Kraft, Peter; Hunter, David J.; Gapstur, Susan; Chanock, Stephen; Berndt, Sonja I.; Albanes, Demetrius; Andriole, Gerald; Schleutker, Johanna; Weischer, Maren; Canzian, Federico; Riboli, Elio; Key, Tim J.; Travis, Ruth C.; Campa, Daniele; Ingles, Sue A.; John, Esther M.; Hayes, Richard B.; Pharoah, Paul; Khaw, Kay-Tee; Stanford, Janet L.; Ostrander, Elaine A.; Signorello, Lisa B.; Thibodeau, Stephen N.; Schaid, Dan; Maier, Christiane; Vogel, Walther; Kibel, Adam S.; Cybulski, Cezary; Lubinski, Jan; Cannon-Albright, Lisa; Brenner, Hermann; Park, Jong Y.; Kaneva, Radka; Batra, Jyotsna; Spurdle, Amanda; Clements, Judith A.; Teixeira, Manuel R.; Govindasami, Koveela; Guy, Michelle; Wilkinson, Rosemary A.; Sawyer, Emma J.; Morgan, Angela; Dicks, Ed; Baynes, Caroline; Conroy, Don; Bojesen, Stig E.; Kaaks, Rudolf; Vincent, Daniel; Bacot, François; Tessier, Daniel C.; Easton, Douglas F.; Eeles, Rosalind A.

    2013-01-01

    Associations between single nucleotide polymorphisms (SNPs) at 5p15 and multiple cancer types have been reported. We have previously shown evidence for a strong association between prostate cancer (PrCa) risk and rs2242652 at 5p15, intronic in the telomerase reverse transcriptase (TERT) gene that encodes TERT. To comprehensively evaluate the association between genetic variation across this region and PrCa, we performed a fine-mapping analysis by genotyping 134 SNPs using a custom Illumina iSelect array or Sequenom MassArray iPlex, followed by imputation of 1094 SNPs in 22 301 PrCa cases and 22 320 controls in The PRACTICAL consortium. Multiple stepwise logistic regression analysis identified four signals in the promoter or intronic regions of TERT that independently associated with PrCa risk. Gene expression analysis of normal prostate tissue showed evidence that SNPs within one of these regions also associated with TERT expression, providing a potential mechanism for predisposition to disease. PMID:23535824

  20. Fine Mapping and Functional Analysis of the Multiple Sclerosis Risk Gene CD6

    Swaminathan, Bhairavi; Cuapio, Angélica; Alloza, Iraide; Matesanz, Fuencisla; Alcina, Antonio; García-Barcina, Maria; Fedetz, Maria; Fernández, Óscar; Lucas, Miguel; Órpez, Teresa; Pinto-Medel, Mª Jesus; Otaegui, David; Olascoaga, Javier; Urcelay, Elena; Ortiz, Miguel A.; Arroyo, Rafael; Oksenberg, Jorge R.; Antigüedad, Alfredo; Tolosa, Eva; Vandenbroeck, Koen

    2013-01-01

    CD6 has recently been identified and validated as risk gene for multiple sclerosis (MS), based on the association of a single nucleotide polymorphism (SNP), rs17824933, located in intron 1. CD6 is a cell surface scavenger receptor involved in T-cell activation and proliferation, as well as in thymocyte differentiation. In this study, we performed a haptag SNP screen of the CD6 gene locus using a total of thirteen tagging SNPs, of which three were non-synonymous SNPs, and replicated the recently reported GWAS SNP rs650258 in a Spanish-Basque collection of 814 controls and 823 cases. Validation of the six most strongly associated SNPs was performed in an independent collection of 2265 MS patients and 2600 healthy controls. We identified association of haplotypes composed of two non-synonymous SNPs [rs11230563 (R225W) and rs2074225 (A257V)] in the 2nd SRCR domain with susceptibility to MS (P max(T) permutation = 1×10−4). The effect of these haplotypes on CD6 surface expression and cytokine secretion was also tested. The analysis showed significantly different CD6 expression patterns in the distinct cell subsets, i.e. – CD4+ naïve cells, P = 0.0001; CD8+ naïve cells, P<0.0001; CD4+ and CD8+ central memory cells, P = 0.01 and 0.05, respectively; and natural killer T (NKT) cells, P = 0.02; with the protective haplotype (RA) showing higher expression of CD6. However, no significant changes were observed in natural killer (NK) cells, effector memory and terminally differentiated effector memory T cells. Our findings reveal that this new MS-associated CD6 risk haplotype significantly modifies expression of CD6 on CD4+ and CD8+ T cells. PMID:23638056

  1. Multiple factors and processes involved in host cell killing by bacteriophage Mu: characterization and mapping.

    Waggoner, B T; Marrs, C F; Howe, M M; Pato, M L

    1984-07-15

    The regions of bacteriophage Mu involved in host cell killing were determined by infection of a lambda-immune host with 12 lambda pMu-transducing phages carrying different amounts of Mu DNA beginning at the left end. Infecting lambda pMu phages containing 5.0 (+/- 0.2) kb or less of the left end of Mu DNA did not kill the lambda-immune host, whereas lambda pMu containing 5.1 kb did kill, thus locating the right end of the kil gene between approximately 5.0 and 5.1 kb. For the Kil+ phages the extent of killing increased as the multiplicity of infection (m.o.i.) increased. In addition, killing was also affected by the presence of at least two other regions of Mu DNA: one, located between 5.1 and 5.8 kb, decreased the extent of killing; the other, located between 6.3 and 7.9 kb, greatly increased host cell killing. Killing was also assayed after lambda pMu infection of a lambda-immune host carrying a mini-Mu deleted for most of the B gene and the middle region of Mu DNA. Complementation of mini-Mu replication by infecting B+ lambda pMu phages resulted in killing of the lambda-immune, mini-Mu-containing host, regardless of the presence or absence of the Mu kil gene. The extent of host cell killing increased as the m.o.i. of the infecting lambda pMu increased, and was further enhanced by both the presence of the kil gene and the region located between 6.3 and 7.9 kb. These distinct processes of kil-mediated killing in the absence of replication and non-kil-mediated killing in the presence of replication were also observed after induction of replication-deficient and kil mutant prophages, respectively.

  2. Global map of physical interactions among differentially expressed genes in multiple sclerosis relapses and remissions.

    Tuller, Tamir; Atar, Shimshi; Ruppin, Eytan; Gurevich, Michael; Achiron, Anat

    2011-09-15

    Multiple sclerosis (MS) is a central nervous system autoimmune inflammatory T-cell-mediated disease with a relapsing-remitting course in the majority of patients. In this study, we performed a high-resolution systems biology analysis of gene expression and physical interactions in MS relapse and remission. To this end, we integrated 164 large-scale measurements of gene expression in peripheral blood mononuclear cells of MS patients in relapse or remission and healthy subjects, with large-scale information about the physical interactions between these genes obtained from public databases. These data were analyzed with a variety of computational methods. We find that there is a clear and significant global network-level signal that is related to the changes in gene expression of MS patients in comparison to healthy subjects. However, despite the clear differences in the clinical symptoms of MS patients in relapse versus remission, the network level signal is weaker when comparing patients in these two stages of the disease. This result suggests that most of the genes have relatively similar expression levels in the two stages of the disease. In accordance with previous studies, we found that the pathways related to regulation of cell death, chemotaxis and inflammatory response are differentially expressed in the disease in comparison to healthy subjects, while pathways related to cell adhesion, cell migration and cell-cell signaling are activated in relapse in comparison to remission. However, the current study includes a detailed report of the exact set of genes involved in these pathways and the interactions between them. For example, we found that the genes TP53 and IL1 are 'network-hub' that interacts with many of the differentially expressed genes in MS patients versus healthy subjects, and the epidermal growth factor receptor is a 'network-hub' in the case of MS patients with relapse versus remission. The statistical approaches employed in this study enabled us

  3. Multiple origins of polyploidy in the phylogeny of southern African barbs (Cyprinidae) as inferred from mtDNA markers.

    Tsigenopoulos, C S; Ráb, P; Naran, D; Berrebi, P

    2002-06-01

    The cyprinid genus Barbus, with more than 800 nominal species, is an apparently polyphyletic assemblage to which a number of unrelated species, groups and/or assemblages have been assigned. It includes species that exhibit three different ploidy levels: diploid, tetraploid and hexaploid. Several lineages of the family Cyprinidae constitute a major component of the African freshwater ichthyofauna, having about 500 species, and fishes assigned to the genus 'Barbus' have the most species on the continent. We used complete sequences of the mitochondrial cytochrome b gene in order to infer phylogenetic relationships between diploid, tetraploid and hexaploid species of 'Barbus' occurring in southern Africa, the only region where representatives of all of the three ploidy levels occur. The results indicate that most of the lineages are incorrectly classified in the genus 'Barbus'. The southern African tetraploids probably originated from southern African diploids. They constitute a monophyletic group distinct from tetraploids occurring in the Euro-Mediterranean region (Barbus sensu stricto). The 'small' African diploid species seem to be paraphyletic, while the 'large' African hexaploid barbs species are of a single, recent origin and form a monophyletic group. The evidence of multiple, independent origins of polyploidy occurring in the African cyprinine cyprinids thus provides a significant contribution to the knowledge on the systematic diversity of these fishes, and warrants a thorough taxonomic reorganization of the genus.

  4. Clinical values of multiple Epstein-Barr virus (EBV serological biomarkers detected by xMAP technology

    Chen Li-Zhen

    2009-08-01

    Full Text Available Abstract Background Serological examination of Epstein-Barr virus (EBV antibodies has been performed for screening nasopharyngeal carcinoma (NPC and other EBV-associated diseases. Methods By using xMAP technology, we examined immunoglobulin (Ig A antibodies against Epstein-Barr virus (EBV VCA-gp125, p18 and IgA/IgG against EA-D, EBNA1 and gp78 in populations with distinct diseases, or with different genetic or geographic background. Sera from Cantonese NPC patients (n = 547 and healthy controls (n = 542, 90 members of high-risk NPC families and 52 non-endemic healthy individuals were tested. Thirty-five of NPC patients were recruited to observe the kinetics of EBV antibody levels during and after treatment. Patients with other EBV-associated diseases were collected, including 16 with infectious mononucleosis, 28 with nasal NK/T cell lymphoma and 14 with Hodgkin's disease. Results Both the sensitivity and specificity of each marker for NPC diagnosis ranged 61–84%, but if combined, they could reach to 84.5% and 92.4%, respectively. Almost half of NPC patients displayed decreased EBV immunoactivities shortly after therapy and tumor recurrence was accompanied with high EBV antibody reactivates. Neither the unaffected members from high-risk NPC families nor non-endemic healthy population showed statistically different EBV antibody levels compared with endemic controls. Moreover, elevated levels of specific antibodies were observed in other EBV-associated diseases, but all were lower than those in NPC. Conclusion Combined EBV serological biomarkers could improve the diagnostic values for NPC. Diverse EBV serological spectrums presented in populations with different EBV-associated diseases, but NPC patients have the highest EBV activity.

  5. Mapping and characterization of positive and negative BOLD responses to visual stimulation in multiple brain regions at 7T.

    Jorge, João; Figueiredo, Patrícia; Gruetter, Rolf; van der Zwaag, Wietske

    2018-02-20

    External stimuli and tasks often elicit negative BOLD responses in various brain regions, and growing experimental evidence supports that these phenomena are functionally meaningful. In this work, the high sensitivity available at 7T was explored to map and characterize both positive (PBRs) and negative BOLD responses (NBRs) to visual checkerboard stimulation, occurring in various brain regions within and beyond the visual cortex. Recently-proposed accelerated fMRI techniques were employed for data acquisition, and procedures for exclusion of large draining vein contributions, together with ICA-assisted denoising, were included in the analysis to improve response estimation. Besides the visual cortex, significant PBRs were found in the lateral geniculate nucleus and superior colliculus, as well as the pre-central sulcus; in these regions, response durations increased monotonically with stimulus duration, in tight covariation with the visual PBR duration. Significant NBRs were found in the visual cortex, auditory cortex, default-mode network (DMN) and superior parietal lobule; NBR durations also tended to increase with stimulus duration, but were significantly less sustained than the visual PBR, especially for the DMN and superior parietal lobule. Responses in visual and auditory cortex were further studied for checkerboard contrast dependence, and their amplitudes were found to increase monotonically with contrast, linearly correlated with the visual PBR amplitude. Overall, these findings suggest the presence of dynamic neuronal interactions across multiple brain regions, sensitive to stimulus intensity and duration, and demonstrate the richness of information obtainable when jointly mapping positive and negative BOLD responses at a whole-brain scale, with ultra-high field fMRI. © 2018 Wiley Periodicals, Inc.

  6. Linking the potato genome to the conserved ortholog set (COS) markers

    2013-01-01

    Background Conserved ortholog set (COS) markers are an important functional genomics resource that has greatly improved orthology detection in Asterid species. A comprehensive list of these markers is available at Sol Genomics Network (http://solgenomics.net/) and many of these have been placed on the genetic maps of a number of solanaceous species. Results We amplified over 300 COS markers from eight potato accessions involving two diploid landraces of Solanum tuberosum Andigenum group (formerly classified as S. goniocalyx, S. phureja), and a dihaploid clone derived from a modern tetraploid cultivar of S. tuberosum and the wild species S. berthaultii, S. chomatophilum, and S. paucissectum. By BLASTn (Basic Local Alignment Search Tool of the NCBI, National Center for Biotechnology Information) algorithm we mapped the DNA sequences of these markers into the potato genome sequence. Additionally, we mapped a subset of these markers genetically in potato and present a comparison between the physical and genetic locations of these markers in potato and in comparison with the genetic location in tomato. We found that most of the COS markers are single-copy in the reference genome of potato and that the genetic location in tomato and physical location in potato sequence are mostly in agreement. However, we did find some COS markers that are present in multiple copies and those that map in unexpected locations. Sequence comparisons between species show that some of these markers may be paralogs. Conclusions The sequence-based physical map becomes helpful in identification of markers for traits of interest thereby reducing the number of markers to be tested for applications like marker assisted selection, diversity, and phylogenetic studies. PMID:23758607

  7. Spatial-area selective retrieval of multiple object-place associations in a hierarchical cognitive map formed by theta phase coding.

    Sato, Naoyuki; Yamaguchi, Yoko

    2009-06-01

    The human cognitive map is known to be hierarchically organized consisting of a set of perceptually clustered landmarks. Patient studies have demonstrated that these cognitive maps are maintained by the hippocampus, while the neural dynamics are still poorly understood. The authors have shown that the neural dynamic "theta phase precession" observed in the rodent hippocampus may be capable of forming hierarchical cognitive maps in humans. In the model, a visual input sequence consisting of object and scene features in the central and peripheral visual fields, respectively, results in the formation of a hierarchical cognitive map for object-place associations. Surprisingly, it is possible for such a complex memory structure to be formed in a few seconds. In this paper, we evaluate the memory retrieval of object-place associations in the hierarchical network formed by theta phase precession. The results show that multiple object-place associations can be retrieved with the initial cue of a scene input. Importantly, according to the wide-to-narrow unidirectional connections among scene units, the spatial area for object-place retrieval can be controlled by the spatial area of the initial cue input. These results indicate that the hierarchical cognitive maps have computational advantages on a spatial-area selective retrieval of multiple object-place associations. Theta phase precession dynamics is suggested as a fundamental neural mechanism of the human cognitive map.

  8. Analysis of the human brain in primary progressive multiple sclerosis with mapping of the spatial distributions using H-1 MR spectroscopy and diffusion tensor imaging

    Sijens, PE; Irwan, R; Potze, JH; Mostert, JP; De Keyser, J; Oudkerk, M

    Primary progressive multiple sclerosis (ppMS; n=4) patients and controls (n=4) were examined by 1H magnetic resonance spectroscopy (MRS) and diffusion tensor imaging (DTI) in order to map choline (Cho), creatine and N-acetylaspartate (NAA), the fractional anisotropy (FA) and the apparent diffusion

  9. The issue of multiple univariate comparisons in the context of neuroelectric brain mapping: an application in a neuromarketing experiment.

    Vecchiato, G; De Vico Fallani, F; Astolfi, L; Toppi, J; Cincotti, F; Mattia, D; Salinari, S; Babiloni, F

    2010-08-30

    This paper presents some considerations about the use of adequate statistical techniques in the framework of the neuroelectromagnetic brain mapping. With the use of advanced EEG/MEG recording setup involving hundred of sensors, the issue of the protection against the type I errors that could occur during the execution of hundred of univariate statistical tests, has gained interest. In the present experiment, we investigated the EEG signals from a mannequin acting as an experimental subject. Data have been collected while performing a neuromarketing experiment and analyzed with state of the art computational tools adopted in specialized literature. Results showed that electric data from the mannequin's head presents statistical significant differences in power spectra during the visualization of a commercial advertising when compared to the power spectra gathered during a documentary, when no adjustments were made on the alpha level of the multiple univariate tests performed. The use of the Bonferroni or Bonferroni-Holm adjustments returned correctly no differences between the signals gathered from the mannequin in the two experimental conditions. An partial sample of recently published literature on different neuroscience journals suggested that at least the 30% of the papers do not use statistical protection for the type I errors. While the occurrence of type I errors could be easily managed with appropriate statistical techniques, the use of such techniques is still not so largely adopted in the literature. Copyright (c) 2010 Elsevier B.V. All rights reserved.

  10. Mapping the structural and dynamical features of multiple p53 DNA binding domains: insights into loop 1 intrinsic dynamics.

    Suryani Lukman

    Full Text Available The transcription factor p53 regulates cellular integrity in response to stress. p53 is mutated in more than half of cancerous cells, with a majority of the mutations localized to the DNA binding domain (DBD. In order to map the structural and dynamical features of the DBD, we carried out multiple copy molecular dynamics simulations (totaling 0.8 μs. Simulations show the loop 1 to be the most dynamic element among the DNA-contacting loops (loops 1-3. Loop 1 occupies two major conformational states: extended and recessed; the former but not the latter displays correlations in atomic fluctuations with those of loop 2 (~24 Å apart. Since loop 1 binds to the major groove whereas loop 2 binds to the minor groove of DNA, our results begin to provide some insight into the possible mechanism underpinning the cooperative nature of DBD binding to DNA. We propose (1 a novel mechanism underlying the dynamics of loop 1 and the possible tread-milling of p53 on DNA and (2 possible mutations on loop 1 residues to restore the transcriptional activity of an oncogenic mutation at a distant site.

  11. Genome-Wide Analysis of Simple Sequence Repeats and Efficient Development of Polymorphic SSR Markers Based on Whole Genome Re-Sequencing of Multiple Isolates of the Wheat Stripe Rust Fungus.

    Huaiyong Luo

    Full Text Available The biotrophic parasitic fungus Puccinia striiformis f. sp. tritici (Pst causes stripe rust, a devastating disease of wheat, endangering global food security. Because the Pst population is highly dynamic, it is difficult to develop wheat cultivars with durable and highly effective resistance. Simple sequence repeats (SSRs are widely used as molecular markers in genetic studies to determine population structure in many organisms. However, only a small number of SSR markers have been developed for Pst. In this study, a total of 4,792 SSR loci were identified using the whole genome sequences of six isolates from different regions of the world, with a marker density of one SSR per 22.95 kb. The majority of the SSRs were di- and tri-nucleotide repeats. A database containing 1,113 SSR markers were established. Through in silico comparison, the previously reported SSR markers were found mainly in exons, whereas the SSR markers in the database were mostly in intergenic regions. Furthermore, 105 polymorphic SSR markers were confirmed in silico by their identical positions and nucleotide variations with INDELs identified among the six isolates. When 104 in silico polymorphic SSR markers were used to genotype 21 Pst isolates, 84 produced the target bands, and 82 of them were polymorphic and revealed the genetic relationships among the isolates. The results show that whole genome re-sequencing of multiple isolates provides an ideal resource for developing SSR markers, and the newly developed SSR markers are useful for genetic and population studies of the wheat stripe rust fungus.

  12. Genome-Wide Analysis of Simple Sequence Repeats and Efficient Development of Polymorphic SSR Markers Based on Whole Genome Re-Sequencing of Multiple Isolates of the Wheat Stripe Rust Fungus.

    Luo, Huaiyong; Wang, Xiaojie; Zhan, Gangming; Wei, Guorong; Zhou, Xinli; Zhao, Jing; Huang, Lili; Kang, Zhensheng

    2015-01-01

    The biotrophic parasitic fungus Puccinia striiformis f. sp. tritici (Pst) causes stripe rust, a devastating disease of wheat, endangering global food security. Because the Pst population is highly dynamic, it is difficult to develop wheat cultivars with durable and highly effective resistance. Simple sequence repeats (SSRs) are widely used as molecular markers in genetic studies to determine population structure in many organisms. However, only a small number of SSR markers have been developed for Pst. In this study, a total of 4,792 SSR loci were identified using the whole genome sequences of six isolates from different regions of the world, with a marker density of one SSR per 22.95 kb. The majority of the SSRs were di- and tri-nucleotide repeats. A database containing 1,113 SSR markers were established. Through in silico comparison, the previously reported SSR markers were found mainly in exons, whereas the SSR markers in the database were mostly in intergenic regions. Furthermore, 105 polymorphic SSR markers were confirmed in silico by their identical positions and nucleotide variations with INDELs identified among the six isolates. When 104 in silico polymorphic SSR markers were used to genotype 21 Pst isolates, 84 produced the target bands, and 82 of them were polymorphic and revealed the genetic relationships among the isolates. The results show that whole genome re-sequencing of multiple isolates provides an ideal resource for developing SSR markers, and the newly developed SSR markers are useful for genetic and population studies of the wheat stripe rust fungus.

  13. Astronomy Map of the World

    Veras, D.

    2017-09-01

    I have created an online clickable and zoom-enabled world map - now viewed over 5,400 times - that contains weblinks to institutions where astronomy is either researched professionally and / or and taught in classrooms at the university level. Not included are stand-alone museums, planetariums, amateur astronomical societies, virtual institutes, nor observatories which do not fulfill this criteria. One can click on a marker to access the relevant institute. The map currently contains 697 institutes, and has multiple potential uses for undergraduate students, graduate students, postdocs, faculty and journal editors.

  14. Multiple-strand displacement and identification of single nucleotide polymorphisms as markers of genotypic variation of Pasteuria penetrans biotypes infecting root-knot nematodes.

    Nong, Guang; Chow, Virginia; Schmidt, Liesbeth M; Dickson, Don W; Preston, James F

    2007-08-01

    Pasteuria species are endospore-forming obligate bacterial parasites of soil-inhabiting nematodes and water-inhabiting cladocerans, e.g. water fleas, and are closely related to Bacillus spp. by 16S rRNA gene sequence. As naturally occurring bacteria, biotypes of Pasteuria penetrans are attractive candidates for the biocontrol of various Meloidogyne spp. (root-knot nematodes). Failure to culture these bacteria outside their hosts has prevented isolation of genomic DNA in quantities sufficient for identification of genes associated with host recognition and virulence. We have applied multiple-strand displacement amplification (MDA) to generate DNA for comparative genomics of biotypes exhibiting different host preferences. Using the genome of Bacillus subtilis as a paradigm, MDA allowed quantitative detection and sequencing of 12 marker genes from 2000 cells. Meloidogyne spp. infected with P. penetrans P20 or B4 contained single nucleotide polymorphisms (SNPs) in the spoIIAB gene that did not change the amino acid sequence, or that substituted amino acids with similar chemical properties. Individual nematodes infected with P. penetrans P20 or B4 contained SNPs in the spoIIAB gene sequenced in MDA-generated products. Detection of SNPs in the spoIIAB gene in a nematode indicates infection by more than one genotype, supporting the need to sequence genomes of Pasteuria spp. derived from single spore isolates.

  15. A de novo 1.58 Mb deletion, including MAP2K6 and mapping 1.28 Mb upstream to SOX9, identified in a patient with Pierre Robin sequence and osteopenia with multiple fractures.

    Smyk, Marta; Roeder, Elizabeth; Cheung, Sau Wai; Szafranski, Przemyslaw; Stankiewicz, Paweł

    2015-08-01

    Defects of long-range regulatory elements of dosage-sensitive genes represent an under-recognized mechanism underlying genetic diseases. Haploinsufficiency of SOX9, the gene essential for development of testes and differentiation of chondrocytes, results in campomelic dysplasia, a skeletal malformation syndrome often associated with sex reversal. Chromosomal rearrangements with breakpoints mapping up to 1.6 Mb up- and downstream to SOX9, and disrupting its distant cis-regulatory elements, have been described in patients with milder forms of campomelic dysplasia, Pierre Robin sequence, and sex reversal. We present an ∼1.58 Mb deletion mapping ∼1.28 Mb upstream to SOX9 that encompasses its putative long-range cis-regulatory element(s) and MAP2K6 in a patient with Pierre Robin sequence and osteopenia with multiple fractures. Low bone mass panel testing using massively parallel sequencing of 23 nuclear genes, including COL1A1 and COL1A2 was negative. Based on the previous mouse model of Map2k6, suggesting that Sox9 is likely a downstream target of the p38 MAPK pathway, and our previous chromosome conformation capture-on-chip (4C) data showing potential interactions between SOX9 promoter and MAP2K6, we hypothesize that deletion of MAP2K6 might have affected SOX9 expression and contributed to our patient's phenotype. © 2015 Wiley Periodicals, Inc.

  16. Fine-scale mapping of 8q24 locus identifies multiple independent risk variants for breast cancer.

    Shi, Jiajun; Zhang, Yanfeng; Zheng, Wei; Michailidou, Kyriaki; Ghoussaini, Maya; Bolla, Manjeet K; Wang, Qin; Dennis, Joe; Lush, Michael; Milne, Roger L; Shu, Xiao-Ou; Beesley, Jonathan; Kar, Siddhartha; Andrulis, Irene L; Anton-Culver, Hoda; Arndt, Volker; Beckmann, Matthias W; Zhao, Zhiguo; Guo, Xingyi; Benitez, Javier; Beeghly-Fadiel, Alicia; Blot, William; Bogdanova, Natalia V; Bojesen, Stig E; Brauch, Hiltrud; Brenner, Hermann; Brinton, Louise; Broeks, Annegien; Brüning, Thomas; Burwinkel, Barbara; Cai, Hui; Canisius, Sander; Chang-Claude, Jenny; Choi, Ji-Yeob; Couch, Fergus J; Cox, Angela; Cross, Simon S; Czene, Kamila; Darabi, Hatef; Devilee, Peter; Droit, Arnaud; Dork, Thilo; Fasching, Peter A; Fletcher, Olivia; Flyger, Henrik; Fostira, Florentia; Gaborieau, Valerie; García-Closas, Montserrat; Giles, Graham G; Guenel, Pascal; Haiman, Christopher A; Hamann, Ute; Hartman, Mikael; Miao, Hui; Hollestelle, Antoinette; Hopper, John L; Hsiung, Chia-Ni; Ito, Hidemi; Jakubowska, Anna; Johnson, Nichola; Torres, Diana; Kabisch, Maria; Kang, Daehee; Khan, Sofia; Knight, Julia A; Kosma, Veli-Matti; Lambrechts, Diether; Li, Jingmei; Lindblom, Annika; Lophatananon, Artitaya; Lubinski, Jan; Mannermaa, Arto; Manoukian, Siranoush; Le Marchand, Loic; Margolin, Sara; Marme, Frederik; Matsuo, Keitaro; McLean, Catriona; Meindl, Alfons; Muir, Kenneth; Neuhausen, Susan L; Nevanlinna, Heli; Nord, Silje; Børresen-Dale, Anne-Lise; Olson, Janet E; Orr, Nick; van den Ouweland, Ans M W; Peterlongo, Paolo; Putti, Thomas Choudary; Rudolph, Anja; Sangrajrang, Suleeporn; Sawyer, Elinor J; Schmidt, Marjanka K; Schmutzler, Rita K; Shen, Chen-Yang; Hou, Ming-Feng; Shrubsole, Matha J; Southey, Melissa C; Swerdlow, Anthony; Teo, Soo Hwang; Thienpont, Bernard; Toland, Amanda E; Tollenaar, Robert A E M; Tomlinson, Ian; Truong, Therese; Tseng, Chiu-Chen; Wen, Wanqing; Winqvist, Robert; Wu, Anna H; Yip, Cheng Har; Zamora, Pilar M; Zheng, Ying; Floris, Giuseppe; Cheng, Ching-Yu; Hooning, Maartje J; Martens, John W M; Seynaeve, Caroline; Kristensen, Vessela N; Hall, Per; Pharoah, Paul D P; Simard, Jacques; Chenevix-Trench, Georgia; Dunning, Alison M; Antoniou, Antonis C; Easton, Douglas F; Cai, Qiuyin; Long, Jirong

    2016-09-15

    Previous genome-wide association studies among women of European ancestry identified two independent breast cancer susceptibility loci represented by single nucleotide polymorphisms (SNPs) rs13281615 and rs11780156 at 8q24. A fine-mapping study across 2.06 Mb (chr8:127,561,724-129,624,067, hg19) in 55,540 breast cancer cases and 51,168 controls within the Breast Cancer Association Consortium was conducted. Three additional independent association signals in women of European ancestry, represented by rs35961416 (OR = 0.95, 95% CI = 0.93-0.97, conditional p = 5.8 × 10(-6) ), rs7815245 (OR = 0.94, 95% CI = 0.91-0.96, conditional p = 1.1 × 10(-6) ) and rs2033101 (OR = 1.05, 95% CI = 1.02-1.07, conditional p = 1.1 × 10(-4) ) were found. Integrative analysis using functional genomic data from the Roadmap Epigenomics, the Encyclopedia of DNA Elements project, the Cancer Genome Atlas and other public resources implied that SNPs rs7815245 in Signal 3, and rs1121948 in Signal 5 (in linkage disequilibrium with rs11780156, r(2)  = 0.77), were putatively functional variants for two of the five independent association signals. The results highlighted multiple 8q24 variants associated with breast cancer susceptibility in women of European ancestry. © 2016 UICC.

  17. SU-G-IeP1-12: Size Selective Arterial Cerebral Blood Volume Mapping Using Multiple Inversion Time Arterial Spin Labeling

    Jung, Y; Johnston, M; Whitlow, C [Wake Forest School of Medicine, Winston-salem, NC (United States); Liu, H [UT MD Anderson Cancer Center, Houston, TX (United States)

    2016-06-15

    Purpose: To demonstrate the feasibility of a novel method for size specific arterial cerebral blood volume (aCBV) mapping using pseudo-continuous arterial spin labeling (PCASL), with multiple TI. Methods: Multiple PCASL images were obtained from a subject with TI of [300, 400, 500, 600, 700, 800, 900, 1000, 1500, 2000, 2500, 3000, 3500, 4000] ms. Each TI pair was averaged six times. Two scans were performed: one without a flow crusher gradient and the other with a crusher gradient (10cm/s in three directions) to remove signals from large arteries. Scan times were 5min. without a crusher gradient and 5.5 min with a crusher gradient. Non-linear fitting algorithm finds the minimum mean squared solution of per-voxel based aCBV, cerebral blood flow, and arterial transit time, and fits the data into a hemodynamic model that represents superposition of blood volume and flow components within a single voxel. Results: aCBV maps with a crusher gradient represent signals from medium and small sized arteries, while those without a crusher gradient represent signals from all sized arteries, indicating that flow crusher gradients can be effectively employed to achieve size-specific aCBV mapping. Regardless of flow crusher, the CBF and ATT maps are very similar in appearance. Conclusion: Quantitative size selective blood volume mapping controlled by a flow crusher is feasible without additional information because the ASL quantification process doesn’t require an arterial input function measured from a large artery. The size specific blood volume mapping is not interfered by sSignals from large arteries do not interfere with size specific aCBV mapping in the applications of interest in for applications in which only medium or small arteries are of interest.

  18. An efficient and reproducible method for in vitro clonal multiplication of Rauvolfia tetraphylla L. and evaluation of genetic stability using DNA-based markers.

    Faisal, Mohammad; Alatar, Abdulrahman A; Ahmad, Naseem; Anis, Mohammad; Hegazy, Ahmad K

    2012-12-01

    An efficient protocol is described for the rapid in vitro clonal propagation of an endangered medicinal plant, Rauvolfia tetraphylla L., through high frequency shoot induction from nodal explants collected from young shoots of a field grown plant. Effects of growth regulators [6-benzyladenine (BA), kinetin (Kin) 2iP, or α-naphthalene acetic acid (NAA)], carbohydrates, different medium [Murashige and Skoog (MS), Woody Plant Medium (WPM), Gamborg medium (B5), Linsmier and Skoog medium (LS)], and various pH levels on in vitro morphogenesis were investigated. The highest frequency of shoot regeneration (90 %) and maximum number of shoot (35.4 ± 2.3) per explant were observed on WPM medium supplemented with 7.5 μM BA, 2.5 μM NAA, and 30 g/l sucrose at pH 5.8. Well-developed shoots, 4-5 cm in length, were successfully rooted ex vitro at 90 % by a 30-min pulse treatment with 150 μM IBA prior to their transfer in planting substrates. The survival rate of transplantation reached 90 % when transferred to field condition. Genetic stability of micropropagated plantlets was assessed and compared with mother plant using Random Amplified Polymorphic DNA and Inter Simple Sequence Repeats markers. No variation was observed in DNA fingerprinting patterns among the micropropagated plants, which were similar to that of the donor plant illustrating their genetic uniformity and clonal fidelity. This confirms that clonal propagation of this plant using axillary shoot buds can be used for commercial exploitation of the selected genotype where a high degree of fidelity is an essential prerequisite. The work contributed to a better in vitro regeneration and clonal mass multiplication of R. tetraphylla and to develop a strategy for the germplasm conservation of this endangered medicinal plant.

  19. A genome-wide transcriptome map of pistachio (Pistacia vera L.) provides novel insights into salinity-related genes and marker discovery.

    Moazzzam Jazi, Maryam; Seyedi, Seyed Mahdi; Ebrahimie, Esmaeil; Ebrahimi, Mansour; De Moro, Gianluca; Botanga, Christopher

    2017-08-17

    Pistachio (Pistacia vera L.) is one of the most important commercial nut crops worldwide. It is a salt-tolerant and long-lived tree, with the largest cultivation area in Iran. Climate change and subsequent increased soil salt content have adversely affected the pistachio yield in recent years. However, the lack of genomic/global transcriptomic sequences on P. vera impedes comprehensive researches at the molecular level. Hence, whole transcriptome sequencing is required to gain insight into functional genes and pathways in response to salt stress. RNA sequencing of a pooled sample representing 24 different tissues of two pistachio cultivars with contrasting salinity tolerance under control and salt treatment by Illumina Hiseq 2000 platform resulted in 368,953,262 clean 100 bp paired-ends reads (90 Gb). Following creating several assemblies and assessing their quality from multiple perspectives, we found that using the annotation-based metrics together with the length-based parameters allows an improved assessment of the transcriptome assembly quality, compared to the solely use of the length-based parameters. The generated assembly by Trinity was adopted for functional annotation and subsequent analyses. In total, 29,119 contigs annotated against all of five public databases, including NR, UniProt, TAIR10, KOG and InterProScan. Among 279 KEGG pathways supported by our assembly, we further examined the pathways involved in the plant hormone biosynthesis and signaling as well as those to be contributed to secondary metabolite biosynthesis due to their importance under salinity stress. In total, 11,337 SSRs were also identified, which the most abundant being dinucleotide repeats. Besides, 13,097 transcripts as candidate stress-responsive genes were identified. Expression of some of these genes experimentally validated through quantitative real-time PCR (qRT-PCR) that further confirmed the accuracy of the assembly. From this analysis, the contrasting expression pattern

  20. A molecular recombination map of Antirrhinum majus

    Hudson Andrew

    2010-12-01

    Full Text Available Abstract Background Genetic recombination maps provide important frameworks for comparative genomics, identifying gene functions, assembling genome sequences and for breeding. The molecular recombination map currently available for the model eudicot Antirrhinum majus is the result of a cross with Antirrhinum molle, limiting its usefulness within A. majus. Results We created a molecular linkage map of A. majus based on segregation of markers in the F2 population of two inbred lab strains of A. majus. The resulting map consisted of over 300 markers in eight linkage groups, which could be aligned with a classical recombination map and the A. majus karyotype. The distribution of recombination frequencies and distorted transmission of parental alleles differed from those of a previous inter-species hybrid. The differences varied in magnitude and direction between chromosomes, suggesting that they had multiple causes. The map, which covered an estimated of 95% of the genome with an average interval of 2 cM, was used to analyze the distribution of a newly discovered family of MITE transposons and tested for its utility in positioning seven mutations that affect aspects of plant size. Conclusions The current map has an estimated interval of 1.28 Mb between markers. It shows a lower level of transmission ratio distortion and a longer length than the previous inter-species map, making it potentially more useful. The molecular recombination map further indicates that the IDLE MITE transposons are distributed throughout the genome and are relatively stable. The map proved effective in mapping classical morphological mutations of A. majus.

  1. Reprint of "A proposed cell model for multiple-occurrence regional landslide events: Implications for landslide susceptibility mapping"

    Crozier, M. J.

    2018-04-01

    Multiple-occurrence regional landslide events (MORLEs) consist of hundreds to thousands of shallow landslides occurring more or less simultaneously within defined areas, ranging from tens to thousands of square kilometres. While MORLEs can be triggered by rainstorms and earthquakes, this paper is confined to those landslide events triggered by rainstorms. Globally, MORLEs occur in a range of geological settings in areas of moderate to steep slopes subject to intense rainstorms. Individual landslides in rainstorm-triggered events are dominantly small, shallow debris and earth flows, and debris and earth slides involving regolith or weathered bedrock. The model used to characterise these events assumes that energy distribution within the event area is represented on the land surface by a cell structure; with maximum energy expenditure within an identifiable core and rapid dissipation concentrically away from the centre. The version of the model presented here has been developed for rainfall-triggered landslide events. It proposes that rainfall intensity can be used to determine different critical landslide response zones within the cell (referred to as core, middle, and periphery zones). These zones are most readily distinguished by two conditions: the proportion of the slope that fails and the particular type of the slope stability factor that assumes dominance in determining specific sites of landslide occurrence. The latter condition means that the power of any slope stability factor to distinguish between stable and unstable sites varies throughout the affected area in accordance with the landslide response zones within the cell; certain factors critical for determining the location of landslide sites in one part of the event area have little influence in other parts of the event area. The implication is that landslide susceptibility maps (and subsequently derived mitigation measures) based on conventional slope stability factors may have only limited validity

  2. Self-excising Cre/mutant lox marker recycling system for multiple gene integrations and consecutive gene deletions in Aspergillus oryzae.

    Zhang, Silai; Ban, Akihiko; Ebara, Naoki; Mizutani, Osamu; Tanaka, Mizuki; Shintani, Takahiro; Gomi, Katsuya

    2017-04-01

    In this study, we developed a self-excising Cre/loxP-mediated marker recycling system with mutated lox sequences to introduce a number of biosynthetic genes into Aspergillus oryzae. To construct the self-excising marker cassette, both the selectable marker, the Aspergillus nidulans adeA gene, and the Cre recombinase gene (cre), conditionally expressed by the xylanase-encoding gene promoter, were designed to be located between the mutant lox sequences, lox66 and lox71. However, construction of the plasmid failed, possibly owing to a slight expression of cre downstream of the fungal gene promoter in Escherichia coli. Hence, to avoid the excision of the cassette in E. coli, a 71-bp intron of the A. oryzae xynG2 gene was inserted into the cre gene. The A. oryzae adeA deletion mutant was transformed with the resulting plasmid in the presence of glucose, and the transformants were cultured in medium containing xylose as the sole carbon source. PCR analysis of genomic DNA from resultant colonies revealed the excision of both the marker and Cre expression construct, indicating that the self-excising marker cassette was efficient at removing the selectable marker. Using the marker recycling system, hyperproduction of kojic acid could be achieved in A. oryzae by the introduction of two genes that encode oxidoreductase and transporter. Furthermore, we also constructed an alternative marker recycling cassette bearing the A. nidulans pyrithiamine resistant gene (ptrA) as a dominant selectable marker. Copyright © 2017 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  3. Convergence of Multiple MAP3Ks on MKK3 Identifies a Set of Novel Stress MAPK Modules

    Colcombet, Jean; Sö zen, Cé cile; Hirt, Heribert

    2016-01-01

    Since its first description in 1995 and functional characterization 12 years later, plant MKK3-type MAP2Ks have emerged as important integrators in plant signaling. Although they have received less attention than the canonical stress-activated

  4. Formal genetic maps

    Mohammad Saad Zaghloul Salem

    2014-12-24

    Dec 24, 2014 ... ome/transcriptome/proteome, experimental induced maps that are intentionally designed and con- ... genetic maps imposed their application in nearly all fields of medical genetics including ..... or genes located adjacent to, or near, them. ...... types of markers, e.g., clinical markers (eye color), genomic.

  5. New algorithm improves fine structure of the barley consensus SNP map

    Endelman Jeffrey B

    2011-08-01

    Full Text Available Abstract Background The need to integrate information from multiple linkage maps is a long-standing problem in genetics. One way to visualize the complex ordinal relationships is with a directed graph, where each vertex in the graph is a bin of markers. When there are no ordering conflicts between the linkage maps, the result is a directed acyclic graph, or DAG, which can then be linearized to produce a consensus map. Results New algorithms for the simplification and linearization of consensus graphs have been implemented as a package for the R computing environment called DAGGER. The simplified consensus graphs produced by DAGGER exactly capture the ordinal relationships present in a series of linkage maps. Using either linear or quadratic programming, DAGGER generates a consensus map with minimum error relative to the linkage maps while remaining ordinally consistent with them. Both linearization methods produce consensus maps that are compressed relative to the mean of the linkage maps. After rescaling, however, the consensus maps had higher accuracy (and higher marker density than the individual linkage maps in genetic simulations. When applied to four barley linkage maps genotyped at nearly 3000 SNP markers, DAGGER produced a consensus map with improved fine structure compared to the existing barley consensus SNP map. The root-mean-squared error between the linkage maps and the DAGGER map was 0.82 cM per marker interval compared to 2.28 cM for the existing consensus map. Examination of the barley hardness locus at the 5HS telomere, for which there is a physical map, confirmed that the DAGGER output was more accurate for fine structure analysis. Conclusions The R package DAGGER is an effective, freely available resource for integrating the information from a set of consistent linkage maps.

  6. Population structure revealed by different marker types (SSR or DArT) has an impact on the results of genome-wide association mapping in European barley cultivars

    Matthies, I.E.; Hintum, van T.J.L.; Weise, S.; Röder, M.S.

    2012-01-01

    Diversity arrays technology (DArT) and simple sequence repeat (SSR) markers were applied to investigate population structure, extent of linkage disequilibrium and genetic diversity (kinship) on a genome-wide level in European barley (Hordeum vulgare L.) cultivars. A set of 183 varieties could be

  7. Convergence of Multiple MAP3Ks on MKK3 Identifies a Set of Novel Stress MAPK Modules

    Colcombet, Jean

    2016-12-22

    Since its first description in 1995 and functional characterization 12 years later, plant MKK3-type MAP2Ks have emerged as important integrators in plant signaling. Although they have received less attention than the canonical stress-activated mitogen-activated protein kinases (MAPKs), several recent publications shed light on their important roles in plant adaptation to environmental conditions. Nevertheless, the MKK3-related literature is complicated. This review summarizes the current knowledge and discrepancies on MKK3 MAPK modules in plants and highlights the singular role of MKK3 in green plants. In the light of the latest data, we hypothesize a general model that all clade-III MAP3Ks converge on MKK3 and C-group MAPKs, thereby defining a set of novel MAPK modules which are activated by stresses and internal signals through the transcriptional regulation of MAP3K genes.

  8. Photolysis of NO2 at multiple wavelengths in the spectral region 200-205 nm - A velocity map imaging study

    Coroiu, A.M.; Parker, D.H.; Groenenboom, G.C.; Barr, J.; Novalbos, I.T.; Whitaker, B.J.

    2006-01-01

    A study of the photodissociation dynamics of NO2 in the 200-205 nm region using resonance enhanced multiphoton ionization (REMPI) in conjunction with the velocity map imaging technique is presented. We chose this region because it allowed the use of a single laser to photodissociate the NO2 molecule

  9. Mapping and characterization of positive and negative BOLD responses to visual stimulation in multiple brain regions at 7T

    Jorge, João; Figueiredo, Patrícia; Gruetter, Rolf; Van der Zwaag, W.

    External stimuli and tasks often elicit negative BOLD responses in various brain regions, and growing experimental evidence supports that these phenomena are functionally meaningful. In this work, the high sensitivity available at 7T was explored to map and characterize both positive (PBRs) and

  10. Fine-scale mapping of 8q24 locus identifies multiple independent risk variants for breast cancer

    J. Shi (Jiajun); Zhang, Y. (Yanfeng); W. Zheng (Wei); K. Michailidou (Kyriaki); M. Ghoussaini (Maya); M.K. Bolla (Manjeet K.); Wang, Q. (Qin); J. Dennis (Joe); Lush, M. (Michael); R.L. Milne (Roger); X.-O. Shu (Xiao-Ou); J. Beesley (Jonathan); S. Kar (Siddhartha); I.L. Andrulis (Irene); H. Anton-Culver (Hoda); Arndt, V. (Volker); M.W. Beckmann (Matthias); Z. Zhao (Zhiguo); Guo, X. (Xingyi); J. Benítez (Javier); A. Beeghly-Fadiel (Alicia); W.J. Blot (William); N.V. Bogdanova (Natalia); S.E. Bojesen (Stig); H. Brauch (Hiltrud); H. Brenner (Hermann); L.A. Brinton (Louise); A. Broeks (Annegien); T. Brüning (Thomas); B. Burwinkel (Barbara); H. Cai (Hui); S. Canisius (Sander); J. Chang-Claude (Jenny); Choi, J.-Y. (Ji-Yeob); F.J. Couch (Fergus); A. Cox (Angela); S.S. Cross (Simon); K. Czene (Kamila); H. Darabi (Hatef); P. Devilee (Peter); A. Droit (Arnaud); T. Dörk (Thilo); P.A. Fasching (Peter); O. Fletcher (Olivia); H. Flyger (Henrik); F. Fostira (Florentia); Gaborieau, V. (Valerie); M. García-Closas (Montserrat); G.G. Giles (Graham); Grip, M. (Mervi); P. Guénel (Pascal); C.A. Haiman (Christopher A.); U. Hamann (Ute); J.M. Hartman (Joost); X. Miao; A. Hollestelle (Antoinette); J.L. Hopper (John); Hsiung, C.-N. (Chia-Ni); H. Ito (Hidemi); A. Jakubowska (Anna); Johnson, N. (Nichola); D. Torres (Diana); M. Kabisch (Maria); D. Kang (Daehee); S. Khan (Sofia); J.A. Knight (Julia); V-M. Kosma (Veli-Matti); Lambrechts, D. (Diether); J. Li (Jingmei); A. Lindblom (Annika); A. Lophatananon (Artitaya); J. Lubinski (Jan); A. Mannermaa (Arto); S. Manoukian (Siranoush); L. Le Marchand (Loic); S. Margolin (Sara); Marme, F. (Frederik); K. Matsuo (Keitaro); C.A. McLean (Catriona Ann); A. Meindl (Alfons); K.R. Muir (K.); S.L. Neuhausen (Susan); H. Nevanlinna (Heli); S. Nord (Silje); A.-L. Borresen-Dale (Anne-Lise); J.E. Olson (Janet); N. Orr (Nick); A.M.W. van den Ouweland (Ans); P. Peterlongo (Paolo); T.C. Putti (Thomas Choudary); Rudolph, A. (Anja); Sangrajrang, S. (Suleeporn); E.J. Sawyer (Elinor); M.K. Schmidt (Marjanka); R.K. Schmutzler (Rita); C.-Y. Shen (Chen-Yang); M.-F. Hou (Ming-Feng); M. Shrubsole (Martha); M.C. Southey (Melissa); A.J. Swerdlow (Anthony ); Hwang Teo, S. (Soo); B. Thienpont (Bernard); A.E. Toland (Amanda); R.A.E.M. Tollenaar (Rob); I.P. Tomlinson (Ian); T. Truong (Thérèse); C.-C. Tseng (Chiu-Chen); W. Wen (Wanqing); R. Winqvist (Robert); A.H. Wu (Anna); C. Har Yip (Cheng); P.M. Zamora (Pilar M.); Zheng, Y. (Ying); O.A.M. Floris; Cheng, C.-Y. (Ching-Yu); M.J. Hooning (Maartje); J.W.M. Martens (John); C.M. Seynaeve (Caroline); V. Kristensen (Vessela); P. Hall (Per); P.D.P. Pharoah (Paul); J. Simard (Jacques); G. Chenevix-Trench (Georgia); A.M. Dunning (Alison); A.C. Antoniou (Antonis C.); D.F. Easton (Douglas F.); Q. Cai (Qiuyin); J. Long (Jirong)

    2016-01-01

    textabstractPrevious genome-wide association studies among women of European ancestry identified two independent breast cancer susceptibility loci represented by single nucleotide polymorphisms (SNPs) rs13281615 and rs11780156 at 8q24. A fine-mapping study across 2.06 Mb

  11. A method for mapping fire hazard and risk across multiple scales and its application in fire management

    Robert E. Keane; Stacy A. Drury; Eva C. Karau; Paul F. Hessburg; Keith M. Reynolds

    2010-01-01

    This paper presents modeling methods for mapping fire hazard and fire risk using a research model called FIREHARM (FIRE Hazard and Risk Model) that computes common measures of fire behavior, fire danger, and fire effects to spatially portray fire hazard over space. FIREHARM can compute a measure of risk associated with the distribution of these measures over time using...

  12. Genomic selection and association mapping in rice (Oryza sativa): effect of trait genetic architecture, training population composition, marker number and statistical model on accuracy of rice genomic selection in elite, tropical rice breeding lines.

    Spindel, Jennifer; Begum, Hasina; Akdemir, Deniz; Virk, Parminder; Collard, Bertrand; Redoña, Edilberto; Atlin, Gary; Jannink, Jean-Luc; McCouch, Susan R

    2015-02-01

    Genomic Selection (GS) is a new breeding method in which genome-wide markers are used to predict the breeding value of individuals in a breeding population. GS has been shown to improve breeding efficiency in dairy cattle and several crop plant species, and here we evaluate for the first time its efficacy for breeding inbred lines of rice. We performed a genome-wide association study (GWAS) in conjunction with five-fold GS cross-validation on a population of 363 elite breeding lines from the International Rice Research Institute's (IRRI) irrigated rice breeding program and herein report the GS results. The population was genotyped with 73,147 markers using genotyping-by-sequencing. The training population, statistical method used to build the GS model, number of markers, and trait were varied to determine their effect on prediction accuracy. For all three traits, genomic prediction models outperformed prediction based on pedigree records alone. Prediction accuracies ranged from 0.31 and 0.34 for grain yield and plant height to 0.63 for flowering time. Analyses using subsets of the full marker set suggest that using one marker every 0.2 cM is sufficient for genomic selection in this collection of rice breeding materials. RR-BLUP was the best performing statistical method for grain yield where no large effect QTL were detected by GWAS, while for flowering time, where a single very large effect QTL was detected, the non-GS multiple linear regression method outperformed GS models. For plant height, in which four mid-sized QTL were identified by GWAS, random forest produced the most consistently accurate GS models. Our results suggest that GS, informed by GWAS interpretations of genetic architecture and population structure, could become an effective tool for increasing the efficiency of rice breeding as the costs of genotyping continue to decline.

  13. Genomic selection and association mapping in rice (Oryza sativa: effect of trait genetic architecture, training population composition, marker number and statistical model on accuracy of rice genomic selection in elite, tropical rice breeding lines.

    Jennifer Spindel

    2015-02-01

    Full Text Available Genomic Selection (GS is a new breeding method in which genome-wide markers are used to predict the breeding value of individuals in a breeding population. GS has been shown to improve breeding efficiency in dairy cattle and several crop plant species, and here we evaluate for the first time its efficacy for breeding inbred lines of rice. We performed a genome-wide association study (GWAS in conjunction with five-fold GS cross-validation on a population of 363 elite breeding lines from the International Rice Research Institute's (IRRI irrigated rice breeding program and herein report the GS results. The population was genotyped with 73,147 markers using genotyping-by-sequencing. The training population, statistical method used to build the GS model, number of markers, and trait were varied to determine their effect on prediction accuracy. For all three traits, genomic prediction models outperformed prediction based on pedigree records alone. Prediction accuracies ranged from 0.31 and 0.34 for grain yield and plant height to 0.63 for flowering time. Analyses using subsets of the full marker set suggest that using one marker every 0.2 cM is sufficient for genomic selection in this collection of rice breeding materials. RR-BLUP was the best performing statistical method for grain yield where no large effect QTL were detected by GWAS, while for flowering time, where a single very large effect QTL was detected, the non-GS multiple linear regression method outperformed GS models. For plant height, in which four mid-sized QTL were identified by GWAS, random forest produced the most consistently accurate GS models. Our results suggest that GS, informed by GWAS interpretations of genetic architecture and population structure, could become an effective tool for increasing the efficiency of rice breeding as the costs of genotyping continue to decline.

  14. Genomic Selection and Association Mapping in Rice (Oryza sativa): Effect of Trait Genetic Architecture, Training Population Composition, Marker Number and Statistical Model on Accuracy of Rice Genomic Selection in Elite, Tropical Rice Breeding Lines

    Spindel, Jennifer; Begum, Hasina; Akdemir, Deniz; Virk, Parminder; Collard, Bertrand; Redoña, Edilberto; Atlin, Gary; Jannink, Jean-Luc; McCouch, Susan R.

    2015-01-01

    Genomic Selection (GS) is a new breeding method in which genome-wide markers are used to predict the breeding value of individuals in a breeding population. GS has been shown to improve breeding efficiency in dairy cattle and several crop plant species, and here we evaluate for the first time its efficacy for breeding inbred lines of rice. We performed a genome-wide association study (GWAS) in conjunction with five-fold GS cross-validation on a population of 363 elite breeding lines from the International Rice Research Institute's (IRRI) irrigated rice breeding program and herein report the GS results. The population was genotyped with 73,147 markers using genotyping-by-sequencing. The training population, statistical method used to build the GS model, number of markers, and trait were varied to determine their effect on prediction accuracy. For all three traits, genomic prediction models outperformed prediction based on pedigree records alone. Prediction accuracies ranged from 0.31 and 0.34 for grain yield and plant height to 0.63 for flowering time. Analyses using subsets of the full marker set suggest that using one marker every 0.2 cM is sufficient for genomic selection in this collection of rice breeding materials. RR-BLUP was the best performing statistical method for grain yield where no large effect QTL were detected by GWAS, while for flowering time, where a single very large effect QTL was detected, the non-GS multiple linear regression method outperformed GS models. For plant height, in which four mid-sized QTL were identified by GWAS, random forest produced the most consistently accurate GS models. Our results suggest that GS, informed by GWAS interpretations of genetic architecture and population structure, could become an effective tool for increasing the efficiency of rice breeding as the costs of genotyping continue to decline. PMID:25689273

  15. Dosing related effects of zoledronic acid on bone markers and creatinine clearance in patients with multiple myeloma and metastatic breast cancer

    Søe, Kent; Delaissé, Jean-Marie; Jakobsen, Erik H

    2014-01-01

    phase II clinical trial we investigated the effect of Zol treatment on the serum levels of the bone markers collagen type 1 cross-linked C-telopeptide (CTX) and bone specific alkaline phosphatase (bALP) as well as on creatinine clearance (kidney function) in response to dosing and duration of treatment...

  16. CD4(+) memory T cells with high CD26 surface expression are enriched for Th1 markers and correlate with clinical severity of multiple sclerosis

    Krakauer, M; Sorensen, P S; Sellebjerg, F

    2006-01-01

    ) memory T lymphocytes contained the high levels of markers of Th1, activation, and effector functions and cell counts of this subset correlated with MS disease severity. This subset had lower expression of PD-1, CCR4, and L-selectin in MS than in controls. These changes were only partially normalised...

  17. Identification and validation of multiple cell surface markers of clinical-grade adipose-derived mesenchymal stromal cells as novel release criteria for good manufacturing practice-compliant production.

    Camilleri, Emily T; Gustafson, Michael P; Dudakovic, Amel; Riester, Scott M; Garces, Catalina Galeano; Paradise, Christopher R; Takai, Hideki; Karperien, Marcel; Cool, Simon; Sampen, Hee-Jeong Im; Larson, A Noelle; Qu, Wenchun; Smith, Jay; Dietz, Allan B; van Wijnen, Andre J

    2016-08-11

    Clinical translation of mesenchymal stromal cells (MSCs) necessitates basic characterization of the cell product since variability in biological source and processing of MSCs may impact therapeutic outcomes. Although expression of classical cell surface markers (e.g., CD90, CD73, CD105, and CD44) is used to define MSCs, identification of functionally relevant cell surface markers would provide more robust release criteria and options for quality control. In addition, cell surface expression may distinguish between MSCs from different sources, including bone marrow-derived MSCs and clinical-grade adipose-derived MSCs (AMSCs) grown in human platelet lysate (hPL). In this work we utilized quantitative PCR, flow cytometry, and RNA-sequencing to characterize AMSCs grown in hPL and validated non-classical markers in 15 clinical-grade donors. We characterized the surface marker transcriptome of AMSCs, validated the expression of classical markers, and identified nine non-classical markers (i.e., CD36, CD163, CD271, CD200, CD273, CD274, CD146, CD248, and CD140B) that may potentially discriminate AMSCs from other cell types. More importantly, these markers exhibit variability in cell surface expression among different cell isolates from a diverse cohort of donors, including freshly prepared, previously frozen, or proliferative state AMSCs and may be informative when manufacturing cells. Our study establishes that clinical-grade AMSCs expanded in hPL represent a homogeneous cell culture population according to classical markers,. Additionally, we validated new biomarkers for further AMSC characterization that may provide novel information guiding the development of new release criteria. Use of Autologous Bone Marrow Aspirate Concentrate in Painful Knee Osteoarthritis (BMAC): Clinicaltrials.gov NCT01931007 . Registered August 26, 2013. MSC for Occlusive Disease of the Kidney: Clinicaltrials.gov NCT01840540 . Registered April 23, 2013. Mesenchymal Stem Cell Therapy in Multiple

  18. Development of simple sequence repeat markers and diversity analysis in alfalfa (Medicago sativa L.).

    Wang, Zan; Yan, Hongwei; Fu, Xinnian; Li, Xuehui; Gao, Hongwen

    2013-04-01

    Efficient and robust molecular markers are essential for molecular breeding in plant. Compared to dominant and bi-allelic markers, multiple alleles of simple sequence repeat (SSR) markers are particularly informative and superior in genetic linkage map and QTL mapping in autotetraploid species like alfalfa. The objective of this study was to enrich SSR markers directly from alfalfa expressed sequence tags (ESTs). A total of 12,371 alfalfa ESTs were retrieved from the National Center for Biotechnology Information. Total 774 SSR-containing ESTs were identified from 716 ESTs. On average, one SSR was found per 7.7 kb of EST sequences. Tri-nucleotide repeats (48.8 %) was the most abundant motif type, followed by di-(26.1 %), tetra-(11.5 %), penta-(9.7 %), and hexanucleotide (3.9 %). One hundred EST-SSR primer pairs were successfully designed and 29 exhibited polymorphism among 28 alfalfa accessions. The allele number per marker ranged from two to 21 with an average of 6.8. The PIC values ranged from 0.195 to 0.896 with an average of 0.608, indicating a high level of polymorphism of the EST-SSR markers. Based on the 29 EST-SSR markers, assessment of genetic diversity was conducted and found that Medicago sativa ssp. sativa was clearly different from the other subspecies. The high transferability of those EST-SSR markers was also found for relative species.

  19. PLOT3D (version-5): a computer code for drawing three dimensional graphs, maps and histograms, in single or multiple colours, for mono or stereoscopic viewing

    Jayaswal, Balhans

    1987-01-01

    PLOT3D series of graphic codes (version 1 to 5) have been developed for drawing three dimensional graphs, maps, histograms and simple layout diagrams on monochrome or colour raster graphic terminal and plotter. Of these, PLOT3D Version-5 is an advanced code, equipped with several features that make it specially suitable for drawing 3D maps, multicolour 3D and contour graphs, and 3D layout diagrams, in axonometric or perspective projection. Prior to drawing, graphic parameters that define orientation, magnification, smoothening, shading, colour-map, etc. of the figure can be selected interactively by means of simple commands on the user terminal, or by reading those commands from an input data file. This code requires linking with any one of three supporting libraries: PLOT 10 TCS, PLOT 10 IGL, and CALCOMP, and the figure can be plotted in single colour, or displayed in single or multiple colours depending upon the type of library support and output device. Furthermore, this code can also be used to plot left and right eye view projections of 3D figure for composing a stereoscopic image from them with the aid of a viewer. 14 figures. (author)

  20. NABIC marker database: A molecular markers information network of agricultural crops.

    Kim, Chang-Kug; Seol, Young-Joo; Lee, Dong-Jun; Jeong, In-Seon; Yoon, Ung-Han; Lee, Gang-Seob; Hahn, Jang-Ho; Park, Dong-Suk

    2013-01-01

    In 2013, National Agricultural Biotechnology Information Center (NABIC) reconstructs a molecular marker database for useful genetic resources. The web-based marker database consists of three major functional categories: map viewer, RSN marker and gene annotation. It provides 7250 marker locations, 3301 RSN marker property, 3280 molecular marker annotation information in agricultural plants. The individual molecular marker provides information such as marker name, expressed sequence tag number, gene definition and general marker information. This updated marker-based database provides useful information through a user-friendly web interface that assisted in tracing any new structures of the chromosomes and gene positional functions using specific molecular markers. The database is available for free at http://nabic.rda.go.kr/gere/rice/molecularMarkers/

  1. Statistical methods for QTL mapping and genomic prediction of multiple traits and environments: case studies in pepper

    Alimi, Nurudeen Adeniyi

    2016-01-01

    In this thesis we describe the results of a number of quantitative techniques that were used to understand the genetics of yield in pepper as an example of complex trait measured in a number of environments. Main objectives were; i) to propose a number of mixed models to detect QTLs for multiple

  2. Fine-scale mapping of 8q24 locus identifies multiple independent risk variants for breast cancer

    Shi, Jiajun; Zhang, Yanfeng; Zheng, Wei

    2016-01-01

    public resources implied that SNPs rs7815245 in Signal 3, and rs1121948 in Signal 5 (in linkage disequilibrium with rs11780156, r(2)  = 0.77), were putatively functional variants for two of the five independent association signals. The results highlighted multiple 8q24 variants associated with breast...

  3. Fine-mapping identifies multiple prostate cancer risk loci at 5p15, one of which associates with TERT expression

    Kote-Jarai, Zsofia; Saunders, Edward J; Leongamornlert, Daniel A

    2013-01-01

    Associations between single nucleotide polymorphisms (SNPs) at 5p15 and multiple cancer types have been reported. We have previously shown evidence for a strong association between prostate cancer (PrCa) risk and rs2242652 at 5p15, intronic in the telomerase reverse transcriptase (TERT) gene that...

  4. Mapping Aquatic Vegetation in a Large, Shallow Eutrophic Lake: A Frequency-Based Approach Using Multiple Years of MODIS Data

    Xiaohan Liu

    2015-08-01

    Full Text Available Aquatic vegetation serves many important ecological and socioeconomic functions in lake ecosystems. The presence of floating algae poses difficulties for accurately estimating the distribution of aquatic vegetation in eutrophic lakes. We present an approach to map the distribution of aquatic vegetation in Lake Taihu (a large, shallow eutrophic lake in China and reduce the influence of floating algae on aquatic vegetation mapping. Our approach involved a frequency analysis over a 2003–2013 time series of the floating algal index (FAI based on moderate-resolution imaging spectroradiometer (MODIS data. Three phenological periods were defined based on the vegetation presence frequency (VPF and the growth of algae and aquatic vegetation: December and January composed the period of wintering aquatic vegetation; February and March composed the period of prolonged coexistence of algal blooms and wintering aquatic vegetation; and June to October was the peak period of the coexistence of algal blooms and aquatic vegetation. By comparing and analyzing the satellite-derived aquatic vegetation distribution and 244 in situ measurements made in 2013, we established a FAI threshold of −0.025 and VPF thresholds of 0.55, 0.45 and 0.85 for the three phenological periods. We validated the accuracy of our approach by comparing the results between the satellite-derived maps and the in situ results obtained from 2008–2012. The overall classification accuracy was 87%, 81%, 77%, 88% and 73% in the five years from 2008–2012, respectively. We then applied the approach to the MODIS images from 2003–2013 and obtained the total area of the aquatic vegetation, which varied from 265.94 km2 in 2007 to 503.38 km2 in 2008, with an average area of 359.62 ± 69.20 km2 over the 11 years. Our findings suggest that (1 the proposed approach can be used to map the distribution of aquatic vegetation in eutrophic algae-rich waters and (2 dramatic changes occurred in the

  5. A phase II clinical trial does not show that high dose simvastatin has beneficial effect on markers of bone turnover in multiple myeloma

    Søndergaard, Teis Esben; Pedersen, PT; Levin Andersen, Thomas

    2008-01-01

    Several studies have evaluated the impact of low dose statin (20-80 mg/day) on bone metabolism with inconclusive results despite promising data of preclinical studies. In this study, we investigated the effect of high dose simvastatin (HD-Sim) on biochemical markers of bone turnover and disease...... acid phosphatase, TRACP); (ii) bone resorption (collagen fragments CTX and NTX); (iii) bone formation (osteocalcin and aminoterminal propeptide of type I collagen PINP); (iv) cholesterol; (v) regulators of bone metabolism [osteoprotegerin (OPG) and Dickkopf-1 (DKK-1)] and (vi) disease activity...... (monoclonal proteins or free light chains in serum). TRACP activity in serum and levels of collagen fragments (NTX) in urine increased for all patients temporarily during the 7 days of treatment with HD-Sim indicating that osteoclasts may have been stimulated rather than inhibited. The other markers of bone...

  6. Gully Erosion Mapping and Monitoring at Multiple Scales Based on Multi-Source Remote Sensing Data of the Sancha River Catchment, Northeast China

    Ranghu Wang

    2016-11-01

    Full Text Available This research is focused on gully erosion mapping and monitoring at multiple spatial scales using multi-source remote sensing data of the Sancha River catchment in Northeast China, where gullies extend over a vast area. A high resolution satellite image (Pleiades 1A, 0.7 m was used to obtain the spatial distribution of the gullies of the overall basin. Image visual interpretation with field verification was employed to map the geometric gully features and evaluate gully erosion as well as the topographic differentiation characteristics. Unmanned Aerial Vehicle (UAV remote sensing data and the 3D photo-reconstruction method were employed for detailed gully mapping at a site scale. The results showed that: (1 the sub-meter image showed a strong ability in the recognition of various gully types and obtained satisfactory results, and the topographic factors of elevation, slope and slope aspects exerted significant influence on the gully spatial distribution at the catchment scale; and (2 at a more detailed site scale, UAV imagery combined with 3D photo-reconstruction provided a Digital Surface Model (DSM and ortho-image at the centimeter level as well as a detailed 3D model. The resulting products revealed the area of agricultural utilization and its shaping by human agricultural activities and water erosion in detail, and also provided the gully volume. The present study indicates that using multi-source remote sensing data, including satellite and UAV imagery simultaneously, results in an effective assessment of gully erosion over multiple spatial scales. The combined approach should be continued to regularly monitor gully erosion to understand the erosion process and its relationship with the environment from a comprehensive perspective.

  7. Single molecule translocation in smectics illustrates the challenge for time-mapping in simulations on multiple scales.

    Mukherjee, Biswaroop; Peter, Christine; Kremer, Kurt

    2017-09-21

    Understanding the connections between the characteristic dynamical time scales associated with a coarse-grained (CG) and a detailed representation is central to the applicability of the coarse-graining methods to understand molecular processes. The process of coarse graining leads to an accelerated dynamics, owing to the smoothening of the underlying free-energy landscapes. Often a single time-mapping factor is used to relate the time scales associated with the two representations. We critically examine this idea using a model system ideally suited for this purpose. Single molecular transport properties are studied via molecular dynamics simulations of the CG and atomistic representations of a liquid crystalline, azobenzene containing mesogen, simulated in the smectic and the isotropic phases. The out-of-plane dynamics in the smectic phase occurs via molecular hops from one smectic layer to the next. Hopping can occur via two mechanisms, with and without significant reorientation. The out-of-plane transport can be understood as a superposition of two (one associated with each mode of transport) independent continuous time random walks for which a single time-mapping factor would be rather inadequate. A comparison of the free-energy surfaces, relevant to the out-of-plane transport, qualitatively supports the above observations. Thus, this work underlines the need for building CG models that exhibit both structural and dynamical consistency to the underlying atomistic model.

  8. Single molecule translocation in smectics illustrates the challenge for time-mapping in simulations on multiple scales

    Mukherjee, Biswaroop; Peter, Christine; Kremer, Kurt

    2017-09-01

    Understanding the connections between the characteristic dynamical time scales associated with a coarse-grained (CG) and a detailed representation is central to the applicability of the coarse-graining methods to understand molecular processes. The process of coarse graining leads to an accelerated dynamics, owing to the smoothening of the underlying free-energy landscapes. Often a single time-mapping factor is used to relate the time scales associated with the two representations. We critically examine this idea using a model system ideally suited for this purpose. Single molecular transport properties are studied via molecular dynamics simulations of the CG and atomistic representations of a liquid crystalline, azobenzene containing mesogen, simulated in the smectic and the isotropic phases. The out-of-plane dynamics in the smectic phase occurs via molecular hops from one smectic layer to the next. Hopping can occur via two mechanisms, with and without significant reorientation. The out-of-plane transport can be understood as a superposition of two (one associated with each mode of transport) independent continuous time random walks for which a single time-mapping factor would be rather inadequate. A comparison of the free-energy surfaces, relevant to the out-of-plane transport, qualitatively supports the above observations. Thus, this work underlines the need for building CG models that exhibit both structural and dynamical consistency to the underlying atomistic model.

  9. Aluminum tolerance association mapping in triticale

    Niedziela Agnieszka

    2012-02-01

    Full Text Available Abstract Background Crop production practices and industrialization processes result in increasing acidification of arable soils. At lower pH levels (below 5.0, aluminum (Al remains in a cationic form that is toxic to plants, reducing growth and yield. The effect of aluminum on agronomic performance is particularly important in cereals like wheat, which has promoted the development of programs directed towards selection of tolerant forms. Even in intermediately tolerant cereals (i.e., triticale, the decrease in yield may be significant. In triticale, Al tolerance seems to be influenced by both wheat and rye genomes. However, little is known about the precise chromosomal location of tolerance-related genes, and whether wheat or rye genomes are crucial for the expression of that trait in the hybrid. Results A mapping population consisting of 232 advanced breeding triticale forms was developed and phenotyped for Al tolerance using physiological tests. AFLP, SSR and DArT marker platforms were applied to obtain a sufficiently large set of molecular markers (over 3000. Associations between the markers and the trait were tested using General (GLM and Multiple (MLM Linear Models, as well as the Statistical Machine Learning (SML approach. The chromosomal locations of candidate markers were verified based on known assignments of SSRs and DArTs or by using genetic maps of rye and triticale. Two candidate markers on chromosome 3R and 9, 15 and 11 on chromosomes 4R, 6R and 7R, respectively, were identified. The r2 values were between 0.066 and 0.220 in most cases, indicating a good fit of the data, with better results obtained with the GML than the MLM approach. Several QTLs on rye chromosomes appeared to be involved in the phenotypic expression of the trait, suggesting that rye genome factors are predominantly responsible for Al tolerance in triticale. Conclusions The Diversity Arrays Technology was applied successfully to association mapping studies

  10. Method to map one-dimensional electronic wave function by using multiple Brillouin zone angle resolved photoemission

    Dong-Wook Lee

    2010-10-01

    Full Text Available Angle resolved photoemission spectroscopy (ARPES is a powerful tool to investigate electronic structures in solids and has been widely used in studying various materials. The electronic structure information by ARPES is obtained in the momentum space. However, in the case of one-dimensional system, we here show that we extract the real space information from ARPES data taken over multiple Brillouin zones (BZs. Intensities in the multiple BZs are proportional to the photoemission matrix element which contains information on the coefficient of the Bloch wave function. It is shown that the Bloch wave function coefficients can be extracted from ARPES data, which allows us to construct the real space wave function. As a test, we use ARPES data from proto-typical one-dimensional system SrCuO2 and construct the real space wave function.

  11. An Integrated Resource for Barley Linkage Map and Malting Quality QTL Alignment

    Péter Szűcs

    2009-07-01

    Full Text Available Barley ( L. is an economically important model plant for genetics research. Barley is currently served by an increasingly comprehensive set of tools for genetic analysis that have recently been augmented by high-density genetic linkage maps built with gene-based single nucleotide polymorphisms (SNPs. These SNP-based maps need to be aligned with earlier generation maps, which were used for quantitative trait locus (QTL detection, by integrating multiple types of markers into a single map. A 2383 locus linkage map was developed using the Oregon Wolfe Barley (OWB Mapping Population to allow such alignments. The map is based on 1472 SNP, 722 DArT, and 189 prior markers which include morphological, simple sequence repeat (SSR, Restriction Fragment Length Polymorphism (RFLP, and sequence tagged site (STS loci. This new OWB map forms, therefore, a useful bridge between high-density SNP-only maps and prior QTL reports. The application of this bridge concept is shown using malting-quality QTLs from multiple mapping populations, as reported in the literature. This is the first step toward developing a Barley QTL Community Curation workbook for all types of QTLs and maps, on the GrainGenes website. The OWB-related resources are available at OWB Data and GrainGenes Tools (OWB-DGGT (.

  12. Fine-mapping and cross-validation of QTLs linked to fatty acid composition in multiple independent interspecific crosses of oil palm.

    Ting, Ngoot-Chin; Yaakub, Zulkifli; Kamaruddin, Katialisa; Mayes, Sean; Massawe, Festo; Sambanthamurthi, Ravigadevi; Jansen, Johannes; Low, Leslie Eng Ti; Ithnin, Maizura; Kushairi, Ahmad; Arulandoo, Xaviar; Rosli, Rozana; Chan, Kuang-Lim; Amiruddin, Nadzirah; Sritharan, Kandha; Lim, Chin Ching; Nookiah, Rajanaidu; Amiruddin, Mohd Din; Singh, Rajinder

    2016-04-14

    The commercial oil palm (Elaeis guineensis Jacq.) produces a mesocarp oil (commonly called 'palm oil') with approximately equal proportions of saturated and unsaturated fatty acids (FAs). An increase in unsaturated FAs content or iodine value (IV) as a measure of the degree of unsaturation would help to open up new markets for the oil. One way to manipulate the fatty acid composition (FAC) in palm oil is through introgression of favourable alleles from the American oil palm, E. oleifera, which has a more unsaturated oil. In this study, a segregating E. oleifera x E. guineensis (OxG) hybrid population for FAC is used to identify quantitative trait loci (QTLs) linked to IV and various FAs. QTL analysis revealed 10 major and two putative QTLs for IV and six FAs, C14:0, C16:0, C16:1, C18:0, C18:1 and C18:2 distributed across six linkage groups (LGs), OT1, T2, T3, OT4, OT6 and T9. The major QTLs for IV and C16:0 on LGOT1 explained 60.0 - 69.0 % of the phenotypic trait variation and were validated in two independent BC2 populations. The genomic interval contains several key structural genes in the FA and oil biosynthesis pathways such as PATE/FATB, HIBCH, BASS2, LACS4 and DGAT1 and also a relevant transcription factor (TF), WRI1. The literature suggests that some of these genes can exhibit pleiotropic effects in the regulatory networks of these traits. Using the whole genome sequence data, markers tightly linked to the candidate genes were also developed. Clustering trait values according to the allelic forms of these candidate markers revealed significant differences in the IV and FAs of the palms in the mapping and validation crosses. The candidate gene approach described and exploited here is useful to identify the potential causal genes linked to FAC and can be adopted for marker-assisted selection (MAS) in oil palm.

  13. YouGenMap: a web platform for dynamic multi-comparative mapping and visualization of genetic maps

    Keith Batesole; Kokulapalan Wimalanathan; Lin Liu; Fan Zhang; Craig S. Echt; Chun Liang

    2014-01-01

    Comparative genetic maps are used in examination of genome organization, detection of conserved gene order, and exploration of marker order variations. YouGenMap is an open-source web tool that offers dynamic comparative mapping capability of users' own genetic mapping between 2 or more map sets. Users' genetic map data and optional gene annotations are...

  14. Comparative genome analysis and resistance gene mapping in grain legumes

    Young, N.D.

    1998-01-01

    Using, DNA markers and genome organization, several important disease resistance genes have been analyzed in mungbean (Vigna radiata), cowpea (Vigna unguiculata), common bean (Phaseolus vulgaris), and soybean (Glycine max). In the process, medium-density linkage maps consisting of restriction fragment length polymorphism (RFLP) markers were constructed for both mungbean and cowpea. Comparisons between these maps, as well as the maps of soybean and common bean, indicate that there is significant conservation of DNA marker order, though the conserved blocks in soybean are much shorter than in the others. DNA mapping results also indicate that a gene for seed weight may be conserved between mungbean and cowpea. Using the linkage maps, genes that control bruchid (genus Callosobruchus) and powdery mildew (Erysiphe polygoni) resistance in mungbean, aphid resistance in cowpea (Aphis craccivora), and cyst nematode (Heterodera glycines) resistance in soybean have all been mapped and characterized. For some of these traits resistance was found to be oligogenic and DNA mapping uncovered multiple genes involved in the phenotype. (author)

  15. Is TrpM5 a reliable marker for chemosensory cells? Multiple types of microvillous cells in the main olfactory epithelium of mice

    Finger Thomas E

    2008-12-01

    Full Text Available Abstract Background In the past, ciliated receptor neurons, basal cells, and supporting cells were considered the principal components of the main olfactory epithelium. Several studies reported the presence of microvillous cells but their function is unknown. A recent report showed cells in the main olfactory epithelium that express the transient receptor potential channel TrpM5 claiming that these cells are chemosensory and that TrpM5 is an intrinsic signaling component of mammalian chemosensory organs. We asked whether the TrpM5-positive cells in the olfactory epithelium are microvillous and whether they belong to a chemosensory system, i.e. are olfactory neurons or trigeminally-innervated solitary chemosensory cells. Results We investigated the main olfactory epithelium of mice at the light and electron microscopic level and describe several subpopulations of microvillous cells. The ultrastructure of the microvillous cells reveals at least three morphologically different types two of which express the TrpM5 channel. None of these cells have an axon that projects to the olfactory bulb. Tests with a large panel of cell markers indicate that the TrpM5-positive cells are not sensory since they express neither neuronal markers nor are contacted by trigeminal nerve fibers. Conclusion We conclude that TrpM5 is not a reliable marker for chemosensory cells. The TrpM5-positive cells of the olfactory epithelium are microvillous and may be chemoresponsive albeit not part of the sensory apparatus. Activity of these microvillous cells may however influence functionality of local elements of the olfactory system.

  16. Mapping cortical hand motor representation using TMS: A method to assess brain plasticity and a surrogate marker for recovery of function after stroke?

    Lüdemann-Podubecká, Jitka; Nowak, Dennis Alexander

    2016-10-01

    Stroke is associated with reorganization within motor areas of both hemispheres. Mapping the cortical hand motor representation using transcranial magnetic stimulation may help to understand the relationship between motor cortex reorganization and motor recovery of the affected hand after stroke. A standardized review of the pertinent literature was performed. We identified 20 trials, which analyzed the relationship between the extent and/or location of cortical hand motor representation using transcranial magnetic stimulation and motor function and recovery of the affected hand. Several correlations were found between cortical reorganization and measures of hand motor impairment and recovery. A better understanding of the relationships between the extent and location of cortical hand motor representation and the motor impairment and motor recovery of the affected hand after stroke may contribute to a targeted use of non-invasive brain stimulation protocols. In the future motor mapping may help to guide brain stimulation techniques to the most effective motor area in an affected individual. Copyright © 2016 Elsevier Ltd. All rights reserved.

  17. Insight into Genotype-Phenotype Associations through eQTL Mapping in Multiple Cell Types in Health and Immune-Mediated Disease.

    James E Peters

    2016-03-01

    Full Text Available Genome-wide association studies (GWAS have transformed our understanding of the genetics of complex traits such as autoimmune diseases, but how risk variants contribute to pathogenesis remains largely unknown. Identifying genetic variants that affect gene expression (expression quantitative trait loci, or eQTLs is crucial to addressing this. eQTLs vary between tissues and following in vitro cellular activation, but have not been examined in the context of human inflammatory diseases. We performed eQTL mapping in five primary immune cell types from patients with active inflammatory bowel disease (n = 91, anti-neutrophil cytoplasmic antibody-associated vasculitis (n = 46 and healthy controls (n = 43, revealing eQTLs present only in the context of active inflammatory disease. Moreover, we show that following treatment a proportion of these eQTLs disappear. Through joint analysis of expression data from multiple cell types, we reveal that previous estimates of eQTL immune cell-type specificity are likely to have been exaggerated. Finally, by analysing gene expression data from multiple cell types, we find eQTLs not previously identified by database mining at 34 inflammatory bowel disease-associated loci. In summary, this parallel eQTL analysis in multiple leucocyte subsets from patients with active disease provides new insights into the genetic basis of immune-mediated diseases.

  18. Tumors markers

    Yamaguchi-Mizumoto, N.H.

    1989-01-01

    In order to study blood and cell components alterations (named tumor markers) that may indicate the presence of a tumor, several methods are presented. Aspects as diagnostic, prognostic, therapeutic value and clinical evaluation are discussed. (M.A.C.)

  19. Multiple sex-associated regions and a putative sex chromosome in zebrafish revealed by RAD mapping and population genomics.

    Jennifer L Anderson

    Full Text Available Within vertebrates, major sex determining genes can differ among taxa and even within species. In zebrafish (Danio rerio, neither heteromorphic sex chromosomes nor single sex determination genes of large effect, like Sry in mammals, have yet been identified. Furthermore, environmental factors can influence zebrafish sex determination. Although progress has been made in understanding zebrafish gonad differentiation (e.g. the influence of germ cells on gonad fate, the primary genetic basis of zebrafish sex determination remains poorly understood. To identify genetic loci associated with sex, we analyzed F(2 offspring of reciprocal crosses between Oregon *AB and Nadia (NA wild-type zebrafish stocks. Genome-wide linkage analysis, using more than 5,000 sequence-based polymorphic restriction site associated (RAD-tag markers and population genomic analysis of more than 30,000 single nucleotide polymorphisms in our *ABxNA crosses revealed a sex-associated locus on the end of the long arm of chr-4 for both cross families, and an additional locus in the middle of chr-3 in one cross family. Additional sequencing showed that two SNPs in dmrt1 previously suggested to be functional candidates for sex determination in a cross of ABxIndia wild-type zebrafish, are not associated with sex in our AB fish. Our data show that sex determination in zebrafish is polygenic and that different genes may influence sex determination in different strains or that different genes become more important under different environmental conditions. The association of the end of chr-4 with sex is remarkable because, unique in the karyotype, this chromosome arm shares features with known sex chromosomes: it is highly heterochromatic, repetitive, late replicating, and has reduced recombination. Our results reveal that chr-4 has functional and structural properties expected of a sex chromosome.

  20. Mapping of wind energy potential over the Gobi Desert in Northwest China based on multiple sources of data

    Li, Li; Wang, Xinyuan; Luo, Lei; Zhao, Yanchuang; Zong, Xin; Bachagha, Nabil

    2018-06-01

    In recent years, wind energy has been a fastgrowing alternative source of electrical power due to its sustainability. In this paper, the wind energy potential over the Gobi Desert in Northwest China is assessed at the patch scale using geographic information systems (GIS). Data on land cover, topography, and administrative boundaries and 11 years (2000‒2010) of wind speed measurements were collected and used to map and estimate the region's wind energy potential. Based on the results, it was found that continuous regions of geographical potential (GeoP) are located in the middle of the research area (RA), with scattered areas of similar GeoP found in other regions. The results also show that the technical potential (TecP) levels are about 1.72‒2.67 times (2.20 times on average) higher than the actual levels. It was found that the GeoP patches can be divided into four classes: unsuitable regions, suitable regions, more suitable regions, and the most suitable regions. The GeoP estimation shows that 0.41 billion kW of wind energy are potentially available in the RA. The suitable regions account for 25.49%, the more suitable regions 24.45%, and the most suitable regions for more than half of the RA. It is also shown that Xinjiang and Gansu are more suitable for wind power development than Ningxia.

  1. Construction of an integrated genetic map for Capsicum baccatum L.

    Moulin, M M; Rodrigues, R; Ramos, H C C; Bento, C S; Sudré, C P; Gonçalves, L S A; Viana, A P

    2015-06-18

    Capsicum baccatum L. is one of the five Capsicum domesticated species and has multiple uses in the food, pharmaceutical and cosmetic industries. This species is also a valuable source of genes for chili pepper breeding, especially genes for disease resistance and fruit quality. However, knowledge of the genetic structure of C. baccatum is limited. A reference map for C. baccatum (2n = 2x = 24) based on 42 microsatellite, 85 inter-simple sequence repeat, and 56 random amplified polymorphic DNA markers was constructed using an F2 population consisting of 203 individuals. The map was generated using the JoinMap software (version 4.0) and the linkage groups were formed and ordered using a LOD score of 3.0 and maximum of 40% recombination. The genetic map consisted of 12 major and four minor linkage groups covering a total genome distance of 2547.5 cM with an average distance of 14.25 cM between markers. Of the 152 pairs of microsatellite markers available for Capsicum annuum, 62 were successfully transferred to C. baccatum, generating polymorphism. Forty-two of these markers were mapped, allowing the introduction of C. baccatum in synteny studies with other species of the genus Capsicum.

  2. Iterative h-minima-based marker-controlled watershed for cell nucleus segmentation.

    Koyuncu, Can Fahrettin; Akhan, Ece; Ersahin, Tulin; Cetin-Atalay, Rengul; Gunduz-Demir, Cigdem

    2016-04-01

    Automated microscopy imaging systems facilitate high-throughput screening in molecular cellular biology research. The first step of these systems is cell nucleus segmentation, which has a great impact on the success of the overall system. The marker-controlled watershed is a technique commonly used by the previous studies for nucleus segmentation. These studies define their markers finding regional minima on the intensity/gradient and/or distance transform maps. They typically use the h-minima transform beforehand to suppress noise on these maps. The selection of the h value is critical; unnecessarily small values do not sufficiently suppress the noise, resulting in false and oversegmented markers, and unnecessarily large ones suppress too many pixels, causing missing and undersegmented markers. Because cell nuclei show different characteristics within an image, the same h value may not work to define correct markers for all the nuclei. To address this issue, in this work, we propose a new watershed algorithm that iteratively identifies its markers, considering a set of different h values. In each iteration, the proposed algorithm defines a set of candidates using a particular h value and selects the markers from those candidates provided that they fulfill the size requirement. Working with widefield fluorescence microscopy images, our experiments reveal that the use of multiple h values in our iterative algorithm leads to better segmentation results, compared to its counterparts. © 2016 International Society for Advancement of Cytometry. © 2016 International Society for Advancement of Cytometry.

  3. How entorhinal grid cells may learn multiple spatial scales from a dorsoventral gradient of cell response rates in a self-organizing map.

    Stephen Grossberg

    Full Text Available Place cells in the hippocampus of higher mammals are critical for spatial navigation. Recent modeling clarifies how this may be achieved by how grid cells in the medial entorhinal cortex (MEC input to place cells. Grid cells exhibit hexagonal grid firing patterns across space in multiple spatial scales along the MEC dorsoventral axis. Signals from grid cells of multiple scales combine adaptively to activate place cells that represent much larger spaces than grid cells. But how do grid cells learn to fire at multiple positions that form a hexagonal grid, and with spatial scales that increase along the dorsoventral axis? In vitro recordings of medial entorhinal layer II stellate cells have revealed subthreshold membrane potential oscillations (MPOs whose temporal periods, and time constants of excitatory postsynaptic potentials (EPSPs, both increase along this axis. Slower (faster subthreshold MPOs and slower (faster EPSPs correlate with larger (smaller grid spacings and field widths. A self-organizing map neural model explains how the anatomical gradient of grid spatial scales can be learned by cells that respond more slowly along the gradient to their inputs from stripe cells of multiple scales, which perform linear velocity path integration. The model cells also exhibit MPO frequencies that covary with their response rates. The gradient in intrinsic rhythmicity is thus not compelling evidence for oscillatory interference as a mechanism of grid cell firing. A response rate gradient combined with input stripe cells that have normalized receptive fields can reproduce all known spatial and temporal properties of grid cells along the MEC dorsoventral axis. This spatial gradient mechanism is homologous to a gradient mechanism for temporal learning in the lateral entorhinal cortex and its hippocampal projections. Spatial and temporal representations may hereby arise from homologous mechanisms, thereby embodying a mechanistic "neural relativity" that

  4. A comparison of multiple regression and neural network techniques for mapping in situ pCO2 data

    Lefevre, Nathalie; Watson, Andrew J.; Watson, Adam R.

    2005-01-01

    Using about 138,000 measurements of surface pCO 2 in the Atlantic subpolar gyre (50-70 deg N, 60-10 deg W) during 1995-1997, we compare two methods of interpolation in space and time: a monthly distribution of surface pCO 2 constructed using multiple linear regressions on position and temperature, and a self-organizing neural network approach. Both methods confirm characteristics of the region found in previous work, i.e. the subpolar gyre is a sink for atmospheric CO 2 throughout the year, and exhibits a strong seasonal variability with the highest undersaturations occurring in spring and summer due to biological activity. As an annual average the surface pCO 2 is higher than estimates based on available syntheses of surface pCO 2 . This supports earlier suggestions that the sink of CO 2 in the Atlantic subpolar gyre has decreased over the last decade instead of increasing as previously assumed. The neural network is able to capture a more complex distribution than can be well represented by linear regressions, but both techniques agree relatively well on the average values of pCO 2 and derived fluxes. However, when both techniques are used with a subset of the data, the neural network predicts the remaining data to a much better accuracy than the regressions, with a residual standard deviation ranging from 3 to 11 μatm. The subpolar gyre is a net sink of CO 2 of 0.13 Gt-C/yr using the multiple linear regressions and 0.15 Gt-C/yr using the neural network, on average between 1995 and 1997. Both calculations were made with the NCEP monthly wind speeds converted to 10 m height and averaged between 1995 and 1997, and using the gas exchange coefficient of Wanninkhof

  5. Landslide Susceptibility Mapping Based on Particle Swarm Optimization of Multiple Kernel Relevance Vector Machines: Case of a Low Hill Area in Sichuan Province, China

    Yongliang Lin

    2016-10-01

    Full Text Available In this paper, we propose a multiple kernel relevance vector machine (RVM method based on the adaptive cloud particle swarm optimization (PSO algorithm to map landslide susceptibility in the low hill area of Sichuan Province, China. In the multi-kernel structure, the kernel selection problem can be solved by adjusting the kernel weight, which determines the single kernel contribution of the final kernel mapping. The weights and parameters of the multi-kernel function were optimized using the PSO algorithm. In addition, the convergence speed of the PSO algorithm was increased using cloud theory. To ensure the stability of the prediction model, the result of a five-fold cross-validation method was used as the fitness of the PSO algorithm. To verify the results, receiver operating characteristic curves (ROC and landslide dot density (LDD were used. The results show that the model that used a heterogeneous kernel (a combination of two different kernel functions had a larger area under the ROC curve (0.7616 and a lower prediction error ratio (0.28% than did the other types of kernel models employed in this study. In addition, both the sum of two high susceptibility zone LDDs (6.71/100 km2 and the sum of two low susceptibility zone LDDs (0.82/100 km2 demonstrated that the landslide susceptibility map based on the heterogeneous kernel model was closest to the historical landslide distribution. In conclusion, the results obtained in this study can provide very useful information for disaster prevention and land-use planning in the study area.

  6. Theory and simulations of covariance mapping in multiple dimensions for data analysis in high-event-rate experiments

    Zhaunerchyk, V.; Frasinski, L. J.; Eland, J. H. D.; Feifel, R.

    2014-05-01

    Multidimensional covariance analysis and its validity for correlation of processes leading to multiple products are investigated from a theoretical point of view. The need to correct for false correlations induced by experimental parameters which fluctuate from shot to shot, such as the intensity of self-amplified spontaneous emission x-ray free-electron laser pulses, is emphasized. Threefold covariance analysis based on simple extension of the two-variable formulation is shown to be valid for variables exhibiting Poisson statistics. In this case, false correlations arising from fluctuations in an unstable experimental parameter that scale linearly with signals can be eliminated by threefold partial covariance analysis, as defined here. Fourfold covariance based on the same simple extension is found to be invalid in general. Where fluctuations in an unstable parameter induce nonlinear signal variations, a technique of contingent covariance analysis is proposed here to suppress false correlations. In this paper we also show a method to eliminate false correlations associated with fluctuations of several unstable experimental parameters.

  7. Rice genetic marker database: An identification of single nucleotide ...

    based genetic marker system to provide information about SNP and QTL markers in rice. The SNP marker database provides 7,227 SNP markers including location information on chromosomes by using genetic map. It allows users to access a ...

  8. Molecular markers linked to apomixis in Panicum maximum Jacq.

    SAM

    2014-05-28

    May 28, 2014 ... The objective of this work was to identify molecular markers linked to apomixis in ... Four RAPD markers linked to apomixis were identified and mapped in this .... Data analysis. The amplification of the potential markers was analyzed as binary, with 1 for presence and 0 for absence of the marker. The binary.

  9. Multiple active myofascial trigger points and pressure pain sensitivity maps in the temporalis muscle are related in women with chronic tension type headache.

    Fernández-de-las-Peñas, César; Caminero, Ana B; Madeleine, Pascal; Guillem-Mesado, Amparo; Ge, Hong-You; Arendt-Nielsen, Lars; Pareja, Juan A

    2009-01-01

    To describe the common locations of active trigger points (TrPs) in the temporalis muscle and their referred pain patterns in chronic tension type headache (CTTH), and to determine if pressure sensitivity maps of this muscle can be used to describe the spatial distribution of active TrPs. Forty women with CTTH were included. An electronic pressure algometer was used to assess pressure pain thresholds (PPT) from 9 points over each temporalis muscle: 3 points in the anterior, medial and posterior part, respectively. Both muscles were examined for the presence of active TrPs over each of the 9 points. The referred pain pattern of each active TrP was assessed. Two-way analysis of variance detected significant differences in mean PPT levels between the measurement points (F=30.3; P<0.001), but not between sides (F=2.1; P=0.2). PPT scores decreased from the posterior to the anterior column (P<0.001). No differences were found in the number of active TrPs (F=0.3; P=0.9) between the dominant side the nondominant side. Significant differences were found in the distribution of the active TrPs (chi2=12.2; P<0.001): active TrPs were mostly found in the anterior column and in the middle of the muscle belly. The analysis of variance did not detect significant differences in the referred pain pattern between active TrPs (F=1.1, P=0.4). The topographical pressure pain sensitivity maps showed the distinct distribution of the TrPs indicated by locations with low PPTs. Multiple active TrPs in the temporalis muscle were found, particularly in the anterior column and in the middle of the muscle belly. Bilateral posterior to anterior decreased distribution of PPTs in the temporalis muscle in women with CTTH was found. The locations of active TrPs in the temporalis muscle corresponded well to the muscle areas with lower PPT, supporting the relationship between multiple active muscle TrPs and topographical pressure sensitivity maps in the temporalis muscle in women with CTTH.

  10. Mapping quantitative trait loci in plant breeding populations : Use of parental haplotype sharing

    Jansen, Ritsert C.; Jannink, Jean-Luc; Beavis, William D.

    2003-01-01

    Applied breeding programs evaluate large numbers of progeny derived from multiple related crosses for a wide range of agronomic traits and for tens to hundreds of molecular markers. This study was conducted to determine how these phenotypic and genetic data could be used for routinely mapping

  11. High Resolution Mapping of Soil Properties Using Remote Sensing Variables in South-Western Burkina Faso: A Comparison of Machine Learning and Multiple Linear Regression Models.

    Forkuor, Gerald; Hounkpatin, Ozias K L; Welp, Gerhard; Thiel, Michael

    2017-01-01

    Accurate and detailed spatial soil information is essential for environmental modelling, risk assessment and decision making. The use of Remote Sensing data as secondary sources of information in digital soil mapping has been found to be cost effective and less time consuming compared to traditional soil mapping approaches. But the potentials of Remote Sensing data in improving knowledge of local scale soil information in West Africa have not been fully explored. This study investigated the use of high spatial resolution satellite data (RapidEye and Landsat), terrain/climatic data and laboratory analysed soil samples to map the spatial distribution of six soil properties-sand, silt, clay, cation exchange capacity (CEC), soil organic carbon (SOC) and nitrogen-in a 580 km2 agricultural watershed in south-western Burkina Faso. Four statistical prediction models-multiple linear regression (MLR), random forest regression (RFR), support vector machine (SVM), stochastic gradient boosting (SGB)-were tested and compared. Internal validation was conducted by cross validation while the predictions were validated against an independent set of soil samples considering the modelling area and an extrapolation area. Model performance statistics revealed that the machine learning techniques performed marginally better than the MLR, with the RFR providing in most cases the highest accuracy. The inability of MLR to handle non-linear relationships between dependent and independent variables was found to be a limitation in accurately predicting soil properties at unsampled locations. Satellite data acquired during ploughing or early crop development stages (e.g. May, June) were found to be the most important spectral predictors while elevation, temperature and precipitation came up as prominent terrain/climatic variables in predicting soil properties. The results further showed that shortwave infrared and near infrared channels of Landsat8 as well as soil specific indices of redness

  12. High Resolution Mapping of Soil Properties Using Remote Sensing Variables in South-Western Burkina Faso: A Comparison of Machine Learning and Multiple Linear Regression Models.

    Gerald Forkuor

    Full Text Available Accurate and detailed spatial soil information is essential for environmental modelling, risk assessment and decision making. The use of Remote Sensing data as secondary sources of information in digital soil mapping has been found to be cost effective and less time consuming compared to traditional soil mapping approaches. But the potentials of Remote Sensing data in improving knowledge of local scale soil information in West Africa have not been fully explored. This study investigated the use of high spatial resolution satellite data (RapidEye and Landsat, terrain/climatic data and laboratory analysed soil samples to map the spatial distribution of six soil properties-sand, silt, clay, cation exchange capacity (CEC, soil organic carbon (SOC and nitrogen-in a 580 km2 agricultural watershed in south-western Burkina Faso. Four statistical prediction models-multiple linear regression (MLR, random forest regression (RFR, support vector machine (SVM, stochastic gradient boosting (SGB-were tested and compared. Internal validation was conducted by cross validation while the predictions were validated against an independent set of soil samples considering the modelling area and an extrapolation area. Model performance statistics revealed that the machine learning techniques performed marginally better than the MLR, with the RFR providing in most cases the highest accuracy. The inability of MLR to handle non-linear relationships between dependent and independent variables was found to be a limitation in accurately predicting soil properties at unsampled locations. Satellite data acquired during ploughing or early crop development stages (e.g. May, June were found to be the most important spectral predictors while elevation, temperature and precipitation came up as prominent terrain/climatic variables in predicting soil properties. The results further showed that shortwave infrared and near infrared channels of Landsat8 as well as soil specific indices

  13. LPmerge: an R package for merging genetic maps by linear programming.

    Endelman, Jeffrey B; Plomion, Christophe

    2014-06-01

    Consensus genetic maps constructed from multiple populations are an important resource for both basic and applied research, including genome-wide association analysis, genome sequence assembly and studies of evolution. The LPmerge software uses linear programming to efficiently minimize the mean absolute error between the consensus map and the linkage maps from each population. This minimization is performed subject to linear inequality constraints that ensure the ordering of the markers in the linkage maps is preserved. When marker order is inconsistent between linkage maps, a minimum set of ordinal constraints is deleted to resolve the conflicts. LPmerge is on CRAN at http://cran.r-project.org/web/packages/LPmerge. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  14. A comparison of multiple indicator kriging and area-to-point Poisson kriging for mapping patterns of herbivore species abundance in Kruger National Park, South Africa.

    Kerry, Ruth; Goovaerts, Pierre; Smit, Izak P J; Ingram, Ben R

    Kruger National Park (KNP), South Africa, provides protected habitats for the unique animals of the African savannah. For the past 40 years, annual aerial surveys of herbivores have been conducted to aid management decisions based on (1) the spatial distribution of species throughout the park and (2) total species populations in a year. The surveys are extremely time consuming and costly. For many years, the whole park was surveyed, but in 1998 a transect survey approach was adopted. This is cheaper and less time consuming but leaves gaps in the data spatially. Also the distance method currently employed by the park only gives estimates of total species populations but not their spatial distribution. We compare the ability of multiple indicator kriging and area-to-point Poisson kriging to accurately map species distribution in the park. A leave-one-out cross-validation approach indicates that multiple indicator kriging makes poor estimates of the number of animals, particularly the few large counts, as the indicator variograms for such high thresholds are pure nugget. Poisson kriging was applied to the prediction of two types of abundance data: spatial density and proportion of a given species. Both Poisson approaches had standardized mean absolute errors (St. MAEs) of animal counts at least an order of magnitude lower than multiple indicator kriging. The spatial density, Poisson approach (1), gave the lowest St. MAEs for the most abundant species and the proportion, Poisson approach (2), did for the least abundant species. Incorporating environmental data into Poisson approach (2) further reduced St. MAEs.

  15. An Evaluation of Population Density Mapping and Built up Area Estimates in Sri Lanka Using Multiple Methodologies

    Engstrom, R.; Soundararajan, V.; Newhouse, D.

    2017-12-01

    In this study we examine how well multiple population density and built up estimates that utilize satellite data compare in Sri Lanka. The population relationship is examined at the Gram Niladhari (GN) level, the lowest administrative unit in Sri Lanka from the 2011 census. For this study we have two spatial domains, the whole country and a 3,500km2 sub-sample, for which we have complete high spatial resolution imagery coverage. For both the entire country and the sub-sample we examine how consistent are the existing publicly available measures of population constructed from satellite imagery at predicting population density? For just the sub-sample we examine how well do a suite of values derived from high spatial resolution satellite imagery predict population density and how does our built up area estimate compare to other publicly available estimates. Population measures were obtained from the Sri Lankan census, and were downloaded from Facebook, WorldPoP, GPW, and Landscan. Percentage built-up area at the GN level was calculated from three sources: Facebook, Global Urban Footprint (GUF), and the Global Human Settlement Layer (GHSL). For the sub-sample we have derived a variety of indicators from the high spatial resolution imagery. Using deep learning convolutional neural networks, an object oriented, and a non-overlapping block, spatial feature approach. Variables calculated include: cars, shadows (a proxy for building height), built up area, and buildings, roof types, roads, type of agriculture, NDVI, Pantex, and Histogram of Oriented Gradients (HOG) and others. Results indicate that population estimates are accurate at the higher, DS Division level but not necessarily at the GN level. Estimates from Facebook correlated well with census population (GN correlation of 0.91) but measures from GPW and WorldPop are more weakly correlated (0.64 and 0.34). Estimates of built-up area appear to be reliable. In the 32 DSD-subsample, Facebook's built- up area measure

  16. Quality Assessment of Kumu Injection, a Traditional Chinese Medicine Preparation, Using HPLC Combined with Chemometric Methods and Qualitative and Quantitative Analysis of Multiple Alkaloids by Single Marker.

    Wang, Ning; Li, Zhi-Yong; Zheng, Xiao-Li; Li, Qiao; Yang, Xin; Xu, Hui

    2018-04-09

    Kumu injection (KMI) is a common-used traditional Chinese medicine (TCM) preparation made from Picrasma quassioides (D. Don) Benn. rich in alkaloids. An innovative technique for quality assessment of KMI was developed using high performance liquid chromatography (HPLC) combined with chemometric methods and qualitative and quantitative analysis of multi-components by single marker (QAMS). Nigakinone (PQ-6, 5-hydroxy-4-methoxycanthin-6-one), one of the most abundant alkaloids responsible for the major pharmacological activities of Kumu, was used as a reference substance. Six alkaloids in KMI were quantified, including 6-hydroxy- β -carboline-1-carboxylic acid (PQ-1), 4,5-dimethoxycanthin-6-one (PQ-2), β -carboline-1-carboxylic acid (PQ-3), β -carboline-1-propanoic acid (PQ-4), 3-methylcanthin-5,6-dione (PQ-5), and PQ-6. Based on the outcomes of twenty batches of KMI samples, the contents of six alkaloids were used for further chemometric analysis. By hierarchical cluster analysis (HCA), radar plots, and principal component analysis (PCA), all the KMI samples could be categorized into three groups, which were closely related to production date and indicated the crucial influence of herbal raw material on end products of KMI. QAMS combined with chemometric analysis could accurately measure and clearly distinguish the different quality samples of KMI. Hence, QAMS is a feasible and promising method for the quality control of KMI.

  17. (SSR) markers

    acer

    2013-06-26

    Jun 26, 2013 ... analysis was in general agreement with PCoA in discrimi- nating the cultivars. Conclusions. Estimation of morphological diversity may provide addi- tional information on the present finding. Nonetheless, the 29 SSR markers provided considerable genetic reso- lution and this genetic diversity analysis ...

  18. (SSR) markers

    SAM

    2014-07-30

    Jul 30, 2014 ... India and the country is currently the leading producer, consumer and exporter of ... registration with the competent authority for plant variety protection. Conventionally ... detection of duplicates, parental verification in crosses, gene tagging in .... allelic patterns as revealed by the current set of SSR markers.

  19. Genome-wide development and deployment of informative intron-spanning and intron-length polymorphism markers for genomics-assisted breeding applications in chickpea.

    Srivastava, Rishi; Bajaj, Deepak; Sayal, Yogesh K; Meher, Prabina K; Upadhyaya, Hari D; Kumar, Rajendra; Tripathi, Shailesh; Bharadwaj, Chellapilla; Rao, Atmakuri R; Parida, Swarup K

    2016-11-01

    ". The designing of multiple ISM and ILP markers (2-5 markers/gene) from an individual gene (transcription factor) with numerous aforementioned desirable genetic attributes can widen the user-preference to select suitable primer combination for simultaneous large-scale assaying of functional allelic variation, natural allelic diversity, molecular mapping and expression profiling of genes among chickpea accessions. This will essentially accelerate the identification of functionally relevant molecular tags regulating vital agronomic traits for genomics-assisted crop improvement by optimal resource expenses in chickpea. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  20. Genetic association of multiple sclerosis with the marker rs391745 near the endogenous retroviral locus HERV-Fc1: analysis of disease subtypes

    Hansen, Bettina; Oturai, Annette Bang; Harbo, Hanne F

    2011-01-01

    We have previously described the occurrence of multiple sclerosis (MS) to be associated with human endogenous retroviruses, specifically the X-linked viral locus HERV-Fc1. The aim of this study was to investigate a possible association of the HERV-Fc1 locus with subtypes of MS. MS patients......-Fc1 locus (p = 0.003), while primary progressive disease was not. The ability to see genetic differences between subtypes of MS near this gene speaks for the involvement of the virus HERV-Fc1 locus in modifying the disease course of MS....

  1. Alteration of Multiple Leukocyte Gene Expression Networks is Linked with Magnetic Resonance Markers of Prognosis After Acute ST-Elevation Myocardial Infarction.

    Teren, A; Kirsten, H; Beutner, F; Scholz, M; Holdt, L M; Teupser, D; Gutberlet, M; Thiery, J; Schuler, G; Eitel, I

    2017-02-03

    Prognostic relevant pathways of leukocyte involvement in human myocardial ischemic-reperfusion injury are largely unknown. We enrolled 136 patients with ST-elevation myocardial infarction (STEMI) after primary angioplasty within 12 h after onset of symptoms. Following reperfusion, whole blood was collected within a median time interval of 20 h (interquartile range: 15-25 h) for genome-wide gene expression analysis. Subsequent CMR scans were performed using a standard protocol to determine infarct size (IS), area at risk (AAR), myocardial salvage index (MSI) and the extent of late microvascular obstruction (lateMO). We found 398 genes associated with lateMO and two genes with IS. Neither AAR, nor MSI showed significant correlations with gene expression. Genes correlating with lateMO were strongly related to several canonical pathways, including positive regulation of T-cell activation (p = 3.44 × 10 -5 ), and regulation of inflammatory response (p = 1.86 × 10 -3 ). Network analysis of multiple gene expression alterations associated with larger lateMO identified the following functional consequences: facilitated utilisation and decreased concentration of free fatty acid, repressed cell differentiation, enhanced phagocyte movement, increased cell death, vascular disease and compensatory vasculogenesis. In conclusion, the extent of lateMO after acute, reperfused STEMI correlated with altered activation of multiple genes related to fatty acid utilisation, lymphocyte differentiation, phagocyte mobilisation, cell survival, and vascular dysfunction.

  2. Herbs and spices: characterization and quantitation of biologically-active markers for routine quality control by multiple headspace solid-phase microextraction combined with separative or non-separative analysis.

    Sgorbini, Barbara; Bicchi, Carlo; Cagliero, Cecilia; Cordero, Chiara; Liberto, Erica; Rubiolo, Patrizia

    2015-01-09

    Herbs and spices are used worldwide as food flavoring, thus determination of their identity, origin, and quality is mandatory for safe human consumption. An analysis strategy based on separative (HS-SPME-GC-MS) and non-separative (HS-SPME-MS) approaches is proposed for the volatile fraction of herbs and spices, for quality control and to quantify the aromatic markers with a single analysis directly on the plant material as such. Eight-to-ten lots of each of the following herbs/spices were considered: cloves (Syzygium aromaticum (L.) Merr. & Perry), American peppertree (Schinus molle L.), black pepper and white pepper (Piper nigrum L.), rosemary (Rosmarinus officinalis L.), sage (Salvia officinalis L.) and thyme (Thymus vulgaris L.). Homogeneity, origin, and chemotypes of the investigated lots of each herb/spice were defined by fingerprinting, through statistical elaboration with principal component analysis (PCA). Characterizing aromatic markers were directly quantified on the solid matrix through multiple headspace extraction-HS-SPME (MHS-SPME). Reliable results were obtained with both separative and non-separative methods (where the latter were applicable); the two were in full agreement, RSD% ranging from 1.8 to 7.7% for eugenol in cloves, 2.2-18.4% for carvacrol+thymol in thyme, and 3.1-16.8% for thujones in sage. Copyright © 2014 Elsevier B.V. All rights reserved.

  3. Maximization of Markers Linked in Coupling for Tetraploid Potatoes via Monoparental Haploids

    Annette M. Bartkiewicz

    2018-05-01

    Full Text Available Haploid potato populations derived from a single tetraploid donor constitute an efficient strategy to analyze markers segregating from a single donor genotype. Analysis of marker segregation in populations derived from crosses between polysomic tetraploids is complicated by a maximum of eight segregating alleles, multiple dosages of the markers and problems related to linkage analysis of marker segregation in repulsion. Here, we present data on two monoparental haploid populations generated by prickle pollination of two tetraploid cultivars with Solanum phureja and genotyped with the 12.8 k SolCAP single nucleotide polymorphism (SNP array. We show that in a population of monoparental haploids, the number of biallelic SNP markers segregating in linkage to loci from the tetraploid donor genotype is much larger than in putative crosses of this genotype to a diverse selection of 125 tetraploid cultivars. Although this strategy is more laborious than conventional breeding, the generation of haploid progeny for efficient marker analysis is straightforward if morphological markers and flow cytometry are utilized to select true haploid progeny. The level of introgressed fragments from S. phureja, the haploid inducer, is very low, supporting its suitability for genetic analysis. Mapping with single-dose markers allowed the analysis of quantitative trait loci (QTL for four phenotypic traits.

  4. A genomic library-based amplification approach (GL-PCR) for the mapping of multiple IS6110 insertion sites and strain differentiation of Mycobacterium tuberculosis.

    Namouchi, Amine; Mardassi, Helmi

    2006-11-01

    Evidence suggests that insertion of the IS6110 element is not without consequence to the biology of Mycobacterium tuberculosis complex strains. Thus, mapping of multiple IS6110 insertion sites in the genome of biomedically relevant clinical isolates would result in a better understanding of the role of this mobile element, particularly with regard to transmission, adaptability and virulence. In the present paper, we describe a versatile strategy, referred to as GL-PCR, that amplifies IS6110-flanking sequences based on the construction of a genomic library. M. tuberculosis chromosomal DNA is fully digested with HincII and then ligated into a plasmid vector between T7 and T3 promoter sequences. The ligation reaction product is transformed into Escherichia coli and selective PCR amplification targeting both 5' and 3' IS6110-flanking sequences are performed on the plasmid library DNA. For this purpose, four separate PCR reactions are performed, each combining an outward primer specific for one IS6110 end with either T7 or T3 primer. Determination of the nucleotide sequence of the PCR products generated from a single ligation reaction allowed mapping of 21 out of the 24 IS6110 copies of two 12 banded M. tuberculosis strains, yielding an overall sensitivity of 87,5%. Furthermore, by simply comparing the migration pattern of GL-PCR-generated products, the strategy proved to be as valuable as IS6110 RFLP for molecular typing of M. tuberculosis complex strains. Importantly, GL-PCR was able to discriminate between strains differing by a single IS6110 band.

  5. Comparison of the sagittal sinus cross-sectional area between patients with multiple sclerosis, hydrocephalus, intracranial hypertension and spontaneous intracranial hypotension: a surrogate marker of venous transmural pressure?

    Bateman, Grant A; Lechner-Scott, Jeannette; Copping, Ross; Moeskops, Christopher; Yap, Swee Leong

    2017-07-06

    There is evidence that patients with multiple sclerosis (MS) and hydrocephalus share some common pathophysiological mechanisms. Alterations in CSF pressure are known to affect cerebral venous sinus geometry. To further explore these mechanisms, we measured the superior sagittal sinus (SSS) cross-sectional area 3 cm above the torcular using T2 images in 20 MS, 10 spontaneous intracranial hypotension (SIH), 21 hydrocephalus and 20 idiopathic intracranial hypertension (IIH) patients and compared with 20 matched controls. The SSS area was reduced by 25% in hydrocephalus (p = 0.0008), increased by 22% (p = 0.037) in SIH and unchanged in IIH compared to matched controls. In MS there was a 16% increase in SSS area (p = 0.01).The findings suggest that changes in SSS cross-sectional are common between MS and SIH patients, while in hydrocephalus and IIH these are different.

  6. Marker lamps

    Watkins, D.V.

    1980-01-01

    A marker lamp is described which consists of a block of transparent plastics material encapsulated in which is a radioactive light source. These lights comprise a small sealed glass capsule, the hollow inside surface of which is coated with phosphor and which contains tritium or similar radioactive gas. The use of such lamps for identification marking of routes, for example roads, and for identification of underwater oil pipelines is envisaged. (U.K.)

  7. A partial least-square approach for modeling gene-gene and gene-environment interactions when multiple markers are genotyped.

    Wang, Tao; Ho, Gloria; Ye, Kenny; Strickler, Howard; Elston, Robert C

    2009-01-01

    Genetic association studies achieve an unprecedented level of resolution in mapping disease genes by genotyping dense single nucleotype polymorphisms (SNPs) in a gene region. Meanwhile, these studies require new powerful statistical tools that can optimally handle a large amount of information provided by genotype data. A question that arises is how to model interactions between two genes. Simply modeling all possible interactions between the SNPs in two gene regions is not desirable because a greatly increased number of degrees of freedom can be involved in the test statistic. We introduce an approach to reduce the genotype dimension in modeling interactions. The genotype compression of this approach is built upon the information on both the trait and the cross-locus gametic disequilibrium between SNPs in two interacting genes, in such a way as to parsimoniously model the interactions without loss of useful information in the process of dimension reduction. As a result, it improves power to detect association in the presence of gene-gene interactions. This approach can be similarly applied for modeling gene-environment interactions. We compare this method with other approaches, the corresponding test without modeling any interaction, that based on a saturated interaction model, that based on principal component analysis, and that based on Tukey's one-degree-of-freedom model. Our simulations suggest that this new approach has superior power to that of the other methods. In an application to endometrial cancer case-control data from the Women's Health Initiative, this approach detected AKT1 and AKT2 as being significantly associated with endometrial cancer susceptibility by taking into account their interactions with body mass index.

  8. Automated genotyping of dinucleotide repeat markers

    Perlin, M.W.; Hoffman, E.P. [Carnegie Mellon Univ., Pittsburgh, PA (United States)]|[Univ. of Pittsburgh, PA (United States)

    1994-09-01

    The dinucleotide repeats (i.e., microsatellites) such as CA-repeats are a highly polymorphic, highly abundant class of PCR-amplifiable markers that have greatly streamlined genetic mapping experimentation. It is expected that over 30,000 such markers (including tri- and tetranucleotide repeats) will be characterized for routine use in the next few years. Since only size determination, and not sequencing, is required to determine alleles, in principle, dinucleotide repeat genotyping is easily performed on electrophoretic gels, and can be automated using DNA sequencers. Unfortunately, PCR stuttering with these markers generates not one band for each allele, but a pattern of bands. Since closely spaced alleles must be disambiguated by human scoring, this poses a key obstacle to full automation. We have developed methods that overcome this obstacle. Our model is that the observed data is generated by arithmetic superposition (i.e., convolution) of multiple allele patterns. By quantitatively measuring the size of each component band, and exploiting the unique stutter pattern associated with each marker, closely spaced alleles can be deconvolved; this unambiguously reconstructs the {open_quotes}true{close_quotes} allele bands, with stutter artifact removed. We used this approach in a system for automated diagnosis of (X-linked) Duchenne muscular dystrophy; four multiplexed CA-repeats within the dystrophin gene were assayed on a DNA sequencer. Our method accurately detected small variations in gel migration that shifted the allele size estimate. In 167 nonmutated alleles, 89% (149/167) showed no size variation, 9% (15/167) showed 1 bp variation, and 2% (3/167) showed 2 bp variation. We are currently developing a library of dinucleotide repeat patterns; together with our deconvolution methods, this library will enable fully automated genotyping of dinucleotide repeats from sizing data.

  9. (SSR) markers for drought tolerance in maize

    use

    2011-11-21

    Nov 21, 2011 ... and dominance gene effects in inheritance are included in almost all traits related to drought (Shiri et al., 2010a, b). Identifying the complete-linked molecular markers with target gene and mapping its chromosome locus is an important goal in plant breeding for gene cloning and marker-aided selection.

  10. 12 Weeks of Combined Endurance and Resistance Training Reduces Innate Markers of Inflammation in a Randomized Controlled Clinical Trial in Patients with Multiple Sclerosis

    Nathalie Deckx

    2016-01-01

    Full Text Available Previously, we reported that patients with multiple sclerosis (MS demonstrate improved muscle strength, exercise tolerance, and lean tissue mass following a combined endurance and resistance exercise program. However, the effect of exercise on the underlying disease pathogenesis remains elusive. Since recent evidence supports a crucial role of dendritic cells (DC in the pathogenesis of MS, we investigated the effect of a 12-week combined exercise program in MS patients on the number and function of DC. We demonstrate an increased number of plasmacytoid DC (pDC following the exercise program. These pDC display an activated phenotype, as evidenced by increased numbers of circulating CD62L+ and CD80+ pDC. Interestingly, the number of CD80+ pDC positively correlates with the presence of IL-10-producing regulatory type 1 cells (Tr1, an important cell type for maintaining peripheral tolerance to self-antigens. In addition, decreased production of the inflammatory mediators, TNF-α and MMP-9, upon Toll-like receptor (TLR stimulation was found at the end of the exercise program. Overall, our findings suggest that the 12-week exercise program reduces the secretion of inflammatory mediators upon TLR stimulation and promotes the immunoregulatory function of circulating pDC, suggestive for a favorable impact of exercise on the underlying immunopathogenesis of MS.

  11. Analysis of the human brain in primary progressive multiple sclerosis with mapping of the spatial distributions using 1H MR spectroscopy and diffusion tensor imaging

    Sijens, Paul E.; Irwan, Roy; Potze, Jan Hendrik; Oudkerk, Matthijs; Mostert, Jop P.; Keyser, Jacques de

    2005-01-01

    Primary progressive multiple sclerosis (ppMS; n=4) patients and controls (n=4) were examined by 1H magnetic resonance spectroscopy (MRS) and diffusion tensor imaging (DTI) in order to map choline (Cho), creatine and N-acetylaspartate (NAA), the fractional anisotropy (FA) and the apparent diffusion constant (ADC). After chemical shift imaging (point-resolved spectroscopy, repetition time/echo time 1,500 ms/135 ms) of a supraventricular volume of interest of 8 x 8 x 2 cm 3 (64 voxels) MRS peak areas were matched to the results of DTI for the corresponding volume elements. Mean FA and NAA values were reduced in the ppMS patients (P<0.01, both) and the ADC increased (P<0.02). The spatial distribution of NAA showed strong correlation to ADC in both ppMS patients and controls (r =-0.74 and r= -0.70; P<0.00001, both), and weaker correlations to FA (r=0.49 and r=0.41; P<0.00001, all). FA and ADC also correlated significantly with Cho in patients and controls (P<0.00001, all). The relationship of Cho and NAA to the ADC and the FA and thus to the content of neuronal structures suggests that these metabolite signals essentially originate from axons (NAA) and the myelin sheath (Cho). This is of interest in view of previous reports in which Cho increases were associated with demyelination and the subsequent breakdown of neurons. (orig.)

  12. Intersection tests for single marker QTL analysis can be more powerful than two marker QTL analysis

    Doerge RW

    2003-06-01

    Full Text Available Abstract Background It has been reported in the quantitative trait locus (QTL literature that when testing for QTL location and effect, the statistical power supporting methodologies based on two markers and their estimated genetic map is higher than for the genetic map independent methodologies known as single marker analyses. Close examination of these reports reveals that the two marker approaches are more powerful than single marker analyses only in certain cases. Simulation studies are a commonly used tool to determine the behavior of test statistics under known conditions. We conducted a simulation study to assess the general behavior of an intersection test and a two marker test under a variety of conditions. The study was designed to reveal whether two marker tests are always more powerful than intersection tests, or whether there are cases when an intersection test may outperform the two marker approach. We present a reanalysis of a data set from a QTL study of ovariole number in Drosophila melanogaster. Results Our simulation study results show that there are situations where the single marker intersection test equals or outperforms the two marker test. The intersection test and the two marker test identify overlapping regions in the reanalysis of the Drosophila melanogaster data. The region identified is consistent with a regression based interval mapping analysis. Conclusion We find that the intersection test is appropriate for analysis of QTL data. This approach has the advantage of simplicity and for certain situations supplies equivalent or more powerful results than a comparable two marker test.

  13. Visual Evoked Potential and Magnetic Resonance Imaging are More Effective Markers of Multiple Sclerosis Progression than Laser Polarimetry with Variable Corneal Compensation.

    Kantorová, Ema; Ziak, Peter; Kurča, Egon; Koyšová, Mária; Hladká, Mária; Zeleňák, Kamil; Michalik, Jozef

    2014-01-01

    The aim of our study was to assess the role of laser polarimetry and visual evoked potentials (VEP) as potential biomarkers of disease progression in multiple sclerosis (MS). A total of 41 patients with MS (82 eyes) and 22 age-related healthy volunteers (44 eyes) completed the study. MS patients were divided into two groups, one (ON) with a history of optic neuritis (17 patients, 34 eyes) and another group (NON) without it (24 patients, 48 eyes). The MS patients and controls underwent laser polarimetry (GDx) examination of the retinal nerve fiber layer (RNFL). In the MS group, we also examined: Kurtzke "expanded disability status scale" (EDSS), the duration of the disorder, VEP - latency and amplitude, and conventional brain magnetic resonance imaging (MRI). Our results were statistically analyzed using ANOVA, Mann-Whitney, and Spearman correlation analyses. In the MS group, brain atrophy and new T2 brain lesions in MRI correlated with both VEP latencies and amplitudes. Separate comparisons revealed VEP latency testing to be less sensitive in ON than in NON-patients. In ON patients, VEP amplitudes correlated mildly with brain atrophy (r = -0.15) and strongly with brain new MRI lesions (r = -0.8). In NON-patients, highly significant correlation of new MRI brain lesions with VEP latencies (r = 0.63, r = 0.6) and amplitudes (r = -0.3, r = -4.2) was found. EDSS also correlated with brain atrophy in this group (r = 0.5). Our study did not find a correlation of GDx measures with MRI tests. The GDx method was not able to detect whole brain demyelinization and the degeneration process, but was only able to reveal the involvement of optic nerves in ON and NON-patients. In our study, we found that both methods (VEP and GDx) can be used for the detection of optic nerve damage, but VEP was found to be superior in evaluating whole brain demyelinization and axonal degeneration. Both VEP and MRI, but not GDx, have an important role in monitoring

  14. Visual evoked potential and magnetic resonance imaging are more effective markers of multiple sclerosis progression than laser polarimetry with variable corneal compensation

    Ema eKantorová

    2014-01-01

    Full Text Available Backround: The aim of our study was to assess the role of laser polarimetry and visual evoked potentials as potential biomarkers of disease progression in multiple sclerosis (MS. Participants: A total of 41 patients with MS (82 eyes and 22 age-related healthy volunteers (44 eyes completed the study. MS patients were divided into two groups, one (ON with a history of optic neuritis (17 patients, 34 eyes and another group (NON without it (24 patients, 48 eyes. The MS patients and controls underwent laser polarimetry (GDx examination of the retinal nerve fibre layer (RNFL. In the MS group we also examined: Kurtzke Expanded disability status scale (EDSS, the duration of the disorder, visual evoked potentials (VEP – latency and amplitude – and conventional brain MRI. Results: In the MS group, brain atrophy and new T2 brain lesions in MRI correlated with both VEP latencies and amplitudes. Separate comparisons revealed VEP latency testing to be less sensitive in ON than in NON patients. In ON patients, VEP amplitudes correlated mildly with brain atrophy (r =-0.15 and strongly with brain new MRI lesions (r = -0.8. In NON patients, highly significant correlation of new MRI brain lesions with VEP latencies (r = 0.63, r = 0.6, and amplitudes ( r = -0.3, r = -4.2 was found. EDSS also correlated with brain atrophy in this group (r = 0.5. Our study did not find a correlation of GDx measures with MRI tests. The GDx method was not able to detect whole brain demyelinisation and the degeneration process, but was only able to reveal the involvement of optic nerves in ON and NON patients.Conclusions: In our study, we found that both methods (VEP and GDx can be used for detection of optic nerve damage, but VEP was found to be superior in evaluating whole brain demyelinisation and axonal degeneration. Both VEP and MRI, but not GDx, have an important role in monitoring disease progression in MS patients, independent of the ON history.

  15. High-intensity resistance training in multiple sclerosis - An exploratory study of effects on immune markers in blood and cerebrospinal fluid, and on mood, fatigue, health-related quality of life, muscle strength, walking and cognition.

    Kierkegaard, Marie; Lundberg, Ingrid E; Olsson, Tomas; Johansson, Sverker; Ygberg, Sofia; Opava, Christina; Holmqvist, Lotta Widén; Piehl, Fredrik

    2016-03-15

    High-intensity resistance training is unexplored in people with multiple sclerosis. To evaluate effects of high-intensity resistance training on immune markers and on measures of mood, fatigue, health-related quality of life, muscle strength, walking and cognition. Further, to describe participants' opinion and perceived changes of the training. Twenty patients with relapsing-remitting multiple sclerosis performed high-intensity resistance training at an intensity of 80% of one-repetition maximum, twice a week for 12 weeks. Blood and optional cerebrospinal fluid samples, and data on secondary outcome measures were collected before and after intervention. A study-specific questionnaire was used for capturing participants' opinion. Seventeen participants completed the study. Plasma cytokine levels of tumor necrosis factor were significantly decreased post-intervention (p=0.001). Exploratory cytokine analyses in cerebrospinal fluid (n=8) did not reveal major changes. Significant and clinically important improvements were found in fatigue (p=0.001) and health-related quality of life (p=0.004). Measures of mood (p=0.002), muscle strength (p ≤ 0.001), walking speed (p=0.013) and cognition (p=0.04) were also improved. A majority of participants evaluated the training as very good and perceived changes to the better. High-intensity resistance training in persons with relapsing remitting multiple sclerosis with low disability had positive effects on peripheral pro-inflammatory cytokine levels, led to clinically relevant improvements in measures of fatigue and health-related quality of life, and was well tolerated. These results provide a basis for a larger randomized trial. Copyright © 2016 Elsevier B.V. All rights reserved.

  16. Genetic Linkage Mapping of Economically Important Traits in Cultivated Tetraploid Potato (Solanum tuberosum L.).

    Massa, Alicia N; Manrique-Carpintero, Norma C; Coombs, Joseph J; Zarka, Daniel G; Boone, Anne E; Kirk, William W; Hackett, Christine A; Bryan, Glenn J; Douches, David S

    2015-09-14

    The objective of this study was to construct a single nucleotide polymorphism (SNP)-based genetic map at the cultivated tetraploid level to locate quantitative trait loci (QTL) contributing to economically important traits in potato (Solanum tuberosum L.). The 156 F1 progeny and parents of a cross (MSL603) between "Jacqueline Lee" and "MSG227-2" were genotyped using the Infinium 8303 Potato Array. Furthermore, the progeny and parents were evaluated for foliar late blight reaction to isolates of the US-8 genotype of Phytophthora infestans (Mont.) de Bary and vine maturity. Linkage analyses and QTL mapping were performed using a novel approach that incorporates allele dosage information. The resulting genetic maps contained 1972 SNP markers with an average density of 1.36 marker per cM. QTL mapping identified the major source of late blight resistance in "Jacqueline Lee." The best SNP marker mapped ~0.54 Mb from a resistance hotspot on the long arm of chromosome 9. For vine maturity, the major-effect QTL was located on chromosome 5 with allelic effects from both parents. A candidate SNP marker for this trait mapped ~0.25 Mb from the StCDF1 gene, which is a candidate gene for the maturity trait. The identification of markers for P. infestans resistance will enable the introgression of multiple sources of resistance through marker-assisted selection. Moreover, the discovery of a QTL for late blight resistance not linked to the QTL for vine maturity provides the opportunity to use marker-assisted selection for resistance independent of the selection for vine maturity classifications. Copyright © 2015 Massa et al.

  17. Simultaneous quantitative determination of multiple bioactive markers in Ocimum sanctum obtained from different locations and its marketed herbal formulations using UPLC-ESI-MS/MS combined with principal component analysis.

    Pandey, Renu; Chandra, Preeti; Srivastava, Mukesh; Mishra, D K; Kumar, Brijesh

    2015-01-01

    Ocimum sanctum L., with phenolic acids, flavonoids, propenyl phenols and terpenoids as active pharmacological constituents, is a popular medicinal herb and is present as an ingredient in many herbal formulations. Therefore, development of a reliable analytical method for simultaneous determination of the pharmacologically active constituents of O. sanctum is of high importance. To develop and validate a new, rapid, sensitive and selective UPLC-ESI/MS/MS method for simultaneous determination of 23 bioactive markers including phenolic acids, flavonoids, propenyl phenol and terpenoid in the leaf extract and marketed herbal formulations of O. sanctum. An UPLC-ESI/MS/MS method using negative electrospray ionisation (ESI) in multiple-reaction-monitoring (MRM) mode was used for simultaneous determination. Chromatographic separation was achieved on an Acquity UPLC BEH C18 -column using a gradient elution with 0.1% formic acid in water and 0.1% formic acid in acetonitrile. Principal component analysis (PCA) was applied to correlate and discriminate eight geographical collections of O. sanctum based on quantitative data of the analytes. The developed method was validated as per International Conference on Harmonization guidelines and found to be accurate, with overall recovery in the range 95.09-104.84% (RSD ≤ 1.85%), precise (RSD ≤ 1.98%) and linear (r(2)  ≥ 0.9971) over the concentration range of 0.5-1000 ng/mL. Ursolic acid was found to be the most abundant marker in all the samples investigated, except for the marketed tablet. The method established is simple, rapid and sensitive, hence it can be reliably utilised for the quality control of O. sanctum and derived herbal formulations. Copyright © 2015 John Wiley & Sons, Ltd.

  18. Isolation and characterization of polymorphic microsatellite markers ...

    Flax (Linum usitatissimum L.) is the third largest natural fiber crop and one of the five major oil crops in the world. ... These novel polymorphic microsatellite loci will be useful in genetic linkage map construction, germplasm classification and identification, gene identification and QTL mapping, and marker-assisted selection ...

  19. Saturation of an intra-gene pool linkage map: towards a unified consensus linkage map for fine mapping and synteny analysis in common bean.

    Galeano, Carlos H; Fernandez, Andrea C; Franco-Herrera, Natalia; Cichy, Karen A; McClean, Phillip E; Vanderleyden, Jos; Blair, Matthew W

    2011-01-01

    Map-based cloning and fine mapping to find genes of interest and marker assisted selection (MAS) requires good genetic maps with reproducible markers. In this study, we saturated the linkage map of the intra-gene pool population of common bean DOR364 × BAT477 (DB) by evaluating 2,706 molecular markers including SSR, SNP, and gene-based markers. On average the polymorphism rate was 7.7% due to the narrow genetic base between the parents. The DB linkage map consisted of 291 markers with a total map length of 1,788 cM. A consensus map was built using the core mapping populations derived from inter-gene pool crosses: DOR364 × G19833 (DG) and BAT93 × JALO EEP558 (BJ). The consensus map consisted of a total of 1,010 markers mapped, with a total map length of 2,041 cM across 11 linkage groups. On average, each linkage group on the consensus map contained 91 markers of which 83% were single copy markers. Finally, a synteny analysis was carried out using our highly saturated consensus maps compared with the soybean pseudo-chromosome assembly. A total of 772 marker sequences were compared with the soybean genome. A total of 44 syntenic blocks were identified. The linkage group Pv6 presented the most diverse pattern of synteny with seven syntenic blocks, and Pv9 showed the most consistent relations with soybean with just two syntenic blocks. Additionally, a co-linear analysis using common bean transcript map information against soybean coding sequences (CDS) revealed the relationship with 787 soybean genes. The common bean consensus map has allowed us to map a larger number of markers, to obtain a more complete coverage of the common bean genome. Our results, combined with synteny relationships provide tools to increase marker density in selected genomic regions to identify closely linked polymorphic markers for indirect selection, fine mapping or for positional cloning.

  20. PAV markers in Sorghum bicolour

    Shen, Xin; Liu, Zhiquan; Mocoeur, Anne Raymonde Joelle

    2015-01-01

    Abstract Genic presence/absence variants (PAVs) correlate closely to the phenotypic variation, impacting plant genome sizes and the adaption to the environment. To shed more light on their genome-wide patterns, functions and to test the possibility of using them as molecular markers, we analyzed...... enriched in stress responses and protein modification. We used 325 polymorphic PAVs in two sorghum inbred lines Ji2731 and E-Tian, together with 49 SSR markers, and constructed a genetic map, which consisted of 10 linkage groups corresponding to the 10 chromosomes of sorghum and spanned 1430.3 cM in length...

  1. The association between intra- and juxta-cortical pathology and cognitive impairment in multiple sclerosis by quantitative T2* mapping at 7 T MRI

    Céline Louapre, MD, PhD

    2016-01-01

    Location of pathology across the cortical width and mantle showed selective correlation with impairment in differing cognitive domains. These findings may guide studies at lower field strength designed to develop surrogate markers of cognitive impairment in MS.

  2. Branched polynomial covering maps

    Hansen, Vagn Lundsgaard

    1999-01-01

    A Weierstrass polynomial with multiple roots in certain points leads to a branched covering map. With this as the guiding example, we formally define and study the notion of a branched polynomial covering map. We shall prove that many finite covering maps are polynomial outside a discrete branch...... set. Particular studies are made of branched polynomial covering maps arising from Riemann surfaces and from knots in the 3-sphere....

  3. Validation of candidate gene markers for marker-assisted selection of potato cultivars with improved tuber quality.

    Li, Li; Tacke, Eckhard; Hofferbert, Hans-Reinhardt; Lübeck, Jens; Strahwald, Josef; Draffehn, Astrid M; Walkemeier, Birgit; Gebhardt, Christiane

    2013-04-01

    Tuber yield, starch content, starch yield and chip color are complex traits that are important for industrial uses and food processing of potato. Chip color depends on the quantity of reducing sugars glucose and fructose in the tubers, which are generated by starch degradation. Reducing sugars accumulate when tubers are stored at low temperatures. Early and efficient selection of cultivars with superior yield, starch yield and chip color is hampered by the fact that reliable phenotypic selection requires multiple year and location trials. Application of DNA-based markers early in the breeding cycle, which are diagnostic for superior alleles of genes that control natural variation of tuber quality, will reduce the number of clones to be evaluated in field trials. Association mapping using genes functional in carbohydrate metabolism as markers has discovered alleles of invertases and starch phosphorylases that are associated with tuber quality traits. Here, we report on new DNA variants at loci encoding ADP-glucose pyrophosphorylase and the invertase Pain-1, which are associated with positive or negative effect with chip color, tuber starch content and starch yield. Marker-assisted selection (MAS) and marker validation were performed in tetraploid breeding populations, using various combinations of 11 allele-specific markers associated with tuber quality traits. To facilitate MAS, user-friendly PCR assays were developed for specific candidate gene alleles. In a multi-parental population of advanced breeding clones, genotypes were selected for having different combinations of five positive and the corresponding negative marker alleles. Genotypes combining five positive marker alleles performed on average better than genotypes with four negative alleles and one positive allele. When tested individually, seven of eight markers showed an effect on at least one quality trait. The direction of effect was as expected. Combinations of two to three marker alleles were

  4. A gene-based SNP resource and linkage map for the copepod Tigriopus californicus

    Foley Brad R

    2011-11-01

    Full Text Available Abstract Background As yet, few genomic resources have been developed in crustaceans. This lack is particularly evident in Copepoda, given the extraordinary numerical abundance, and taxonomic and ecological diversity of this group. Tigriopus californicus is ideally suited to serve as a genetic model copepod and has been the subject of extensive work in environmental stress and reproductive isolation. Accordingly, we set out to develop a broadly-useful panel of genetic markers and to construct a linkage map dense enough for quantitative trait locus detection in an interval mapping framework for T. californicus--a first for copepods. Results One hundred and ninety Single Nucleotide Polymorphisms (SNPs were used to genotype our mapping population of 250 F2 larvae. We were able to construct a linkage map with an average intermarker distance of 1.8 cM, and a maximum intermarker distance of 10.3 cM. All markers were assembled into linkage groups, and the 12 linkage groups corresponded to the 12 known chromosomes of T. californicus. We estimate a total genome size of 401.0 cM, and a total coverage of 73.7%. Seventy five percent of the mapped markers were detected in 9 additional populations of T. californicus. Of available model arthropod genomes, we were able to show more colocalized pairs of homologues between T. californicus and the honeybee Apis mellifera, than expected by chance, suggesting preserved macrosynteny between Hymenoptera and Copepoda. Conclusions Our study provides an abundance of linked markers spanning all chromosomes. Many of these markers are also found in multiple populations of T. californicus, and in two other species in the genus. The genomic resource we have developed will enable mapping throughout the geographical range of this species and in closely related species. This linkage map will facilitate genome sequencing, mapping and assembly in an ecologically and taxonomically interesting group for which genomic resources are

  5. A gene-based SNP resource and linkage map for the copepod Tigriopus californicus

    2011-01-01

    Background As yet, few genomic resources have been developed in crustaceans. This lack is particularly evident in Copepoda, given the extraordinary numerical abundance, and taxonomic and ecological diversity of this group. Tigriopus californicus is ideally suited to serve as a genetic model copepod and has been the subject of extensive work in environmental stress and reproductive isolation. Accordingly, we set out to develop a broadly-useful panel of genetic markers and to construct a linkage map dense enough for quantitative trait locus detection in an interval mapping framework for T. californicus--a first for copepods. Results One hundred and ninety Single Nucleotide Polymorphisms (SNPs) were used to genotype our mapping population of 250 F2 larvae. We were able to construct a linkage map with an average intermarker distance of 1.8 cM, and a maximum intermarker distance of 10.3 cM. All markers were assembled into linkage groups, and the 12 linkage groups corresponded to the 12 known chromosomes of T. californicus. We estimate a total genome size of 401.0 cM, and a total coverage of 73.7%. Seventy five percent of the mapped markers were detected in 9 additional populations of T. californicus. Of available model arthropod genomes, we were able to show more colocalized pairs of homologues between T. californicus and the honeybee Apis mellifera, than expected by chance, suggesting preserved macrosynteny between Hymenoptera and Copepoda. Conclusions Our study provides an abundance of linked markers spanning all chromosomes. Many of these markers are also found in multiple populations of T. californicus, and in two other species in the genus. The genomic resource we have developed will enable mapping throughout the geographical range of this species and in closely related species. This linkage map will facilitate genome sequencing, mapping and assembly in an ecologically and taxonomically interesting group for which genomic resources are currently under development

  6. Frameworking memory and serotonergic markers.

    Meneses, Alfredo

    2017-07-26

    The evidence for neural markers and memory is continuously being revised, and as evidence continues to accumulate, herein, we frame earlier and new evidence. Hence, in this work, the aim is to provide an appropriate conceptual framework of serotonergic markers associated with neural activity and memory. Serotonin (5-hydroxytryptamine [5-HT]) has multiple pharmacological tools, well-characterized downstream signaling in mammals' species, and established 5-HT neural markers showing new insights about memory functions and dysfunctions, including receptors (5-HT1A/1B/1D, 5-HT2A/2B/2C, and 5-HT3-7), transporter (serotonin transporter [SERT]) and volume transmission present in brain areas involved in memory. Bidirectional influence occurs between 5-HT markers and memory/amnesia. A growing number of researchers report that memory, amnesia, or forgetting modifies neural markers. Diverse approaches support the translatability of using neural markers and cerebral functions/dysfunctions, including memory formation and amnesia. At least, 5-HT1A, 5-HT4, 5-HT6, and 5-HT7 receptors and SERT seem to be useful neural markers and therapeutic targets. Hence, several mechanisms cooperate to achieve synaptic plasticity or memory, including changes in the expression of neurotransmitter receptors and transporters.

  7. Mapping out Map Libraries

    Ferjan Ormeling

    2008-09-01

    Full Text Available Discussing the requirements for map data quality, map users and their library/archives environment, the paper focuses on the metadata the user would need for a correct and efficient interpretation of the map data. For such a correct interpretation, knowledge of the rules and guidelines according to which the topographers/cartographers work (such as the kind of data categories to be collected, and the degree to which these rules and guidelines were indeed followed are essential. This is not only valid for the old maps stored in our libraries and archives, but perhaps even more so for the new digital files as the format in which we now have to access our geospatial data. As this would be too much to ask from map librarians/curators, some sort of web 2.0 environment is sought where comments about data quality, completeness and up-to-dateness from knowledgeable map users regarding the specific maps or map series studied can be collected and tagged to scanned versions of these maps on the web. In order not to be subject to the same disadvantages as Wikipedia, where the ‘communis opinio’ rather than scholarship, seems to be decisive, some checking by map curators of this tagged map use information would still be needed. Cooperation between map curators and the International Cartographic Association ( ICA map and spatial data use commission to this end is suggested.

  8. Molecular marker systems for Oenothera genetics.

    Rauwolf, Uwe; Golczyk, Hieronim; Meurer, Jörg; Herrmann, Reinhold G; Greiner, Stephan

    2008-11-01

    The genus Oenothera has an outstanding scientific tradition. It has been a model for studying aspects of chromosome evolution and speciation, including the impact of plastid nuclear co-evolution. A large collection of strains analyzed during a century of experimental work and unique genetic possibilities allow the exchange of genetically definable plastids, individual or multiple chromosomes, and/or entire haploid genomes (Renner complexes) between species. However, molecular genetic approaches for the genus are largely lacking. In this study, we describe the development of efficient PCR-based marker systems for both the nuclear genome and the plastome. They allow distinguishing individual chromosomes, Renner complexes, plastomes, and subplastomes. We demonstrate their application by monitoring interspecific exchanges of genomes, chromosome pairs, and/or plastids during crossing programs, e.g., to produce plastome-genome incompatible hybrids. Using an appropriate partial permanent translocation heterozygous hybrid, linkage group 7 of the molecular map could be assigned to chromosome 9.8 of the classical Oenothera map. Finally, we provide the first direct molecular evidence that homologous recombination and free segregation of chromosomes in permanent translocation heterozygous strains is suppressed.

  9. Branched polynomial covering maps

    Hansen, Vagn Lundsgaard

    2002-01-01

    A Weierstrass polynomial with multiple roots in certain points leads to a branched covering map. With this as the guiding example, we formally define and study the notion of a branched polynomial covering map. We shall prove that many finite covering maps are polynomial outside a discrete branch ...... set. Particular studies are made of branched polynomial covering maps arising from Riemann surfaces and from knots in the 3-sphere. (C) 2001 Elsevier Science B.V. All rights reserved.......A Weierstrass polynomial with multiple roots in certain points leads to a branched covering map. With this as the guiding example, we formally define and study the notion of a branched polynomial covering map. We shall prove that many finite covering maps are polynomial outside a discrete branch...

  10. Mapping earthworm communities in Europe

    Rutgers, M.; Orgiazzi, A.; Gardi, C.; Römbke, J.; Jansch, S.; Keith, A.; Neilson, R.; Boag, B.; Schmidt, O.; Murchie, A.K.; Blackshaw, R.P.; Pérès, G.; Cluzeau, D.; Guernion, M.; Briones, M.J.I.; Rodeiro, J.; Pineiro, R.; Diaz Cosin, D.J.; Sousa, J.P.; Suhadolc, M.; Kos, I.; Krogh, P.H.; Faber, J.H.; Mulder, C.; Bogte, J.J.; Wijnen, van H.J.; Schouten, A.J.; Zwart, de D.

    2016-01-01

    Existing data sets on earthworm communities in Europe were collected, harmonized, collated, modelled and depicted on a soil biodiversity map. Digital Soil Mapping was applied using multiple regressions relating relatively low density earthworm community data to soil characteristics, land use,

  11. An Ultra-High-Density, Transcript-Based, Genetic Map of Lettuce

    Truco, Maria José; Ashrafi, Hamid; Kozik, Alexander; van Leeuwen, Hans; Bowers, John; Wo, Sebastian Reyes Chin; Stoffel, Kevin; Xu, Huaqin; Hill, Theresa; Van Deynze, Allen; Michelmore, Richard W.

    2013-01-01

    We have generated an ultra-high-density genetic map for lettuce, an economically important member of the Compositae, consisting of 12,842 unigenes (13,943 markers) mapped in 3696 genetic bins distributed over nine chromosomal linkage groups. Genomic DNA was hybridized to a custom Affymetrix oligonucleotide array containing 6.4 million features representing 35,628 unigenes of Lactuca spp. Segregation of single-position polymorphisms was analyzed using 213 F7:8 recombinant inbred lines that had been generated by crossing cultivated Lactuca sativa cv. Salinas and L. serriola acc. US96UC23, the wild progenitor species of L. sativa. The high level of replication of each allele in the recombinant inbred lines was exploited to identify single-position polymorphisms that were assigned to parental haplotypes. Marker information has been made available using GBrowse to facilitate access to the map. This map has been anchored to the previously published integrated map of lettuce providing candidate genes for multiple phenotypes. The high density of markers achieved in this ultradense map allowed syntenic studies between lettuce and Vitis vinifera as well as other plant species. PMID:23550116

  12. An Ultra-High-Density, Transcript-Based, Genetic Map of Lettuce.

    Truco, Maria José; Ashrafi, Hamid; Kozik, Alexander; van Leeuwen, Hans; Bowers, John; Wo, Sebastian Reyes Chin; Stoffel, Kevin; Xu, Huaqin; Hill, Theresa; Van Deynze, Allen; Michelmore, Richard W

    2013-04-09

    We have generated an ultra-high-density genetic map for lettuce, an economically important member of the Compositae, consisting of 12,842 unigenes (13,943 markers) mapped in 3696 genetic bins distributed over nine chromosomal linkage groups. Genomic DNA was hybridized to a custom Affymetrix oligonucleotide array containing 6.4 million features representing 35,628 unigenes of Lactuca spp. Segregation of single-position polymorphisms was analyzed using 213 F 7:8 recombinant inbred lines that had been generated by crossing cultivated Lactuca sativa cv. Salinas and L. serriola acc. US96UC23, the wild progenitor species of L. sativa The high level of replication of each allele in the recombinant inbred lines was exploited to identify single-position polymorphisms that were assigned to parental haplotypes. Marker information has been made available using GBrowse to facilitate access to the map. This map has been anchored to the previously published integrated map of lettuce providing candidate genes for multiple phenotypes. The high density of markers achieved in this ultradense map allowed syntenic studies between lettuce and Vitis vinifera as well as other plant species. Copyright © 2013 Truco et al.

  13. Towards mapping the Dioscorea genome

    Terauchi, R.; Kahl, G.

    1998-01-01

    Yams are important starchy tuber crops in (sub-) tropical countries of the world. Despite their importance in the regional economy, no serious attempt has been made toward their improvement. In order to obtain basic knowledge of the genetics of yams, we are trying to establish a linkage map of a wild yam species, Dioscorea tokoro. So far, six allozyme markers, six STMS markers and twenty AFLP markers have been identified. They will be used for linkage mapping of a population comprising 80 progeny obtained from a controlled cross. (author)

  14. Identification of a two-marker-haplotype on Bos taurus autosome 18 associated with somatic cell score in German Holstein cattle

    Reinsch Norbert

    2009-09-01

    Full Text Available Abstract Background The somatic cell score (SCS is implemented in routine sire evaluations in many countries as an indicator trait for udder health. Somatic cell score is highly correlated with clinical mastitis, and in the German Holstein population quantitative trait loci (QTL for SCS have been repeatedly mapped on Bos taurus autosome 18 (BTA18. In the present study, we report a refined analysis of previously detected QTL regions on BTA18 with the aim of identifying marker and marker haplotypes in linkage disequilibrium with SCS. A combined linkage and linkage disequilibrium approach was implemented, and association analyses of marker genotypes and maternally inherited two-marker-haplotypes were conducted to identify marker and haplotypes in linkage disequilibrium with a locus affecting SCS in the German Holstein population. Results We detected a genome-wide significant QTL within marker interval 9 (HAMP_c.366+109G>A - BMS833 in the middle to telomeric region on BTA18 and a second putative QTL in marker interval 12-13 (BB710 - PVRL2_c.392G>A. Association analyses with genotypes of markers flanking the most likely QTL positions revealed the microsatellite marker BMS833 (interval 9 to be associated with a locus affecting SCS within the families investigated. A further analysis of maternally inherited two-marker haplotypes and effects of maternally inherited two-marker-interval gametes indicated haplotype 249-G in marker interval 12-13 (BB710 - PVRL2_c.392G>A to be associated with SCS in the German Holstein population. Conclusion Our results confirmed previous QTL mapping results for SCS and support the hypothesis that more than one locus presumably affects udder health in the middle to telomeric region of BTA18. However, a subsequent investigation of the reported QTL regions is necessary to verify the two-QTL hypothesis and confirm the association of two-marker-haplotype 249-G in marker interval 12-13 (BB710 - PVRL2_c.392G>A with SCS. For this

  15. Genome-wide generation and use of informative intron-spanning and intron-length polymorphism markers for high-throughput genetic analysis in rice

    Badoni, Saurabh; Das, Sweta; Sayal, Yogesh K.; Gopalakrishnan, S.; Singh, Ashok K.; Rao, Atmakuri R.; Agarwal, Pinky; Parida, Swarup K.; Tyagi, Akhilesh K.

    2016-01-01

    We developed genome-wide 84634 ISM (intron-spanning marker) and 16510 InDel-fragment length polymorphism-based ILP (intron-length polymorphism) markers from genes physically mapped on 12 rice chromosomes. These genic markers revealed much higher amplification-efficiency (80%) and polymorphic-potential (66%) among rice accessions even by a cost-effective agarose gel-based assay. A wider level of functional molecular diversity (17–79%) and well-defined precise admixed genetic structure was assayed by 3052 genome-wide markers in a structured population of indica, japonica, aromatic and wild rice. Six major grain weight QTLs (11.9–21.6% phenotypic variation explained) were mapped on five rice chromosomes of a high-density (inter-marker distance: 0.98 cM) genetic linkage map (IR 64 x Sonasal) anchored with 2785 known/candidate gene-derived ISM and ILP markers. The designing of multiple ISM and ILP markers (2 to 4 markers/gene) in an individual gene will broaden the user-preference to select suitable primer combination for efficient assaying of functional allelic variation/diversity and realistic estimation of differential gene expression profiles among rice accessions. The genomic information generated in our study is made publicly accessible through a user-friendly web-resource, “Oryza ISM-ILP marker” database. The known/candidate gene-derived ISM and ILP markers can be enormously deployed to identify functionally relevant trait-associated molecular tags by optimal-resource expenses, leading towards genomics-assisted crop improvement in rice. PMID:27032371

  16. Simple sequence repeat marker loci discovery using SSR primer.

    Robinson, Andrew J; Love, Christopher G; Batley, Jacqueline; Barker, Gary; Edwards, David

    2004-06-12

    Simple sequence repeats (SSRs) have become important molecular markers for a broad range of applications, such as genome mapping and characterization, phenotype mapping, marker assisted selection of crop plants and a range of molecular ecology and diversity studies. With the increase in the availability of DNA sequence information, an automated process to identify and design PCR primers for amplification of SSR loci would be a useful tool in plant breeding programs. We report an application that integrates SPUTNIK, an SSR repeat finder, with Primer3, a PCR primer design program, into one pipeline tool, SSR Primer. On submission of multiple FASTA formatted sequences, the script screens each sequence for SSRs using SPUTNIK. The results are parsed to Primer3 for locus-specific primer design. The script makes use of a Web-based interface, enabling remote use. This program has been written in PERL and is freely available for non-commercial users by request from the authors. The Web-based version may be accessed at http://hornbill.cspp.latrobe.edu.au/

  17. Sonification of reference markers for auditory graphs: effects on non-visual point estimation tasks

    Oussama Metatla

    2016-04-01

    Full Text Available Research has suggested that adding contextual information such as reference markers to data sonification can improve interaction with auditory graphs. This paper presents results of an experiment that contributes to quantifying and analysing the extent of such benefits for an integral part of interacting with graphed data: point estimation tasks. We examine three pitch-based sonification mappings; pitch-only, one-reference, and multiple-references that we designed to provide information about distance from an origin. We assess the effects of these sonifications on users’ performances when completing point estimation tasks in a between-subject experimental design against visual and speech control conditions. Results showed that the addition of reference tones increases users accuracy with a trade-off for task completion times, and that the multiple-references mapping is particularly effective when dealing with points that are positioned at the midrange of a given axis.

  18. High-throughput development of genome-wide locus-specific informative SSR markers in wheat

    Although simple sequence repeat (SSR) markers are not new, they are still useful and often used markers in molecular mapping and marker-assisted breeding, particularly in developing countries. However, locus-specific SSR markers could be more useful and informative in wheat breeding and genetic stud...

  19. Towards a unified genetic map of diploid roses

    Spiller, M.; Hibrand-Saint Oyant, L.; Tsai, C.; Byrne, D.H.; Smulders, M.J.M.; Foucher, A.L.J.L.; Debener, T.

    2011-01-01

    We have constructed the first integrated consensus map (ICM) for rose, based on the information of four diploid populations and more than 1,000 initial markers. The single population maps are linked via 59 bridge markers, on average 8.4 per linkage group (LG). The integrated map comprises 597

  20. Diagnostic markers of infection in curret pediatric practice | Chiabia ...

    chemokines, cytokines, adhesion molecules, cell surface markers and polymerase chain reaction are expensive and available only in specialised research laboratories. Optimal benefit can be obtained from rational use of currently available markers either by multiple marker assays or serial measurements which increase ...

  1. The role of Molecular Markers in Improvement of Fruit Crops

    Zahoor Ahmad BHAT

    2010-06-01

    Full Text Available Markers have been used over the years for the classification of plants. Markers are any trait of an organism that can be identified with confidence and relative easy, and can be followed in a mapping population on another hand markers be defined as heritable entities associated with the economically important trait under the control of polygenes. Morphological markers can be detected with naked eye (naked eye polymorphism or as difference in physical or chemical properties of the macromolecules. In other words, there are two types of genetic markers viz. morphological markers or naked eye polymorphism and non-morphological markers or molecular markers. Morphological markers include traits such as plant height, disease response, photoperiod, sensitivity, shape or colour of flowers, fruits or seeds etc. Molecular markers include biochemical constituents. Morphological markers have many limitations for being used as markers particularly in fruit crops because of long generation time and large size of fruit trees besides being influenced by environment. Consequently, molecular markers could be appropriate choice to study and preserve the diversity in any germplasm. Molecular markers have diverse applications in fruit crop improvement, particularly in the areas of genetic diversity and varietal identification studies, gene tagging, disease diagnostics, pedigree analysis, hybrid detection, sex differentiation and marker assisted selection.

  2. A review of microsatellite markers and their applications in rice breeding programs to improve blast disease resistance.

    Miah, Gous; Rafii, Mohd Y; Ismail, Mohd R; Puteh, Adam B; Rahim, Harun A; Islam, Kh Nurul; Latif, Mohammad Abdul

    2013-11-14

    Over the last few decades, the use of molecular markers has played an increasing role in rice breeding and genetics. Of the different types of molecular markers, microsatellites have been utilized most extensively, because they can be readily amplified by PCR and the large amount of allelic variation at each locus. Microsatellites are also known as simple sequence repeats (SSR), and they are typically composed of 1-6 nucleotide repeats. These markers are abundant, distributed throughout the genome and are highly polymorphic compared with other genetic markers, as well as being species-specific and co-dominant. For these reasons, they have become increasingly important genetic markers in rice breeding programs. The evolution of new biotypes of pests and diseases as well as the pressures of climate change pose serious challenges to rice breeders, who would like to increase rice production by introducing resistance to multiple biotic and abiotic stresses. Recent advances in rice genomics have now made it possible to identify and map a number of genes through linkage to existing DNA markers. Among the more noteworthy examples of genes that have been tightly linked to molecular markers in rice are those that confer resistance or tolerance to blast. Therefore, in combination with conventional breeding approaches, marker-assisted selection (MAS) can be used to monitor the presence or lack of these genes in breeding populations. For example, marker-assisted backcross breeding has been used to integrate important genes with significant biological effects into a number of commonly grown rice varieties. The use of cost-effective, finely mapped microsatellite markers and MAS strategies should provide opportunities for breeders to develop high-yield, blast resistance rice cultivars. The aim of this review is to summarize the current knowledge concerning the linkage of microsatellite markers to rice blast resistance genes, as well as to explore the use of MAS in rice breeding

  3. A Review of Microsatellite Markers and Their Applications in Rice Breeding Programs to Improve Blast Disease Resistance

    Mohammad Abdul Latif

    2013-11-01

    Full Text Available Over the last few decades, the use of molecular markers has played an increasing role in rice breeding and genetics. Of the different types of molecular markers, microsatellites have been utilized most extensively, because they can be readily amplified by PCR and the large amount of allelic variation at each locus. Microsatellites are also known as simple sequence repeats (SSR, and they are typically composed of 1–6 nucleotide repeats. These markers are abundant, distributed throughout the genome and are highly polymorphic compared with other genetic markers, as well as being species-specific and co-dominant. For these reasons, they have become increasingly important genetic markers in rice breeding programs. The evolution of new biotypes of pests and diseases as well as the pressures of climate change pose serious challenges to rice breeders, who would like to increase rice production by introducing resistance to multiple biotic and abiotic stresses. Recent advances in rice genomics have now made it possible to identify and map a number of genes through linkage to existing DNA markers. Among the more noteworthy examples of genes that have been tightly linked to molecular markers in rice are those that confer resistance or tolerance to blast. Therefore, in combination with conventional breeding approaches, marker-assisted selection (MAS can be used to monitor the presence or lack of these genes in breeding populations. For example, marker-assisted backcross breeding has been used to integrate important genes with significant biological effects into a number of commonly grown rice varieties. The use of cost-effective, finely mapped microsatellite markers and MAS strategies should provide opportunities for breeders to develop high-yield, blast resistance rice cultivars. The aim of this review is to summarize the current knowledge concerning the linkage of microsatellite markers to rice blast resistance genes, as well as to explore the use of MAS

  4. A general pipeline for the development of anchor markers for comparative genomics in plants

    Stougaard Jens

    2006-08-01

    Full Text Available Abstract Background Complete or near-complete genomic sequence information is presently only available for a few plant species representing a large phylogenetic diversity among plants. In order to effectively transfer this information to species lacking sequence information, comparative genomic tools need to be developed. Molecular markers permitting cross-species mapping along co-linear genomic regions are central to comparative genomics. These "anchor" markers, defining unique loci in genetic linkage maps of multiple species, are gene-based and possess a number of features that make them relatively sparse. To identify potential anchor marker sequences more efficiently, we have established an automated bioinformatic pipeline that combines multi-species Expressed Sequence Tags (EST and genome sequence data. Results Taking advantage of sequence data from related species, the pipeline identifies evolutionarily conserved sequences that are likely to define unique orthologous loci in most species of the same phylogenetic clade. The key features are the identification of evolutionarily conserved sequences followed by automated design of intron-flanking Polymerase Chain Reaction (PCR primer pairs. Polymorphisms can subsequently be identified by size- or sequence variation of PCR products, amplified from mapping parents or populations. We illustrate our procedure in legumes and grasses and exemplify its application in legumes, where model plant studies and the genome- and EST-sequence data available have a potential impact on the breeding of crop species and on our understanding of the evolution of this large and diverse family. Conclusion We provide a database of 459 candidate anchor loci which have the potential to serve as map anchors in more than 18,000 legume species, a number of which are of agricultural importance. For grasses, the database contains 1335 candidate anchor loci. Based on this database, we have evaluated 76 candidate anchor loci

  5. Detection of Sequence Polymorphism in Rubus Occidentalis L. Monomorphic Microsatellite Markers by High Resolution Melting

    Microsatellite, or simple sequence repeat (SSR) markers, are valuable as co-dominant genetic markers with a variety of applications such as DNA fingerprinting, linkage mapping, and population structure analysis. Development of microsatellite primers through the identification of appropriate repeate...

  6. Genetic studies and a search for molecular markers that are linked ...

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    Instead, linkage analysis resulted in the construction of a molecular marker linkage map consisting of 45 ..... This limits the application of this marker type, particularly in ... primer design when one uses RAPDs. .... Concepts of Genetics. Fourth.