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Sample records for line mapping population

  1. QTL mapping of fruit rot resistance to the plant pathogen Phytophthora capsici in a recombinant inbred line Capsicum annuum population.

    Science.gov (United States)

    Naegele, R P; Ashrafi, H; Hill, T A; Chin-Wo, S Reyes; Van Deynze, A E; Hausbeck, M K

    2014-05-01

    Phytophthora capsici is an important pepper (Capsicum annuum) pathogen causing fruit and root rot, and foliar blight in field and greenhouse production. Previously, an F6 recombinant inbred line population was evaluated for fruit rot susceptibility. Continuous variation among lines and partial and isolate-specific resistance were found. In this study, Phytophthora fruit rot resistance was mapped in the same F6 population between Criollo del Morelos 334 (CM334), a landrace from Mexico, and 'Early Jalapeno' using a high-density genetic map. Isolate-specific resistance was mapped independently in 63 of the lines evaluated and the two parents. Heritability of the resistance for each isolate at 3 and 5 days postinoculation (dpi) was high (h(2) = 0.63 to 0.68 and 0.74 to 0.83, respectively). Significant additive and epistatic quantitative trait loci (QTL) were identified for resistance to isolates OP97 and 13709 (3 and 5 dpi) and 12889 (3 dpi only). Mapping of fruit traits showed potential linkage with few disease resistance QTL. The partial fruit rot resistance from CM334 suggests that this may not be an ideal source for fruit rot resistance in pepper.

  2. Bike Map Lines

    Data.gov (United States)

    Town of Chapel Hill, North Carolina — Chapel Hill Bike Map Lines from KMZ file.This data came from the wiki comment board for the public, not an “official map” showing the Town of Chapel Hill's plans or...

  3. The SAURON project - XI. Stellar populations from absorption-line strength maps of 24 early-type spirals

    NARCIS (Netherlands)

    Peletier, Reynier F.; Falcon-Barroso, Jesus; Bacon, Roland; Cappellari, Michele; Davies, Roger L.; de Zeeuw, P. T.; Emsellem, Eric; Ganda, Katia; Krajnovic, Davor; Kuntschner, Harald; McDermid, Richard M.; Sarzi, Marc; van de Ven, Glenn

    2007-01-01

    We present absorption-line strength maps of a sample of 24 representative early-type spiral galaxies, mostly of type Sa, obtained as part of the SAURON (Spectrographic Areal Unit for Research on Optical Nebulae) survey of nearby galaxies using our custom-built integral-field spectrograph. Using

  4. Whole genome re-sequencing reveals genome-wide variations among parental lines of 16 mapping populations in chickpea (Cicer arietinum L.).

    Science.gov (United States)

    Thudi, Mahendar; Khan, Aamir W; Kumar, Vinay; Gaur, Pooran M; Katta, Krishnamohan; Garg, Vanika; Roorkiwal, Manish; Samineni, Srinivasan; Varshney, Rajeev K

    2016-01-27

    Chickpea (Cicer arietinum L.) is the second most important grain legume cultivated by resource poor farmers in South Asia and Sub-Saharan Africa. In order to harness the untapped genetic potential available for chickpea improvement, we re-sequenced 35 chickpea genotypes representing parental lines of 16 mapping populations segregating for abiotic (drought, heat, salinity), biotic stresses (Fusarium wilt, Ascochyta blight, Botrytis grey mould, Helicoverpa armigera) and nutritionally important (protein content) traits using whole genome re-sequencing approach. A total of 192.19 Gb data, generated on 35 genotypes of chickpea, comprising 973.13 million reads, with an average sequencing depth of ~10 X for each line. On an average 92.18 % reads from each genotype were aligned to the chickpea reference genome with 82.17 % coverage. A total of 2,058,566 unique single nucleotide polymorphisms (SNPs) and 292,588 Indels were detected while comparing with the reference chickpea genome. Highest number of SNPs were identified on the Ca4 pseudomolecule. In addition, copy number variations (CNVs) such as gene deletions and duplications were identified across the chickpea parental genotypes, which were minimum in PI 489777 (1 gene deletion) and maximum in JG 74 (1,497). A total of 164,856 line specific variations (144,888 SNPs and 19,968 Indels) with the highest percentage were identified in coding regions in ICC 1496 (21 %) followed by ICCV 97105 (12 %). Of 539 miscellaneous variations, 339, 138 and 62 were inter-chromosomal variations (CTX), intra-chromosomal variations (ITX) and inversions (INV) respectively. Genome-wide SNPs, Indels, CNVs, PAVs, and miscellaneous variations identified in different mapping populations are a valuable resource in genetic research and helpful in locating genes/genomic segments responsible for economically important traits. Further, the genome-wide variations identified in the present study can be used for developing high density SNP arrays for

  5. Quantitative Trait Loci Mapping of Western Corn Rootworm (Coleoptera: Chrysomelidae) Host Plant Resistance in Two Populations of Doubled Haploid Lines in Maize (Zea mays L.).

    Science.gov (United States)

    Bohn, Martin O; Marroquin, Juan J; Flint-Garcia, Sherry; Dashiell, Kenton; Willmot, David B; Hibbard, Bruce E

    2018-02-09

    Over the last 70 yr, more than 12,000 maize accessions have been screened for their level of resistance to western corn rootworm, Diabrotica virgifera virgifera (LeConte; Coleoptera: Chrysomelidae), larval feeding. Less than 1% of this germplasm was selected for initiating recurrent selection or other breeding programs. Selected genotypes were mostly characterized by large root systems and superior root regrowth after root damage caused by western corn rootworm larvae. However, no hybrids claiming native (i.e., host plant) resistance to western corn rootworm larval feeding are currently commercially available. We investigated the genetic basis of western corn rootworm resistance in maize materials with improved levels of resistance using linkage disequilibrium mapping approaches. Two populations of topcrossed doubled haploid maize lines (DHLs) derived from crosses between resistant and susceptible maize lines were evaluated for their level of resistance in three to four different environments. For each DHL topcross an average root damage score was estimated and used for quantitative trait loci (QTL) analysis. We found genomic regions contributing to western corn rootworm resistance on all maize chromosomes, except for chromosome 4. Models fitting all QTL simultaneously explained about 30 to 50% of the genotypic variance for root damage scores in both mapping populations. Our findings confirm the complex genetic structure of host plant resistance against western corn rootworm larval feeding in maize. Interestingly, three of these QTL regions also carry genes involved in ascorbate biosynthesis, a key compound we hypothesize is involved in the expression of western corn rootworm resistance. © The Author(s) 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  6. Line Generalization and AutoCAD Map

    Directory of Open Access Journals (Sweden)

    Nada Vučetić

    2001-01-01

    Full Text Available The paper offers the results of original research made on the application of AutoCAD Map in line generalisation. The differences and similarities have been found out between the Douglas-Peucker method and the method of line simplification that is incorporated in AutoCAD Map. There have been also the inaccuracies found out in AutoCAD Map manual relating to the issues of buffer width and tolerance, and the line width before and after simplification. The paper gives recommendations about pseudo nodes dissolving. It has been noticed that AutoCAD Map simplification method is not independent of the order of points. The application of the method is illustrated by an example of coastal line of Istria.

  7. Reconstruction of multiple line source attenuation maps

    International Nuclear Information System (INIS)

    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

  8. Variability among inbred lines and RFLP mapping of sunflower isozymes

    Directory of Open Access Journals (Sweden)

    Carrera Alicia D.

    2002-01-01

    Full Text Available Eight isozyme systems were used in this study: acid phosphatase (ACP, alcohol dehydrogenase (ADH, esterase (EST, glutamate dehydrogenase (GDH, malate dehydrogenase (MDH, phosphoglucoisomerase (PGI, 6-phosphogluconate dehydrogenase (PGD, and phosphoglucomutase (PGM. The polymorphism of these enzyme systems was studied in 25 elite inbred lines. A total of 19 loci were identified, but only eight of them were polymorphic in the germplasm tested. The polymorphic index for the eight informative markers ranged from 0.08 to 0.57, with a mean value of 0.36. Five isozyme loci were mapped in F2:3 populations with existing RFLP data. Est-1, Gdh-2 and Pgi-2 were mapped to linkage groups 3, 14 and 9, respectively. As in previous reports, an ACP locus and a PGD locus were found to be linked, both located in linkage group 2 of the public sunflower map.

  9. A New Advanced Backcross Tomato Population Enables High Resolution Leaf QTL Mapping and Gene Identification

    Directory of Open Access Journals (Sweden)

    Daniel Fulop

    2016-10-01

    Full Text Available Quantitative Trait Loci (QTL mapping is a powerful technique for dissecting the genetic basis of traits and species differences. Established tomato mapping populations between domesticated tomato (Solanum lycopersicum and its more distant interfertile relatives typically follow a near isogenic line (NIL design, such as the S. pennellii Introgression Line (IL population, with a single wild introgression per line in an otherwise domesticated genetic background. Here, we report on a new advanced backcross QTL mapping resource for tomato, derived from a cross between the M82 tomato cultivar and S. pennellii. This so-called Backcrossed Inbred Line (BIL population is comprised of a mix of BC2 and BC3 lines, with domesticated tomato as the recurrent parent. The BIL population is complementary to the existing S. pennellii IL population, with which it shares parents. Using the BILs, we mapped traits for leaf complexity, leaflet shape, and flowering time. We demonstrate the utility of the BILs for fine-mapping QTL, particularly QTL initially mapped in the ILs, by fine-mapping several QTL to single or few candidate genes. Moreover, we confirm the value of a backcrossed population with multiple introgressions per line, such as the BILs, for epistatic QTL mapping. Our work was further enabled by the development of our own statistical inference and visualization tools, namely a heterogeneous hidden Markov model for genotyping the lines, and by using state-of-the-art sparse regression techniques for QTL mapping.

  10. Registration of Wyandot × PI 567301B soybean recombinant inbred line population

    Science.gov (United States)

    A soybean [Glycine max (L.) Merr] mapping population (Reg. No., SNL MAP) consisting of 357 F7-derived recombinant inbred lines (RILs) was jointly developed by the USDA-Agricultural Research Service and the Ohio Agricultural Research and Development Center (OARDC) in Wooster, OH. The population was ...

  11. Estimation of Initial Position Using Line Segment Matching in Maps

    Directory of Open Access Journals (Sweden)

    Chongyang Wei

    2016-06-01

    Full Text Available While navigating in a typical traffic scene, with a drastic drift or sudden jump in its Global Positioning System (GPS position, the localization based on such an initial position is unable to extract precise overlapping data from the prior map in order to match the current data, thus rendering the localization as unfeasible. In this paper, we first propose a new method to estimate an initial position by matching the infrared reflectivity maps. The maps consist of a highly precise prior map, built with the offline simultaneous localization and mapping (SLAM technique, and a smooth current map, built with the integral over velocities. Considering the attributes of the maps, we first propose to exploit the stable, rich line segments to match the lidar maps. To evaluate the consistency of the candidate line pairs in both maps, we propose to adopt the local appearance, pairwise geometric attribute and structural likelihood to construct an affinity graph, as well as employ a spectral algorithm to solve the graph efficiently. The initial position is obtained according to the relationship between the vehicle's current position and matched lines. Experiments on the campus with a GPS error of dozens of metres show that our algorithm can provide an accurate initial value with average longitudinal and lateral errors being 1.68m and 1.04m, respectively.

  12. On Estimation of Contamination from Hydrogen Cyanide in Carbon Monoxide Line-intensity Mapping

    Energy Technology Data Exchange (ETDEWEB)

    Chung, Dongwoo T.; Li, Tony Y.; Viero, Marco P.; Church, Sarah E.; Wechsler, Risa H., E-mail: dongwooc@stanford.edu [Kavli Institute for Particle Astrophysics and Cosmology, Physics Department, Stanford University, Stanford, CA 94305 (United States)

    2017-09-01

    Line-intensity mapping surveys probe large-scale structure through spatial variations in molecular line emission from a population of unresolved cosmological sources. Future such surveys of carbon monoxide line emission, specifically the CO(1-0) line, face potential contamination from a disjointed population of sources emitting in a hydrogen cyanide emission line, HCN(1-0). This paper explores the potential range of the strength of HCN emission and its effect on the CO auto power spectrum, using simulations with an empirical model of the CO/HCN–halo connection. We find that effects on the observed CO power spectrum depend on modeling assumptions but are very small for our fiducial model, which is based on current understanding of the galaxy–halo connection. Given the fiducial model, we expect the bias in overall CO detection significance due to HCN to be less than 1%.

  13. A new population growth map with variable coefficients

    International Nuclear Information System (INIS)

    Jannussis, A.

    1986-01-01

    In the present paper it is investigated a simple population growth map with variable coefficients. Moreover, it is studied the new population map of the form xsub(j+1) = axsub(j) (1/(1 + bxsub(j)) -1/(1 + cxsub(j))), c not= b, j = 0, 1,..., which is transformed in an equivalent logistic map

  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.

    Science.gov (United States)

    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.

  15. 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.

    Directory of Open Access Journals (Sweden)

    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.

  16. 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

    Science.gov (United States)

    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

  17. Field line mapping results in the CNT stellarator

    International Nuclear Information System (INIS)

    Sarasola, X.; Pedersen, T. Sunn; Kremer, J.P.; Lefrancois, R.G.; Marksteiner, Q.; Ahmad, N.

    2005-01-01

    The Columbia Non-neutral Torus (CNT), located at Columbia University, is a toroidal, ultra-high vacuum stellarator designed to confine pure electron and other non-neutral plasmas. Its coil configuration is the simplest of any stellarator constructed, since it consists only of two pairs of circular planar copper coils. CNT started operation in November 2004. During its first months of operation a detailed mapping of the nested magnetic surfaces has been developed using the fluorescent method. An electron beam was emitted along a field line by a small moveable electron gun. Different beam energies (ranging from 50 to 200 eV) were used to perform the field line mapping. The e- beam emitted by the electron gun followed the field lines around the torus and hit two moveable ZnO coated aluminum rods that emit visible light when struck by the e-beam. For each position of the e- gun, the phosphor rods scanned the cross-section of the torus allowing a standard digital camera to record a single magnetic surface in a five second exposure. Multiple photos were taken and then manipulated and superposed using IDL software to create composite images of the nested magnetic surfaces. Detailed mapping of the magnetic flux surfaces was completed at a variety of magnetic configurations and at pressures in the 10 -8 Torr range. The experimental results were compared with numerical calculations demonstrating that the obtained measurements agree very well with numerical predictions. In particular, the current configuration has an ultralow aspect ratio (A≤ 1.9) and excellent magnetic surface quality with no detectable island structures or stochastic regions, except at the edge of the plasma where a predicted island chain is present. These experimental results will be presented along with details of the field line mapping system. (author)

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

    Directory of Open Access Journals (Sweden)

    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.

  19. Reverberation Mapping of Optical Emission Lines in Five Active Galaxies

    Energy Technology Data Exchange (ETDEWEB)

    Fausnaugh, M. M.; Denney, K. D.; Peterson, B. M.; Kochanek, C. S.; Pogge, R. W.; Brown, Jonathan S.; Coker, C. T. [Department of Astronomy, The Ohio State University, 140 W. 18th Avenue, Columbus, OH 43210 (United States); Grier, C. J.; Beatty, Thomas G. [Department of Astronomy and Astrophysics, The Pennsylvania State University, 525 Davey Laboratory, University Park, PA 16802 (United States); Bentz, M. C. [Department of Physics and Astronomy, Georgia State University, Atlanta, GA 30303 (United States); Rosa, G. De [Space Telescope Science Institute, 3700 San Martin Drive, Baltimore, MD 21218 (United States); Adams, S. M. [Cahill Center for Astrophysics, California Institute of Technology, Pasadena, CA 91125 (United States); Barth, A. J. [Department of Physics and Astronomy, 4129 Frederick Reines Hall, University of California, Irvine, CA 92697 (United States); Bhattacharjee, A.; Brotherton, M. S. [Department of Physics and Astronomy, University of Wyoming, 1000 E. University Avenue, Laramie, WY (United States); Borman, G. A. [Crimean Astrophysical Observatory, P/O Nauchny, Crimea 298409 (Russian Federation); Boroson, T. A. [Las Cumbres Global Telescope Network, 6740 Cortona Drive, Suite 102, Santa Barbara, CA 93117 (United States); Bottorff, M. C. [Fountainwood Observatory, Department of Physics FJS 149, Southwestern University, 1011 E. University Avenue, Georgetown, TX 78626 (United States); Brown, Jacob E. [Department of Physics and Astronomy, University of Missouri, Columbia (United States); Crawford, S. M. [South African Astronomical Observatory, P.O. Box 9, Observatory 7935, Cape Town (South Africa); and others

    2017-05-10

    We present the first results from an optical reverberation mapping campaign executed in 2014 targeting the active galactic nuclei (AGNs) MCG+08-11-011, NGC 2617, NGC 4051, 3C 382, and Mrk 374. Our targets have diverse and interesting observational properties, including a “changing look” AGN and a broad-line radio galaxy. Based on continuum-H β lags, we measure black hole masses for all five targets. We also obtain H γ and He ii λ 4686 lags for all objects except 3C 382. The He ii λ 4686 lags indicate radial stratification of the BLR, and the masses derived from different emission lines are in general agreement. The relative responsivities of these lines are also in qualitative agreement with photoionization models. These spectra have extremely high signal-to-noise ratios (100–300 per pixel) and there are excellent prospects for obtaining velocity-resolved reverberation signatures.

  20. Reverberation Mapping of Optical Emission Lines in Five Active Galaxies

    International Nuclear Information System (INIS)

    Fausnaugh, M. M.; Denney, K. D.; Peterson, B. M.; Kochanek, C. S.; Pogge, R. W.; Brown, Jonathan S.; Coker, C. T.; Grier, C. J.; Beatty, Thomas G.; Bentz, M. C.; Rosa, G. De; Adams, S. M.; Barth, A. J.; Bhattacharjee, A.; Brotherton, M. S.; Borman, G. A.; Boroson, T. A.; Bottorff, M. C.; Brown, Jacob E.; Crawford, S. M.

    2017-01-01

    We present the first results from an optical reverberation mapping campaign executed in 2014 targeting the active galactic nuclei (AGNs) MCG+08-11-011, NGC 2617, NGC 4051, 3C 382, and Mrk 374. Our targets have diverse and interesting observational properties, including a “changing look” AGN and a broad-line radio galaxy. Based on continuum-H β lags, we measure black hole masses for all five targets. We also obtain H γ and He ii λ 4686 lags for all objects except 3C 382. The He ii λ 4686 lags indicate radial stratification of the BLR, and the masses derived from different emission lines are in general agreement. The relative responsivities of these lines are also in qualitative agreement with photoionization models. These spectra have extremely high signal-to-noise ratios (100–300 per pixel) and there are excellent prospects for obtaining velocity-resolved reverberation signatures.

  1. Mapping of imprinted quantitative trait loci using immortalized F2 populations.

    Directory of Open Access Journals (Sweden)

    Yongxian Wen

    Full Text Available Mapping of imprinted quantitative trait loci (iQTLs is helpful for understanding the effects of genomic imprinting on complex traits in animals and plants. At present, the experimental designs and corresponding statistical methods having been proposed for iQTL mapping are all based on temporary populations including F2 and BC1, which can be used only once and suffer some other shortcomings respectively. In this paper, we propose a framework for iQTL mapping, including methods of interval mapping (IM and composite interval mapping (CIM based on conventional low-density genetic maps and point mapping (PM and composite point mapping (CPM based on ultrahigh-density genetic maps, using an immortalized F2 (imF2 population generated by random crosses between recombinant inbred lines or doubled haploid lines. We demonstrate by simulations that imF2 populations are very desirable and the proposed statistical methods (especially CIM and CPM are very powerful for iQTL mapping, with which the imprinting effects as well as the additive and dominance effects of iQTLs can be unbiasedly estimated.

  2. Mapping of a rice thermosensitive genic male sterility gene from a TGMS mutant line

    Energy Technology Data Exchange (ETDEWEB)

    Vu Duc Quang; Nguyen Van Dong; Pham Ngoc Luong; Tran Duy Quy [Argicultural Genetics Institute, Hanoi (Viet Nam); Nguyen, Henry T. [Texas Tech Univ., Department of Plant and Soil Science, Lubbock TX (United States)

    2001-03-01

    At the Agricultural Genetics Institute (AGI), Hanoi, Vietnam, a number of thermo-sensitive genic male sterility (TGMS) homozygous rice lines have been developed by means of experimental mutagenesis followed by anther culture techniques. One of them (TGMS-1 indica mutant line) was used in this research. The critical temperature (at the period from pollen mother cell formation to the beginning of meiotic division) for TGMS-1 sterility was 24-25degC, below which the plants were fertile and above which the plants became sterile. Segregation analysis showed that the TGMS trait of the TGMS-1 mutant line was controlled by a single recessive gene. An F{sub 2} mapping population from a cross between TGMS-1 mutant line and CH1 (a fertile indica line) was developed for tagging and mapping the TGMS gene. From survey of 200 AFLP primer combinations in a bulked segregant analysis, 4 AFLP markers (E2/M5-200, E3/M16-400, E5/M12-600 and E5/M12-200) linked to TGMS-1 gene were identified and cloned. All except E2/M5-200 were found to be low-copy number sequences. The marker E5/M12-600 showed polymorphism in RFLP analysis and was closely linked to the TGMS gene at a distance of 3.3cM. This marker was subsequently mapped on chromosome 2 using doubled-haploid mapping populations derived from the crosses IR64xAzucena and CT9993xIR62666. Linkage of microsatellite marker RM27 with the TGMS gene further confirmed its location on chromosome 2. The closest marker, E5/M12-600, was sequenced so that a PCR marker can be developed for the use in marker-assisted breeding. The application of TGMS genes to the commercial two-line hybrid rice breeding system was discussed. (author)

  3. Mapping of a rice thermosensitive genic male sterility gene from a TGMS mutant line

    International Nuclear Information System (INIS)

    Vu Duc Quang; Nguyen Van Dong; Pham Ngoc Luong; Tran Duy Quy; Nguyen, Henry T.

    2001-01-01

    At the Agricultural Genetics Institute (AGI), Hanoi, Vietnam, a number of thermo-sensitive genic male sterility (TGMS) homozygous rice lines have been developed by means of experimental mutagenesis followed by anther culture techniques. One of them (TGMS-1 indica mutant line) was used in this research. The critical temperature (at the period from pollen mother cell formation to the beginning of meiotic division) for TGMS-1 sterility was 24-25degC, below which the plants were fertile and above which the plants became sterile. Segregation analysis showed that the TGMS trait of the TGMS-1 mutant line was controlled by a single recessive gene. An F 2 mapping population from a cross between TGMS-1 mutant line and CH1 (a fertile indica line) was developed for tagging and mapping the TGMS gene. From survey of 200 AFLP primer combinations in a bulked segregant analysis, 4 AFLP markers (E2/M5-200, E3/M16-400, E5/M12-600 and E5/M12-200) linked to TGMS-1 gene were identified and cloned. All except E2/M5-200 were found to be low-copy number sequences. The marker E5/M12-600 showed polymorphism in RFLP analysis and was closely linked to the TGMS gene at a distance of 3.3cM. This marker was subsequently mapped on chromosome 2 using doubled-haploid mapping populations derived from the crosses IR64xAzucena and CT9993xIR62666. Linkage of microsatellite marker RM27 with the TGMS gene further confirmed its location on chromosome 2. The closest marker, E5/M12-600, was sequenced so that a PCR marker can be developed for the use in marker-assisted breeding. The application of TGMS genes to the commercial two-line hybrid rice breeding system was discussed. (author)

  4. Mapping population-based structural connectomes.

    Science.gov (United States)

    Zhang, Zhengwu; Descoteaux, Maxime; Zhang, Jingwen; Girard, Gabriel; Chamberland, Maxime; Dunson, David; Srivastava, Anuj; Zhu, Hongtu

    2018-05-15

    Advances in understanding the structural connectomes of human brain require improved approaches for the construction, comparison and integration of high-dimensional whole-brain tractography data from a large number of individuals. This article develops a population-based structural connectome (PSC) mapping framework to address these challenges. PSC simultaneously characterizes a large number of white matter bundles within and across different subjects by registering different subjects' brains based on coarse cortical parcellations, compressing the bundles of each connection, and extracting novel connection weights. A robust tractography algorithm and streamline post-processing techniques, including dilation of gray matter regions, streamline cutting, and outlier streamline removal are applied to improve the robustness of the extracted structural connectomes. The developed PSC framework can be used to reproducibly extract binary networks, weighted networks and streamline-based brain connectomes. We apply the PSC to Human Connectome Project data to illustrate its application in characterizing normal variations and heritability of structural connectomes in healthy subjects. Copyright © 2018 Elsevier Inc. All rights reserved.

  5. A protein interaction map of the kalimantacin biosynthesis assembly line

    Directory of Open Access Journals (Sweden)

    Birgit Uytterhoeven

    2016-11-01

    Full Text Available The antimicrobial secondary metabolite kalimantacin is produced by a hybrid polyketide/ non-ribosomal peptide system in Pseudomonas fluorescens BCCM_ID9359. In this study, the kalimantacin biosynthesis gene cluster is analyzed by yeast two-hybrid analysis, creating a protein-protein interaction map of the entire assembly line. In total, 28 potential interactions were identified, of which 13 could be confirmed further. These interactions include the dimerization of ketosynthase domains, a link between assembly line modules 9 and 10, and a specific interaction between the trans-acting enoyl reductase BatK and the carrier proteins of modules 8 and 10. These interactions reveal fundamental insight into the biosynthesis of secondary metabolites.This study is the first to reveal interactions in a complete biosynthetic pathway. Similar future studies could build a strong basis for engineering strategies in such clusters.

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Science.gov (United States)

    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.

  8. Integrated genetic linkage map of cultivated peanut by three RIL populations

    Institute of Scientific and Technical Information of China (English)

    Yanbin Song; Huifang Jiang; Huaiyong Luo; Li Huang; Yuning Chen; Weigang Chen; Nian Liu; Xiaoping Ren; Bolun Yu; Jianbin Guo

    2017-01-01

    High-density and precise genetic linkage map is fundamental to detect quanti-tative trait locus (QTL) of agronomic and quality related traits in cultivated peanut (Arachis hypogaea L.). In this study, three linkage maps from three RIL (recombinant inbred line) populations were used to construct an integrated map. A total of 2,069 SSR and transposon markers were anchored on the high-density integrated map which covered 2,231.53 cM with 20 linkage groups. Totally, 92 QTLs correlating with pod length (PL), pod width (PW), hun-dred pods weight (HPW) and plant height (PH) from above RIL populations were mapped on it. Seven intervals were found to harbor QTLs controlling the same traits in different pop-ulations, including one for PL, three for PW, two for HPW, and one for PH. Besides, QTLs controlling different traits in different populations were found to be overlapped in four inter-vals. Interval on A05 contains 17 QTLs for different traits from two RIL populations. New markers were added to these intervals to detect QTLs with narrow confidential intervals. Results obtained in this study may facilitate future genomic researches such as QTL study, fine mapping, positional cloning and marker-assisted selection (MAS) in peanut.

  9. A map of copy number variations in Chinese populations.

    Directory of Open Access Journals (Sweden)

    Haiyi Lou

    Full Text Available It has been shown that the human genome contains extensive copy number variations (CNVs. Investigating the medical and evolutionary impacts of CNVs requires the knowledge of locations, sizes and frequency distribution of them within and between populations. However, CNV study of Chinese minorities, which harbor the majority of genetic diversity of Chinese populations, has been underrepresented considering the same efforts in other populations. Here we constructed, to our knowledge, a first CNV map in seven Chinese populations representing the major linguistic groups in China with 1,440 CNV regions identified using Affymetrix SNP 6.0 Array. Considerable differences in distributions of CNV regions between populations and substantial population structures were observed. We showed that ∼35% of CNV regions identified in minority ethnic groups are not shared by Han Chinese population, indicating that the contribution of the minorities to genetic architecture of Chinese population could not be ignored. We further identified highly differentiated CNV regions between populations. For example, a common deletion in Dong and Zhuang (44.4% and 50%, which overlaps two keratin-associated protein genes contributing to the structure of hair fibers, was not observed in Han Chinese. Interestingly, the most differentiated CNV deletion between HapMap CEU and YRI containing CCL3L1 gene reported in previous studies was also the highest differentiated regions between Tibetan and other populations. Besides, by jointly analyzing CNVs and SNPs, we found a CNV region containing gene CTDSPL were in almost perfect linkage disequilibrium between flanking SNPs in Tibetan while not in other populations except HapMap CHD. Furthermore, we found the SNP taggability of CNVs in Chinese populations was much lower than that in European populations. Our results suggest the necessity of a full characterization of CNVs in Chinese populations, and the CNV map we constructed serves as a

  10. A Map of Copy Number Variations in Chinese Populations

    Science.gov (United States)

    Yang, Yajun; Kang, Longli; Zhang, Xin; Jin, Wenfei; Wu, Bailin; Jin, Li; Xu, Shuhua

    2011-01-01

    It has been shown that the human genome contains extensive copy number variations (CNVs). Investigating the medical and evolutionary impacts of CNVs requires the knowledge of locations, sizes and frequency distribution of them within and between populations. However, CNV study of Chinese minorities, which harbor the majority of genetic diversity of Chinese populations, has been underrepresented considering the same efforts in other populations. Here we constructed, to our knowledge, a first CNV map in seven Chinese populations representing the major linguistic groups in China with 1,440 CNV regions identified using Affymetrix SNP 6.0 Array. Considerable differences in distributions of CNV regions between populations and substantial population structures were observed. We showed that ∼35% of CNV regions identified in minority ethnic groups are not shared by Han Chinese population, indicating that the contribution of the minorities to genetic architecture of Chinese population could not be ignored. We further identified highly differentiated CNV regions between populations. For example, a common deletion in Dong and Zhuang (44.4% and 50%), which overlaps two keratin-associated protein genes contributing to the structure of hair fibers, was not observed in Han Chinese. Interestingly, the most differentiated CNV deletion between HapMap CEU and YRI containing CCL3L1 gene reported in previous studies was also the highest differentiated regions between Tibetan and other populations. Besides, by jointly analyzing CNVs and SNPs, we found a CNV region containing gene CTDSPL were in almost perfect linkage disequilibrium between flanking SNPs in Tibetan while not in other populations except HapMap CHD. Furthermore, we found the SNP taggability of CNVs in Chinese populations was much lower than that in European populations. Our results suggest the necessity of a full characterization of CNVs in Chinese populations, and the CNV map we constructed serves as a useful resource in

  11. Integrating population dynamics into mapping human exposure to seismic hazard

    Directory of Open Access Journals (Sweden)

    S. Freire

    2012-11-01

    Full Text Available Disaster risk is not fully characterized without taking into account vulnerability and population exposure. Assessment of earthquake risk in urban areas would benefit from considering the variation of population distribution at more detailed spatial and temporal scales, and from a more explicit integration of this improved demographic data with existing seismic hazard maps. In the present work, "intelligent" dasymetric mapping is used to model population dynamics at high spatial resolution in order to benefit the analysis of spatio-temporal exposure to earthquake hazard in a metropolitan area. These night- and daytime-specific population densities are then classified and combined with seismic intensity levels to derive new spatially-explicit four-class-composite maps of human exposure. The presented approach enables a more thorough assessment of population exposure to earthquake hazard. Results show that there are significantly more people potentially at risk in the daytime period, demonstrating the shifting nature of population exposure in the daily cycle and the need to move beyond conventional residence-based demographic data sources to improve risk analyses. The proposed fine-scale maps of human exposure to seismic intensity are mainly aimed at benefiting visualization and communication of earthquake risk, but can be valuable in all phases of the disaster management process where knowledge of population densities is relevant for decision-making.

  12. Environmental DNA mapping of Zebra Mussel populations

    Science.gov (United States)

    Amberg, Jon J.; Merkes, Christopher

    2016-01-01

    Environmental DNA (eDNA) has become a popular tool for detecting aquatic invasive species, but advancements have made it possible to potentially answer other questions like reproduction, movement, and abundance of the targeted organism. In this study we developed a Zebra Mussel (Dreissena polymorpha) eDNA protocol. We then determined if this assay could be used to help determine Zebra Mussel biomass in a lake with a well-established population of Zebra Mussels and a lake with an emerging population of mussels. Our eDNA assay detected DNA of Zebra Mussels but not DNA from more than 20 other species of fish and mussels, many commonly found in Minnesota waters. Our assay did not predict biomass. We did find that DNA from Zebra Mussels accumulated in softer substrates in both lakes, even though the mussels were predominately on the harder substrates. Therefore, we concluded that eDNA may be useful to detect the presence of Zebra Mussels in these lakes but our assay/approach could not predict biomass.

  13. IDENTIFICATION AND MAPPING OF A GENE FOR RICE SLENDER KERNEL USING Oryza glumaepatula INTROGRESSION LINES

    Directory of Open Access Journals (Sweden)

    Sobrizal Sobrizal

    2016-10-01

    Full Text Available World demand for superior rice grain quality tends to increase. One of the  criteria of appearance quality of rice grain is grain shape. Rice consumers  exhibit wide preferences for grain shape, but most Indonesian rice consumers prefer long and slender grain. The objectives of this study were to identify and map a gene for rice slender kernel trait using Oryza  glumaepatula introgression lines with O. sativa cv. Taichung 65 genetic background. A segregation analysis of BC4F2 population derived from backcrosses of a donor parent O. glumaepatula into a recurrent parent Taichung 65 showed that the slender kernel was controlled by a single recessive gene. This new identified gene was designated as sk1 (slender kernel 1. Moreover, based on the RFLP analyses using 14 RFLP markers located on chromosomes 2, 8, 9, and 10 in which the O. glumaepatula chromosomal segments were retained in BC4F2 population, the sk1 was located between RFLP markers C679 and C560 on the long arm of chromosome 2, with map distances of 2.8 and 1.5 cM, respectively. The wild rice O. glumaepatula carried a recessive allele for slender kernel. This allele may be useful in breeding of rice with slender kernel types. In addition, the development of plant materials and RFLP map associated with slender kernel in this study is the preliminary works in the effort to isolate this important grain shape gene.

  14. Mapping QTLs controlling kernel dimensions in a wheat inter-varietal RIL mapping population.

    Science.gov (United States)

    Cheng, Ruiru; Kong, Zhongxin; Zhang, Liwei; Xie, Quan; Jia, Haiyan; Yu, Dong; Huang, Yulong; Ma, Zhengqiang

    2017-07-01

    Seven kernel dimension QTLs were identified in wheat, and kernel thickness was found to be the most important dimension for grain weight improvement. Kernel morphology and weight of wheat (Triticum aestivum L.) affect both yield and quality; however, the genetic basis of these traits and their interactions has not been fully understood. In this study, to investigate the genetic factors affecting kernel morphology and the association of kernel morphology traits with kernel weight, kernel length (KL), width (KW) and thickness (KT) were evaluated, together with hundred-grain weight (HGW), in a recombinant inbred line population derived from Nanda2419 × Wangshuibai, with data from five trials (two different locations over 3 years). The results showed that HGW was more closely correlated with KT and KW than with KL. A whole genome scan revealed four QTLs for KL, one for KW and two for KT, distributed on five different chromosomes. Of them, QKl.nau-2D for KL, and QKt.nau-4B and QKt.nau-5A for KT were newly identified major QTLs for the respective traits, explaining up to 32.6 and 41.5% of the phenotypic variations, respectively. Increase of KW and KT and reduction of KL/KT and KW/KT ratios always resulted in significant higher grain weight. Lines combining the Nanda 2419 alleles of the 4B and 5A intervals had wider, thicker, rounder kernels and a 14% higher grain weight in the genotype-based analysis. A strong, negative linear relationship of the KW/KT ratio with grain weight was observed. It thus appears that kernel thickness is the most important kernel dimension factor in wheat improvement for higher yield. Mapping and marker identification of the kernel dimension-related QTLs definitely help realize the breeding goals.

  15. Nebular Continuum and Line Emission in Stellar Population Synthesis Models

    Energy Technology Data Exchange (ETDEWEB)

    Byler, Nell; Dalcanton, Julianne J. [Department of Astronomy, University of Washington, Box 351580, Seattle, WA 98195 (United States); Conroy, Charlie; Johnson, Benjamin D., E-mail: ebyler@astro.washington.edu [Department of Astronomy, Harvard University, Cambridge, MA 02138 (United States)

    2017-05-01

    Accounting for nebular emission when modeling galaxy spectral energy distributions (SEDs) is important, as both line and continuum emissions can contribute significantly to the total observed flux. In this work, we present a new nebular emission model integrated within the Flexible Stellar Population Synthesis code that computes the line and continuum emission for complex stellar populations using the photoionization code Cloudy. The self-consistent coupling of the nebular emission to the matched ionizing spectrum produces emission line intensities that correctly scale with the stellar population as a function of age and metallicity. This more complete model of galaxy SEDs will improve estimates of global gas properties derived with diagnostic diagrams, star formation rates based on H α , and physical properties derived from broadband photometry. Our models agree well with results from other photoionization models and are able to reproduce observed emission from H ii regions and star-forming galaxies. Our models show improved agreement with the observed H ii regions in the Ne iii/O ii plane and show satisfactory agreement with He ii emission from z = 2 galaxies, when including rotating stellar models. Models including post-asymptotic giant branch stars are able to reproduce line ratios consistent with low-ionization emission regions. The models are integrated into current versions of FSPS and include self-consistent nebular emission predictions for MIST and Padova+Geneva evolutionary tracks.

  16. Effect of small mapping population sizes on reliability of quantitative ...

    African Journals Online (AJOL)

    A limitation of quantitative trait loci (QTL) mapping is that accuracy of determining QTL position and effects are largely determined by population size. Despite the importance of this concept, known as the "Beavis effect there has generally been a lack of understanding by molecular geneticists and breeders. One possible ...

  17. Long-distance pulse propagation on high-frequency dissipative nonlinear transmission lines/resonant tunneling diode line cascaded maps

    International Nuclear Information System (INIS)

    Klofai, Yerima; Essimbi, B Z; Jaeger, D

    2011-01-01

    Pulse propagation on high-frequency dissipative nonlinear transmission lines (NLTLs)/resonant tunneling diode line cascaded maps is investigated for long-distance propagation of short pulses. Applying perturbative analysis, we show that the dynamics of each line is reduced to an expanded Korteweg-de Vries-Burgers equation. Moreover, it is found by computer experiments that the soliton developed in NLTLs experiences an exponential amplitude decay on the one hand and an exponential amplitude growth on the other. As a result, the behavior of a pulse in special electrical networks made of concatenated pieces of lines is closely similar to the transmission of information in optical/electrical communication systems.

  18. Long-distance pulse propagation on high-frequency dissipative nonlinear transmission lines/resonant tunneling diode line cascaded maps

    Energy Technology Data Exchange (ETDEWEB)

    Klofai, Yerima [Department of Physics, Higher Teacher Training College, University of Maroua, PO Box 46 Maroua (Cameroon); Essimbi, B Z [Department of Physics, Faculty of Science, University of Yaounde 1, PO Box 812 Yaounde (Cameroon); Jaeger, D, E-mail: bessimb@yahoo.fr [ZHO, Optoelectronik, Universitaet Duisburg-Essen, D-47048 Duisburg (Germany)

    2011-10-15

    Pulse propagation on high-frequency dissipative nonlinear transmission lines (NLTLs)/resonant tunneling diode line cascaded maps is investigated for long-distance propagation of short pulses. Applying perturbative analysis, we show that the dynamics of each line is reduced to an expanded Korteweg-de Vries-Burgers equation. Moreover, it is found by computer experiments that the soliton developed in NLTLs experiences an exponential amplitude decay on the one hand and an exponential amplitude growth on the other. As a result, the behavior of a pulse in special electrical networks made of concatenated pieces of lines is closely similar to the transmission of information in optical/electrical communication systems.

  19. Approaches in Characterizing Genetic Structure and Mapping in a Rice Multiparental Population.

    Science.gov (United States)

    Raghavan, Chitra; Mauleon, Ramil; Lacorte, Vanica; Jubay, Monalisa; Zaw, Hein; Bonifacio, Justine; Singh, Rakesh Kumar; Huang, B Emma; Leung, Hei

    2017-06-07

    Multi-parent Advanced Generation Intercross (MAGIC) populations are fast becoming mainstream tools for research and breeding, along with the technology and tools for analysis. This paper demonstrates the analysis of a rice MAGIC population from data filtering to imputation and processing of genetic data to characterizing genomic structure, and finally quantitative trait loci (QTL) mapping. In this study, 1316 S6:8 indica MAGIC (MI) lines and the eight founders were sequenced using Genotyping by Sequencing (GBS). As the GBS approach often includes missing data, the first step was to impute the missing SNPs. The observable number of recombinations in the population was then explored. Based on this case study, a general outline of procedures for a MAGIC analysis workflow is provided, as well as for QTL mapping of agronomic traits and biotic and abiotic stress, using the results from both association and interval mapping approaches. QTL for agronomic traits (yield, flowering time, and plant height), physical (grain length and grain width) and cooking properties (amylose content) of the rice grain, abiotic stress (submergence tolerance), and biotic stress (brown spot disease) were mapped. Through presenting this extensive analysis in the MI population in rice, we highlight important considerations when choosing analytical approaches. The methods and results reported in this paper will provide a guide to future genetic analysis methods applied to multi-parent populations. Copyright © 2017 Raghavan et al.

  20. Approaches in Characterizing Genetic Structure and Mapping in a Rice Multiparental Population

    Directory of Open Access Journals (Sweden)

    Chitra Raghavan

    2017-06-01

    Full Text Available Multi-parent Advanced Generation Intercross (MAGIC populations are fast becoming mainstream tools for research and breeding, along with the technology and tools for analysis. This paper demonstrates the analysis of a rice MAGIC population from data filtering to imputation and processing of genetic data to characterizing genomic structure, and finally quantitative trait loci (QTL mapping. In this study, 1316 S6:8 indica MAGIC (MI lines and the eight founders were sequenced using Genotyping by Sequencing (GBS. As the GBS approach often includes missing data, the first step was to impute the missing SNPs. The observable number of recombinations in the population was then explored. Based on this case study, a general outline of procedures for a MAGIC analysis workflow is provided, as well as for QTL mapping of agronomic traits and biotic and abiotic stress, using the results from both association and interval mapping approaches. QTL for agronomic traits (yield, flowering time, and plant height, physical (grain length and grain width and cooking properties (amylose content of the rice grain, abiotic stress (submergence tolerance, and biotic stress (brown spot disease were mapped. Through presenting this extensive analysis in the MI population in rice, we highlight important considerations when choosing analytical approaches. The methods and results reported in this paper will provide a guide to future genetic analysis methods applied to multi-parent populations.

  1. Single-molecule optical genome mapping of a human HapMap and a colorectal cancer cell line.

    Science.gov (United States)

    Teo, Audrey S M; Verzotto, Davide; Yao, Fei; Nagarajan, Niranjan; Hillmer, Axel M

    2015-01-01

    Next-generation sequencing (NGS) technologies have changed our understanding of the variability of the human genome. However, the identification of genome structural variations based on NGS approaches with read lengths of 35-300 bases remains a challenge. Single-molecule optical mapping technologies allow the analysis of DNA molecules of up to 2 Mb and as such are suitable for the identification of large-scale genome structural variations, and for de novo genome assemblies when combined with short-read NGS data. Here we present optical mapping data for two human genomes: the HapMap cell line GM12878 and the colorectal cancer cell line HCT116. High molecular weight DNA was obtained by embedding GM12878 and HCT116 cells, respectively, in agarose plugs, followed by DNA extraction under mild conditions. Genomic DNA was digested with KpnI and 310,000 and 296,000 DNA molecules (≥ 150 kb and 10 restriction fragments), respectively, were analyzed per cell line using the Argus optical mapping system. Maps were aligned to the human reference by OPTIMA, a new glocal alignment method. Genome coverage of 6.8× and 5.7× was obtained, respectively; 2.9× and 1.7× more than the coverage obtained with previously available software. Optical mapping allows the resolution of large-scale structural variations of the genome, and the scaffold extension of NGS-based de novo assemblies. OPTIMA is an efficient new alignment method; our optical mapping data provide a resource for genome structure analyses of the human HapMap reference cell line GM12878, and the colorectal cancer cell line HCT116.

  2. The Genetic Basis of Plant Architecture in 10 Maize Recombinant Inbred Line Populations.

    Science.gov (United States)

    Pan, Qingchun; Xu, Yuancheng; Li, Kun; Peng, Yong; Zhan, Wei; Li, Wenqiang; Li, Lin; Yan, Jianbing

    2017-10-01

    Plant architecture is a key factor affecting planting density and grain yield in maize ( Zea mays ). However, the genetic mechanisms underlying plant architecture in diverse genetic backgrounds have not been fully addressed. Here, we performed a large-scale phenotyping of 10 plant architecture-related traits and dissected the genetic loci controlling these traits in 10 recombinant inbred line populations derived from 14 diverse genetic backgrounds. Nearly 800 quantitative trait loci (QTLs) with major and minor effects were identified as contributing to the phenotypic variation of plant architecture-related traits. Ninety-two percent of these QTLs were detected in only one population, confirming the diverse genetic backgrounds of the mapping populations and the prevalence of rare alleles in maize. The numbers and effects of QTLs are positively associated with the phenotypic variation in the population, which, in turn, correlates positively with parental phenotypic and genetic variations. A large proportion (38.5%) of QTLs was associated with at least two traits, suggestive of the frequent occurrence of pleiotropic loci or closely linked loci. Key developmental genes, which previously were shown to affect plant architecture in mutant studies, were found to colocalize with many QTLs. Five QTLs were further validated using the segregating populations developed from residual heterozygous lines present in the recombinant inbred line populations. Additionally, one new plant height QTL, qPH3 , has been fine-mapped to a 600-kb genomic region where three candidate genes are located. These results provide insights into the genetic mechanisms controlling plant architecture and will benefit the selection of ideal plant architecture in maize breeding. © 2017 American Society of Plant Biologists. All Rights Reserved.

  3. Population structure and linkage disequilibrium in Lupinus albus L. germplasm and its implication for association mapping.

    Science.gov (United States)

    Iqbal, Muhammad Javed; Mamidi, Sujan; Ahsan, Rubina; Kianian, Shahryar F; Coyne, Clarice J; Hamama, Anwar A; Narina, Satya S; Bhardwaj, Harbans L

    2012-08-01

    White lupin (Lupinus albus L.) has been around since 300 B.C. and is recognized for its ability to grow on poor soils and application as green manure in addition to seed harvest. The seed has very high levels of protein (33-47 %) and oil (6-13 %). It also has many secondary metabolites that are potentially of nutraceutical value to animals and humans. Despite such a great potential, lupins role in modern agriculture began only in the twentieth century. Although a large collection of Lupinus germplasm accessions is available worldwide, rarely have they been genetically characterized. Additionally, scarce genomic resources in terms of recombinant populations and genome information have been generated for L. albus. With the advancement in association mapping methods, the natural populations have the potential to replace the recombinant populations in gene mapping and marker-trait associations. Therefore, we studied the genetic similarity, population structure and marker-trait association in a USDA germplasm collection for their current and future application in this crop improvement. A total of 122 PI (Plant Inventory) lines were screened with 18 AFLP primer pairs that generated 2,277 fragments. A subset of 892 polymorphic markers with MAF >0.05 (minor allele frequency) were used for association mapping. The cluster analysis failed to group accessions on the basis of their passport information, and a weak structure and low linkage disequilibrium (LD) were observed indicating the usefulness of the collection for association mapping. Moreover, we were also able to identify two markers (a p value of 1.53 × 10(-4) and 2.3 × 10(-4)) that explained 22.69 and 20.5 % of seed weight variation determined using R (LR) (2) . The implications of lack of geographic clustering, population structure, low LD and the ability of AFLP to map seed weight trait using association mapping and the usefulness of the PI collections in breeding programs are discussed.

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

    Indian Academy of Sciences (India)

    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  ...

  5. Molecular mapping and improvement of leaf rust resistance in wheat breeding lines.

    Science.gov (United States)

    Tsilo, Toi J; Kolmer, James A; Anderson, James A

    2014-08-01

    Leaf rust, caused by Puccinia triticina, is the most common and widespread disease of wheat (Triticum aestivum) worldwide. Deployment of host-plant resistance is one of the strategies to reduce losses due to leaf rust disease. The objective of this study was to map genes for adult-plant resistance to leaf rust in a recombinant inbred line (RIL) population originating from MN98550-5/MN99394-1. The mapping population of 139 RILs and five checks were evaluated in 2005, 2009, and 2010 in five environments. Natural infection occurred in the 2005 trials and trials in 2009 and 2010 were inoculated with leaf rust. Four quantitative trait loci (QTL) on chromosomes 2BS, 2DS, 7AL, and 7DS were detected. The QTL on 2BS explained up to 33.6% of the phenotypic variation in leaf rust response, whereas the QTL on 2DS, 7AL, and 7DS explained up to 15.7, 8.1, and 34.2%, respectively. Seedling infection type tests conducted with P. triticina races BBBD and SBDG confirmed that the QTL on 2BS and 2DS were Lr16 and Lr2a, respectively, and these genes were expressed in the seedling and field plot tests. The Lr2a gene mapped at the same location as Sr6. The QTL on 7DS was Lr34. The QTL on 7AL is a new QTL for leaf rust resistance. The joint effects of all four QTL explained 74% of the total phenotypic variation in leaf rust severity. Analysis of different combinations of QTL showed that the RILs containing all four or three of the QTL had the lowest average leaf rust severity in all five environments. Deployment of these QTL in combination or with other effective genes will lead to successful control of leaf rust.

  6. On Line Segment Length and Mapping 4-regular Grid Structures in Network Infrastructures

    DEFF Research Database (Denmark)

    Riaz, Muhammad Tahir; Nielsen, Rasmus Hjorth; Pedersen, Jens Myrup

    2006-01-01

    The paper focuses on mapping the road network into 4-regular grid structures. A mapping algorithm is proposed. To model the road network GIS data have been used. The Geographic Information System (GIS) data for the road network are composed with different size of line segment lengths...

  7. Estimating and mapping the population at risk of sleeping sickness.

    Directory of Open Access Journals (Sweden)

    Pere P Simarro

    Full Text Available Human African trypanosomiasis (HAT, also known as sleeping sickness, persists as a public health problem in several sub-Saharan countries. Evidence-based, spatially explicit estimates of population at risk are needed to inform planning and implementation of field interventions, monitor disease trends, raise awareness and support advocacy. Comprehensive, geo-referenced epidemiological records from HAT-affected countries were combined with human population layers to map five categories of risk, ranging from "very high" to "very low," and to estimate the corresponding at-risk population.Approximately 70 million people distributed over a surface of 1.55 million km(2 are estimated to be at different levels of risk of contracting HAT. Trypanosoma brucei gambiense accounts for 82.2% of the population at risk, the remaining 17.8% being at risk of infection from T. b. rhodesiense. Twenty-one million people live in areas classified as moderate to very high risk, where more than 1 HAT case per 10,000 inhabitants per annum is reported.Updated estimates of the population at risk of sleeping sickness were made, based on quantitative information on the reported cases and the geographic distribution of human population. Due to substantial methodological differences, it is not possible to make direct comparisons with previous figures for at-risk population. By contrast, it will be possible to explore trends in the future. The presented maps of different HAT risk levels will help to develop site-specific strategies for control and surveillance, and to monitor progress achieved by ongoing efforts aimed at the elimination of sleeping sickness.

  8. Solar monochromatic images in magneto-sensitive spectral lines and maps of vector magnetic fields

    Science.gov (United States)

    Shihui, Y.; Jiehai, J.; Minhan, J.

    1985-01-01

    A new method which allows by use of the monochromatic images in some magneto-sensitive spectra line to derive both the magnetic field strength as well as the angle between magnetic field lines and line of sight for various places in solar active regions is described. In this way two dimensional maps of vector magnetic fields may be constructed. This method was applied to some observational material and reasonable results were obtained. In addition, a project for constructing the three dimensional maps of vector magnetic fields was worked out.

  9. An integrated genetic map based on four mapping populations and quantitative trait loci associated with economically important traits in watermelon (Citrullus lanatus)

    Science.gov (United States)

    2014-01-01

    Background Modern watermelon (Citrullus lanatus L.) cultivars share a narrow genetic base due to many years of selection for desirable horticultural qualities. Wild subspecies within C. lanatus are important potential sources of novel alleles for watermelon breeding, but successful trait introgression into elite cultivars has had limited success. The application of marker assisted selection (MAS) in watermelon is yet to be realized, mainly due to the past lack of high quality genetic maps. Recently, a number of useful maps have become available, however these maps have few common markers, and were constructed using different marker sets, thus, making integration and comparative analysis among maps difficult. The objective of this research was to use single-nucleotide polymorphism (SNP) anchor markers to construct an integrated genetic map for C. lanatus. Results Under the framework of the high density genetic map, an integrated genetic map was constructed by merging data from four independent mapping experiments using a genetically diverse array of parental lines, which included three subspecies of watermelon. The 698 simple sequence repeat (SSR), 219 insertion-deletion (InDel), 36 structure variation (SV) and 386 SNP markers from the four maps were used to construct an integrated map. This integrated map contained 1339 markers, spanning 798 cM with an average marker interval of 0.6 cM. Fifty-eight previously reported quantitative trait loci (QTL) for 12 traits in these populations were also integrated into the map. In addition, new QTL identified for brix, fructose, glucose and sucrose were added. Some QTL associated with economically important traits detected in different genetic backgrounds mapped to similar genomic regions of the integrated map, suggesting that such QTL are responsible for the phenotypic variability observed in a broad array of watermelon germplasm. Conclusions The integrated map described herein enhances the utility of genomic tools over

  10. An integrated genetic map based on four mapping populations and quantitative trait loci associated with economically important traits in watermelon (Citrullus lanatus).

    Science.gov (United States)

    Ren, Yi; McGregor, Cecilia; Zhang, Yan; Gong, Guoyi; Zhang, Haiying; Guo, Shaogui; Sun, Honghe; Cai, Wantao; Zhang, Jie; Xu, Yong

    2014-01-20

    Modern watermelon (Citrullus lanatus L.) cultivars share a narrow genetic base due to many years of selection for desirable horticultural qualities. Wild subspecies within C. lanatus are important potential sources of novel alleles for watermelon breeding, but successful trait introgression into elite cultivars has had limited success. The application of marker assisted selection (MAS) in watermelon is yet to be realized, mainly due to the past lack of high quality genetic maps. Recently, a number of useful maps have become available, however these maps have few common markers, and were constructed using different marker sets, thus, making integration and comparative analysis among maps difficult. The objective of this research was to use single-nucleotide polymorphism (SNP) anchor markers to construct an integrated genetic map for C. lanatus. Under the framework of the high density genetic map, an integrated genetic map was constructed by merging data from four independent mapping experiments using a genetically diverse array of parental lines, which included three subspecies of watermelon. The 698 simple sequence repeat (SSR), 219 insertion-deletion (InDel), 36 structure variation (SV) and 386 SNP markers from the four maps were used to construct an integrated map. This integrated map contained 1339 markers, spanning 798 cM with an average marker interval of 0.6 cM. Fifty-eight previously reported quantitative trait loci (QTL) for 12 traits in these populations were also integrated into the map. In addition, new QTL identified for brix, fructose, glucose and sucrose were added. Some QTL associated with economically important traits detected in different genetic backgrounds mapped to similar genomic regions of the integrated map, suggesting that such QTL are responsible for the phenotypic variability observed in a broad array of watermelon germplasm. The integrated map described herein enhances the utility of genomic tools over previous watermelon genetic maps. A

  11. Identification and evaluation of resistance to powdery mildew and yellow rust in a wheat mapping population.

    Directory of Open Access Journals (Sweden)

    Lijun Yang

    Full Text Available Deployment of cultivars with genetic resistance is an effective approach to control the diseases of powdery mildew (PM and yellow rust (YR. Chinese wheat cultivar XK0106 exhibits high levels of resistance to both diseases, while cultivar E07901 has partial, adult plant resistance (APR. The aim of this study was to map resistance loci derived from the two cultivars and analyze their effects against PM and YR in a range of environments. A doubled haploid population (388 lines was used to develop a framework map consisting of 117 SSR markers, while a much higher density map using the 90K Illumina iSelect SNP array was produced with a subset of 80 randomly selected lines. Seedling resistance was characterized against a range of PM and YR isolates, while field scores in multiple environments were used to characterize APR. Composite interval mapping (CIM of seedling PM scores identified two QTLs (QPm.haas-6A and QPm.haas-2A, the former being located at the Pm21 locus. These QTLs were also significant in field scores, as were Qpm.haas-3A and QPm.haas-5A. QYr.haas-1B-1 and QYr.haas-2A were identified in field scores of YR and were located at the Yr24/26 and Yr17 chromosomal regions respectively. A second 1B QTL, QYr.haas-1B-2 was also identified. QPm.haas-2A and QYr.haas-1B-2 are likely to be new QTLs that have not been previously identified. Effects of the QTLs were further investigated in multiple environments through the testing of selected lines predicted to contain various QTL combinations. Significant additive interactions between the PM QTLs highlighted the ability to pyramid these loci to provide higher level of resistance. Interactions between the YR QTLs gave insights into the pathogen populations in the different locations as well as showing genetic interactions between these loci.

  12. Genomic Dissection of Leaf Angle in Maize (Zea mays L. Using a Four-Way Cross Mapping Population.

    Directory of Open Access Journals (Sweden)

    Junqiang Ding

    Full Text Available Increasing grain yield by the selection for optimal plant architecture has been the key focus in modern maize breeding. As a result, leaf angle, an important determinant of plant architecture, has been significantly improved to adapt to the ever-increasing plant density in maize production over the past several decades. To extend our understanding on the genetic mechanisms of leaf angle in maize, we developed the first four-way cross mapping population, consisting of 277 lines derived from four maize inbred lines with varied leaf angles. The four-way cross mapping population together with the four parental lines were evaluated for leaf angle in two environments. In this study, we reported linkage maps built in the population and quantitative trait loci (QTL on leaf angle detected by inclusive composite interval mapping (ICIM. ICIM applies a two-step strategy to effectively separate the cofactor selection from the interval mapping, which controls the background additive and dominant effects at the same time. A total of 14 leaf angle QTL were identified, four of which were further validated in near-isogenic lines (NILs. Seven of the 14 leaf angle QTL were found to overlap with the published leaf angle QTL or genes, and the remaining QTL were unique to the four-way population. This study represents the first example of QTL mapping using a four-way cross population in maize, and demonstrates that the use of specially designed four-way cross is effective in uncovering the basis of complex and polygenetic trait like leaf angle in maize.

  13. Genetic loci mapping for ear axis weight using recombinant inbred line

    African Journals Online (AJOL)

    Jane

    2011-08-08

    Aug 8, 2011 ... mays L.) ear-related traits were concentrated on yield per ... but the studies on using different N environments to map. QTL for .... ANOVA of the RIL population on EAW under two N regimes. ... (2007), but our study was different from theirs in many ... Mapping QTLs for grain yield and yield components under.

  14. Regional analysis assessment of landslide hazard and zoning map for transmission line route selection using GIS

    International Nuclear Information System (INIS)

    Baharuddin, I N Z; Omar, R C; Usman, F; Mejan, M A; Halim, M K Abd; Zainol, M A; Zulkarnain, M S

    2013-01-01

    The stability of ground as foundation for infrastructure development is always associated with geology and geomorphology aspects. Failure to carefully analyze these aspects may induce ground instability such subsidence and landslide which eventually can cause catastrophe to the infrastructure i.e. instability of transmission tower. However, in some cases such as the study area this is unavoidable. A GIS system for analysis of route was favoured to perform optimal route predictions based selection by incorporating multiple influence factors into its analysis by incorporating the Landslide Hazard Map (LHM) that was produced on basis of slope map, aspect map, land use map and geological map with the help of ArcGIS using weighted overlay method. Based on LHM it is safe to conclude that the proposed route for Ulu Jelai- Neggiri-Lebir-LILO transmission line has very low risk in term of landslides.

  15. Ultrasound line-by-line scanning method of spatial-temporal active cavitation mapping for high-intensity focused ultrasound.

    Science.gov (United States)

    Ding, Ting; Zhang, Siyuan; Fu, Quanyou; Xu, Zhian; Wan, Mingxi

    2014-01-01

    This paper presented an ultrasound line-by-line scanning method of spatial-temporal active cavitation mapping applicable in a liquid or liquid filled tissue cavities exposed by high-intensity focused ultrasound (HIFU). Scattered signals from cavitation bubbles were obtained in a scan line immediately after one HIFU exposure, and then there was a waiting time of 2 s long enough to make the liquid back to the original state. As this pattern extended, an image was built up by sequentially measuring a series of such lines. The acquisition of the beamformed radiofrequency (RF) signals for a scan line was synchronized with HIFU exposure. The duration of HIFU exposure, as well as the delay of the interrogating pulse relative to the moment while HIFU was turned off, could vary from microseconds to seconds. The feasibility of this method was demonstrated in tap-water and a tap-water filled cavity in the tissue-mimicking gelatin-agar phantom as capable of observing temporal evolutions of cavitation bubble cloud with temporal resolution of several microseconds, lateral and axial resolution of 0.50 mm and 0.29 mm respectively. The dissolution process of cavitation bubble cloud and spatial distribution affected by cavitation previously generated were also investigated. Although the application is limited by the requirement for a gassy fluid (e.g. tap water, etc.) that allows replenishment of nuclei between HIFU exposures, the technique may be a useful tool in spatial-temporal cavitation mapping for HIFU with high precision and resolution, providing a reference for clinical therapy. Copyright © 2013 Elsevier B.V. All rights reserved.

  16. A new set of BXD recombinant inbred lines from advanced intercross populations in mice

    Directory of Open Access Journals (Sweden)

    Gu Jing

    2004-04-01

    Full Text Available Abstract Background Recombinant inbred (RI strains are an important resource for mapping complex traits in many species. While large RI panels are available for Arabidopsis, maize, C. elegans, and Drosophila, mouse RI panels typically consist of fewer than 30 lines. This is a severe constraint on the power and precision of mapping efforts and greatly hampers analysis of epistatic interactions. Results In order to address these limitations and to provide the community with a more effective collaborative RI mapping panel we generated new BXD RI strains from two independent advanced intercrosses (AI between C57BL/6J (B6 and DBA/2J (D2 progenitor strains. Progeny were intercrossed for 9 to 14 generations before initiating inbreeding, which is still ongoing for some strains. Since this AI base population is highly recombinant, the 46 advanced recombinant inbred (ARI strains incorporate approximately twice as many recombinations as standard RI strains, a fraction of which are inevitably shared by descent. When combined with the existing BXD RI strains, the merged BXD strain set triples the number of previously available unique recombinations and quadruples the total number of recombinations in the BXD background. Conclusion The combined BXD strain set is the largest mouse RI mapping panel. It is a powerful tool for collaborative analysis of quantitative traits and gene function that will be especially useful to study variation in transcriptome and proteome data sets under multiple environments. Additional strains also extend the value of the extensive phenotypic characterization of the previously available strains. A final advantage of expanding the BXD strain set is that both progenitors have been sequenced, and approximately 1.8 million SNPs have been characterized. This provides unprecedented power in screening candidate genes and can reduce the effective length of QTL intervals. It also makes it possible to reverse standard mapping strategies and

  17. Dissecting genomic hotspots underlying seed protein, oil, and sucrose content in an interspecific mapping population of soybean using high-density linkage mapping.

    Science.gov (United States)

    Patil, Gunvant; Vuong, Tri D; Kale, Sandip; Valliyodan, Babu; Deshmukh, Rupesh; Zhu, Chengsong; Wu, Xiaolei; Bai, Yonghe; Yungbluth, Dennis; Lu, Fang; Kumpatla, Siva; Grover Shannon, J; Varshney, Rajeev K; Nguyen, Henry T

    2018-04-04

    The cultivated [Glycine max (L) Merr.] and wild [Glycine soja Siebold & Zucc.] soybean species comprise wide variation in seed composition traits. Compared to wild soybean, cultivated soybean contains low protein, high oil and high sucrose. In this study, an inter-specific population was derived from a cross between G. max (Williams 82) and G. soja (PI 483460B). This recombinant inbred line (RIL) population of 188 lines was sequenced at 0.3x depth. Based on 91,342 single nucleotide polymorphisms (SNPs), recombination events in RILs were defined, and a high-resolution bin map was developed (4,070 bins). In addition to bin mapping, QTL analysis for protein, oil and sucrose was performed using 3,343 polymorphic SNPs (3K-SNP), derived from Illumina Infinium BeadChip sequencing platform. The QTL regions from both platforms were compared and a significant concordance was observed between bin and 3K-SNP markers. Importantly, the bin map derived from next generation sequencing technology enhanced mapping resolution (from 1325 Kb to 50 Kb). A total of 5, 9 and 4 QTLs were identified for protein, oil and sucrose content, respectively and some of the QTLs coincided with soybean domestication related genomic loci. The major QTL for protein and oil was mapped on Chr. 20 (qPro_20) and suggested negative correlation between oil and protein. In terms of sucrose content, a novel and major QTL was identified on Chr. 8 (qSuc_08) and harbors putative genes involved in sugar transport. In addition, genome-wide association (GWAS) using 91,342 SNPs confirmed the genomic loci derived from QTL mapping. A QTL based haplotype using whole genome resequencing of 106 diverse soybean lines identified unique allelic variation in wild soybean that could be utilized to widen the genetic base in cultivated soybean. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  18. Aerial image geolocalization by matching its line structure with route map

    Science.gov (United States)

    Kunina, I. A.; Terekhin, A. P.; Khanipov, T. M.; Kuznetsova, E. G.; Nikolaev, D. P.

    2017-03-01

    The classic way of aerial photographs geolocation is to bind their local coordinates to a geographic coordinate system using GPS and IMU data. At the same time the possibility of geolocation in a jammed navigation field is also of interest for practical purposes. In this paper we consider one approach to visual localization relatively to a vector road map without GPS. We suggest a geolocalization algorithm which detects image line segments and looks for a geometrical transformation which provides the best mapping between the obtained segments set and line segments in the road map. We consider IMU and altimeter data still known which allows to work with orthorectified images. The problem is hence reduced to a search for a transformation which contains an arbitrary shift and bounded rotation and scaling relatively to the vector map. These parameters are estimated using RANSAC by matching straight line segments from the image to vector map segments. We also investigate how the proposed algorithm's stability is influenced by segment coordinates (two spatial and one angular).

  19. On Line Neutron Flux Mapping in Fuel Coolant Channels of a Research Reactor

    International Nuclear Information System (INIS)

    Barbot, Loic; Domergue, Christophe; Villard, Jean-Francois; Destouches, Christophe; Braoudakis, George; Wassink, David; Sinclair, Bradley; Osborn, John-C.; Wu, Huayou; Blandin, C.; Thevenin, Mathieu; Corre, Gwenole; Normand, Stephane

    2013-06-01

    This work deals with the on-line neutron flux mapping of the OPAL research reactor. A specific irradiation device has been set up to investigate fuel coolant channels using subminiature fission chambers to get thermal neutron flux profiles. Experimental results are compared to first neutronic calculations and show good agreement (C/E ∼0.97). (authors)

  20. The SAURON project - VI. Line strength maps of 48 elliptical and lenticular galaxies

    NARCIS (Netherlands)

    Kuntschner, Harald; Emsellem, Eric; Bacon, R.; Bureau, M.; Cappellari, Michele; Davies, Roger L.; de Zeeuw, P. T.; Falcon-Barroso, Jesus; Krajnovic, Davor; McDermid, Richard M.; Peletier, Reynier F.; Sarzi, Marc

    2006-01-01

    We present absorption line strength maps of 48 representative elliptical and lenticular galaxies obtained as part of a survey of nearby galaxies using our custom-built integral-field spectrograph, SAURON, operating on the William Herschel Telescope. Using high-quality spectra, spatially binned to a

  1. Spitzer spectral line mapping of the HH211 outflow

    DEFF Research Database (Denmark)

    Dionatos, Odyssefs; Nisini, Brunella; Cabrit, Sylvie

    2010-01-01

    of emission line diagnostics and an existing grid of molecular shock models. The physical properties of the warm gas are compared against other molecular jet tracers and to the results of a similar study towards the L1448-C outflow. Results: We have detected and mapped the v=0-0 S(0) - S(7) H2 lines and fine...... compared to solar abundances by a factor ~10-50. Conclusions: Spitzer spectral mapping observations reveal for the first time a cool H$_2$ component towards the CO jet of HH211 consistent with the CO material being fully molecular and warm at ~ 300 K. The maps also reveal for the first time the existence...... uncertainties on jet speed and shock conditions are too large for a definite conclusion....

  2. Developmental and Architectural Principles of the Lateral-line Neural Map

    Directory of Open Access Journals (Sweden)

    Hernan eLopez-Schier

    2013-03-01

    Full Text Available The transmission and central representation of sensory cues through the accurate construction of neural maps is essential for animals to react to environmental stimuli. Structural diversity of sensorineural maps along a continuum between discrete- and continuous-map architectures can influence behavior. The mechanosensory lateral line of fishes and amphibians, for example, detects complex hydrodynamics occurring around the animal body. It. It triggers innate fast escape reactions but also modulates complex navigation behaviors that require constant knowledge about the environment. The aim of this article is to summarize recent work in the zebrafish that has shed light on the development and structure of the lateralis neural map, which is helping to understand how individual sensory modalities generate appropriate behavioral responses to the sensory context.

  3. Construction of chromosome segment substitution lines enables QTL mapping for flowering and morphological traits in Brassica rapa

    Directory of Open Access Journals (Sweden)

    Xiaonan eLi

    2015-06-01

    Full Text Available Chromosome segment substitution lines (CSSLs represent a powerful method for precise quantitative trait loci (QTL detection of complex agronomical traits in plants. In this study, we used a marker-assisted backcrossing strategy to develop a population consisting of 63 CSSLs, derived from backcrossing of the F1 generated from a cross between two Brassica rapa subspecies: ‘Chiifu’ (ssp. pekinensis, the Brassica A genome-represented line used as the donor, and ‘49caixin’ (ssp. parachinensis, a non-heading cultivar used as the recipient. The 63 CSSLs covered 87.95% of the B. rapa genome. Among them, 39 lines carried a single segment; 15 lines, two segments; and nine lines, three or more segments of the donor parent chromosomes. To verify the potential advantage of these CSSL lines, we used them to locate QTL for six morphology-related traits. A total of 58 QTL were located on eight chromosomes for all six traits: 17 for flowering time, 14 each for bolting time and plant height, 6 for plant diameter, 2 for leaf width, and 5 for flowering stalk diameter. Co-localized QTL were mainly distributed on eight genomic regions in A01, A02, A05, A06, A08, A09, and A10, present in the corresponding CSSLs. Moreover, new chromosomal fragments that harbored QTL were identified using the findings of previous studies. The CSSL population constructed in our study paves the way for fine mapping and cloning of candidate genes involved in late bolting, flowering, and plant architecture-related traits in B. rapa. Furthermore, it has great potential for future marker-aided gene/QTL pyramiding of other interesting traits in B. rapa breeding.

  4. Wild boar mapping using population-density statistics: From polygons to high resolution raster maps.

    Science.gov (United States)

    Pittiglio, Claudia; Khomenko, Sergei; Beltran-Alcrudo, Daniel

    2018-01-01

    The wild boar is an important crop raider as well as a reservoir and agent of spread of swine diseases. Due to increasing densities and expanding ranges worldwide, the related economic losses in livestock and agricultural sectors are significant and on the rise. Its management and control would strongly benefit from accurate and detailed spatial information on species distribution and abundance, which are often available only for small areas. Data are commonly available at aggregated administrative units with little or no information about the distribution of the species within the unit. In this paper, a four-step geostatistical downscaling approach is presented and used to disaggregate wild boar population density statistics from administrative units of different shape and size (polygons) to 5 km resolution raster maps by incorporating auxiliary fine scale environmental variables. 1) First a stratification method was used to define homogeneous bioclimatic regions for the analysis; 2) Under a geostatistical framework, the wild boar densities at administrative units, i.e. subnational areas, were decomposed into trend and residual components for each bioclimatic region. Quantitative relationships between wild boar data and environmental variables were estimated through multiple regression and used to derive trend components at 5 km spatial resolution. Next, the residual components (i.e., the differences between the trend components and the original wild boar data at administrative units) were downscaled at 5 km resolution using area-to-point kriging. The trend and residual components obtained at 5 km resolution were finally added to generate fine scale wild boar estimates for each bioclimatic region. 3) These maps were then mosaicked to produce a final output map of predicted wild boar densities across most of Eurasia. 4) Model accuracy was assessed at each different step using input as well as independent data. We discuss advantages and limits of the method and its

  5. The Mapping of On-Line Learning to Flipped Classroom: Small Private Online Course

    Directory of Open Access Journals (Sweden)

    Muqiang Zheng

    2018-03-01

    Full Text Available This study uses an integrated pedagogical tool for knowledge learning as an on-line tool for flipped classroom activities and as an off-line capability training tool. Theoretically, the Experiential Learning Cycle (ELC plays a critical role in promoting students learning effectiveness and performance. However, a dearth of research has applied M-learning and flipped classroom in combination with the ELC stages such as concrete experience, reflective observation, abstract conceptualization, and active experimentation to examine the knowledge and ability learning outcomes for students. This study integrates the On line to Off line (O2O classroom development and usage derived from the four stages of ELC based on on-line knowledge learning and off-line ability training in Microeconomics courses. The results revealed significant improvements in students learning outcomes after O2O mode was implemented. In comparison with traditional teaching methods, not only does O2O teaching significantly improve the students’ learning result of professional knowledge, but O2O teaching also significantly enhanced the capabilities of the students. Furthermore, this study reports the findings from major activities of each ELC stage in O2O classroom practice along with the mapping of on-line learning and off-line training included in the aforementioned stages. Finally, the study provides pedagogical implications and future research directions.

  6. Off-line mapping of multi-rate dependent task sets to many-core platforms

    DEFF Research Database (Denmark)

    Puffitsch, Wolfgang; Noulard, Eric; Pagetti, Claire

    2015-01-01

    This paper presents an approach to execute safety-critical applications on multi- and many-core processors in a predictable manner. We investigate three concrete platforms: the Intel Single-chip Cloud Computer, the Texas Instruments TMS320C6678 and the Tilera TILEmpower-Gx36. We define an execution...... model to safely execute dependent periodic task sets on these platforms. The four rules of the execution model entail that an off-line mapping of the application to the platform must be computed. The paper details our approach to automatically compute a valid mapping. Furthermore, we evaluate our...

  7. Emission-line maps with OSIRIS-TF: The case of M101

    Science.gov (United States)

    Méndez-Abreu, J.

    2013-05-01

    We investigate the suitability of GTC/OSIRIS Tunable Filters (TFs) for obtaining emission-line maps of extended objects. We developed a technique to reconstruct an emission-line image from a set of images taken at consecutive central wavelengths. We demonstrate the feasibility of the reconstruction method by generating a flux calibrated Hα image of the well-known spiral galaxy M101. We tested our emission-line fluxes and ratios by using data present in the literature. We found that the differences in both Hα fluxes and N II/Hα line ratios are ~15% and ~50%, respectively. These results are fully in agreement with the expected values for our observational setup. The proposed methodology will allow us to use OSIRIS/GTC to perform accurate spectrophotometric studies of extended galaxies in the local Universe.

  8. Population weighted raster maps can communicate findings of social audits: examples from three continents.

    Science.gov (United States)

    Mitchell, Steven; Cockcroft, Anne; Andersson, Neil

    2011-12-21

    Maps can portray trends, patterns, and spatial differences that might be overlooked in tabular data and are now widely used in health research. Little has been reported about the process of using maps to communicate epidemiological findings. Population weighted raster maps show colour changes over the study area. Similar to the rasters of barometric pressure in a weather map, data are the health occurrence--a peak on the map represents a higher value of the indicator in question. The population relevance of each sentinel site, as determined in the stratified last stage random sample, combines with geography (inverse-distance weighting) to provide a population-weighted extension of each colour. This transforms the map to show population space rather than simply geographic space. Maps allowed discussion of strategies to reduce violence against women in a context of political sensitivity about quoting summary indicator figures. Time-series maps showed planners how experiences of health services had deteriorated despite a reform programme; where in a country HIV risk behaviours were improving; and how knowledge of an economic development programme quickly fell off across a region. Change maps highlighted where indicators were improving and where they were deteriorating. Maps of potential impact of interventions, based on multivariate modelling, displayed how partial and full implementation of programmes could improve outcomes across a country. Scale depends on context. To support local planning, district maps or local government authority maps of health indicators were more useful than national maps; but multinational maps of outcomes were more useful for regional institutions. Mapping was useful to illustrate in which districts enrolment in religious schools--a rare occurrence--was more prevalent. Population weighted raster maps can present social audit findings in an accessible and compelling way, increasing the use of evidence by planners with limited numeracy

  9. Rhumb lines and map wars a social history of the Mercator projection

    CERN Document Server

    Monmonier, Mark

    2010-01-01

    In Rhumb Lines and Map Wars, Mark Monmonier offers an insightful, richly illustrated account of the controversies surrounding Flemish cartographer Gerard Mercator's legacy. He takes us back to 1569, when Mercator announced a clever method of portraying the earth on a flat surface, creating the first projection to take into account the earth's roundness. As Monmonier shows, mariners benefited most from Mercator's projection, which allowed for easy navigation of the high seas with rhumb lines-clear-cut routes with a constant compass bearing-for true direction. But the projection's popularity amo

  10. The symmetric quartic map for trajectories of magnetic field lines in elongated divertor tokamak plasmas

    Science.gov (United States)

    Jones, Morgin; Wadi, Hasina; Ali, Halima; Punjabi, Alkesh

    2009-04-01

    The coordinates of the area-preserving map equations for integration of magnetic field line trajectories in divertor tokamaks can be any coordinates for which a transformation to (ψt,θ,φ) coordinates exists [A. Punjabi, H. Ali, T. Evans, and A. Boozer, Phys. Lett. A 364, 140 (2007)]. ψt is toroidal magnetic flux, θ is poloidal angle, and φ is toroidal angle. This freedom is exploited to construct the symmetric quartic map such that the only parameter that determines magnetic geometry is the elongation of the separatrix surface. The poloidal flux inside the separatrix, the safety factor as a function of normalized minor radius, and the magnetic perturbation from the symplectic discretization are all held constant, and only the elongation is κ varied. The width of stochastic layer, the area, and the fractal dimension of the magnetic footprint and the average radial diffusion coefficient of magnetic field lines from the stochastic layer; and how these quantities scale with κ is calculated. The symmetric quartic map gives the correct scalings which are consistent with the scalings of coordinates with κ. The effects of m =1, n =±1 internal perturbation with the amplitude that is expected to occur in tokamaks are calculated by adding a term [H. Ali, A. Punjabi, A. H. Boozer, and T. Evans, Phys. Plasmas 11, 1908 (2004)] to the symmetric quartic map. In this case, the width of stochastic layer scales as 0.35 power of κ. The area of the footprint is roughly constant. The average radial diffusion coefficient of field lines near the X-point scales linearly with κ. The low mn perturbation changes the quasisymmetric structure of the footprint, and reorganizes it into a single, large scale, asymmetric structure. The symmetric quartic map is combined with the dipole map [A. Punjabi, H. Ali, and A. H. Boozer, Phys. Plasmas 10, 3992 (2003)] to calculate the effects of magnetic perturbation from a current carrying coil. The coil position and coil current coil are

  11. The symmetric quartic map for trajectories of magnetic field lines in elongated divertor tokamak plasmas

    International Nuclear Information System (INIS)

    Jones, Morgin; Wadi, Hasina; Ali, Halima; Punjabi, Alkesh

    2009-01-01

    The coordinates of the area-preserving map equations for integration of magnetic field line trajectories in divertor tokamaks can be any coordinates for which a transformation to (ψ t ,θ,φ) coordinates exists [A. Punjabi, H. Ali, T. Evans, and A. Boozer, Phys. Lett. A 364, 140 (2007)]. ψ t is toroidal magnetic flux, θ is poloidal angle, and φ is toroidal angle. This freedom is exploited to construct the symmetric quartic map such that the only parameter that determines magnetic geometry is the elongation of the separatrix surface. The poloidal flux inside the separatrix, the safety factor as a function of normalized minor radius, and the magnetic perturbation from the symplectic discretization are all held constant, and only the elongation is κ varied. The width of stochastic layer, the area, and the fractal dimension of the magnetic footprint and the average radial diffusion coefficient of magnetic field lines from the stochastic layer; and how these quantities scale with κ is calculated. The symmetric quartic map gives the correct scalings which are consistent with the scalings of coordinates with κ. The effects of m=1, n=±1 internal perturbation with the amplitude that is expected to occur in tokamaks are calculated by adding a term [H. Ali, A. Punjabi, A. H. Boozer, and T. Evans, Phys. Plasmas 11, 1908 (2004)] to the symmetric quartic map. In this case, the width of stochastic layer scales as 0.35 power of κ. The area of the footprint is roughly constant. The average radial diffusion coefficient of field lines near the X-point scales linearly with κ. The low mn perturbation changes the quasisymmetric structure of the footprint, and reorganizes it into a single, large scale, asymmetric structure. The symmetric quartic map is combined with the dipole map [A. Punjabi, H. Ali, and A. H. Boozer, Phys. Plasmas 10, 3992 (2003)] to calculate the effects of magnetic perturbation from a current carrying coil. The coil position and coil current coil are

  12. Genetic Analysis of Fusarium Head Blight Resistance in CIMMYT Bread Wheat Line C615 Using Traditional and Conditional QTL Mapping.

    Science.gov (United States)

    Yi, Xin; Cheng, Jingye; Jiang, Zhengning; Hu, Wenjing; Bie, Tongde; Gao, Derong; Li, Dongsheng; Wu, Ronglin; Li, Yuling; Chen, Shulin; Cheng, Xiaoming; Liu, Jian; Zhang, Yong; Cheng, Shunhe

    2018-01-01

    Fusarium head blight (FHB) is a destructive wheat disease present throughout the world, and host resistance is an effective and economical strategy used to control FHB. Lack of adequate resistance resource is still a main bottleneck for FHB genetics and wheat breeding research. The synthetic-derived bread wheat line C615, which does not carry the Fhb1 gene, is a promising source of FHB resistance for breeding. A population of 198 recombinant inbred lines (RILs) produced by crossing C615 with the susceptible cultivar Yangmai 13 was evaluated for FHB response using point and spray inoculations. As the disease phenotype is frequently complicated by other agronomic traits, we used both traditional and multivariate conditional QTL mapping approaches to investigate the genetic relationships (at the individual QTL level) between FHB resistance and plant height (PH), spike compactness (SC), and days to flowering (FD). A linkage map was constructed from 3,901 polymorphic SNP markers, which covered 2,549.2 cM. Traditional and conditional QTL mapping analyses found 13 and 22 QTL for FHB, respectively; 10 were identified by both methods. Among these 10, three QTL from C615 were detected in multiple years; these QTL were located on chromosomes 2AL, 2DS, and 2DL. Conditional QTL mapping analysis indicated that, at the QTL level, SC strongly influenced FHB in point inoculation; whereas PH and SC contributed more to FHB than did FD in spray inoculation. The three stable QTL ( QFhbs-jaas.2AL, QFhbp-jaas.2DS , and QFhbp-jaas.2DL ) for FHB were partly affected by or were independent of the three agronomic traits. The QTL detected in this study improve our understanding of the genetic relationships between FHB response and related traits at the QTL level and provide useful information for marker-assisted selection for the improvement of FHB resistance in breeding.

  13. Genetic Analysis of Fusarium Head Blight Resistance in CIMMYT Bread Wheat Line C615 Using Traditional and Conditional QTL Mapping

    Science.gov (United States)

    Yi, Xin; Cheng, Jingye; Jiang, Zhengning; Hu, Wenjing; Bie, Tongde; Gao, Derong; Li, Dongsheng; Wu, Ronglin; Li, Yuling; Chen, Shulin; Cheng, Xiaoming; Liu, Jian; Zhang, Yong; Cheng, Shunhe

    2018-01-01

    Fusarium head blight (FHB) is a destructive wheat disease present throughout the world, and host resistance is an effective and economical strategy used to control FHB. Lack of adequate resistance resource is still a main bottleneck for FHB genetics and wheat breeding research. The synthetic-derived bread wheat line C615, which does not carry the Fhb1 gene, is a promising source of FHB resistance for breeding. A population of 198 recombinant inbred lines (RILs) produced by crossing C615 with the susceptible cultivar Yangmai 13 was evaluated for FHB response using point and spray inoculations. As the disease phenotype is frequently complicated by other agronomic traits, we used both traditional and multivariate conditional QTL mapping approaches to investigate the genetic relationships (at the individual QTL level) between FHB resistance and plant height (PH), spike compactness (SC), and days to flowering (FD). A linkage map was constructed from 3,901 polymorphic SNP markers, which covered 2,549.2 cM. Traditional and conditional QTL mapping analyses found 13 and 22 QTL for FHB, respectively; 10 were identified by both methods. Among these 10, three QTL from C615 were detected in multiple years; these QTL were located on chromosomes 2AL, 2DS, and 2DL. Conditional QTL mapping analysis indicated that, at the QTL level, SC strongly influenced FHB in point inoculation; whereas PH and SC contributed more to FHB than did FD in spray inoculation. The three stable QTL (QFhbs-jaas.2AL, QFhbp-jaas.2DS, and QFhbp-jaas.2DL) for FHB were partly affected by or were independent of the three agronomic traits. The QTL detected in this study improve our understanding of the genetic relationships between FHB response and related traits at the QTL level and provide useful information for marker-assisted selection for the improvement of FHB resistance in breeding. PMID:29780395

  14. GRILLIX. A 3D turbulence code for magnetic fusion devices based on a field line map

    International Nuclear Information System (INIS)

    Stegmeir, Andreas Korbinian

    2015-01-01

    The complex geometry in the scrape-off layer of tokamaks poses problems to existing turbulence codes. The usually employed field aligned coordinates become ill defined at the separatrix. Therefore the parallel code GRILLIX was developed, which is based on a field line map. This allows simulations in additional complex geometries, especially across the separatrix. A new discretisation, based on the support operator method, for the highly anisotropic diffusion was developed and applied to a simple turbulence model (Hasegawa-Wakatani).

  15. A Population of Deletion Mutants and an Integrated Mapping and Exome-seq Pipeline for Gene Discovery in Maize

    Science.gov (United States)

    Jia, Shangang; Li, Aixia; Morton, Kyla; Avoles-Kianian, Penny; Kianian, Shahryar F.; Zhang, Chi; Holding, David

    2016-01-01

    To better understand maize endosperm filling and maturation, we used γ-irradiation of the B73 maize reference line to generate mutants with opaque endosperm and reduced kernel fill phenotypes, and created a population of 1788 lines including 39 Mo17 × F2s showing stable, segregating, and viable kernel phenotypes. For molecular characterization of the mutants, we developed a novel functional genomics platform that combined bulked segregant RNA and exome sequencing (BSREx-seq) to map causative mutations and identify candidate genes within mapping intervals. To exemplify the utility of the mutants and provide proof-of-concept for the bioinformatics platform, we present detailed characterization of line 937, an opaque mutant harboring a 6203 bp in-frame deletion covering six exons within the Opaque-1 gene. In addition, we describe mutant line 146 which contains a 4.8 kb intragene deletion within the Sugary-1 gene and line 916 in which an 8.6 kb deletion knocks out a Cyclin A2 gene. The publically available algorithm developed in this work improves the identification of causative deletions and its corresponding gaps within mapping peaks. This study demonstrates the utility of γ-irradiation for forward genetics in large nondense genomes such as maize since deletions often affect single genes. Furthermore, we show how this classical mutagenesis method becomes applicable for functional genomics when combined with state-of-the-art genomics tools. PMID:27261000

  16. High Resolution Population Maps for Low Income Nations: Combining Land Cover and Census in East Africa

    Science.gov (United States)

    Tatem, Andrew J.; Noor, Abdisalan M.; von Hagen, Craig; Di Gregorio, Antonio; Hay, Simon I.

    2007-01-01

    Background Between 2005 and 2050, the human population is forecast to grow by 2.7 billion, with the vast majority of this growth occurring in low income countries. This growth is likely to have significant social, economic and environmental impacts, and make the achievement of international development goals more difficult. The measurement, monitoring and potential mitigation of these impacts require high resolution, contemporary data on human population distributions. In low income countries, however, where the changes will be concentrated, the least information on the distribution of population exists. In this paper we investigate whether satellite imagery in combination with land cover information and census data can be used to create inexpensive, high resolution and easily-updatable settlement and population distribution maps over large areas. Methodology/Principal Findings We examine various approaches for the production of maps of the East African region (Kenya, Uganda, Burundi, Rwanda and Tanzania) and where fine resolution census data exists, test the accuracies of map production approaches and existing population distribution products. The results show that combining high resolution census, settlement and land cover information is important in producing accurate population distribution maps. Conclusions We find that this semi-automated population distribution mapping at unprecedented spatial resolution produces more accurate results than existing products and can be undertaken for as little as $0.01 per km2. The resulting population maps are a product of the Malaria Atlas Project (MAP: http://www.map.ox.ac.uk) and are freely available. PMID:18074022

  17. High resolution population maps for low income nations: combining land cover and census in East Africa.

    Directory of Open Access Journals (Sweden)

    Andrew J Tatem

    2007-12-01

    Full Text Available Between 2005 and 2050, the human population is forecast to grow by 2.7 billion, with the vast majority of this growth occurring in low income countries. This growth is likely to have significant social, economic and environmental impacts, and make the achievement of international development goals more difficult. The measurement, monitoring and potential mitigation of these impacts require high resolution, contemporary data on human population distributions. In low income countries, however, where the changes will be concentrated, the least information on the distribution of population exists. In this paper we investigate whether satellite imagery in combination with land cover information and census data can be used to create inexpensive, high resolution and easily-updatable settlement and population distribution maps over large areas.We examine various approaches for the production of maps of the East African region (Kenya, Uganda, Burundi, Rwanda and Tanzania and where fine resolution census data exists, test the accuracies of map production approaches and existing population distribution products. The results show that combining high resolution census, settlement and land cover information is important in producing accurate population distribution maps.We find that this semi-automated population distribution mapping at unprecedented spatial resolution produces more accurate results than existing products and can be undertaken for as little as $0.01 per km(2. The resulting population maps are a product of the Malaria Atlas Project (MAP: http://www.map.ox.ac.uk and are freely available.

  18. MAPPING THE LINEARLY POLARIZED SPECTRAL LINE EMISSION AROUND THE EVOLVED STAR IRC+10216

    Energy Technology Data Exchange (ETDEWEB)

    Girart, J. M. [Institut de Ciencies de l' Espai, (CSIC-IEEC), Campus UAB, Facultat de Ciencies, C5p 2, 08193 Bellaterra, Catalunya (Spain); Patel, N. [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States); Vlemmings, W. H. T. [Department of Earth and Space Sciences, Chalmers University of Technology, Onsala Space Observatory, SE-439 92 Onsala (Sweden); Rao, Ramprasad, E-mail: girart@ice.cat [Submillimeter Array, Academia Sinica Institute of Astronomy and Astrophysics, 645 N. Aohoku Place, Hilo, HI 96720 (United States)

    2012-05-20

    We present spectro-polarimetric observations of several molecular lines obtained with the Submillimeter Array toward the carbon-rich asymptotic giant branch star IRC+10216. We have detected and mapped the linear polarization of the CO 3-2, SiS 19-18, and CS 7-6 lines. The polarization arises at a distance of {approx_equal} 450 AU from the star and is blueshifted with respect to the Stokes I. The SiS 19-18 polarization pattern appears to be consistent with a locally radial magnetic field configuration. However, the CO 3-2 and CS 7-6 line polarization suggests an overall complex magnetic field morphology within the envelope. This work demonstrates the feasibility of using spectro-polarimetric observations to carry out tomographic imaging of the magnetic field in circumstellar envelopes.

  19. Residential mobility of populations near UK power lines and implications for childhood leukaemia

    International Nuclear Information System (INIS)

    Swanson, John

    2013-01-01

    Epidemiological studies suggest associations between childhood leukaemia and living near high-voltage power lines, but the most obvious potential causative agent, the magnetic fields produced by the power lines, is not supported by laboratory studies or a known mechanism. An alternative hypothesised explanation is if there is greater population mobility near power lines, linking to the findings of Kinlen that population mixing increases leukaemia rates. We used the names recorded in electoral registers to see whether people near power lines move house more often than the population as a whole. We did find variations, but only small ones, and not such as to support the hypothesis. (note)

  20. Mapping the Antarctic grounding line with CryoSat-2 radar altimetry

    Science.gov (United States)

    Bamber, J. L.; Dawson, G. J.

    2017-12-01

    The grounding line, where grounded ice begins to float, is the boundary at which the ocean has the greatest influence on the ice-sheet. Its position and dynamics are critical in assessing the stability of the ice-sheet, for mass budget calculations and as an input into numerical models. The most reliable approaches to map the grounding line remotely are to measure the limit of tidal flexure of the ice shelf using differential synthetic aperture radar interferometry (DInSAR) or ICESat repeat-track measurements. However, these methods are yet to provide satisfactory spatial and temporal coverage of the whole of the Antarctic grounding zone. It has not been possible to use conventional radar altimetry to map the limit of tidal flexure of the ice shelf because it performs poorly near breaks in slope, commonly associated with the grounding zone. The synthetic aperture radar interferometric (SARin) mode of CryoSat-2, performs better over steeper margins of the ice sheet and allows us to achieve this. The SARin mode combines "delay Doppler" processing with a cross-track interferometer, and enables us to use elevations based on the first return (point of closest approach or POCA) and "swath processed" elevations derived from the time-delayed waveform beyond the first return, to significantly improve coverage. Here, we present a new method to map the limit of tidal motion from a combination of POCA and swath data. We test this new method on the Siple Coast region of the Ross Ice Shelf, and the mapped grounding line is in good agreement with previous observations from DinSAR and ICESat measurements. There is, however, an approximately constant seaward offset between these methods and ours, which we believe is due to the poorer precision of CryoSat-2. This new method has improved the coverage of the grounding zone across the Siple Coast, and can be applied to the rest of Antarctica.

  1. Spatially associated clump populations in Rosette from CO and dust maps

    Science.gov (United States)

    Veltchev, Todor V.; Ossenkopf-Okada, Volker; Stanchev, Orlin; Schneider, Nicola; Donkov, Sava; Klessen, Ralf S.

    2018-04-01

    Spatial association of clumps from different tracers turns out to be a valuable tool to determine the physical properties of molecular clouds. It provides a reliable estimate for the X-factors, serves to trace the density of clumps seen in column densities only, and allows one to measure the velocity dispersion of clumps identified in dust emission. We study the spatial association between clump populations, extracted by use of the GAUSSCLUMPS technique from 12CO (1-0), 13CO (1-0) line maps and Herschel dust-emission maps of the star-forming region Rosette, and analyse their physical properties. All CO clumps that overlap with another CO or dust counterpart are found to be gravitationally bound and located in the massive star-forming filaments of the molecular cloud. They obey a single mass-size relation M_cl∝ R_cl^γ with γ ≃ 3 (implying constant mean density) and display virtually no velocity-size relation. We interpret their population as low-density structures formed through compression by converging flows and still not evolved under the influence of self-gravity. The high-mass parts of their clump mass functions are fitted by a power law dN_cl/d log M_cl∝ M_cl^{Γ } and display a nearly Salpeter slope Γ ˜ -1.3. On the other hand, clumps extracted from the dust-emission map exhibit a shallower mass-size relation with γ = 2.5 and mass functions with very steep slopes Γ ˜ -2.3 even if associated with CO clumps. They trace density peaks of the associated CO clumps at scales of a few tenths of pc where no single density scaling law should be expected.

  2. Genetic dissection of maize plant architecture with an ultra-high density bin map based on recombinant inbred lines.

    Science.gov (United States)

    Zhou, Zhiqiang; Zhang, Chaoshu; Zhou, Yu; Hao, Zhuanfang; Wang, Zhenhua; Zeng, Xing; Di, Hong; Li, Mingshun; Zhang, Degui; Yong, Hongjun; Zhang, Shihuang; Weng, Jianfeng; Li, Xinhai

    2016-03-03

    Plant architecture attributes, such as plant height, ear height, and internode number, have played an important role in the historical increases in grain yield, lodging resistance, and biomass in maize (Zea mays L.). Analyzing the genetic basis of variation in plant architecture using high density QTL mapping will be of benefit for the breeding of maize for many traits. However, the low density of molecular markers in existing genetic maps has limited the efficiency and accuracy of QTL mapping. Genotyping by sequencing (GBS) is an improved strategy for addressing a complex genome via next-generation sequencing technology. GBS has been a powerful tool for SNP discovery and high-density genetic map construction. The creation of ultra-high density genetic maps using large populations of advanced recombinant inbred lines (RILs) is an efficient way to identify QTL for complex agronomic traits. A set of 314 RILs derived from inbreds Ye478 and Qi319 were generated and subjected to GBS. A total of 137,699,000 reads with an average of 357,376 reads per individual RIL were generated, which is equivalent to approximately 0.07-fold coverage of the maize B73 RefGen_V3 genome for each individual RIL. A high-density genetic map was constructed using 4183 bin markers (100-Kb intervals with no recombination events). The total genetic distance covered by the linkage map was 1545.65 cM and the average distance between adjacent markers was 0.37 cM with a physical distance of about 0.51 Mb. Our results demonstrated a relatively high degree of collinearity between the genetic map and the B73 reference genome. The quality and accuracy of the bin map for QTL detection was verified by the mapping of a known gene, pericarp color 1 (P1), which controls the color of the cob, with a high LOD value of 80.78 on chromosome 1. Using this high-density bin map, 35 QTL affecting plant architecture, including 14 for plant height, 14 for ear height, and seven for internode number were detected

  3. THE APPLICATION OF DIGITAL LINE GRAPHS AND MAP IN THE NETWORK ENVIRONMENT

    Directory of Open Access Journals (Sweden)

    X. Guo

    2012-07-01

    Full Text Available WebGIS is an important research field in GIS. W3C organization established SVG standard, which laid a foundation for WebGIS based on vector data. In China, Digital Line Graphs(DLG is a significant GIS product and it has been used in many medium and large WebGIS system. Geographic information-portrayal is the common method of DLG visualization. However, the inherent characteristics of Geographic information-portrayal may lead to a relatively higher data production input, still, the visualization effect is not ideal. We put forward a new product named Digital Line Graphs and Map(DLGM, which consists of DLG and DLG's cartographic presentation data. It provides visualization data based on the cartographic standards. Due to the manufacture and management of DLGM data that are independent from software and platform, its data can be used in many fields. Network application is one of them. This paper is to use DLGM in the network applications. First it reveals the connotation and characteristics of DLGM then analyses the model that DLGM organizes, manages DLG and map symbol data. After that, combined with SVG standards, we put forward DLGM’s SVG encoding method without any information loss. Finally we provide a web map system based on local area network by using 1:10000 DLGM data of a certain area. Based on this study, we conclude that DLGM can be used in the network environment providing high quality DLG and cartographic data for WebGIS.

  4. Genetic map of Triticum turgidum based on a hexaploid wheat population without genetic recombination for D genome

    Directory of Open Access Journals (Sweden)

    Zhang Li

    2012-08-01

    Full Text Available Abstract Background A synthetic doubled-haploid hexaploid wheat population, SynDH1, derived from the spontaneous chromosome doubling of triploid F1 hybrid plants obtained from the cross of hybrids Triticum turgidum ssp. durum line Langdon (LDN and ssp. turgidum line AS313, with Aegilops tauschii ssp. tauschii accession AS60, was previously constructed. SynDH1 is a tetraploidization-hexaploid doubled haploid (DH population because it contains recombinant A and B chromosomes from two different T. turgidum genotypes, while all the D chromosomes from Ae. tauschii are homogenous across the whole population. This paper reports the construction of a genetic map using this population. Results Of the 606 markers used to assemble the genetic map, 588 (97% were assigned to linkage groups. These included 513 Diversity Arrays Technology (DArT markers, 72 simple sequence repeat (SSR, one insertion site-based polymorphism (ISBP, and two high-molecular-weight glutenin subunit (HMW-GS markers. These markers were assigned to the 14 chromosomes, covering 2048.79 cM, with a mean distance of 3.48 cM between adjacent markers. This map showed good coverage of the A and B genome chromosomes, apart from 3A, 5A, 6A, and 4B. Compared with previously reported maps, most shared markers showed highly consistent orders. This map was successfully used to identify five quantitative trait loci (QTL, including two for spikelet number on chromosomes 7A and 5B, two for spike length on 7A and 3B, and one for 1000-grain weight on 4B. However, differences in crossability QTL between the two T. turgidum parents may explain the segregation distortion regions on chromosomes 1A, 3B, and 6B. Conclusions A genetic map of T. turgidum including 588 markers was constructed using a synthetic doubled haploid (SynDH hexaploid wheat population. Five QTLs for three agronomic traits were identified from this population. However, more markers are needed to increase the density and resolution of

  5. Genetic map of Triticum turgidum based on a hexaploid wheat population without genetic recombination for D genome.

    Science.gov (United States)

    Zhang, Li; Luo, Jiang-Tao; Hao, Ming; Zhang, Lian-Quan; Yuan, Zhong-Wei; Yan, Ze-Hong; Liu, Ya-Xi; Zhang, Bo; Liu, Bao-Long; Liu, Chun-Ji; Zhang, Huai-Gang; Zheng, You-Liang; Liu, Deng-Cai

    2012-08-13

    A synthetic doubled-haploid hexaploid wheat population, SynDH1, derived from the spontaneous chromosome doubling of triploid F1 hybrid plants obtained from the cross of hybrids Triticum turgidum ssp. durum line Langdon (LDN) and ssp. turgidum line AS313, with Aegilops tauschii ssp. tauschii accession AS60, was previously constructed. SynDH1 is a tetraploidization-hexaploid doubled haploid (DH) population because it contains recombinant A and B chromosomes from two different T. turgidum genotypes, while all the D chromosomes from Ae. tauschii are homogenous across the whole population. This paper reports the construction of a genetic map using this population. Of the 606 markers used to assemble the genetic map, 588 (97%) were assigned to linkage groups. These included 513 Diversity Arrays Technology (DArT) markers, 72 simple sequence repeat (SSR), one insertion site-based polymorphism (ISBP), and two high-molecular-weight glutenin subunit (HMW-GS) markers. These markers were assigned to the 14 chromosomes, covering 2048.79 cM, with a mean distance of 3.48 cM between adjacent markers. This map showed good coverage of the A and B genome chromosomes, apart from 3A, 5A, 6A, and 4B. Compared with previously reported maps, most shared markers showed highly consistent orders. This map was successfully used to identify five quantitative trait loci (QTL), including two for spikelet number on chromosomes 7A and 5B, two for spike length on 7A and 3B, and one for 1000-grain weight on 4B. However, differences in crossability QTL between the two T. turgidum parents may explain the segregation distortion regions on chromosomes 1A, 3B, and 6B. A genetic map of T. turgidum including 588 markers was constructed using a synthetic doubled haploid (SynDH) hexaploid wheat population. Five QTLs for three agronomic traits were identified from this population. However, more markers are needed to increase the density and resolution of this map in the future study.

  6. LINES

    Directory of Open Access Journals (Sweden)

    Minas Bakalchev

    2015-10-01

    Full Text Available The perception of elements in a system often creates their interdependence, interconditionality, and suppression. The lines from a basic geometrical element have become the model of a reductive world based on isolation according to certain criteria such as function, structure, and social organization. Their traces are experienced in the contemporary world as fragments or ruins of a system of domination of an assumed hierarchical unity. How can one release oneself from such dependence or determinism? How can the lines become less “systematic” and forms more autonomous, and less reductive? How is a form released from modernistic determinism on the new controversial ground? How can these elements or forms of representation become forms of action in the present complex world? In this paper, the meaning of lines through the ideas of Le Corbusier, Leonidov, Picasso, and Hitchcock is presented. Spatial research was made through a series of examples arising from the projects of the architectural studio “Residential Transformations”, which was a backbone for mapping the possibilities ranging from playfulness to exactness, as tactics of transformation in the different contexts of the contemporary world.

  7. Transient Cnp expression by early progenitors causes Cre-Lox-based reporter lines to map profoundly different fates.

    Science.gov (United States)

    Tognatta, Reshmi; Sun, Wenjing; Goebbels, Sandra; Nave, Klaus-Armin; Nishiyama, Akiko; Schoch, Susanne; Dimou, Leda; Dietrich, Dirk

    2017-02-01

    NG2 expressing oligodendroglial precursor cells are ubiquitous in the central nervous system and the only cell type cycling throughout life. Previous fate mapping studies have remained inconsistent regarding the question whether NG2 cells are capable of generating certain types of neurons. Here, we use CNP-Cre mice to map the fate of a sub-population of NG2 cells assumed to be close to differentiation. When crossing these mice with the ROSA26/YFP Cre-reporter line we discovered large numbers of reporter-expressing pyramidal neurons in the piriform and dorsal cortex. In contrast, when using Z/EG reporter mice to track the fate of Cnp-expressing NG2 cells only oligodendroglial cells were found reporter positive. Using BrdU-based birth dating protocols and inducible NG2CreER:ROSA26/YFP mice we show that YFP positive neurons are generated from radial glial cells and that these radial glial cells display temporary and low level activity of certain oligodendroglial genes sufficient to recombine the Cre-inducible reporter gene in ROSA26/YFP but not in Z/EG mice. Taken together, we did not obtain evidence for generation of neurons from NG2 cells. Our results suggest that with an appropriate reporter system Cnp activity can be used to define a proliferative subpopulation of NG2 cells committed to generate oligodendrocytes. However, the strikingly different results obtained from ROSA26/YFP versus Z/EG mice demonstrate that the choice of Cre-reporter line can be of crucial importance for fate mapping studies and other applications of the Cre-lox technology. GLIA 2017;65:342-359. © 2016 Wiley Periodicals, Inc.

  8. A symplectic map for trajectories of magnetic field lines in double-null divertor tokamaks

    Science.gov (United States)

    Crank, Willie; Ali, Halima; Punjabi, Alkesh

    2009-11-01

    The coordinates of the area-preserving map equations for integration of magnetic field line trajectories in tokamaks can be any coordinates for which a transformation to (ψ,θ,φ) coordinates exists [A. Punjabi, H. Ali, T. Evans, and A. Boozer, Phys. Lett. A 364, 140 (2007)]. ψ is toroidal magnetic flux, θ is poloidal angle, and φ is toroidal angle. This freedom is exploited to construct a map that represents the magnetic topology of double-null divertor tokamaks. For this purpose, the generating function of the simple map [A. Punjabi, A. Verma, and A. Boozer, Phys. Rev. Lett. 69, 3322 (1992)] is slightly modified. The resulting map equations for the double-null divertor tokamaks are: x1=x0-ky0(1-y0^2 ), y1=y0+kx1. k is the map parameter. It represents the generic topological effects of toroidal asymmetries. The O-point is at (0.0). The X-points are at (0,±1). The equilibrium magnetic surfaces are calculated. These surfaces are symmetric about the x- and y- axes. The widths of stochastic layer near the X-points in the principal plane, and the fractal dimensions of the magnetic footprints on the inboard and outboard side of upper and lower X-points are calculated from the map. This work is supported by US Department of Energy grants DE-FG02-07ER54937, DE-FG02-01ER54624 and DE-FG02-04ER54793.

  9. On a Hopping-Points SVD and Hough Transform-Based Line Detection Algorithm for Robot Localization and Mapping

    Directory of Open Access Journals (Sweden)

    Abhijeet Ravankar

    2016-05-01

    Full Text Available Line detection is an important problem in computer vision, graphics and autonomous robot navigation. Lines detected using a laser range sensor (LRS mounted on a robot can be used as features to build a map of the environment, and later to localize the robot in the map, in a process known as Simultaneous Localization and Mapping (SLAM. We propose an efficient algorithm for line detection from LRS data using a novel hopping-points Singular Value Decomposition (SVD and Hough transform-based algorithm, in which SVD is applied to intermittent LRS points to accelerate the algorithm. A reverse-hop mechanism ensures that the end points of the line segments are accurately extracted. Line segments extracted from the proposed algorithm are used to form a map and, subsequently, LRS data points are matched with the line segments to localize the robot. The proposed algorithm eliminates the drawbacks of point-based matching algorithms like the Iterative Closest Points (ICP algorithm, the performance of which degrades with an increasing number of points. We tested the proposed algorithm for mapping and localization in both simulated and real environments, and found it to detect lines accurately and build maps with good self-localization.

  10. Genetic analysis of morphological traits in a new, versatile, rapid-cycling Brassica rapa recombinant inbred line population

    Directory of Open Access Journals (Sweden)

    Hedayat eBagheri

    2012-08-01

    Full Text Available A recombinant inbred line (RIL population was produced based on a wide cross between the rapid-cycling and self-compatible genotypes L58, a Caixin vegetable type, and R-o-18, a yellow sarson oil type. A linkage map based on 160 F7 lines was constructed using 100 SNP, 130 AFLP®, 27 InDel and 13 publicly available SSR markers. The map covers a total length of 1150 cM with an average resolution of 4.3 cM/marker. To demonstrate the versatility of this new population, 17 traits, related to plant architecture and seed characteristics, were subjected to QTL analysis. A total of 47 QTLs were detected, each explaining between 6 to 54% of the total phenotypic variance for the concerned trait. The genetic analysis shows that this population is a useful new tool for analyzing genetic variation for interesting traits in B. rapa, and for further exploitation of the recent availability of the B. rapa whole genome sequence for gene cloning and gene function analysis.

  11. QTL mapping for combining ability in different population-based ...

    Indian Academy of Sciences (India)

    2013-12-13

    Dec 13, 2013 ... ability and for geneticists to research the genetic basis of combining ability. [Li L., Sun C., ... population-based NCII designs by a simulation study. J. Genet. ... combining ability could also be applied to other population- based NCII ... was to estimate how different base populations, sample sizes, heritability ...

  12. Mapping copy number variation by population-scale genome sequencing

    DEFF Research Database (Denmark)

    Mills, Ryan E.; Walter, Klaudia; Stewart, Chip

    2011-01-01

    Genomic structural variants (SVs) are abundant in humans, differing from other forms of variation in extent, origin and functional impact. Despite progress in SV characterization, the nucleotide resolution architecture of most SVs remains unknown. We constructed a map of unbalanced SVs (that is......, copy number variants) based on whole genome DNA sequencing data from 185 human genomes, integrating evidence from complementary SV discovery approaches with extensive experimental validations. Our map encompassed 22,025 deletions and 6,000 additional SVs, including insertions and tandem duplications...

  13. Mapping low- and high-density clouds in astrophysical nebulae by imaging forbidden line emission

    Science.gov (United States)

    Steiner, J. E.; Menezes, R. B.; Ricci, T. V.; Oliveira, A. S.

    2009-06-01

    Emission line ratios have been essential for determining physical parameters such as gas temperature and density in astrophysical gaseous nebulae. With the advent of panoramic spectroscopic devices, images of regions with emission lines related to these physical parameters can, in principle, also be produced. We show that, with observations from modern instruments, it is possible to transform images taken from density-sensitive forbidden lines into images of emission from high- and low-density clouds by applying a transformation matrix. In order to achieve this, images of the pairs of density-sensitive lines as well as the adjacent continuum have to be observed and combined. We have computed the critical densities for a series of pairs of lines in the infrared, optical, ultraviolet and X-rays bands, and calculated the pair line intensity ratios in the high- and low-density limit using a four- and five-level atom approximation. In order to illustrate the method, we applied it to Gemini Multi-Object Spectrograph (GMOS) Integral Field Unit (GMOS-IFU) data of two galactic nuclei. We conclude that this method provides new information of astrophysical interest, especially for mapping low- and high-density clouds; for this reason, we call it `the ld/hd imaging method'. Based on observations obtained at the Gemini Observatory, which is operated by the Association of Universities for Research in Astronomy, Inc., under a cooperative agreement with the National Science Foundation on behalf of the Gemini partnership: the National Science Foundation (United States); the Science and Technology Facilities Council (United Kingdom); the National Research Council (Canada), CONICYT (Chile); the Australian Research Council (Australia); Ministério da Ciência e Tecnologia (Brazil) and Secretaria de Ciencia y Tecnologia (Argentina). E-mail: steiner@astro.iag.usp.br

  14. Population weighted raster maps can communicate findings of social audits: examples from three continents

    Directory of Open Access Journals (Sweden)

    Mitchell Steven

    2011-12-01

    Full Text Available Abstract Background Maps can portray trends, patterns, and spatial differences that might be overlooked in tabular data and are now widely used in health research. Little has been reported about the process of using maps to communicate epidemiological findings. Method Population weighted raster maps show colour changes over the study area. Similar to the rasters of barometric pressure in a weather map, data are the health occurrence – a peak on the map represents a higher value of the indicator in question. The population relevance of each sentinel site, as determined in the stratified last stage random sample, combines with geography (inverse-distance weighting to provide a population-weighted extension of each colour. This transforms the map to show population space rather than simply geographic space. Results Maps allowed discussion of strategies to reduce violence against women in a context of political sensitivity about quoting summary indicator figures. Time-series maps showed planners how experiences of health services had deteriorated despite a reform programme; where in a country HIV risk behaviours were improving; and how knowledge of an economic development programme quickly fell off across a region. Change maps highlighted where indicators were improving and where they were deteriorating. Maps of potential impact of interventions, based on multivariate modelling, displayed how partial and full implementation of programmes could improve outcomes across a country. Scale depends on context. To support local planning, district maps or local government authority maps of health indicators were more useful than national maps; but multinational maps of outcomes were more useful for regional institutions. Mapping was useful to illustrate in which districts enrolment in religious schools – a rare occurrence - was more prevalent. Conclusions Population weighted raster maps can present social audit findings in an accessible and compelling

  15. QTL MAPPING FOR GRAIN QUALITY TRAITS IN TESTCROSSES OF A MAIZE BIPARENTAL POPULATION USING GENOTYPING-BY-SEQUENCING DATA

    Directory of Open Access Journals (Sweden)

    Mario Franić

    2017-01-01

    Full Text Available We performed QTL mapping in testcrosses of maize population IBMSyn4 for three grain quality traits: oil and protein contents and test weight. 191 phenotyped and genotyped lines were used as a training set while 85 genotyped only lines comprised a validation set used to calculate best linear unbiased predictions (BLUP, making a total of 276 phenotypes for the QTL analysis. 92000 filtered Genotyping-By-Sequencing (GBS SNP markers were used to calculate BLUPs, while a set of 2178 genetically mapped SSRs was used in QTL analysis. By simple QTL scan, we scored several minor effect QTLs: one for oil content (chromosome 1, one for protein content (chromosome 10 and four for test weight (chromosomes 1, 3, 5 and 10. QTLs associated with test weight were found to be additive, and 18.25% of phenotypic variance was explained by their joint effect. Only one QTL for test weight was found to be significant in composite interval mapping and it was mapped on chromosome 5. This QTL accounted for 9.97% of phenotypic variance. QTLs detected in this study represent monitoring of commercially most successful elite maize germplasm for grain quality traits.

  16. Impact of population structure, effective bottleneck time, and allele frequency on linkage disequilibrium maps.

    Science.gov (United States)

    Zhang, Weihua; Collins, Andrew; Gibson, Jane; Tapper, William J; Hunt, Sarah; Deloukas, Panos; Bentley, David R; Morton, Newton E

    2004-12-28

    Genetic maps in linkage disequilibrium (LD) units play the same role for association mapping as maps in centimorgans provide at much lower resolution for linkage mapping. Association mapping of genes determining disease susceptibility and other phenotypes is based on the theory of LD, here applied to relations with three phenomena. To test the theory, markers at high density along a 10-Mb continuous segment of chromosome 20q were studied in African-American, Asian, and Caucasian samples. Population structure, whether created by pooling samples from divergent populations or by the mating pattern in a mixed population, is accurately bioassayed from genotype frequencies. The effective bottleneck time for Eurasians is substantially less than for migration out of Africa, reflecting later bottlenecks. The classical dependence of allele frequency on mutation age does not hold for the generally shorter time span of inbreeding and LD. Limitation of the classical theory to mutation age justifies the assumption of constant time in a LD map, except for alleles that were rare at the effective bottleneck time or have arisen since. This assumption is derived from the Malecot model and verified in all samples. Tested measures of relative efficiency, support intervals, and localization error determine the operating characteristics of LD maps that are applicable to every sexually reproducing species, with implications for association mapping, high-resolution linkage maps, evolutionary inference, and identification of recombinogenic sequences.

  17. CD4+ T-cell lines used to evaluate a Mycobacterium avium subsp. paratuberculosis (MAP) peptide vaccine

    DEFF Research Database (Denmark)

    Lybeck, Kari; Sjurseth, Siri K.; Al-Touama, Zainab

    The aim of the study was to establish a protocol for generation of MAP-specific T-cell lines and to use these lines for evaluation of a peptide vaccine. A protocol for culturing T-cell lines from peripheral blood of goats naturally infected with MAP was established. CD4+ T cells were positively...... selected using an anti CD4 mAb and Dynabeads. Sorted CD4+ cells were cultivated with purified protein derivative from MAP (PPDj) or E. coli sonicate, IL-2, and IL-15. After two cultivation cycles, T cells were tested for recall responses in a proliferative T-cell assay. T-cell line responses were...... in average 92 % for PPDj, and -3 % for E. coli sonicate. CD4+ T-cell lines stimulated with PPDj showed a 6 fold increase in IFN- γ production compared to controls. These results indicated that the T-cell lines were MAP-specific. The protocol was subsequently used to evaluate MAP-specific peptides as vaccine...

  18. NeuroLines: A Subway Map Metaphor for Visualizing Nanoscale Neuronal Connectivity

    KAUST Repository

    Al-Awami, Ali K.

    2014-12-31

    We present NeuroLines, a novel visualization technique designed for scalable detailed analysis of neuronal connectivity at the nanoscale level. The topology of 3D brain tissue data is abstracted into a multi-scale, relative distance-preserving subway map visualization that allows domain scientists to conduct an interactive analysis of neurons and their connectivity. Nanoscale connectomics aims at reverse-engineering the wiring of the brain. Reconstructing and analyzing the detailed connectivity of neurons and neurites (axons, dendrites) will be crucial for understanding the brain and its development and diseases. However, the enormous scale and complexity of nanoscale neuronal connectivity pose big challenges to existing visualization techniques in terms of scalability. NeuroLines offers a scalable visualization framework that can interactively render thousands of neurites, and that supports the detailed analysis of neuronal structures and their connectivity. We describe and analyze the design of NeuroLines based on two real-world use-cases of our collaborators in developmental neuroscience, and investigate its scalability to large-scale neuronal connectivity data.

  19. NeuroLines: A Subway Map Metaphor for Visualizing Nanoscale Neuronal Connectivity

    KAUST Repository

    Al-Awami, Ali K.; Beyer, Johanna; Strobelt, Hendrik; Kasthuri, Narayanan; Lichtman, Jeff W.; Pfister, Hanspeter; Hadwiger, Markus

    2014-01-01

    We present NeuroLines, a novel visualization technique designed for scalable detailed analysis of neuronal connectivity at the nanoscale level. The topology of 3D brain tissue data is abstracted into a multi-scale, relative distance-preserving subway map visualization that allows domain scientists to conduct an interactive analysis of neurons and their connectivity. Nanoscale connectomics aims at reverse-engineering the wiring of the brain. Reconstructing and analyzing the detailed connectivity of neurons and neurites (axons, dendrites) will be crucial for understanding the brain and its development and diseases. However, the enormous scale and complexity of nanoscale neuronal connectivity pose big challenges to existing visualization techniques in terms of scalability. NeuroLines offers a scalable visualization framework that can interactively render thousands of neurites, and that supports the detailed analysis of neuronal structures and their connectivity. We describe and analyze the design of NeuroLines based on two real-world use-cases of our collaborators in developmental neuroscience, and investigate its scalability to large-scale neuronal connectivity data.

  20. THE SLOAN DIGITAL SKY SURVEY REVERBERATION MAPPING PROJECT: RAPID C iv BROAD ABSORPTION LINE VARIABILITY

    International Nuclear Information System (INIS)

    Grier, C. J.; Brandt, W. N.; Trump, J. R.; Schneider, D. P.; Hall, P. B.; Shen, Yue; Vivek, M.; Dawson, K. S.; Ak, N. Filiz; Chen, Yuguang; Denney, K. D.; Kochanek, C. S.; Peterson, B. M.; Green, Paul J.; Jiang, Linhua; McGreer, Ian D.; Pâris, I.; Tao, Charling; Wood-Vasey, W. M.; Bizyaev, Dmitry

    2015-01-01

    We report the discovery of rapid variations of a high-velocity C iv broad absorption line trough in the quasar SDSS J141007.74+541203.3. This object was intensively observed in 2014 as a part of the Sloan Digital Sky Survey Reverberation Mapping Project, during which 32 epochs of spectroscopy were obtained with the Baryon Oscillation Spectroscopic Survey spectrograph. We observe significant (>4σ) variability in the equivalent width (EW) of the broad (∼4000 km s −1 wide) C iv trough on rest-frame timescales as short as 1.20 days (∼29 hr), the shortest broad absorption line variability timescale yet reported. The EW varied by ∼10% on these short timescales, and by about a factor of two over the duration of the campaign. We evaluate several potential causes of the variability, concluding that the most likely cause is a rapid response to changes in the incident ionizing continuum. If the outflow is at a radius where the recombination rate is higher than the ionization rate, the timescale of variability places a lower limit on the density of the absorbing gas of n e ≳ 3.9 × 10 5 cm −3 . The broad absorption line variability characteristics of this quasar are consistent with those observed in previous studies of quasars, indicating that such short-term variability may in fact be common and thus can be used to learn about outflow characteristics and contributions to quasar/host-galaxy feedback scenarios

  1. NeuroLines: A Subway Map Metaphor for Visualizing Nanoscale Neuronal Connectivity.

    Science.gov (United States)

    Al-Awami, Ali K; Beyer, Johanna; Strobelt, Hendrik; Kasthuri, Narayanan; Lichtman, Jeff W; Pfister, Hanspeter; Hadwiger, Markus

    2014-12-01

    We present NeuroLines, a novel visualization technique designed for scalable detailed analysis of neuronal connectivity at the nanoscale level. The topology of 3D brain tissue data is abstracted into a multi-scale, relative distance-preserving subway map visualization that allows domain scientists to conduct an interactive analysis of neurons and their connectivity. Nanoscale connectomics aims at reverse-engineering the wiring of the brain. Reconstructing and analyzing the detailed connectivity of neurons and neurites (axons, dendrites) will be crucial for understanding the brain and its development and diseases. However, the enormous scale and complexity of nanoscale neuronal connectivity pose big challenges to existing visualization techniques in terms of scalability. NeuroLines offers a scalable visualization framework that can interactively render thousands of neurites, and that supports the detailed analysis of neuronal structures and their connectivity. We describe and analyze the design of NeuroLines based on two real-world use-cases of our collaborators in developmental neuroscience, and investigate its scalability to large-scale neuronal connectivity data.

  2. Line-Based Registration of Panoramic Images and LiDAR Point Clouds for Mobile Mapping

    Directory of Open Access Journals (Sweden)

    Tingting Cui

    2016-12-01

    Full Text Available For multi-sensor integrated systems, such as the mobile mapping system (MMS, data fusion at sensor-level, i.e., the 2D-3D registration between an optical camera and LiDAR, is a prerequisite for higher level fusion and further applications. This paper proposes a line-based registration method for panoramic images and a LiDAR point cloud collected by a MMS. We first introduce the system configuration and specification, including the coordinate systems of the MMS, the 3D LiDAR scanners, and the two panoramic camera models. We then establish the line-based transformation model for the panoramic camera. Finally, the proposed registration method is evaluated for two types of camera models by visual inspection and quantitative comparison. The results demonstrate that the line-based registration method can significantly improve the alignment of the panoramic image and the LiDAR datasets under either the ideal spherical or the rigorous panoramic camera model, with the latter being more reliable.

  3. The frequency of allelic lethals and complementation maps in natural populations of drosophila melanogaster from Mexico

    Directory of Open Access Journals (Sweden)

    Salceda Victor M.

    2004-01-01

    Full Text Available Departing from a previous study on the genetic loads affecting the second chromosome of Drosophila melanogaster in four natural populations, 171 lethal chromosomes were recovered and maintained as a balanced stocks in the condition Cy L / 1 (l=lethal; of those lethais 24 correspond to population A, 50 to populations B and C and 47 to population D. later on an intra-population allelism test for the four populations was performed for each one. A total of 3807 inter lethal crosses were done yielding a total of i 10 allelic combinations, from them the respective percentage of allelism for each population was calculated and they are as follow: 3.98 % for population A, 1.80 % for population B, 3.67 % for population C and 2.96 % for population D. the observed values for the frequency of allelism in these populations are not significantly different from those reported by other authors in similar studies in natural and/or experimental populations. Beside these values the frequency for singles, doubles, triplets and even quadruplets present in each population were determined, they shown the presence of various complementation maps due to the clustering of few different lethals: also a large complementation map formed by a large cluster involving the presence of 26 different lethals found in population D all of them combined constituting a single unit was found.

  4. Construction of an almond linkage map in an Australian population Nonpareil × Lauranne

    Science.gov (United States)

    2010-01-01

    Background Despite a high genetic similarity to peach, almonds (Prunus dulcis) have a fleshless fruit and edible kernel, produced as a crop for human consumption. While the release of peach genome v1.0 provides an excellent opportunity for almond genetic and genomic studies, well-assessed segregating populations and the respective saturated genetic linkage maps lay the foundation for such studies to be completed in almond. Results Using an almond intraspecific cross between 'Nonpareil' and 'Lauranne' (N × L), we constructed a moderately saturated map with SSRs, SNPs, ISSRs and RAPDs. The N × L map covered 591.4 cM of the genome with 157 loci. The average marker distance of the map was 4.0 cM. The map displayed high synteny and colinearity with the Prunus T × E reference map in all eight linkage groups (G1-G8). The positions of 14 mapped gene-anchored SNPs corresponded approximately with the positions of homologous sequences in the peach genome v1.0. Analysis of Mendelian segregation ratios showed that 17.9% of markers had significantly skewed genotype ratios at the level of P almond map, which is highly syntenic and collinear with the Prunus reference map and peach genome V1.0. Therefore, the well-assessed almond population reported here can be used to investigate the traits of interest under Australian growing conditions, and provides more information on the almond genome for the international community. PMID:20932335

  5. THE STRUCTURE OF THE BROAD-LINE REGION IN ACTIVE GALACTIC NUCLEI. I. RECONSTRUCTED VELOCITY-DELAY MAPS

    International Nuclear Information System (INIS)

    Grier, C. J.; Peterson, B. M.; Pogge, R. W.; De Rosa, G.; Martini, Paul; Kochanek, C. S.; Zu, Y.; Shappee, B.; Beatty, T. G.; Salvo, C. Araya; Bird, J. C.; Horne, Keith; Bentz, M. C.; Denney, K. D.; Siverd, R.; Sergeev, S. G.; Borman, G. A.; Kaspi, S.; Bord, D. J.; Che, X.

    2013-01-01

    We present velocity-resolved reverberation results for five active galactic nuclei. We recovered velocity-delay maps using the maximum entropy method for four objects: Mrk 335, Mrk 1501, 3C 120, and PG 2130+099. For the fifth, Mrk 6, we were only able to measure mean time delays in different velocity bins of the Hβ emission line. The four velocity-delay maps show unique dynamical signatures for each object. For 3C 120, the Balmer lines show kinematic signatures consistent with both an inclined disk and infalling gas, but the He II λ4686 emission line is suggestive only of inflow. The Balmer lines in Mrk 335, Mrk 1501, and PG 2130+099 show signs of infalling gas, but the He II emission in Mrk 335 is consistent with an inclined disk. We also see tentative evidence of combined virial motion and infalling gas from the velocity-binned analysis of Mrk 6. The maps for 3C 120 and Mrk 335 are two of the most clearly defined velocity-delay maps to date. These maps constitute a large increase in the number of objects for which we have resolved velocity-delay maps and provide evidence supporting the reliability of reverberation-based black hole mass measurements.

  6. THE STRUCTURE OF THE BROAD-LINE REGION IN ACTIVE GALACTIC NUCLEI. I. RECONSTRUCTED VELOCITY-DELAY MAPS

    Energy Technology Data Exchange (ETDEWEB)

    Grier, C. J.; Peterson, B. M.; Pogge, R. W.; De Rosa, G.; Martini, Paul; Kochanek, C. S.; Zu, Y.; Shappee, B.; Beatty, T. G.; Salvo, C. Araya; Bird, J. C. [Department of Astronomy, The Ohio State University, 140 W 18th Ave, Columbus, OH 43210 (United States); Horne, Keith [SUPA Physics and Astronomy, University of St. Andrews, Fife, KY16 9SS Scotland (United Kingdom); Bentz, M. C. [Department of Physics and Astronomy, Georgia State University, Astronomy Offices, One Park Place South SE, Suite 700, Atlanta, GA 30303 (United States); Denney, K. D. [Marie Curie Fellow at the Dark Cosmology Centre, Niels Bohr Institute, University of Copenhagen, Juliane Maries Vej 30, DK-2100 Copenhagen (Denmark); Siverd, R. [Department of Physics and Astronomy, Vanderbilt University, 5301 Stevenson Center, Nashville, TN 37235 (United States); Sergeev, S. G.; Borman, G. A. [Crimean Astrophysical Observatory, P/O Nauchny Crimea 98409 (Ukraine); Kaspi, S. [School of Physics and Astronomy, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978 (Israel); Bord, D. J. [Department of Natural Sciences, The University of Michigan - Dearborn, 4901 Evergreen Rd, Dearborn, MI 48128 (United States); Che, X. [Department of Astronomy, University of Michigan, 500 Church Street, Ann Arbor, MI 41809 (United States); and others

    2013-02-10

    We present velocity-resolved reverberation results for five active galactic nuclei. We recovered velocity-delay maps using the maximum entropy method for four objects: Mrk 335, Mrk 1501, 3C 120, and PG 2130+099. For the fifth, Mrk 6, we were only able to measure mean time delays in different velocity bins of the H{beta} emission line. The four velocity-delay maps show unique dynamical signatures for each object. For 3C 120, the Balmer lines show kinematic signatures consistent with both an inclined disk and infalling gas, but the He II {lambda}4686 emission line is suggestive only of inflow. The Balmer lines in Mrk 335, Mrk 1501, and PG 2130+099 show signs of infalling gas, but the He II emission in Mrk 335 is consistent with an inclined disk. We also see tentative evidence of combined virial motion and infalling gas from the velocity-binned analysis of Mrk 6. The maps for 3C 120 and Mrk 335 are two of the most clearly defined velocity-delay maps to date. These maps constitute a large increase in the number of objects for which we have resolved velocity-delay maps and provide evidence supporting the reliability of reverberation-based black hole mass measurements.

  7. Mapping young stellar populations towards Orion with Gaia DR1

    Science.gov (United States)

    Zari, Eleonora; Brown, Anthony G. A.

    2018-04-01

    OB associations are prime sites for the study of star formation processes and of the interaction between young massive stars with the interstellar medium. Furthermore, the kinematics and structure of the nearest OB associations provide detailed insight into the properties and origin of the Gould Belt. In this context, the Orion complex has been extensively studied. However, the spatial distribution of the stellar population is still uncertain: in particular, the distances and ages of the various sub-groups composing the Orion OB association, and their connection to the surrounding interstellar medium, are not well determined. We used the first Gaia data release to characterize the stellar population in Orion, with the goal to obtain new distance and age estimates of the numerous stellar groups composing the Orion OB association. We found evidence of the existence of a young and rich population spread over the entire region, loosely clustered around some known groups. This newly discovered population of young stars provides a fresh view of the star formation history of the Orion region.

  8. QTL Mapping of Agronomic Waterlogging Tolerance Using Recombinant Inbred Lines Derived from Tropical Maize (Zea mays L) Germplasm

    Science.gov (United States)

    Zaidi, Pervez Haider; Rashid, Zerka; Vinayan, Madhumal Thayil; Almeida, Gustavo Dias; Phagna, Ramesh Kumar; Babu, Raman

    2015-01-01

    Waterlogging is an important abiotic stress constraint that causes significant yield losses in maize grown throughout south and south-east Asia due to erratic rainfall patterns. The most economic option to offset the damage caused by waterlogging is to genetically incorporate tolerance in cultivars that are grown widely in the target agro-ecologies. We assessed the genetic variation in a population of recombinant inbred lines (RILs) derived from crossing a waterlogging tolerant line (CAWL-46-3-1) to an elite but sensitive line (CML311-2-1-3) and observed significant range of variation for grain yield (GY) under waterlogging stress along with a number of other secondary traits such as brace roots (BR), chlorophyll content (SPAD), % stem and root lodging (S&RL) among the RILs. Significant positive correlation of GY with BR and SPAD and negative correlation with S&RL indicated the potential use of these secondary traits in selection indices under waterlogged conditions. RILs were genotyped with 331 polymorphic single nucleotide polymorphism (SNP) markers using KASP (Kompetitive Allele Specific PCR) Platform. QTL mapping revealed five QTL on chromosomes 1, 3, 5, 7 and 10, which together explained approximately 30% of phenotypic variance for GY based on evaluation of RIL families under waterlogged conditions, with effects ranging from 520 to 640 kg/ha for individual genomic regions. 13 QTL were identified for various secondary traits associated with waterlogging tolerance, each individually explaining from 3 to 14% of phenotypic variance. Of the 22 candidate genes with known functional domains identified within the physical intervals delimited by the flanking markers of the QTL influencing GY and other secondary traits, six have previously been demonstrated to be associated with anaerobic responses in either maize or other model species. A pair of flanking SNP markers has been identified for each of the QTL and high throughput marker assays were developed to facilitate

  9. Climate Signals: An On-Line Digital Platform for Mapping Climate Change Impacts in Real Time

    Science.gov (United States)

    Cutting, H.

    2016-12-01

    Climate Signals is an on-line digital platform for cataloging and mapping the impacts of climate change. The CS platform specifies and details the chains of connections between greenhouse gas emissions and individual climate events. Currently in open-beta release, the platform is designed to to engage and serve the general public, news media, and policy-makers, particularly in real-time during extreme climate events. Climate Signals consists of a curated relational database of events and their links to climate change, a mapping engine, and a gallery of climate change monitors offering real-time data. For each event in the database, an infographic engine provides a custom attribution "tree" that illustrates the connections to climate change. In addition, links to key contextual resources are aggregated and curated for each event. All event records are fully annotated with detailed source citations and corresponding hyper links. The system of attribution used to link events to climate change in real-time is detailed here. This open-beta release is offered for public user testing and engagement. Launched in May 2016, the operation of this platform offers lessons for public engagement in climate change impacts.

  10. THE SLOAN DIGITAL SKY SURVEY REVERBERATION MAPPING PROJECT: RAPID C iv BROAD ABSORPTION LINE VARIABILITY

    Energy Technology Data Exchange (ETDEWEB)

    Grier, C. J.; Brandt, W. N.; Trump, J. R.; Schneider, D. P. [Department of Astronomy and Astrophysics and Institute for Gravitation and the Cosmos, The Pennsylvania State University, 525 Davey Laboratory, University Park, PA 16802 (United States); Hall, P. B. [Department of Physics and Astronomy, York University, Toronto, ON M3J 1P3 (Canada); Shen, Yue [Carnegie Observatories, 813 Santa Barbara Street, Pasadena, CA 91101 (United States); Vivek, M.; Dawson, K. S. [Department of Physics and Astronomy, University of Utah, Salt Lake City, UT 84112 (United States); Ak, N. Filiz [Faculty of Sciences, Department of Astronomy and Space Sciences, Erciyes University, 38039 Kayseri (Turkey); Chen, Yuguang [Department of Astronomy, School of Physics, Peking University, Beijing 100871 (China); Denney, K. D.; Kochanek, C. S.; Peterson, B. M. [Department of Astronomy, The Ohio State University, 140 West 18th Avenue, Columbus, OH 43210 (United States); Green, Paul J. [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States); Jiang, Linhua [Kavli Institute for Astronomy and Astrophysics, Peking University, Beijing 100871 (China); McGreer, Ian D. [Steward Observatory, The University of Arizona, 933 North Cherry Avenue, Tucson, AZ 85721-0065 (United States); Pâris, I. [INAF-Osservatorio Astronomico di Trieste, Via G. B. Tiepolo 11, I-34131 Trieste (Italy); Tao, Charling [Centre de Physique des Particules de Marseille, Aix-Marseille Universite, CNRS /IN2P3, 163, avenue de Luminy, Case 902, F-13288 Marseille Cedex 09 (France); Wood-Vasey, W. M. [PITT PACC, Department of Physics and Astronomy, University of Pittsburgh, 3941 O’Hara Street, Pittsburgh, PA 15260 (United States); Bizyaev, Dmitry, E-mail: grier@psu.edu [Apache Point Observatory and New Mexico State University, P.O. Box 59, Sunspot, NM, 88349-0059 (United States); and others

    2015-06-10

    We report the discovery of rapid variations of a high-velocity C iv broad absorption line trough in the quasar SDSS J141007.74+541203.3. This object was intensively observed in 2014 as a part of the Sloan Digital Sky Survey Reverberation Mapping Project, during which 32 epochs of spectroscopy were obtained with the Baryon Oscillation Spectroscopic Survey spectrograph. We observe significant (>4σ) variability in the equivalent width (EW) of the broad (∼4000 km s{sup −1} wide) C iv trough on rest-frame timescales as short as 1.20 days (∼29 hr), the shortest broad absorption line variability timescale yet reported. The EW varied by ∼10% on these short timescales, and by about a factor of two over the duration of the campaign. We evaluate several potential causes of the variability, concluding that the most likely cause is a rapid response to changes in the incident ionizing continuum. If the outflow is at a radius where the recombination rate is higher than the ionization rate, the timescale of variability places a lower limit on the density of the absorbing gas of n{sub e} ≳ 3.9 × 10{sup 5} cm{sup −3}. The broad absorption line variability characteristics of this quasar are consistent with those observed in previous studies of quasars, indicating that such short-term variability may in fact be common and thus can be used to learn about outflow characteristics and contributions to quasar/host-galaxy feedback scenarios.

  11. Development of a sensor platform for roadway mapping : part b - mapping the road fog lines : final report.

    Science.gov (United States)

    2015-04-01

    Our objective is the development and evaluation of a low-cost, vehicle-mounted sensor suite capable of generating : map data with lane and road boundary information accurate to the 10 cm (4 in) level. Such a map could be used for : a number of differ...

  12. Comparison of association mapping methods in a complex pedigreed population

    DEFF Research Database (Denmark)

    Sahana, Goutam; Guldbrandtsen, Bernt; Janss, Luc

    2010-01-01

    to collect SNP signals in intervals, to avoid the scattering of a QTL signal over multiple neighboring SNPs. Methods not accounting for genetic background (full pedigree information) performed worse, and methods using haplotypes were considerably worse with a high false-positive rate, probably due...... to the presence of low-frequency haplotypes. It was necessary to account for full relationships among individuals to avoid excess false discovery. Although the methods were tested on a cattle pedigree, the results are applicable to any population with a complex pedigree structure...

  13. QTL Analysis and Nested Association Mapping for Adult Plant Resistance to Powdery Mildew in Two Bread Wheat Populations

    Directory of Open Access Journals (Sweden)

    Yan Ren

    2017-07-01

    Full Text Available CIMMYT wheat (Triticum aestivum L. lines Francolin#1 and Quaiu#3 displayed effective and stable adult plant resistance (APR to Chinese Blumeria graminis f. sp. tritici isolates in the field. To elucidate their genetic basis of resistance, two recombinant inbred line (RIL populations of their crosses with Avocet, the susceptible parent, were phenotyped in Zhengzhou and Shangqiu in the 2014–2015 and 2015–2016 cropping seasons. These populations were also genotyped with SSR (simple sequence repeat markers and DArT (diversity arrays technology markers. Two common significant quantitative trait loci (QTL on wheat chromosomes 1BL and 4BL were detected in both populations by joint and individual inclusive composite interval mapping, explaining 20.3–28.7% and 9.6–15.9% of the phenotypic variance in Avocet × Francolin#1 and 4.8–11.5% and 10.8–18.9% in Avocet × Quaiu#3, respectively. Additional QTL were mapped on chromosomes 1DL and 5BL in Avocet × Francolin#1 and on 2DL and 6BS in Avocet × Quaiu#3. Among these, QPm.heau-1DL is probably a novel APR gene contributing 6.1–8.5% of total phenotypic variance. The QTL on 1BL corresponds to the pleiotropic multi-pathogen resistance gene Yr29/Lr46/Pm39, whereas the QTL on 2DL maps to a similar region where stripe rust resistance gene Yr54 is located. The QTL identified can potentially be used for the improvement of powdery mildew and rust resistance in wheat breeding.

  14. Identification and validation of quantitative trait loci for seed yield, oil and protein contents in two recombinant inbred line populations of soybean.

    Science.gov (United States)

    Wang, Xianzhi; Jiang, Guo-Liang; Green, Marci; Scott, Roy A; Song, Qijian; Hyten, David L; Cregan, Perry B

    2014-10-01

    Soybean seeds contain high levels of oil and protein, and are the important sources of vegetable oil and plant protein for human consumption and livestock feed. Increased seed yield, oil and protein contents are the main objectives of soybean breeding. The objectives of this study were to identify and validate quantitative trait loci (QTLs) associated with seed yield, oil and protein contents in two recombinant inbred line populations, and to evaluate the consistency of QTLs across different environments, studies and genetic backgrounds. Both the mapping population (SD02-4-59 × A02-381100) and validation population (SD02-911 × SD00-1501) were phenotyped for the three traits in multiple environments. Genetic analysis indicated that oil and protein contents showed high heritabilities while yield exhibited a lower heritability in both populations. Based on a linkage map constructed previously with the mapping population and using composite interval mapping and/or interval mapping analysis, 12 QTLs for seed yield, 16 QTLs for oil content and 11 QTLs for protein content were consistently detected in multiple environments and/or the average data over all environments. Of the QTLs detected in the mapping population, five QTLs for seed yield, eight QTLs for oil content and five QTLs for protein content were confirmed in the validation population by single marker analysis in at least one environment and the average data and by ANOVA over all environments. Eight of these validated QTLs were newly identified. Compared with the other studies, seven QTLs for seed yield, eight QTLs for oil content and nine QTLs for protein content further verified the previously reported QTLs. These QTLs will be useful for breeding higher yield and better quality cultivars, and help effectively and efficiently improve yield potential and nutritional quality in soybean.

  15. Inbreeding depression in maize populations and its effects on the obtention of promising inbred lines

    Directory of Open Access Journals (Sweden)

    Deoclecio Domingos Garbuglio

    2017-10-01

    Full Text Available Inbreeding can potentially be used for the development of inbred lines containing alleles of interest, but the genetic causes that control inbreeding depression are not completely known, and there are few studies found in the literature. The present study aimed to obtain estimates of inbreeding depression for eight traits in seven tropical maize populations, analyze the effects of inbreeding over generations and environments, and predict the behavior of inbred lines in future generation S? through linear regression methods. It was found that regardless of the base population used, prediction values could vary when the model was based on only 2 generations of inbreeding due to the environmental component. The influence of the environment in this type of study could be reduced when considering 3 generations of inbreeding, allowing greater precision in predicting the phenotypes of inbred lines. The use of linear regression was effective for inbred line prediction for the different agronomic traits evaluated. The use of 3 levels of inbreeding minimizes the effects of the environmental component in inbred line prediction for grain yield. GO-S was the most promising population for inbred line extraction.

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

    Directory of Open Access Journals (Sweden)

    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.

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

    DEFF Research Database (Denmark)

    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...

  18. Wired: impacts of increasing power line use by a growing bird population

    Science.gov (United States)

    Moreira, Francisco; Encarnação, Vitor; Rosa, Gonçalo; Gilbert, Nathalie; Infante, Samuel; Costa, Julieta; D'Amico, Marcello; Martins, Ricardo C.; Catry, Inês

    2017-02-01

    Power lines are increasingly widespread across many regions of the planet. Although these linear infrastructures are known for their negative impacts on bird populations, through collision and electrocution, some species take advantage of electricity pylons for nesting. In this case, estimation of the net impact of these infrastructures at the population level requires an assessment of trade-offs between positive and negative impacts. We compiled historical information (1958-2014) of the Portuguese white stork Ciconia ciconia population to analyze long-term changes in numbers, distribution range and use of nesting structures. White stork population size increased 660% up to 12000 breeding pairs between 1984 and 2014. In the same period, the proportion of nests on electricity pylons increased from 1% to 25%, likely facilitated by the 60% increase in the length of the very high tension power line grid (holding the majority of the nests) in the stork’s distribution range. No differences in breeding success were registered for storks nesting on electricity pylons versus other structures, but a high risk of mortality by collision and electrocution with power lines was estimated. We discuss the implications of this behavioral change, and of the management responses by power line companies, both for stork populations and for managers.

  19. An Atlas of ShakeMaps and population exposure catalog for earthquake loss modeling

    Science.gov (United States)

    Allen, T.I.; Wald, D.J.; Earle, P.S.; Marano, K.D.; Hotovec, A.J.; Lin, K.; Hearne, M.G.

    2009-01-01

    We present an Atlas of ShakeMaps and a catalog of human population exposures to moderate-to-strong ground shaking (EXPO-CAT) for recent historical earthquakes (1973-2007). The common purpose of the Atlas and exposure catalog is to calibrate earthquake loss models to be used in the US Geological Survey's Prompt Assessment of Global Earthquakes for Response (PAGER). The full ShakeMap Atlas currently comprises over 5,600 earthquakes from January 1973 through December 2007, with almost 500 of these maps constrained-to varying degrees-by instrumental ground motions, macroseismic intensity data, community internet intensity observations, and published earthquake rupture models. The catalog of human exposures is derived using current PAGER methodologies. Exposure to discrete levels of shaking intensity is obtained by correlating Atlas ShakeMaps with a global population database. Combining this population exposure dataset with historical earthquake loss data, such as PAGER-CAT, provides a useful resource for calibrating loss methodologies against a systematically-derived set of ShakeMap hazard outputs. We illustrate two example uses for EXPO-CAT; (1) simple objective ranking of country vulnerability to earthquakes, and; (2) the influence of time-of-day on earthquake mortality. In general, we observe that countries in similar geographic regions with similar construction practices tend to cluster spatially in terms of relative vulnerability. We also find little quantitative evidence to suggest that time-of-day is a significant factor in earthquake mortality. Moreover, earthquake mortality appears to be more systematically linked to the population exposed to severe ground shaking (Modified Mercalli Intensity VIII+). Finally, equipped with the full Atlas of ShakeMaps, we merge each of these maps and find the maximum estimated peak ground acceleration at any grid point in the world for the past 35 years. We subsequently compare this "composite ShakeMap" with existing global

  20. High resolution population distribution maps for Southeast Asia in 2010 and 2015.

    Science.gov (United States)

    Gaughan, Andrea E; Stevens, Forrest R; Linard, Catherine; Jia, Peng; Tatem, Andrew J

    2013-01-01

    Spatially accurate, contemporary data on human population distributions are vitally important to many applied and theoretical researchers. The Southeast Asia region has undergone rapid urbanization and population growth over the past decade, yet existing spatial population distribution datasets covering the region are based principally on population count data from censuses circa 2000, with often insufficient spatial resolution or input data to map settlements precisely. Here we outline approaches to construct a database of GIS-linked circa 2010 census data and methods used to construct fine-scale (∼100 meters spatial resolution) population distribution datasets for each country in the Southeast Asia region. Landsat-derived settlement maps and land cover information were combined with ancillary datasets on infrastructure to model population distributions for 2010 and 2015. These products were compared with those from two other methods used to construct commonly used global population datasets. Results indicate mapping accuracies are consistently higher when incorporating land cover and settlement information into the AsiaPop modelling process. Using existing data, it is possible to produce detailed, contemporary and easily updatable population distribution datasets for Southeast Asia. The 2010 and 2015 datasets produced are freely available as a product of the AsiaPop Project and can be downloaded from: www.asiapop.org.

  1. High resolution population distribution maps for Southeast Asia in 2010 and 2015.

    Directory of Open Access Journals (Sweden)

    Andrea E Gaughan

    Full Text Available Spatially accurate, contemporary data on human population distributions are vitally important to many applied and theoretical researchers. The Southeast Asia region has undergone rapid urbanization and population growth over the past decade, yet existing spatial population distribution datasets covering the region are based principally on population count data from censuses circa 2000, with often insufficient spatial resolution or input data to map settlements precisely. Here we outline approaches to construct a database of GIS-linked circa 2010 census data and methods used to construct fine-scale (∼100 meters spatial resolution population distribution datasets for each country in the Southeast Asia region. Landsat-derived settlement maps and land cover information were combined with ancillary datasets on infrastructure to model population distributions for 2010 and 2015. These products were compared with those from two other methods used to construct commonly used global population datasets. Results indicate mapping accuracies are consistently higher when incorporating land cover and settlement information into the AsiaPop modelling process. Using existing data, it is possible to produce detailed, contemporary and easily updatable population distribution datasets for Southeast Asia. The 2010 and 2015 datasets produced are freely available as a product of the AsiaPop Project and can be downloaded from: www.asiapop.org.

  2. Method for mapping population-based case-control studies: an application using generalized additive models

    Directory of Open Access Journals (Sweden)

    Aschengrau Ann

    2006-06-01

    Full Text Available Abstract Background Mapping spatial distributions of disease occurrence and risk can serve as a useful tool for identifying exposures of public health concern. Disease registry data are often mapped by town or county of diagnosis and contain limited data on covariates. These maps often possess poor spatial resolution, the potential for spatial confounding, and the inability to consider latency. Population-based case-control studies can provide detailed information on residential history and covariates. Results Generalized additive models (GAMs provide a useful framework for mapping point-based epidemiologic data. Smoothing on location while controlling for covariates produces adjusted maps. We generate maps of odds ratios using the entire study area as a reference. We smooth using a locally weighted regression smoother (loess, a method that combines the advantages of nearest neighbor and kernel methods. We choose an optimal degree of smoothing by minimizing Akaike's Information Criterion. We use a deviance-based test to assess the overall importance of location in the model and pointwise permutation tests to locate regions of significantly increased or decreased risk. The method is illustrated with synthetic data and data from a population-based case-control study, using S-Plus and ArcView software. Conclusion Our goal is to develop practical methods for mapping population-based case-control and cohort studies. The method described here performs well for our synthetic data, reproducing important features of the data and adequately controlling the covariate. When applied to the population-based case-control data set, the method suggests spatial confounding and identifies statistically significant areas of increased and decreased odds ratios.

  3. Construction of an almond linkage map in an Australian population Nonpareil × Lauranne

    Directory of Open Access Journals (Sweden)

    Gibson John P

    2010-10-01

    Full Text Available Abstract Background Despite a high genetic similarity to peach, almonds (Prunus dulcis have a fleshless fruit and edible kernel, produced as a crop for human consumption. While the release of peach genome v1.0 provides an excellent opportunity for almond genetic and genomic studies, well-assessed segregating populations and the respective saturated genetic linkage maps lay the foundation for such studies to be completed in almond. Results Using an almond intraspecific cross between 'Nonpareil' and 'Lauranne' (N × L, we constructed a moderately saturated map with SSRs, SNPs, ISSRs and RAPDs. The N × L map covered 591.4 cM of the genome with 157 loci. The average marker distance of the map was 4.0 cM. The map displayed high synteny and colinearity with the Prunus T × E reference map in all eight linkage groups (G1-G8. The positions of 14 mapped gene-anchored SNPs corresponded approximately with the positions of homologous sequences in the peach genome v1.0. Analysis of Mendelian segregation ratios showed that 17.9% of markers had significantly skewed genotype ratios at the level of P ® 3 were compared, and their high degree of similarity was evident despite the positional inconsistency of a few markers. Conclusions We presented a moderately saturated Australian almond map, which is highly syntenic and collinear with the Prunus reference map and peach genome V1.0. Therefore, the well-assessed almond population reported here can be used to investigate the traits of interest under Australian growing conditions, and provides more information on the almond genome for the international community.

  4. Genetic Analysis of Health-Related Secondary Metabolites in a Brassica rapa Recombinant Inbred Line Population

    NARCIS (Netherlands)

    Bagheri, H.; Soda, El M.; Kim, H.K.; Fritsche, S.; Jung, C.; Aarts, M.G.M.

    2013-01-01

    The genetic basis of the wide variation for nutritional traits in Brassica rapa is largely unknown. A new Recombinant Inbred Line (RIL) population was profiled using High Performance Liquid Chromatography (HPLC) and Nuclear Magnetic Resonance (NMR) analysis to detect quantitative trait loci (QTLs)

  5. Pipeline mapping and strain assessment using ILI (In-line Inspection) tolls

    Energy Technology Data Exchange (ETDEWEB)

    Purvis, Brian [GE PII Pipeline Solutions, Rio de Janeiro, RJ (Brazil); Huewener, Thomas [E.ON Ruhrgas AG, Essen (Germany)

    2009-07-01

    GE PII IMU Mapping inspection system measures pipeline location coordinates (x, y, z) and provides data for determining pipeline curvature and consequential pipeline bending strain. The changes in strain can be used in the application of structural analyses and integrity evaluation of pipeline systems. This paper reviews the Inertia Measuring Unit (IMU) system and field investigation works performed on a high-pressure gas pipeline for E.ON Ruhrgas AG. The Inertial Measuring Unit of the pipeline inspection tool provides continuous measurement of the pipeline centreline coordinates. More than one inspection run was performed which allowed a more accurate strain comparison to be made. Repeatability is important to establish the reasons for increasing strain values detected at specific pipeline sections through in-line inspection surveys conducted in regular intervals over many years. Moreover, the flexibility resulting from a combination of different sensor technologies, makes it possible to provide a more complete picture of the overall situation. This paper reviews the work involved in detecting, locating and determining the magnitude and type of strain corresponding to the pipeline movement in field. (author)

  6. LINE-1 Hypomethylation is Associated with the Risk of Coronary Heart Disease in Chinese Population

    Energy Technology Data Exchange (ETDEWEB)

    Wei, Li [Department of Cardiology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin (China); Liu, Shuchuan [Department of Hematology, The First Affiliated Hospital of Harbin Medical University, Harbin (China); Su, Zhendong; Cheng, Rongchao; Bai, Xiuping; Li, Xueqi, E-mail: xueqi-li@163.com [Department of Cardiology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin (China)

    2014-05-15

    Global methylation level in blood leukocyte DNA has been associated with the risk of coronary heart disease (CHD), with inconsistent results in various populations. Similar data are lacking in Chinese population where different genetic, lifestyle and environmental factors may affect DNA methylation and its risk relationship with CHD. To examine whether global methylation is associated with the risk of CHD in Chinese population. A total of 334 cases with CHD and 788 healthy controls were included. Global methylation in blood leukocyte DNA was estimated by analyzing LINE-1 repeats using bisulfite pyrosequencing. In an initial analysis restricted to control subjects, LINE-1 level reduced significantly with aging, elevated total cholesterol, and diagnosis of diabetes. In the case-control analysis, reduced LINE-1 methylation was associated with increased risk of CHD; analysis by quartile revealed odds ratios (95%CI) of 0.9 (0.6-1.4), 1.9 (1.3-2.9) and 2.3 (1.6-3.5) for the third, second and first (lowest) quartile (P{sub trend} < 0.001), respectively, compared to the fourth (highest) quartile. Lower (LINE-1 methylation was associated with a 2.2-fold (95%CI = 1.7-3.0) increased risk of CHD. The lower LINE-1-related CHD risk estimates tended to be stronger among subjects with the highest tertile of homocysteine (P{sub interaction} = 0.042) and those with diagnosis of hypertension (P{sub interaction} = 0.012). LINE-1 hypomethylation is associated with the risk of CHD in Chinese population. Potential CHD risk factors such as older age, elevated total cholesterol, and diagnosis of diabetes may have impact on global DNA methylation, whereby exerting their effect on CHD risk.

  7. LINE-1 Hypomethylation is Associated with the Risk of Coronary Heart Disease in Chinese Population

    International Nuclear Information System (INIS)

    Wei, Li; Liu, Shuchuan; Su, Zhendong; Cheng, Rongchao; Bai, Xiuping; Li, Xueqi

    2014-01-01

    Global methylation level in blood leukocyte DNA has been associated with the risk of coronary heart disease (CHD), with inconsistent results in various populations. Similar data are lacking in Chinese population where different genetic, lifestyle and environmental factors may affect DNA methylation and its risk relationship with CHD. To examine whether global methylation is associated with the risk of CHD in Chinese population. A total of 334 cases with CHD and 788 healthy controls were included. Global methylation in blood leukocyte DNA was estimated by analyzing LINE-1 repeats using bisulfite pyrosequencing. In an initial analysis restricted to control subjects, LINE-1 level reduced significantly with aging, elevated total cholesterol, and diagnosis of diabetes. In the case-control analysis, reduced LINE-1 methylation was associated with increased risk of CHD; analysis by quartile revealed odds ratios (95%CI) of 0.9 (0.6-1.4), 1.9 (1.3-2.9) and 2.3 (1.6-3.5) for the third, second and first (lowest) quartile (P trend < 0.001), respectively, compared to the fourth (highest) quartile. Lower (LINE-1 methylation was associated with a 2.2-fold (95%CI = 1.7-3.0) increased risk of CHD. The lower LINE-1-related CHD risk estimates tended to be stronger among subjects with the highest tertile of homocysteine (P interaction = 0.042) and those with diagnosis of hypertension (P interaction = 0.012). LINE-1 hypomethylation is associated with the risk of CHD in Chinese population. Potential CHD risk factors such as older age, elevated total cholesterol, and diagnosis of diabetes may have impact on global DNA methylation, whereby exerting their effect on CHD risk

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

    Science.gov (United States)

    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.

  9. First light - II. Emission line extinction, population III stars, and X-ray binaries

    Science.gov (United States)

    Barrow, Kirk S. S.; Wise, John H.; Aykutalp, Aycin; O'Shea, Brian W.; Norman, Michael L.; Xu, Hao

    2018-02-01

    We produce synthetic spectra and observations for metal-free stellar populations and high-mass X-ray binaries in the Renaissance Simulations at a redshift of 15. We extend our methodology from the first paper in the series by modelling the production and extinction of emission lines throughout a dusty and metal-enriched interstellar and circum-galactic media extracted from the simulation, using a Monte Carlo calculation. To capture the impact of high-energy photons, we include all frequencies from hard X-ray to far-infrared with enough frequency resolution to discern line emission and absorption profiles. The most common lines in our sample in order of their rate of occurrence are Ly α, the C IV λλ1548, 1551 doublet, H α, and the Ca II λλλ8498, 8542, 8662 triplet. The best scenario for a direct observation of a metal-free stellar population is a merger between two Population III Galaxies. In mergers between metal-enriched and metal-free stellar populations, some characteristics may be inferred indirectly. Single Population III galaxies are too dim to be observed photometrically at z = 15. Ly α emission is discernible by JWST as an increase in J200w - J277w colour off the intrinsic stellar tracks. Observations of metal-free stars will be difficult, though not impossible, with the next generation of space telescopes.

  10. Analysis of aneuploid lines of bread wheat to map chromosomal locations of genes controlling root hair length.

    Science.gov (United States)

    Liu, Miao; Rathjen, Tina; Weligama, Kumara; Forrest, Kerrie; Hayden, Matthew; Delhaize, Emmanuel

    2017-06-01

    Long root hairs enable the efficient uptake of poorly mobile nutrients such as phosphorus. Mapping the chromosomal locations of genes that control root hair length can help exploit the natural variation within crops to develop improved cultivars. Genetic stocks of the wheat cultivar 'Chinese Spring' were used to map genes that control root hair length. Aneuploid stocks of 'Chinese Spring' were screened using a rapid method based on rhizosheath size and then selected lines were assayed for root hair length to identify chromosomes harbouring genes controlling root hair length. A series of lines with various fractional deletions of candidate chromosomes were then screened to map the root hair loci more accurately. A line with a deletion in chromosome 5A was analysed with a 90 000 single nucleotide polymorphism (SNP) array. The phosphorus acquisition efficiency (PAE) of one deletion line was compared with that of euploid 'Chinese Spring' by growing the seedlings in pots at low and luxury phosphorus supplies. Chromosomes 1A, 1D and 5A were found to harbour genes controlling root hair length. The 90 000 SNP array identified two candidate genes controlling root hair length located on chromosome 5A. The line with a deletion in chromosome 5A had root hairs that were approx. 20 % shorter than euploid 'Chinese Spring', but this was insufficient to reduce its PAE. A rapid screen for rhizosheath size enabled chromosomal regions controlling root hair length to be mapped in the wheat cultivar 'Chinese Spring' and subsequent analysis with an SNP array identified candidate genes controlling root hair length. The difference in root hair length between euploid 'Chinese Spring' and a deletion line identified in the rapid screen was still apparent, albeit attenuated, when the seedlings were grown on a fully fertilized soil. © The Author 2017. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  11. Mapping quantitative trait loci in a selectively genotyped outbred population using a mixture model approach

    NARCIS (Netherlands)

    Johnson, David L.; Jansen, Ritsert C.; Arendonk, Johan A.M. van

    1999-01-01

    A mixture model approach is employed for the mapping of quantitative trait loci (QTL) for the situation where individuals, in an outbred population, are selectively genotyped. Maximum likelihood estimation of model parameters is obtained from an Expectation-Maximization (EM) algorithm facilitated by

  12. Linkage mapping in a watermelon population segregating for fusarium wilt resistance

    Science.gov (United States)

    Leigh K. Hawkins; Fenny Dane; Thomas L. Kubisiak; Billy B. Rhodes; Robert L. Jarret

    2001-01-01

    Isozyme, randomly amplified polymorphic DNA (RAPD), and simple sequence repeats (SSR) markers were used to generate a linkage map in an F2 and F3 watermelon (Citrullus lanatus (Thumb.) Matsum. & Nakai) population derived from a cross between the fusarium wilt (Fusarium oxysporum f....

  13. Mapping the distinctive populations of lymphatic endothelial cells in different zones of human lymph nodes.

    Directory of Open Access Journals (Sweden)

    Saem Mul Park

    Full Text Available The lymphatic sinuses in human lymph nodes (LNs are crucial to LN function yet their structure remains poorly defined. Much of our current knowledge of lymphatic sinuses derives from rodent models, however human LNs differ substantially in their sinus structure, most notably due to the presence of trabeculae and trabecular lymphatic sinuses that rodent LNs lack. Lymphatic sinuses are bounded and traversed by lymphatic endothelial cells (LECs. A better understanding of LECs in human LNs is likely to improve our understanding of the regulation of cell trafficking within LNs, now an important therapeutic target, as well as disease processes that involve lymphatic sinuses. We therefore sought to map all the LECs within human LNs using multicolor immunofluorescence microscopy to visualize the distribution of a range of putative markers. PROX1 was the only marker that uniquely identified the LECs lining and traversing all the sinuses in human LNs. In contrast, LYVE1 and STAB2 were only expressed by LECs in the paracortical and medullary sinuses in the vast majority of LNs studied, whilst the subcapsular and trabecular sinuses lacked these molecules. These data highlight the existence of at least two distinctive populations of LECs within human LNs. Of the other LEC markers, we confirmed VEGFR3 was not specific for LECs, and CD144 and CD31 stained both LECs and blood vascular endothelial cells (BECs; in contrast, CD59 and CD105 stained BECs but not LECs. We also showed that antigen-presenting cells (APCs in the sinuses could be clearly distinguished from LECs by their expression of CD169, and their lack of expression of PROX1 and STAB2, or endothelial markers such as CD144. However, both LECs and sinus APCs were stained with DCN46, an antibody commonly used to detect CD209.

  14. FEDERAL USERS CONFERENCE PRODUCT LINE TOOL SET (PLTS) MAP PRODUCTION SYSTEM (MPS) ATLAS CUSTOM GRIDS [Rev 0 was draft

    Energy Technology Data Exchange (ETDEWEB)

    HAYENGA, J.L.

    2006-12-19

    Maps, and more importantly Atlases, are assisting the user community in managing a large land area with complex issues, the most complex of which is the management of nuclear waste. The techniques and experiences discussed herein were gained while developing several atlases for use at the US Department of Energy's Hanford Site. The user community requires the ability to locate not only waste sites, but other features as well. Finding a specific waste site on a map and in the field is a difficult task at a site the size of Hanford. To find a specific waste site, the user begins by locating the item or object in an index, then locating the feature on the corresponding map within an atlas. Locating features requires a method for indexing them. The location index and how to place it on a map or atlas is the central theme presented in this article. The user requirements for atlases forced the design team to develop new and innovative solutions for requirements that Product Line Tool Set (PLTS) Map Production System (MPS)-Atlas was not designed to handle. The layout of the most complex atlases includes custom reference grids, multiple data frames, multiple map series, and up to 250 maps. All of these functional requirements are at the extreme edge of the capabilities of PLTS MPS-Atlas. This document outlines the setup of an atlas using PLTS MPS-Atlas to meet these requirements.

  15. FEDERAL USERS CONFERENCE PRODUCT LINE TOOL SET (PLTS) MAP PRODUCTION SYSTEM (MPS) ATLAS CUSTOM GRIDS [Rev 0 was draft

    International Nuclear Information System (INIS)

    HAYENGA, J.L.

    2006-01-01

    Maps, and more importantly Atlases, are assisting the user community in managing a large land area with complex issues, the most complex of which is the management of nuclear waste. The techniques and experiences discussed herein were gained while developing several atlases for use at the US Department of Energy's Hanford Site. The user community requires the ability to locate not only waste sites, but other features as well. Finding a specific waste site on a map and in the field is a difficult task at a site the size of Hanford. To find a specific waste site, the user begins by locating the item or object in an index, then locating the feature on the corresponding map within an atlas. Locating features requires a method for indexing them. The location index and how to place it on a map or atlas is the central theme presented in this article. The user requirements for atlases forced the design team to develop new and innovative solutions for requirements that Product Line Tool Set (PLTS) Map Production System (MPS)-Atlas was not designed to handle. The layout of the most complex atlases includes custom reference grids, multiple data frames, multiple map series, and up to 250 maps. All of these functional requirements are at the extreme edge of the capabilities of PLTS MPS-Atlas. This document outlines the setup of an atlas using PLTS MPS-Atlas to meet these requirements

  16. A simple highly accurate field-line mapping technique for three-dimensional Monte Carlo modeling of plasma edge transport

    International Nuclear Information System (INIS)

    Feng, Y.; Sardei, F.; Kisslinger, J.

    2005-01-01

    The paper presents a new simple and accurate numerical field-line mapping technique providing a high-quality representation of field lines as required by a Monte Carlo modeling of plasma edge transport in the complex magnetic boundaries of three-dimensional (3D) toroidal fusion devices. Using a toroidal sequence of precomputed 3D finite flux-tube meshes, the method advances field lines through a simple bilinear, forward/backward symmetric interpolation at the interfaces between two adjacent flux tubes. It is a reversible field-line mapping (RFLM) algorithm ensuring a continuous and unique reconstruction of field lines at any point of the 3D boundary. The reversibility property has a strong impact on the efficiency of modeling the highly anisotropic plasma edge transport in general closed or open configurations of arbitrary ergodicity as it avoids artificial cross-field diffusion of the fast parallel transport. For stellarator-symmetric magnetic configurations, which are the standard case for stellarators, the reversibility additionally provides an average cancellation of the radial interpolation errors of field lines circulating around closed magnetic flux surfaces. The RFLM technique has been implemented in the 3D edge transport code EMC3-EIRENE and is used routinely for plasma transport modeling in the boundaries of several low-shear and high-shear stellarators as well as in the boundary of a tokamak with 3D magnetic edge perturbations

  17. Population trapping: The mechanism for the lost resonance lines in Pm-like ions

    Science.gov (United States)

    Kato, Daiji; Sakaue, Hiroyuki A.; Murakami, Izumi; Nakamura, Nobuyuki

    2017-10-01

    We report a population kinetics study on line emissions of the Pm-like Bi22+ performed by using a collisional-radiative (CR) model. Population rates of excited levels are analyzed to explain the population trapping in the 4f135s2 state which causes the loss of the 5s - 5p resonance lines in emission spectra. Based on the present analysis, we elucidate why the population trapping is not facilitated for a meta-stable excited level of the Sm-like Bi21+. The emission line spectra are calculated for the Pm-like isoelectronic sequence from Au18+ through W13+ and compared with experimental measurements by electron-beam-ion-traps (EBITs). Structures of the spectra are similar for all of the cases except for calculated W13+ spectra. The calculated spectra are hardly reconciled with the measured W13+ spectrum using the compact electron-beam-ion-trap (CoBIT) [Phys. Rev. A 92 (2015) 022510].

  18. Analysis of cytoplasmic effects and fine-mapping of a genic male sterile line in rice.

    Directory of Open Access Journals (Sweden)

    Peng Qin

    Full Text Available Cytoplasm has substantial genetic effects on progeny and is important for yield improvement in rice breeding. Studies on the cytoplasmic effects of cytoplasmic male sterility (CMS show that most types of CMS have negative effects on yield-related traits and that these negative effects vary among CMS. Some types of genic male sterility (GMS, including photo-thermo sensitive male sterility (PTMS, have been widely used in rice breeding, but the cytoplasmic effects of GMS remain unknown. Here, we identified a GMS mutant line, h2s, which exhibited small, white anthers and failed to produce mature pollen. Unlike CMS, the h2s had significant positive cytoplasmic effects on the seed set rate, weight per panicle, yield, and general combining ability (GCA for plant height, seed set rate, weight per panicle, and yield. These effects indicated that h2s cytoplasm may show promise for the improvement of rice yield. Genetic analysis suggested that the phenotype of h2s was controlled by a single recessive locus. We mapped h2s to a 152 kb region on chromosome 6, where 22 candidate genes were predicted. None of the 22 genes had previously been reported to be responsible for the phenotypes of h2s. Sequencing analysis showed a 12 bp deletion in the sixth exon of Loc_Os06g40550 in h2s in comparison to wild type, suggesting that Loc_Os06g40550 is the best candidate gene. These results lay a strong foundation for cloning of the H2S gene to elucidate the molecular mechanism of male reproduction.

  19. Evaluation of Intrinsic Water Use Efficiency and Ecophysiological Modelling on a Potato Dihaploid Mapping Population

    DEFF Research Database (Denmark)

    Topbjerg, Henrik Bak

    of the solution the crop has to be able to tolerate drought. In this study, a dihaploid potato mapping population has been used to investigate clonal performance in intrinsic water use efficiency (WUEi) under progressive drought achieved in greenhouse and under field conditions. The mapping population revealed...... on environmental sustainability. Future growth in the global population predicts that the agricultural output will have to increase considerably if malnutrition and famine are to be prevented. On this basis, the development of crops capable of producing higher yields under water scarce situations is being...... progression in the development of drought tolerant crop cultivars, faster screening methods have to be developed. Here, it was found that the chlorophyll content index could be a useful screening method for higher WUEi under greenhouse conditions. However, such methods must rely on physiological trait...

  20. Interindividual registration and dose mapping for voxelwise population analysis of rectal toxicity in prostate cancer radiotherapy

    Energy Technology Data Exchange (ETDEWEB)

    Dréan, Gaël; Acosta, Oscar, E-mail: Oscar.Acosta@univ-rennes1.fr; Simon, Antoine; Haigron, Pascal [INSERM, U1099, Rennes F-35000 (France); Université de Rennes 1, LTSI, Rennes F-35000 (France); Lafond, Caroline; Crevoisier, Renaud de [INSERM, U1099, Rennes F-35000 (France); Université de Rennes 1, LTSI, Rennes F-35000 (France); Département de Radiothérapie, Center Eugène Marquis, Rennes F-35000 (France)

    2016-06-15

    Purpose: Recent studies revealed a trend toward voxelwise population analysis in order to understand the local dose/toxicity relationships in prostate cancer radiotherapy. Such approaches require, however, an accurate interindividual mapping of the anatomies and 3D dose distributions toward a common coordinate system. This step is challenging due to the high interindividual variability. In this paper, the authors propose a method designed for interindividual nonrigid registration of the rectum and dose mapping for population analysis. Methods: The method is based on the computation of a normalized structural description of the rectum using a Laplacian-based model. This description takes advantage of the tubular structure of the rectum and its centerline to be embedded in a nonrigid registration-based scheme. The performances of the method were evaluated on 30 individuals treated for prostate cancer in a leave-one-out cross validation. Results: Performance was measured using classical metrics (Dice score and Hausdorff distance), along with new metrics devised to better assess dose mapping in relation with structural deformation (dose-organ overlap). Considering these scores, the proposed method outperforms intensity-based and distance maps-based registration methods. Conclusions: The proposed method allows for accurately mapping interindividual 3D dose distributions toward a single anatomical template, opening the way for further voxelwise statistical analysis.

  1. Internal electric-field-lines distribution in CdZnTe detectors measured using X-ray mapping

    International Nuclear Information System (INIS)

    Bolotnikov, A.E.; Camarda, G.S.; Cui, Y.; Hossain, A.; Yang, G.; Yao, H.W.; James, R.B.

    2009-01-01

    The ideal operation of CdZnTe devices entails having a uniformly distributed internal electric field. Such uniformity especially is critical for thick long-drift-length detectors, such as large-volume CPG and 3-D multi-pixel devices. Using a high-spatial resolution X-ray mapping technique, we investigated the distribution of the electric field in real devices. Our measurements demonstrate that in thin detectors, 1 cm, with a large aspect ratio (thickness-to-width ratio), we observed two effects: the electric field lines bending away from or towards the side surfaces, which we called, respectively, the focusing field-line distribution and the defocusing field-line distribution. In addition to these large-scale variations, the field-line distributions were locally perturbed by the presence of extended defects and residual strains existing inside the crystals. We present our data clearly demonstrating the non-uniformity of the internal electric field

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

    Science.gov (United States)

    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

  3. Emission-line diagnostics of nearby H II regions including interacting binary populations

    Science.gov (United States)

    Xiao, Lin; Stanway, Elizabeth R.; Eldridge, J. J.

    2018-06-01

    We present numerical models of the nebular emission from H II regions around young stellar populations over a range of compositions and ages. The synthetic stellar populations include both single stars and interacting binary stars. We compare these models to the observed emission lines of 254 H II regions of 13 nearby spiral galaxies and 21 dwarf galaxies drawn from archival data. The models are created using the combination of the BPASS (Binary Population and Spectral Synthesis) code with the photoionization code CLOUDY to study the differences caused by the inclusion of interacting binary stars in the stellar population. We obtain agreement with the observed emission line ratios from the nearby star-forming regions and discuss the effect of binary-star evolution pathways on the nebular ionization of H II regions. We find that at population ages above 10 Myr, single-star models rapidly decrease in flux and ionization strength, while binary-star models still produce strong flux and high [O III]/H β ratios. Our models can reproduce the metallicity of H II regions from spiral galaxies, but we find higher metallicities than previously estimated for the H II regions from dwarf galaxies. Comparing the equivalent width of H β emission between models and observations, we find that accounting for ionizing photon leakage can affect age estimates for H II regions. When it is included, the typical age derived for H II regions is 5 Myr from single-star models, and up to 10 Myr with binary-star models. This is due to the existence of binary-star evolution pathways, which produce more hot Wolf-Rayet and helium stars at older ages. For future reference, we calculate new BPASS binary maximal starburst lines as a function of metallicity, and for the total model population, and present these in Appendix A.

  4. Mapping genes governing flower architecture and pollen development in a double mutant population of carrot

    Directory of Open Access Journals (Sweden)

    Holger eBudahn

    2014-10-01

    Full Text Available A linkage map of carrot (Daucus carota L. was developed in order to study reproductive traits. The F2 mapping population derived from an initial cross between a yellow leaf (yel chlorophyll mutant and a compressed lamina (cola mutant with unique flower defects of the sporophytic parts of male and female organs. The genetic map has a total length of 781 cM and included 285 loci. The length of the nine linkage groups ranged between 65 cM and 145 cM. All linkage groups have been anchored to the reference map. The objective of this study was the generation of a well-saturated linkage map of D. carota. Mapping of the cola-locus associated with flower development and fertility was successfully demonstrated. Two MADS-box genes (DcMADS3, DcMADS5 with prominent roles in flowering and reproduction as well as three additional genes (DcAOX2a, DcAOX2b, DcCHS2 with further importance for male reproduction were assigned to different loci that did not co-segregate with the cola-locus.

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

    DEFF Research Database (Denmark)

    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...

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

    Directory of Open Access Journals (Sweden)

    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.

  7. Yield-related salinity tolerance traits identified in a nested association mapping (NAM) population of wild barley

    KAUST Repository

    Saade, Stephanie

    2016-09-02

    Producing sufficient food for nine billion people by 2050 will be constrained by soil salinity, especially in irrigated systems. To improve crop yield, greater understanding of the genetic control of traits contributing to salinity tolerance in the field is needed. Here, we exploit natural variation in exotic germplasm by taking a genome-wide association approach to a new nested association mapping population of barley called HEB-25. The large population (1,336 genotypes) allowed cross-validation of loci, which, along with two years of phenotypic data collected from plants irrigated with fresh and saline water, improved statistical power. We dissect the genetic architecture of flowering time under high salinity and we present genes putatively affecting this trait and salinity tolerance. In addition, we identify a locus on chromosome 2H where, under saline conditions, lines homozygous for the wild allele yielded 30% more than did lines homozygous for the Barke allele. Introgressing this wild allele into elite cultivars could markedly improve yield under saline conditions. © 2016 The Author(s).

  8. Modelling cell population growth with applications to cancer therapy in human tumour cell lines.

    Science.gov (United States)

    Basse, Britta; Baguley, Bruce C; Marshall, Elaine S; Wake, Graeme C; Wall, David J N

    2004-01-01

    In this paper we present an overview of the work undertaken to model a population of cells and the effects of cancer therapy. We began with a theoretical one compartment size structured cell population model and investigated its asymptotic steady size distributions (SSDs) (On a cell growth model for plankton, MMB JIMA 21 (2004) 49). However these size distributions are not similar to the DNA (size) distributions obtained experimentally via the flow cytometric analysis of human tumour cell lines (data obtained from the Auckland Cancer Society Research Centre, New Zealand). In our one compartment model, size was a generic term, but in order to obtain realistic steady size distributions we chose size to be DNA content and devised a multi-compartment mathematical model for the cell division cycle where each compartment corresponds to a distinct phase of the cell cycle (J. Math. Biol. 47 (2003) 295). We then incorporated another compartment describing the possible induction of apoptosis (cell death) from mitosis phase (Modelling cell death in human tumour cell lines exposed to anticancer drug paclitaxel, J. Math. Biol. 2004, in press). This enabled us to compare our model to flow cytometric data of a melanoma cell line where the anticancer drug, paclitaxel, had been added. The model gives a dynamic picture of the effects of paclitaxel on the cell cycle. We hope to use the model to describe the effects of other cancer therapies on a number of different cell lines. Copyright 2004 Elsevier Ltd.

  9. Epidemiological geomatics in evaluation of mine risk education in Afghanistan: introducing population weighted raster maps

    Directory of Open Access Journals (Sweden)

    Andersson Neil

    2006-01-01

    Full Text Available Abstract Evaluation of mine risk education in Afghanistan used population weighted raster maps as an evaluation tool to assess mine education performance, coverage and costs. A stratified last-stage random cluster sample produced representative data on mine risk and exposure to education. Clusters were weighted by the population they represented, rather than the land area. A "friction surface" hooked the population weight into interpolation of cluster-specific indicators. The resulting population weighted raster contours offer a model of the population effects of landmine risks and risk education. Five indicator levels ordered the evidence from simple description of the population-weighted indicators (level 0, through risk analysis (levels 1–3 to modelling programme investment and local variations (level 4. Using graphic overlay techniques, it was possible to metamorphose the map, portraying the prediction of what might happen over time, based on the causality models developed in the epidemiological analysis. Based on a lattice of local site-specific predictions, each cluster being a small universe, the "average" prediction was immediately interpretable without losing the spatial complexity.

  10. GPR applied to mapping utilities along the route of the Line 4 (yellow) subway tunnel construction in São Paulo City, Brazil

    Science.gov (United States)

    Porsani, Jorge Luís; Ruy, Yang Boo; Ramos, Fernanda Pereira; Yamanouth, Gisele R. B.

    2012-05-01

    The rapid industrial development and disorganized population growth in huge cities bring about various urban problems due to intense use of physical space on and below the surface. Subsurface problems in metropolitan areas are caused by subway line construction, which often follows the routes of utility networks, such as electric and telephone cables, water and gas pipes, storm sewers, etc. Usually, the main problems are related to damage or destruction of preexisting utilities, often putting human lives at risk. With the purpose of minimizing risks, GPR-profiling with 200 MHz antennae was done at two sites, both located in downtown São Paulo, Brazil. The objectives of this work were to map utilities or existing infrastructure in the subsurface in order to orient the construction of the Line 4 (yellow) subway tunnel in São Paulo. GPR profiles can detect water pipes, utility networks in the subsurface, and concrete foundation columns or pilings in subsoil up to 2 m depth. In addition, the GPR profiles also provided details of the target shapes in the subsurface. GPR interpretations combined with lithological information from boreholes and trenches opened in the study areas were extremely important in mapping of the correct spatial distribution of buried utilities at these two sites in São Paulo. This information improves and updates maps of utility placement, serves as a basis for planning of the geotechnical excavation of the Line 4 (yellow) subway tunnel in São Paulo, helps minimize problems related to destruction of preexisting utilities in the subsoil, and avoids risk of dangerous accidents.

  11. Mapping of stripe rust resistance gene in an Aegilops caudate introgression line in wheat and its genetic association with leaf rust resistance.

    Science.gov (United States)

    Toor, Puneet Inder; Kaur, Satinder; Bansal, Mitaly; Yadav, Bharat; Chhuneja, Parveen

    2016-12-01

    A pair of stripe rust and leaf rust resistance genes was introgressed from Aegilops caudata, a nonprogenitor diploid species with the CC genome, to cultivated wheat. Inheritance and genetic mapping of stripe rust resistance gene in backcrossrecombinant inbred line (BC-RIL) population derived from the cross of a wheat-Ae. caudata introgression line (IL) T291- 2(pau16060) with wheat cv. PBW343 is reported here. Segregation of BC-RILs for stripe rust resistance depicted a single major gene conditioning adult plant resistance (APR) with stripe rust reaction varying from TR-20MS in resistant RILs signifying the presence of some minor genes as well. Genetic association with leaf rust resistance revealed that two genes are located at a recombination distance of 13%. IL T291-2 had earlier been reported to carry introgressions on wheat chromosomes 2D, 3D, 4D, 5D, 6D and 7D. Genetic mapping indicated the introgression of stripe rust resistance gene on wheat chromosome 5DS in the region carrying leaf rust resistance gene LrAc, but as an independent introgression. Simple sequence repeat (SSR) and sequence-tagged site (STS) markers designed from the survey sequence data of 5DS enriched the target region harbouring stripe and leaf rust resistance genes. Stripe rust resistance locus, temporarily designated as YrAc, mapped at the distal most end of 5DS linked with a group of four colocated SSRs and two resistance gene analogue (RGA)-STS markers at a distance of 5.3 cM. LrAc mapped at a distance of 9.0 cM from the YrAc and at 2.8 cM from RGA-STS marker Ta5DS_2737450, YrAc and LrAc appear to be the candidate genes for marker-assisted enrichment of the wheat gene pool for rust resistance.

  12. Model-driven product line engineering for mapping parallel algorithms to parallel computing platforms

    NARCIS (Netherlands)

    Arkin, Ethem; Tekinerdogan, Bedir

    2016-01-01

    Mapping parallel algorithms to parallel computing platforms requires several activities such as the analysis of the parallel algorithm, the definition of the logical configuration of the platform, the mapping of the algorithm to the logical configuration platform and the implementation of the

  13. QTL mapping for yield components and agronomic traits in a Brazilian soybean population

    Directory of Open Access Journals (Sweden)

    Josiane Isabela da Silva Rodrigues

    2016-11-01

    Full Text Available The objective of this work was to map QTL for agronomic traits in a Brazilian soybean population. For this, 207 F2:3 progenies from the cross CS3035PTA276-1-5-2x UFVS2012 were genotyped and cultivated in Viçosa-MG, using randomized block design with three replications. QTL detection was carried out by linear regression and composite interval mapping. Thirty molecular markers linked to QTL were detected by linear regression for the total of nine agronomic traits. QTL for SWP (seed weight per plant, W100S (weight of 100 seeds, NPP (number of pods per plant, and NSP (number of seeds per plant were detected by composite interval mapping. Four QTL with additive effect are promising for marker-assisted selection (MAS. Particularly, the markers Satt155 and Satt300 could be useful in simultaneous selection for greater SWP, NPP, and NSP.

  14. Map generation in unknown environments by AUKF-SLAM using line segment-type and point-type landmarks

    Science.gov (United States)

    Nishihta, Sho; Maeyama, Shoichi; Watanebe, Keigo

    2018-02-01

    Recently, autonomous mobile robots that collect information at disaster sites are being developed. Since it is difficult to obtain maps in advance in disaster sites, the robots being capable of autonomous movement under unknown environments are required. For this objective, the robots have to build maps, as well as the estimation of self-location. This is called a SLAM problem. In particular, AUKF-SLAM which uses corners in the environment as point-type landmarks has been developed as a solution method so far. However, when the robots move in an environment like a corridor consisting of few point-type features, the accuracy of self-location estimated by the landmark is decreased and it causes some distortions in the map. In this research, we propose AUKF-SLAM which uses walls in the environment as a line segment-type landmark. We demonstrate that the robot can generate maps in unknown environment by AUKF-SLAM, using line segment-type and point-type landmarks.

  15. Linkage analysis by genotyping of sibling populations: a genetic map for the potato cyst nematode constructed using a "pseudo-F2" mapping strategy.

    Science.gov (United States)

    Rouppe van der Voort, J N; van Eck, H J; van Zandvoort, P M; Overmars, H; Helder, J; Bakker, J

    1999-07-01

    A mapping strategy is described for the construction of a linkage map of a non-inbred species in which individual offspring genotypes are not amenable to marker analysis. After one extra generation of random mating, the segregating progeny was propagated, and bulked populations of offspring were analyzed. Although the resulting population structure is different from that of commonly used mapping populations, we show that the maximum likelihood formula for a normal F2 is applicable for the estimation of recombination. This "pseudo-F2" mapping strategy, in combination with the development of an AFLP assay for single cysts, facilitated the construction of a linkage map for the potato cyst nematode Globodera rostochiensis. Using 12 pre-selected AFLP primer combinations, a total of 66 segregating markers were identified, 62 of which were mapped to nine linkage groups. These 62 AFLP markers are randomly distributed and cover about 65% of the genome. An estimate of the physical size of the Globodera genome was obtained from comparisons of the number of AFLP fragments obtained with the values for Caenorhabditis elegans. The methodology presented here resulted in the first genomic map for a cyst nematode. The low value of the kilobase/centimorgan (kb/cM) ratio for the Globodera genome will facilitate map-based cloning of genes that mediate the interaction between the nematode and its host plant.

  16. Mapping of the stochastic Lotka-Volterra model to models of population genetics and game theory

    Science.gov (United States)

    Constable, George W. A.; McKane, Alan J.

    2017-08-01

    The relationship between the M -species stochastic Lotka-Volterra competition (SLVC) model and the M -allele Moran model of population genetics is explored via timescale separation arguments. When selection for species is weak and the population size is large but finite, precise conditions are determined for the stochastic dynamics of the SLVC model to be mappable to the neutral Moran model, the Moran model with frequency-independent selection, and the Moran model with frequency-dependent selection (equivalently a game-theoretic formulation of the Moran model). We demonstrate how these mappings can be used to calculate extinction probabilities and the times until a species' extinction in the SLVC model.

  17. Mapping Landscape Friction to Locate Isolated Tsetse Populations that are Candidates for Elimination

    International Nuclear Information System (INIS)

    Bouyer, Jérémy; Dicko, Ahmadou H.; Cecchi, Giuliano; Ravel, Sophie; Solano, Philippe; Guerrini, Laure; Vreysen, Marc J. B.; De Meeûs, Thierry; Lancelot, Renaud

    2016-01-01

    Tsetse flies are the cyclical vectors of deadly human and animal trypanosomes in sub-Saharan Africa. Tsetse control is a key component for the integrated management of both plagues, but local eradication successes have been limited to less than 2% of the infested area. This is attributed to either resurgence of residual populations that were omitted from the eradication campaign or reinvasion from neighboring infested areas. Here we focused on Glossina palpalis gambiensis, a riverine tsetse species representing the main vector of trypanosomoses in West Africa. We mapped landscape resistance to tsetse genetic flow, hereafter referred to as friction, to identify natural barriers that isolate tsetse populations. For this purpose, we fitted a statistical model of the genetic distance between 37 tsetse populations sampled in the region, using a set of remotely sensed environmental data as predictors. The least-cost path between these populations was then estimated using the predicted friction map. The method enabled us to avoid the subjectivity inherent in the expert-based weighting of environmental parameters. Finally, we identified potentially isolated clusters of G. p. gambiensis habitat based on a species distribution model and ranked them according to their predicted genetic distance to the main tsetse population. The methodology presented here will inform the choice on the most appropriate intervention strategies to be implemented against tsetse flies in different parts of Africa. It can also be used to control other pests and to support conservation of endangered species. (author)

  18. Cross-Population Joint Analysis of eQTLs: Fine Mapping and Functional Annotation

    Science.gov (United States)

    Wen, Xiaoquan; Luca, Francesca; Pique-Regi, Roger

    2015-01-01

    Mapping expression quantitative trait loci (eQTLs) has been shown as a powerful tool to uncover the genetic underpinnings of many complex traits at molecular level. In this paper, we present an integrative analysis approach that leverages eQTL data collected from multiple population groups. In particular, our approach effectively identifies multiple independent cis-eQTL signals that are consistent across populations, accounting for population heterogeneity in allele frequencies and linkage disequilibrium patterns. Furthermore, by integrating genomic annotations, our analysis framework enables high-resolution functional analysis of eQTLs. We applied our statistical approach to analyze the GEUVADIS data consisting of samples from five population groups. From this analysis, we concluded that i) jointly analysis across population groups greatly improves the power of eQTL discovery and the resolution of fine mapping of causal eQTL ii) many genes harbor multiple independent eQTLs in their cis regions iii) genetic variants that disrupt transcription factor binding are significantly enriched in eQTLs (p-value = 4.93 × 10-22). PMID:25906321

  19. LARGE-AREA [Fe II] LINE MAPPING OF THE SUPERNOVA REMNANT IC 443 WITH THE IRSF/SIRIUS

    Energy Technology Data Exchange (ETDEWEB)

    Kokusho, Takuma; Nagayama, Takahiro; Kaneda, Hidehiro; Ishihara, Daisuke [Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602 (Japan); Lee, Ho-Gyu; Onaka, Takashi, E-mail: kokusho@u.phys.nagoya-u.ac.jp [Department of Astronomy, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo 113-0033 (Japan)

    2013-05-01

    We present the results of near-infrared (near-IR) [Fe II] line mapping of the supernova remnant IC 443 with IRSF/SIRIUS, using the two narrow-band filters tuned for the [Fe II] 1.257 {mu}m and [Fe II] 1.644 {mu}m lines. Covering a large area of 30' Multiplication-Sign 35', our observations reveal that [Fe II] filamentary structures exist all over the remnant, not only in an ionic shock shell, but also in a molecular shock shell and a central region inside the shells. With the two [Fe II] lines, we performed corrections for dust extinction to derive the intrinsic line intensities. We also obtained the intensities of thermal emission from the warm dust associated with IC 443, using the far- and mid-IR images taken with AKARI and Spitzer, respectively. As a result, we find that the [Fe II] line emission relative to the dust emission notably enhances in the inner central region. We discuss causes of the enhanced [Fe II] line emission, estimating the Fe{sup +} and dust masses.

  20. A Multidisciplinary Phenotyping and Genotyping Analysis of a Mapping Population Enables Quality to Be Combined with Yield in Rice

    Directory of Open Access Journals (Sweden)

    Mariafe Calingacion

    2017-05-01

    Full Text Available In this study a mapping population (F8 of ca 200 progeny from a cross between the commercial rice varieties Apo and IR64 has been both genotyped and phenotyped. A genotyping-by-sequencing approach was first used to identify 2,681 polymorphic SNP markers which gave dense coverage of the genome with a good distribution across all 12 chromosomes. The coefficient of parentage was also low, at 0.13, confirming that the parents are genetically distant from each other. The progeny, together with both parents, were grown under irrigated and water restricted conditions in a randomised block design. All grain was harvested to determine variation in yield across the population. The grains were then polished following standard procedures prior to performing the phenotyping analyses. A Gas Chromatography—Mass Spectrometry approach was used to determine the volatile biochemical profiles of each line and after data curation and processing, discriminatory metabolites were putatively identified based on in-house and commercial spectral libraries. These data were used to predict the potential role of these metabolites in determining differences in aroma between genotypes. A number of QTLs for yield and for individual metabolites have been identified. Following these combined multi-disciplinary analyses, it proved possible to identify a number of lines which appeared to combine the favourable aroma attributes of IR64 with the favourable (higher yield potential of Apo. As such, these lines are excellent candidates to assess further as potential genotypes to work up into a new variety of rice which has both good yield and good quality, thus meeting the needs of both farmer and consumer alike.

  1. Derivation and characterization of human embryonic stem cell lines from the Chinese population

    Institute of Scientific and Technical Information of China (English)

    Zhao Wu; Huimin Dai; Lei Qian; Qing Tian; Lei Xiao; Xiaojun Tan; Hui Li; Lingjun Rao; Lixiazi He; Lei Bao; Jing Liao; Chun Cui; Zhenyu Zuo; Qiao Li

    2011-01-01

    Human embryonic stem cells (hESCs) can self-renew indefinitely and differentiate into all cell types in the human body. Therefore, they are valuable in regenerative medicine, human developmental biology and drug discovery. A number of hESC lines have been derived from the Chinese population,but limited of them are available for research purposes. Here we report the derivation and characterization of two hESC lines derived from human blastocysts of Chinese origin. These hESCs express alkaline phosphatase and hESC-specific markers, including Oct4, Nanog, SSEA-3, SSEA-4,TRA-1-60 and TRA-1-81. They also have high levels of telomerase activity and normal karyotypes. These cells can form embryoid body in vitro and can be differentiated into all three germ layers in vivo by teratoma formation. The newly established hESCs will be distributed for research purposes.The availability of hESC lines from the Chinese population will facilitate studies on the differences in hESCs from different ethnic groups.

  2. Genome-wide association mapping for yield and other agronomic traits in an elite breeding population of tropical rice (Oryza sativa).

    Science.gov (United States)

    Begum, Hasina; Spindel, Jennifer E; Lalusin, Antonio; Borromeo, Teresita; Gregorio, Glenn; Hernandez, Jose; Virk, Parminder; Collard, Bertrand; McCouch, Susan R

    2015-01-01

    Genome-wide association mapping studies (GWAS) are frequently used to detect QTL in diverse collections of crop germplasm, based on historic recombination events and linkage disequilibrium across the genome. Generally, diversity panels genotyped with high density SNP panels are utilized in order to assay a wide range of alleles and haplotypes and to monitor recombination breakpoints across the genome. By contrast, GWAS have not generally been performed in breeding populations. In this study we performed association mapping for 19 agronomic traits including yield and yield components in a breeding population of elite irrigated tropical rice breeding lines so that the results would be more directly applicable to breeding than those from a diversity panel. The population was genotyped with 71,710 SNPs using genotyping-by-sequencing (GBS), and GWAS performed with the explicit goal of expediting selection in the breeding program. Using this breeding panel we identified 52 QTL for 11 agronomic traits, including large effect QTLs for flowering time and grain length/grain width/grain-length-breadth ratio. We also identified haplotypes that can be used to select plants in our population for short stature (plant height), early flowering time, and high yield, and thus demonstrate the utility of association mapping in breeding populations for informing breeding decisions. We conclude by exploring how the newly identified significant SNPs and insights into the genetic architecture of these quantitative traits can be leveraged to build genomic-assisted selection models.

  3. Experience of MAPS in monitoring of personnel movement with on-line database management system

    International Nuclear Information System (INIS)

    Rajendran, T.S.; Anand, S.D.

    1992-01-01

    As a part of physical protection system, access control system has been installed in Madras Atomic Power Station(MAPS) to monitor and regulate the movement of persons within MAPS. The present system in its original form was meant only for security monitoring. A PC based database management system was added to this to computerize the availability of work force for actual work. (author). 2 annexures

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

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

  6. Prospects and pitfalls of occupational hazard mapping: 'between these lines there be dragons'.

    Science.gov (United States)

    Koehler, Kirsten A; Volckens, John

    2011-10-01

    Hazard data mapping is a promising new technique that can enhance the process of occupational exposure assessment and risk communication. Hazard maps have the potential to improve worker health by providing key input for the design of hazard intervention and control strategies. Hazard maps are developed with aid from direct-reading instruments, which can collect highly spatially and temporally resolved data in a relatively short period of time. However, quantifying spatial-temporal variability in the occupational environment is not a straightforward process, and our lack of understanding of how to ascertain and model spatial and temporal variability is a limiting factor in the use and interpretation of workplace hazard maps. We provide an example of how sources of and exposures to workplace hazards may be mischaracterized in a hazard map due to a lack of completeness and representativeness of collected measurement data. Based on this example, we believe that a major priority for research in this emerging area should focus on the development of a statistical framework to quantify uncertainty in spatially and temporally varying data. In conjunction with this need is one for the development of guidelines and procedures for the proper sampling, generation, and evaluation of workplace hazard maps.

  7. The SLUGGS survey: globular cluster stellar population trends from weak absorption lines in stacked spectra

    Science.gov (United States)

    Usher, Christopher; Forbes, Duncan A.; Brodie, Jean P.; Romanowsky, Aaron J.; Strader, Jay; Conroy, Charlie; Foster, Caroline; Pastorello, Nicola; Pota, Vincenzo; Arnold, Jacob A.

    2015-01-01

    As part of the SAGES Legacy Unifying Globulars and GalaxieS (SLUGGS) survey, we stack 1137 Keck DEIMOS (Deep Imaging Multi-Object Spectrograph) spectra of globular clusters from 10 galaxies to study their stellar populations in detail. The stacked spectra have median signal-to-noise ratios of ˜90 Å-1. Besides the calcium triplet, we study weaker sodium, magnesium, titanium and iron lines as well as the Hα and higher order Paschen hydrogen lines. In general, the stacked spectra are consistent with old ages and a Milky Way-like initial mass function. However, we see different metal line index strengths at fixed colour and magnitude, and differences in the calcium triplet-colour relation from galaxy to galaxy. We interpret this as strong evidence for variations in the globular cluster colour-metallicity relation between galaxies. Two possible explanations for the colour-metallicity relation variations are that the average ages of globular clusters vary from galaxy to galaxy or that the average abundances of light elements (i.e. He, C, N and O) differ between galaxies. Stacking spectra by magnitude, we see that the colours become redder and metal line indices stronger with brighter magnitudes. These trends are consistent with the previously reported `blue tilts' being mass-metallicity relations.

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

    Science.gov (United States)

    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.

  9. Ovulation rate and early embryonic survival rate in female rabbits of a synthetic line and a local Algerian population

    Directory of Open Access Journals (Sweden)

    R. Belabbas

    2016-12-01

    Full Text Available A higher litter size at birth has been reported in female rabbits from a Synthetic line than in those of the Local Algerian population. The aim of this work was to analyse whether this difference in litter size was due to a higher ovulation rate and/or embryonic survival rate in Synthetic line than in Local Algerian population. In total, 24 multiparous female rabbits from Synthetic line and 23 from Local population were used in this experiment. Litter size at birth was recorded up to the first 3 parities. Litter size was 20% higher in Synthetic line than Local population. At their 4th gestation, the females were euthanized at 72 h post coitum. Synthetic line females had 50% more ova and embryos than those of Local population (+4.42 ova and +3.92 embryos, respectively. Synthetic line displayed a lower percentage of normal embryos and a larger number of unfertilized oocytes than Local population (–2.81% and +0.64 oocytes, respectively, but differences were not relevant. Synthetic line showed a lesser embryonic stage of development at 72 h post coitum, showing a higher percentage of early morulae (31.50 vs. 8.50% and a lower percentage of compact morulae (51.45 vs. 78.65% than Local population. No relevant difference was found for early embryonic survival rate between Synthetic line and Local population. In conclusion, the difference in litter size was mainly due to a higher ovulation rate in the Synthetic line, allowing more embryos to develop in this line.

  10. Genomewide Linkage Disequilibrium Mapping of Severe Bipolar Disorder in a Population Isolate

    Science.gov (United States)

    Ophoff, Roel A.; Escamilla, Michael A.; Service, Susan K.; Spesny, Mitzi; Meshi, Dar B.; Poon, Wingman; Molina, Julio; Fournier, Eduardo; Gallegos, Alvaro; Mathews, Carol; Neylan, Thomas; Batki, Steven L.; Roche, Erin; Ramirez, Margarita; Silva, Sandra; De Mille, Melissa C.; Dong, Penny; Leon, Pedro E.; Reus, Victor I.; Sandkuijl, Lodewijk A.; Freimer, Nelson B.

    2002-01-01

    Genomewide association studies may offer the best promise for genetic mapping of complex traits. Such studies in outbred populations require very densely spaced single-nucleotide polymorphisms. In recently founded population isolates, however, extensive linkage disequilibrium (LD) may make these studies feasible with currently available sets of short tandem repeat markers, spaced at intervals as large as a few centimorgans. We report the results of a genomewide association study of severe bipolar disorder (BP-I), using patients from the isolated population of the central valley of Costa Rica. We observed LD with BP-I on several chromosomes; the most striking results were in proximal 8p, a region that has previously shown linkage to schizophrenia. This region could be important for severe psychiatric disorders, rather than for a specific phenotype. PMID:12119601

  11. Mapping and validation of a new QTL for adult-plant resistance to powdery mildew in Chinese elite bread wheat line Zhou8425B.

    Science.gov (United States)

    Jia, Aolin; Ren, Yan; Gao, Fengmei; Yin, Guihong; Liu, Jindong; Guo, Lu; Zheng, Jizhou; He, Zhonghu; Xia, Xianchun

    2018-05-01

    Four QTLs for adult-plant resistance to powdery mildew were mapped in the Zhou8425B/Chinese Spring population, and a new QTL on chromosome 3B was validated in 103 wheat cultivars derived from Zhou8425B. Zhou8425B is an elite wheat (Triticum aestivum L.) line widely used as a parent in Chinese wheat breeding programs. Identification of genes for adult-plant resistance (APR) to powdery mildew in Zhou8425B is of high importance for continued controlling the disease. In the current study, the high-density Illumina iSelect 90K single-nucleotide polymorphism (SNP) array was used to map quantitative trait loci (QTL) for APR to powdery mildew in 244 recombinant inbred lines derived from the cross Zhou8425B/Chinese Spring. Inclusive composite interval mapping identified QTL on chromosomes 1B, 3B, 4B, and 7D, designated as QPm.caas-1BL.1, QPm.caas-3BS, QPm.caas-4BL.2, and QPm.caas-7DS, respectively. Resistance alleles at the QPm.caas-1BL.1, QPm.caas-3BS, and QPm.caas-4BL.2 loci were contributed by Zhou8425B, whereas that at QPm.caas-7DS was from Chinese Spring. QPm.caas-3BS, likely to be a new APR gene for powdery mildew resistance, was detected in all four environments. One SNP marker closely linked to QPm.caas-3BS was transferred into a semi-thermal asymmetric reverse PCR (STARP) marker and tested on 103 commercial wheat cultivars derived from Zhou8425B. Cultivars with the resistance allele at the QPm.caas-3BS locus had averaged maximum disease severity reduced by 5.3%. This STARP marker can be used for marker-assisted selection in improvement of the level of powdery mildew resistance in wheat breeding.

  12. Characterization and Mapping of Leaf Rust and Stripe Rust Resistance Loci in Hexaploid Wheat Lines UC1110 and PI610750 under Mexican Environments.

    Science.gov (United States)

    Lan, Caixia; Hale, Iago L; Herrera-Foessel, Sybil A; Basnet, Bhoja R; Randhawa, Mandeep S; Huerta-Espino, Julio; Dubcovsky, Jorge; Singh, Ravi P

    2017-01-01

    Growing resistant wheat varieties is a key method of minimizing the extent of yield losses caused by the globally important wheat leaf rust (LR) and stripe rust (YR) diseases. In this study, a population of 186 F 8 recombinant inbred lines (RILs) derived from a cross between a synthetic wheat derivative (PI610750) and an adapted common wheat line (cv. "UC1110") were phenotyped for LR and YR response at both seedling and adult plant stages over multiple seasons. Using a genetic linkage map consisting of single sequence repeats and diversity arrays technology markers, in combination with inclusive composite interval mapping analysis, we detected a new LR adult plant resistance (APR) locus, QLr.cim-2DS , contributed by UC1110. One co-located resistance locus to both rusts, QLr.cim-3DC/QYr.cim-3DC , and the known seedling resistance gene Lr26 were also mapped. QLr.cim-2DS and QLr.cim-3DC showed a marginally significant interaction for LR resistance in the adult plant stage. In addition, two previously reported YR APR loci, QYr.ucw-3BS and Yr48 , were found to exhibit stable performances in rust environments in both Mexico and the United States and showed a highly significant interaction in the field. Yr48 was also observed to confer intermediate seedling resistance against Mexican YR races, thus suggesting it should be re-classified as an all-stage resistance gene. We also identified 5 and 2 RILs that possessed all detected YR and LR resistance loci, respectively. With the closely linked molecular markers reported here, these RILs could be used as donors for multiple resistance loci to both rusts in wheat breeding programs.

  13. Estimating population size of a nocturnal burrow-nesting seabird using acoustic monitoring and habitat mapping

    Directory of Open Access Journals (Sweden)

    Steffen Oppel

    2014-04-01

    Full Text Available Population size assessments for nocturnal burrow-nesting seabirds are logistically challenging because these species are active in colonies only during darkness and often nest on remote islands where manual inspections of breeding burrows are not feasible. Many seabird species are highly vocal, and recent technological innovations now make it possible to record and quantify vocal activity in seabird colonies. Here we test the hypothesis that remotely recorded vocal activity in Cory’s shearwater (Calonectris borealis breeding colonies in the North Atlantic increases with nest density, and combined this relationship with cliff habitat mapping to estimate the population size of Cory’s shearwaters on the island of Corvo (Azores. We deployed acoustic recording devices in 9 Cory’s shearwater colonies of known size to establish a relationship between vocal activity and local nest density (slope = 1.07, R2 = 0.86, p < 0.001. We used this relationship to predict the nest density in various cliff habitat types and produced a habitat map of breeding cliffs to extrapolate nest density around the island of Corvo. The mean predicted nest density on Corvo ranged from 6.6 (2.1–16.2 to 27.8 (19.5–36.4 nests/ha. Extrapolation of habitat-specific nest densities across the cliff area of Corvo resulted in an estimate of 6326 Cory’s shearwater nests (95% confidence interval: 3735–10,524. This population size estimate is similar to previous assessments, but is too imprecise to detect moderate changes in population size over time. While estimating absolute population size from acoustic recordings may not be sufficiently precise, the strong positive relationship that we found between local nest density and recorded calling rate indicates that passive acoustic monitoring may be useful to document relative changes in seabird populations over time.

  14. Comparison between electric-field-navigated and line-navigated TMS for cortical motor mapping in patients with brain tumors.

    Science.gov (United States)

    Sollmann, Nico; Goblirsch-Kolb, Moritz F; Ille, Sebastian; Butenschoen, Vicki M; Boeckh-Behrens, Tobias; Meyer, Bernhard; Ringel, Florian; Krieg, Sandro M

    2016-12-01

    For the navigation of transcranial magnetic stimulation (TMS), various techniques are available. Yet, there are two basic principles underlying them all: electric-field-navigated transcranial magnetic stimulation (En-TMS) and line-navigated transcranial magnetic stimulation (Ln-TMS). The current study was designed to compare both methods. To explore whether there is a difference in clinical applicability, workflow, and mapping results of both techniques, we systematically compared motor mapping via En-TMS and Ln-TMS in 12 patients suffering from brain tumors. The number of motor-positive stimulation spots and the ratio of positive spots per overall stimulation numbers were significantly higher for En-TMS (motor-positive spots: En-TMS vs. Ln-TMS: 128.3 ± 35.0 vs. 41.3 ± 26.8, p mapping in the neurosurgical context for the first time. Although both TMS systems tested in the present study are explicitly designed for application during motor mapping in patients with brain lesions, there are differences in applicability, workflow, and results between En-TMS and Ln-TMS, which should be distinctly considered during clinical use of the technique. However, to draw final conclusions about accuracy, confirmation of motor-positive Ln-TMS spots by intraoperative stimulation is crucial within the scope of upcoming investigations.

  15. Harris lines of the tibia across centuries: a comparison of two populations, medieval and contemporary in Central Europe

    Energy Technology Data Exchange (ETDEWEB)

    Ameen, S.; Vock, P.; Anderson, S.E. [University Hospital of Bern, Department of Diagnostic Radiology, Bern (Switzerland); Staub, L.; Ulrich, S. [University of Bern, Institute of Historical Medicine, Bern (Switzerland); Ballmer, F. [University Hospital of Bern, Department of Orthopaedics, Bern (Switzerland)

    2005-05-01

    To determine the incidence of Harris lines in two medieval populations which inhabited the Canton of Berne, in Central Switzerland, and to compare the results with those of a contemporary population living in the same geographical area. A simplified method is described for measuring the age of the individual at the time of formation of Harris lines, with possible future applications. Radiographs of 112 well-preserved tibiae of skeletons of two medieval populations from the eighth to fifteenth centuries were reviewed for the incidence of Harris lines. The results were compared with those of 138 current patients living in the same geographic location in Central Switzerland. Age and gender of the medieval individual were determined using known anthropological methods. Age of bone at the time of formation of Harris lines was estimated according to the method of Maat. Harris lines were found in 88 of 112 (80%) of the examined medieval skeletons and in 28 of 138 (20%) of the living individuals. Higher incidences of Harris lines were found at the age of 2 years and at ages between 8 and 12 years in both populations. No gender difference was found regarding the incidence of Harris lines. In both populations the occurrence of Harris lines was associated with certain diseases such as degenerative bone disease, trauma, osteoporosis, rheumatoid arthritis, peripheral vascular diseases, rickets and bony deformities. (orig.)

  16. Harris lines of the tibia across centuries: a comparison of two populations, medieval and contemporary in Central Europe

    International Nuclear Information System (INIS)

    Ameen, S.; Vock, P.; Anderson, S.E.; Staub, L.; Ulrich, S.; Ballmer, F.

    2005-01-01

    To determine the incidence of Harris lines in two medieval populations which inhabited the Canton of Berne, in Central Switzerland, and to compare the results with those of a contemporary population living in the same geographical area. A simplified method is described for measuring the age of the individual at the time of formation of Harris lines, with possible future applications. Radiographs of 112 well-preserved tibiae of skeletons of two medieval populations from the eighth to fifteenth centuries were reviewed for the incidence of Harris lines. The results were compared with those of 138 current patients living in the same geographic location in Central Switzerland. Age and gender of the medieval individual were determined using known anthropological methods. Age of bone at the time of formation of Harris lines was estimated according to the method of Maat. Harris lines were found in 88 of 112 (80%) of the examined medieval skeletons and in 28 of 138 (20%) of the living individuals. Higher incidences of Harris lines were found at the age of 2 years and at ages between 8 and 12 years in both populations. No gender difference was found regarding the incidence of Harris lines. In both populations the occurrence of Harris lines was associated with certain diseases such as degenerative bone disease, trauma, osteoporosis, rheumatoid arthritis, peripheral vascular diseases, rickets and bony deformities. (orig.)

  17. Test of the Capability of Laser Line Scan Technology to Support Benthic Habitat Mapping in Coral Reef Ecosystems, Maui Island, November 2006

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The utility of Laser Line Scan (LLS) Technology for optical validation of benthic habitat map data from coral reef ecosystems was tested with a deployment of a...

  18. Power Lines: The Rhetoric of Maps as Social Change in the Post-Cold War Landscape

    Science.gov (United States)

    Barney, Timothy

    2009-01-01

    After the fall of the Berlin Wall and the collapse of state socialism in Eastern and Central Europe, cartographers were faced with choices on how the new post-Cold War political landscape would be mapped. One such group called the Pluto Project had been producing atlases since 1981 with a progressive point of view about the nature of state power…

  19. Information Security Awareness On-Line Materials Design with Knowledge Maps

    Science.gov (United States)

    Shaw, Ruey-Shiang; Keh, Huan-Chao; Huang, Nan-Ching; Huang, Tien-Chuan

    2011-01-01

    Information Security Awareness, though known as a primary and important issue in the domain of Information Security, CSI computer crime and security survey showed poor security awareness training in public and private sectors. In many studies, the authors have found that the usage of knowledge maps helps the process of learning and conception…

  20. Provision of the population of Kazakhstan with qualitative drinking water by the main water lines

    International Nuclear Information System (INIS)

    Tastanov, K.Kh; Tokmurzin, Zh.T.; Baibatyrov, E.N.; Taubaldiev, T.S.; Murinov, S.K.; But, A. A.

    2002-01-01

    In the paper the status of drinking water supply of the Kazakhstan Caspian region is revealed. It is noted, that on the Kazakhstan coast of the Caspian sea by reason of lack of local water resources suitable for economic-consumption and technical usage water-supply is generally made with the Volga waters by water line 'Astrakhan-Mangistau', flow of the Ural river with very low water quality and sea water after water preparation on the Mangistau atomic energetic plant (for technical aims). By reason of lack of proper water preparation an intensive processes of corrosion of internal uninsulated surface in pipeline is coming. Water is enriched with iron lower water sanitary-hygienic norms and gets a stagnant smell. Nowadays half of population of Caspian region uses water which does not meet standard of quality, or is faced with lack of water what negatively results in human health. Large concentration of iron in drinking water is causing of illness of liver, blood and allergy reactions. Raised content of strontium results in development of rickets and other skeletal diseases. At present plants for treatment and disinfecting of water in water-line 'Astrakhan-Mangistau' were elaborated and put into operation for supply of population of several villages of Western Kazakhstan with drinking water of quarantined quality and necessary quantity

  1. A POPULATION OF WEAK METAL-LINE ABSORBERS SURROUNDING THE MILKY WAY

    International Nuclear Information System (INIS)

    Richter, Philipp; Charlton, Jane C.; Fangano, Alessio P. M.; Bekhti, Nadya Ben; Masiero, Joseph R.

    2009-01-01

    We report on the detection of a population of weak metal-line absorbers in the halo or nearby intergalactic environment of the Milky Way. Using high-resolution ultraviolet absorption-line spectra of bright quasars (QSO) obtained with the Space Telescope Imaging Spectrograph (STIS), along six sight lines we have observed unsaturated, narrow absorption in O I and Si II, together with mildly saturated C II absorption at high radial velocities (|v LSR | = 100-320 km s -1 ). The measured O I column densities lie in the range N(O I) 14 cm -2 implying that these structures represent Lyman limit Systems and sub-Lyman limit System with H I column densities between 10 16 and 3 x 10 18 cm -2 , thus below the detection limits of current 21 cm all-sky surveys of high-velocity clouds (HVCs). The absorbers apparently are not directly associated with any of the large high column density HVC complexes, but rather represent isolated, partly neutral gas clumps embedded in a more tenuous, ionized gaseous medium situated in the halo or nearby intergalactic environment of the Galaxy. Photoionization modeling of the observed low ion ratios suggests typical hydrogen volume densities of n H > 0.02 cm -3 and characteristic thicknesses of a several parsec down to subparsec scales. For three absorbers, metallicities are constrained in the range of 0.1-1.0 solar, implying that these gaseous structures may have multiple origins inside and outside the Milky Way. Using supplementary optical absorption-line data, we find for two other absorbers Ca II/O I column-density ratios that correspond to solar Ca/O abundance ratios. This finding indicates that these clouds do not contain significant amounts of dust. This population of low column density gas clumps in the circumgalactic environment of the Milky Way is indicative of the various processes that contribute to the circulation of neutral gas in the extended halos of spiral galaxies. These processes include the accretion of gas from the

  2. THE LICK AGN MONITORING PROJECT: REVERBERATION MAPPING OF OPTICAL HYDROGEN AND HELIUM RECOMBINATION LINES

    International Nuclear Information System (INIS)

    Bentz, Misty C.; Walsh, Jonelle L.; Barth, Aaron J.; Thornton, Carol E.; Yoshii, Yuzuru; Sakata, Yu; Minezaki, Takeo; Woo, Jong-Hak; Malkan, Matthew A.; Wang, Xiaofeng; Steele, Thea N.; Silverman, Jeffrey M.; Serduke, Frank J. D.; Li, Weidong; Lee, Nicholas; Treu, Tommaso; Street, Rachel A.; Hidas, Marton G.; Hiner, Kyle D.; Greene, Jenny E.

    2010-01-01

    We have recently completed a 64-night spectroscopic monitoring campaign at the Lick Observatory 3 m Shane telescope with the aim of measuring the masses of the black holes in 12 nearby (z 6 -10 7 M sun and also the well-studied nearby active galactic nucleus (AGN) NGC 5548. Nine of the objects in the sample (including NGC 5548) showed optical variability of sufficient strength during the monitoring campaign to allow for a time lag to be measured between the continuum fluctuations and the response to these fluctuations in the broad Hβ emission, which we have previously reported. We present here the light curves for the Hα, Hγ, He II λ4686, and He I λ5876 emission lines and the time lags for the emission-line responses relative to changes in the continuum flux. Combining each emission-line time lag with the measured width of the line in the variable part of the spectrum, we determine a virial mass of the central supermassive black hole from several independent emission lines. We find that the masses are generally consistent within the uncertainties. The time-lag response as a function of velocity across the Balmer line profiles is examined for six of the AGNs. We find similar responses across all three Balmer lines for Arp 151, which shows a strongly asymmetric profile, and for SBS 1116+583A and NGC 6814, which show a symmetric response about zero velocity. For the other three AGNs, the data quality is somewhat lower and the velocity-resolved time-lag response is less clear. Finally, we compare several trends seen in the data set against the predictions from photoionization calculations as presented by Korista and Goad. We confirm several of their predictions, including an increase in responsivity and a decrease in the mean time lag as the excitation and ionization level for the species increases. Specifically, we find the time lags of the optical recombination lines to have weighted mean ratios of τ(Hα):τ(Hβ):τ(Hγ):τ(He I):τ(He II) = 1

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

    Science.gov (United States)

    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.

  4. Intensity Mapping of the [CII] Fine Structure Line during the Epoch of Reionization

    Science.gov (United States)

    Gong, Yan; Cooray, A.; Silva, M.; Santos, M. G.; Bock, J.; Bradford, M.; Zemcov, M.

    2012-01-01

    The atomic CII fine-structure line is one of the brightest lines in a typical star-forming galaxy spectrum with a luminosity 0.1% to 1% of the bolometric luminosity. It is otentially a reliable tracer of the dense gas distribution at high edshifts and could provide an additional probe to the era of reionization. By taking into account of the spontaneous, stimulated and collisional emission of the CII line, we calculate the spin temperature and the mean intensity as a function of the redshift. When averaged over a cosmologically large volume, we find that the CII emission from ionized carbon in individual galaxies is larger than the signal generated by carbon in the intergalactic medium (IGM). Assuming that the CII luminosity is proportional to the carbon mass in dark matter halos, we also compute the power spectrum of the CII line intensity at various redshifts. In order to avoid the contamination from CO rotational lines at low redshift when targeting a CII survey at high redshifts, we propose the cross-correlation of CII and 21-cm line emission from high redshifts. To explore the detectability of the CII signal from reionization, we also evaluate the expected errors on the CII power spectrum and CII-21 cm cross power spectrum based on the design of the future milimeter surveys. We note that the CII-21 cm cross power spectrum contains interesting features that captures physics during reionization, including the ionized bubble sizes and the mean ionization fraction, which are challenging to measure from 21-cm data alone. We propose an instrumental concept for the reionization CII experiment targeting the frequency range of 200 to 300 GHz with 1, 3 and 10 meter apertures and a bolometric spectrometer array with 64 independent spectral pixels with about 20,000 bolometers.

  5. Body-Map Storytelling as a Health Research Methodology: Blurred Lines Creating Clear Pictures

    Directory of Open Access Journals (Sweden)

    Denise Gastaldo

    2018-03-01

    Full Text Available In this article we review the literature on body-mapping (BM as an approach to health research in order to systematize recent advancements and to contribute to its development. We conducted a critical narrative synthesis of the literature published until September 2016 guided by two questions: 1. How has BM been utilized in health research? 2. How does BM advance a decolonization agenda? Twenty-seven studies in English, Spanish, and Portuguese were analyzed. Most of them were published between 2011 and 2016 and were conducted in South Africa, Canada, Australia, Brazil, Chile, and USA. They narrate stories of marginalized groups and commonly focus on the social determinants of health. Data generation, analysis, and knowledge mobilization strategies differ considerably. Recent developments show that body-mapping is a visual, narrative, and participatory methodology that has several names and is used unevenly by health researchers. Despite its diversity, core methodological elements reveal that participants are considered knowledgeable, reflexive individuals who can better articulate their complex life journeys when painting and drawing their bodies and social circumstances. The decolonization of health research occurs when these unlikely protagonists tell their stories producing counter-hegemonic discourses to exclusionary capitalist, patriarchal and colonialist rationalities. We call this methodology body-map storytelling.

  6. Density-independent population projection trajectories of chromosome-substituted lines resistant and susceptible to organophosphate insecticides in Drosophila melanogaster

    Directory of Open Access Journals (Sweden)

    Miyo Takahiro

    2004-11-01

    Full Text Available Abstract Background Seasonal fluctuations in susceptibility to organophosphate insecticides were observed in the Katsunuma population of Drosophila melanogaster for two consecutive years; susceptibility to three organophosphates tended to increase in the fall. To examine the hypothesis that variation in fitness among resistant and susceptible genotypes could trigger the change of genetic constitution within the fall population, we investigated density-independent population projection trajectories starting from single adult females with characteristics of chromosome-substituted lines resistant and susceptible to the three organophosphates. Results Density-independent population projection trajectories, expressed as the ratios of the number of each chromosome-substituted line to that of line SSS, for which all chromosomes were derived from the susceptible line, showed significant declines in numbers with time for all the resistant chromosome-substituted lines. Conclusion The declining tendency in the density-independent population projection trajectories of the resistant chromosome-substituted lines could explain the simultaneous decline in the levels of resistance to the three organophosphates, observed in the Katsunuma population in the fall.

  7. QTL analysis of seed dormancy in Arabidopsis using recombinant inbred lines and MQM mapping

    NARCIS (Netherlands)

    Schaar, Wybe van der; Alonso-Blanco, Carlos; Léon-Kloosterziel, Karen M.; Jansen, Ritsert C.; Ooijen, Johan W. van; Koornneef, Maarten

    1997-01-01

    The genetic differences for seed germination between two commonly used Arabidopsis thaliana ecotypes Ler and Col, both showing a low level of seed dormancy, were investigated. The analysis was performed with 98 recombinant inbred lines (RILs) derived from the cross between the two ecotypes, and

  8. Inheritance and molecular mapping of anthracnose resistance gene present in the differential line PI533918

    Science.gov (United States)

    Anthracnose (Collectrotichum sublineolum) is considered one of the most destructive diseases of sorghum (Sorghum bicolor L. Moench) because it infects all aerial tissues of the plant. The best strategy to control the disease is the incorporation of resistance genes. At present, eighteen sorghum line...

  9. A second-order orientation-contrast stimulus for population-receptive-field-based retinotopic mapping.

    Science.gov (United States)

    Yildirim, Funda; Carvalho, Joana; Cornelissen, Frans W

    2018-01-01

    Visual field or retinotopic mapping is one of the most frequently used paradigms in fMRI. It uses activity evoked by position-varying high luminance contrast visual patterns presented throughout the visual field for determining the spatial organization of cortical visual areas. While the advantage of using high luminance contrast is that it tends to drive a wide range of neural populations - thus resulting in high signal-to-noise BOLD responses - this may also be a limitation, especially for approaches that attempt to squeeze more information out of the BOLD response, such as population receptive field (pRF) mapping. In that case, more selective stimulation of a subset of neurons - despite reduced signals - could result in better characterization of pRF properties. Here, we used a second-order stimulus based on local differences in orientation texture - to which we refer as orientation contrast - to perform retinotopic mapping. Participants in our experiment viewed arrays of Gabor patches composed of a foreground (a bar) and a background. These could only be distinguished on the basis of a difference in patch orientation. In our analyses, we compare the pRF properties obtained using this new orientation contrast-based retinotopy (OCR) to those obtained using classic luminance contrast-based retinotopy (LCR). Specifically, in higher order cortical visual areas such as LO, our novel approach resulted in non-trivial reductions in estimated population receptive field size of around 30%. A set of control experiments confirms that the most plausible cause for this reduction is that OCR mainly drives neurons sensitive to orientation contrast. We discuss how OCR - by limiting receptive field scatter and reducing BOLD displacement - may result in more accurate pRF localization as well. Estimation of neuronal properties is crucial for interpreting cortical function. Therefore, we conclude that using our approach, it is possible to selectively target particular neuronal

  10. polymapR - linkage analysis and genetic map construction from F1 populations of outcrossing polyploids.

    Science.gov (United States)

    Bourke, Peter M; van Geest, Geert; Voorrips, Roeland E; Jansen, Johannes; Kranenburg, Twan; Shahin, Arwa; Visser, Richard G F; Arens, Paul; Smulders, Marinus J M; Maliepaard, Chris

    2018-05-02

    Polyploid species carry more than two copies of each chromosome, a condition found in many of the world's most important crops. Genetic mapping in polyploids is more complex than in diploid species, resulting in a lack of available software tools. These are needed if we are to realise all the opportunities offered by modern genotyping platforms for genetic research and breeding in polyploid crops. polymapR is an R package for genetic linkage analysis and integrated genetic map construction from bi-parental populations of outcrossing autopolyploids. It can currently analyse triploid, tetraploid and hexaploid marker datasets and is applicable to various crops including potato, leek, alfalfa, blueberry, chrysanthemum, sweet potato or kiwifruit. It can detect, estimate and correct for preferential chromosome pairing, and has been tested on high-density marker datasets from potato, rose and chrysanthemum, generating high-density integrated linkage maps in all of these crops. polymapR is freely available under the general public license from the Comprehensive R Archive Network (CRAN) at http://cran.r-project.org/package=polymapR. Chris Maliepaard chris.maliepaard@wur.nl or Roeland E. Voorrips roeland.voorrips@wur.nl. Supplementary data are available at Bioinformatics online.

  11. QTL Mapping of Grain Quality Traits Using Introgression Lines Carrying Oryza rufipogon Chromosome Segments in Japonica Rice.

    Science.gov (United States)

    Yun, Yeo-Tae; Chung, Chong-Tae; Lee, Young-Ju; Na, Han-Jung; Lee, Jae-Chul; Lee, Sun-Gye; Lee, Kwang-Won; Yoon, Young-Hwan; Kang, Ju-Won; Lee, Hyun-Sook; Lee, Jong-Yeol; Ahn, Sang-Nag

    2016-12-01

    Improved eating quality is a major breeding target in japonica rice due to market demand. Consequently, quantitative trait loci (QTL) for glossiness of cooked rice and amylose content associated with eating quality have received much research focus because of their importance in rice quality. In this study, QTL associated with 12 grain quality traits were identified using 96 introgression lines (IL) of rice developed from an interspecific cross between the Korean elite O. sativa japonica cultivar 'Hwaseong' and O. rufipogon over 7 years. QTL analyses indicated that QTL qDTH6 for heading date, detected on chromosome 6 is associated with variance in grain traits. Most QTLs detected in this study clustered near the qDTH6 locus on chromosome 6, suggesting the effect of qDTH6. O. rufipogon alleles negatively affected grain quality traits except for a few QTLs, including qGCR9 for glossiness of cooked rice on chromosome 9. To characterize the effect of the O. rufipogon locus harboring qGCR9, four lines with a single but different O. rufipogon segment near qGCR9 were compared to Hwaseong. Three lines (O. rufipopgon ILs) having O. rufipogon segment between RM242 and RM245 in common showed higher glossiness of cooked rice than Hwaseong and the other line (Hwaseong IL), indicating that qGCR9 is located in the 3.4-Mb region between RM242 and RM245. Higher glossiness of cooked rice conferred by the O. rufipogon allele might be associated with protein content considering that three lines had lower protein content than Hwaseong (P < 0.1). These three O. rufipogon ILs showed higher yield than Hwaseong and Hwaseong IL due to increase in spikelets per panicle and grain weight indicating the linkage of qGCR9 and yield component QTLs. The qGCR9 locus is of particular interest because of its independence from other undesirable grain quality traits in O. rufipogon. SSR markers linked to qGCR9 can be used to develop high-quality japonica lines and offer a starting point for map

  12. Generalization and fine mapping of European ancestry-based central adiposity variants in African ancestry populations.

    Science.gov (United States)

    Yoneyama, S; Yao, J; Guo, X; Fernandez-Rhodes, L; Lim, U; Boston, J; Buzková, P; Carlson, C S; Cheng, I; Cochran, B; Cooper, R; Ehret, G; Fornage, M; Gong, J; Gross, M; Gu, C C; Haessler, J; Haiman, C A; Henderson, B; Hindorff, L A; Houston, D; Irvin, M R; Jackson, R; Kuller, L; Leppert, M; Lewis, C E; Li, R; Le Marchand, L; Matise, T C; Nguyen, K-Dh; Chakravarti, A; Pankow, J S; Pankratz, N; Pooler, L; Ritchie, M D; Bien, S A; Wassel, C L; Chen, Y-D I; Taylor, K D; Allison, M; Rotter, J I; Schreiner, P J; Schumacher, F; Wilkens, L; Boerwinkle, E; Kooperberg, C; Peters, U; Buyske, S; Graff, M; North, K E

    2017-02-01

    Central adiposity measures such as waist circumference (WC) and waist-to-hip ratio (WHR) are associated with cardiometabolic disorders independently of body mass index (BMI) and are gaining clinically utility. Several studies report genetic variants associated with central adiposity, but most utilize only European ancestry populations. Understanding whether the genetic associations discovered among mainly European descendants are shared with African ancestry populations will help elucidate the biological underpinnings of abdominal fat deposition. To identify the underlying functional genetic determinants of body fat distribution, we conducted an array-wide association meta-analysis among persons of African ancestry across seven studies/consortia participating in the Population Architecture using Genomics and Epidemiology (PAGE) consortium. We used the Metabochip array, designed for fine-mapping cardiovascular-associated loci, to explore novel array-wide associations with WC and WHR among 15 945 African descendants using all and sex-stratified groups. We further interrogated 17 known WHR regions for African ancestry-specific variants. Of the 17 WHR loci, eight single-nucleotide polymorphisms (SNPs) located in four loci were replicated in the sex-combined or sex-stratified meta-analyses. Two of these eight independently associated with WHR after conditioning on the known variant in European descendants (rs12096179 in TBX15-WARS2 and rs2059092 in ADAMTS9). In the fine-mapping assessment, the putative functional region was reduced across all four loci but to varying degrees (average 40% drop in number of putative SNPs and 20% drop in genomic region). Similar to previous studies, the significant SNPs in the female-stratified analysis were stronger than the significant SNPs from the sex-combined analysis. No novel associations were detected in the array-wide analyses. Of 17 previously identified loci, four loci replicated in the African ancestry populations of this

  13. Generalization and fine mapping of European ancestry-based central adiposity variants in African ancestry populations

    Science.gov (United States)

    Yoneyama, Sachiko; Yao, Jie; Guo, Xiuqing; Fernandez-Rhodes, Lindsay; Lim, Unhee; Boston, Jonathan; Buzková, Petra; Carlson, Christopher S.; Cheng, Iona; Cochran, Barbara; Cooper, Richard; Ehret, Georg; Fornage, Myriam; Gong, Jian; Gross, Myron; Gu, C. Charles; Haessler, Jeff; Haiman, Christopher A.; Henderson, Brian; Hindorff, Lucia A.; Houston, Denise; Irvin, Marguerite R.; Jackson, Rebecca; Kuller, Lew; Leppert, Mark; Lewis, Cora E.; Li, Rongling; Le Marchand, Loic; Matise, Tara C.; Nguyen, Khanh-Dung H.; Chakravarti, Aravinda; Pankow, James S.; Pankratz, Nathan; Pooler, Loreall; Ritchie, Marylyn D.; Bien, Stephanie A.; Wassel, Christina L.; Chen, Yii-Der I.; Taylor, Kent D.; Allison, Matthew; Rotter, Jerome I.; Schreiner, Pamela J.; Schumacher, Fredrick; Wilkens, Lynne; Boerwinkle, Eric; Kooperberg, Charles; Peters, Ulrike; Buyske, Steven; Graff, Mariaelisa; North, Kari E.

    2016-01-01

    Background/Objectives Central adiposity measures such as waist circumference (WC) and waist-to-hip ratio (WHR) are associated with cardiometabolic disorders independently of BMI and are gaining clinically utility. Several studies report genetic variants associated with central adiposity, but most utilize only European ancestry populations. Understanding whether the genetic associations discovered among mainly European descendants are shared with African ancestry populations will help elucidate the biological underpinnings of abdominal fat deposition. Subjects/Methods To identify the underlying functional genetic determinants of body fat distribution, we conducted an array-wide association meta-analysis among persons of African ancestry across seven studies/consortia participating in the Population Architecture using Genomics and Epidemiology (PAGE) consortium. We used the Metabochip array, designed for fine mapping cardiovascular associated loci, to explore novel array-wide associations with WC and WHR among 15 945 African descendants using all and sex-stratified groups. We further interrogated 17 known WHR regions for African ancestry-specific variants. Results Of the 17 WHR loci, eight SNPs located in four loci were replicated in the sex-combined or sex-stratified meta-analyses. Two of these eight independently associated with WHR after conditioning on the known variant in European descendants (rs12096179 in TBX15-WARS2 and rs2059092 in ADAMTS9). In the fine mapping assessment, the putative functional region was reduced across all four loci but to varying degrees (average 40% drop in number of putative SNPs and 20% drop in genomic region). Similar to previous studies, the significant SNPs in the female stratified analysis were stronger than the significant SNPs from the sex-combined analysis. No novel associations were detected in the array-wide analyses. Conclusions Of 17 previously identified loci, four loci replicated in the African ancestry populations of

  14. Unexpected Relationships and Inbreeding in HapMap Phase III Populations

    Science.gov (United States)

    Stevens, Eric L.; Baugher, Joseph D.; Shirley, Matthew D.; Frelin, Laurence P.; Pevsner, Jonathan

    2012-01-01

    Correct annotation of the genetic relationships between samples is essential for population genomic studies, which could be biased by errors or omissions. To this end, we used identity-by-state (IBS) and identity-by-descent (IBD) methods to assess genetic relatedness of individuals within HapMap phase III data. We analyzed data from 1,397 individuals across 11 ethnic populations. Our results support previous studies (Pemberton et al., 2010; Kyriazopoulou-Panagiotopoulou et al., 2011) assessing unknown relatedness present within this population. Additionally, we present evidence for 1,657 novel pairwise relationships across 9 populations. Surprisingly, significant Cotterman's coefficients of relatedness K1 (IBD1) values were detected between pairs of known parents. Furthermore, significant K2 (IBD2) values were detected in 32 previously annotated parent-child relationships. Consistent with a hypothesis of inbreeding, regions of homozygosity (ROH) were identified in the offspring of related parents, of which a subset overlapped those reported in previous studies (Gibson et al. 2010; Johnson et al. 2011). In total, we inferred 28 inbred individuals with ROH that overlapped areas of relatedness between the parents and/or IBD2 sharing at a different genomic locus between a child and a parent. Finally, 8 previously annotated parent-child relationships had unexpected K0 (IBD0) values (resulting from a chromosomal abnormality or genotype error), and 10 previously annotated second-degree relationships along with 38 other novel pairwise relationships had unexpected IBD2 (indicating two separate paths of recent ancestry). These newly described types of relatedness may impact the outcome of previous studies and should inform the design of future studies relying on the HapMap Phase III resource. PMID:23185369

  15. Central Masses and Broad-Line Region Sizes of Active Galactic Nuclei. II. A Homogeneous Analysis of a Large Reverberation-Mapping Database

    DEFF Research Database (Denmark)

    Peterson, B. M.; Ferrarese, L.; Gilbert, K. M.

    2004-01-01

    We present improved black hole masses for 35 active galactic nuclei (AGNs) based on a complete and consistent reanalysis of broad emission-line reverberation-mapping data. From objects with multiple line measurements, we find that the highest precision measure of the virial product is obtained...

  16. Grain orientation mapping of passivated aluminum interconnect lines with X-ray micro-diffraction

    International Nuclear Information System (INIS)

    Chang, C.H.; Patel, J.R.; MacDowell, A.A.; Padmore, H.A.; Thompson, A.C.

    1998-01-01

    A micro x-ray diffraction facility is under development at the Advanced Light Source. Spot sizes are typically about 1-microm size generated by means of grazing incidence Kirkpatrick-Baez focusing mirrors. Photon energy is either white of energy range 6--14 keV or monochromatic generated from a pair of channel cut crystals. Laue diffraction pattern from a single grain in a passivated 2-microm wide bamboo structured Aluminum interconnect line has been recorded. Acquisition times are of the order of seconds. The Laue pattern has allowed the determination of the crystallographic orientation of individual grains along the line length. The experimental and analysis procedure used is described, as is the latest grain orientation result. The impact of x-ray micro-diffraction and its possible future direction are discussed in the context of other developments in the area of electromigration, and other technological problems

  17. Grain orientation mapping of passivated aluminum interconnect lines by x-ray micro-diffraction

    International Nuclear Information System (INIS)

    Chang, C. H.; Patel, J. R.; MacDowell, A. A.; Padmore, H. A.; Thompson, A. C.

    1998-01-01

    A micro x-ray diffraction facility is under development at the Advanced Light Source. Spot sizes are typically about 1-μm size generated by means of grazing incidence Kirkpatrick-Baez focusing mirrors. Photon energy is either white of energy range 6-14 keV or monochromatic generated from a pair of channel cut crystals. Laue diffraction pattern from a single grain in a passivated 2-μm wide bamboo structured Aluminum interconnect line has been recorded. Acquisition times are of the order of seconds. The Laue pattern has allowed the determination of the crystallographic orientation of individual grains along the line length. The experimental and analysis procedure used is described, as is the latest grain orientation result. The impact of x-ray micro-diffraction and its possible future direction are discussed in the context of other developments in the area of electromigration, and other technological problems

  18. Fine resolution mapping of population age-structures for health and development applications.

    Science.gov (United States)

    Alegana, V A; Atkinson, P M; Pezzulo, C; Sorichetta, A; Weiss, D; Bird, T; Erbach-Schoenberg, E; Tatem, A J

    2015-04-06

    The age-group composition of populations varies considerably across the world, and obtaining accurate, spatially detailed estimates of numbers of children under 5 years is important in designing vaccination strategies, educational planning or maternal healthcare delivery. Traditionally, such estimates are derived from population censuses, but these can often be unreliable, outdated and of coarse resolution for resource-poor settings. Focusing on Nigeria, we use nationally representative household surveys and their cluster locations to predict the proportion of the under-five population in 1 × 1 km using a Bayesian hierarchical spatio-temporal model. Results showed that land cover, travel time to major settlements, night-time lights and vegetation index were good predictors and that accounting for fine-scale variation, rather than assuming a uniform proportion of under 5 year olds can result in significant differences in health metrics. The largest gaps in estimated bednet and vaccination coverage were in Kano, Katsina and Jigawa. Geolocated household surveys are a valuable resource for providing detailed, contemporary and regularly updated population age-structure data in the absence of recent census data. By combining these with covariate layers, age-structure maps of unprecedented detail can be produced to guide the targeting of interventions in resource-poor settings.

  19. Association Mapping of Biomass Yield and Stem Composition in a Tetraploid Alfalfa Breeding Population

    Directory of Open Access Journals (Sweden)

    Xuehui Li

    2011-03-01

    Full Text Available Alfalfa ( L., an important forage crop that is also a potential biofuel crop, has advantages of high yield, high lignocellulose concentration in stems, and has low input costs. In this study, we investigated population structure and linkage disequilibrium (LD patterns in a tetraploid alfalfa breeding population using genome-wide simple sequence repeat (SSR markers and identified markers related to yield and cell wall composition by association mapping. No obvious population structure was found in our alfalfa breeding population, which could be due to the relatively narrow genetic base of the founders and/or due to two generations of random mating. We found significant LD ( 10% alleles across the 71 SSR markers, 15 showed strong association ( < 0.005 with yield in at least one of five environments, and most of the 15 alleles were identified in multiple environments. Only one allele showed strong association with acid detergent fiber (ADF and one allele with acid detergent lignin (ADL. Alleles associated with traits could be directly applied in a breeding program using marker-assisted selection. However, based on our estimated LD level, we would need about 1000 markers to explore the whole alfalfa genome for association between markers and traits.

  20. SPITZER MAPPING OF MOLECULAR HYDROGEN PURE ROTATIONAL LINES IN NGC 1333: A DETAILED STUDY OF FEEDBACK IN STAR FORMATION

    International Nuclear Information System (INIS)

    Maret, Sebastien; Bergin, Edwin A.; Neufeld, David A.; Sonnentrucker, Paule; Yuan Yuan; Green, Joel D.; Watson, Dan M.; Harwit, Martin O.; Kristensen, Lars E.; Melnick, Gary J.; Tolls, Volker; Werner, Michael W.; Willacy, Karen

    2009-01-01

    We present mid-infrared spectral maps of the NGC 1333 star-forming region, obtained with the infrared spectrometer on board the Spitzer Space Telescope. Eight pure H 2 rotational lines, from S(0) to S(7), are detected and mapped. The H 2 emission appears to be associated with the warm gas shocked by the multiple outflows present in the region. A comparison between the observed intensities and the predictions of detailed shock models indicates that the emission arises in both slow (12-24 km s -1 ) and fast (36-53 km s -1 ) C-type shocks with an initial ortho-to-para ratio (opr) ∼ 2 opr exhibits a large degree of spatial variations. In the postshocked gas, it is usually about 2, i.e., close to the equilibrium value (∼3). However, around at least two outflows, we observe a region with a much lower (∼0.5) opr. This region probably corresponds to gas which has been heated up recently by the passage of a shock front, but whose ortho-to-para has not reached equilibrium yet. This, together with the low initial opr needed to reproduce the observed emission, provide strong evidence that H 2 is mostly in para form in cold molecular clouds. The H 2 lines are found to contribute to 25%-50% of the total outflow luminosity, and thus can be used to ascertain the importance of star formation feedback on the natal cloud. From these lines, we determine the outflow mass loss rate and, indirectly, the stellar infall rate, the outflow momentum and the kinetic energy injected into the cloud over the embedded phase. The latter is found to exceed the binding energy of individual cores, suggesting that outflows could be the main mechanism for core disruption.

  1. Mapping populations at risk: improving spatial demographic data for infectious disease modeling and metric derivation

    Directory of Open Access Journals (Sweden)

    Tatem Andrew J

    2012-05-01

    Full Text Available Abstract The use of Global Positioning Systems (GPS and Geographical Information Systems (GIS in disease surveys and reporting is becoming increasingly routine, enabling a better understanding of spatial epidemiology and the improvement of surveillance and control strategies. In turn, the greater availability of spatially referenced epidemiological data is driving the rapid expansion of disease mapping and spatial modeling methods, which are becoming increasingly detailed and sophisticated, with rigorous handling of uncertainties. This expansion has, however, not been matched by advancements in the development of spatial datasets of human population distribution that accompany disease maps or spatial models. Where risks are heterogeneous across population groups or space or dependent on transmission between individuals, spatial data on human population distributions and demographic structures are required to estimate infectious disease risks, burdens, and dynamics. The disease impact in terms of morbidity, mortality, and speed of spread varies substantially with demographic profiles, so that identifying the most exposed or affected populations becomes a key aspect of planning and targeting interventions. Subnational breakdowns of population counts by age and sex are routinely collected during national censuses and maintained in finer detail within microcensus data. Moreover, demographic and health surveys continue to collect representative and contemporary samples from clusters of communities in low-income countries where census data may be less detailed and not collected regularly. Together, these freely available datasets form a rich resource for quantifying and understanding the spatial variations in the sizes and distributions of those most at risk of disease in low income regions, yet at present, they remain unconnected data scattered across national statistical offices and websites. In this paper we discuss the deficiencies of existing

  2. Genetic analysis in maize foundation parents with mapping population and testcross population: Ye478 carried more favorable alleles and using QTL information could improve foundation parents

    Directory of Open Access Journals (Sweden)

    Yinghong Liu

    2016-09-01

    Full Text Available The development of maize foundation parents is an important part of genetics and breeding research, and applying new genetic information to produce foundation parents has been challenging. In this study, we focused on quantitative trait loci (QTLs and general combining ability (GCA of Ye478, a widely used foundation parent in China. We developed three sets of populations for QTL mapping and to analyze the GCA for some agronomic traits. The assessment of 15 traits resulted in the detection of 251 QTLs in six tested environments, with 119 QTLs identified through a joint analysis across all environments. Further analyses revealed that most favorable alleles for plant type-related traits were from Ye478, and more than half of the favorable alleles for yield-related traits were from R08, another foundation parent used in southwestern China, suggesting that different types of foundation parents carried different favorable alleles. We observed that the GCA for most traits (e.g., plant height and 100-kernel weight was maintained in the inbred lines descended from the foundation parents. Additionally, the continuous improvement in the GCA of the descendants of the foundation parents was consistent with the main trend in maize breeding programs. We identified three significant genomic regions that were highly conserved in three Ye478 descendants, including the stable QTL for plant height. The GCA for the traits in the F7 generation revealed that the QTLs for the given traits per se were affected by additive effects in the same way in different populations.

  3. Pooled population pharmacokinetic model of imipenem in plasma and the lung epithelial lining fluid.

    Science.gov (United States)

    van Hasselt, J G Coen; Rizk, Matthew L; Lala, Mallika; Chavez-Eng, Cynthia; Visser, Sandra A G; Kerbusch, Thomas; Danhof, Meindert; Rao, Gauri; van der Graaf, Piet H

    2016-06-01

    Several clinical trials have confirmed the therapeutic benefit of imipenem for treatment of lung infections. There is however no knowledge of the penetration of imipenem into the lung epithelial lining fluid (ELF), the site of action relevant for lung infections. Furthermore, although the plasma pharmacokinetics (PK) of imipenem has been widely studied, most studies have been based on selected patient groups. The aim of this analysis was to characterize imipenem plasma PK across populations and to quantify imipenem ELF penetration. A population model for imipenem plasma PK was developed using data obtained from healthy volunteers, elderly subjects and subjects with renal impairment, in order to identify predictors for inter-individual variability (IIV) of imipenem PK. Subsequently, a clinical study which measured plasma and ELF concentrations of imipenem was included in order to quantify lung penetration. A two compartmental model best described the plasma PK of imipenem. Creatinine clearance and body weight were included as subject characteristics predictive for IIV on clearance. Typical estimates for clearance, central and peripheral volume, and inter-compartmental clearance were 11.5 l h(-1) , 9.37 l, 6.41 l, 13.7 l h(-1) , respectively (relative standard error (RSE) imipenem into ELF was described using a time-independent penetration coefficient of 0.44 (RSE 14%). The identified lung penetration coefficient confirms the clinical relevance of imipenem for treatment of lung infections, while the population PK model provided insights into predictors of IIV for imipenem PK and may be of relevance to support dose optimization in various subject groups. © 2016 The British Pharmacological Society.

  4. HLA haplotype map of river valley populations with hemochromatosis traced through five centuries in Central Sweden.

    Science.gov (United States)

    Olsson, K Sigvard; Ritter, Bernd; Hansson, Norbeth; Chowdhury, Ruma R

    2008-07-01

    The hemochromatosis mutation, C282Y of the HFE gene, seems to have originated from a single event which once occurred in a person living in the north west of Europe carrying human leukocyte antigen (HLA)-A3-B7. In descendants of this ancestor also other haplotypes appear probably caused by local recombinations and founder effects. The background of these associations is unknown. Isolated river valley populations may be fruitful for the mapping of genetic disorders such as hemochromatosis. In this study, we try to test this hypothesis in a study from central Sweden where the haplotyope A1-B8 was common. HLA haplotypes and HFE mutations were studied in hemochromatosis patients with present or past parental origin in a sparsely populated (1/km(2)) rural district (n = 8366 in the year of 2005), in central Sweden. Pedigrees were constructed from the Swedish church book registry. Extended haplotypes were studied to evaluate origin of recombinations. There were 87 original probands, 36 females and 51 males identified during 30 yr, of whom 86% carried C282Y/C282Y and 14% C282Y/H63D. Of 32 different HLA haplotypes A1-B8 was the most common (34%), followed by A3-B7 (16%), both in strong linkage disequilibrium with controls, (P females. River valley populations may contain HLA haplotypes reflecting their demographic history. This study has demonstrated that the resistance against recombinations between HLA-A and HFE make HLA haplotypes excellent markers for population movements. Founder effects and genetic drift from bottleneck populations (surviving the plague?) may explain the commonness of the mutation in central Scandinavia. The intergenerational time difference >30 yr was greater than expected and means that the age of the original mutation may be underestimated.

  5. Adaptive divergence in flowering time among natural populations of Arabidopsis thaliana: Estimates of selection and QTL mapping.

    Science.gov (United States)

    Ågren, Jon; Oakley, Christopher G; Lundemo, Sverre; Schemske, Douglas W

    2017-03-01

    To identify the ecological and genetic mechanisms of local adaptation requires estimating selection on traits, identifying their genetic basis, and evaluating whether divergence in adaptive traits is due to conditional neutrality or genetic trade-offs. To this end, we conducted field experiments for three years using recombinant inbred lines (RILs) derived from two ecotypes of Arabidopsis thaliana (Italy, Sweden), and at each parental site examined selection on flowering time and mapped quantitative trait loci (QTL). There was strong selection for early flowering in Italy, but weak selection in Sweden. Eleven distinct flowering time QTL were detected, and for each the Italian genotype caused earlier flowering. Twenty-seven candidate genes were identified, two of which (FLC and VIN3) appear under major flowering time QTL in Italy. Seven of eight QTL in Italy with narrow credible intervals colocalized with previously reported fitness QTL, in comparison to three of four in Sweden. The results demonstrate that the magnitude of selection on flowering time differs strikingly between our study populations, that the genetic basis of flowering time variation is multigenic with some QTL of large effect, and suggest that divergence in flowering time between ecotypes is due mainly to conditional neutrality. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

  6. Mitochondrial DNA mapping of social-biological interactions in Brazilian Amazonian African-descendant populations

    Directory of Open Access Journals (Sweden)

    Bruno Maia Carvalho

    2008-01-01

    Full Text Available The formation of the Brazilian Amazonian population has historically involved three main ethnic groups, Amerindian, African and European. This has resulted in genetic investigations having been carried out using classical polymorphisms and molecular markers. To better understand the genetic variability and the micro-evolutionary processes acting in human groups in the Brazilian Amazon region we used mitochondrial DNA to investigate 159 maternally unrelated individuals from five Amazonian African-descendant communities. The mitochondrial lineage distribution indicated a contribution of 50.2% from Africans (L0, L1, L2, and L3, 46.6% from Amerindians (haplogroups A, B, C and D and a small European contribution of 1.3%. These results indicated high genetic diversity in the Amerindian and African lineage groups, suggesting that the Brazilian Amazonian African-descendant populations reflect a possible population amalgamation of Amerindian women from different Amazonian indigenous tribes and African women from different geographic regions of Africa who had been brought to Brazil as slaves. The present study partially mapped the historical biological and social interactions that had occurred during the formation and expansion of Amazonian African-descendant communities.

  7. Tumourigenic canine osteosarcoma cell lines associated with frizzled-6 up-regulation and enhanced side population cell frequency.

    Science.gov (United States)

    de Sá Rodrigues, L C; Holmes, K E; Thompson, V; Newton, M A; Stein, T J

    2017-03-01

    An increased serum alkaline phosphatase concentration is known to be associated with a negative prognosis in canine and human osteosarcoma. To expand upon previous studies regarding the biological relevance of increased serum alkaline phosphatase as a negative prognostic factor, xenogeneic heterotopic transplants were performed using six canine primary osteosarcoma cell lines generated from patients with differing serum alkaline phosphatase concentrations (three normal and three increased). Three of the six cell lines were capable of generating tumours and tumour formation was independent of the serum alkaline phosphatase status of the cell line. Microarray analysis identified 379 genes as being differentially expressed between the tumourigenic and non-tumourigenic cell lines. Frizzled-6 was upregulated to the greatest extent (7.78-fold) in tumourigenic cell lines compared with non-tumourigenic cell lines. Frizzled-6, a co-receptor for Wnt ligands has been associated with enhanced tumour-initiating cells and poor prognosis for other tumours. The increased expression of frizzled-6 was confirmed by quantitative reverse transcription polymerase chain reaction (QPCR) and Western blot analysis. Additionally, the tumourigenic cell lines also had an increase in the percentage of side population cells compared with non-tumourigenic cell lines (5.89% versus 1.58%, respectively). There were no differences in tumourigenicity, frizzled-6 or percentage of side population cells noted between osteosarcoma cell lines generated from patients of differing serum alkaline phosphatase concentration. However, to our knowledge this is the first study to identified frizzled-6 as a possible marker of osteosarcoma cell populations with enhanced tumourigenicity and side population cells. Future work will focus on defining the role of frizzled-6 in osteosarcoma tumourigenesis and tumour-initiating cells. © 2015 John Wiley & Sons Ltd.

  8. THE LICK AGN MONITORING PROJECT: BROAD-LINE REGION RADII AND BLACK HOLE MASSES FROM REVERBERATION MAPPING OF Hβ

    International Nuclear Information System (INIS)

    Bentz, Misty C.; Walsh, Jonelle L.; Barth, Aaron J.; Baliber, Nairn; Bennert, Vardha Nicola; Greene, Jenny E.; Hidas, Marton G.; Canalizo, Gabriela; Hiner, Kyle D.; Filippenko, Alexei V.; Ganeshalingam, Mohan; Lee, Nicholas; Li, Weidong; Serduke, Frank J. D.; Silverman, Jeffrey M.; Steele, Thea N.; Gates, Elinor L.; Malkan, Matthew A.; Minezaki, Takeo; Sakata, Yu

    2009-01-01

    We have recently completed a 64-night spectroscopic monitoring campaign at the Lick Observatory 3-m Shane telescope with the aim of measuring the masses of the black holes in 12 nearby (z 6 -10 7 M sun and also the well-studied nearby active galactic nucleus (AGN) NGC 5548. Nine of the objects in the sample (including NGC 5548) showed optical variability of sufficient strength during the monitoring campaign to allow for a time lag to be measured between the continuum fluctuations and the response to these fluctuations in the broad Hβ emission. We present here the light curves for all the objects in this sample and the subsequent Hβ time lags for the nine objects where these measurements were possible. The Hβ lag time is directly related to the size of the broad-line region (BLR) in AGNs, and by combining the Hβ lag time with the measured width of the Hβ emission line in the variable part of the spectrum, we determine the virial mass of the central supermassive black hole in these nine AGNs. The absolute calibration of the black hole masses is based on the normalization derived by Onken et al., which brings the masses determined by reverberation mapping into agreement with the local M BH -σ * relationship for quiescent galaxies. We also examine the time lag response as a function of velocity across the Hβ line profile for six of the AGNs. The analysis of four leads to rather ambiguous results with relatively flat time lags as a function of velocity. However, SBS 1116+583A exhibits a symmetric time lag response around the line center reminiscent of simple models for circularly orbiting BLR clouds, and Arp 151 shows an asymmetric profile that is most easily explained by a simple gravitational infall model. Further investigation will be necessary to fully understand the constraints placed on the physical models of the BLR by the velocity-resolved response in these objects.

  9. Bird on the wire: Landscape planning considering costs and benefits for bird populations coexisting with power lines.

    Science.gov (United States)

    D'Amico, Marcello; Catry, Inês; Martins, Ricardo C; Ascensão, Fernando; Barrientos, Rafael; Moreira, Francisco

    2018-02-24

    Power-line grids are increasingly expanding worldwide, as well as their negative impacts on avifauna, namely the direct mortality through collision and electrocution, the reduction of breeding performance, and the barrier effect. On the other hand, some bird species can apparently benefit from the presence of power lines, for example perching for hunting purposes or nesting on electricity towers. In this perspective essay, we reviewed the scientific literature on both costs and benefits for avifauna coexisting with power lines. Overall, we detected a generalized lack of studies focusing on these costs or benefits at a population level. We suggest that a switch in research approach to a larger spatio-temporal scale would greatly improve our knowledge about the actual effects of power lines on bird populations. This research approach would facilitate suitable landscape planning encompassing both mitigation of costs and promotion of benefits for bird populations coexisting with power lines. For example, the strategic route planning of electricity infrastructures would limit collision risk or barrier effects for threatened bird populations. Concurrently, this strategic route planning would promote the range expansion of threatened populations of other bird species, by providing nesting structures in treeless but potentially suitable landscapes. We suggest establishing a collaborative dialogue among the scientific community, governments, and electricity companies, with the aim to produce a win-win scenario in which both biodiversity conservation and infrastructure development are integrated in a common strategy.

  10. A comparison of genetic map distance and linkage disequilibrium between 15 polymorphic dinucleotide repeat loci in two populations

    Energy Technology Data Exchange (ETDEWEB)

    Urbanek, M.; Goldman, D.; Long, J.C. [Lab. of Neurogenetics, Rockville, MD (United States)

    1994-09-01

    Linkage disequilibrium has recently been used to map the diastrophic dysplasia gene in a Finnish sample. One advantage of this method is that the large pedigrees required by some other methods are unnecessary. Another advantage is that linkage disequilibrium mapping capitalizes on the cumulative history of recombination events, rather than those occurring within the sampled individuals. A potential limitation of linkage disequilibrium mapping is that linkage equilibrium is likely to prevail in all but the most isolated populations, e.g., those which have recently experienced founder effects or severe population bottlenecks. In order to test the method`s generality, we examined patterns of linkage disequilibrium between pairs of loci within a known genetic map. Two populations were analyzed. The first population, Navajo Indians (N=45), is an isolate that experienced a severe bottleneck in the 1860`s. The second population, Maryland Caucasians (N=45), is cosmopolitan. We expected the Navajo sample to display more linkage disequilibrium than the Caucasian sample, and possibly that the Navajo disequilibrium pattern would reflect the genetic map. Linkage disequilibrium coefficients were estimated between pairs of alleles at different loci using maximum likelihood. The genetic isolate structure of Navajo Indians is confirmed by the DNA typings. Heterozygosity is lower than in the Caucasians, and fewer different alleles are observed. However, a relationship between genetic map distance and linkage disequilibrium could be discerned in neither the Navajo nor the Maryland samples. Slightly more linkage disequilibrium was observed in the Navajos, but both data sets were characterized by very low disequilibrium levels. We tentatively conclude that linkage disequilibrium mapping with dinucleotide repeats will only be useful with close linkage between markers and diseases, even in very isolated populations.

  11. High-precision genetic mapping of behavioral traits in the diversity outbred mouse population

    Science.gov (United States)

    Logan, R W; Robledo, R F; Recla, J M; Philip, V M; Bubier, J A; Jay, J J; Harwood, C; Wilcox, T; Gatti, D M; Bult, C J; Churchill, G A; Chesler, E J

    2013-01-01

    Historically our ability to identify genetic variants underlying complex behavioral traits in mice has been limited by low mapping resolution of conventional mouse crosses. The newly developed Diversity Outbred (DO) population promises to deliver improved resolution that will circumvent costly fine-mapping studies. The DO is derived from the same founder strains as the Collaborative Cross (CC), including three wild-derived strains. Thus the DO provides more allelic diversity and greater potential for discovery compared to crosses involving standard mouse strains. We have characterized 283 male and female DO mice using open-field, light–dark box, tail-suspension and visual-cliff avoidance tests to generate 38 behavioral measures. We identified several quantitative trait loci (QTL) for these traits with support intervals ranging from 1 to 3 Mb in size. These intervals contain relatively few genes (ranging from 5 to 96). For a majority of QTL, using the founder allelic effects together with whole genome sequence data, we could further narrow the positional candidates. Several QTL replicate previously published loci. Novel loci were also identified for anxiety- and activity-related traits. Half of the QTLs are associated with wild-derived alleles, confirming the value to behavioral genetics of added genetic diversity in the DO. In the presence of wild-alleles we sometimes observe behaviors that are qualitatively different from the expected response. Our results demonstrate that high-precision mapping of behavioral traits can be achieved with moderate numbers of DO animals, representing a significant advance in our ability to leverage the mouse as a tool for behavioral genetics PMID:23433259

  12. Comparing different stimulus configurations for population receptive field mapping in human fMRI

    Directory of Open Access Journals (Sweden)

    Ivan eAlvarez

    2015-02-01

    Full Text Available Population receptive field (pRF mapping is a widely used approach to measuring aggregate human visual receptive field properties by recording non-invasive signals using functional MRI. Despite growing interest, no study to date has systematically investigated the effects of different stimulus configurations on pRF estimates from human visual cortex. Here we compared the effects of three different stimulus configurations on a model-based approach to pRF estimation: size-invariant bars and eccentricity-scaled bars defined in Cartesian coordinates and traveling along the cardinal axes, and a novel simultaneous ‘wedge and ring’ stimulus defined in polar coordinates, systematically covering polar and eccentricity axes. We found that the presence or absence of eccentricity scaling had a significant effect on goodness of fit and pRF size estimates. Further, variability in pRF size estimates was directly influenced by stimulus configuration, particularly for higher visual areas including V5/MT+. Finally, we compared eccentricity estimation between phase-encoded and model-based pRF approaches. We observed a tendency for more peripheral eccentricity estimates using phase-encoded methods, independent of stimulus size. We conclude that both eccentricity scaling and polar rather than Cartesian stimulus configuration are important considerations for optimal experimental design in pRF mapping. While all stimulus configurations produce adequate estimates, simultaneous wedge and ring stimulation produced higher fit reliability, with a significant advantage in reduced acquisition time.

  13. Mapping of Novel QTL Regulating Grain Shattering Using Doubled Haploid Population in Rice (Oryza sativa L.

    Directory of Open Access Journals (Sweden)

    Gyu-Ho Lee

    2016-01-01

    Full Text Available The critical evolutionary step during domestication of major cereals was elimination of seed shattering because the easy-to-shatter trait in wild relatives results in a severe reduction in yield. In this study, we analyzed the QTLs associated with shattering employing a high-density genetic map in doubled haploid (DH population of rice (Oryza sativa L.. A genetic linkage map was generated with 217 microsatellite markers spanning 2082.4 cM and covering 12 rice chromosomes with an average interval of 9.6 cM between markers based on 120 DHLs derived from a cross between Cheongcheong indica type cultivar and Nagdong japonica type cultivar. In the QTL analysis, five QTLs pertaining to the breaking tensile strength (BTS were detected in 2013 and 2015. Two regions of the QTLs related to BTS on chromosome 1 and chromosome 6 were detected. Several important genes are distributed in 1 Mbp region of the QTL on chromosome 6 and they are related to the formation of abscission layer. We decide to name this QTL qSh6 and the candidate genes in the qSh6 region can be employed usefully in further research for cloning.

  14. Geospatial Technology in Disease Mapping, E- Surveillance and Health Care for Rural Population in South India

    Science.gov (United States)

    Praveenkumar, B. A.; Suresh, K.; Nikhil, A.; Rohan, M.; Nikhila, B. S.; Rohit, C. K.; Srinivas, A.

    2014-11-01

    Providing Healthcare to rural population has been a challenge to the medical service providers especially in developing countries. For this to be effective, scalable and sustainable, certain strategic decisions have to be taken during the planning phase. Also, there is a big gap between the services available and the availability of doctors and medical resources in rural areas. Use of Information Technology can aid this deficiency to a good extent. In this paper, a mobile application has been developed to gather data from the field. A cloud based interface has been developed to store the data in the cloud for effective usage and management of the data. A decision tree based solution developed in this paper helps in diagnosing a patient based on his health parameters. Interactive geospatial maps have been developed to provide effective data visualization facility. This will help both the user community as well as decision makers to carry out long term strategy planning.

  15. Mean-field dynamics of a population of stochastic map neurons

    Science.gov (United States)

    Franović, Igor; Maslennikov, Oleg V.; Bačić, Iva; Nekorkin, Vladimir I.

    2017-07-01

    We analyze the emergent regimes and the stimulus-response relationship of a population of noisy map neurons by means of a mean-field model, derived within the framework of cumulant approach complemented by the Gaussian closure hypothesis. It is demonstrated that the mean-field model can qualitatively account for stability and bifurcations of the exact system, capturing all the generic forms of collective behavior, including macroscopic excitability, subthreshold oscillations, periodic or chaotic spiking, and chaotic bursting dynamics. Apart from qualitative analogies, we find a substantial quantitative agreement between the exact and the approximate system, as reflected in matching of the parameter domains admitting the different dynamical regimes, as well as the characteristic properties of the associated time series. The effective model is further shown to reproduce with sufficient accuracy the phase response curves of the exact system and the assembly's response to external stimulation of finite amplitude and duration.

  16. Improved Mapping of Human Population and Settlements through Integration of Remote Sensing and Socioeconomic Data

    Science.gov (United States)

    de Sherbinin, A. M.; Yetman, G.; MacManus, K.; Vinay, S.

    2017-12-01

    The diversity of data on human settlements, infrastructure, and population continues to grow rapidly, with recent releases of data products based on a range of different remote sensing data sources as well as census and administrative data. We report here on recent improvements in data from the NASA Socioeconomic Data and Applications Center (SEDAC) and partner organizations, aimed at supporting both interdisciplinary research and real-world applications. The fourth version of SEDAC's Gridded Population of the World (GPWv4) now includes variables for age categories, gender, and urban/rural location, and has also been integrated with the Global Human Settlements (GHS) data developed by the Joint Research Centre of the European Commission to produce a GHS-POP grid for the years 1975, 1990, 2000 and 2015. Through a collaboration between Facebook's Connectivity Lab and the Center for International Earth Science Information Network (CIESIN), High Resolution Settlement Layer (HRSL) data derived from 50-cm DigitalGlobe imagery are now available for selected developing countries at 30-m resolution. SEDAC is also developing interactive mapping and analysis tools to facilitate visualization and access to these often large and complex data products. For example, SEDAC has collaborated with scientists from NASA's Goddard Space Flight Center to release the Global Man-made Impervious Surfaces & Settlement Extents from Landsat data at 30-m resolution through an innovative map interface. We also summarize recent progress in developing an international data collective that is bringing together both data developers and data users from the public and private sectors to collaborate on expanding data access and use, improving data quality and documentation, facilitating data intercomparison and integration, and sharing of resources and capabilities.

  17. The Global Trachoma Mapping Project: Methodology of a 34-Country Population-Based Study

    Science.gov (United States)

    Solomon, Anthony W.; Pavluck, Alexandre L.; Courtright, Paul; Aboe, Agatha; Adamu, Liknaw; Alemayehu, Wondu; Alemu, Menbere; Alexander, Neal D. E.; Kello, Amir Bedri; Bero, Berhanu; Brooker, Simon J.; Chu, Brian K.; Dejene, Michael; Emerson, Paul M.; Flueckiger, Rebecca M.; Gadisa, Solomon; Gass, Katherine; Gebre, Teshome; Habtamu, Zelalem; Harvey, Erik; Haslam, Dominic; King, Jonathan D.; Mesurier, Richard Le; Lewallen, Susan; Lietman, Thomas M.; MacArthur, Chad; Mariotti, Silvio P.; Massey, Anna; Mathieu, Els; Mekasha, Addis; Millar, Tom; Mpyet, Caleb; Muñoz, Beatriz E.; Ngondi, Jeremiah; Ogden, Stephanie; Pearce, Joseph; Sarah, Virginia; Sisay, Alemayehu; Smith, Jennifer L.; Taylor, Hugh R.; Thomson, Jo; West, Sheila K.; Willis, Rebecca; Bush, Simon; Haddad, Danny; Foster, Allen

    2015-01-01

    ABSTRACT Purpose: To complete the baseline trachoma map worldwide by conducting population-based surveys in an estimated 1238 suspected endemic districts of 34 countries. Methods: A series of national and sub-national projects owned, managed and staffed by ministries of health, conduct house-to-house cluster random sample surveys in evaluation units, which generally correspond to “health district” size: populations of 100,000–250,000 people. In each evaluation unit, we invite all residents aged 1 year and older from h households in each of c clusters to be examined for clinical signs of trachoma, where h is the number of households that can be seen by 1 team in 1 day, and the product h × c is calculated to facilitate recruitment of 1019 children aged 1–9 years. In addition to individual-level demographic and clinical data, household-level water, sanitation and hygiene data are entered into the purpose-built LINKS application on Android smartphones, transmitted to the Cloud, and cleaned, analyzed and ministry-of-health-approved via a secure web-based portal. The main outcome measures are the evaluation unit-level prevalence of follicular trachoma in children aged 1–9 years, prevalence of trachomatous trichiasis in adults aged 15 + years, percentage of households using safe methods for disposal of human feces, and percentage of households with proximate access to water for personal hygiene purposes. Results: In the first year of fieldwork, 347 field teams commenced work in 21 projects in 7 countries. Conclusion: With an approach that is innovative in design and scale, we aim to complete baseline mapping of trachoma throughout the world in 2015. PMID:26158580

  18. Quantitative Trait Loci in Inbred Lines

    NARCIS (Netherlands)

    Jansen, R.C.

    2001-01-01

    Quantitative traits result from the influence of multiple genes (quantitative trait loci) and environmental factors. Detecting and mapping the individual genes underlying such 'complex' traits is a difficult task. Fortunately, populations obtained from crosses between inbred lines are relatively

  19. Mapping analysis of scaffold/matrix attachment regions (s/MARs) from two different mammalian cell lines

    Energy Technology Data Exchange (ETDEWEB)

    Pilus, Nur Shazwani Mohd; Ahmad, Azrin; Yusof, Nurul Yuziana Mohd [School of Bioscience and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor (Malaysia); Johari, Norazfa [Department of Chemical and Process Engineering, Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor (Malaysia)

    2014-09-03

    Scaffold/matrix attachment regions (S/MARs) are potential element that can be integrated into expression vector to increase expression of recombinant protein. Many studies on S/MAR have been done but none has revealed the distribution of S/MAR in a genome. In this study, we have isolated S/MAR sequences from HEK293 and Chinese hamster ovary cell lines (CHO DG44) using two different methods utilizing 2 M NaCl and lithium-3,5-diiodosalicylate (LIS). The isolated S/MARs were sequenced using Next Generation Sequencing (NGS) platform. Based on reference mapping analysis against human genome database, a total of 8,994,856 and 8,412,672 contigs of S/MAR sequences were retrieved from 2M NaCl and LIS extraction of HEK293 respectively. On the other hand, reference mapping analysis of S/MAR derived from CHO DG44 against our own CHO DG44 database have generated a total of 7,204,348 and 4,672,913 contigs from 2 M NaCl and LIS extraction method respectively.

  20. Mapping analysis of scaffold/matrix attachment regions (s/MARs) from two different mammalian cell lines

    International Nuclear Information System (INIS)

    Pilus, Nur Shazwani Mohd; Ahmad, Azrin; Yusof, Nurul Yuziana Mohd; Johari, Norazfa

    2014-01-01

    Scaffold/matrix attachment regions (S/MARs) are potential element that can be integrated into expression vector to increase expression of recombinant protein. Many studies on S/MAR have been done but none has revealed the distribution of S/MAR in a genome. In this study, we have isolated S/MAR sequences from HEK293 and Chinese hamster ovary cell lines (CHO DG44) using two different methods utilizing 2 M NaCl and lithium-3,5-diiodosalicylate (LIS). The isolated S/MARs were sequenced using Next Generation Sequencing (NGS) platform. Based on reference mapping analysis against human genome database, a total of 8,994,856 and 8,412,672 contigs of S/MAR sequences were retrieved from 2M NaCl and LIS extraction of HEK293 respectively. On the other hand, reference mapping analysis of S/MAR derived from CHO DG44 against our own CHO DG44 database have generated a total of 7,204,348 and 4,672,913 contigs from 2 M NaCl and LIS extraction method respectively

  1. Molecular-cloud-scale Chemical Composition. II. Mapping Spectral Line Survey toward W3(OH) in the 3 mm Band

    Energy Technology Data Exchange (ETDEWEB)

    Nishimura, Yuri [Institute of Astronomy, The University of Tokyo, 2-21-1, Osawa, Mitaka, Tokyo 181-0015 (Japan); Watanabe, Yoshimasa; Yamamoto, Satoshi [Department of Physics, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan); Harada, Nanase [Academia Sinica Institute of Astronomy and Astrophysics, No.1, Sec. 4, Roosevelt Road, 10617 Taipei, Taiwan, R.O.C. (China); Shimonishi, Takashi [Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Aramakiazaaoba 6-3, Aoba-ku, Sendai, Miyagi 980-8578 (Japan); Sakai, Nami [RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan); Aikawa, Yuri [Department of Astronomy, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan); Kawamura, Akiko [Chile Observatory, National Astronomical Observatory of Japan, 2-21-1, Osawa, Mitaka, Tokyo 181-8588 (Japan)

    2017-10-10

    To study a molecular-cloud-scale chemical composition, we conducted a mapping spectral line survey toward the Galactic molecular cloud W3(OH), which is one of the most active star-forming regions in the Perseus arm. We conducted our survey through the use of the Nobeyama Radio Observatory 45 m telescope, and observed the area of 16′ × 16′, which corresponds to 9.0 pc × 9.0 pc. The observed frequency ranges are 87–91, 96–103, and 108–112 GHz. We prepared the spectrum averaged over the observed area, in which eight molecular species (CCH, HCN, HCO{sup +}, HNC, CS, SO, C{sup 18}O, and {sup 13}CO) are identified. On the other hand, the spectrum of the W3(OH) hot core observed at a 0.17 pc resolution shows the lines of various molecules such as OCS, H{sub 2}CS CH{sub 3}CCH, and CH{sub 3}CN in addition to the above species. In the spatially averaged spectrum, emission of the species concentrated just around the star-forming core, such as CH{sub 3}OH and HC{sub 3}N, is fainter than in the hot core spectrum, whereas emission of the species widely extended over the cloud such as CCH is relatively brighter. We classified the observed area into five subregions according to the integrated intensity of {sup 13}CO, and evaluated the contribution to the averaged spectrum from each subregion. The CCH, HCN, HCO{sup +}, and CS lines can be seen even in the spectrum of the subregion with the lowest {sup 13}CO integrated intensity range (<10 K km s{sup −1}). Thus, the contributions of the spatially extended emission is confirmed to be dominant in the spatially averaged spectrum.

  2. Transverse--Harris--lines in a skeletal population from the 1711 Danish plague site

    DEFF Research Database (Denmark)

    Fiscella, Gabriela N; Bennike, Pia; Lynnerup, Niels

    2008-01-01

    This study examines the occurrence and distribution of transverse lines in skeletal remains from the Copenhagen site, a plague cemetery dated 1711 AD. A relatively low frequency for evidence of line formation was observed in the individuals comprising the total sample and no transverse lines were...

  3. Population-Based Trachoma Mapping in Six Evaluation Units of Papua New Guinea.

    Science.gov (United States)

    Ko, Robert; Macleod, Colin; Pahau, David; Sokana, Oliver; Keys, Drew; Burnett, Anthea; Willis, Rebecca; Wabulembo, Geoffrey; Garap, Jambi; Solomon, Anthony W

    2016-01-01

    We sought to determine the prevalence of trachomatous inflammation - follicular (TF) in children aged 1-9 years, and trachomatous trichiasis (TT) in those aged ≥15 years, in suspected trachoma-endemic areas of Papua New Guinea (PNG). We carried out six population-based prevalence surveys using the protocol developed as part of the Global Trachoma Mapping Project. A total of 19,013 individuals were sampled for inclusion, with 15,641 (82.3%) consenting to participate. Four evaluation units had prevalences of TF in children ≥10%, above which threshold the World Health Organization (WHO) recommends mass drug administration (MDA) of azithromycin for at least three years; Western Province (South Fly/Daru) 11.2% (95% confidence interval, CI, 6.9-17.0%), Southern Highlands (East) 12.2% (95% CI 9.6-15.0%), Southern Highlands (West) 11.7% (95% CI 8.5-15.3%), and West New Britain 11.4% (95% CI 8.7-13.9%). TF prevalence was 5.0-9.9% in Madang (9.4%, 95% CI 6.1-13.0%) and National Capital District (6.0%. 95% CI 3.2-9.1%) where consideration of a single round of MDA is warranted. Cases of TT were not found outside West New Britain, in which four cases were seen, generating an estimated population-level prevalence of TT in adults of 0.10% (95% CI 0.00-0.40%) for West New Britain, below the WHO elimination threshold of 0.2% of those aged ≥15 years. Trachoma is a public health issue in PNG. However, other than in West New Britain, there are few data to support the idea that trachoma is a cause of blindness in PNG. Further research is needed to understand the stimulus for the active trachoma phenotype in these populations.

  4. Mapping of stripe rust resistance QTL in Cappelle-Desprez × PBW343 RIL population effective in northern wheat belt of India.

    Science.gov (United States)

    Pawar, Sushma Kumari; Sharma, Davinder; Duhan, Joginder Singh; Saharan, Mahender Singh; Tiwari, Ratan; Sharma, Indu

    2016-06-01

    Stripe rust caused by Puccinia striiformis f. sp. tritici is most important and devastating disease of wheat worldwide, which affects the grain yields, quality and nutrition. To elucidate, the genetic basis of resistance, a mapping population of recombinant inbred lines was developed from a cross between resistant Cappelle-Desprez and susceptible cultivar PBW343 using single-seed descent. Variety PBW343 had been one of the most popular cultivars of North Western Plains Zone, for more than a decade, before succumbing to the stripe rust. Cappelle-Desprez, a source of durable adult plant resistance, has maintained its resistance against stripe rust for a long time in Europe. Map construction and QTL analysis were completed with 1012 polymorphic (DArT and SSR) markers. Screenings for stripe rust disease were carried out in field condition for two consecutive crop seasons (2012-2013 and 2013-2014). Susceptible parent (PBW343) achieved a significant level of disease i.e., 100 % in both the years. In present investigations, resistance in Cappelle-Desprez was found stable and response to the rust ranged from 0 to 1.5 % over the years. The estimated broad-sense heritability (h 2 ) of stripe rust rAUDPC in the mapping population was 0.82. The relative area under the disease progress curve data showed continuous distributions, indicating that trait was controlled multigenically. Genomic region identified on chromosome 2D, was located within the short arm, with flanking markers (Xgwm484-Xcfd73), explained phenotypic variation (PVE) ranged from 13.9 to 31.8 %. The genomic region identified on chromosome 5B was found with the effect of maximum contribution with flanking DArT markers (1376633|F|0-1207571|F|0), PVE ranged from 24 to 27.0 %. This can, therefore, be utilized for marker assisted selection in developing much needed stripe rust resistant lines for the northern wheat belt of India.

  5. Biologic characteristics of the side population of human small cell lung cancer cell line H446.

    Science.gov (United States)

    Wang, Bo; Yang, Huan; Huang, Yu-Zheng; Yan, Ru-Hong; Liu, Fen-Ju; Zhang, Jun-Ning

    2010-03-01

    Recently, the theory of cancer stem cells (CSCs) has presented new targets and orientations for tumor therapy. The major difficulties in researching CSCs include their isolation and purification. The aim of this study is to identify and characterize the side population (SP) cells in small cell lung cancer (SCLC) cell line H446, which lays the foundation for the isolation and purification of CSCs. Fluorescence-activated cell sorting (FACS) was used to sort SP and non-SP (NSP) cells from H446. Both subgroups were cultivated to survey the capacity to form into suspended tumor cell spheres. Reverse transcription-polymerase chain reaction (RT-PCR) and real-time PCR were used to evaluate the expression levels of the mRNA of CD133, ABCG2, and nucleostemin in both subgroups. The capacity of proliferation and the differences in drug resistance of both subgroups and unsorted cells were tested by the MTT method. The differentiation ability of both subgroups was determined by FACS. Proliferation was determined by subcutaneous tumor formation in nude mice. The percent of Hoechst 33342 negative cells was about (5.1 +/- 0.2)% in H446 by fluorescence microscopy. The percent of SP cells was (6.3 +/- 0.1)% by flow cytometry. SP cells had a stronger capability of forming into tumor spheres than NSP cells. The mRNA expression levels of ABCG2, CD133, and nucleostemin in SP cells were 21.60 +/- 0.26, 7.10 +/- 0.14, and 1.02 +/- 0.08 folds higher than that in NSP cells (P 0.05, respectively). In vivo, SP cells showed better proliferative ability and tougher viability when treated with drugs. SP cells can differentiate into NSP cells, but NSP cells cannot differentiate into SP cells. SP cells had a greater ability to form tumors. The H446 cell line contained some SP cells with stem cell properties. CD133 and ABCG2 may be cancer stem cell markers of SCLC.

  6. QTL mapping of combining ability and heterosis of agronomic traits in rice backcross recombinant inbred lines and hybrid crosses.

    Directory of Open Access Journals (Sweden)

    Zhen Qu

    Full Text Available BACKGROUND: Combining ability effects are very effective genetic parameters in deciding the next phase of breeding programs. Although some breeding strategies on the basis of evaluating combining ability have been utilized extensively in hybrid breeding, little is known about the genetic basis of combining ability. Combining ability is a complex trait that is controlled by polygenes. With the advent and development of molecular markers, it is feasible to evaluate the genetic bases of combining ability and heterosis of elite rice hybrids through QTL analysis. METHODOLOGY/PRINCIPAL FINDINGS: In the present study, we first developed a QTL-mapping method for dissecting combining ability and heterosis of agronomic traits. With three testcross populations and a BCRIL population in rice, biometric and QTL analyses were conducted for ten agronomic traits. The significance of general combining ability and special combining ability for most of the traits indicated the importance of both additive and non-additive effects on expression levels. A large number of additive effect QTLs associated with performance per se of BCRIL and general combining ability, and dominant effect QTLs associated with special combining ability and heterosis were identified for the ten traits. CONCLUSIONS/SIGNIFICANCE: The combining ability of agronomic traits could be analyzed by the QTL mapping method. The characteristics revealed by the QTLs for combining ability of agronomic traits were similar with those by multitudinous QTLs for agronomic traits with performance per se of BCRIL. Several QTLs (1-6 in this study were identified for each trait for combining ability. It demonstrated that some of the QTLs were pleiotropic or linked tightly with each other. The identification of QTLs responsible for combining ability and heterosis in the present study provides valuable information for dissecting genetic basis of combining ability.

  7. Guide for developing an information technology investment road map for population health management.

    Science.gov (United States)

    Hunt, Jacquelyn S; Gibson, Richard F; Whittington, John; Powell, Kitty; Wozney, Brad; Knudson, Susan

    2015-06-01

    Many health systems recovering from a massive investment in electronic health records are now faced with the prospect of maturing into accountable care organizations. This maturation includes the need to cooperate with new partners, involve substantially new data sources, require investment in additional information technology (IT) solutions, and become proficient in managing care from a new perspective. Adding to the confusion, there are hundreds of population health management (PHM) vendors with overlapping product functions. This article proposes an organized approach to investing in PHM IT. The steps include assessing the organization's business and clinical goals, establishing governance, agreeing on business requirements, evaluating the ability of current IT systems to meet those requirements, setting time lines and budgets, rationalizing current and future needs and capabilities, and installing the new systems in the context of a continuously learning organization. This article will help organizations chart their position on the population health readiness spectrum and enhance their chances for a successful transition from volume-based to value-based care.

  8. An evaluation of the performance of tag SNPs derived from HapMap in a Caucasian population.

    Directory of Open Access Journals (Sweden)

    Alexandre Montpetit

    2006-03-01

    Full Text Available The Haplotype Map (HapMap project recently generated genotype data for more than 1 million single-nucleotide polymorphisms (SNPs in four population samples. The main application of the data is in the selection of tag single-nucleotide polymorphisms (tSNPs to use in association studies. The usefulness of this selection process needs to be verified in populations outside those used for the HapMap project. In addition, it is not known how well the data represent the general population, as only 90-120 chromosomes were used for each population and since the genotyped SNPs were selected so as to have high frequencies. In this study, we analyzed more than 1,000 individuals from Estonia. The population of this northern European country has been influenced by many different waves of migrations from Europe and Russia. We genotyped 1,536 randomly selected SNPs from two 500-kbp ENCODE regions on Chromosome 2. We observed that the tSNPs selected from the CEPH (Centre d'Etude du Polymorphisme Humain from Utah (CEU HapMap samples (derived from US residents with northern and western European ancestry captured most of the variation in the Estonia sample. (Between 90% and 95% of the SNPs with a minor allele frequency of more than 5% have an r2 of at least 0.8 with one of the CEU tSNPs. Using the reverse approach, tags selected from the Estonia sample could almost equally well describe the CEU sample. Finally, we observed that the sample size, the allelic frequency, and the SNP density in the dataset used to select the tags each have important effects on the tagging performance. Overall, our study supports the use of HapMap data in other Caucasian populations, but the SNP density and the bias towards high-frequency SNPs have to be taken into account when designing association studies.

  9. Determining phenological patterns associated with the onset of senescence in a wheat MAGIC mapping population

    Directory of Open Access Journals (Sweden)

    Anyela Valentina Camargo Rodriguez

    2016-10-01

    Full Text Available The appropriate timing of developmental transitions is critical for adapting many crops to their local climatic conditions. Therefore, understanding the genetic basis of different aspects of phenology could be useful in highlighting mechanisms underpinning adaptation, with implications in breeding for climate change. For bread wheat (Triticum aestivum, the transition from vegetative to reproductive growth, the start and rate of leaf senescence and the relative timing of different stages of flowering and grain filling all contribute to plant performance. In this study we screened under Smart house conditions a large, multi-founder ‘NIAB elite MAGIC’ wheat population, to evaluate the genetic elements that influence the timing of developmental stages in European elite varieties. This panel of recombinant inbred lines was derived from eight parents that are or recently have been grown commercially in the UK and Northern Europe. We undertook a detailed temporal phenotypic analysis under Smart house conditions of the population and its parents, to try to identify known or novel Quantitative Trait Loci associated with variation in the timing of key phenological stages in senescence. This analysis resulted in the detection of QTL interactions with novel traits such the time between ‘half of ear emergence above flag leaf ligule’ and the onset of senescence at the flag leaf as well as traits associated with plant morphology such as stem height. In addition, strong correlations between several traits and the onset of senescence of the flag leaf were identified. This work establishes the value of systematically phenotyping genetically unstructured populations to reveal the genetic architecture underlying morphological variation in commercial wheat.

  10. Mapping low-frequency carbon radio recombination lines towards Cassiopeia A at 340, 148, 54, and 43 MHz

    Science.gov (United States)

    Salas, P.; Oonk, J. B. R.; van Weeren, R. J.; Wolfire, M. G.; Emig, K. L.; Toribio, M. C.; Röttgering, H. J. A.; Tielens, A. G. G. M.

    2018-04-01

    Quantitative understanding of the interstellar medium requires knowledge of its physical conditions. Low-frequency carbon radio recombination lines (CRRLs) trace cold interstellar gas and can be used to determine its physical conditions (e.g. electron temperature and density). In this work, we present spatially resolved observations of the low-frequency (≤390 MHz) CRRLs centred around C268α, C357α, C494α, and C539α towards Cassiopeia A on scales of ≤1.2 pc. We compare the spatial distribution of CRRLs with other interstellar medium tracers. This comparison reveals a spatial offset between the peak of the CRRLs and other tracers, which is very characteristic for photodissociation regions and that we take as evidence for CRRLs being preferentially detected from the surfaces of molecular clouds. Using the CRRLs, we constrain the gas electron temperature and density. These constraints on the gas conditions suggest variations of less than a factor of 2 in pressure over ˜1 pc scales, and an average hydrogen density of 200-470 cm-3. From the electron temperature and density maps, we also constrain the ionized carbon emission measure, column density, and path length. Based on these, the hydrogen column density is larger than 1022 cm-2, with a peak of ˜4 × 1022 cm-2 towards the south of Cassiopeia A. Towards the southern peak, the line-of-sight length is ˜40 pc over a ˜2 pc wide structure, which implies that the gas is a thin surface layer on a large (molecular) cloud that is only partially intersected by Cassiopeia A. These observations highlight the utility of CRRLs as tracers of low-density extended H I and CO-dark gas halo's around molecular clouds.

  11. High Density Linkage Map Construction and QTL Detection for Three Silique-Related Traits in Orychophragmus violaceus Derived Brassica napus Population

    Directory of Open Access Journals (Sweden)

    Yi Yang

    2017-09-01

    Full Text Available Seeds per silique (SS, seed weight (SW, and silique length (SL are important determinant traits of seed yield potential in rapeseed (Brassica napus L., and are controlled by naturally occurring quantitative trait loci (QTLs. Mapping QTLs to narrow chromosomal regions provides an effective means of characterizing the genetic basis of these complex traits. Orychophragmus violaceus is a crucifer with long siliques, many SS, and heavy seeds. A novel B. napus introgression line with many SS was previously selected from multiple crosses (B. rapa ssp. chinesis × O. violaceus × B. napus. In present study, a doubled haploid (DH population with 167 lines was established from a cross between the introgression line and a line with far fewer SS, in order to detect QTLs for silique-related traits. By screening with a Brassica 60K single nucleotide polymorphism (SNP array, a high-density linkage map consisting of 1,153 bins and spanning a cumulative length of 2,209.1 cM was constructed, using 12,602 high-quality polymorphic SNPs in the DH population. The average recombination bin densities of the A and C subgenomes were 1.7 and 2.4 cM, respectively. 45 QTLs were identified for the three traits in all, which explained 4.0–34.4% of the total phenotypic variation; 20 of them were integrated into three unique QTLs by meta-analysis. These unique QTLs revealed a significant positive correlation between SS and SL and a significant negative correlation between SW and SS, and were mapped onto the linkage groups A05, C08, and C09. A trait-by-trait meta-analysis revealed eight, four, and seven consensus QTLs for SS, SW, and SL, respectively, and five major QTLs (cqSS.A09b, cqSS.C09, cqSW.A05, cqSW.C09, and cqSL.C09 were identified. Five, three, and four QTLs for SS, SW, and SL, respectively, might be novel QTLs because of the existence of alien genetic loci for these traits in the alien introgression. Thirty-eight candidate genes underlying nine QTLs for silique

  12. Genetic mapping of QTLs associated with seed macronutrients accumulation in 'MD96-5722' by 'Spencer' recombinant inbred lines of soybean

    Science.gov (United States)

    Research of genetic mapping of QTLs for macronutrient accumulation in soybean seed is limited. Therefore, the objective of this research was to identify QTLs related to macronutrients (N, C, S, P, K, Ca, and Mg) in seeds in 92 F5:7 recombinant inbred lines developed from a cross between MD 96-5722 (...

  13. Fracture network evaluation program (FraNEP): A software for analyzing 2D fracture trace-line maps

    Science.gov (United States)

    Zeeb, Conny; Gomez-Rivas, Enrique; Bons, Paul D.; Virgo, Simon; Blum, Philipp

    2013-10-01

    Fractures, such as joints, faults and veins, strongly influence the transport of fluids through rocks by either enhancing or inhibiting flow. Techniques used for the automatic detection of lineaments from satellite images and aerial photographs, LIDAR technologies and borehole televiewers significantly enhanced data acquisition. The analysis of such data is often performed manually or with different analysis software. Here we present a novel program for the analysis of 2D fracture networks called FraNEP (Fracture Network Evaluation Program). The program was developed using Visual Basic for Applications in Microsoft Excel™ and combines features from different existing software and characterization techniques. The main novelty of FraNEP is the possibility to analyse trace-line maps of fracture networks applying the (1) scanline sampling, (2) window sampling or (3) circular scanline and window method, without the need of switching programs. Additionally, binning problems are avoided by using cumulative distributions, rather than probability density functions. FraNEP is a time-efficient tool for the characterisation of fracture network parameters, such as density, intensity and mean length. Furthermore, fracture strikes can be visualized using rose diagrams and a fitting routine evaluates the distribution of fracture lengths. As an example of its application, we use FraNEP to analyse a case study of lineament data from a satellite image of the Oman Mountains.

  14. C II forbidden-line 158 micron mapping in Sagittarius A Rotation curve and mass distribution in the galactic center

    Science.gov (United States)

    Lugten, J. B.; Genzel, R.; Crawford, M. K.; Townes, C. H.

    1986-01-01

    Based on data obtained with the NASA Kuiper Airborne Observatory 91.4 cm telescope, the 158-micron fine structure line emission of C(+) is mapped near the galactic center. The strongest emission comes from a 10-pc FWHM diameter disk centered on Sgr A West whose dominant motion is rotation. Extended C(+) emission is also found from the +50 km/s galactic center molecular cloud, and a second cloud at v(LSR) of about -35 km/s. The rotation curve and mass distribution within 10 pc of the galactic center are derived, and the C(+) profiles show a drop-off of rotation velocity between 2 and 10 pc. A mass model is suggested with 2-4 million solar masses in a central point mass, and a M/L ratio of the central stellar cluster of 0.5 solar masses/solar luminosities, suggesting a large abundance of giants and relatively recent star formation in the center.

  15. CD133 expression is not selective for tumor initiating or radioresistant cell populations in the CRC line HCT-116

    International Nuclear Information System (INIS)

    Seidel, Claudia; Dietrich, Antje; Wondrak, Marit; Kunz-Schughart, Leoni A.; Grade, Marian; Ried, Thomas

    2009-01-01

    The hypothesis of certain subpopulations of cancer cells with stem-cell like characteristics that might be responsible for treatment resistance and recurrence of disease is still challenging and under quite controversial discussion. In most studies, surrogate cell surface antigens such as the 92-110 kDa transmembrane glycoprotein CD133 (human Prominin-1) were labeled to isolate particular small cancer cell populations for studying their tumorigenic potential. In colorectal carcinomas (CRC) for example, a small CD133 positive (CD133 + ) cell population has recently been described to be enriched for tumor-initiating/cancer stem cells (TIC/CSC) as compared to the CD133 negative (CD133) population. Furthermore, it was documented that the CD133 + subpopulation could exclusively be maintained in culture as spheres under serum-free conditions. Addition of serum resulted in cell differentiation, growth in 2-D and downregulation of CD133 expression. This would imply that established colorectal cancer (CRC) cell lines that have been grown under adherent, serum-supplemented conditions for years should be devoid of CD133 + cells and TIC/CSC, respectively, which seems contradictory to the finding that many CRC lines produce tumors in nude mice models. In order to gain insight into this paradox, we studied the expression of CD133 in numerous established CRC lines under standard culture conditions and chose one particular cell line based on its expression pattern to study the behavior of CD133 + / CD133 - subpopulations

  16. Allelism analysis of BrRfp locus in different restorer lines and map-based cloning of a fertility restorer gene, BrRfp1, for pol CMS in Chinese cabbage (Brassica rapa L.).

    Science.gov (United States)

    Zhang, Huamin; Wu, Junqing; Dai, Zihui; Qin, Meiling; Hao, Lingyu; Ren, Yanjing; Li, Qingfei; Zhang, Lugang

    2017-03-01

    In Chinese cabbage, there are two Rf loci for pol CMS and one of them was mapped to a 12.6-kb region containing a potential candidate gene encoding PPR protein. In Chinese cabbage (Brassica rapa), polima cytoplasmic male sterility (pol CMS) is an important CMS type and is widely used for hybrid breeding. By extensive test crossing in Chinese cabbage, four restorer lines (92s105, 01s325, 00s109, and 88s148) for pol CMS were screened. By analyzing the allelism of the four restorer lines, it was found that 92s105, 01s325, and 00s109 had the same "restorers of fertility" (Rf) locus (designated as BrRfp1), but 88s148 had a different Rf locus (designated as BrRfp2). For fine mapping the BrRfp1 locus of 92s105, a BC 1 F 1 population with 487 individuals and a BC 1 F 2 population with 2485 individuals were successively constructed. Using simple sequence repeat (SSR) markers developed from Brassica rapa reference genome and InDel markers derived from whole-genome resequencing data of 94c9 and 92s105, BrRfp1 was mapped to a 12.6-kb region containing a potential candidate gene encoding pentatricopeptide repeat-containing protein. Based on the nucleotide polymorphisms of the candidate gene sequence between the restoring and nonrestoring alleles, a co-segregating marker SC718 was developed, which would be helpful for hybrid breeding by marker-assisted screening and for detecting new restorer lines.

  17. CRED REA Coral Population Parameters at Palmyra Atoll, Line Islands, 2004

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Belt transects along 2 consecutively-placed, 25m transect lines were surveyed as part of Rapid Ecological Assessments conducted at 9 sites at Palmyra Atoll in the...

  18. Mitochondrial Mutation Rate, Spectrum and Heteroplasmy in Caenorhabditis elegans Spontaneous Mutation Accumulation Lines of Differing Population Size.

    Science.gov (United States)

    Konrad, Anke; Thompson, Owen; Waterston, Robert H; Moerman, Donald G; Keightley, Peter D; Bergthorsson, Ulfar; Katju, Vaishali

    2017-06-01

    Mitochondrial genomes of metazoans, given their elevated rates of evolution, have served as pivotal markers for phylogeographic studies and recent phylogenetic events. In order to determine the dynamics of spontaneous mitochondrial mutations in small populations in the absence and presence of selection, we evolved mutation accumulation (MA) lines of Caenorhabditis elegans in parallel over 409 consecutive generations at three varying population sizes of N = 1, 10, and 100 hermaphrodites. The N =1 populations should have a minimal influence of natural selection to provide the spontaneous mutation rate and the expected rate of neutral evolution, whereas larger population sizes should experience increasing intensity of selection. New mutations were identified by Illumina paired-end sequencing of 86 mtDNA genomes across 35 experimental lines and compared with published genomes of natural isolates. The spontaneous mitochondrial mutation rate was estimated at 1.05 × 10-7/site/generation. A strong G/C→A/T mutational bias was observed in both the MA lines and the natural isolates. This suggests that the low G + C content at synonymous sites is the product of mutation bias rather than selection as previously proposed. The mitochondrial effective population size per worm generation was estimated to be 62. Although it was previously concluded that heteroplasmy was rare in C. elegans, the vast majority of mutations in this study were heteroplasmic despite an experimental regime exceeding 400 generations. The frequencies of frameshift and nonsynonymous mutations were negatively correlated with population size, which suggests their deleterious effects on fitness and a potent role for selection in their eradication. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  19. Strategies for haplotype-based association mapping in complex pedigreed populations

    DEFF Research Database (Denmark)

    Boleckova, J; Christensen, Ole Fredslund; Sørensen, Peter

    2012-01-01

    In association mapping, haplotype-based methods are generally regarded to provide higher power and increased precision than methods based on single markers. For haplotype-based association mapping most studies use a fixed haplotype effect in the model. However, an increase in haplotype length inc...

  20. An integrated interspecific AFLP map of lettuce (Lactuca) based on two L. Saligna x L. sativa F2-populations

    NARCIS (Netherlands)

    Jeuken, M.; Wijk, van R.; Peleman, J.; Lindhout, P.

    2001-01-01

    AFLP markers were obtained with 12 EcoRI/ MseI primer combinations on two independent F2 populations of Lactuca sativa 2 Lactuca saligna. The polymorphism rates of the AFLP products between the two different L. saligna lines was 39°between the two different L. sativa cultivars 13 nd between the L.

  1. [Visualizing Research Lines in Public Health: An analysis Based on Bibliometric Maps Applied to the Revista Española de Salud Pública (2006-2015)].

    Science.gov (United States)

    Gálvez, Carmen

    2016-12-01

    Identifying research lines is essential to understand the knowledge structure of a scientific domain. The aim of this study was to identify the main research topics of within the domain of public health, in the Revista Española de Saslud Pública during 2006-2015. Original articles included in the Social Sciences Citation Index (SSCI) database, available online through the Web of Science (WoS), were selected. The analysis units used were the keywords, KeyWords Plus (KW+), extracted automatically by SSCI. With KW+ obtained bibliometric, maps were created using a methodology based on the combination of co-word analysis, co-word analysis, clustering techniques and visualization techniques. We analyzed 512 documents, of which 176 KW+ were obtained with a frequency greater than or equal to 3. The results were bidimensional bibliometric maps with thematic groupings of KW+, representing the main research fronts: i) epidemiology, risk control programs disease and, in general, service organization and health policies; ii) infectious diseases, principally HIV; iii) a progressive increase in several lines interrelated with cardiovascular diseases (CVD); iv) a line multidimensional dedicated to different aspects associated to the quality of life related to health (HRQoL); and v) an emerging line linked to binge drinking. For the multidisciplinary and multidimensional nature of public health, the construction of bibliometric maps is an appropriate methodology to understand the knowledge structure of this scientific domain.

  2. Identification of candidate genes associated with cell wall digestibility and eQTL (expression quantitative trait loci analysis in a Flint × Flint maize recombinant inbred line population

    Directory of Open Access Journals (Sweden)

    Wenzel Gerhard

    2007-01-01

    Full Text Available Abstract Background Cell-wall digestibility is the major target for improving the feeding value of forage maize. An understanding of the molecular basis for cell-wall digestibility is crucial towards breeding of highly digestible maize. Results 865 candidate ESTs for cell-wall digestibility were selected according to the analysis of expression profiles in 1 three sets of brown-midrib isogenic lines in the genetic background of inbreds 1332 (1332 and 1332 bm3, 5361 (5361 and 5361 bm3, and F2 (F2, F2 bm1, F2 bm2, and F2 bm3, 2 the contrasting extreme lines of FD (Flint × Dent, AS08 × AS 06, DD1 (Dent × Dent, AS11 × AS09, and DD2 (Dent × Dent, AS29 × AS30 mapping populations, and 3 two contrasting isogenic inbreds, AS20 and AS21. Out of those, 439 ESTs were assembled on our "Forage Quality Array", a small microarray specific for cell wall digestibility related experiments. Transcript profiles of 40 lines of a Flint × Flint population were monitored using the Forage Quality Array, which were contrasting for cell wall digestibility. Using t-tests (p Conclusion 102 candidate genes for cell-wall digestibility were validated by genetical genomics approach. Although the cDNA array highlights gene types (the tested gene and any close family members, trans-acting factors or metabolic bottlenecks seem to play the major role in controlling heritable variation of gene expression related to cell-wall digestibility, since no in silico mapped ESTs were in the same location as their own eQTL. Transcriptional variation was generally found to be oligogenic rather than monogenic inherited due to only 26% ESTs detected a single eQTL in the present study. One eQTL hotspot was co-localized with cell wall digestibility related QTL cluster on bins 3.05, implying that in this case the gene(s underlying QTL and eQTL are identical. As the field of genetical genomics develops, it is expected to significantly improve our knowledge about complex traits, such as cell

  3. Identification of quantitative trait Loci for resistance to southern leaf blight and days to anthesis in a maize recombinant inbred line population.

    Science.gov (United States)

    Balint-Kurti, P J; Krakowsky, M D; Jines, M P; Robertson, L A; Molnár, T L; Goodman, M M; Holl, J B

    2006-10-01

    ABSTRACT A recombinant inbred line population derived from a cross between the maize lines NC300 (resistant) and B104 (susceptible) was evaluated for resistance to southern leaf blight (SLB) disease caused by Cochliobolus heterostrophus race O and for days to anthesis in four environments (Clayton, NC, and Tifton, GA, in both 2004 and 2005). Entry mean and average genetic correlations between disease ratings in different environments were high (0.78 to 0.89 and 0.9, respectively) and the overall entry mean heritability for SLB resistance was 0.89. When weighted mean disease ratings were fitted to a model using multiple interval mapping, seven potential quantitative trait loci (QTL) were identified, the two strongest being on chromosomes 3 (bin 3.04) and 9 (bin 9.03-9.04). These QTL explained a combined 80% of the phenotypic variation for SLB resistance. Some time-point-specific SLB resistance QTL were also identified. There was no significant correlation between disease resistance and days to anthesis. Six putative QTL for time to anthesis were identified, none of which coincided with any SLB resistance QTL.

  4. THE ALMA SPECTROSCOPIC SURVEY IN THE HUBBLE ULTRA DEEP FIELD: IMPLICATIONS FOR SPECTRAL LINE INTENSITY MAPPING AT MILLIMETER WAVELENGTHS AND CMB SPECTRAL DISTORTIONS

    Energy Technology Data Exchange (ETDEWEB)

    Carilli, C. L.; Walter, F. [National Radio Astronomy Observatory, P.O. Box 0, Socorro, NM 87801 (United States); Chluba, J. [Jodrell Bank Centre for Astrophysics, University of Manchester, Oxford Road, M13 9PL (United Kingdom); Decarli, R. [Max-Planck Institute for Astronomy, D-69117 Heidelberg (Germany); Aravena, M. [Nucleo de Astronomia, Facultad de Ingenieria, Universidad Diego Portales, Av. Ejercito 441, Santiago (Chile); Wagg, J. [Square Kilometre Array Organisation, Lower Withington, Cheshire (United Kingdom); Popping, G. [European Southern Observatory, Karl-Schwarzschild-Strasse 2, D-85748, Garching (Germany); Cortes, P. [Joint ALMA Observatory—ESO, Av. Alonso de Cordova, 3104, Santiago (Chile); Hodge, J. [Leiden Observatory, Leiden University, Niels Bohrweg 2, NL2333 RA Leiden (Netherlands); Weiss, A. [Max-Planck-Institut für Radioastronomie, Auf dem Hügel 69, D-53121 Bonn (Germany); Bertoldi, F. [Argelander Institute for Astronomy, University of Bonn, Auf dem Hügel 71, D-53121 Bonn (Germany); Riechers, D., E-mail: ccarilli@aoc.nrao.edu [Cornell University, 220 Space Sciences Building, Ithaca, NY 14853 (United States)

    2016-12-10

    We present direct estimates of the mean sky brightness temperature in observing bands around 99 and 242 GHz due to line emission from distant galaxies. These values are calculated from the summed line emission observed in a blind, deep survey for spectral line emission from high redshift galaxies using ALMA (the ALMA spectral deep field observations “ASPECS” survey). In the 99 GHz band, the mean brightness will be dominated by rotational transitions of CO from intermediate and high redshift galaxies. In the 242 GHz band, the emission could be a combination of higher order CO lines, and possibly [C ii] 158 μ m line emission from very high redshift galaxies ( z  ∼ 6–7). The mean line surface brightness is a quantity that is relevant to measurements of spectral distortions of the cosmic microwave background, and as a potential tool for studying large-scale structures in the early universe using intensity mapping. While the cosmic volume and the number of detections are admittedly small, this pilot survey provides a direct measure of the mean line surface brightness, independent of conversion factors, excitation, or other galaxy formation model assumptions. The mean surface brightness in the 99 GHZ band is: T{sub B}  = 0.94 ± 0.09 μ K. In the 242 GHz band, the mean brightness is: T{sub B}  = 0.55 ± 0.033 μ K. These should be interpreted as lower limits on the average sky signal, since we only include lines detected individually in the blind survey, while in a low resolution intensity mapping experiment, there will also be the summed contribution from lower luminosity galaxies that cannot be detected individually in the current blind survey.

  5. Resource mapping and emergency preparedness to infectious diseases in human and animal populations in Kibaha and Ngorongoro districts, Tanzania

    OpenAIRE

    E.D. Karimuribo; B. Jones; M.I. Matee; D.M. Kambarage; S. Mounier-Jack; M.M. Rweyemamu

    2012-01-01

    A rapid situation analysis was conducted in Kibaha and Ngorongoro districts in Tanzania to map resources as well as analysing emergency preparedness to infectious diseases in animal (domestic and wild) and human populations. Kibaha was chosen as a district close to a commercial city (Dar es Salaam) while Ngorongoro represented a remote, border district with high interactions between humans, domestic and wild animals. In this study, data on resources and personnel as well as emergency pre...

  6. Association mapping for #Phytophthora# pod rot resistance in a cacao (#Theobroma cacao# L.) population grown in farmers' field

    OpenAIRE

    Efombagn, Mousseni Ives Bruno; Sounigo, Olivier; Courtois, Brigitte; Fouet, Olivier; Jeanneau, Mélanie; Lemainque, Arnaud; Pavek, Sylvana; Lanaud, Claire

    2016-01-01

    Phytophthora pod rot (PPR) caused by the specie Phytophthora megakarya is an important disease of cacao tree. Association mapping identified markers linked to PPR resistance in a cacao population of 260 trees planted under high disease pressure in a single plantation in a farmer's field. These cacao trees were derived from both selfing and full-sib progenies. The resistance traits were assessed through field observations of the natural pod attacks of the disease on the trunk (PRTnk) or the ca...

  7. Heritability and demographic analyses in the large isolated population of Val Borbera suggest advantages in mapping complex traits genes.

    Directory of Open Access Journals (Sweden)

    Michela Traglia

    2009-10-01

    Full Text Available Isolated populations are a useful resource for mapping complex traits due to shared stable environment, reduced genetic complexity and extended Linkage Disequilibrium (LD compared to the general population. Here we describe a large genetic isolate from the North West Apennines, the mountain range that runs through Italy from the North West Alps to the South.The study involved 1,803 people living in 7 villages of the upper Borbera Valley. For this large population cohort, data from genealogy reconstruction, medical questionnaires, blood, anthropometric and bone status QUS parameters were evaluated. Demographic and epidemiological analyses indicated a substantial genetic component contributing to each trait variation as well as overlapping genetic determinants and family clustering for some traits.The data provide evidence for significant heritability of medical relevant traits that will be important in mapping quantitative traits. We suggest that this population isolate is suitable to identify rare variants associated with complex phenotypes that may be difficult to study in larger but more heterogeneous populations.

  8. Resource mapping and emergency preparedness to infectious diseases in human and animal populations in Kibaha and Ngorongoro districts, Tanzania

    Directory of Open Access Journals (Sweden)

    E.D. Karimuribo

    2012-06-01

    Full Text Available A rapid situation analysis was conducted in Kibaha and Ngorongoro districts in Tanzania to map resources as well as analysing emergency preparedness to infectious diseases in animal (domestic and wild and human populations. Kibaha was chosen as a district close to a commercial city (Dar es Salaam while Ngorongoro represented a remote, border district with high interactions between humans, domestic and wild animals. In this study, data on resources and personnel as well as emergency preparedness were collected from all wards (n = 22, human health facilities (n = 40 and livestock facilities in the two districts using interview checklists and questionnaires. Descriptive statistics for resources were calculated and mapped by district. Kibaha district had a higher human population density, more health workers, better equipped health facilities and better communication and transport systems. On the other hand, Ngorongoro had a higher population of livestock and more animal health facilities but a poorer ratio of animal health workers to livestock. The average ratio of health personnel to population in catchment areas of the health facilities was 1:147 (range of 1:17−1:1200. The ratio of personnel to human population was significantly higher in Kibaha (1:95 than in Ngorongoro (1:203 district (p = 0 < 0.001. Considering the limited resources available to both human and animal health sectors and their different strengths and weaknesses there are opportunities for greater collaboration and resource-sharing between human and animal health for improved surveillance and emergency-preparedness.

  9. Are Proplyds the Low-Energy Counterpart of Clouds Populating the AGNs Broad Line Region?

    Science.gov (United States)

    Dottori, H.

    2000-11-01

    The stability of the clouds producing the broadening of permitted lines in A GNs is a challenge for the persistence of these features during the galactic nucleus active fase lifetime. The formation of succesive generations of clouds in this very agressive enviroment, seems not to be the more adequated scenarion to explain this phenomenon. Why should new clouds be formed in regions where the UV radiation is so intense as to destroy the previously existing ones? The discovery of proplyds in Orion and NGC3603, as well as in 30Dor, shows that the formation of stars with protostars with surrounding disk is a common phenomenon in HII regions with very different radiation fields. We discuss that as a mechanism to explain the persistence of the clouds in the AGNs broad line regions.

  10. The regrowth kinetic of the surviving population is independent of acute and chronic responses to temozolomide in glioblastoma cell lines

    International Nuclear Information System (INIS)

    Silva, Andrew Oliveira; Dalsin, Eloisa; Onzi, Giovana Ravizzoni; Filippi-Chiela, Eduardo Cremonese; Lenz, Guido

    2016-01-01

    Chemotherapy acts on cancer cells by producing multiple effects on a cell population including cell cycle arrest, necrosis, apoptosis and senescence. However, often a subpopulation of cells survives and the behavior of this subpopulation, which is responsible for cancer recurrence, remains obscure. Here we investigated the in vitro short- and long-term responses of six glioblastoma cell lines to clinically relevant doses of temozolomide for 5 days followed by 23 days of recovery, mimicking the standard schedule used in glioblastoma patient for this drug. These cells presented different profiles of sensitivity to temozolomide with varying levels of cell cycle arrest, autophagy and senescence, followed by a regrowth of the surviving cells. The initial reduction in cell number and the subsequent regrowth was analyzed with four new parameters applied to Cumulative Population Doubling (CPD) curves that describe the overall sensitivity of the population and the characteristic of the regrowth: the relative end point CPD (RendCPD); the relative Area Under Curve (rAUC); the Relative Time to Cross a Threshold (RTCT); and the Relative Proliferation Rate (RPR). Surprisingly, the kinetics of regrowth were not predicted by the mechanisms activated after treatment nor by the acute or overall sensitivity. With this study we added new parameters that describe key responses of glioblastoma cell populations to temozolomide treatment. These parameters can also be applied to other cell types and treatments and will help to understand the behavior of the surviving cancer cells after treatment and shed light on studies of cancer resistance and recurrence. - Highlights: • Little is known about the behavior of the glioma cells surviving to TMZ. • The short- and long-term response of six glioma cells lines to TMZ varies considerably. • These glioma cells lines recovered proliferation after therapeutic levels of TMZ. • The growth velocity of the surviving cells was different from the

  11. The regrowth kinetic of the surviving population is independent of acute and chronic responses to temozolomide in glioblastoma cell lines

    Energy Technology Data Exchange (ETDEWEB)

    Silva, Andrew Oliveira, E-mail: andrewbiomed@gmail.com [Department of Biophysics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS (Brazil); Dalsin, Eloisa, E-mail: dalsineloisa@gmail.com [Department of Biophysics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS (Brazil); Onzi, Giovana Ravizzoni, E-mail: gioonzi@gmail.com [Department of Biophysics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS (Brazil); Center of Biotechnology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS (Brazil); Filippi-Chiela, Eduardo Cremonese, E-mail: eduardochiela@gmail.com [Department of Biophysics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS (Brazil); Lenz, Guido, E-mail: lenz@ufrgs.br [Department of Biophysics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS (Brazil); Center of Biotechnology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS (Brazil)

    2016-11-01

    Chemotherapy acts on cancer cells by producing multiple effects on a cell population including cell cycle arrest, necrosis, apoptosis and senescence. However, often a subpopulation of cells survives and the behavior of this subpopulation, which is responsible for cancer recurrence, remains obscure. Here we investigated the in vitro short- and long-term responses of six glioblastoma cell lines to clinically relevant doses of temozolomide for 5 days followed by 23 days of recovery, mimicking the standard schedule used in glioblastoma patient for this drug. These cells presented different profiles of sensitivity to temozolomide with varying levels of cell cycle arrest, autophagy and senescence, followed by a regrowth of the surviving cells. The initial reduction in cell number and the subsequent regrowth was analyzed with four new parameters applied to Cumulative Population Doubling (CPD) curves that describe the overall sensitivity of the population and the characteristic of the regrowth: the relative end point CPD (RendCPD); the relative Area Under Curve (rAUC); the Relative Time to Cross a Threshold (RTCT); and the Relative Proliferation Rate (RPR). Surprisingly, the kinetics of regrowth were not predicted by the mechanisms activated after treatment nor by the acute or overall sensitivity. With this study we added new parameters that describe key responses of glioblastoma cell populations to temozolomide treatment. These parameters can also be applied to other cell types and treatments and will help to understand the behavior of the surviving cancer cells after treatment and shed light on studies of cancer resistance and recurrence. - Highlights: • Little is known about the behavior of the glioma cells surviving to TMZ. • The short- and long-term response of six glioma cells lines to TMZ varies considerably. • These glioma cells lines recovered proliferation after therapeutic levels of TMZ. • The growth velocity of the surviving cells was different from the

  12. A donor-specific QTL, exhibiting allelic variation for leaf sheath hairiness in a nested association mapping population, is located on barley chromosome 4H

    KAUST Repository

    Saade, Stephanie; Kutlu, Burcu; Draba, Vera; Fö rster, Karin; Schumann, Erika; Tester, Mark A.; Pillen, Klaus; Maurer, Andreas

    2017-01-01

    Leaf sheath hairiness is a morphological trait associated with various advantages, including tolerance to both abiotic and biotic stresses, thereby increasing yield. Understanding the genetic basis of this trait in barley can therefore improve the agronomic performance of this economically important crop. We scored leaf sheath hairiness in a two-year field trial in 1,420 BC1S3 lines from the wild barley nested association mapping (NAM) population HEB-25. Leaf sheath hairiness segregated in six out of 25 families with the reference parent Barke being glabrous. We detected the major hairy leaf sheath locus Hs (syn. Hsh) on chromosome 4H (111.3 cM) with high precision. The effects of the locus varied across the six different wild barley donors, with donor of HEB family 11 conferring the highest score of leaf sheath hairiness. Due to the high mapping resolution present in HEB-25, we were able to discuss physically linked pentatricopeptide repeat genes and subtilisin-like proteases as potential candidate genes underlying this locus. In this study, we proved that HEB-25 provides an appropriate tool to further understand the genetic control of leaf sheath hairiness in barley. Furthermore, our work represents a perfect starting position to clone the gene responsible for the 4H locus observed.

  13. A donor-specific QTL, exhibiting allelic variation for leaf sheath hairiness in a nested association mapping population, is located on barley chromosome 4H

    KAUST Repository

    Saade, Stephanie

    2017-12-07

    Leaf sheath hairiness is a morphological trait associated with various advantages, including tolerance to both abiotic and biotic stresses, thereby increasing yield. Understanding the genetic basis of this trait in barley can therefore improve the agronomic performance of this economically important crop. We scored leaf sheath hairiness in a two-year field trial in 1,420 BC1S3 lines from the wild barley nested association mapping (NAM) population HEB-25. Leaf sheath hairiness segregated in six out of 25 families with the reference parent Barke being glabrous. We detected the major hairy leaf sheath locus Hs (syn. Hsh) on chromosome 4H (111.3 cM) with high precision. The effects of the locus varied across the six different wild barley donors, with donor of HEB family 11 conferring the highest score of leaf sheath hairiness. Due to the high mapping resolution present in HEB-25, we were able to discuss physically linked pentatricopeptide repeat genes and subtilisin-like proteases as potential candidate genes underlying this locus. In this study, we proved that HEB-25 provides an appropriate tool to further understand the genetic control of leaf sheath hairiness in barley. Furthermore, our work represents a perfect starting position to clone the gene responsible for the 4H locus observed.

  14. Population pharmacokinetics and limited sampling strategy for first-line tuberculosis drugs and moxifloxacin

    NARCIS (Netherlands)

    Magis-Escurra, C.; Later-Nijland, H. M. J.; Alffenaar, J. W. C.; Broeders, J.; Burger, D. M.; van Crevel, R.; Boeree, M. J.; Donders, A. R. T.; van Altena, R.; van der Werf, T. S.; Aarnoutse, R. E.

    Therapeutic drug monitoring (TDM) of tuberculosis (TB) drugs currently focuses on peak plasma concentrations, yet total exposure [area under the 24-h concentration-time curve (AUC(0-24))] is probably most relevant to the efficacy of these drugs. We therefore assessed population AUC(0-24) data for

  15. Evolutionary stellar population synthesis with MILES : I. The base models and a new line index system

    NARCIS (Netherlands)

    Vazdekis, A.; Sanchez-Blazquez, P.; Falcon-Barroso, J.; Cenarro, A. J.; Beasley, M. A.; Cardiel, N.; Gorgas, J.; Peletier, R. F.

    2010-01-01

    We present synthetic spectral energy distributions (SEDs) for single-age, single-metallicity stellar populations (SSPs) covering the full optical spectral range at moderately high resolution [full width at half-maximum (FWHM) = 2.3Å]. These SEDs constitute our base models, as they combine

  16. A high resolution spatial population database of Somalia for disease risk mapping.

    Science.gov (United States)

    Linard, Catherine; Alegana, Victor A; Noor, Abdisalan M; Snow, Robert W; Tatem, Andrew J

    2010-09-14

    Millions of Somali have been deprived of basic health services due to the unstable political situation of their country. Attempts are being made to reconstruct the health sector, in particular to estimate the extent of infectious disease burden. However, any approach that requires the use of modelled disease rates requires reasonable information on population distribution. In a low-income country such as Somalia, population data are lacking, are of poor quality, or become outdated rapidly. Modelling methods are therefore needed for the production of contemporary and spatially detailed population data. Here land cover information derived from satellite imagery and existing settlement point datasets were used for the spatial reallocation of populations within census units. We used simple and semi-automated methods that can be implemented with free image processing software to produce an easily updatable gridded population dataset at 100 × 100 meters spatial resolution. The 2010 population dataset was matched to administrative population totals projected by the UN. Comparison tests between the new dataset and existing population datasets revealed important differences in population size distributions, and in population at risk of malaria estimates. These differences are particularly important in more densely populated areas and strongly depend on the settlement data used in the modelling approach. The results show that it is possible to produce detailed, contemporary and easily updatable settlement and population distribution datasets of Somalia using existing data. The 2010 population dataset produced is freely available as a product of the AfriPop Project and can be downloaded from: http://www.afripop.org.

  17. Mapping quantitative trait loci in plant breeding populations : Use of parental haplotype sharing

    NARCIS (Netherlands)

    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

  18. QTL mapping for test weight by using F2:3 population in maize

    Indian Academy of Sciences (India)

    Based on the genetic map containing 180 polymorphic SSR markers with an average linkage ... Introduction ... determining the corn market grades for milling, export and ... However, little is known about the importance of additive ... Journal of Genetics, Vol. .... It should be noted in these digenic interactions, a relatively.

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

    Czech Academy of Sciences Publication Activity Database

    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

  20. Scaling results for the magnetic field line trajectories in the stochastic layer near the separatrix in divertor tokamaks with high magnetic shear using the higher shear map

    International Nuclear Information System (INIS)

    Punjabi, Alkesh; Ali, Halima; Farhat, Hamidullah

    2009-01-01

    Extra terms are added to the generating function of the simple map (Punjabi et al 1992 Phys. Rev. Lett. 69 3322) to adjust shear of magnetic field lines in divertor tokamaks. From this new generating function, a higher shear map is derived from a canonical transformation. A continuous analog of the higher shear map is also derived. The method of maps (Punjabi et al 1994 J. Plasma Phys. 52 91) is used to calculate the average shear, stochastic broadening of the ideal separatrix near the X-point in the principal plane of the tokamak, loss of poloidal magnetic flux from inside the ideal separatrix, magnetic footprint on the collector plate, and its area, and the radial diffusion coefficient of magnetic field lines near the X-point. It is found that the width of the stochastic layer near the X-point and the loss of poloidal flux from inside the ideal separatrix scale linearly with average shear. The area of magnetic footprints scales roughly linearly with average shear. Linear scaling of the area is quite good when the average shear is greater than or equal to 1.25. When the average shear is in the range 1.1-1.25, the area of the footprint fluctuates (as a function of average shear) and scales faster than linear scaling. Radial diffusion of field lines near the X-point increases very rapidly by about four orders of magnitude as average shear increases from about 1.15 to 1.5. For higher values of average shear, diffusion increases linearly, and comparatively very slowly. The very slow scaling of the radial diffusion of the field can flatten the plasma pressure gradient near the separatrix, and lead to the elimination of type-I edge localized modes.

  1. Climate change and population dynamics at the tree line: the importance of long-term studies

    Directory of Open Access Journals (Sweden)

    Anfodillo T

    2007-01-01

    Full Text Available Temperature-limited ecosystems are believed to be extremely sensitive to global warming and the upward treeline migration is one of the most relevant phenomenon. Long term monitoring of demographic trends appears essential in order to understand possible effects of higher temperatures on cold ecosystems. Long-term monitoring of natality and mortality of a Pinus sylvestris population in the Swedish Scandes from 1973 to 2005 (Kullman 2007 showed that number of trees increased in the study plots due to higher natality rate, especially in the last decade. This reverses a natural trend of treeline decline and recession occurred in the past.

  2. Analysis and Mapping of Flood Line and Flood Zones within the Godavari River in Nasik Municipal Corporation

    Science.gov (United States)

    Thakre, Deepak

    2010-05-01

    Analysis and Mapping of Flood Line within the Godavari River in Nasik(Municipal Corporation Area) Dr.Deepak N.Thakre Lecturer in Geography L.V.H.College, Nasik-3, Maharashtra, India A flood is an overflow or accumulation of an expanse of water that submerges land when the discharge of a river can not be accommodated within the margins of its normal channel so that water spreads over adjoining area and creates havoc. Problem: Since last few years there has been a sudden increase in rainfall,quite intense during a certain period in monsoon,as a result of which the discharge in river Godavari increases and creates problems in low lying areas on the banks of river Godavari like: submergence of houses,major loss of lives,management failure(due to unexpected dimension of floods)and the disruption of normal life. This paper attempts to analyse and draw an averege flood zone and sudden flood zone on the basis of : 1) Actual field work and survey with the help of Dumpy level and GPS 2) Field interviews of affected people 3) Data available from Meteorological and Irrigation department Among several districts that have flourished in the soils of Indian subcontinent the name of Nashik has drawn the attention of people all over the world. Geographical location of Nashik is 20° 01' to 20° 02' North and 73° 30' to 73° 50'East. Nashik city is situated on the banks of river Godavari and tributaries namely Nasardi, Waghadi, Darna and Walvadi.The total area of Nasik is 264.23 Sq.km (102 Sq.mt) and height from M.S.L is 3284 feet (1001 Mt). River Godavari originates in Western mountain range and flows towards East up to Bay of Bengal. On the upstream of Nasik city dams like Gangapur, Darna, Alandi, Kasyapi and Gautami-Godavari are constructed on river Godavari and its tributaries. Gangapur dam is the nearest storage dam constructed 15km away from Nasik city at source area in the year 1965. Due to moderation of floods and construction of dam there is encroachment in low lying areas

  3. China Dimensions Data Collection: China County-Level Data on Population (Census) and Agriculture, Keyed to 1:1M GIS Map

    Data.gov (United States)

    National Aeronautics and Space Administration — China County-Level Data on Population (Census) and Agriculture, Keyed To 1:1M GIS Map consists of census, agricultural economic, and boundary data for the...

  4. Differential screening and mass mapping of proteins from premalignant and cancer cell lines using nonporous reversed-phase HPLC coupled with mass spectrometric analysis.

    Science.gov (United States)

    Chong, B E; Hamler, R L; Lubman, D M; Ethier, S P; Rosenspire, A J; Miller, F R

    2001-03-15

    Nonporous (NPS) RP-HPLC has been used to rapidly separate proteins from whole cell lysates of human breast cell lines. The nonporous separation involves the use of hard-sphere silica beads of 1.5-microm diameter coated with C18, which can be used to separate proteins ranging from 5 to 90 kDa. Using only 30-40 microg of total protein, the protein molecular weights are detectable on-line using an ESI-oaTOF MS. Of hundreds of proteins detected in this mass range, approxinately 75-80 are more highly expressed. The molecular weight profiles can be displayed as a mass map analogous to a virtual "1-D gel" and differentially expressed proteins can be compared by image analysis. The separated proteins can also be detected by UV absorption and differentially expressed proteins quantified. The eluting proteins can be collected in the liquid phase and the molecular weight and peptide maps determined by MALDI-TOF MS for identification. It is demonstrated that the expressed protein profiles change during neoplastic progression and that many oncoproteins are readily detected. It is also shown that the response of premalignant cancer cells to estradiol can be rapidly screened by this method, demonstrating significant changes in response to an external agent. Ultimately, the proteins can be studied by peptide mapping to search for posttranslational modifications of the oncoproteins accompanying progression.

  5. VERY LARGE ARRAY MAPPING OF THE CO(1-0) LINE IN SMM J14011+0252

    Energy Technology Data Exchange (ETDEWEB)

    Sharon, Chelsea E.; Baker, Andrew J. [Department of Physics and Astronomy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854-8019 (United States); Harris, Andrew I. [Department of Astronomy, University of Maryland, College Park, MD 20742 (United States); Thomson, Alasdair P., E-mail: csharon@physics.rutgers.edu, E-mail: ajbaker@physics.rutgers.edu, E-mail: harris@astro.umd.edu, E-mail: at@roe.ac.uk [Institute for Astronomy, University of Edinburgh, Blackford Hill, Edinburgh EH9 3HJ (United Kingdom)

    2013-03-01

    We present high-resolution CO(1-0) observations of the lensed submillimeter galaxy (SMG) SMM J14011+0252 at z = 2.6. Comparison to the previously detected CO(3-2) line gives an intensity ratio of r {sub 3,1} = 0.97 {+-} 0.16 in temperature units, larger than is typical for SMGs but within the range seen in the low-z ultraluminous infrared galaxy population. Combining our new data with previous mid-J CO observations, we perform a single-phase large velocity gradient (LVG) analysis to constrain the physical conditions of the molecular gas. Acceptable models have significant degeneracies between parameters, even when we rule out all models that produce optically thin emission, but we find that the bulk of the molecular gas has T {sub kin} = 20-60 K, n{sub H{sub 2}}{approx}10{sup 4}-10{sup 5} cm{sup -3}, and N {sub CO}/{Delta}v = 10{sup 17.00{+-}0.25} cm{sup -2} km{sup -1} s. For our best-fit models to self-consistently recover a typical CO-to-H{sub 2} abundance and a plausible degree of virialization, the local velocity gradient in the molecular gas must be substantially larger than its galaxy-wide average. This conclusion is consistent with a scenario in which SMM J14011+0252 has a fairly face-on orientation and a molecular interstellar medium composed of many unresolved clouds. Using previous H{alpha} observations, we find that SMM J14011+0252 has a spatially resolved star formation rate versus molecular gas surface density relation inconsistent with those of 'normal' local star-forming galaxies, even if we adopt a local 'disk-like' CO-to-H{sub 2} conversion factor as motivated by our LVG analysis. This discrepancy supports the inference of a star formation relation for high-z starbursts distinct from the local relation that is not solely due to differing choices of gas mass conversion factor.

  6. Deciphering Natural Allelic Variation in Switchgrass for Biomass Yield and Quality Using a Nested Association Mapping Population

    Energy Technology Data Exchange (ETDEWEB)

    Saha, Malay C. [The Samuel Roberts Noble Foundation, Inc., Ardmore, OK (United States). Forage Improvement Division (FID); Brummer, E. Charles [The Samuel Roberts Noble Foundation, Inc., Ardmore, OK (United States); Kaeppler, Shawn [Univ. of Wisconsin, Madison, WI (United States); Bhandari, Hem S. [Univ. of Tennessee, Knoxville, TN (United States)

    2016-10-28

    Switchgrass (Panicum virgatum L.) is a C4 grass with high biomass yield potential and a model species for bioenergy feedstock development. Understanding the genetic basis of quantitative traits is essential to facilitate genome-enabled breeding programs. The nested association mapping (NAM) analysis combines the best features of both bi-parental and association analyses and can provide high power and high resolution in QTL detection and will ensure significant improvements in biomass yield and quality. To develop a NAM population of switchgrass, 15 highly diverse genotypes with specific characteristics were selected from a diversity panel and crossed to a recurrent parent, AP13, a genotype selected for whole genome sequencing and parent of a mapping population. Ten genotypes from each of the 15 F1 families were then chain crossed. Progenies form each family were randomly selected to develop the NAM population. The switchgrass NAM population consists of a total of 2000 genotypes from 15 families. All the progenies, founder parents, F1 parents (n=2350) were evaluated in replicated field trials at Ardmore, OK and Knoxville, TN. Phenotypic data on plant height, tillering ability, regrowth, flowering time, and biomass yield were collected. Dried biomass samples were also analyzed using prediction equations of NIRS at the Noble Foundation and for lignin content, S/G ratio, and sugar release characteristics at the NREL. Genomic shotgun sequencing of 15 switchgrass NAM founder parental genomes at JGI produced 28-66 Gb high-quality sequence data. Alignment of these sequences with the reference genome, AP13 (v3.0), revealed that up to 99% of the genomic sequences mapped to the reference genome. A total of 2,149 individuals from NAM populations were sequenced by exome capture and two sets of 15 SNP matrices (one for each family) were generated. QTL associated with important traits have been identified and verified in breeding populations. The QTL detected and their associated

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

    Science.gov (United States)

    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.

  8. A comparison of bivariate and univariate QTL mapping in livestock populations

    Directory of Open Access Journals (Sweden)

    Sorensen Daniel

    2003-11-01

    Full Text Available Abstract This study presents a multivariate, variance component-based QTL mapping model implemented via restricted maximum likelihood (REML. The method was applied to investigate bivariate and univariate QTL mapping analyses, using simulated data. Specifically, we report results on the statistical power to detect a QTL and on the precision of parameter estimates using univariate and bivariate approaches. The model and methodology were also applied to study the effectiveness of partitioning the overall genetic correlation between two traits into a component due to many genes of small effect, and one due to the QTL. It is shown that when the QTL has a pleiotropic effect on two traits, a bivariate analysis leads to a higher statistical power of detecting the QTL and to a more precise estimate of the QTL's map position, in particular in the case when the QTL has a small effect on the trait. The increase in power is most marked in cases where the contributions of the QTL and of the polygenic components to the genetic correlation have opposite signs. The bivariate REML analysis can successfully partition the two components contributing to the genetic correlation between traits.

  9. Modelling risk of tick exposure in southern Scandinavia using machine learning techniques, satellite imagery, and human population density maps

    DEFF Research Database (Denmark)

    Kjær, Lene Jung; Korslund, L.; Kjelland, V.

    30 sites (forests and meadows) in each of Denmark, southern Norway and south-eastern Sweden. At each site we measured presence/absence of ticks, and used the data obtained along with environmental satellite images to run Boosted Regression Tree machine learning algorithms to predict overall spatial...... and Sweden), areas with high population densities tend to overlap with these zones.Machine learning techniques allow us to predict for larger areas without having to perform extensive sampling all over the region in question, and we were able to produce models and maps with high predictive value. The results...

  10. Park Facilities, Boundaries were determined from parcel mapping lines & site specific items, such as shelter locations, were obtained by field GPS observation, Published in 2010, Not Applicable scale, Chippewa County Government.

    Data.gov (United States)

    NSGIC Local Govt | GIS Inventory — Park Facilities dataset current as of 2010. Boundaries were determined from parcel mapping lines & site specific items, such as shelter locations, were obtained...

  11. Delineation of high tide line using DGPS and laser trak instruments: With special reference to mapping techniqus

    Digital Repository Service at National Institute of Oceanography (India)

    Ganesan, P.

    output. A suggestion is being made in this report for an urgent need that CRZ issues should be taken up as a national programme with all mapping agencies using same methodology, same datum, same projection and with similar interpretation, so that, uniform...

  12. The structure of the broad-line region in active galactic nuclei. I. Reconstructed velocity-delay maps

    DEFF Research Database (Denmark)

    Grier, C.J.; Peterson, B.M.; Pogge, R.W.

    2013-01-01

    We present velocity-resolved reverberation results for five active galactic nuclei. We recovered velocity-delay maps using the maximum entropy method for four objects: Mrk 335, Mrk 1501, 3C 120, and PG 2130+099. For the fifth, Mrk 6, we were only able to measure mean time delays in different velo...

  13. Mapping cell populations in flow cytometry data for cross-sample comparison using the Friedman-Rafsky test statistic as a distance measure.

    Science.gov (United States)

    Hsiao, Chiaowen; Liu, Mengya; Stanton, Rick; McGee, Monnie; Qian, Yu; Scheuermann, Richard H

    2016-01-01

    Flow cytometry (FCM) is a fluorescence-based single-cell experimental technology that is routinely applied in biomedical research for identifying cellular biomarkers of normal physiological responses and abnormal disease states. While many computational methods have been developed that focus on identifying cell populations in individual FCM samples, very few have addressed how the identified cell populations can be matched across samples for comparative analysis. This article presents FlowMap-FR, a novel method for cell population mapping across FCM samples. FlowMap-FR is based on the Friedman-Rafsky nonparametric test statistic (FR statistic), which quantifies the equivalence of multivariate distributions. As applied to FCM data by FlowMap-FR, the FR statistic objectively quantifies the similarity between cell populations based on the shapes, sizes, and positions of fluorescence data distributions in the multidimensional feature space. To test and evaluate the performance of FlowMap-FR, we simulated the kinds of biological and technical sample variations that are commonly observed in FCM data. The results show that FlowMap-FR is able to effectively identify equivalent cell populations between samples under scenarios of proportion differences and modest position shifts. As a statistical test, FlowMap-FR can be used to determine whether the expression of a cellular marker is statistically different between two cell populations, suggesting candidates for new cellular phenotypes by providing an objective statistical measure. In addition, FlowMap-FR can indicate situations in which inappropriate splitting or merging of cell populations has occurred during gating procedures. We compared the FR statistic with the symmetric version of Kullback-Leibler divergence measure used in a previous population matching method with both simulated and real data. The FR statistic outperforms the symmetric version of KL-distance in distinguishing equivalent from nonequivalent cell

  14. Diagnosing the Kinematics of the Tori in Active Galactic Nuclei with the Velocity-resolved Reverberation Mapping of the Narrow Iron K α Line

    Energy Technology Data Exchange (ETDEWEB)

    Liu Yuan; Li Xiaobo, E-mail: liuyuan@ihep.ac.cn, E-mail: lixb@ihep.ac.cn [Key Laboratory of Particle Astrophysics, Institute of High Energy Physics, Chinese Academy of Sciences, P.O. Box 918-3, Beijing 100049 (China)

    2017-07-20

    The properties of the dusty tori in active galactic nuclei (AGNs) have been investigated in detail, mainly focusing on the geometry and components; however, the kinematics of the torus are still not clear. The narrow iron K α line at 6.4 keV is thought to be produced by the X-ray reflection from the torus. Thus, the velocity-resolved reverberation mapping of it is able to constrain the kinematics of the torus. Such effort is limited by the spectral resolution of current charged coupled device (CCD) detectors and should be possible with the microcalorimeter on the next generation X-ray satellite. In this paper, we first construct the response functions of the torus under a uniform inflow, a Keplerian rotation, and a uniform outflow. Then the energy-dependent light curve of the narrow iron K α line is simulated according to the performance of the X-ray Integral Field Unit in Athena. Finally, the energy-dependent cross-correlation function is calculated to reveal the kinematic signal. According to our results, 100 observations with 5 ks exposure of each are sufficient to distinguish the above three velocity fields. Although the real geometry and velocity field of the torus could be more complex than we assumed, the present result proves the feasibility of the velocity-resolved reverberation mapping of the narrow iron K α line. The combination of the dynamics of the torus with those of the broad-line region and the host galaxy is instructive for the understanding of the feeding and feedback process of AGNs.

  15. Genetic mapping of variation in dauer larvae development in growing populations of Caenorhabditis elegans

    NARCIS (Netherlands)

    Green, J.W.M.; Snoek, L.B.; Kammenga, J.E.; Harvey, S.C.

    2013-01-01

    In the nematode Caenorhabditis elegans, the appropriate induction of dauer larvae development within growing populations is likely to be a primary determinant of genotypic fitness. The underlying genetic architecture of natural genetic variation in dauer formation has, however, not been thoroughly

  16. Mapping the genetic diversity of HLA haplotypes in the Japanese populations

    Science.gov (United States)

    Saw, Woei-Yuh; Liu, Xuanyao; Khor, Chiea-Chuen; Takeuchi, Fumihiko; Katsuya, Tomohiro; Kimura, Ryosuke; Nabika, Toru; Ohkubo, Takayoshi; Tabara, Yasuharu; Yamamoto, Ken; Yokota, Mitsuhiro; Akiyama, Koichi; Asano, Hiroyuki; Asayama, Kei; Haga, Toshikazu; Hara, Azusa; Hirose, Takuo; Hosaka, Miki; Ichihara, Sahoko; Imai, Yutaka; Inoue, Ryusuke; Ishiguro, Aya; Isomura, Minoru; Isono, Masato; Kamide, Kei; Kato, Norihiro; Katsuya, Tomohiro; Kikuya, Masahiro; Kohara, Katsuhiko; Matsubara, Tatsuaki; Matsuda, Ayako; Metoki, Hirohito; Miki, Tetsuro; Murakami, Keiko; Nabika, Toru; Nakatochi, Masahiro; Ogihara, Toshio; Ohnaka, Keizo; Ohkubo, Takayoshi; Rakugi, Hiromi; Satoh, Michihiro; Shiwaku, Kunihiro; Sugimoto, Ken; Tabara, Yasuharu; Takami, Yoichi; Takayanagi, Ryoichi; Takeuchi, Fumihiko; Tsubota-Utsugi, Megumi; Yamamoto, Ken; Yamamoto, Koichi; Yamasaki, Masayuki; Yasui, Daisaku; Yokota, Mitsuhiro; Teo, Yik-Ying; Kato, Norihiro

    2015-01-01

    Japan has often been viewed as an Asian country that possesses a genetically homogenous community. The basis for partitioning the country into prefectures has largely been geographical, although cultural and linguistic differences still exist between some of the districts/prefectures, especially between Okinawa and the mainland prefectures. The Major Histocompatibility Complex (MHC) region has consistently emerged as the most polymorphic region in the human genome, harbouring numerous biologically important variants; nevertheless the presence of population-specific long haplotypes hinders the imputation of SNPs and classical HLA alleles. Here, we examined the extent of genetic variation at the MHC between eight Japanese populations sampled from Okinawa, and six other prefectures located in or close to the mainland of Japan, specifically focusing at the haplotypes observed within each population, and what the impact of any variation has on imputation. Our results indicated that Okinawa was genetically farther to the mainland Japanese than were Gujarati Indians from Tamil Indians, while the mainland Japanese from six prefectures were more homogeneous than between northern and southern Han Chinese. The distribution of haplotypes across Japan was similar, although imputation was most accurate for Okinawa and several mainland prefectures when population-specific panels were used as reference. PMID:26648100

  17. Genome mapping in F 1 population of crossbred Italia and Mercan ...

    African Journals Online (AJOL)

    ... and Mercan), 60 F1 (Italia × Mercan population) and two reference grape cultivar (Cabarnet Sauvignon and Merlot), successfully amplifying 112 markers. When the resistance traits to fungal diseases were analyzed during the study, no markers related with resistance to Botrytis cinerea and downy mildew could be found.

  18. Using SNA to map participation and non-participation in vulnerable populations

    DEFF Research Database (Denmark)

    Hindhede, Anette Lykke

    in health. This has led to the implementation of various health promoting activities within these areas. Community health promotion requires the participation of local leadership and social networks to facilitate the transmission and uptake of interventions for the overall population to achieve social...

  19. Therapeutic implications of an enriched cancer stem-like cell population in a human osteosarcoma cell line

    International Nuclear Information System (INIS)

    Martins-Neves, Sara R; Lopes, Áurio O; Carmo, Anália do; Paiva, Artur A; Simões, Paulo C; Abrunhosa, Antero J; Gomes, Célia MF

    2012-01-01

    Osteosarcoma is a bone-forming tumor of mesenchymal origin that presents a clinical pattern that is consistent with the cancer stem cell model. Cells with stem-like properties (CSCs) have been identified in several tumors and hypothesized as the responsible for the relative resistance to therapy and tumor relapses. In this study, we aimed to identify and characterize CSCs populations in a human osteosarcoma cell line and to explore their role in the responsiveness to conventional therapies. CSCs were isolated from the human MNNG/HOS cell line using the sphere formation assay and characterized in terms of self-renewal, mesenchymal stem cell properties, expression of pluripotency markers and ABC transporters, metabolic activity and tumorigenicity. Cell's sensitivity to conventional chemotherapeutic agents and to irradiation was analyzed and related with cell cycle-induced alterations and apoptosis. The isolated CSCs were found to possess self-renewal and multipotential differentiation capabilities, express markers of pluripotent embryonic stem cells Oct4 and Nanog and the ABC transporters P-glycoprotein and BCRP, exhibit low metabolic activity and induce tumors in athymic mice. Compared with parental MNNG/HOS cells, CSCs were relatively more resistant to both chemotherapy and irradiation. None of the treatments have induced significant cell-cycle alterations and apoptosis in CSCs. MNNG/HOS osteosarcoma cells contain a stem-like cell population relatively resistant to conventional chemotherapeutic agents and irradiation. This resistant phenotype appears to be related with some stem features, namely the high expression of the drug efflux transporters P-glycoprotein and BCRP and their quiescent nature, which may provide a biological basis for resistance to therapy and recurrence commonly observed in osteosarcoma

  20. Therapeutic implications of an enriched cancer stem-like cell population in a human osteosarcoma cell line

    Directory of Open Access Journals (Sweden)

    Martins-Neves Sara R

    2012-04-01

    Full Text Available Abstract Background Osteosarcoma is a bone-forming tumor of mesenchymal origin that presents a clinical pattern that is consistent with the cancer stem cell model. Cells with stem-like properties (CSCs have been identified in several tumors and hypothesized as the responsible for the relative resistance to therapy and tumor relapses. In this study, we aimed to identify and characterize CSCs populations in a human osteosarcoma cell line and to explore their role in the responsiveness to conventional therapies. Methods CSCs were isolated from the human MNNG/HOS cell line using the sphere formation assay and characterized in terms of self-renewal, mesenchymal stem cell properties, expression of pluripotency markers and ABC transporters, metabolic activity and tumorigenicity. Cell's sensitivity to conventional chemotherapeutic agents and to irradiation was analyzed and related with cell cycle-induced alterations and apoptosis. Results The isolated CSCs were found to possess self-renewal and multipotential differentiation capabilities, express markers of pluripotent embryonic stem cells Oct4 and Nanog and the ABC transporters P-glycoprotein and BCRP, exhibit low metabolic activity and induce tumors in athymic mice. Compared with parental MNNG/HOS cells, CSCs were relatively more resistant to both chemotherapy and irradiation. None of the treatments have induced significant cell-cycle alterations and apoptosis in CSCs. Conclusions MNNG/HOS osteosarcoma cells contain a stem-like cell population relatively resistant to conventional chemotherapeutic agents and irradiation. This resistant phenotype appears to be related with some stem features, namely the high expression of the drug efflux transporters P-glycoprotein and BCRP and their quiescent nature, which may provide a biological basis for resistance to therapy and recurrence commonly observed in osteosarcoma.

  1. Metabolic profiling of a mapping population exposes new insights in the regulation of seed metabolism and seed, fruit, and plant relations.

    Directory of Open Access Journals (Sweden)

    David Toubiana

    Full Text Available To investigate the regulation of seed metabolism and to estimate the degree of metabolic natural variability, metabolite profiling and network analysis were applied to a collection of 76 different homozygous tomato introgression lines (ILs grown in the field in two consecutive harvest seasons. Factorial ANOVA confirmed the presence of 30 metabolite quantitative trait loci (mQTL. Amino acid contents displayed a high degree of variability across the population, with similar patterns across the two seasons, while sugars exhibited significant seasonal fluctuations. Upon integration of data for tomato pericarp metabolite profiling, factorial ANOVA identified the main factor for metabolic polymorphism to be the genotypic background rather than the environment or the tissue. Analysis of the coefficient of variance indicated greater phenotypic plasticity in the ILs than in the M82 tomato cultivar. Broad-sense estimate of heritability suggested that the mode of inheritance of metabolite traits in the seed differed from that in the fruit. Correlation-based metabolic network analysis comparing metabolite data for the seed with that for the pericarp showed that the seed network displayed tighter interdependence of metabolic processes than the fruit. Amino acids in the seed metabolic network were shown to play a central hub-like role in the topology of the network, maintaining high interactions with other metabolite categories, i.e., sugars and organic acids. Network analysis identified six exceptionally highly co-regulated amino acids, Gly, Ser, Thr, Ile, Val, and Pro. The strong interdependence of this group was confirmed by the mQTL mapping. Taken together these results (i reflect the extensive redundancy of the regulation underlying seed metabolism, (ii demonstrate the tight co-ordination of seed metabolism with respect to fruit metabolism, and (iii emphasize the centrality of the amino acid module in the seed metabolic network. Finally, the study

  2. Quantitative trait loci underlying resistance to sudden death syndrome (SDS) in MD96-5722 by 'Spencer' recombinant inbred line population of soybean.

    Science.gov (United States)

    Anderson, J; Akond, M; Kassem, M A; Meksem, K; Kantartzi, S K

    2015-04-01

    The best way to protect yield loss of soybean [Glycine max (L.) Merr.] due to sudden death syndrome (SDS), caused by Fusarium virguliforme (Aoki, O'Donnel, Homma & Lattanzi), is the development and use of resistant lines. Mapping quantitative trait loci (QTL) linked to SDS help developing resistant soybean germplasm through molecular marker-assisted selection strategy. QTL for SDS presented herein are from a high-density SNP-based genetic linkage map of MD 96-5722 (a.k.a 'Monocacy') by 'Spencer' recombinant inbred line using SoySNP6K Illumina Infinium BeadChip genotyping array. Ninety-four F 5:7 lines were evaluated for 2 years (2010 and 2011) at two locations (Carbondale and Valmeyer) in southern Illinois, USA to identify QTL controlling SDS resistance using disease index (DX). Composite interval mapping identified 19 SDS controlling QTL which were mapped on 11 separate linkage group (LG) or chromosomes (Chr) out of 20 LG or Chr of soybean genome. Many of these significant QTL identified in one environment/year were confirmed in another year or environment, which suggests a common genetic effects and modes of the pathogen. These new QTL are useful sources for SDS resistance studies in soybean breeding, complementing previously reported loci.

  3. QTL mapping of downy and powdery mildew resistances in PI 197088 cucumber with genotyping-by-sequencing in RIL population.

    Science.gov (United States)

    Wang, Yuhui; VandenLangenberg, Kyle; Wen, Changlong; Wehner, Todd C; Weng, Yiqun

    2018-03-01

    Host resistances in PI 197088 cucumber to downy and powdery mildew pathogens are conferred by 11 (3 with major effect) and 4 (1 major effect) QTL, respectively, and three of which are co-localized. The downy mildew (DM) and powdery mildew (PM) are the two most important foliar diseases of cucurbit crops worldwide. The cucumber accession PI 197088 exhibits high-level resistances to both pathogens. Here, we reported QTL mapping results for DM and PM resistances with 148 recombinant inbred lines from a cross between PI 197088 and the susceptible line 'Coolgreen'. Phenotypic data on responses to natural DM and PM infection were collected in multi-year and multi-location replicated field trials. A high-density genetic map with 2780 single nucleotide polymorphisms (SNPs) from genotyping-by-sequencing and 55 microsatellite markers was developed, which revealed genomic regions with segregation distortion and mis-assemblies in the '9930' cucumber draft genome. QTL analysis identified 11 and 4 QTL for DM and PM resistances accounting for more than 73.5 and 63.0% total phenotypic variance, respectively. Among the 11 DM resistance QTL, dm5.1, dm5.2, and dm5.3 were major-effect contributing QTL, whereas dm1.1, dm2.1, and dm6.2 conferred susceptibility. Of the 4 QTL for PM resistance, pm5.1 was the major-effect QTL explaining 32.4% phenotypic variance and the minor-effect QTL pm6.1 contributed to disease susceptibility. Three PM QTL, pm2.1, pm5.1, and pm6.1, were co-localized with DM QTL dm2.1, dm5.2, and dm6.1, respectively, which was consistent with the observed linkage of PM and DM resistances in PI 197088. The genetic architecture of DM resistance in PI 197088 and another resistant line WI7120 (PI 330628) was compared, and the potential of using PI 197088 in cucumber breeding for downy and powdery mildew resistances is discussed.

  4. Reconstructing human pancreatic differentiation by mapping specific cell populations during development

    DEFF Research Database (Denmark)

    Ramond, Cyrille; Glaser, Nicolas; Berthault, Claire

    2017-01-01

    . Endocrine maturation progresses by up-regulating SUSD2 and lowering ECAD levels. Finally, in vitro differentiation of pancreatic endocrine cells derived from human pluripotent stem cells mimics key in vivo events. Our work paves the way to extend our understanding of the origin of mature human pancreatic......Information remains scarce on human development compared to animal models. Here, we reconstructed human fetal pancreatic differentiation using cell surface markers. We demonstrate that at 7weeks of development, the glycoprotein 2 (GP2) marks a multipotent cell population that will differentiate...... cell types and how such lineage decisions are regulated....

  5. Animals’ population on the glades of electric power line-500 kw in fir and pine formations of the southern taiga

    Directory of Open Access Journals (Sweden)

    A. S. Shishikin

    2016-04-01

    Full Text Available The test groups of animals showed different reaction on the presence of electric power line (EPL glades, which cross light and dark conifer formations. The microarthropods react on the changes of hydrotermic soil conditions in a higher degree. The direct influence of electromagnetic field on the population density of soil invertebrates has place in both forest formations, but with opposite consequences. The same is demonstrated by herpetobium elements: the clear dominance of «meadow» species in fir formations and the absence of this in pine parts. Small mammals on the LEP glades increase their abundance and species diversity. They also demonstrate that their distribution is dominated by food and protection conditions. But at the same time, the distribution of constant rodent winter refuges demonstrate the negative effects of EPL existence. The analysis of bird populations on the basis of optimal life conditions demonstrated a highest negative effect of electromagnetic field of EPL. Independently of the creation of good protection, food and nesting conditions for birds, which usually occupy open biotopes and bush with herb thickets, they avoid the EPL glades. The first results showed the dual effect of EPL glades on animal populations. It is necessary to take into account the forming of intrazonal locations and real electromagnetic effects. The significant conclusions are found for birds, because they receive more irradiation. Also some biological peculiarities are important: the migratory species have a possibility to react immediately, according to the season, on the changing of biotopes. As for other animal groups, it is necessary to prolong the study of seasonal changes. For the invertebrates it must be performed the instrumental analysis of the differences of hydrotermic conditions of EPL glades and native biotopes.

  6. Biocultural research in global mental health: mapping idioms of distress onto blood pressure in a population survey.

    Science.gov (United States)

    Sancilio, Amelia; Eggerman, Mark; Panter-Brick, Catherine

    2017-01-01

    Biocultural research remains a challenge in the field of global mental health. We sought to test associations between blood pressure and idioms of distress in a population survey. We drew on a randomly selected sample of 991 adults (498 men, 493 women) in Afghanistan, for whom physiological and psychosocial data were systematically collected. Assessment of mental health (Self-Reported Questionnaire, Afghan Symptom Checklist) included conceptualizations of distress related to pressure (fishar), anxiety, and dysphoria, as well as dimensions of negative affect and aggression. We used principal component analysis to map survey responses to fishar, and multiple regressions to examine associations with systolic/diastolic blood pressure, controlling for age, body mass index, and wealth, and differentiating by gender, mental health, and medication. The Afghan sample averaged 129/80 mmHg, with 27.14% of hypertensive individuals. SBP showed inverse associations with reports of low fishar (β = -4.58, P < .001) and high fishar (β = 6.90, P < .001), as did DPB with low fishar (β = -1.55, P < .001) and high fishar (β = 3.77, P < .001). Low and high fishar responses accounted for substantial proportions of SBP data variation (R 2  = 20% and R 2  = 24%), especially in adults on blood pressure medication (R 2  = 58% and R 2  = 49%). Subjective reports of fishar map onto physiological blood pressure more robustly than other conceptualizations of mental distress related to anxiety, dysphoria, negative affect, or aggression. Our results point to the utility of mapping biological and cultural measures of stress and distress, advancing biopsychosocial understandings of wellbeing in global mental health surveys. © 2016 Wiley Periodicals, Inc.

  7. Mapping the exposure of the Brazilian population to natural background radiation - cosmic radiation

    International Nuclear Information System (INIS)

    Rochedo, Elaine R.R.; Salles, Krause C.S.; Prado, Nadya M.C.

    2013-01-01

    The main objective of this work is to statically and graphically describe the exposure of the Brazilian population to natural background radiation. in this stage, doses due to cosmic rays is being assessed based on sea level dose rates, corrected by latitude and altitude, according to the model recommended by UNSCEAR. In this work, the doses were estimated for ali Brazilian municipalities with more than 100.000 inhabitants. The 253 municipalities selected for this study include about 52% of the Brazilian population. Average dose rate was estimated to be about 50 n Sv/h with a variation coefficient of 31%. The estimated doses have shown a strong influence of altitude on dose rates, with a correlation coefficient of 0,998 for ao exponential fit. This result confirms previous studies that show a large effect of the altitude 00 exposure from cosmic radiation. Considering the same occupation and shielding conditions used by UNSCEAR as global averages, average annual dose was estimated to be 0,37 (0,24 - 0,76) mSv/y, very close to UNSCEAR worldwide average of 0,38 (0,3 - 1,0) mSv/y. (author)

  8. Sub-national mapping of population pyramids and dependency ratios in Africa and Asia

    Science.gov (United States)

    Pezzulo, Carla; Hornby, Graeme M.; Sorichetta, Alessandro; Gaughan, Andrea E.; Linard, Catherine; Bird, Tomas J.; Kerr, David; Lloyd, Christopher T.; Tatem, Andrew J.

    2017-07-01

    The age group composition of populations varies substantially across continents and within countries, and is linked to levels of development, health status and poverty. The subnational variability in the shape of the population pyramid as well as the respective dependency ratio are reflective of the different levels of development of a country and are drivers for a country's economic prospects and health burdens. Whether measured as the ratio between those of working age and those young and old who are dependent upon them, or through separate young and old-age metrics, dependency ratios are often highly heterogeneous between and within countries. Assessments of subnational dependency ratio and age structure patterns have been undertaken for specific countries and across high income regions, but to a lesser extent across the low income regions. In the framework of the WorldPop Project, through the assembly of over 100 million records across 6,389 subnational administrative units, subnational dependency ratio and high resolution gridded age/sex group datasets were produced for 87 countries in Africa and Asia.

  9. Mapping the exposure of the Brazilian population to natural background radiation - cosmic radiation

    Energy Technology Data Exchange (ETDEWEB)

    Rochedo, Elaine R.R., E-mail: elaine@ird.gov.br [Instituto de Radioprotecao e Dosimetria (lRD/CNEN-RJ), Rio de Janeiro, RJ (Brazil); Salles, Krause C.S.; Prado, Nadya M.C., E-mail: krausesalles@yahoo.com.br, E-mail: nadya@ime.ib.br [Instituto Militar de Engenharia (IME), Rio de Janeiro, RJ (Brazil)

    2013-07-01

    The main objective of this work is to statically and graphically describe the exposure of the Brazilian population to natural background radiation. in this stage, doses due to cosmic rays is being assessed based on sea level dose rates, corrected by latitude and altitude, according to the model recommended by UNSCEAR. In this work, the doses were estimated for ali Brazilian municipalities with more than 100.000 inhabitants. The 253 municipalities selected for this study include about 52% of the Brazilian population. Average dose rate was estimated to be about 50 n Sv/h with a variation coefficient of 31%. The estimated doses have shown a strong influence of altitude on dose rates, with a correlation coefficient of 0,998 for ao exponential fit. This result confirms previous studies that show a large effect of the altitude 00 exposure from cosmic radiation. Considering the same occupation and shielding conditions used by UNSCEAR as global averages, average annual dose was estimated to be 0,37 (0,24 - 0,76) mSv/y, very close to UNSCEAR worldwide average of 0,38 (0,3 - 1,0) mSv/y. (author)

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

    Institute of Scientific and Technical Information of China (English)

    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.

  11. A map of human genome variation from population-scale sequencing.

    Science.gov (United States)

    Abecasis, Gonçalo R; Altshuler, David; Auton, Adam; Brooks, Lisa D; Durbin, Richard M; Gibbs, Richard A; Hurles, Matt E; McVean, Gil A

    2010-10-28

    The 1000 Genomes Project aims to provide a deep characterization of human genome sequence variation as a foundation for investigating the relationship between genotype and phenotype. Here we present results of the pilot phase of the project, designed to develop and compare different strategies for genome-wide sequencing with high-throughput platforms. We undertook three projects: low-coverage whole-genome sequencing of 179 individuals from four populations; high-coverage sequencing of two mother-father-child trios; and exon-targeted sequencing of 697 individuals from seven populations. We describe the location, allele frequency and local haplotype structure of approximately 15 million single nucleotide polymorphisms, 1 million short insertions and deletions, and 20,000 structural variants, most of which were previously undescribed. We show that, because we have catalogued the vast majority of common variation, over 95% of the currently accessible variants found in any individual are present in this data set. On average, each person is found to carry approximately 250 to 300 loss-of-function variants in annotated genes and 50 to 100 variants previously implicated in inherited disorders. We demonstrate how these results can be used to inform association and functional studies. From the two trios, we directly estimate the rate of de novo germline base substitution mutations to be approximately 10(-8) per base pair per generation. We explore the data with regard to signatures of natural selection, and identify a marked reduction of genetic variation in the neighbourhood of genes, due to selection at linked sites. These methods and public data will support the next phase of human genetic research.

  12. Mapping of Powdery Mildew Resistance Gene pmCH89 in a Putative Wheat-Thinopyrum intermedium Introgression Line.

    Science.gov (United States)

    Hou, Liyuan; Zhang, Xiaojun; Li, Xin; Jia, Juqing; Yang, Huizhen; Zhan, Haixian; Qiao, Linyi; Guo, Huijuan; Chang, Zhijian

    2015-07-28

    Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is a globally serious disease adversely affecting wheat production. The Bgt-resistant wheat breeding line CH09W89 was derived after backcrossing a Bgt resistant wheat-Thinopyrum intermedium partial amphiploid TAI7045 with susceptible wheat cultivars. At the seedling stage, CH09W89 exhibited immunity or high resistance to Bgt pathotypes E09, E20, E21, E23, E26, Bg1, and Bg2, similar to its donor line TAI7045 and Th. intermedium. No Th. intermedium chromatin was detected based on genomic in situ hybridization of mitotic chromosomes. To determine the mode of inheritance of the Bgt resistance and the chromosomal location of the resistance gene, CH09W89 was crossed with two susceptible wheat cultivars. The results of the genetic analysis showed that the adult resistance to Bgt E09 in CH09W89 was controlled by a single recessive gene, which was tentatively designated as pmCH89. Two polymorphic SSR markers, Xwmc310 and Xwmc125, were linked to the resistance gene with genetic distances 3.1 and 2.7 cM, respectively. Using the Chinese Spring aneuploid and deletion lines, the resistance gene and its linked markers were assigned to chromosome arm 4BL in the bin 0.68-0.78. Due to its unique position on chromosome 4BL, pmCH89 appears to be a new locus for resistance to powdery mildew. These results will be of benefit for improving powdery mildew resistance in wheat breeding programs.

  13. Mapping of Powdery Mildew Resistance Gene pmCH89 in a Putative Wheat-Thinopyrum intermedium Introgression Line

    Directory of Open Access Journals (Sweden)

    Liyuan Hou

    2015-07-01

    Full Text Available Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt, is a globally serious disease adversely affecting wheat production. The Bgt-resistant wheat breeding line CH09W89 was derived after backcrossing a Bgt resistant wheat-Thinopyrum intermedium partial amphiploid TAI7045 with susceptible wheat cultivars. At the seedling stage, CH09W89 exhibited immunity or high resistance to Bgt pathotypes E09, E20, E21, E23, E26, Bg1, and Bg2, similar to its donor line TAI7045 and Th. intermedium. No Th. intermedium chromatin was detected based on genomic in situ hybridization of mitotic chromosomes. To determine the mode of inheritance of the Bgt resistance and the chromosomal location of the resistance gene, CH09W89 was crossed with two susceptible wheat cultivars. The results of the genetic analysis showed that the adult resistance to Bgt E09 in CH09W89 was controlled by a single recessive gene, which was tentatively designated as pmCH89. Two polymorphic SSR markers, Xwmc310 and Xwmc125, were linked to the resistance gene with genetic distances 3.1 and 2.7 cM, respectively. Using the Chinese Spring aneuploid and deletion lines, the resistance gene and its linked markers were assigned to chromosome arm 4BL in the bin 0.68–0.78. Due to its unique position on chromosome 4BL, pmCH89 appears to be a new locus for resistance to powdery mildew. These results will be of benefit for improving powdery mildew resistance in wheat breeding programs.

  14. Microbeam X-ray fluorescence mapping of Cu and Fe in human prostatic carcinoma cell lines using synchrotron radiation

    Energy Technology Data Exchange (ETDEWEB)

    Rocha, K.M.J.; Leitao, R.G.; Oliveira-Barros, E.G.; Oliveira, M.A.; Canellas, C.G.L.; Anjos, M.J.; Nasciutti, L.E.; Lopes, R.T., E-mail: kjose@nuclear.ufrj.br, E-mail: marcelin@lin.ufrj.br, E-mail: ricardo@lin.ufrj.br, E-mail: roberta@lin.ufrj.br, E-mail: eligouveab@gmail.com, E-mail: maria_aparecida_ufrj@yahoo.com.br, E-mail: luiz.nasciutti@histo.ufrj.br, E-mail: roberta.leitao@uerj.br, E-mail: marcelin@uerj.br [Universidade Federal do Rio de Janeiro (UFRJ), RJ (Brazil). Laboratorio de Instrumentacao Nuclear; Universidade Federal do Rio de Janeiro (UFRJ), RJ (Brazil). Instituto de Ciencias Biomedicas; Universidade do Estado do Rio de Janeiro (UERJ), RJ (Brazil). Instituto de Fisica

    2017-11-01

    Cancer is a worldwide public health problem and prostate cancer continues to be one of the most common fatal cancers in men. Copper plays an important role in the aetiology and growth of tumours however, whether intratumoral copper is actually elevated in prostate cancer patients has not been established. Iron, an important trace element, plays a vital function in oxygen metabolism, oxygen uptake, and electron transport in mitochondria, energy metabolism, muscle function, and hematopoiesis. The X-ray microfluorescence technique (μXRF) is a rapid and non-destructive method of elemental analysis that provides useful elemental information about samples without causing damage or requiring extra sample preparations. This study investigated the behavior of cells in spheroids of human prostate cells, tumour cell line (DU145) and normal cell line (RWPE-1), after supplementation with zinc chloride by 24 hours using synchrotron X-ray microfluorescence (μSRXRF). The measurements were performed with a standard geometry of 45 deg of incidence, excited by a white beam using a pixel of 25 μm and a time of 300 ms/pixel at the XRF beamline at the Synchrotron Light National Laboratory (Campinas, Brazil). The results by SRμXRF showed non-uniform Cu and Fe distributions in all the spheroids analyzed. (author)

  15. Microbeam X-ray fluorescence mapping of Cu and Fe in human prostatic carcinoma cell lines using synchrotron radiation

    International Nuclear Information System (INIS)

    Rocha, K.M.J.; Leitao, R.G.; Oliveira-Barros, E.G.; Oliveira, M.A.; Canellas, C.G.L.; Anjos, M.J.; Nasciutti, L.E.; Lopes, R.T.; Universidade Federal do Rio de Janeiro; Universidade do Estado do Rio de Janeiro

    2017-01-01

    Cancer is a worldwide public health problem and prostate cancer continues to be one of the most common fatal cancers in men. Copper plays an important role in the aetiology and growth of tumours however, whether intratumoral copper is actually elevated in prostate cancer patients has not been established. Iron, an important trace element, plays a vital function in oxygen metabolism, oxygen uptake, and electron transport in mitochondria, energy metabolism, muscle function, and hematopoiesis. The X-ray microfluorescence technique (μXRF) is a rapid and non-destructive method of elemental analysis that provides useful elemental information about samples without causing damage or requiring extra sample preparations. This study investigated the behavior of cells in spheroids of human prostate cells, tumour cell line (DU145) and normal cell line (RWPE-1), after supplementation with zinc chloride by 24 hours using synchrotron X-ray microfluorescence (μSRXRF). The measurements were performed with a standard geometry of 45 deg of incidence, excited by a white beam using a pixel of 25 μm and a time of 300 ms/pixel at the XRF beamline at the Synchrotron Light National Laboratory (Campinas, Brazil). The results by SRμXRF showed non-uniform Cu and Fe distributions in all the spheroids analyzed. (author)

  16. RelocaTE2: a high resolution transposable element insertion site mapping tool for population resequencing

    Directory of Open Access Journals (Sweden)

    Jinfeng Chen

    2017-01-01

    Full Text Available Background Transposable element (TE polymorphisms are important components of population genetic variation. The functional impacts of TEs in gene regulation and generating genetic diversity have been observed in multiple species, but the frequency and magnitude of TE variation is under appreciated. Inexpensive and deep sequencing technology has made it affordable to apply population genetic methods to whole genomes with methods that identify single nucleotide and insertion/deletion polymorphisms. However, identifying TE polymorphisms, particularly transposition events or non-reference insertion sites can be challenging due to the repetitive nature of these sequences, which hamper both the sensitivity and specificity of analysis tools. Methods We have developed the tool RelocaTE2 for identification of TE insertion sites at high sensitivity and specificity. RelocaTE2 searches for known TE sequences in whole genome sequencing reads from second generation sequencing platforms such as Illumina. These sequence reads are used as seeds to pinpoint chromosome locations where TEs have transposed. RelocaTE2 detects target site duplication (TSD of TE insertions allowing it to report TE polymorphism loci with single base pair precision. Results and Discussion The performance of RelocaTE2 is evaluated using both simulated and real sequence data. RelocaTE2 demonstrate high level of sensitivity and specificity, particularly when the sequence coverage is not shallow. In comparison to other tools tested, RelocaTE2 achieves the best balance between sensitivity and specificity. In particular, RelocaTE2 performs best in prediction of TSDs for TE insertions. Even in highly repetitive regions, such as those tested on rice chromosome 4, RelocaTE2 is able to report up to 95% of simulated TE insertions with less than 0.1% false positive rate using 10-fold genome coverage resequencing data. RelocaTE2 provides a robust solution to identify TE insertion sites and can be

  17. Mapping human temporal and parietal neuronal population activity and functional coupling during mathematical cognition

    Science.gov (United States)

    Daitch, Amy L.; Foster, Brett L.; Schrouff, Jessica; Rangarajan, Vinitha; Kaşikçi, Itır; Gattas, Sandra; Parvizi, Josef

    2016-01-01

    Brain areas within the lateral parietal cortex (LPC) and ventral temporal cortex (VTC) have been shown to code for abstract quantity representations and for symbolic numerical representations, respectively. To explore the fast dynamics of activity within each region and the interaction between them, we used electrocorticography recordings from 16 neurosurgical subjects implanted with grids of electrodes over these two regions and tracked the activity within and between the regions as subjects performed three different numerical tasks. Although our results reconfirm the presence of math-selective hubs within the VTC and LPC, we report here a remarkable heterogeneity of neural responses within each region at both millimeter and millisecond scales. Moreover, we show that the heterogeneity of response profiles within each hub mirrors the distinct patterns of functional coupling between them. Our results support the existence of multiple bidirectional functional loops operating between discrete populations of neurons within the VTC and LPC during the visual processing of numerals and the performance of arithmetic functions. These findings reveal information about the dynamics of numerical processing in the brain and also provide insight into the fine-grained functional architecture and connectivity within the human brain. PMID:27821758

  18. Comparison of Antidepressant Efficacy-related SNPs Among Taiwanese and Four Populations in the HapMap Database

    Directory of Open Access Journals (Sweden)

    Mei-Hung Chi

    2011-07-01

    Full Text Available The genetic influence of single nucleotide polymorphisms (SNPs on antidepressant efficacy has been previously demonstrated. To evaluate whether there are ethnic differences, we compared the allele frequencies of antidepressant efficacy-related SNPs between the Taiwanese population and four other populations in the HapMap database. We recruited 198 Taiwanese major depression patients and 106 Taiwanese controls. A panel of possible relevant SNPs (in brain-derived neurotrophic factor, 5-hydroxytryptamine receptor 2A, interleukin 1 beta, and G-protein beta 3 subunit genes was selected for comparisons of allele frequencies using the χ2 test. Our results suggested no difference between Taiwanese patients and controls, but there were significant differences among Taiwanese controls and the other four ethnic groups in brain-derived neurotrophic factor, 5-hydroxytryptamine receptor 2A, interleukin 1 beta and G-protein beta 3 subunit genes. We conclude that there are ethnic differences in the allele frequencies of antidepressant efficacy-related SNPs, and that the degree of variations is consistent with geographic distances. Further investigation is required to verify the attribution of genetic differences to ethnic-specific antidepressant responses.

  19. Mapping Application for Penguin Populations and Projected Dynamics (MAPPPD): Data and Tools for Dynamic Management and Decision Support

    Science.gov (United States)

    Humphries, G. R. W.; Naveen, R.; Schwaller, M.; Che-Castaldo, C.; McDowall, P.; Schrimpf, M.; Schrimpf, Michael; Lynch, H. J.

    2017-01-01

    The Mapping Application for Penguin Populations and Projected Dynamics (MAPPPD) is a web-based, open access, decision-support tool designed to assist scientists, non-governmental organizations and policy-makers working to meet the management objectives as set forth by the Commission for the Conservation of Antarctic Marine Living Resources (CCAMLR) and other components of the Antarctic Treaty System (ATS) (that is, Consultative Meetings and the ATS Committee on Environmental Protection). MAPPPD was designed specifically to complement existing efforts such as the CCAMLR Ecosystem Monitoring Program (CEMP) and the ATS site guidelines for visitors. The database underlying MAPPPD includes all publicly available (published and unpublished) count data on emperor, gentoo, Adelie) and chinstrap penguins in Antarctica. Penguin population models are used to assimilate available data into estimates of abundance for each site and year.Results are easily aggregated across multiple sites to obtain abundance estimates over any user-defined area of interest. A front end web interface located at www.penguinmap.com provides free and ready access to the most recent count and modelled data, and can act as a facilitator for data transfer between scientists and Antarctic stakeholders to help inform management decisions for the continent.

  20. About Non-Line-Of-Sight Satellite Detection and Exclusion in a 3D Map-Aided Localization Algorithm

    Directory of Open Access Journals (Sweden)

    François Peyret

    2013-01-01

    Full Text Available Reliable GPS positioning in city environment is a key issue: actually, signals are prone to multipath, with poor satellite geometry in many streets. Using a 3D urban model to forecast satellite visibility in urban contexts in order to improve GPS localization is the main topic of the present article. A virtual image processing that detects and eliminates possible faulty measurements is the core of this method. This image is generated using the position estimated a priori by the navigation process itself, under road constraints. This position is then updated by measurements to line-of-sight satellites only. This closed-loop real-time processing has shown very first promising full-scale test results.

  1. About Non-Line-Of-Sight Satellite Detection and Exclusion in a 3D Map-Aided Localization Algorithm

    Science.gov (United States)

    Peyraud, Sébastien; Bétaille, David; Renault, Stéphane; Ortiz, Miguel; Mougel, Florian; Meizel, Dominique; Peyret, François

    2013-01-01

    Reliable GPS positioning in city environment is a key issue actually, signals are prone to multipath, with poor satellite geometry in many streets. Using a 3D urban model to forecast satellite visibility in urban contexts in order to improve GPS localization is the main topic of the present article. A virtual image processing that detects and eliminates possible faulty measurements is the core of this method. This image is generated using the position estimated a priori by the navigation process itself, under road constraints. This position is then updated by measurements to line-of-sight satellites only. This closed-loop real-time processing has shown very first promising full-scale test results. PMID:23344379

  2. Integration of population census and water point mapping data-A case study of Cambodia, Liberia and Tanzania.

    Science.gov (United States)

    Yu, Weiyu; Wardrop, Nicola A; Bain, Robert; Wright, Jim A

    2017-07-01

    Sustainable Development Goal (SDG) 6 has expanded the Millennium Development Goals' focus from improved drinking-water to safely managed water services. This expanded focus to include issues such as water quality requires richer monitoring data and potentially integration of datasets from different sources. Relevant data sets include water point mapping (WPM), the survey of boreholes, wells and other water points, census and household survey data. This study examined inconsistencies between population census and WPM datasets for Cambodia, Liberia and Tanzania, and identified potential barriers to integrating the two datasets to meet monitoring needs. Literatures on numbers of people served per water point were used to convert WPM data to population served by water source type per area and compared with census reports. For Cambodia and Tanzania, discrepancies with census data suggested incomplete WPM coverage. In Liberia, where the data sets were consistent, WPM-derived data on functionality, quantity and quality of drinking water were further combined with census area statistics to generate an enhanced drinking-water access measure for protected wells and springs. The process revealed barriers to integrating census and WPM data, including exclusion of water points not used for drinking by households, matching of census and WPM source types; temporal mismatches between data sources; data quality issues such as missing or implausible data values, and underlying assumptions about population served by different water point technologies. However, integration of these two data sets could be used to identify and rectify gaps in WPM coverage. If WPM databases become more complete and the above barriers are addressed, it could also be used to develop more realistic measures of household drinking-water access for monitoring. Copyright © 2017 Elsevier GmbH. All rights reserved.

  3. Unconditional and Conditional QTL Mapping for Tiller Numbers at Various Stages with Single Segment Substitution Lines in Rice (Oryza sativa L.)

    Institute of Scientific and Technical Information of China (English)

    ZHAO Fang-ming; LIU Gui-fu; ZHU Hai-tao; DING Xiao-hua; ZENG Rui-zhen; ZHANG Ze-min; LI Wen-tao; ZHANG Gui-quan

    2008-01-01

    Tiller is one of the most important agronomic traits which influences quantity and quality of effective panicles and finally influences yield in rice.It is important to understand "static" and "dynamic" information of the QTLs for tillers in rice.This work was the first time to simultaneously map unconditional and conditional QTLs for tiller numbers at various stages by using single segment substitution lines in rice.Fourteen QTLs for tiller number,distributing on the corresponding substitution segments of chromosomes 1,2,3,4,6,7 and 8 were detected.Both the number and the effect of the QTLs for tiller number were various at different stages,from 6 to 9 in the number and from 1.49 to 3.49 in the effect,respectively. Tiller number QTLs expressed in a time order,mainly detected at three stages of 0-7d,14-21d and 35-42d after transplanting with 6 positive,9 random and 6 negative expressing QTLs,respectively.Each of the QTLs expressed one time at least during the whole duration of rice.The tiller number at a specific stage was determined by sum of QTL effects estimated by the unconditional method,while the increasing or decreasing number in a given time interval was controlled by the total of QTL effects estimated by the conditional method.These results demonstrated that it is highly effective and accurate for mapping of the QTLs by using single segment substitution lines and the conditional analysis methodology.

  4. GIS Database and Google Map of the Population at Risk of Cholangiocarcinoma in Mueang Yang District, Nakhon Ratchasima Province of Thailand.

    Science.gov (United States)

    Kaewpitoon, Soraya J; Rujirakul, Ratana; Joosiri, Apinya; Jantakate, Sirinun; Sangkudloa, Amnat; Kaewthani, Sarochinee; Chimplee, Kanokporn; Khemplila, Kritsakorn; Kaewpitoon, Natthawut

    2016-01-01

    Cholangiocarcinoma (CCA) is a serious problem in Thailand, particularly in the northeastern and northern regions. Database of population at risk are need required for monitoring, surveillance, home health care, and home visit. Therefore, this study aimed to develop a geographic information system (GIS) database and Google map of the population at risk of CCA in Mueang Yang district, Nakhon Ratchasima province, northeastern Thailand during June to October 2015. Populations at risk were screened using the Korat CCA verbal screening test (KCVST). Software included Microsoft Excel, ArcGIS, and Google Maps. The secondary data included the point of villages, sub-district boundaries, district boundaries, point of hospital in Mueang Yang district, used for created the spatial databese. The populations at risk for CCA and opisthorchiasis were used to create an arttribute database. Data were tranfered to WGS84 UTM ZONE 48. After the conversion, all of the data were imported into Google Earth using online web pages www.earthpoint.us. Some 222 from a 4,800 population at risk for CCA constituted a high risk group. Geo-visual display available at following www.google.com/maps/d/u/0/ edit?mid=zPxtcHv_iDLo.kvPpxl5mAs90 and hl=th. Geo-visual display 5 layers including: layer 1, village location and number of the population at risk for CCA; layer 2, sub-district health promotion hospital in Mueang Yang district and number of opisthorchiasis; layer 3, sub-district district and the number of population at risk for CCA; layer 4, district hospital and the number of population at risk for CCA and number of opisthorchiasis; and layer 5, district and the number of population at risk for CCA and number of opisthorchiasis. This GIS database and Google map production process is suitable for further monitoring, surveillance, and home health care for CCA sufferers.

  5. Cytogenetic analysis and mapping of leaf rust resistance in Aegilops speltoides Tausch derived bread wheat line Selection2427 carrying putative gametocidal gene(s).

    Science.gov (United States)

    Niranjana, M; Vinod; Sharma, J B; Mallick, Niharika; Tomar, S M S; Jha, S K

    2017-12-01

    Leaf rust (Puccinia triticina) is a major biotic stress affecting wheat yields worldwide. Host-plant resistance is the best method for controlling leaf rust. Aegilops speltoides is a good source of resistance against wheat rusts. To date, five Lr genes, Lr28, Lr35, Lr36, Lr47, and Lr51, have been transferred from Ae. speltoides to bread wheat. In Selection2427, a bread wheat introgresed line with Ae. speltoides as the donor parent, a dominant gene for leaf rust resistance was mapped to the long arm of chromosome 3B (LrS2427). None of the Lr genes introgressed from Ae. speltoides have been mapped to chromosome 3B. Since none of the designated seedling leaf rust resistance genes have been located on chromosome 3B, LrS2427 seems to be a novel gene. Selection2427 showed a unique property typical of gametocidal genes, that when crossed to other bread wheat cultivars, the F 1 showed partial pollen sterility and poor seed setting, whilst Selection2427 showed reasonable male and female fertility. Accidental co-transfer of gametocidal genes with LrS2427 may have occurred in Selection2427. Though LrS2427 did not show any segregation distortion and assorted independently of putative gametocidal gene(s), its utilization will be difficult due to the selfish behavior of gametocidal genes.

  6. Flood-inundation maps for the Hoosic River, North Adams and Williamstown, Massachusetts, from the confluence with the North Branch Hoosic River to the Vermont State line

    Science.gov (United States)

    Lombard, Pamela J.; Bent, Gardner C.

    2015-01-01

    A series of nine digital flood-inundation maps were developed for an 8-mile reach of the Hoosic River in North Adams and Williamstown, Massachusetts, by the U.S. Geological Survey (USGS) in cooperation with the Federal Emergency Management Agency. The coverage of the maps extends from the confluence with the North Branch Hoosic River to the Vermont State line. Peak flows with 20-, 10-, 4-, 2-, 1-, 0.5-, and 0.2-percent annual exceedance probabilities were computed for the reach from updated flood-frequency analyses. These peak flows were routed through a one-dimensional step-backwater hydraulic model to obtain the corresponding peak water-surface elevations, and to place the tropical storm Irene flood of August 28, 2011 into historical context. The hydraulic model was calibrated by using the current (2014) stage-discharge relation at the USGS streamgage Hoosic River near Williamstown, Massachusetts (01332500), and from documented high-water marks from the tropical storm Irene flood, which had approximately a 1-percent annual exceedance probability.

  7. Construction of a dense genetic linkage map and mapping quantitative trait loci for economic traits of a doubled haploid population of Pyropia haitanensis (Bangiales, Rhodophyta).

    Science.gov (United States)

    Xu, Yan; Huang, Long; Ji, Dehua; Chen, Changsheng; Zheng, Hongkun; Xie, Chaotian

    2015-09-21

    Pyropia haitanensis is one of the most economically important mariculture crops in China. A high-density genetic map has not been published yet and quantitative trait locus (QTL) mapping has not been undertaken for P. haitanensis because of a lack of sufficient molecular markers. Specific length amplified fragment sequencing (SLAF-seq) was developed recently for large-scale, high resolution de novo marker discovery and genotyping. In this study, SLAF-seq was used to obtain mass length polymorphic markers to construct a high-density genetic map for P. haitanensis. In total, 120.33 Gb of data containing 75.21 M pair-end reads was obtained after sequencing. The average coverage for each SLAF marker was 75.50-fold in the male parent, 74.02-fold in the female parent, and 6.14-fold average in each double haploid individual. In total, 188,982 SLAFs were detected, of which 6731 were length polymorphic SLAFs that could be used to construct a genetic map. The final map included 4550 length polymorphic markers that were combined into 740 bins on five linkage groups, with a length of 874.33 cM and an average distance of 1.18 cM between adjacent bins. This map was used for QTL mapping to identify chromosomal regions associated with six economically important traits: frond length, width, thickness, fresh weight, growth rates of frond length and growth rates of fresh weight. Fifteen QTLs were identified for these traits. The value of phenotypic variance explained by an individual QTL ranged from 9.59 to 16.61 %, and the confidence interval of each QTL ranged from 0.97 cM to 16.51 cM. The first high-density genetic linkage map for P. haitanensis was constructed, and fifteen QTLs associated with six economically important traits were identified. The results of this study not only provide a platform for gene and QTL fine mapping, map-based gene isolation, and molecular breeding for P. haitanensis, but will also serve as a reference for positioning sequence scaffolds on a physical

  8. Mapping the end points of large deletions affecting the hprt locus in human peripheral blood cells and cell lines

    International Nuclear Information System (INIS)

    Nelson, S.L.; Grosovsky, A.J.; Jones, I.M.; Burkhart-Schultz, K.; Fuscoe, J.C.

    1995-01-01

    We have examined the extent of of HPRT - total gene deletions in three mutant collections: spontaneous and X-ray-induced deletions in TK6 human B lymphoblasts, and HPRT - deletions arising in vivo in T cells. A set of 13 Xq26 STS markers surrounding hprt and spanning approximately 3.3 Mb was used. Each marker used was observed to be missing in at least one of the hprt deletion mutants analyzed. The largest deletion observed encompassed at least 3 Mb. Nine deletions extended outside of the mapped region in the centromeric direction (>1.7 Mb). In contrast, only two telomeric deletions extended to marker 342R (1.26 Mb), and both exhibited slowed or limited cell growth. These data suggest the existence of a gene, within the vicinity of 342R, which establishes the telomeric limit of recoverable deletions. Most (25/41) X-ray-induced total gene deletion mutants exhibited marker loss, but only 1/8 of the spontaneous deletions encompassed any Xq26 markers (P = 0.0187). Furthermore, nearly half (3/8) of the spontaneous 3' total deletion breakpoints were within 14 kb of the hprt coding sequence. In contrast, 40/41 X-ray-induced HPRT - total deletions extended beyond this point (P = 0.011). Although the overall representation of total gene deletions in the in vivo spectrum is low, 4/5 encompass Xq26 markers flanking hprt. This pattern differs significantly from spontaneous HPRT - large deletions occurring in vitro (P = 0.032) but resembles the spectrum of X-ray-induced deletions. 24 refs., 6 figs., 1 tab

  9. Pepsin immobilized in dextran-modified fused-silica capillaries for on-line protein digestion and peptide mapping.

    Science.gov (United States)

    Stigter, E C A; de Jong, G J; van Bennekom, W P

    2008-07-07

    On-line digestion of proteins under acidic conditions was studied using micro-reactors consisting of dextran-modified fused-silica capillaries with covalently immobilized pepsin. The proteins used in this study differed in molecular weight, isoelectric point and sample composition. The injected protein samples were completely digested in 3 min and the digest was analyzed with micro-high performance liquid chromatography (HPLC) and tandem mass spectrometry (MS/MS). The different proteins present in the samples could be identified with a Mascot database search on the basis of auto-MS/MS data. It proved also to be possible to digest and analyze protein mixtures with a sequence coverage of 55% and 97% for the haemoglobin beta- and alpha-chain, respectively, and 35-55% for the various casein variants. Protease auto-digestion, sample carry-over and loss of signal due to adsorption of the injected proteins were not observed. The backpressure of the reactor is low which makes coupling to systems such as Surface Plasmon Resonance biosensors, which do not tolerate too high pressure, possible. The reactor was stable for at least 40 days when used continuously.

  10. Pepsin immobilized in dextran-modified fused-silica capillaries for on-line protein digestion and peptide mapping

    Energy Technology Data Exchange (ETDEWEB)

    Stigter, E.C.A. [Division of Biomedical Analysis, Department of Pharmaceutical Sciences, Faculty of Science, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht (Netherlands)], E-mail: e.c.a.stigter@uu.nl; Jong, G.J. de; Bennekom, W.P. van [Division of Biomedical Analysis, Department of Pharmaceutical Sciences, Faculty of Science, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht (Netherlands)

    2008-07-07

    On-line digestion of proteins under acidic conditions was studied using micro-reactors consisting of dextran-modified fused-silica capillaries with covalently immobilized pepsin. The proteins used in this study differed in molecular weight, isoelectric point and sample composition. The injected protein samples were completely digested in 3 min and the digest was analyzed with micro-high performance liquid chromatography (HPLC) and tandem mass spectrometry (MS/MS). The different proteins present in the samples could be identified with a Mascot database search on the basis of auto-MS/MS data. It proved also to be possible to digest and analyze protein mixtures with a sequence coverage of 55% and 97% for the haemoglobin {beta}- and {alpha}-chain, respectively, and 35-55% for the various casein variants. Protease auto-digestion, sample carry-over and loss of signal due to adsorption of the injected proteins were not observed. The backpressure of the reactor is low which makes coupling to systems such as Surface Plasmon Resonance biosensors, which do not tolerate too high pressure, possible. The reactor was stable for at least 40 days when used continuously.

  11. Fidaxomicin versus Vancomycin as a First-Line Treatment for Clostridium difficile-Associated Diarrhea in Specific Patient Populations: A Pharmacoeconomic Evaluation.

    Science.gov (United States)

    Reveles, Kelly R; Backo, Jennifer L; Corvino, Frank A; Zivkovic, Marko; Broderick, Kelly C

    2017-12-01

    The reduction in recurrent Clostridium difficile-associated diarrhea (CDAD) with fidaxomicin therapy may reduce hospital readmissions and lead to lower overall CDAD costs. However, studies assessing the cost-effectiveness of fidaxomicin as first-line therapy from the U.S. hospital perspective are lacking. This study evaluated the costs associated with utilizing fidaxomicin or vancomycin as a first-line therapy for CDAD in specific patient populations from a U.S. hospital perspective. A decision-analytic model was developed to estimate total costs (hospitalization and drug costs) associated with using fidaxomicin or vancomycin as first-line therapy for a first episode and up to two recurrences of CDAD in five patient populations: general population, elderly, patients receiving concomitant antibiotics, and patients with renal impairment or cancer. The total cost of CDAD treatment using fidaxomicin first line in the general population was $14,442 per patient versus $14,179 per patient with vancomycin first line. In subgroup analyses, fidaxomicin use resulted in total hospital cost savings of $616 per patient in patients with cancer and $312 in patients with concomitant antibiotic use; vancomycin use was associated with total hospital cost savings of $243 per patient in the elderly and $371 in patients with renal impairment. Fidaxomicin as first-line CDAD therapy is associated with similar total costs as compounded vancomycin oral solution in the general population. In elderly and renally impaired patients, slight increases in hospital cost were observed with fidaxomicin therapy, and in patients with cancer or concomitant antibiotic use, hospital cost savings were observed. © 2017 Pharmacotherapy Publications, Inc.

  12. Fine-scale mapping of a locus for severe bipolar mood disorder on chromosome 18p11.3 in the Costa Rican population

    Science.gov (United States)

    McInnes, L. Alison; Service, Susan K.; Reus, Victor I.; Barnes, Glenn; Charlat, Olga; Jawahar, Satya; Lewitzky, Steve; Yang, Qing; Duong, Quyen; Spesny, Mitzi; Araya, Carmen; Araya, Xinia; Gallegos, Alvaro; Meza, Luis; Molina, Julio; Ramirez, Rolando; Mendez, Roxana; Silva, Sandra; Fournier, Eduardo; Batki, Steven L.; Mathews, Carol A.; Neylan, Thomas; Glatt, Charles E.; Escamilla, Michael A.; Luo, David; Gajiwala, Paresh; Song, Terry; Crook, Stephen; Nguyen, Jasmine B.; Roche, Erin; Meyer, Joanne M.; Leon, Pedro; Sandkuijl, Lodewijk A.; Freimer, Nelson B.; Chen, Hong

    2001-01-01

    We have searched for genes predisposing to bipolar disorder (BP) by studying individuals with the most extreme form of the affected phenotype, BP-I, ascertained from the genetically isolated population of the Central Valley of Costa Rica (CVCR). The results of a previous linkage analysis on two extended CVCR BP-I pedigrees, CR001 and CR004, and of linkage disequilibrium (LD) analyses of a CVCR population sample of BP-I patients implicated a candidate region on 18p11.3. We further investigated this region by creating a physical map and developing 4 new microsatellite and 26 single-nucleotide polymorphism markers for typing in the pedigree and population samples. We report the results of fine-scale association analyses in the population sample, as well as evaluation of haplotypes in pedigree CR001. Our results suggest a candidate region containing six genes but also highlight the complexities of LD mapping of common disorders. PMID:11572994

  13. Implementation of lean manufacturing to reduce waste in production line with value stream mapping approach and Kaizen in division sanding upright piano, case study in: PT. X

    Directory of Open Access Journals (Sweden)

    Santosa W. A.

    2018-01-01

    Full Text Available PT. XY produces musical instruments such as Upright Pianos and Grand Pianos. Due to a competitive competition, a good quality product is highly required as well as increasing the production scale. To achieve these objectives, company needs to reduce wastes occurred in its production lines, particularly in the division of sanding panel upright piano (UP which produces type of PE B1 pianos. High cycle time and lead-time are caused by wastes in UP panel sanding division. Therefore, it is needed improvements to be applied here so that the production lines will be run more effectively and efficiently. This study aims to identify wastes using Value Stream Mapping (VSM as a tool of lean manufacturing and to implement the improvements using Kaizen. It is found that the wastes are motion and waiting. Furthermore, the improvements (kaizen are focused on reducing motion and waiting wastes. It is shown that cycle time decreased from 51.16 minutes to 41.90 minutes, work in process or inventory can be reduced to 24 pcs over 32 pcs, and the lead-time is 0.167 days of 0.222 days.

  14. Comparative mapping in intraspecific populations uncovers a high degree of macrosynteny between A- and B-genome diploid species of peanut

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    Guo Yufang

    2012-11-01

    Full Text Available Abstract Background Cultivated peanut or groundnut (Arachis hypogaea L. is an important oilseed crop with an allotetraploid genome (AABB, 2n = 4x = 40. Both the low level of genetic variation within the cultivated gene pool and its polyploid nature limit the utilization of molecular markers to explore genome structure and facilitate genetic improvement. Nevertheless, a wealth of genetic diversity exists in diploid Arachis species (2n = 2x = 20, which represent a valuable gene pool for cultivated peanut improvement. Interspecific populations have been used widely for genetic mapping in diploid species of Arachis. However, an intraspecific mapping strategy was essential to detect chromosomal rearrangements among species that could be obscured by mapping in interspecific populations. To develop intraspecific reference linkage maps and gain insights into karyotypic evolution within the genus, we comparatively mapped the A- and B-genome diploid species using intraspecific F2 populations. Exploring genome organization among diploid peanut species by comparative mapping will enhance our understanding of the cultivated tetraploid peanut genome. Moreover, new sources of molecular markers that are highly transferable between species and developed from expressed genes will be required to construct saturated genetic maps for peanut. Results A total of 2,138 EST-SSR (expressed sequence tag-simple sequence repeat markers were developed by mining a tetraploid peanut EST assembly including 101,132 unigenes (37,916 contigs and 63,216 singletons derived from 70,771 long-read (Sanger and 270,957 short-read (454 sequences. A set of 97 SSR markers were also developed by mining 9,517 genomic survey sequences of Arachis. An SSR-based intraspecific linkage map was constructed using an F2 population derived from a cross between K 9484 (PI 298639 and GKBSPSc 30081 (PI 468327 in the B-genome species A. batizocoi. A high degree of macrosynteny was observed

  15. ActionMap: A web-based software that automates loci assignments to framework maps.

    Science.gov (United States)

    Albini, Guillaume; Falque, Matthieu; Joets, Johann

    2003-07-01

    Genetic linkage computation may be a repetitive and time consuming task, especially when numerous loci are assigned to a framework map. We thus developed ActionMap, a web-based software that automates genetic mapping on a fixed framework map without adding the new markers to the map. Using this tool, hundreds of loci may be automatically assigned to the framework in a single process. ActionMap was initially developed to map numerous ESTs with a small plant mapping population and is limited to inbred lines and backcrosses. ActionMap is highly configurable and consists of Perl and PHP scripts that automate command steps for the MapMaker program. A set of web forms were designed for data import and mapping settings. Results of automatic mapping can be displayed as tables or drawings of maps and may be exported. The user may create personal access-restricted projects to store raw data, settings and mapping results. All data may be edited, updated or deleted. ActionMap may be used either online or downloaded for free (http://moulon.inra.fr/~bioinfo/).

  16. Comparison of gene-based rare variant association mapping methods for quantitative traits in a bovine population with complex familial relationships.

    Science.gov (United States)

    Zhang, Qianqian; Guldbrandtsen, Bernt; Calus, Mario P L; Lund, Mogens Sandø; Sahana, Goutam

    2016-08-17

    There is growing interest in the role of rare variants in the variation of complex traits due to increasing evidence that rare variants are associated with quantitative traits. However, association methods that are commonly used for mapping common variants are not effective to map rare variants. Besides, livestock populations have large half-sib families and the occurrence of rare variants may be confounded with family structure, which makes it difficult to disentangle their effects from family mean effects. We compared the power of methods that are commonly applied in human genetics to map rare variants in cattle using whole-genome sequence data and simulated phenotypes. We also studied the power of mapping rare variants using linear mixed models (LMM), which are the method of choice to account for both family relationships and population structure in cattle. We observed that the power of the LMM approach was low for mapping a rare variant (defined as those that have frequencies lower than 0.01) with a moderate effect (5 to 8 % of phenotypic variance explained by multiple rare variants that vary from 5 to 21 in number) contributing to a QTL with a sample size of 1000. In contrast, across the scenarios studied, statistical methods that are specialized for mapping rare variants increased power regardless of whether multiple rare variants or a single rare variant underlie a QTL. Different methods for combining rare variants in the test single nucleotide polymorphism set resulted in similar power irrespective of the proportion of total genetic variance explained by the QTL. However, when the QTL variance is very small (only 0.1 % of the total genetic variance), these specialized methods for mapping rare variants and LMM generally had no power to map the variants within a gene with sample sizes of 1000 or 5000. We observed that the methods that combine multiple rare variants within a gene into a meta-variant generally had greater power to map rare variants compared

  17. Resistance to gray leaf spot of maize: genetic architecture and mechanisms elucidated through nested association mapping and near-isogenic line analysis.

    Science.gov (United States)

    Benson, Jacqueline M; Poland, Jesse A; Benson, Brent M; Stromberg, Erik L; Nelson, Rebecca J

    2015-03-01

    Gray leaf spot (GLS), caused by Cercospora zeae-maydis and Cercospora zeina, is one of the most important diseases of maize worldwide. The pathogen has a necrotrophic lifestyle and no major genes are known for GLS. Quantitative resistance, although poorly understood, is important for GLS management. We used genetic mapping to refine understanding of the genetic architecture of GLS resistance and to develop hypotheses regarding the mechanisms underlying quantitative disease resistance (QDR) loci. Nested association mapping (NAM) was used to identify 16 quantitative trait loci (QTL) for QDR to GLS, including seven novel QTL, each of which demonstrated allelic series with significant effects above and below the magnitude of the B73 reference allele. Alleles at three QTL, qGLS1.04, qGLS2.09, and qGLS4.05, conferred disease reductions of greater than 10%. Interactions between loci were detected for three pairs of loci, including an interaction between iqGLS4.05 and qGLS7.03. Near-isogenic lines (NILs) were developed to confirm and fine-map three of the 16 QTL, and to develop hypotheses regarding mechanisms of resistance. qGLS1.04 was fine-mapped from an interval of 27.0 Mb to two intervals of 6.5 Mb and 5.2 Mb, consistent with the hypothesis that multiple genes underlie highly significant QTL identified by NAM. qGLS2.09, which was also associated with maturity (days to anthesis) and with resistance to southern leaf blight, was narrowed to a 4-Mb interval. The distance between major leaf veins was strongly associated with resistance to GLS at qGLS4.05. NILs for qGLS1.04 were treated with the C. zeae-maydis toxin cercosporin to test the role of host-specific toxin in QDR. Cercosporin exposure increased expression of a putative flavin-monooxygenase (FMO) gene, a candidate detoxification-related gene underlying qGLS1.04. This integrated approach to confirming QTL and characterizing the potential underlying mechanisms advances the understanding of QDR and will facilitate the

  18. Resistance to gray leaf spot of maize: genetic architecture and mechanisms elucidated through nested association mapping and near-isogenic line analysis.

    Directory of Open Access Journals (Sweden)

    Jacqueline M Benson

    2015-03-01

    Full Text Available Gray leaf spot (GLS, caused by Cercospora zeae-maydis and Cercospora zeina, is one of the most important diseases of maize worldwide. The pathogen has a necrotrophic lifestyle and no major genes are known for GLS. Quantitative resistance, although poorly understood, is important for GLS management. We used genetic mapping to refine understanding of the genetic architecture of GLS resistance and to develop hypotheses regarding the mechanisms underlying quantitative disease resistance (QDR loci. Nested association mapping (NAM was used to identify 16 quantitative trait loci (QTL for QDR to GLS, including seven novel QTL, each of which demonstrated allelic series with significant effects above and below the magnitude of the B73 reference allele. Alleles at three QTL, qGLS1.04, qGLS2.09, and qGLS4.05, conferred disease reductions of greater than 10%. Interactions between loci were detected for three pairs of loci, including an interaction between iqGLS4.05 and qGLS7.03. Near-isogenic lines (NILs were developed to confirm and fine-map three of the 16 QTL, and to develop hypotheses regarding mechanisms of resistance. qGLS1.04 was fine-mapped from an interval of 27.0 Mb to two intervals of 6.5 Mb and 5.2 Mb, consistent with the hypothesis that multiple genes underlie highly significant QTL identified by NAM. qGLS2.09, which was also associated with maturity (days to anthesis and with resistance to southern leaf blight, was narrowed to a 4-Mb interval. The distance between major leaf veins was strongly associated with resistance to GLS at qGLS4.05. NILs for qGLS1.04 were treated with the C. zeae-maydis toxin cercosporin to test the role of host-specific toxin in QDR. Cercosporin exposure increased expression of a putative flavin-monooxygenase (FMO gene, a candidate detoxification-related gene underlying qGLS1.04. This integrated approach to confirming QTL and characterizing the potential underlying mechanisms advances the understanding of QDR and will

  19. Accentuated lines in the enamel of primary incisors from skeletal remains: A contribution to the explanation of early childhood mortality in a medieval population from Poland.

    Science.gov (United States)

    Żądzińska, Elżbieta; Lorkiewicz, Wiesław; Kurek, Marta; Borowska-Strugińska, Beata

    2015-07-01

    Physiological disruptions resulting from an impoverished environment during the first years of life are of key importance for the health and biological status of individuals and populations. Studies of growth processes in archaeological populations point to the fact that the main causes of childhood mortality in the past are to be sought among extrinsic factors. Based on this assumption, one would expect random mortality of children, with the deceased individuals representing the entire subadult population. The purpose of this study is to explore whether differences in early childhood survival are reflected in differences in deciduous tooth enamel, which can provide an insight into the development of an individual during prenatal and perinatal ontogeny. Deciduous incisors were taken from 83 individuals aged 2.0-6.5 years from a medieval inhumation cemetery dated AD 1300-1600. Prenatal and postnatal enamel formation time, neonatal line width, and the number of accentuated lines were measured using an optical microscope. The significantly wider neonatal line and the higher frequency of accentuated lines in the enamel of the incisors of children who died at the age of 2-3 years suggest the occurrence of stronger or more frequent stress events in this group. These results indicate that in skeletal populations mortality was not exclusively determined by random external factors. Individuals predisposed by an unfavorable course of prenatal and perinatal growth were more likely to die in early childhood. © 2015 Wiley Periodicals, Inc.

  20. Mapping the Centimeter-Scale Spatial Variability of PAHs and Microbial Populations in the Rhizosphere of Two Plants.

    Directory of Open Access Journals (Sweden)

    Amélia Bourceret

    Full Text Available Rhizoremediation uses root development and exudation to favor microbial activity. Thus it can enhance polycyclic aromatic hydrocarbon (PAH biodegradation in contaminated soils. Spatial heterogeneity of rhizosphere processes, mainly linked to the root development stage and to the plant species, could explain the contrasted rhizoremediation efficiency levels reported in the literature. Aim of the present study was to test if spatial variability in the whole plant rhizosphere, explored at the centimetre-scale, would influence the abundance of microorganisms (bacteria and fungi, and the abundance and activity of PAH-degrading bacteria, leading to spatial variability in PAH concentrations. Two contrasted rhizospheres were compared after 37 days of alfalfa or ryegrass growth in independent rhizotron devices. Almost all spiked PAHs were degraded, and the density of the PAH-degrading bacterial populations increased in both rhizospheres during the incubation period. Mapping of multiparametric data through geostatistical estimation (kriging revealed that although root biomass was spatially structured, PAH distribution was not. However a greater variability of the PAH content was observed in the rhizosphere of alfalfa. Yet, in the ryegrass-planted rhizotron, the Gram-positive PAH-degraders followed a reverse depth gradient to root biomass, but were positively correlated to the soil pH and carbohydrate concentrations. The two rhizospheres structured the microbial community differently: a fungus-to-bacterium depth gradient similar to the root biomass gradient only formed in the alfalfa rhizotron.

  1. Comparison of T1rho and T2 mapping of knee articular cartilage in an asymptomatic population

    Energy Technology Data Exchange (ETDEWEB)

    Yoon, Min A; Hong, Suk Joo; Im, A Lan [Dept. of Radiology, Korea University Guro Hospital, Korea University College of Medicine, Seoul (Korea, Republic of); Kang, Chang Ho [Dept. of Radiology, Korea University Anam Hospital, Korea University College of Medicine, Seoul (Korea, Republic of); Kim, Baek Hyun [Dept. of Radiology, Korea University Ansan Hospital, Korea University College of Medicine, Ansan (Korea, Republic of); Kim, In Seong [Siemens Healthcare, Seoul (Korea, Republic of)

    2016-11-15

    To analyze subregional differences in T1rho (T1ρ) and T2 values and their correlation in asymptomatic knee cartilage, and to evaluate angular dependence with magic angles. Six asymptomatic volunteers underwent knee MRI with T1ρ and T2 mapping. T1ρ and T2 values were measured by two radiologists independently, at nine subregions in the medial femoral condyle (MFC) cartilage, at angles of ± 0°, 15°, 35°, 55°, 75° respective to a vertical line (B0) bisecting the width of the distal femur, and at two locations in the patella. Subregional values of T1ρ and T2 were analyzed and significant differences in three divided portions of the MFC (anterior, central, and posterior) were statistically evaluated. Correlation between T1ρ and T2 and angular dependence with magic angles were also assessed for statistical significance. T1ρ values were lowest at +15° and highest at -55°. T2 values were lowest at +75° and highest at +35°. Both T1ρ and T2 were higher in superior patella than inferior patella. T1ρ showed significant differences in the three divided portions of the MFC, while T2 showed significant differences only between central and posterior portions. There was a weak correlation between T1ρ and T2 (r = 0.217, p = 0.127). T1ρ showed more angular dependence than T2. T1ρ and T2 showed different subregional values and angular dependence in asymptomatic knee cartilage with a weak correlation. Awareness of these differences will aid in assessment of cartilage in a specific subregion of the knee.

  2. Mapping the factors affecting the frequency and types of micronuclei in an elderly population from Southern Bohemia

    Energy Technology Data Exchange (ETDEWEB)

    Rossnerova, Andrea, E-mail: andrearo@biomed.cas.cz [Department of Genetic Toxicology and Nanotoxicology, Institute of Experimental Medicine, Czech Academy of Sciences, 14220 Prague 4 (Czech Republic); Honkova, Katerina; Pavlikova, Jitka [Department of Genetic Toxicology and Nanotoxicology, Institute of Experimental Medicine, Czech Academy of Sciences, 14220 Prague 4 (Czech Republic); Skalicka, Zuzana Freitinger; Havrankova, Renata [Institute of Radiology, Toxicology and Civil Protection, University of South Bohemia, 37005 Ceske Budejovice (Czech Republic); Solansky, Ivo; Rossner, Pavel; Sram, Radim J. [Department of Genetic Toxicology and Nanotoxicology, Institute of Experimental Medicine, Czech Academy of Sciences, 14220 Prague 4 (Czech Republic); Zölzer, Friedo [Institute of Radiology, Toxicology and Civil Protection, University of South Bohemia, 37005 Ceske Budejovice (Czech Republic)

    2016-11-15

    Highlights: • Factors affecting the frequency and types of micronuclei were mapped. • The effect of former uranium exposure and later X-ray examination was studied. • An increase of CEN+ MN (chromosome losses) in the fall season was observed. • Lower DNA damage after X-ray examination was found in cases of previous exposure. - Abstract: The micronucleus assay is one of the most common methods used to assess chromosomal damage (losses or breaks) in human peripheral blood lymphocytes (PBL) in genetic toxicology. Most studies have focused on analyzing total micronuclei (MN), but identifying the content of MN can provide more detailed information. The main aim of this study was to map the factors affecting the frequency and types of micronuclei in binucleated cells (BNC) in elderly population. Fluorescence in situ hybridization using Human Pan Centromeric Chromosome Paint was used to identify centromere positive (CEN+) or centromere negative (CEN-) MN. A group of 95 men from Southern Bohemia, Czech Republic (average age 68.0 ± 6.8 years) was followed repeatedly, in spring and fall 2014. The study participants were former workers of the uranium plant “MAPE Mydlovary” (processing uranium ore from 1962 to 1991), and controls. The general profile of individual types of MN, and the effect of the season, former uranium exposure, age, smoking status, weight, and X-ray examination on the level and type of MN were analyzed. The results of this study showed: (i) a stable profile of BNC with MN based on the number of MN during two seasons; (ii) an increase of the number of CEN+ MN from spring to fall; (iii) a lower frequency of the total MN in the exposed group than in controls with a significant difference in the percentage of aberrant cells (%AB.C.) in the fall; (iv) no clear effect of age, smoking and BMI on DNA damage in this group; (v) lower DNA damage levels in former uranium workers who received X-ray examination later in life. In summary, the results indicate

  3. Identification of a unique hepatocellular carcinoma line, Li-7, with CD13(+) cancer stem cells hierarchy and population change upon its differentiation during culture and effects of sorafenib.

    Science.gov (United States)

    Yamada, Takeshi; Abei, Masato; Danjoh, Inaho; Shirota, Ryoko; Yamashita, Taro; Hyodo, Ichinosuke; Nakamura, Yukio

    2015-04-11

    Cancer stem cell (CSC) research has highlighted the necessity of developing drugs targeting CSCs. We investigated a hepatocellular carcinoma (HCC) cell line that not only has CSC hierarchy but also shows phenotypic changes (population changes) upon differentiation of CSC during culture and can be used for screening drugs targeting CSC. Based on a hypothesis that the CSC proportion should decrease upon its differentiation into progenitors (population change), we tested HCC cell lines (HuH-7, Li-7, PLC/PRF/5, HLF, HLE) before and after 2 months culture for several markers (CD13, EpCAM, CD133, CD44, CD90, CD24, CD166). Tumorigenicity was tested using nude mice. To evaluate the CSC hierarchy, we investigated reconstructivity, proliferation, ALDH activity, spheroid formation, chemosensitivity and microarray analysis of the cell populations sorted by FACS. Only Li-7 cells showed a population change during culture: the proportion of CD13 positive cells decreased, while that of CD166 positive cells increased. The high tumorigenicity of the Li-7 was lost after the population change. CD13(+)/CD166(-) cells showed slow growth and reconstructed the bulk Li-7 populations composed of CD13(+)/CD166(-), CD13(-)/CD166(-) and CD13(-)/CD166(+) fractions, whereas CD13(-)/CD166(+) cells showed rapid growth but could not reproduce any other population. CD13(+)/CD166(-) cells showed high ALDH activity, spheroid forming ability and resistance to 5-fluorouracil. Microarray analysis demonstrated higher expression of stemness-related genes in CD166(-) than CD166(+) fraction. These results indicated a hierarchy in Li-7 cells, in which CD13(+)/CD166(-) and CD13(-)/CD166(+) cells serve as slow growing CSCs and rapid growing progenitors, respectively. Sorafenib selectively targeted the CD166(-) fraction, including CD13(+) CSCs, which exhibited higher mRNA expression for FGF3 and FGF4, candidate biomarkers for sorafenib. 5-fluorouracil followed by sorafenib inhibited the growth of bulk Li-7

  4. Genomic analysis of CD8+ NK/T cell line, ‘SRIK-NKL’, with array-based CGH (aCGH), SKY/FISH and molecular mapping

    Science.gov (United States)

    Rossi, Michael; LaDuca, Jeff; Cowell, John; Srivastava, Bejai I.S.; Matsui, Sei-ichi

    2010-01-01

    We performed aCGH, SKY /FISH, molecular mapping and expression analyses on a permanent CD8+ NK/T cell line, ‘SRIK-NKL’ established from a lymphoma (ALL) patient, in attempt to define the fundamental genetic profile of its unique NK phenotypes. aCGH revealed hemizygous deletion of 6p containing genes responsible for hematopoietic functions. The SKY demonstrated that a constitutive reciprocal translocation, rcpt(5;14)(p13.2;q11) is a stable marker. Using somatic hybrids containing der(5) derived from SRIK-NKL, we found that the breakpoint in one homologue of no. 5 is located upstream of IL7R and also that the breakpoint in no. 14 is located within TRA@. The FISH analysis using BAC which contains TRA@ and its flanking region further revealed a ~231 kb deletion within 14q11 in the der(5) but not in the normal homologue of no. 14. The RT-PCR analysis detected mRNA for TRA@ transcripts which were extending across, but not including, the deleted region. IL7R was detected at least at mRNA levels. These findings were consistent with the immunological findings that TRA@ and IL7R are both expressed at mRNA levels and TRA@ at cytoplasmic protein levels in SRIK-NKL cells. In addition to rept(5;14), aCGH identified novel copy number abnormalities suggesting that the unique phenotype of the SRIK-NKL cell line is not solely due to the TRA@ rearrangement. These findings provide supportive evidence for the notion that SRIK-NKL cells may be useful for studying not only the function of NK cells but also genetic deregulations associated with leukemiogenesis. PMID:17640729

  5. Properties of Dense Cores Embedded in Musca Derived from Extinction Maps and {sup 13}CO, C{sup 18}O, and NH{sub 3} Emission Lines

    Energy Technology Data Exchange (ETDEWEB)

    Machaieie, Dinelsa A.; Vilas-Boas, José W.; Wuensche, Carlos A. [Instituto Nacional de Pesquisas Espaciais, Av. dos Astronautas 1.758—Jardim da Granja, CEP-12227-010, São José dos Campos, SP (Brazil); Racca, Germán A. [Universidade do Estado do Rio Grande do Norte, Faculdade de Ciências Exatas e Naturais/Depto. de Física, Campus Universitário Central, Setor II BR 110, KM 48, Rua Prof. António Campos, Costa e Silva 59610-090—Mossoró-RN (Brazil); Myers, Philip C. [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States); Hickel, Gabriel R., E-mail: dinelsa.machaieie@inpe.br [Universidade Federal de Itajubá, Departamento de Física, Av. BPS, 1303, Pinheirinho, Itajubá, MG (Brazil)

    2017-02-10

    Using near-infrared data from the Two Micron All Sky Survey catalog and the Near Infrared Color Excess method, we studied the extinction distribution in five dense cores of Musca, which show visual extinction greater than 10 mag and are potential sites of star formation. We analyzed the stability in four of them, fitting their radial extinction profiles with Bonnor–Ebert isothermal spheres, and explored their properties using the J = 1–0 transition of {sup 13}CO and C{sup 18}O and the J = K = 1 transition of NH{sub 3}. One core is not well described by the model. The stability parameter of the fitted cores ranges from 4.5 to 5.7 and suggests that all cores are stable, including Mu13, which harbors one young stellar object (YSO), the IRAS 12322-7023 source. However, the analysis of the physical parameters shows that Mu13 tends to have larger A {sub V}, n {sub c}, and P {sub ext} than the remaining starless cores. The other physical parameters do not show any trend. It is possible that those are the main parameters to explore in active star-forming cores. Mu13 also shows the most intense emission of NH{sub 3}. Its {sup 13}CO and C{sup 18}O lines have double peaks, whose integrated intensity maps suggest that they are due to the superposition of clouds with different radial velocities seen in the line of sight. It is not possible to state whether these clouds are colliding and inducing star formation or are related to a physical process associated with the formation of the YSO.

  6. Assessment of the effects and limitations of the 1998 to 2008 Abbreviated Injury Scale map using a large population-based dataset

    Directory of Open Access Journals (Sweden)

    Franklyn Melanie

    2011-01-01

    Full Text Available Abstract Background Trauma systems should consistently monitor a given trauma population over a period of time. The Abbreviated Injury Scale (AIS and derived scores such as the Injury Severity Score (ISS are commonly used to quantify injury severities in trauma registries. To reflect contemporary trauma management and treatment, the most recent version of the AIS (AIS08 contains many codes which differ in severity from their equivalents in the earlier 1998 version (AIS98. Consequently, the adoption of AIS08 may impede comparisons between data coded using different AIS versions. It may also affect the number of patients classified as major trauma. Methods The entire AIS98-coded injury dataset of a large population based trauma registry was retrieved and mapped to AIS08 using the currently available AIS98-AIS08 dictionary map. The percentage of codes which had increased or decreased in severity, or could not be mapped, was examined in conjunction with the effect of these changes to the calculated ISS. The potential for free text information accompanying AIS coding to improve the quality of AIS mapping was explored. Results A total of 128280 AIS98-coded injuries were evaluated in 32134 patients, 15471 patients of whom were classified as major trauma. Although only 4.5% of dictionary codes decreased in severity from AIS98 to AIS08, this represented almost 13% of injuries in the registry. In 4.9% of patients, no injuries could be mapped. ISS was potentially unreliable in one-third of patients, as they had at least one AIS98 code which could not be mapped. Using AIS08, the number of patients classified as major trauma decreased by between 17.3% and 30.3%. Evaluation of free text descriptions for some injuries demonstrated the potential to improve mapping between AIS versions. Conclusions Converting AIS98-coded data to AIS08 results in a significant decrease in the number of patients classified as major trauma. Many AIS98 codes are missing from the

  7. Visual cortex in aging and Alzheimer’s disease: Changes in visual field maps and population receptive fields

    Directory of Open Access Journals (Sweden)

    Alyssa A. Brewer

    2014-02-01

    Full Text Available Although several studies have suggested that cortical alterations underlie such age-related visual deficits as decreased acuity, little is known about what changes actually occur in visual cortex during healthy aging. Two recent studies showed changes in primary visual cortex (V1 during normal aging; however, no studies have characterized the effects of aging on visual cortex beyond V1, important measurements both for understanding the aging process and for comparison to changes in age-related diseases. Similarly, there is almost no information about changes in visual cortex in Alzheimer’s disease (AD, the most common form of dementia. Because visual deficits are often reported as one of the first symptoms of AD, measurements of such changes in the visual cortex of AD patients might improve our understanding of how the visual system is affected by neurodegeneration as well as aid early detection, accurate diagnosis and timely treatment of AD. Here we use fMRI to first compare the visual field map (VFM organization and population receptive fields (pRFs between young adults and healthy aging subjects for occipital VFMs V1, V2, V3, and hV4. Healthy aging subjects do not show major VFM organizational deficits, but do have reduced surface area and increased pRF sizes in the foveal representations of V1, V2, and hV4 relative to healthy young control subjects. These measurements are consistent with behavioral deficits seen in healthy aging. We then demonstrate the feasibility and first characterization of these measurements in two patients with mild AD, which reveal potential changes in visual cortex as part of the pathophysiology of AD. Our data aid in our understanding of the changes in the visual processing pathways in normal aging and provide the foundation for future research into earlier and more definitive detection of AD.

  8. Association Mapping of Ferrous, Zinc, and Aluminum Tolerance at the Seedling Stage in Indica Rice using MAGIC Populations

    Directory of Open Access Journals (Sweden)

    Lijun Meng

    2017-10-01

    Full Text Available Excessive amounts of metal are toxic and severely affect plant growth and development. Understanding the genetic control of metal tolerance is crucial to improve rice resistance to Fe, Zn, and Al toxicity. The multi-parent advanced generation inter-cross (MAGIC populations were genotyped using a 55 K rice SNP array and screened at the seedling stage for Fe, Zn, and Al toxicity using a hydroponics system. Association analysis was conducted by implementing a mixed linear model (MLM for each of the five MAGIC populations double cross DC1 (founders were SAGC-08, HHZ5-SAL9-Y3-Y1, BP1976B-2-3-7-TB-1-1, PR33282-B-8-1-1-1-1-1, double cross DC2 (founders of double cross were FFZ1, CT 16658-5-2-2SR-2-3-6MP, IR 68, IR 02A127, eight parents population 8way (founders were SAGC-08, HHZ5-SAL9-Y3-Y1, BP1976B-2-3-7-TB-1-1, PR33282-B-8-1-1-1-1-1, FFZ1, CT 16658-5-2-2SR-2-3-6MP, IR 68, IR 02A127, DC12 (DC1+DC2 and rice multi-parent recombinant inbred line population RMPRIL (DC1+DC2+8way. A total of 21, 30, and 21 QTL were identified for Fe, Zn, and Al toxicity tolerance, respectively. For multi tolerance (MT as Fe, Zn, and Al tolerance-related traits, three genomic regions, MT1.1 (chr.1: 35.4–36.3 Mb, MT1.2 (chr.1: 35.4–36.3 Mb, and MT3.2 (chr.3: 35.4-36.2 Mb harbored QTL. The chromosomal regions MT2.1 (chr.2: 2.4–2.8 Mb, MT2.2 (chr.2: 24.5–25.8 Mb, MT4 (chr.4: 1.2 Mb Mb, MT8.1 (chr.8: 0.7–0.9 Mb, and MT8.2 (chr.8: 2.2–2.4 Mb harbored QTL for Fe and Zn tolerance, while MT2.3 (chr.2: 30.5–31.6 Mb, MT3.1 (chr.3: 12.5–12.8 Mb, and MT6 (chr.6: 2.0–3.0 Mb possessed QTL for Al and Zn tolerance. The chromosomal region MT9.1 (chr.9: 14.2–14.7 Mb possessed QTL for Fe and Al tolerance. A total of 11 QTL were detected across different MAGIC populations and 12 clustered regions were detected under different metal conditions, suggesting that these genomic regions might constitute valuable regions for further marker-assisted selection (MAS in breeding

  9. Some AFLP amplicons are highly conserved DNA sequences mapping to the same linkage groups in two F2 populations of carrot

    Directory of Open Access Journals (Sweden)

    Santos Carlos A.F.

    2002-01-01

    Full Text Available Amplified fragment length polymorphism (AFLP is a fast and reliable tool to generate a large number of DNA markers. In two unrelated F2 populations of carrot (Daucus carota L., Brasilia x HCM and B493 x QAL (wild carrot, it was hypothesized that DNA 1 digested with the same restriction endonuclease enzymes and amplified with the same primer combination and 2 sharing the same position in polyacrylamide gels should be conserved sequences. To test this hypothesis AFLP fragments from polyacrylamide gels were eluted, reamplified, separated in agarose gels, purified, cloned and sequenced. Among thirty-one paired fragments from each F2 population, twenty-six had identity greater than 91% and five presented identity of 24% to 44%. Among the twenty-six conserved AFLPs only one mapped to different linkage groups in the two populations while four of the five less-conserved bands mapped to different linkage groups. Of eight SCAR (sequence characterized amplified regions primers tested, one conserved AFLP resulted in co-dominant markers in both populations. Screening among 14 carrot inbreds or cultivars with three AFLP-SCAR primers revealed clear and polymorphic PCR products, with similar molecular sizes on agarose gels. The development of co-dominant markers based on conserved AFLP fragments will be useful to detect seed mixtures among hybrids, to improve and to merge linkage maps and to study diversity and phylogenetic relationships.

  10. Mapping of PARK2 and PACRG overlapping regulatory region reveals LD structure and functional variants in association with leprosy in unrelated indian population groups.

    Science.gov (United States)

    Chopra, Rupali; Ali, Shafat; Srivastava, Amit K; Aggarwal, Shweta; Kumar, Bhupender; Manvati, Siddharth; Kalaiarasan, Ponnusamy; Jena, Mamta; Garg, Vijay K; Bhattacharya, Sambit N; Bamezai, Rameshwar N K

    2013-01-01

    Leprosy is a chronic infectious disease caused by Mycobacterium Leprae, where the host genetic background plays an important role toward the disease pathogenesis. Various studies have identified a number of human genes in association with leprosy or its clinical forms. However, non-replication of results has hinted at the heterogeneity among associations between different population groups, which could be due to differently evolved LD structures and differential frequencies of SNPs within the studied regions of the genome. A need for systematic and saturated mapping of the associated regions with the disease is warranted to unravel the observed heterogeneity in different populations. Mapping of the PARK2 and PACRG gene regulatory region with 96 SNPs, with a resolution of 1 SNP per 1 Kb for PARK2 gene regulatory region in a North Indian population, showed an involvement of 11 SNPs in determining the susceptibility towards leprosy. The association was replicated in a geographically distinct and unrelated population from Orissa in eastern India. In vitro reporter assays revealed that the two significantly associated SNPs, located 63.8 kb upstream of PARK2 gene and represented in a single BIN of 8 SNPs, influenced the gene expression. A comparison of BINs between Indian and Vietnamese populations revealed differences in the BIN structures, explaining the heterogeneity and also the reason for non-replication of the associated genomic region in different populations.

  11. Identification of candidate genes involved in Witches' broom disease resistance in a segregating mapping population of Theobroma cacao L. in Brazil.

    Science.gov (United States)

    Royaert, Stefan; Jansen, Johannes; da Silva, Daniela Viana; de Jesus Branco, Samuel Martins; Livingstone, Donald S; Mustiga, Guiliana; Marelli, Jean-Philippe; Araújo, Ioná Santos; Corrêa, Ronan Xavier; Motamayor, Juan Carlos

    2016-02-11

    Witches' broom disease (WBD) caused by the fungus Moniliophthora perniciosa is responsible for considerable economic losses for cacao producers. One of the ways to combat WBD is to plant resistant cultivars. Resistance may be governed by a few genetic factors, mainly found in wild germplasm. We developed a dense genetic linkage map with a length of 852.8 cM that contains 3,526 SNPs and is based on the MP01 mapping population, which counts 459 trees from a cross between the resistant 'TSH 1188' and the tolerant 'CCN 51' at the Mars Center for Cocoa Science in Barro Preto, Bahia, Brazil. Seven quantitative trait loci (QTL) that are associated with WBD were identified on five different chromosomes using a multi-trait QTL analysis for outbreeders. Phasing of the haplotypes at the major QTL region on chromosome IX on a diversity panel of genotypes clearly indicates that the major resistance locus comes from a well-known source of WBD resistance, the clone 'SCAVINA 6'. Various potential candidate genes identified within all QTL may be involved in different steps leading to disease resistance. Preliminary expression data indicate that at least three of these candidate genes may play a role during the first 12 h after infection, with clear differences between 'CCN 51' and 'TSH 1188'. We combined the information from a large mapping population with very distinct parents that segregate for WBD, a dense set of mapped markers, rigorous phenotyping capabilities and the availability of a sequenced genome to identify several genomic regions that are involved in WBD resistance. We also identified a novel source of resistance that most likely comes from the 'CCN 51' parent. Thanks to the large population size of the MP01 population, we were able to pick up QTL and markers with relatively small effects that can contribute to the creation and selection of more tolerant/resistant plant material.

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

    Science.gov (United States)

    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.

  13. Discrimination of candidate subgenome-specific loci by linkage map construction with an S1 population of octoploid strawberry (Fragaria × ananassa).

    Science.gov (United States)

    Nagano, Soichiro; Shirasawa, Kenta; Hirakawa, Hideki; Maeda, Fumi; Ishikawa, Masami; Isobe, Sachiko N

    2017-05-12

    The strawberry, Fragaria × ananassa, is an allo-octoploid (2n = 8x = 56) and outcrossing species. Although it is the most widely consumed berry crop in the world, its complex genome structure has hindered its genetic and genomic analysis, and thus discrimination of subgenome-specific loci among the homoeologous chromosomes is needed. In the present study, we identified candidate subgenome-specific single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) loci, and constructed a linkage map using an S 1 mapping population of the cultivar 'Reikou' with an IStraw90 Axiom® SNP array and previously published SSR markers. The 'Reikou' linkage map consisted of 11,574 loci (11,002 SNPs and 572 SSR loci) spanning 2816.5 cM of 31 linkage groups. The 11,574 loci were located on 4738 unique positions (bin) on the linkage map. Of the mapped loci, 8999 (8588 SNPs and 411 SSR loci) showed a 1:2:1 segregation ratio of AA:AB:BB allele, which suggested the possibility of deriving loci from candidate subgenome-specific sequences. In addition, 2575 loci (2414 SNPs and 161 SSR loci) showed a 3:1 segregation of AB:BB allele, indicating they were derived from homoeologous genomic sequences. Comparative analysis of the homoeologous linkage groups revealed differences in genome structure among the subgenomes. Our results suggest that candidate subgenome-specific loci are randomly located across the genomes, and that there are small- to large-scale structural variations among the subgenomes. The mapped SNPs and SSR loci on the linkage map are expected to be seed points for the construction of pseudomolecules in the octoploid strawberry.

  14. Geostatistical analysis of disease data: accounting for spatial support and population density in the isopleth mapping of cancer mortality risk using area-to-point Poisson kriging

    Directory of Open Access Journals (Sweden)

    Goovaerts Pierre

    2006-11-01

    Full Text Available Abstract Background Geostatistical techniques that account for spatially varying population sizes and spatial patterns in the filtering of choropleth maps of cancer mortality were recently developed. Their implementation was facilitated by the initial assumption that all geographical units are the same size and shape, which allowed the use of geographic centroids in semivariogram estimation and kriging. Another implicit assumption was that the population at risk is uniformly distributed within each unit. This paper presents a generalization of Poisson kriging whereby the size and shape of administrative units, as well as the population density, is incorporated into the filtering of noisy mortality rates and the creation of isopleth risk maps. An innovative procedure to infer the point-support semivariogram of the risk from aggregated rates (i.e. areal data is also proposed. Results The novel methodology is applied to age-adjusted lung and cervix cancer mortality rates recorded for white females in two contrasted county geographies: 1 state of Indiana that consists of 92 counties of fairly similar size and shape, and 2 four states in the Western US (Arizona, California, Nevada and Utah forming a set of 118 counties that are vastly different geographical units. Area-to-point (ATP Poisson kriging produces risk surfaces that are less smooth than the maps created by a naïve point kriging of empirical Bayesian smoothed rates. The coherence constraint of ATP kriging also ensures that the population-weighted average of risk estimates within each geographical unit equals the areal data for this unit. Simulation studies showed that the new approach yields more accurate predictions and confidence intervals than point kriging of areal data where all counties are simply collapsed into their respective polygon centroids. Its benefit over point kriging increases as the county geography becomes more heterogeneous. Conclusion A major limitation of choropleth

  15. Geostatistical analysis of disease data: accounting for spatial support and population density in the isopleth mapping of cancer mortality risk using area-to-point Poisson kriging

    Science.gov (United States)

    Goovaerts, Pierre

    2006-01-01

    Background Geostatistical techniques that account for spatially varying population sizes and spatial patterns in the filtering of choropleth maps of cancer mortality were recently developed. Their implementation was facilitated by the initial assumption that all geographical units are the same size and shape, which allowed the use of geographic centroids in semivariogram estimation and kriging. Another implicit assumption was that the population at risk is uniformly distributed within each unit. This paper presents a generalization of Poisson kriging whereby the size and shape of administrative units, as well as the population density, is incorporated into the filtering of noisy mortality rates and the creation of isopleth risk maps. An innovative procedure to infer the point-support semivariogram of the risk from aggregated rates (i.e. areal data) is also proposed. Results The novel methodology is applied to age-adjusted lung and cervix cancer mortality rates recorded for white females in two contrasted county geographies: 1) state of Indiana that consists of 92 counties of fairly similar size and shape, and 2) four states in the Western US (Arizona, California, Nevada and Utah) forming a set of 118 counties that are vastly different geographical units. Area-to-point (ATP) Poisson kriging produces risk surfaces that are less smooth than the maps created by a naïve point kriging of empirical Bayesian smoothed rates. The coherence constraint of ATP kriging also ensures that the population-weighted average of risk estimates within each geographical unit equals the areal data for this unit. Simulation studies showed that the new approach yields more accurate predictions and confidence intervals than point kriging of areal data where all counties are simply collapsed into their respective polygon centroids. Its benefit over point kriging increases as the county geography becomes more heterogeneous. Conclusion A major limitation of choropleth maps is the common biased

  16. Quantitative trait loci mapping of calving and conformation traits on Bos taurus autosome 18 in the German Holstein population.

    Science.gov (United States)

    Brand, B; Baes, C; Mayer, M; Reinsch, N; Seidenspinner, T; Thaller, G; Kühn, Ch

    2010-03-01

    Linkage, linkage disequilibrium, and combined linkage and linkage disequilibrium analyses were performed to map quantitative trait loci (QTL) affecting calving and conformation traits on Bos taurus autosome 18 (BTA18) in the German Holstein population. Six paternal half-sib families consisting of a total of 1,054 animals were genotyped on 28 genetic markers in the telomeric region on BTA18 spanning approximately 30 Mb. Calving traits, body type traits, and udder type traits were investigated. Using univariately estimated breeding values, maternal and direct effects on calving ease and stillbirth were analyzed separately for first- and further-parity calvings. The QTL initially identified by separate linkage and linkage disequilibrium analyses could be confirmed by a combined linkage and linkage disequilibrium analysis for udder composite index, udder depth, fore udder attachment, front teat placement, body depth, rump angle, and direct effects on calving ease and stillbirth. Concurrence of QTL peaks and a similar shape of restricted log-likelihood ratio profiles were observed between udder type traits and for body depth and calving traits, respectively. Association analyses were performed for markers flanking the most likely QTL positions by applying a mixed model including a fixed allele effect of the maternally inherited allele and a random polygenic effect. Results indicated that microsatellite marker DIK4234 (located at 53.3 Mb) is associated with maternal effects on stillbirth, direct effects on calving ease, and body depth. A comparison of effects for maternally inherited DIK4234 alleles indicated a favorable, positive correlation of maternal and direct effects on calving. Additionally, the association of maternally inherited DIK4234 marker alleles with body depth implied that conformation traits might provide the functional background of the QTL for calving traits. For udder type traits, the strong coincidence of QTL peaks and the position of the QTL in a

  17. Linkage Maps of a Mediterranean × Continental Tall Fescue Population and their Comparative Analysis with Other Poaceae Species

    Directory of Open Access Journals (Sweden)

    Ryan Dierking

    2015-03-01

    Full Text Available Temperate grasses belonging to the complex are important throughout the world in pasture and grassland agriculture. Tall fescue ( Schreb. is the predominant species in the United States, covering approximately 15 million ha. Tall fescue has distinctive morphotypes, two of which are Continental (summer active and Mediterranean (summer semidormant. This is the first report of a linkage map created for Mediterranean tall fescue, while updating the Continental map with additional simple sequence repeat and sequence-tagged site markers. Additionally, this is the first time that diversity arrays technology (DArT markers were used in the construction of a tall fescue map. The male parent (Continental, R43-64, map consisted of 594 markers arranged in 22 linkage groups (LGs and covered a total of 1577 cM. The female parent (Mediterranean, 103-2, map was shorter (1258 cM and consisted of only 208 markers arranged in 29 LGs. Marker densities for R43-64 and 103-2 were 2.65 and 6.08 cM per marker, respectively. When compared with the other Poaceae species, meadow fescue ( Huds., annual ryegrass ( Lam., perennial ryegrass ( L., (L. Beauv., and barley ( L., a total of 171 and 98 orthologous or homologous sequences, identified by DArT analysis, were identified in R43-64 and 103-2, respectively. By using genomic in situ hybridization, we aimed to identify potential progenitors of both morphotypes. However, no clear conclusion on genomic constitution was reached. These maps will aid in the search for quantitative trait loci of various traits as well as help define and distinguish genetic differences between the two morphotypes.

  18. NKX6.1 induced pluripotent stem cell reporter lines for isolation and analysis of functionally relevant neuronal and pancreas populations

    Directory of Open Access Journals (Sweden)

    Shailesh Kumar Gupta

    2018-05-01

    Full Text Available Recent studies have reported significant advances in the differentiation of human pluripotent stem cells to clinically relevant cell types such as the insulin producing beta-like cells and motor neurons. However, many of the current differentiation protocols lead to heterogeneous cell cultures containing cell types other than the targeted cell fate. Genetically modified human pluripotent stem cells reporting the expression of specific genes are of great value for differentiation protocol optimization and for the purification of relevant cell populations from heterogeneous cell cultures. Here we present the generation of human induced pluripotent stem cell (iPSC lines with a GFP reporter inserted in the endogenous NKX6.1 locus. Characterization of the reporter lines demonstrated faithful GFP labelling of NKX6.1 expression during pancreas and motor neuron differentiation. Cell sorting and gene expression profiling by RNA sequencing revealed that NKX6.1-positive cells from pancreatic differentiations closely resemble human beta cells. Furthermore, functional characterization of the isolated cells demonstrated that glucose-stimulated insulin secretion is mainly confined to the NKX6.1-positive cells. We expect that the NKX6.1-GFP iPSC lines and the results presented here will contribute to the further refinement of differentiation protocols and characterization of hPSC-derived beta cells and motor neurons for disease modelling and cell replacement therapies. Keywords: Human induced pluripotent stem cells, NKX6.1, Reporter cell line, Directed differentiation, hiPSC-derived beta cells

  19. Genetic mapping and QTL analysis of agronomic traits in Indian Mucuna pruriens using an intraspecific F₂population.

    Science.gov (United States)

    Mahesh, S; Leelambika, M; Jaheer, Md; Anithakumari, A M; Sathyanarayana, N

    2016-03-01

    Mucuna pruriens is a well-recognized agricultural and horticultural crop with important medicinal use. However, antinutritional factors in seed and adverse morphological characters have negatively affected its cultivation. To elucidate the genetic control of agronomic traits, an intraspecific genetic linkage map of Indian M. pruriens has been developed based on amplified fragment length polymorphism (AFLP) markers using 200 F₂ progenies derived from a cross between wild and cultivated genotypes. The resulting linkage map comprised 129 AFLP markers dispersed over 13 linkage groups spanning a total distance of 618.88 cM with an average marker interval of 4.79 cM. For the first time, three QTLs explaining about 6.05-14.77% of the corresponding total phenotypic variation for three quantitative (seed) traits and, eight QTLs explaining about 25.96% of the corresponding total phenotypic variation for three qualitative traits have been detected on four linkage groups. The map presented here will pave a way for mapping of genes/QTLs for the important agronomic and horticultural traits contrasting between the parents used in this study.

  20. The development of insecticide-treated durable wall lining for malaria control: insights from rural and urban populations in Angola and Nigeria

    Directory of Open Access Journals (Sweden)

    Messenger Louisa A

    2012-09-01

    Full Text Available Abstract Background Durable lining (DL is a deltamethrin-impregnated polyethylene material, which is designed to cover domestic walls that would normally be sprayed with residual insecticide. The operational success of DL as a long-lasting insecticidal substrate will be dependent on a high level of user acceptability as households must maintain correctly installed linings on their walls for several years. Preliminary trials were undertaken to identify a material to develop into a marketable wall lining and to assess its level of acceptability among rural and urban populations. Methods In Angola (n=60, prototype DL and insecticide-treated plastic sheeting (ITPS were installed on urban house walls and ceilings, respectively, and acceptability was compared to indoor residual spraying (IRS (n=20 using a knowledge, attitude and practice (KAP questionnaire. In Nigeria (n=178, three materials (prototype DL, ITPS and insecticide-treated wall netting were distributed among rural and urban households. User opinions were gathered from focus group discussions, in-depth interviews and KAP questionnaires. Results In Angola, after two weeks, the majority of participants (98% expressed satisfaction with the products and identified the killing of insects as the materials’ principal benefits (73%. After one year, despite a loss of almost 50% of households to refugee repatriation, all 32 remaining households still asserted that they had liked the DL/ITPS in their homes and given the choice of intervention preferred DL/ITPS to IRS (94% or insecticide-treated nets (78%. In Nigeria, a dichotomy between rural and urban respondents emerged. Rural participants favoured wall adornments and accepted wall linings because of their perceived decorative value and entomological efficacy. By contrast, urban households preferred minimal wall decoration and rejected the materials based upon objections to their aesthetics and installation feasibility. Conclusions The high level

  1. The development of insecticide-treated durable wall lining for malaria control: insights from rural and urban populations in Angola and Nigeria

    Science.gov (United States)

    2012-01-01

    Background Durable lining (DL) is a deltamethrin-impregnated polyethylene material, which is designed to cover domestic walls that would normally be sprayed with residual insecticide. The operational success of DL as a long-lasting insecticidal substrate will be dependent on a high level of user acceptability as households must maintain correctly installed linings on their walls for several years. Preliminary trials were undertaken to identify a material to develop into a marketable wall lining and to assess its level of acceptability among rural and urban populations. Methods In Angola (n=60), prototype DL and insecticide-treated plastic sheeting (ITPS) were installed on urban house walls and ceilings, respectively, and acceptability was compared to indoor residual spraying (IRS) (n=20) using a knowledge, attitude and practice (KAP) questionnaire. In Nigeria (n=178), three materials (prototype DL, ITPS and insecticide-treated wall netting) were distributed among rural and urban households. User opinions were gathered from focus group discussions, in-depth interviews and KAP questionnaires. Results In Angola, after two weeks, the majority of participants (98%) expressed satisfaction with the products and identified the killing of insects as the materials’ principal benefits (73%). After one year, despite a loss of almost 50% of households to refugee repatriation, all 32 remaining households still asserted that they had liked the DL/ITPS in their homes and given the choice of intervention preferred DL/ITPS to IRS (94%) or insecticide-treated nets (78%). In Nigeria, a dichotomy between rural and urban respondents emerged. Rural participants favoured wall adornments and accepted wall linings because of their perceived decorative value and entomological efficacy. By contrast, urban households preferred minimal wall decoration and rejected the materials based upon objections to their aesthetics and installation feasibility. Conclusions The high level of acceptability

  2. Dislocation density and Burgers vector population in fiber-textured Ni thin films determined by high-resolution X-ray line profile analysis

    DEFF Research Database (Denmark)

    Csiszár, Gábor; Pantleon, Karen; Alimadadi, Hossein

    2012-01-01

    distribution are determined by high-resolution X-ray diffraction line profile analysis. The substructure parameters are correlated with the strength of the films by using the combined Taylor and Hall-Petch relations. The convolutional multiple whole profile method is used to obtain the substructure parameters......Nanocrystalline Ni thin films have been produced by direct current electrodeposition with different additives and current density in order to obtain 〈100〉, 〈111〉 and 〈211〉 major fiber textures. The dislocation density, the Burgers vector population and the coherently scattering domain size...

  3. Three millimeter molecular line observations in Sagittarius B2. 1: Full synthesis mapping study of HNO, CCS, and HC(13)CCN

    Science.gov (United States)

    Kuan, Yi-Jehng; Snyder, Lewis E.

    1994-01-01

    We present the first full synthesis maps of the small molecules HNO, CCS, and HC(13)CCN in Sgr B2. We have observed the 3.8 mm continuum, the HNO J(sub K(sub -1)K(sub 1)) = 1(sub O1)-0(sub OO), the CCS J(sub N) = 7(sub 6)-6(sub 5), and the HC(13)CCN J = 9-8 transitions in the core of the Sgr B2 molecular cloud, using the Berkeley Illinois Maryland Association (BIMA) millimeter array and the NRAO 12 m telescope. We have found that HNO exists in five major gas clumps in the Sgr B2 region, which we have labeled HNO(N), HNO(NW), HNO(E), HNO(M), and HNO(S). Of particular interest is HNO(M), a major molecular gas concentration approximately 15 sec west of Sgr B2(M) in a region of young star formation. HNO is found to be closely associated with the ionized gas and might be depleted around bright H II complexes. In general, the peak intensity of the HNO emission is found to be offset from the peak of the continuum emission. We found evidence for some chemical differentiation among the three species, HNO, CCS, and HC(13)CCN, but the abundance ratios are in fair agreement with theoretical models. Two unidentified lines, U81420 and U81518, were observed, and a previously unknown compact dust source was detected. Our HNO data indicate the presence of a rotating approximately (2.2-4.4) x 10(exp 3)solar mass gas envelope surrounding Sgr B2(N), a possible bipolar gas outflow in HNO(M), and possibly a large (approximately 4.2 x 10(exp 4)solar mass) extended rotating disk associated with HNO(S). In addition, the CCS and HC(13)CCN data approximately outline the extended component of Sgr B2 and clearly show that the southern continuum source Sgr B2(S) is actually a major molecular source as well. Consequently, the kinematics of the Sgr B2 molecular cloud is quite complex, but in moving from the northwest to south, the LSR velocity generally changes from 79 to 46 km/s.

  4. The effective size of the Icelandic population and the prospects for LD mapping: inference from unphased microsatellite markers

    DEFF Research Database (Denmark)

    Bataillon, Thomas; Mailund, Thomas; Thorlacius, Steinunn

    2006-01-01

    on scaled recombination rates from patterns of LD. Patterns of LD in Iceland suggest a genome-wide scaled recombination rate of ρ* = 200 [130–330] per cM which is equivalent to a long term effective population size of ~5000 in the range of estimates recently reported in three populations using extensive...

  5. Satellite line mapping in Eu3+–Ce3+ and Pr3+–Ce3+ codoped Y2SiO5

    International Nuclear Information System (INIS)

    Serrano, D.; Karlsson, J.; Zheng, L.; Dong, Y.; Ferrier, A.; Goldner, P.; Walther, A.; Rippe, L.; Kröll, S.

    2016-01-01

    In this work we perform a high-resolution spectroscopic investigation of Eu 3+ –Ce 3+ and Pr 3+ –Ce 3+ codoped Y 2 SiO 5 crystals. Satellite line spectra were recorded at low temperatures around the Eu 3+ : 7 F 0 → 5 D 0 and the Pr 3+ : 3 H 4 → 1 D 2 transitions. It is observed that the incorporation of Ce 3+ as a codopant notably changes the Eu 3+ and Pr 3+ satellite line patterns. Satellite lines measured in singly doped Eu 3+ :Y 2 SiO 5 were found at the same spectral positions in Eu 3+ –Ce 3+ codoped crystals. These coincident lines were concluded to be due to pairs of Eu 3+ ions. Extra satellite lines appeared in the codoped crystals, which were assigned to Ce 3+ related structures such as Ce 3+ –Eu 3+ pairs. The analysis of the Pr 3+ satellite line spectra presents further challenges. Satellite lines associated to Pr 3+ pairs show weaker intensity, presumably due to the efficient quenching of the Pr 3+1 D 2 emission through cross-relaxation paths ( 1 D 2 → 1 G 4 ; 3 H 4 → 3 F 4 ). The investigation of the Eu 3+ and Pr 3+ satellite line patterns in Y 2 SiO 5 is particularly interesting for their exploitation in rare-earth based quantum computation schemes. - Highlights: • We recorded Eu and Pr satellite lines in Y 2 SiO 5 with and without Ce as a codopant. • The presence of Ce leads to the appearance of extra satellite lines in the spectra. • The satellite lines are associated to minor crystal sites such as ion pairs. • Less than 100 ion pairs were detected per satellite line. • The exploitation of the satellite line structure is proposed for quantum computing.

  6. Assessing the value of phenotypic information from non-genotyped animals for QTL mapping of complex traits in real and simulated populations.

    Science.gov (United States)

    Melo, Thaise P; Takada, Luciana; Baldi, Fernando; Oliveira, Henrique N; Dias, Marina M; Neves, Haroldo H R; Schenkel, Flavio S; Albuquerque, Lucia G; Carvalheiro, Roberto

    2016-06-21

    QTL mapping through genome-wide association studies (GWAS) is challenging, especially in the case of low heritability complex traits and when few animals possess genotypic and phenotypic information. When most of the phenotypic information is from non-genotyped animals, GWAS can be performed using the weighted single-step GBLUP (WssGBLUP) method, which permits to combine all available information, even that of non-genotyped animals. However, it is not clear to what extent phenotypic information from non-genotyped animals increases the power of QTL detection, and whether factors such as the extent of linkage disequilibrium (LD) in the population and weighting SNPs in WssGBLUP affect the importance of using information from non-genotyped animals in GWAS. These questions were investigated in this study using real and simulated data. Analysis of real data showed that the use of phenotypes of non-genotyped animals affected SNP effect estimates and, consequently, QTL mapping. Despite some coincidence, the most important genomic regions identified by the analyses, either using or ignoring phenotypes of non-genotyped animals, were not the same. The simulation results indicated that the inclusion of all available phenotypic information, even that of non-genotyped animals, tends to improve QTL detection for low heritability complex traits. For populations with low levels of LD, this trend of improvement was less pronounced. Stronger shrinkage on SNPs explaining lower variance was not necessarily associated with better QTL mapping. The use of phenotypic information from non-genotyped animals in GWAS may improve the ability to detect QTL for low heritability complex traits, especially in populations in which the level of LD is high.

  7. Epitope mapping of the major allergen from Atlantic cod in Spanish population reveals different IgE-binding patterns.

    Science.gov (United States)

    Perez-Gordo, Marina; Pastor-Vargas, Carlos; Lin, Jing; Bardina, Ludmilla; Cases, Barbara; Ibáñez, Maria Dolores; Vivanco, Fernando; Cuesta-Herranz, Javier; Sampson, Hugh A

    2013-07-01

    IgE-epitope mapping of allergens reveal important information about antigen components involved in allergic reactions. The peptide-based microarray immunoassay has been used to map epitopes of some food allergens. We developed a peptide microarray immunoassay to map allergenic epitopes in parvalbumin from Atlantic cod (Gad m 1), the most consumed cod species in Spain. Sera from 13 fish-allergic patients with specific IgE to cod parvalbumin were used. A library of overlapping peptides was synthesized, representing the primary sequence of Gad m 1. Peptides were used to analyze allergen-specific IgE antibodies in patient sera. 100% of the patients recognized one antigenic region of 15 amino acids in length in Gad m 1. This region only partially correlated with one of the three antigenic determinants of Gad c 1 (Allergen M), parvalbumin from Baltic cod (Gadus callarias). In the 3D model of the protein, this region was located on the surface of the protein. We have identified a relevant antigenic region in Gad m 1. This epitope could be considered as a severity marker and provides additional information to improve fish allergy diagnosis and the design of safe immunotherapeutic tools. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Physiological factors affecting intrinsic water use efficiency of potato clones within a dihaploid mapping population under well-watered and drought-stressed conditions

    DEFF Research Database (Denmark)

    Topbjerg, Henrik Bak; Kaminski, Kacper Piotr; Markussen, Bo

    2014-01-01

    ) within a dihaploid potato (Solanum tuberosum L.) mapping population under well-watered (WW) and drought-stress (DS) conditions. The factorial dependency of WUEi on several plant bio-physiological traits was analyzed, and clonal difference of WUEi was compared. Significant differences in WUEi were found......Optimizing crops water use is essential for ensuring food production under future climate scenarios. Therefore, new cultivars that are capable of maintaining production under limited water resource are needed. This study screened for clonal differences in intrinsic water use efficiency (WUEi...

  9. Improved resolution in the position of drought-related QTLs in a single mapping population of rice by meta-analysis

    Directory of Open Access Journals (Sweden)

    Courtois Brigitte

    2009-06-01

    Full Text Available Abstract Background Meta-analysis of QTLs combines the results of several QTL detection studies and provides narrow confidence intervals for meta-QTLs, permitting easier positional candidate gene identification. It is usually applied to multiple mapping populations, but can be applied to one. Here, a meta-analysis of drought related QTLs in the Bala × Azucena mapping population compiles data from 13 experiments and 25 independent screens providing 1,650 individual QTLs separated into 5 trait categories; drought avoidance, plant height, plant biomass, leaf morphology and root traits. A heat map of the overlapping 1 LOD confidence intervals provides an overview of the distribution of QTLs. The programme BioMercator is then used to conduct a formal meta-analysis at example QTL clusters to illustrate the value of meta-analysis of QTLs in this population. Results The heat map graphically illustrates the genetic complexity of drought related traits in rice. QTLs can be linked to their physical position on the rice genome using Additional file 1 provided. Formal meta-analysis on chromosome 1, where clusters of QTLs for all trait categories appear close, established that the sd1 semi-dwarfing gene coincided with a plant height meta-QTL, that the drought avoidance meta-QTL was not likely to be associated with this gene, and that this meta-QTL was not pleiotropic with close meta-QTLs for leaf morphology and root traits. On chromosome 5, evidence suggests that a drought avoidance meta-QTL was pleiotropic with leaf morphology and plant biomass meta-QTLs, but not with meta-QTLs for root traits and plant height 10 cM lower down. A region of dense root QTL activity graphically visible on chromosome 9 was dissected into three meta-QTLs within a space of 35 cM. The confidence intervals for meta-QTLs obtained ranged from 5.1 to 14.5 cM with an average of 9.4 cM, which is approximately 180 genes in rice. Additional file 1 Alignment of markers on the Bala

  10. A population-based study of first and second-line drug-resistant tuberculosis in a high-burden area of the Mexico/United States border

    Directory of Open Access Journals (Sweden)

    Pola Becerril-Montes

    2013-04-01

    Full Text Available The resistance of 139 Mycobacterium tuberculosis (MTB isolates from the city of Monterrey, Northeast Mexico, to first and second-line anti-TB drugs was analysed. A total of 73 isolates were susceptible and 66 were resistant to anti-TB drugs. Monoresistance to streptomycin, isoniazid (INH and ethambutol was observed in 29 cases. Resistance to INH was found in 52 cases and in 29 cases INH resistance was combined with resistance to two or three drugs. A total of 24 isolates were multidrug-resistant (MDR resistant to at least INH and rifampicin and 11 MDR cases were resistant to five drugs. The proportion of MDR-TB among new TB cases in our target population was 0.72% (1/139 cases. The proportion of MDR-TB among previously treated cases was 25.18% (35/139 cases. The 13 polyresistant and 24 MDR isolates were assayed against the following seven second-line drugs: amikacin (AMK, kanamycin (KAN, capreomycin (CAP, clofazimine (CLF, ethionamide (ETH, ofloxacin (OFL and cycloserine (CLS. Resistance to CLF, OFL or CLS was not observed. Resistance was detected to ETH (10.80% and to AMK (2.70%, KAN (2.70% and CAP (2.70%. One isolate of MDR with primary resistance was also resistant to three second-line drugs. Monterrey has a high prevalence of MDR-TB among previously treated cases and extensively drug-resistant-MTB strains may soon appear.

  11. BOOSTING LY α   AND He ii λ 1640 LINE FLUXES FROM POPULATION III GALAXIES: STOCHASTIC IMF SAMPLING AND DEPARTURES FROM CASE-B

    International Nuclear Information System (INIS)

    Mas-Ribas, Lluís; Dijkstra, Mark; Forero-Romero, Jaime E.

    2016-01-01

    We revisit calculations of nebular hydrogen Ly α and He ii λ 1640 line strengths for Population III (Pop III) galaxies, undergoing continuous, and bursts of, star formation. We focus on initial mass functions (IMFs) motivated by recent theoretical studies, which generally span a lower range of stellar masses than earlier works. We also account for case-B departures and the stochastic sampling of the IMF. In agreement with previous work, we find that departures from case-B can enhance the Ly α flux by a factor of a few, but we argue that this enhancement is driven mainly by collisional excitation and ionization, and not due to photoionization from the n  = 2 state of atomic hydrogen. The increased sensitivity of the Ly α flux to the high-energy end of the galaxy spectrum makes it more subject to stochastic sampling of the IMF. The latter introduces a dispersion in the predicted nebular line fluxes around the deterministic value by as much as a factor of ∼4. In contrast, the stochastic sampling of the IMF has less impact on the emerging Lyman Werner photon flux. When case-B departures and stochasticity effects are combined, nebular line emission from Pop III galaxies can be up to one order of magnitude brighter than predicted by “standard” calculations that do not include these effects. This enhances the prospects for detection with future facilities such as the James Webb Space Telescope and large, ground-based telescopes.

  12. Boosting Lyα and He II λ1640 Line Fluxes from Population III Galaxies: Stochastic IMF Sampling and Departures from Case-B

    Science.gov (United States)

    Mas-Ribas, Lluís; Dijkstra, Mark; Forero-Romero, Jaime E.

    2016-12-01

    We revisit calculations of nebular hydrogen Lyα and He II λ1640 line strengths for Population III (Pop III) galaxies, undergoing continuous, and bursts of, star formation. We focus on initial mass functions (IMFs) motivated by recent theoretical studies, which generally span a lower range of stellar masses than earlier works. We also account for case-B departures and the stochastic sampling of the IMF. In agreement with previous work, we find that departures from case-B can enhance the Lyα flux by a factor of a few, but we argue that this enhancement is driven mainly by collisional excitation and ionization, and not due to photoionization from the n = 2 state of atomic hydrogen. The increased sensitivity of the Lyα flux to the high-energy end of the galaxy spectrum makes it more subject to stochastic sampling of the IMF. The latter introduces a dispersion in the predicted nebular line fluxes around the deterministic value by as much as a factor of ˜4. In contrast, the stochastic sampling of the IMF has less impact on the emerging Lyman Werner photon flux. When case-B departures and stochasticity effects are combined, nebular line emission from Pop III galaxies can be up to one order of magnitude brighter than predicted by “standard” calculations that do not include these effects. This enhances the prospects for detection with future facilities such as the James Webb Space Telescope and large, ground-based telescopes.

  13. Regulation of voltage-gated potassium channels attenuates resistance of side-population cells to gefitinib in the human lung cancer cell line NCI-H460.

    Science.gov (United States)

    Choi, Seon Young; Kim, Hang-Rae; Ryu, Pan Dong; Lee, So Yeong

    2017-02-21

    Side-population (SP) cells that exclude anti-cancer drugs have been found in various tumor cell lines. Moreover, SP cells have a higher proliferative potential and drug resistance than main population cells (Non-SP cells). Also, several ion channels are responsible for the drug resistance and proliferation of SP cells in cancer. To confirm the expression and function of voltage-gated potassium (Kv) channels of SP cells, these cells, as well as highly expressed ATP-binding cassette (ABC) transporters and stemness genes, were isolated from a gefitinib-resistant human lung adenocarcinoma cell line (NCI-H460), using Hoechst 33342 efflux. In the present study, we found that mRNA expression of Kv channels in SP cells was different compared to Non-SP cells, and the resistance of SP cells to gefitinib was weakened with a combination treatment of gefitinib and Kv channel blockers or a Kv7 opener, compared to single-treatment gefitinib, through inhibition of the Ras-Raf signaling pathway. The findings indicate that Kv channels in SP cells could be new targets for reducing the resistance to gefitinib.

  14. GIS-Mapping and Statistical Analyses to Identify Climate-Vulnerable Communities and Populations Exposed to Superfund Sites

    Science.gov (United States)

    Climate change-related cumulative health risks are expected to be disproportionately greater for overburdened communities, due to differential proximity and exposures to chemical sources and flood zones. Communities and populations vulnerable to climate change-associated impacts ...

  15. High-Resolution Genome-Wide Linkage Mapping Identifies Susceptibility Loci for BMI in the Chinese Population

    DEFF Research Database (Denmark)

    Zhang, Dong Feng; Pang, Zengchang; Li, Shuxia

    2012-01-01

    The genetic loci affecting the commonly used BMI have been intensively investigated using linkage approaches in multiple populations. This study aims at performing the first genome-wide linkage scan on BMI in the Chinese population in mainland China with hypothesis that heterogeneity in genetic...... linkage could exist in different ethnic populations. BMI was measured from 126 dizygotic twins in Qingdao municipality who were genotyped using high-resolution Affymetrix Genome-Wide Human SNP arrays containing about 1 million single-nucleotide polymorphisms (SNPs). Nonparametric linkage analysis...... in western countries. Multiple loci showing suggestive linkage were found on chromosome 1 (lod score 2.38 at 242 cM), chromosome 8 (2.48 at 95 cM), and chromosome 14 (2.2 at 89.4 cM). The strong linkage identified in the Chinese subjects that is consistent with that found in populations of European origin...

  16. Low Elevation Coastal Zone (LECZ) Urban-Rural Population Estimates, Global Rural-Urban Mapping Project (GRUMP), Alpha Version

    Data.gov (United States)

    National Aeronautics and Space Administration — The Low Elevation Coastal Zone (LECZ) Urban-Rural Estimates consists of country-level estimates of urban, rural and total population and land area country-wide and...

  17. Measuring urban agglomeration using a city-scale dasymetric population map: A study in the Pearl River Delta, China

    OpenAIRE

    Wei, Chunzhu; Taubenböck, Hannes; Blaschke, Thomas

    2017-01-01

    The rates of urbanization and increase in urban sprawl that have occurred in China over the past thirty years have been unprecedented. This article presents a new city-scale dasymetric modelling approach that incorporates historical census data for 28 cities in the Pearl River Delta area of southern China. It combines Landsat imagery (from 2000, 2005, 2010, and 2015) with a ‘limiting variable’ estimation al-gorithm to generate a gridded estimate of population density. These gridded population...

  18. Berberine diminishes side population and down-regulates stem cell-associated genes in the pancreatic cancer cell lines PANC-1 and MIA PaCa-2.

    Science.gov (United States)

    Park, S H; Sung, J H; Chung, N

    2014-09-01

    Cancer stem cells play an important role in metastasis and the relapse of drug resistant cancers. Side-population (SP) cells are capable of effluxing Hoechst 33342 dye and are referred to as cancer stem cells. We investigated the effect of berberine on pancreatic cancer stem cells of PANC-1 and MIA PaCa-2. For both cell lines, the proportions of SP cells in the presence of berberine were investigated and compared to the proportions in the presence of gemcitabine, a standard pancreatic anti-cancer drug. The proportions of SP cells in the PANC-1 and MIA PaCa-2 cell lines were about 9 and PANC-1 decreased to 5.7 ± 2.0 and 6.8 ± 0.8%, respectively, which compares to the control proportion of (9.7 ± 1.7). After berberine and gemcitabine treatment of PANC-1, of the four stem cell-associated genes (SOX2, POU5F1, NANOG, and NOTCH1), all but NOTCH1 were down-regulated. Unfortunately, the effect of berberine and gemcitabine treatments on MIA PaCa-2 SP cells could not be clearly observed because SP cells represented only a very small proportion of MIA PaCa-2 cells. However, SOX2, POU5F1, and NANOG genes were shown to be effectively down-regulated in the MIA PaCa-2 cell line as a whole. Taken together, these results indicate that berberine is as effective at targeting pancreatic cancer cell lines as gemcitabine. Therefore, we believe that POU5F1, SOX2, and NANOG can serve as potential markers, and berberine may be an effective anti-cancer agent when targeting human pancreatic cancer cells and/or their cancer stem cells.

  19. Biomarker screening of oral cancer cell lines revealed sub-populations of CD133-, CD44-, CD24- and ALDH1- positive cancer stem cells

    Directory of Open Access Journals (Sweden)

    Kendall K

    2013-05-01

    Full Text Available Head and neck squamous cell carcinoma (HNSCC ranks sixth worldwide for cancer-related mortality. For the past several decades the mainstay of treatment for HNSCC has been surgery and external beam radiation, although more recent trials combining chemotherapy and radiation have demonstrated improvements. However, cancer recurrence and treatment failures continue to occur in a significant percentage of patients. Recent advances in tumor biology have led to the discovery that many cancers, including HNSCC, may contain subpopulations of cells with stem cell-like properties that may explain relapse and recurrence. The objective of this study was to screen existing oral cancer cell lines for biomarkers specific for cells with stem cell-like properties. RNA was isolated for RT-PCR screening using primers for specific mRNA of the biomarkers: CD44, CD24, CD133, NANOG, Nestin, ALDH1, and ABCG2 in CAL27, SCC25 and SCC15 cells. This analysis revealed that some oral cancer cell lines (CAL27 and SCC25 may contain small subpopulations of adhesion- and contact-independent cells (AiDC that also express tumor stem cell markers, including CD44, CD133, and CD24. In addition, CAL27 cells also expressed the intracellular tumor stem cell markers, ALDH1 and ABCG2. Isolation and culture of the adhesion- and contact-independent cells from CAL27 and SCC25 populations revealed differential proliferation rates and more robust inhibition by the MEK inhibitor PD98059, as well as the chemotherapeutic agents Cisplatin and Paclitaxel, within the AiDC CAL27 cells. At least one oral cancer cell line (CAL27 contained subpopulations of cells that express specific biomarkers associated with tumor stem cells which were morphologically and phenotypically distinct from other cells within this cell line.

  20. Mapping cell populations in flow cytometry data for cross‐sample comparison using the Friedman–Rafsky test statistic as a distance measure

    Science.gov (United States)

    Hsiao, Chiaowen; Liu, Mengya; Stanton, Rick; McGee, Monnie; Qian, Yu

    2015-01-01

    Abstract Flow cytometry (FCM) is a fluorescence‐based single‐cell experimental technology that is routinely applied in biomedical research for identifying cellular biomarkers of normal physiological responses and abnormal disease states. While many computational methods have been developed that focus on identifying cell populations in individual FCM samples, very few have addressed how the identified cell populations can be matched across samples for comparative analysis. This article presents FlowMap‐FR, a novel method for cell population mapping across FCM samples. FlowMap‐FR is based on the Friedman–Rafsky nonparametric test statistic (FR statistic), which quantifies the equivalence of multivariate distributions. As applied to FCM data by FlowMap‐FR, the FR statistic objectively quantifies the similarity between cell populations based on the shapes, sizes, and positions of fluorescence data distributions in the multidimensional feature space. To test and evaluate the performance of FlowMap‐FR, we simulated the kinds of biological and technical sample variations that are commonly observed in FCM data. The results show that FlowMap‐FR is able to effectively identify equivalent cell populations between samples under scenarios of proportion differences and modest position shifts. As a statistical test, FlowMap‐FR can be used to determine whether the expression of a cellular marker is statistically different between two cell populations, suggesting candidates for new cellular phenotypes by providing an objective statistical measure. In addition, FlowMap‐FR can indicate situations in which inappropriate splitting or merging of cell populations has occurred during gating procedures. We compared the FR statistic with the symmetric version of Kullback–Leibler divergence measure used in a previous population matching method with both simulated and real data. The FR statistic outperforms the symmetric version of KL‐distance in distinguishing

  1. An Evaluation of Population Density Mapping and Built up Area Estimates in Sri Lanka Using Multiple Methodologies

    Science.gov (United States)

    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

  2. Excitation of plasma waves by unstable photoelectron and thermal electron populations on closed magnetic field lines in the Martian ionosphere

    Directory of Open Access Journals (Sweden)

    N. Borisov

    2005-06-01

    Full Text Available It is argued that anisotropic electron pitch angle distributions in the closed magnetic field regions of the Martian ionosphere gives rise to excitation of plasma instabilities. We discuss two types of instabilities that are excited by two different populations of electrons. First, the generation of Langmuir waves by photoelectrons with energies of the order of 10eV is investigated. It is predicted that the measured anisotropy of their pitch angle distribution at the heights z≈400km causes excitation of waves with frequencies f~30kHz and wavelengths λ~30m. Near the terminators the instability of the electrostatic waves with frequencies of the order of or less than the electron gyrofrequency exited by thermal electrons is predicted. The typical frequencies of these waves depend on the local magnitude of the magnetic field and can achieve values f~3-5kHz above strong crustal magnetic fields.

  3. Labelling subway lines

    NARCIS (Netherlands)

    Garrido, M.A.; Iturriaga, C.; Márquez, A.; Portillo, J.R.; Reyes, P.; Wolff, A.; Eades, P.; Takaoka, T.

    2001-01-01

    Graphical features on map, charts, diagrams and graph drawings usually must be annotated with text labels in order to convey their meaning. In this paper we focus on a problem that arises when labeling schematized maps, e.g. for subway networks. We present algorithms for labeling points on a line

  4. Quantitative trait loci mapping of heat tolerance in a doubled haploid population of broccoli using genotyping-by-sequencing

    Science.gov (United States)

    Broccoli is a cool weather vegetable crop with a vernalization requirement to initiate and maintain floral development. Breeding for heat tolerance in broccoli has the potential to both expand viable production areas and extend the growing season. A doubled haploid (DH) population of broccoli (Bras...

  5. Mapping the social network: tracking lice in a wild primate (Microcebus rufus population to infer social contacts and vector potential

    Directory of Open Access Journals (Sweden)

    Zohdy Sarah

    2012-03-01

    Full Text Available Abstract Background Studies of host-parasite interactions have the potential to provide insights into the ecology of both organisms involved. We monitored the movement of sucking lice (Lemurpediculus verruculosus, parasites that require direct host-host contact to be transferred, in their host population of wild mouse lemurs (Microcebus rufus. These lemurs live in the rainforests of Madagascar, are small (40 g, arboreal, nocturnal, solitary foraging primates for which data on population-wide interactions are difficult to obtain. We developed a simple, cost effective method exploiting the intimate relationship between louse and lemur, whereby individual lice were marked, without removal from their host, with an individualized code, and tracked throughout the lemur population. We then tested the hypotheses that 1 the frequency of louse transfers, and thus interactions, would decrease with increasing distance between paired individual lemurs; 2 due to host polygynandry, social interactions and hence louse transfers would increase during the onset of the breeding season; and 3 individual mouse lemurs would vary in their contributions to the spread of lice. Results We show that louse transfers involved 43.75% of the studied lemur population, exclusively males. Louse transfers peaked during the breeding season, perhaps due to increased social interactions between lemurs. Although trap-based individual lemur ranging patterns are restricted, louse transfer rate does not correlate with the distance between lemur trapping locales, indicating wider host ranging behavior and a greater risk of rapid population-wide pathogen transmission than predicted by standard trapping data alone. Furthermore, relatively few lemur individuals contributed disproportionately to the rapid spread of lice throughout the population. Conclusions Using a simple method, we were able to visualize exchanges of lice in a population of cryptic wild primates. This method not only

  6. HapMap-based study of the DNA repair gene ERCC2 and lung cancer susceptibility in a Chinese population

    DEFF Research Database (Denmark)

    Yin, Jiaoyang; Vogel, Ulla Birgitte; Ma, Yegang

    2009-01-01

    -nucleotide polymorphisms (htSNPs) (rs238403, rs50871, rs3916840, rs238415, rs3916874 and rs1799787) from HapMap database were analyzed, which provide an almost complete coverage of the genetic variations in the ERCC2 gene. Although none of the six htSNPs was individually associated with lung cancer risk, we found that two...... ratio, OR (95% confidence interval, CI) = 2.62 (1.53–4.50), P = 0.0003 for hap4; OR (95% CI) = 3.01 (1.36–6.63), P = 0.004 for hap7]. Furthermore, diplotype analyses also strengthened the significant associations of risk haplotype 4 [OR (95% CI) = 3.56 (2.12–5.87), P

  7. Illicit Drug Users in the Tanzanian Hinterland: Population Size Estimation Through Key Informant-Driven Hot Spot Mapping.

    Science.gov (United States)

    Ndayongeje, Joel; Msami, Amani; Laurent, Yovin Ivo; Mwankemwa, Syangu; Makumbuli, Moza; Ngonyani, Alois M; Tiberio, Jenny; Welty, Susie; Said, Christen; Morris, Meghan D; McFarland, Willi

    2018-02-12

    We mapped hot spots and estimated the numbers of people who use drugs (PWUD) and who inject drugs (PWID) in 12 regions of Tanzania. Primary (ie, current and past PWUD) and secondary (eg, police, service providers) key informants identified potential hot spots, which we visited to verify and count the number of PWUD and PWID present. Adjustments to counts and extrapolation to regional estimates were done by local experts through iterative rounds of discussion. Drug use, specifically cocaine and heroin, occurred in all regions. Tanga had the largest numbers of PWUD and PWID (5190 and 540, respectively), followed by Mwanza (3300 and 300, respectively). Findings highlight the need to strengthen awareness of drug use and develop prevention and harm reduction programs with broader reach in Tanzania. This exercise provides a foundation for understanding the extent and locations of drug use, a baseline for future size estimations, and a sampling frame for future research.

  8. Quantitative trait loci mapping and genetic dissection for lint ...

    Indian Academy of Sciences (India)

    2014-08-01

    Aug 1, 2014 ... hirsutum, as parents to construct a mapping populations in upland ... that could be candidate markers affecting cotton fibre development. .... F2:3 family line seeds were harvested. ... long). All activities were performed as per the normal mana- ... times, and the QTL with a LOD value of more than the LOD.

  9. Mapping the Human Planet: Integrating Settlement, Infrastructure, and Population Data to Support Sustainable Development, Climate, and Disaster Data Needs

    Science.gov (United States)

    Chen, R. S.; de Sherbinin, A. M.; Yetman, G.; Downs, R. R.

    2017-12-01

    A central issue in international efforts to address climate change, large-scale disaster risk, and overall sustainable development is the exposure of human settlements and population to changing climate patterns and a range of geological, climatological, technological, and other hazards. The present and future location of human activities is also important in mitigation and adaptation to climate change, and to ensuring that we "leave no one behind" in achieving the Sustainable Development Goals adopted by the international community in September 2015. The extent and quality of built infrastructure are key factors in the mortality, morbidity, and economic impacts of disasters, and are simultaneously essential to sustainable development. Earth observations have great potential to improve the coverage, consistency, timeliness, and richness of data on settlements, infrastructure, and population, in ways that complement existing and emerging forms of socioeconomic data collection such as censuses, surveys, and cell phone and Internet traffic. Night-time lights from the Suomi-NPP satellite may be able to provide near real-time data on occupance and economic activity. New "big data" capabilities make it possible to rapidly process high-resolution (50-cm) imagery to detect structures and changes in structures, especially in rural areas where other data are limited. A key challenge is to ensure that these types of data can be translated into forms useful in a range of applications and for diverse user communities, including national statistical offices, local government planners, development and humanitarian organizations, community groups, and the private sector. We report here on efforts, in coordination with the GEO Human Planet Initiative, to develop new data on settlements, infrastructure, and population, together with open data services and tools, to support disaster risk assessment, climate vulnerability analysis, and sustainable development decision making.

  10. Local Genealogies in a Linear Mixed Model for Genome-wide Association Mapping in Complex Pedigreed Populations

    DEFF Research Database (Denmark)

    Sahana, Goutam; Mailund, Thomas; Lund, Mogens Sandø

    2011-01-01

    be extended to incorporate other effects in a straightforward and rigorous fashion. Here, we present a complementary approach, called ‘GENMIX (genealogy based mixed model)’ which combines advantages from two powerful GWAS methods: genealogy-based haplotype grouping and MMA. Subjects and Methods: We validated......Introduction: The state-of-the-art for dealing with multiple levels of relationship among the samples in genome-wide association studies (GWAS) is unified mixed model analysis (MMA). This approach is very flexible, can be applied to both family-based and population-based samples, and can...

  11. Use of linkage mapping and centrality analysis across habitat gradients to conserve connectivity of gray wolf populations in western North America.

    Science.gov (United States)

    Carroll, Carlos; McRae, Brad H; Brookes, Allen

    2012-02-01

    Centrality metrics evaluate paths between all possible pairwise combinations of sites on a landscape to rank the contribution of each site to facilitating ecological flows across the network of sites. Computational advances now allow application of centrality metrics to landscapes represented as continuous gradients of habitat quality. This avoids the binary classification of landscapes into patch and matrix required by patch-based graph analyses of connectivity. It also avoids the focus on delineating paths between individual pairs of core areas characteristic of most corridor- or linkage-mapping methods of connectivity analysis. Conservation of regional habitat connectivity has the potential to facilitate recovery of the gray wolf (Canis lupus), a species currently recolonizing portions of its historic range in the western United States. We applied 3 contrasting linkage-mapping methods (shortest path, current flow, and minimum-cost-maximum-flow) to spatial data representing wolf habitat to analyze connectivity between wolf populations in central Idaho and Yellowstone National Park (Wyoming). We then applied 3 analogous betweenness centrality metrics to analyze connectivity of wolf habitat throughout the northwestern United States and southwestern Canada to determine where it might be possible to facilitate range expansion and interpopulation dispersal. We developed software to facilitate application of centrality metrics. Shortest-path betweenness centrality identified a minimal network of linkages analogous to those identified by least-cost-path corridor mapping. Current flow and minimum-cost-maximum-flow betweenness centrality identified diffuse networks that included alternative linkages, which will allow greater flexibility in planning. Minimum-cost-maximum-flow betweenness centrality, by integrating both land cost and habitat capacity, allows connectivity to be considered within planning processes that seek to maximize species protection at minimum cost

  12. Genetic dissection of the maize kernel development process via conditional QTL mapping for three developing kernel-related traits in an immortalized F2 population.

    Science.gov (United States)

    Zhang, Zhanhui; Wu, Xiangyuan; Shi, Chaonan; Wang, Rongna; Li, Shengfei; Wang, Zhaohui; Liu, Zonghua; Xue, Yadong; Tang, Guiliang; Tang, Jihua

    2016-02-01

    Kernel development is an important dynamic trait that determines the final grain yield in maize. To dissect the genetic basis of maize kernel development process, a conditional quantitative trait locus (QTL) analysis was conducted using an immortalized F2 (IF2) population comprising 243 single crosses at two locations over 2 years. Volume (KV) and density (KD) of dried developing kernels, together with kernel weight (KW) at different developmental stages, were used to describe dynamic changes during kernel development. Phenotypic analysis revealed that final KW and KD were determined at DAP22 and KV at DAP29. Unconditional QTL mapping for KW, KV and KD uncovered 97 QTLs at different kernel development stages, of which qKW6b, qKW7a, qKW7b, qKW10b, qKW10c, qKV10a, qKV10b and qKV7 were identified under multiple kernel developmental stages and environments. Among the 26 QTLs detected by conditional QTL mapping, conqKW7a, conqKV7a, conqKV10a, conqKD2, conqKD7 and conqKD8a were conserved between the two mapping methodologies. Furthermore, most of these QTLs were consistent with QTLs and genes for kernel development/grain filling reported in previous studies. These QTLs probably contain major genes associated with the kernel development process, and can be used to improve grain yield and quality through marker-assisted selection.

  13. RECORD-4 multicenter phase 2 trial of second-line everolimus in patients with metastatic renal cell carcinoma: Asian versus non-Asian population subanalysis.

    Science.gov (United States)

    Yang, Lin; Alyasova, Anna; Ye, Dingwei; Ridolfi, Antonia; Dezzani, Luca; Motzer, Robert J

    2018-02-17

    RECORD-4 assessed everolimus in patients with metastatic renal cell carcinoma (mRCC) who progressed after 1 prior anti-vascular endothelial growth factor (VEGF) or cytokine and reinforced the clinical benefit of second-line everolimus. Because of the high percentage of patients from China enrolled in RECORD-4 (41%) and some reported differences in responses to certain targeted agents between Chinese and Western patients, this subanalysis evaluated outcomes in Asian versus non-Asian patients. RECORD-4 enrolled patients with clear cell mRCC into 3 cohorts based on prior first-line therapy: sunitinib, other anti-VEGF (sorafenib, bevacizumab, pazopanib, other), or cytokines. Patients received everolimus 10 mg/d until progression of disease (RECIST, v1.0) or intolerance. Primary end point was progression-free survival per investigator review. Data cutoff was Sept 1, 2014. Among Asian (n = 55) versus non-Asian (n = 79) patients, 98% versus 84% had good/intermediate MSKCC prognosis; 73% versus 65% were men, and 85% versus 73% were < 65 years of age. All (100%) Asian patients were of Chinese ethnicity. Median duration of exposure was 5.5 mo for Asian and 6.0 mo for non-Asian patients. Among Asian versus non-Asian patients, median progression-free survival (months) was 7.4 versus 7.8 overall, 7.4 versus 4.0 with prior sunitinib, and 5.7 versus 9.2 with prior other anti-VEGFs. Clinical benefit rate was similar between populations: 74.5% (95% CI 61.0-85.3) for Asian patients and 74.7% (95% CI 63.6-83.8) for non-Asian patients. Most patients achieved stable disease as best overall response (Asian, 63.6%; non-Asian, 69.6%). Overall rate of grade 3/4 adverse events appeared similar for Asian (58%) and non-Asian patients (54%). This RECORD-4 subanalysis demonstrated comparable efficacy and adverse event profiles of second-line everolimus in Asian and non-Asian patients. Efficacy and safety outcomes by prior therapy should be interpreted with caution because of small

  14. Mapping socio-environmentally vulnerable populations access and exposure to ecosystem services at the U.S.-Mexico borderlands

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    Norman, Laura M.; Villarreal, Miguel L.; Lara-Valencia, Francisco; Yuan, Yongping; Nie, Wenming; Wilson, Sylvia; Amaya, Gladys; Sleeter, Rachel

    2012-01-01

    Socio-environmental vulnerable populations are often unrepresented in land-use planning yet have great potential for loss when exposed to changes in ecosystem services. Administrative boundaries, cultural differences, and language barriers increase the disassociation between land-use management and marginalized populations living in the U.S.–Mexico borderlands. This paper describes the development of a Modified Socio-Environmental Vulnerability Index (M-SEVI), using determinants from binational census and neighborhood data that describe levels of education, access to resources, migratory status, housing, and number of dependents, to provide a simplified snapshot of the region's populace that can be used in binational planning efforts. We apply this index at the SCW, located on the border between Arizona, USA and Sonora, Mexico. For comparison, the Soil and Water Assessment Tool is concurrently applied to assess the provision of erosion- and flood control services over a 9-year period. We describe how this coupling of data can form the base for an ecosystem services assessment across political boundaries that can be used by land-use planners. Results reveal potential disparities in environmental risks and burdens throughout the binational watershed in residential districts surrounding and between urban centers. The M-SEVI can be used as an important first step in addressing environmental justice for binational decision-making.

  15. Molecular Mapping of QTLs for Yield and Yield-Related Traits in Oryza sativa cv Swarna × O. nivara (IRGC81848 Backcross Population

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    B.P. MALLIKARJUNA SWAMY

    2011-09-01

    Full Text Available Advanced backcross QTL analysis was used to identify QTLs for seven yield and yield-related traits in a BC2F2 population from the cross between a popular Oryza sativa cv Swarna and O. nivara IRGC81848. Transgressive segregants with more than 15% increased effect over Swarna were observed for all the traits except days to heading and days to 50% flowering. Thirty QTLs were detected for seven yield and yield-related traits using interval and composite interval mapping. Enhancing alleles at 13 (45% of these QTLs were derived from O. nivara, and enhancing alleles at all the QTLs for stem diameter and rachis diameter were derived from O. nivara. Three stem diameter QTLs, two rachis diameter QTLs and one number of secondary branches QTL identified by both Interval and composite interval mapping contributed more than 15% of the total phenotypic variance. The QTL epistasis was significant for stem diameter and plot yield. The most significant QTLs qSD7.2, qSD8.1 and qSD9.1 for stem diameter, qRD9.1 for rachis diameter and qNSB1.1 for number of secondary branches are good targets to evaluate their use in marker-assisted selection. O. nivara is a good source of novel alleles for yield related traits and reveals major effect QTLs suitable for marker-assisted selection.

  16. Mapping out Map Libraries

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    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.

  17. Real-life 10-year retention rate of first-line anti-TNF drugs for inflammatory arthritides in adult- and juvenile-onset populations: similarities and differences.

    Science.gov (United States)

    Favalli, Ennio Giulio; Pontikaki, Irene; Becciolini, Andrea; Biggioggero, Martina; Ughi, Nicola; Romano, Micol; Crotti, Chiara; Gattinara, Maurizio; Gerloni, Valeria; Marchesoni, Antonio; Meroni, Pier Luigi

    2017-08-01

    The aim of this study is to retrospectively analyze 10-year drug survival of first-line TNF inhibitor (TNFi) in rheumatoid arthritis (RA), ankylosing spondylitis (AS), psoriatic arthritis (PsA), and juvenile idiopathic arthritis (JIA) patients, comparing withdrawal rates and discontinuation pattern between adult- and juvenile-onset populations. RA, AS, PsA, and JIA patients treated with infliximab, etanercept, or adalimumab as first TNFi between 1999 and 2015 were extracted from a local registry. Drug survival up to 10-year follow-up was evaluated by the Kaplan-Meier method and compared according to age (adult vs juvenile onset), TNFi agent, and discontinuation reason by a stratified log-rank test. Three hundred sixty JIA (205 etanercept, 66 adalimumab, and 89 infliximab) and 951 (607 RA, 188 AS, and 156 PsA) adult patients (464 infliximab, 262 adalimumab, and 225 etanercept) were included. After exclusion of systemic-onset JIA (18.5%), overall 10-year retention rate was 31.8%, with no difference between adult- and juvenile-onset patients (32.1 and 30.2%, respectively; HR 0.938 [95% CI 0.782-1.125]). Etanercept showed the highest drug survival in adult-onset population (p adult population (29.75%) with a significantly higher risk of discontinuation than in juvenile-onset subgroup (HR 1.390 [95% CI 1.060-1.824]). Serious infections and malignancies caused TNFi withdrawal only in adult whereas gastrointestinal, neuropsychiatric, and ocular complications quite only in juvenile patients. Despite a similar 10-year drug survival, adult- and juvenile-onset subpopulations showed a significantly different pattern of TNFi reasons for discontinuation.

  18. Mapping SLCO1B1 Genetic Variation for Global Precision Medicine in Understudied Regions in Africa: A Focus on Zulu and Cape Admixed Populations.

    Science.gov (United States)

    Hoosain, Nisreen; Pearce, Brendon; Jacobs, Clifford; Benjeddou, Mongi

    2016-09-01

    The U.S. President Barack Obama has announced, in his State of the Union address on January 20, 2015, the Precision Medicine Initiative, a US$215-million program. For global precision medicine to become a reality, however, biological and environmental "variome" in previously understudied populations ought to be mapped and catalogued. Chief among the molecular targets that warrant global mapping is the organic anion-transporting polypeptide 1B1 (OATP1B1), encoded by solute carrier organic anion transporter family member 1B1 (SLCO1B1), a hepatic uptake transporter predominantly expressed in the basolateral side of hepatocytes. Human OATP1B1 plays a crucial role in the transport of a wide variety of substrates. This includes endogenous compounds such as bile salts as well as medicines, including benzylpenicillin, methotrexate, pravastatin, and rifampicin, and natural toxins microcystin and phalloidin. Genetic variations observed in the SLCO1B1 gene have been associated with altered in vitro and in vivo OATP1B1 transport activity, and consequently influencing patients' response to medicines, toxins, and susceptibility to common complex diseases. Well-characterized haplotypes, *5 (RS4149056C) and *15 (RS4149056T), have been associated with a strikingly reduced uptake of multiple OATP1B1 substrates, including estrone-3-sulfate, estradiol-17β-d-glucuronide, atorvastatin, cerivastatin, pravastatin, and rifampicin. In particular, RS4149056C is observed in 60% of the Cape admixed (CA) population and is associated with increased plasma concentrations of many statins as well as fexofenadine and repaglinide. We designed and optimized a SNaPshot minisequencing panel to characterize the variants of relevance for precision medicine in the clinic. We report here the first study on allele and genotype frequencies for 10 nonsynonymous, 4 synonymous, and 6 intronic single-nucleotide polymorphisms of SLCO1B1 in the Zulu and CA populations of South Africa. These variants are further

  19. Mapping the low palmitate fap1 mutation and validation of its effects in soybean oil and agronomic traits in three soybean populations.

    Science.gov (United States)

    Cardinal, Andrea J; Whetten, Rebecca; Wang, Sanbao; Auclair, Jérôme; Hyten, David; Cregan, Perry; Bachlava, Eleni; Gillman, Jason; Ramirez, Martha; Dewey, Ralph; Upchurch, Greg; Miranda, Lilian; Burton, Joseph W

    2014-01-01

    fap 1 mutation is caused by a G174A change in GmKASIIIA that disrupts a donor splice site recognition and creates a GATCTG motif that enhanced its expression. Soybean oil with reduced palmitic acid content is desirable to reduce the health risks associated with consumption of this fatty acid. The objectives of this study were: to identify the genomic location of the reduced palmitate fap1 mutation, determine its molecular basis, estimate the amount of phenotypic variation in fatty acid composition explained by this locus, determine if there are epistatic interactions between the fap1 and fap nc loci and, determine if the fap1 mutation has pleiotropic effects on seed yield, oil and protein content in three soybean populations. This study detected two major QTL for 16:0 content located in chromosome 5 (GmFATB1a, fap nc) and chromosome 9 near BARCSOYSSR_09_1707 that explained, with their interaction, 66-94 % of the variation in 16:0 content in the three populations. Sequencing results of a putative candidate gene, GmKASIIIA, revealed a single unique polymorphism in the germplasm line C1726, which was predicted to disrupt the donor splice site recognition between exon one and intron one and produce a truncated KASIIIA protein. This G to A change also created the GATCTG motif that enhanced gene expression of the mutated GmKASIIIA gene. Lines homozygous for the GmKASIIIA mutation (fap1) had a significant reduction in 16:0, 18:0, and oil content; and an increase in unsaturated fatty acids content. There were significant epistatic interactions between GmKASIIIA (fap1) and fap nc for 16:0 and oil contents, and seed yield in two populations. In conclusion, the fap1 phenotype is caused by a single unique SNP in the GmKASIIIA gene.

  20. Differential equilibration and intergranular diffusion of trace elements during rapid regional metamorphism: constraints from LA-ICP-MS mapping of a garnet population

    Science.gov (United States)

    George, F. R.; Gaidies, F.

    2017-12-01

    Trace element zoning contained within a metapelitic garnet population yields information pertaining to a more complex prograde reaction history than is evident in major element zoning patterns and other conventional analyses. In particular, while trace elements may not act as a rate-limiting component for garnet crystallization, their incorporation into garnet growth surfaces provides a nuanced insight into the crystallization history of the population, and the extent of equilibration of trace elements in the matrix. In this study, we present LA-ICP-MS raster maps of trace element concentrations from several population-representative, centrally sectioned garnets from a garnet-grade metapelite of the Sikkim Himalaya, India. Equilibrium forward modeling of garnet crystallization and simulation of diffusional modification indicates that the garnet population crystallized rapidly over <1 Myr between 515 °C/4.5 kbar and 565 °C/5.5 kbar, as a consequence of high heating rates during regional amphibolite-facies metamorphism. While the rate of diffusional homogenization of major divalent cations is interpreted to have exceeded the rate of interfacial advance (yielding simple prograde growth zoning), trace element distributions record a more complex transport history. In particular, yttrium and the heavy rare earth elements (HREE) document a transition from an overprinted sigmoidal core to concentric repeated HREE and yttrium annuli in all crystals. This suggests that there was a discrete increase in the length scale of equilibration along the advancing garnet interface at some point in the growth history. However, there is no evidence for a coeval change in HREE transport thorough the intergranular network. Conversely, spiral core-to-rim zoning of chromium indicates the element remains almost completely immobile in the matrix over the duration of garnet growth.

  1. A consensus genetic map for Pinus taeda and Pinus elliottii and extent of linkage disequilibrium in two genotype-phenotype discovery populations of Pinua taeda

    Science.gov (United States)

    Jared W. Westbrook; Vikram E. Chhatre; Le-Shin Wu; Srikar Chamala; Leandro Gomide Neves; Patricio Munoz; Pedro J. Martinez-Garcia; David B. Neale; Matias Kirst; Keithanne Mockaitis; C. Dana Nelson; Gary F. Peter; John M. Davis; Craig S. Echt

    2015-01-01

    A consensus genetic map for Pinus taeda (loblolly pine) and Pinus elliottii (slash pine) was constructed by merging three previously published P. taeda maps with a map from a pseudo-backcross between P. elliottii and P. taeda. The consensus map positioned 3856 markers via...

  2. Using remote sensing to map larval and adult populations of Anopheles hyrcanus (Diptera: Culicidae a potential malaria vector in Southern France

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    Roger François

    2008-02-01

    Full Text Available Abstract Background Although malaria disappeared from southern France more than 60 years ago, suspicions of recent autochthonous transmission in the French Mediterranean coast support the idea that the area could still be subject to malaria transmission. The main potential vector of malaria in the Camargue area, the largest river delta in southern France, is the mosquito Anopheles hyrcanus (Diptera: Culicidae. In the context of recent climatic and landscape changes, the evaluation of the risk of emergence or re-emergence of such a major disease is of great importance in Europe. When assessing the risk of emergence of vector-borne diseases, it is crucial to be able to characterize the arthropod vector's spatial distribution. Given that remote sensing techniques can describe some of the environmental parameters which drive this distribution, satellite imagery or aerial photographs could be used for vector mapping. Results In this study, we propose a method to map larval and adult populations of An. hyrcanus based on environmental indices derived from high spatial resolution imagery. The analysis of the link between entomological field data on An. hyrcanus larvae and environmental indices (biotopes, distance to the nearest main productive breeding sites of this species i.e., rice fields led to the definition of a larval index, defined as the probability of observing An. hyrcanus larvae in a given site at least once over a year. Independent accuracy assessments showed a good agreement between observed and predicted values (sensitivity and specificity of the logistic regression model being 0.76 and 0.78, respectively. An adult index was derived from the larval index by averaging the larval index within a buffer around the trap location. This index was highly correlated with observed adult abundance values (Pearson r = 0.97, p An. hyrcanus larval and adult populations from the landscape indices. Conclusion This work shows that it is possible to use

  3. Mapping in an apple (Malus x domestica) F1 segregating population based on physical clustering of differentially expressed genes.

    Science.gov (United States)

    Jensen, Philip J; Fazio, Gennaro; Altman, Naomi; Praul, Craig; McNellis, Timothy W

    2014-04-04

    Apple tree breeding is slow and difficult due to long generation times, self-incompatibility, and complex genetics. The identification of molecular markers linked to traits of interest is a way to expedite the breeding process. In the present study, we aimed to identify genes whose steady-state transcript abundance was associated with inheritance of specific traits segregating in an apple (Malus × domestica) rootstock F1 breeding population, including resistance to powdery mildew (Podosphaera leucotricha) disease and woolly apple aphid (Eriosoma lanigerum). Transcription profiling was performed for 48 individual F1 apple trees from a cross of two highly heterozygous parents, using RNA isolated from healthy, actively-growing shoot tips and a custom apple DNA oligonucleotide microarray representing 26,000 unique transcripts. Genome-wide expression profiles were not clear indicators of powdery mildew or woolly apple aphid resistance phenotype. However, standard differential gene expression analysis between phenotypic groups of trees revealed relatively small sets of genes with trait-associated expression levels. For example, thirty genes were identified that were differentially expressed between trees resistant and susceptible to powdery mildew. Interestingly, the genes encoding twenty-four of these transcripts were physically clustered on chromosome 12. Similarly, seven genes were identified that were differentially expressed between trees resistant and susceptible to woolly apple aphid, and the genes encoding five of these transcripts were also clustered, this time on chromosome 17. In each case, the gene clusters were in the vicinity of previously identified major quantitative trait loci for the corresponding trait. Similar results were obtained for a series of molecular traits. Several of the differentially expressed genes were used to develop DNA polymorphism markers linked to powdery mildew disease and woolly apple aphid resistance. Gene expression profiling

  4. Review Article: Mapping of children's health and development data on population level using the classification system ICF-CY.

    Science.gov (United States)

    Ståhl, Ylva; Granlund, Mats; Gäre-Andersson, Boel; Enskär, Karin

    2011-02-01

    The aim of this study was to investigate if essential health and development data of all children in Sweden in the Child Health Service (CHS) and School Health Service (SHS) can be linked to the classification system International Classification of Functioning, Disability and Health--Children and Youth (ICF-CY). Lists of essential health terms, compiled by professionals from CHS and SHS, expected to be used in the national standardised records form the basis for the analysis in this study. The essential health terms have been linked to the codes of ICF-CY by using linking rules and a verification procedure. After exclusion of terms not directly describing children's health, a majority of the health terms could be linked into the ICF-CY with a high proportion of terms in body functions and a lower proportion in activity/participation and environment respectively. Some health terms had broad description and were linked to several ICF-CY codes. The precision of the health terms was at a medium level of detail. ICF-CY can be useful as a tool for documenting child health. It provides not only a code useful for statistical purposes but also a language useful for the CHS and SHS in their work on individual as well as population levels. It was noted that the health terms used by services mainly focused on health related to body function. This indicates that more focus is needed on health data related to child's functioning in everyday life situations.

  5. Genetic Diversity and Phenotypic Variation in an Introgression Line Population Derived from an Interspecific Cross between Oryza glaberrima and Oryza sativa.

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    Caijin Chen

    Full Text Available The introduction of closely related species genomic fragments is an effective way to enrich genetic diversity and creates new germplasms in crops. Here, we studied the genetic diversity of an introgression line (IL population composed of 106 ILs derived from an interspecific tetra cross between O. glaberrima and O. sativa (RAM3/Jin23B//Jin23B///YuetaiB. The proportion of O. glaberrima genome (PGG in the ILs ranged from 0.3% to 36.7%, with an average value of 12.32% which is close to the theoretically expected proportion. A total of 250 polymorphic alleles were amplified by 21 AFLP primer combinations with an average of 12 alleles per primer. Population structure analysis revealed that the IL population can be divided into four genetically distinct subpopulations. Both principal component analysis and neighbor-joining tree analysis showed that ILs with a higher PGG displayed greater genetic diversity. Canonical discriminant analysis identified six phenotypic traits (plant height, yield per plant, filled grain percentage, panicle length, panicle number and days to flowering as the main discriminatory traits among the ILs and between the subpopulations and showed significant phenotypic distances between subpopulations. The effects of PGG on phenotypic traits in the ILs were estimated using a linear admixed model, which showed a significant positive effect on grain yield per plant (0.286±0.117, plant height (0.418 ± 0.132, panicle length (0.663 ± 0.107, and spikelet number per panicle (0.339 ± 0.128, and a significant negative effect on filled grain percentage (-0.267 ± 0.123 and days to flowering (-0.324 ± 0.075. We found that an intermediate range (10% - 20% of PGG was more effective for producing ILs with favorable integrated agronomic traits. Our results confirm that construction of IL population carrying O. glaberrima genomic fragments could be an effective approach to increase the genetic diversity of O. sativa genome and an appropriate

  6. A microsatellite linkage map for Drosophila montana shows large variation in recombination rates, and a courtship song trait maps to an area of low recombination.

    Science.gov (United States)

    Schäfer, M A; Mazzi, D; Klappert, K; Kauranen, H; Vieira, J; Hoikkala, A; Ritchie, M G; Schlötterer, C

    2010-03-01

    Current advances in genetic analysis are opening up our knowledge of the genetics of species differences, but challenges remain, particularly for out-bred natural populations. We constructed a microsatellite-based linkage map for two out-bred lines of Drosophila montana derived from divergent populations by taking advantage of the Drosophila virilis genome and available cytological maps of both species. Although the placement of markers was quite consistent with cytological predictions, the map indicated large heterogeneity in recombination rates along chromosomes. We also performed a quantitative trait locus (QTL) analysis on a courtship song character (carrier frequency), which differs between populations and is subject to strong sexual selection. Linkage mapping yielded two significant QTLs, which explained 3% and 14% of the variation in carrier frequency, respectively. Interestingly, as in other recent studies of traits which can influence speciation, the strongest QTL mapped to a genomic region partly covered by an inversion polymorphism.

  7. Replication and fine mapping for association of the C2orf43, FOXP4, GPRC6A and RFX6 genes with prostate cancer in the Chinese population.

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    Qing-Zhi Long

    Full Text Available Prostate cancer represents the leading cause of male death across the world. A recent genome-wide association study (GWAS identified five novel susceptibility loci for prostate cancer in the Japanese population. This study is to replicate and fine map the potential association of these five loci with prostate cancer in the Chinese Han population.In Phase I of the study, we tested the five single nucleotide polymorphisms (SNPs which showed the strongest association evidence in the original GWAS in Japanese. The study sample consists of 1,169 Chinese Hans, comprising 483 patients and 686 healthy controls. Then in phase II, flanking SNPs of the successfully replicated SNPs in Phase I were genotyped and tested for association with prostate cancer to fine map those significant association signals.We successfully replicated the association of rs13385191 (located in the C2orf43 gene, P = 8.60×10(-5, rs12653946 (P = 1.33×10(-6, rs1983891 (FOXP4, P = 6.22×10(-5, and rs339331 (GPRC6A/RFX6, P = 1.42×10(-5 with prostate cancer. The most significant odds ratio (OR was recorded as 1.41 (95% confidence interval 1.18-1.68 for rs12653946. Rs9600079 did not show significant association (P = 8.07×10(-2 with prostate cancer in this study. The Phase II study refined these association signals, and identified several SNPs showing more significant association with prostate cancer than the very SNPs tested in Phase I.Our results provide further support for association of the C2orf43, FOXP4, GPRC6A and RFX6 genes with prostate cancer in Eastern Asian populations. This study also characterized the novel loci reported in the original GWAS with more details. Further work is still required to determine the functional variations and finally clarify the underlying biological mechanisms.

  8. Multiple sex-associated regions and a putative sex chromosome in zebrafish revealed by RAD mapping and population genomics.

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    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.

  9. Local genealogies in a linear mixed model for genome-wide association mapping in complex pedigreed populations.

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    Goutam Sahana

    Full Text Available INTRODUCTION: The state-of-the-art for dealing with multiple levels of relationship among the samples in genome-wide association studies (GWAS is unified mixed model analysis (MMA. This approach is very flexible, can be applied to both family-based and population-based samples, and can be extended to incorporate other effects in a straightforward and rigorous fashion. Here, we present a complementary approach, called 'GENMIX (genealogy based mixed model' which combines advantages from two powerful GWAS methods: genealogy-based haplotype grouping and MMA. SUBJECTS AND METHODS: We validated GENMIX using genotyping data of Danish Jersey cattle and simulated phenotype and compared to the MMA. We simulated scenarios for three levels of heritability (0.21, 0.34, and 0.64, seven levels of MAF (0.05, 0.10, 0.15, 0.20, 0.25, 0.35, and 0.45 and five levels of QTL effect (0.1, 0.2, 0.5, 0.7 and 1.0 in phenotypic standard deviation unit. Each of these 105 possible combinations (3 h(2 x 7 MAF x 5 effects of scenarios was replicated 25 times. RESULTS: GENMIX provides a better ranking of markers close to the causative locus' location. GENMIX outperformed MMA when the QTL effect was small and the MAF at the QTL was low. In scenarios where MAF was high or the QTL affecting the trait had a large effect both GENMIX and MMA performed similarly. CONCLUSION: In discovery studies, where high-ranking markers are identified and later examined in validation studies, we therefore expect GENMIX to enrich candidates brought to follow-up studies with true positives over false positives more than the MMA would.

  10. High resolution spatio-temporal mapping of NO2 pollution for estimating personal exposures of the Dutch population

    Science.gov (United States)

    Soenario, Ivan; Helbich, Marco; Schmitz, Oliver; Strak, Maciek; Hoek, Gerard; Karssenberg, Derek

    2017-04-01

    Air pollution has been associated with adverse health effects (e.g., cardiovascular and respiration diseases) in the urban environments. Therefore, the assessment of people's exposure to air pollution is central in epidemiological studies. The estimation of exposures on an individual level can be done by combining location information across space and over time with spatio-temporal data on air pollution concentrations. When detailed information on peoples' space-time paths (e.g. commuting patterns calculated by means of spatial routing algorithms or tracked through GPS) and peoples' major activity locations (e.g. home location, work location) are available, it is possible to calculate more precise personal exposure levels depending on peoples' individual space-time mobility patterns. This requires air pollution values not only at a high level of spatial accuracy and high temporal granularity but such data also needs to be available on a nation-wide scale. As current data is seriously limited in this respect, we introduce a novel data set of NO2 levels across the Netherlands. The provided NO2 concentrations are accessible on hourly timestamps on a 5 meter grid cell resolution for weekdays and weekends, and each month of the year. We modeled a single Land Use Regression model using a five year average of NO2 data from the Dutch NO2 measurement network consisting of N=46 sampling locations distributed over the country. Predictor variables for this model were selected in a data-driven manner using an Elastic Net and Best Subset Selection procedure from 70 candidate predictors including traffic, industry, infrastructure and population-based variables. Subsequently, to model NO2 for each time scale (hour, week, month), the LUR coefficients were fitted using the NO2 data, aggregated per time scale. Model validation was grounded on independent data collected in an ad hoc measurement campaign. Our results show a considerable difference in urban concentrations between

  11. A high-density consensus map of barley to compare the distribution of QTLs for partial resistance to Puccinia hordei and of defence gene homologues

    NARCIS (Netherlands)

    Marcel, T.C.; Varshney, R.K.; Barbieri, M.; Jafary, H.; Kock, de M.J.D.; Graner, A.; Niks, R.E.

    2007-01-01

    A consensus map of barley was constructed based on three reference doubled haploid (DH) populations and three recombinant inbred line (RIL) populations. Several sets of microsatellites were used as bridge markers in the integration of those populations previously genotyped with RFLP or with AFLP

  12. QTLs for agronomic traits in the Mediterranean environment identified in recombinant inbred lines of the cross 'Arta' × ¤H. spontaneum¤ 41-1

    DEFF Research Database (Denmark)

    Baum, M.; Grando, S.; Backes, G.

    2003-01-01

    A genetic linkage map has been developed for recombinant inbred lines (RILs) of the cross 'Arta' x Hordeum spontaneum 41-1. One hundred and ninety four RILs, randomly chosen from a population of 494 RILs, were mapped with 189 markers including one morphological trait (btr = brittle rachis locus...

  13. Development and Genetic Characterization of Advanced Backcross Materials and An Introgression Line Population of Solanum incanum in a S. melongena Background

    Directory of Open Access Journals (Sweden)

    Pietro Gramazio

    2017-08-01

    Full Text Available Advanced backcrosses (ABs and introgression lines (ILs of eggplant (Solanum melongena can speed up genetics and genomics studies and breeding in this crop. We have developed the first full set of ABs and ILs in eggplant using Solanum incanum, a wild eggplant that has a relatively high tolerance to drought, as a donor parent. The development of these ABs and IL eggplant populations had a low efficiency in the early stages, because of the lack of molecular markers and genomic tools. However, this dramatically improved after performing genotyping-by-sequencing in the first round of selfing, followed by high-resolution-melting single nucleotide polymorphism genotyping in subsequent selection steps. A set of 73 selected ABs covered 99% of the S. incanum genome, while 25 fixed immortal ILs, each carrying a single introgressed fragment in homozygosis, altogether spanned 61.7% of the S. incanum genome. The introgressed size fragment in the ILs contained between 0.1 and 10.9% of the S. incanum genome, with a mean value of 4.3%. Sixty-eight candidate genes involved in drought tolerance were identified in the set of ILs. This first set of ABs and ILs of eggplant will be extremely useful for the genetic dissection of traits of interest for eggplant, and represents an elite material for introduction into the breeding pipelines for developing new eggplant cultivars adapted to the challenges posed by the climate-change scenario.

  14. Quantitative trait loci mapping of western corn rootworm (Coleoptera: Chrysomelidae) host plant resistance in two populations of doubled haploid lines in maize (Zea mays L.)

    Science.gov (United States)

    Over the last 70 years, more than 12,000 maize accessions have been screened for their level of resistance to western corn rootworm, Diabrotica virgifera virgifera LeConte, larval feeding. Less than 1% of this germplasm was selected for initiating recurrent selection or other breeding programs. Sele...

  15. Crop characteristics and weed Interactions of diverse Rrecurrent Inbred Lines (RILs) from a weed-suppressive x non-suppressive rice mapping population

    Science.gov (United States)

    ndica rice genotypes with enhanced weed suppression traits have been previously identified as potentially useful in supplementing weed control efforts in drill-seeded systems in the southern USA. A particularly weed-suppressive indica genotype (PI 312777) that was also high tillering and high yield...

  16. Genetic Analysis of Recombinant Inbred Lines for Sorghum bicolor ? Sorghum propinquum

    OpenAIRE

    Kong, Wenqian; Jin, Huizhe; Franks, Cleve D.; Kim, Changsoo; Bandopadhyay, Rajib; Rana, Mukesh K.; Auckland, Susan A.; Goff, Valorie H.; Rainville, Lisa K.; Burow, Gloria B.; Woodfin, Charles; Burke, John J.; Paterson, Andrew H.

    2013-01-01

    We describe a recombinant inbred line (RIL) population of 161 F5 genotypes for the widest euploid cross that can be made to cultivated sorghum (Sorghum bicolor) using conventional techniques, S. bicolor ? Sorghum propinquum, that segregates for many traits related to plant architecture, growth and development, reproduction, and life history. The genetic map of the S. bicolor ? S. propinquum RILs contains 141 loci on 10 linkage groups collectively spanning 773.1 cM. Although the genetic map ha...

  17. Mapping of QTL on chromosomes 1, 2, 3, 12, 14, 15 and X in pigs: characteristics carcass and quality of meat

    NARCIS (Netherlands)

    Paixao, D.M.; Carneiro, P.L.S.; Paiva, S.R.; Sousa, K.R.S.; Verardo, L.L.; Braccini Neto, J.; Pinto, A.P.G.; Marubayashi Hidalgo, A.; Nascimento, C.; Périssé, I.V.; Lopes, P.S.; Guimaraes, S.E.F.

    2012-01-01

    The accomplishment of the present study had as objective to map Quantitative Trait Loci (QTL) associated to carcass and quality traits in a F2 pig population developed by mating two Brazilian Piau breed sires with 18 dams from a commercial line (Landrace × Large White × Pietrain). The linkage map

  18. Trans-ethnic fine-mapping of lipid loci identifies population-specific signals and allelic heterogeneity that increases the trait variance explained.

    Directory of Open Access Journals (Sweden)

    Ying Wu

    2013-03-01

    Full Text Available Genome-wide association studies (GWAS have identified ~100 loci associated with blood lipid levels, but much of the trait heritability remains unexplained, and at most loci the identities of the trait-influencing variants remain unknown. We conducted a trans-ethnic fine-mapping study at 18, 22, and 18 GWAS loci on the Metabochip for their association with triglycerides (TG, high-density lipoprotein cholesterol (HDL-C, and low-density lipoprotein cholesterol (LDL-C, respectively, in individuals of African American (n = 6,832, East Asian (n = 9,449, and European (n = 10,829 ancestry. We aimed to identify the variants with strongest association at each locus, identify additional and population-specific signals, refine association signals, and assess the relative significance of previously described functional variants. Among the 58 loci, 33 exhibited evidence of association at P<1 × 10(-4 in at least one ancestry group. Sequential conditional analyses revealed that ten, nine, and four loci in African Americans, Europeans, and East Asians, respectively, exhibited two or more signals. At these loci, accounting for all signals led to a 1.3- to 1.8-fold increase in the explained phenotypic variance compared to the strongest signals. Distinct signals across ancestry groups were identified at PCSK9 and APOA5. Trans-ethnic analyses narrowed the signals to smaller sets of variants at GCKR, PPP1R3B, ABO, LCAT, and ABCA1. Of 27 variants reported previously to have functional effects, 74% exhibited the strongest association at the respective signal. In conclusion, trans-ethnic high-density genotyping and analysis confirm the presence of allelic heterogeneity, allow the identification of population-specific variants, and limit the number of candidate SNPs for functional studies.

  19. Genome-wide association mapping identifies the genetic basis of discrete and quantitative variation in sexual weaponry in a wild sheep population.

    Science.gov (United States)

    Johnston, Susan E; McEwan, John C; Pickering, Natalie K; Kijas, James W; Beraldi, Dario; Pilkington, Jill G; Pemberton, Josephine M; Slate, Jon

    2011-06-01

    Understanding the genetic architecture of phenotypic variation in natural populations is a fundamental goal of evolutionary genetics. Wild Soay sheep (Ovis aries) have an inherited polymorphism for horn morphology in both sexes, controlled by a single autosomal locus, Horns. The majority of males have large normal horns, but a small number have vestigial, deformed horns, known as scurs; females have either normal horns, scurs or no horns (polled). Given that scurred males and polled females have reduced fitness within each sex, it is counterintuitive that the polymorphism persists within the population. Therefore, identifying the genetic basis of horn type will provide a vital foundation for understanding why the different morphs are maintained in the face of natural selection. We conducted a genome-wide association study using ∼36000 single nucleotide polymorphisms (SNPs) and determined the main candidate for Horns as RXFP2, an autosomal gene with a known involvement in determining primary sex characters in humans and mice. Evidence from additional SNPs in and around RXFP2 supports a new model of horn-type inheritance in Soay sheep, and for the first time, sheep with the same horn phenotype but different underlying genotypes can be identified. In addition, RXFP2 was shown to be an additive quantitative trait locus (QTL) for horn size in normal-horned males, accounting for up to 76% of additive genetic variation in this trait. This finding contrasts markedly from genome-wide association studies of quantitative traits in humans and some model species, where it is often observed that mapped loci only explain a modest proportion of the overall genetic variation. © 2011 Blackwell Publishing Ltd.

  20. Zero-inflated Poisson regression models for QTL mapping applied to tick-resistance in a Gyr x Holstein F2 population

    Directory of Open Access Journals (Sweden)

    Fabyano Fonseca Silva

    2011-01-01

    Full Text Available Nowadays, an important and interesting alternative in the control of tick-infestation in cattle is to select resistant animals, and identify the respective quantitative trait loci (QTLs and DNA markers, for posterior use in breeding programs. The number of ticks/animal is characterized as a discrete-counting trait, which could potentially follow Poisson distribution. However, in the case of an excess of zeros, due to the occurrence of several noninfected animals, zero-inflated Poisson and generalized zero-inflated distribution (GZIP may provide a better description of the data. Thus, the objective here was to compare through simulation, Poisson and ZIP models (simple and generalized with classical approaches, for QTL mapping with counting phenotypes under different scenarios, and to apply these approaches to a QTL study of tick resistance in an F2 cattle (Gyr x Holstein population. It was concluded that, when working with zero-inflated data, it is recommendable to use the generalized and simple ZIP model for analysis. On the other hand, when working with data with zeros, but not zero-inflated, the Poisson model or a data-transformation-approach, such as square-root or Box-Cox transformation, are applicable.

  1. Zero-inflated Poisson regression models for QTL mapping applied to tick-resistance in a Gyr × Holstein F2 population

    Science.gov (United States)

    Silva, Fabyano Fonseca; Tunin, Karen P.; Rosa, Guilherme J.M.; da Silva, Marcos V.B.; Azevedo, Ana Luisa Souza; da Silva Verneque, Rui; Machado, Marco Antonio; Packer, Irineu Umberto

    2011-01-01

    Now a days, an important and interesting alternative in the control of tick-infestation in cattle is to select resistant animals, and identify the respective quantitative trait loci (QTLs) and DNA markers, for posterior use in breeding programs. The number of ticks/animal is characterized as a discrete-counting trait, which could potentially follow Poisson distribution. However, in the case of an excess of zeros, due to the occurrence of several noninfected animals, zero-inflated Poisson and generalized zero-inflated distribution (GZIP) may provide a better description of the data. Thus, the objective here was to compare through simulation, Poisson and ZIP models (simple and generalized) with classical approaches, for QTL mapping with counting phenotypes under different scenarios, and to apply these approaches to a QTL study of tick resistance in an F2 cattle (Gyr × Holstein) population. It was concluded that, when working with zero-inflated data, it is recommendable to use the generalized and simple ZIP model for analysis. On the other hand, when working with data with zeros, but not zero-inflated, the Poisson model or a data-transformation-approach, such as square-root or Box-Cox transformation, are applicable. PMID:22215960

  2. IMPLEMENTASI POPULATION RESIZING ON FITNESS IMPROVEMENT GENETIC ALGORITHM (PROFIGA UNTUK OPTIMASI RUTE KUNJUNGAN PROMOSI UNIVERSITAS MURIA KUDUS BERBASIS ANDROID DAN GOOGLE MAPS API

    Directory of Open Access Journals (Sweden)

    Tri Listyorini

    2016-04-01

    Full Text Available Tim Promosi Universitas Muria Kudus (UMK melakukan kunjungan promosi ke sekolah menengah atas pada setiap tahun. Kunjungan tersebut dilakukan ke sekolah-sekolah menengah atas di wilayah Kudus, Jepara, Pati, Demak, Rembang dan Purwodadi. Untuk memudahkan kunjungan, setiap kunjungan dibatasi sekitar 15 (lima belas sekolah. Namun pada saat melakukan kunjungan, tim tersebut mengalami kesulitan dalam menentukan rute kunjungan sekolah. Hal ini dikarenakan jarak sekolah yang dikunjungi cukup jauh atau memiliki rute yang rumit sehingga menyebabkan waktu kunjungan yang molor dan biaya pengeluaran bahan bakar yang cukup boros. Untuk menyelesaikan masalah tersebut, dikembangkan suatu aplikasi menggunakan metode heuristik algoritma genetika dengan dinamisasi ukuran populasi atau Population Resizing on Fitness Improvement Genetic Algorithm (PRoFIGA. Aplikasi dikembangkan dengan basis android digunakan untuk memudahkan mencari rute kunjungan terpendek bagi tim promosi UMK sehingga waktu kunjungan menjadi efektif dan efisien. Hasil dari penelitian adalah aplikasi berbasis android untuk penentuan rute kunjungan sekolah terpendek menggunakan metode heuristik yang efisien dan efektif yang dikombinasikan dengan Google Maps Application Programming Interface (API untuk display rute kunjungan sehingga lebih memudahkan bagi tim promosi UMK. Kata kunci: optimasi rute kunjungan, algoritma fuzzy evolusi, optimasi rute android.

  3. Rationale and development of an on-line quality assurance programme for colposcopy in a population-based cervical screening setting in Italy

    Science.gov (United States)

    2013-01-01

    Background Colposcopy, the key step in the management of women with abnormal Pap smear results, is a visual technique prone to observer variation, which implies the need for prolonged apprenticeship, continuous training, and quality assurance (QA) measures. Colposcopy QA programmes vary in level of responsibility of organizing subjects, geographic coverage, scope, model, and type of actions. The programmes addressing the clinical standards of colposcopy (quality of examination and appropriateness of clinical decisions) are more limited in space and less sustainable over time than those focused on the provision of the service (resources, accessibility, etc.). This article reports on the protocol of a QA programme targeting the clinical quality of colposcopy in a population-based cervical screening service in an administrative region of northern Italy. Methods/design After a situation analysis of local colposcopy audit practices and previous QA initiatives, a permanent web-based QA programme was developed. The design places more emphasis on providing education and feedback to participants than on testing them. The technical core is a log-in web application accessible on the website of the regional Administration. The primary objectives are to provide (1) a practical opportunity for retraining of screening colposcopists, and (2) a platform for them to interact with colposcopists from other settings and regions through exchange and discussion of digital colposcopic images. The retraining function is based on repeated QA sessions in which the registered colposcopists log-in, classify a posted set of colpophotographs, and receive on line a set of personal feedback data. Each session ends with a plenary seminar featuring the presentation of overall results and an interactive review of the test set of colpophotographs. This is meant to be a forum for an open exchange of views that may lead to more knowledge and more diagnostic homogeneity. The protocol includes the

  4. Rationale and development of an on-line quality assurance programme for colposcopy in a population-based cervical screening setting in Italy.

    Science.gov (United States)

    Bucchi, Lauro; Cristiani, Paolo; Costa, Silvano; Schincaglia, Patrizia; Garutti, Paola; Sassoli de Bianchi, Priscilla; Naldoni, Carlo; Olea, Oswaldo; Sideri, Mario

    2013-06-28

    Colposcopy, the key step in the management of women with abnormal Pap smear results, is a visual technique prone to observer variation, which implies the need for prolonged apprenticeship, continuous training, and quality assurance (QA) measures. Colposcopy QA programmes vary in level of responsibility of organizing subjects, geographic coverage, scope, model, and type of actions. The programmes addressing the clinical standards of colposcopy (quality of examination and appropriateness of clinical decisions) are more limited in space and less sustainable over time than those focused on the provision of the service (resources, accessibility, etc.). This article reports on the protocol of a QA programme targeting the clinical quality of colposcopy in a population-based cervical screening service in an administrative region of northern Italy. After a situation analysis of local colposcopy audit practices and previous QA initiatives, a permanent web-based QA programme was developed. The design places more emphasis on providing education and feedback to participants than on testing them. The technical core is a log-in web application accessible on the website of the regional Administration. The primary objectives are to provide (1) a practical opportunity for retraining of screening colposcopists, and (2) a platform for them to interact with colposcopists from other settings and regions through exchange and discussion of digital colposcopic images. The retraining function is based on repeated QA sessions in which the registered colposcopists log-in, classify a posted set of colpophotographs, and receive on line a set of personal feedback data. Each session ends with a plenary seminar featuring the presentation of overall results and an interactive review of the test set of colpophotographs. This is meant to be a forum for an open exchange of views that may lead to more knowledge and more diagnostic homogeneity. The protocol includes the criteria for selection of

  5. Analysis of some coplanar transmission lines: coplanar coupled lines, coplanar coupled striplines, and coplanar coupled lines with rectangular microshield

    Science.gov (United States)

    Yuan, Naichang; He, Jianguo; Yao, Demiao; Dai, Qin; Lin, Weigan

    1995-06-01

    Two types of coplanar transmission lines, rectangular microshield coplanar coupled lines (RMCCL) and coplanar coupled rectangular microshield lines (CCRML), are proposed for MMIC applications. These are developed from coplanar coupled lines (CCL) and coplanar coupled strip lines (CCS). Analytic formulas are presented for calculating the quasistatic TEM parameters of these coupled lines by means of exact conformal mapping techniques. Numerical results are also presented to illustrate the properties of these coplanar transmission lines.

  6. Map of Nasca Geoglyphs

    Science.gov (United States)

    Hanzalová, K.; Pavelka, K.

    2013-07-01

    The Czech Technical University in Prague in the cooperation with the University of Applied Sciences in Dresden (Germany) work on the Nasca Project. The cooperation started in 2004 and much work has been done since then. All work is connected with Nasca lines in southern Peru. The Nasca project started in 1995 and its main target is documentation and conservation of the Nasca lines. Most of the project results are presented as WebGIS application via Internet. In the face of the impending destruction of the soil drawings, it is possible to preserve this world cultural heritage for the posterity at least in a digital form. Creating of Nasca lines map is very useful. The map is in a digital form and it is also available as a paper map. The map contains planimetric component of the map, map lettering and altimetry. Thematic folder in this map is a vector layer of the geoglyphs in Nasca/Peru. Basis for planimetry are georeferenced satellite images, altimetry is created from digital elevation model. This map was created in ArcGis software.

  7. MAP OF NASCA GEOGLYPHS

    Directory of Open Access Journals (Sweden)

    K. Hanzalová

    2013-07-01

    Full Text Available The Czech Technical University in Prague in the cooperation with the University of Applied Sciences in Dresden (Germany work on the Nasca Project. The cooperation started in 2004 and much work has been done since then. All work is connected with Nasca lines in southern Peru. The Nasca project started in 1995 and its main target is documentation and conservation of the Nasca lines. Most of the project results are presented as WebGIS application via Internet. In the face of the impending destruction of the soil drawings, it is possible to preserve this world cultural heritage for the posterity at least in a digital form. Creating of Nasca lines map is very useful. The map is in a digital form and it is also available as a paper map. The map contains planimetric component of the map, map lettering and altimetry. Thematic folder in this map is a vector layer of the geoglyphs in Nasca/Peru. Basis for planimetry are georeferenced satellite images, altimetry is created from digital elevation model. This map was created in ArcGis software.

  8. Drawing subway maps : a survey

    NARCIS (Netherlands)

    Wolff, A.

    2007-01-01

    This paper deals with automating the drawing of subway maps. There are two features of schematic subway maps that make them different from drawings of other networks such as flow charts or organigrams. First, most schematic subway maps use not only horizontal and vertical lines, but also diagonals.

  9. A spatially encoded dose difference maximal intensity projection map for patient dose evaluation: A new first line patient quality assurance tool

    Energy Technology Data Exchange (ETDEWEB)

    Hu Weigang; Graff, Pierre; Boettger, Thomas; Pouliot, Jean [Department of Radiation Oncology, University of California, San Francisco, San Francisco, California 94143 (United States); and others

    2011-04-15

    Purpose: To develop a spatially encoded dose difference maximal intensity projection (DD-MIP) as an online patient dose evaluation tool for visualizing the dose differences between the planning dose and dose on the treatment day. Methods: Megavoltage cone-beam CT (MVCBCT) images acquired on the treatment day are used for generating the dose difference index. Each index is represented by different colors for underdose, acceptable, and overdose regions. A maximal intensity projection (MIP) algorithm is developed to compress all the information of an arbitrary 3D dose difference index into a 2D DD-MIP image. In such an algorithm, a distance transformation is generated based on the planning CT. Then, two new volumes representing the overdose and underdose regions of the dose difference index are encoded with the distance transformation map. The distance-encoded indices of each volume are normalized using the skin distance obtained on the planning CT. After that, two MIPs are generated based on the underdose and overdose volumes with green-to-blue and green-to-red lookup tables, respectively. Finally, the two MIPs are merged with an appropriate transparency level and rendered in planning CT images. Results: The spatially encoded DD-MIP was implemented in a dose-guided radiotherapy prototype and tested on 33 MVCBCT images from six patients. The user can easily establish the threshold for the overdose and underdose. A 3% difference between the treatment and planning dose was used as the threshold in the study; hence, the DD-MIP shows red or blue color for the dose difference >3% or {<=}3%, respectively. With such a method, the overdose and underdose regions can be visualized and distinguished without being overshadowed by superficial dose differences. Conclusions: A DD-MIP algorithm was developed that compresses information from 3D into a single or two orthogonal projections while hinting the user whether the dose difference is on the skin surface or deeper.

  10. A spatially encoded dose difference maximal intensity projection map for patient dose evaluation: a new first line patient quality assurance tool.

    Science.gov (United States)

    Hu, Weigang; Graff, Pierre; Boettger, Thomas; Pouliot, Jean

    2011-04-01

    To develop a spatially encoded dose difference maximal intensity projection (DD-MIP) as an online patient dose evaluation tool for visualizing the dose differences between the planning dose and dose on the treatment day. Megavoltage cone-beam CT (MVCBCT) images acquired on the treatment day are used for generating the dose difference index. Each index is represented by different colors for underdose, acceptable, and overdose regions. A maximal intensity projection (MIP) algorithm is developed to compress all the information of an arbitrary 3D dose difference index into a 2D DD-MIP image. In such an algorithm, a distance transformation is generated based on the planning CT. Then, two new volumes representing the overdose and underdose regions of the dose difference index are encoded with the distance transformation map. The distance-encoded indices of each volume are normalized using the skin distance obtained on the planning CT. After that, two MIPs are generated based on the underdose and overdose volumes with green-to-blue and green-to-red lookup tables, respectively. Finally, the two MIPs are merged with an appropriate transparency level and rendered in planning CT images. The spatially encoded DD-MIP was implemented in a dose-guided radiotherapy prototype and tested on 33 MVCBCT images from six patients. The user can easily establish the threshold for the overdose and underdose. A 3% difference between the treatment and planning dose was used as the threshold in the study; hence, the DD-MIP shows red or blue color for the dose difference > 3% or < or = 3%, respectively. With such a method, the overdose and underdose regions can be visualized and distinguished without being overshadowed by superficial dose differences. A DD-MIP algorithm was developed that compresses information from 3D into a single or two orthogonal projections while hinting the user whether the dose difference is on the skin surface or deeper.

  11. Mapping quantitative trait loci affecting fatness and breast muscle weight in meat-type chicken lines divergently selected on abdominal fatness

    Directory of Open Access Journals (Sweden)

    Neau André

    2006-01-01

    Full Text Available Abstract Quantitative trait loci (QTL for abdominal fatness and breast muscle weight were investigated in a three-generation design performed by inter-crossing two experimental meat-type chicken lines that were divergently selected on abdominal fatness. A total of 585 F2 male offspring from 5 F1 sires and 38 F1 dams were recorded at 8 weeks of age for live body, abdominal fat and breast muscle weights. One hundred-twenty nine microsatellite markers, evenly located throughout the genome and heterozygous for most of the F1 sires, were used for genotyping the F2 birds. In each sire family, those offspring exhibiting the most extreme values for each trait were genotyped. Multipoint QTL analyses using maximum likelihood methods were performed for abdominal fat and breast muscle weights, which were corrected for the effects of 8-week body weight, dam and hatching group. Isolated markers were assessed by analyses of variance. Two significant QTL were identified on chromosomes 1 and 5 with effects of about one within-family residual standard deviation. One breast muscle QTL was identified on GGA1 with an effect of 2.0 within-family residual standard deviation.

  12. Digital Line Graphs (DLG) 24K

    Data.gov (United States)

    Kansas Data Access and Support Center — Digital line graph (DLG) data are digital representations of cartographic information. DLG's of map features are converted to digital form from maps and related...

  13. Digital Line Graphs (DLG) 100K

    Data.gov (United States)

    Kansas Data Access and Support Center — Digital line graph (DLG) data are digital representations of cartographic information. DLG's of map features are converted to digital form from maps and related...

  14. How to perform RT-qPCR accurately in plant species? A case study on flower colour gene expression in an azalea (Rhododendron simsii hybrids) mapping population.

    Science.gov (United States)

    De Keyser, Ellen; Desmet, Laurence; Van Bockstaele, Erik; De Riek, Jan

    2013-06-24

    Flower colour variation is one of the most crucial selection criteria in the breeding of a flowering pot plant, as is also the case for azalea (Rhododendron simsii hybrids). Flavonoid biosynthesis was studied intensively in several species. In azalea, flower colour can be described by means of a 3-gene model. However, this model does not clarify pink-coloration. The last decade gene expression studies have been implemented widely for studying flower colour. However, the methods used were often only semi-quantitative or quantification was not done according to the MIQE-guidelines. We aimed to develop an accurate protocol for RT-qPCR and to validate the protocol to study flower colour in an azalea mapping population. An accurate RT-qPCR protocol had to be established. RNA quality was evaluated in a combined approach by means of different techniques e.g. SPUD-assay and Experion-analysis. We demonstrated the importance of testing noRT-samples for all genes under study to detect contaminating DNA. In spite of the limited sequence information available, we prepared a set of 11 reference genes which was validated in flower petals; a combination of three reference genes was most optimal. Finally we also used plasmids for the construction of standard curves. This allowed us to calculate gene-specific PCR efficiencies for every gene to assure an accurate quantification. The validity of the protocol was demonstrated by means of the study of six genes of the flavonoid biosynthesis pathway. No correlations were found between flower colour and the individual expression profiles. However, the combination of early pathway genes (CHS, F3H, F3'H and FLS) is clearly related to co-pigmentation with flavonols. The late pathway genes DFR and ANS are to a minor extent involved in differentiating between coloured and white flowers. Concerning pink coloration, we could demonstrate that the lower intensity in this type of flowers is correlated to the expression of F3'H. Currently in plant

  15. Exploring the power of rice (O. sativa x O. rufipogon) chromosome segment substitution line libraries

    Science.gov (United States)

    Transgressive variation was reported as an increase in grain yield for several rice (Oryza sativa x O. rufipogon) advanced backcross mapping populations. The objective of this study was to develop chromosome segment substitution line (CSSL) libraries to further dissect the reported transgressive var...

  16. Absorption-line strengths of 18 late-type spiral galaxies observed with SAURON

    NARCIS (Netherlands)

    Ganda, Katia; Peletier, Reynier F.; McDermid, Richard M.; Falcon-Barroso, Jesus; de Zeeuw, P. T.; Bacon, Roland; Cappellari, Michele; Davies, Roger L.; Emsellem, Eric; Krajnovic, Davor; Kuntschner, Harald; Sarzi, Marc; van de Ven, Glenn

    2007-01-01

    We present absorption line strength maps for a sample of 18 Sb-Sd galaxies observed using the integral-field spectrograph SAURON operating at the William Herschel Telescope on La Palma, as part of a project devoted to the investigation of the kinematics and stellar populations of late-type spirals,

  17. Mapping Mammalian Cell-type-specific Transcriptional Regulatory Networks Using KD-CAGE and ChIP-seq Data in the TC-YIK Cell Line

    Science.gov (United States)

    Lizio, Marina; Ishizu, Yuri; Itoh, Masayoshi; Lassmann, Timo; Hasegawa, Akira; Kubosaki, Atsutaka; Severin, Jessica; Kawaji, Hideya; Nakamura, Yukio; Suzuki, Harukazu; Hayashizaki, Yoshihide; Carninci, Piero; Forrest, Alistair R. R.

    2015-01-01

    Mammals are composed of hundreds of different cell types with specialized functions. Each of these cellular phenotypes are controlled by different combinations of transcription factors. Using a human non islet cell insulinoma cell line (TC-YIK) which expresses insulin and the majority of known pancreatic beta cell specific genes as an example, we describe a general approach to identify key cell-type-specific transcription factors (TFs) and their direct and indirect targets. By ranking all human TFs by their level of enriched expression in TC-YIK relative to a broad collection of samples (FANTOM5), we confirmed known key regulators of pancreatic function and development. Systematic siRNA mediated perturbation of these TFs followed by qRT-PCR revealed their interconnections with NEUROD1 at the top of the regulation hierarchy and its depletion drastically reducing insulin levels. For 15 of the TF knock-downs (KD), we then used Cap Analysis of Gene Expression (CAGE) to identify thousands of their targets genome-wide (KD-CAGE). The data confirm NEUROD1 as a key positive regulator in the transcriptional regulatory network (TRN), and ISL1, and PROX1 as antagonists. As a complimentary approach we used ChIP-seq on four of these factors to identify NEUROD1, LMX1A, PAX6, and RFX6 binding sites in the human genome. Examining the overlap between genes perturbed in the KD-CAGE experiments and genes with a ChIP-seq peak within 50 kb of their promoter, we identified direct transcriptional targets of these TFs. Integration of KD-CAGE and ChIP-seq data shows that both NEUROD1 and LMX1A work as the main transcriptional activators. In the core TRN (i.e., TF-TF only), NEUROD1 directly transcriptionally activates the pancreatic TFs HSF4, INSM1, MLXIPL, MYT1, NKX6-3, ONECUT2, PAX4, PROX1, RFX6, ST18, DACH1, and SHOX2, while LMX1A directly transcriptionally activates DACH1, SHOX2, PAX6, and PDX1. Analysis of these complementary datasets suggests the need for caution in interpreting Ch

  18. Characterization of the RAPD for 6 Durum wheat lines (Triticum durum desf.) selected from M4-irradiated population under drought conditions

    International Nuclear Information System (INIS)

    Kalil, M.K.; Nesiem, M.R.A.; Kassem, M.K.M.; Basyouny, M.A.E.

    2012-01-01

    Grains of two durum wheat cultivars Sohag 3 and Beni Suef 3 were irradiated with different doses of gamma ray 0, 150, 250 and 350 Gy to obtain new durum wheat lines characterized by high yielding and drought tolerance. Irradiated grins were cultivated in the field under normal and drought conditions during 2005-2009 Results of field experiments showed that there were new six putative lines S1, S2, S3, S4, B1 and B2. Each putative line had superiority than its parent in grain yield / plant. The putative lines S1 and S2 had superiority over their parent Sohag 3 under normal conditions in grain yield per plant this increase equal 52 and 60% respectively. The putative lines S3 and S4 had superiority in grain yield per plan as compared to Sohag 3 under drought conditions this increase equal 75 to 58% respectively. The putative lines B1 and B2 had superiority in grain yield per plant than their parent Beni Suef 3 under normal condition this increase equal 46 and 12% respectively. Results for RAPD markers showed that each putative line was characterized by positive and negative unique marker. The putative line S1: characterized by four negative marker amplified by OPM-05, OPN-04, OPA-18 and OPB-12 primers. The putative line S2: characterized by one negative unique marker amplified by OPQ-14 marker. The putative line S3: characterized by two positive markers amplified by OPB-07 and OPG-12 markers and one negative unique marker amplified by OPA-10 marker. The putative line S4: characterized by four negative markers amplified by OPM-05, OPN-13, OPQ-12 and OPQ-14 markers and one positive unique marker amplified by OPC-05 marker. The putative line B1: characterized by four positive markers amplified by OPA-10, OPG-12, OPB-07 and OPA-18 markers and three negative markers amplified with OPM-05, OPC-05 and OPB-12 markers. The putative line B2: characterized by three positive unique marker amplified by OPB-07, OPN-04, OPN-10 markers and four negative markers amplified with OPA-10

  19. Base Flood Elevation (BFE) Lines

    Data.gov (United States)

    Department of Homeland Security — The Base Flood Elevation (BFE) table is required for any digital data where BFE lines will be shown on the corresponding Flood Insurance Rate Map (FIRM). Normally if...

  20. Shortest-paths preserving metro maps

    NARCIS (Netherlands)

    Milea, T.Y.; Schrijvers, O.J.; Buchin, K.; Haverkort, H.J.; Kreveld, van M.J.; Speckmann, B.

    2012-01-01

    A metro map, or subway map, is a schematic representation of a metro system of a city. The main goal of a metro map is to provide a traveler with information on which lines to take to get from station A to station B, and at which stations he needs to switch lines. It is often not beneficial to use

  1. System of automated map design

    International Nuclear Information System (INIS)

    Ponomarjov, S.Yu.; Rybalko, S.I.; Proskura, N.I.

    1992-01-01

    Preprint 'System of automated map design' contains information about the program shell for construction of territory map, performing level line drawing of arbitrary two-dimension field (in particular, the radionuclide concentration field). The work schedule and data structures are supplied, as well as data on system performance. The preprint can become useful for experts in radioecology and for all persons involved in territory pollution mapping or multi-purpose geochemical mapping. (author)

  2. Comparison of gene-based rare variant association mapping methods for quantitative traits in a bovine population with complex familial relationships

    NARCIS (Netherlands)

    Zhang, Qianqian; Guldbrandtsen, Bernt; Calus, Mario P.L.; Lund, Mogens Sandø; Sahana, Goutam

    2016-01-01

    Background: There is growing interest in the role of rare variants in the variation of complex traits due to increasing evidence that rare variants are associated with quantitative traits. However, association methods that are commonly used for mapping common variants are not effective to map

  3. Combined linkage and association mapping of flowering time in Sunflower (Helianthus annuus L.).

    Science.gov (United States)

    Cadic, Elena; Coque, Marie; Vear, Felicity; Grezes-Besset, Bruno; Pauquet, Jerôme; Piquemal, Joël; Lippi, Yannick; Blanchard, Philippe; Romestant, Michel; Pouilly, Nicolas; Rengel, David; Gouzy, Jerôme; Langlade, Nicolas; Mangin, Brigitte; Vincourt, Patrick

    2013-05-01

    Association mapping and linkage mapping were used to identify quantitative trait loci (QTL) and/or causative mutations involved in the control of flowering time in cultivated sunflower Helianthus annuus. A panel of 384 inbred lines was phenotyped through testcrosses with two tester inbred lines across 15 location × year combinations. A recombinant inbred line (RIL) population comprising 273 lines was phenotyped both per se and through testcrosses with one or two testers in 16 location × year combinations. In the association mapping approach, kinship estimation using 5,923 single nucleotide polymorphisms was found to be the best covariate to correct for effects of panel structure. Linkage disequilibrium decay ranged from 0.08 to 0.26 cM for a threshold of 0.20, after correcting for structure effects, depending on the linkage group (LG) and the ancestry of inbred lines. A possible hitchhiking effect is hypothesized for LG10 and LG08. A total of 11 regions across 10 LGs were found to be associated with flowering time, and QTLs were mapped on 11 LGs in the RIL population. Whereas eight regions were demonstrated to be common between the two approaches, the linkage disequilibrium approach did not detect a documented QTL that was confirmed using the linkage mapping approach.

  4. TIGER/Line Shapefile, 2010, Series Information File for the 2010 Census Block State-based Shapefile with Housing and Population Data

    Data.gov (United States)

    US Census Bureau, Department of Commerce — The TIGER/Line Files are shapefiles and related database files (.dbf) that are an extract of selected geographic and cartographic information from the U.S. Census...

  5. Study the chemical composition and agronomic traits for some durum wheat lines (Triticum durum) selected from M4-irradiated populations under drought stress

    International Nuclear Information System (INIS)

    Khalil, M.K.; Nesiem, M.R.A.; Kasem, M.K.M.; Basyouny, M.A.E.

    2010-01-01

    Field and laboratory experiments were carried out during four successive seasons 2005-2009 to access the effectiveness of gamma rays on inducing new drought tolerance lines from two durum wheat cultivars, i.e. Sohag 3 and Beni Suef 3. Irradiated grains (0, 150, 250 and 350 Gy) of both cultivars were sown and at harvest, 20 grains (M1) from each treatment were planted as in the first season. In the second season, grains of 61 plants were selected as they had the following higher criteria, i.e. yield, grain yield/plant, plant height, tillering and 100 grains weight. The selected variants should exceed by 50 % or more the control. Grains of the 61 selected plants were individually sown under drought or non-stress conditions, at the end of this season, six selected putative lines had superiority over their parents. The S1 and S2 lines have an excellent grain yield per plant under non stress condition as compared to Sohag3. The S3 and S4 lines have the superiority for grain yield per plant under drought condition as compared to Sohag 3. The B1 and B2 lines have the superiority for grain yield per plant under non stress condition comparing with Beni Suef 3. In the fourth season, growth, chemical composition and yield of the six putative lines as well as Sohag 3 and Beni Suef 3 were determined under non stress and drought conditions. The results showed a significant increase in the number of leaves on the main stem and tillering number/plant for S1, S2, B1 and B2 as compared each with their corresponding parent under non stress condition. Also, S3 and S4 lines had the same results comparing with Sohag 3 under drought condition. The results of S3 and S4 showed and accumulation of organic protective osmolytes such as sugar proline and free amino acids. As well as N, P, K and Ca concentrations in shoots and roots as compared to Sohag 3 .The putative lines S1, S2 and B1 showed a significant increase for grain yield per plant comparing with their controls under non stress

  6. The construction of a Solanum habrochaites LYC4 introgression line population and the identification of QTLs for resistance to Botrytis cinerea

    NARCIS (Netherlands)

    Finkers, H.J.; Heusden, van A.W.; Meijer-Dekens, R.G.; Kan, van J.A.L.; Maris, P.C.; Lindhout, P.

    2007-01-01

    Tomato (Solanum lycopersicum) is susceptible to grey mold (Botrytis cinerea). Partial resistance to this fungus has been identified in accessions of wild relatives of tomato such as Solanum habrochaites LYC4. In a previous F-2 mapping study, three QTLs conferring resistance to B. cinerea (Rbcq1,

  7. Analysis of natural allelic variation of Arabidopsis seed germination and seed longevity traits between the accessions Landberg erecta and Shakdara, using a new recombinant inbred line population

    NARCIS (Netherlands)

    Clerkx, E.J.M.; El-Lithy, M.E.M.; Vierling, E.; Ruijs, G.J.; Vries, de M.H.C.; Groot, S.P.C.; Vreugdenhil, D.; Koornneef, M.

    2004-01-01

    Quantitative trait loci (QTL) mapping was used to identify loci controlling various aspects of seed longevity during storage and germination. Similar locations for QTLs controlling different traits might be an indication for a common genetic control of such traits. For this analysis we used a new

  8. Evaluation of growth characters and yield components for six durum wheat lines (triticum durum deaf) selected from M4 and M5 - irradiated population under drought conditions

    International Nuclear Information System (INIS)

    Nesiem, M. R. A.; Kassem, M. K. M.; Basyouny, M. A. E.

    2012-12-01

    Grain of two durum wheat cultivars, Sohag 3 and Beni Suef 3 were irradiated with gamma ray doses 0, 150, 250 and 350 Gy to obtain new durum wheat lines, characterized by high yielding and drought tolerance. Irradiated grains were cultivated in the field under normal and drought conditions 2005 - 2010 seasons. 20 grain (M 1 ) from each treatment was planed as in the first season. In the second season (M 2 ), grains of 61 plants were selected as thy had the following higher criteria, i.e yield, grain yield / plant, plant height, tillering and 100 grains weight. The selected variants should exceed by 50% or more than control. Grains of the 61 selected plants were individually sown under normal and drought condition. At the end of this season, six selected putative line had superiority over their parents. The S1 and S2 lines had an excellent grain yield per plant under normal condition but S3 and S4 lines had superiority for grain yield per plant under drought condition as compared to parents Sohag3. B1 and B2 lines had the superiority for grain per plant under normal condition comparing with the parent Beni Suef3. In the fourth season (M4),growth, chemical compositions and yield as well as its components of the six putative lines as well as the parents Sohag 3 and Beni Suef 3 were determined under normal and drought conditions. The results showed a significant under normal and drought conditions. The results showed a significant increase in the number of leaves on the main stem and tillering number / plant for S1, S2, B1, B2 as compared with their corresponding parent under normal condition. Also, S3 and S4 line shad the same results comparing with the parent Sohag3 under drought condition. The results of S3 and S4 showed an accumulation of organic protective asmolytes such as sugar, proline and free amino acid. As well as N, P, K, and Ca concentrations in shoots and roots as compared to the parent Sohag 3 . The putative line S1, A2 and B1 showed significant increase

  9. Genome-wide interval mapping using SNPs identifies new QTL for growth, body composition and several physiological variables in an F2 intercross between fat and lean chicken lines.

    Science.gov (United States)

    Demeure, Olivier; Duclos, Michel J; Bacciu, Nicola; Le Mignon, Guillaume; Filangi, Olivier; Pitel, Frédérique; Boland, Anne; Lagarrigue, Sandrine; Cogburn, Larry A; Simon, Jean; Le Roy, Pascale; Le Bihan-Duval, Elisabeth

    2013-09-30

    For decades, genetic improvement based on measuring growth and body composition traits has been successfully applied in the production of meat-type chickens. However, this conventional approach is hindered by antagonistic genetic correlations between some traits and the high cost of measuring body composition traits. Marker-assisted selection should overcome these problems by selecting loci that have effects on either one trait only or on more than one trait but with a favorable genetic correlation. In the present study, identification of such loci was done by genotyping an F2 intercross between fat and lean lines divergently selected for abdominal fatness genotyped with a medium-density genetic map (120 microsatellites and 1302 single nucleotide polymorphisms). Genome scan linkage analyses were performed for growth (body weight at 1, 3, 5, and 7 weeks, and shank length and diameter at 9 weeks), body composition at 9 weeks (abdominal fat weight and percentage, breast muscle weight and percentage, and thigh weight and percentage), and for several physiological measurements at 7 weeks in the fasting state, i.e. body temperature and plasma levels of IGF-I, NEFA and glucose. Interval mapping analyses were performed with the QTLMap software, including single-trait analyses with single and multiple QTL on the same chromosome. Sixty-seven QTL were detected, most of which had never been described before. Of these 67 QTL, 47 were detected by single-QTL analyses and 20 by multiple-QTL analyses, which underlines the importance of using different statistical models. Close analysis of the genes located in the defined intervals identified several relevant functional candidates, such as ACACA for abdominal fatness, GHSR and GAS1 for breast muscle weight, DCRX and ASPSCR1 for plasma glucose content, and ChEBP for shank diameter. The medium-density genetic map enabled us to genotype new regions of the chicken genome (including micro-chromosomes) that influenced the traits

  10. Derivation of the dipole map

    International Nuclear Information System (INIS)

    Ali, Halima; Punjabi, Alkesh; Boozer, Allen

    2004-01-01

    In our method of maps [Punjabi et al., Phy. Rev. Lett. 69, 3322 (1992), and Punjabi et al., J. Plasma Phys. 52, 91 (1994)], symplectic maps are used to calculate the trajectories of magnetic field lines in divertor tokamaks. Effects of the magnetic perturbations are calculated using the low MN map [Ali et al., Phys. Plasmas 11, 1908 (2004)] and the dipole map [Punjabi et al., Phys. Plasmas 10, 3992 (2003)]. The dipole map is used to calculate the effects of externally located current carrying coils on the trajectories of the field lines, the stochastic layer, the magnetic footprint, and the heat load distribution on the collector plates in divertor tokamaks [Punjabi et al., Phys. Plasmas 10, 3992 (2003)]. Symplectic maps are general, efficient, and preserve and respect the Hamiltonian nature of the dynamics. In this brief communication, a rigorous mathematical derivation of the dipole map is given

  11. Construction of a high-density DArTseq SNP-based genetic map and identification of genomic regions with segregation distortion in a genetic population derived from a cross between feral and cultivated-type watermelon.

    Science.gov (United States)

    Ren, Runsheng; Ray, Rumiana; Li, Pingfang; Xu, Jinhua; Zhang, Man; Liu, Guang; Yao, Xiefeng; Kilian, Andrzej; Yang, Xingping

    2015-08-01

    Watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai] is an economically important vegetable crop grown extensively worldwide. To facilitate the identification of agronomically important traits and provide new information for genetic and genomic research on this species, a high-density genetic linkage map of watermelon was constructed using an F2 population derived from a cross between elite watermelon cultivar K3 and wild watermelon germplasm PI 189225. Based on a sliding window approach, a total of 1,161 bin markers representing 3,465 SNP markers were mapped onto 11 linkage groups corresponding to the chromosome pair number of watermelon. The total length of the genetic map is 1,099.2 cM, with an average distance between bins of 1.0 cM. The number of markers in each chromosome varies from 62 in chromosome 07 to 160 in chromosome 05. The length of individual chromosomes ranged between 61.8 cM for chromosome 07 and 140.2 cM for chromosome 05. A total of 616 SNP bin markers showed significant (P watermelon cultivar K3 allele and 103 were skewed toward PI 189225. The number of SNPs and InDels per Mb varied considerably across the segregation distorted regions (SDRs) on each chromosome, and a mixture of dense and sparse SNPs and InDel SDRs coexisted on some chromosomes suggesting that SDRs were randomly distributed throughout the genome. Recombination rates varied greatly among each chromosome, from 2.0 to 4.2 centimorgans per megabase (cM/Mb). An inconsistency was found between the genetic and physical positions on the map for a segment on chromosome 11. The high-density genetic map described in the present study will facilitate fine mapping of quantitative trait loci, the identification of candidate genes, map-based cloning, as well as marker-assisted selection (MAS) in watermelon breeding programs.

  12. VT National Wetlands Inventory Map Data - lines

    Data.gov (United States)

    Vermont Center for Geographic Information — (Link to Metadata) VCGI downloaded NWI quads from the US FWS web site and reprojected to VCS NAD83. NWI digital data files are records of wetlands location and...

  13. Changes of heterogeneous cell populations in the Ishikawa cell line during long-term culture: Proposal for an in vitro clonal evolution model of tumor cells.

    Science.gov (United States)

    Kasai, Fumio; Hirayama, Noriko; Ozawa, Midori; Iemura, Masashi; Kohara, Arihiro

    2016-06-01

    Genomic changes in tumor cell lines can occur during culture, leading to differences between cell lines carrying the same name. In this study, genome profiles between low and high passages were investigated in the Ishikawa 3-H-12 cell line (JCRB1505). Cells contained between 43 and 46 chromosomes and the modal number changed from 46 to 45 during culture. Cytogenetic analysis revealed that a translocation t(9;14), observed in all metaphases, is a robust marker for this cell line. Single-nucleotide polymorphism microarrays showed a heterogeneous copy number in the early passages and distinct profiles at late passages. These results demonstrate that cell culture can lead to elimination of ancestral clones by sequential selection, resulting in extensive replacement with a novel clone. Our observations on Ishikawa cells in vitro are different from the in vivo heterogeneity in which ancestral clones are often retained during tumor evolution and suggest a model for in vitro clonal evolution. Copyright © 2016 Elsevier Inc. All rights reserved.

  14. Comparative mapping in watermelon [Citrullus lanatus (Thunb.) Matsum. et Nakai].

    Science.gov (United States)

    Sandlin, Katherine; Prothro, Jason; Heesacker, Adam; Khalilian, Nelly; Okashah, Rebecca; Xiang, Wenwen; Bachlava, Eleni; Caldwell, David G; Taylor, Chris A; Seymour, Danelle K; White, Victoria; Chan, Eva; Tolla, Greg; White, Cathy; Safran, Dolores; Graham, Elaine; Knapp, Steven; McGregor, Cecilia

    2012-12-01

    The first single-nucleotide polymorphism (SNP) maps for watermelon [Citrullus lanatus (Thunb.) Matsum. et Nakai] were constructed and compared. Three populations were developed from crosses between two elite cultivars, Klondike Black Seeded × New Hampshire Midget (KBS × NHM), an elite cultivar and wild egusi accession, Strain II × PI 560023 (SII × Egusi) and an elite cultivar and a wild citron accession, ZWRM50 × PI 244019 (ZWRM × Citroides). The SII × Egusi and ZWRM × Citroides F(2) populations consisted of 187 and 182 individuals respectively while the KBS × NHM recombinant inbred line (RIL) population consisted of 164 lines. The length of the genetic maps were 1,438, 1,514 and 1,144 cM with average marker distances of 3.8, 4.2, and 3.4 cM for the KBS × NHM, SII × Egusi and ZWRM × Citroides populations, respectively. Shared markers were used to align the three maps so that the linkage groups (LGs) represented the 11 chromosomes of the species. Marker segregation distortion were observed in all three populations, but was highest (12.7 %) in the ZWRM × Citroides population, where Citroides alleles were favored. The three maps were used to construct a consensus map containing 378 SNP markers with an average distance of 5.1 cM between markers. Phenotypic data was collected for fruit weight (FWT), fruit length (FL), fruit width (FWD), fruit shape index (FSI), rind thickness (RTH) and Brix (BRX) and analyzed for quantitative trait loci (QTL) associated with these traits. A total of 40 QTL were identified in the three populations, including major QTL for fruit size and shape that were stable across genetic backgrounds and environments. The present study reports the first SNP maps for Citrullus and the first map constructed using two elite parents. We also report the first stable QTL associated with fruit size and shape in Citrullus lanatus. These maps, QTL and SNPs should be useful for the watermelon community and represent a significant step towards the

  15. Planetary maps - Passports for the mind

    International Nuclear Information System (INIS)

    Anderson, C.M.

    1990-01-01

    The various types of planetary maps are reviewed. Included are basic descriptions of planimetric, topographic, geologic, and digital maps. It is noted that planimetric maps are pictorial representations of a planet's round surface flattened into a plane, such as controlled photomosaic maps and shaded relief maps. Topographic maps, those usually made with data from altimeters and stereoscopic images, have contour lines indicating the shapes and elevations of landforms. Geologic maps carry additional information about landforms, such as rock types, the processes that formed them, and their relative ages. The International Astronomical Union nomenclature system is briefly discussed, pointing out that the Union often assigns themes to areas to be mapped

  16. Mapping of Vegetation with the Geoinformation System and Determining of Carrying Capacity of the Pre-Urals Steppe area for a Newly Establishing Population of the Przewalski Horse Equus ferus przewalskii at the Orenburg State Nature Reserve

    Science.gov (United States)

    Fedorov, N. I.; Mikhailenko, O. I.; Zharkikh, T. L.; Bakirova, R. T.

    2018-01-01

    Mapping of the vegetation (1:25000) of the Pre-Urals Steppe area at the Orenburg State Nature Reserve was completed in 2016. A map created with the geoinformation system contains 1931 simple and complex polygons for 25 types of vegetation. In a drought year, the average stock of palatable vegetation of the whole area is estimated at 8380 tons dry weight. The estimation is based on the size of areas covered by different types of vegetation, their grass production, the correction coefficients for decreasing of pasture forage stocks in winter and decreasing of production of grass communities in dry years. Based on pasture forage stocks the area could tolerate the maximum population size of 1769 individuals of the Przewalski horse, their average density could be 0.11 horse per ha. Yet, as watering places for animals are limited in Pre-Urals Steppe, grazing pressures on the vegetation next to the water sources may increase in dry years. That is why the above-mentioned calculated maximum population size and density must be reduced at least by half until some additional watering places are established and monitoring of the grazing effect on the vegetation next to the places is carried out regularly. Thus, the maximum size of the population is estimated at 800 to 900 individuals, which is almost 1.5 times more than necessary to establish a self-sustained population of the Przewalski horse.

  17. Allegheny County Map Index Grid

    Data.gov (United States)

    Allegheny County / City of Pittsburgh / Western PA Regional Data Center — Map Index Sheets from Block and Lot Grid of Property Assessment and based on aerial photography, showing 1983 datum with solid line and NAD 27 with 5 second grid...

  18. Examining the Influence of a New Light Rail Line on the Health of a Demographically Diverse and Understudied Population within the Washington, D.C. Metropolitan Area: A Protocol for a Natural Experiment Study

    Science.gov (United States)

    Saksvig, Brit Irene; Brachman, Micah L.; Durand, Casey P.

    2018-01-01

    Approximately two-thirds of adults and youth in Prince George’s County, Maryland, a suburb of Washington, D.C. are overweight or obese and less than half are achieving daily physical activity recommendations. Active transportation (AT), such as walking, biking or using public transportation (PT), is a strategic pathway to improving physical activity levels and thus reducing excess weight. Utilizing an expansion of the Washington, D.C. area transportation system with a new light rail line, the Purple Line Outcomes on Transportation (PLOT) Study will exam pre- and post-Purple Line PT use, AT behaviors and attitudes and physical activity among Prince George’s County adults and youth. The PLOT Study will take advantage of this natural experiment in an area enduring significant racial/ethnic and gender-based overweight or obesity and physical inactivity disparities. While similar natural experiments on AT have been conducted in other U.S. cities, those studies lacked diverse and representative samples. To effectively evaluate these physical activity outcomes among this population, efforts will be used to recruit African American and Latino populations, the first and second most common racial/ethnic groups in Prince George’s County. Finally, the PLOT Study will also examine how contextual effects (e.g., neighborhood built environment) impact PT, AT and physical activity.

  19. Examining the Influence of a New Light Rail Line on the Health of a Demographically Diverse and Understudied Population within the Washington, D.C. Metropolitan Area: A Protocol for a Natural Experiment Study

    Directory of Open Access Journals (Sweden)

    Jennifer D. Roberts

    2018-02-01

    Full Text Available Approximately two-thirds of adults and youth in Prince George’s County, Maryland, a suburb of Washington, D.C. are overweight or obese and less than half are achieving daily physical activity recommendations. Active transportation (AT, such as walking, biking or using public transportation (PT, is a strategic pathway to improving physical activity levels and thus reducing excess weight. Utilizing an expansion of the Washington, D.C. area transportation system with a new light rail line, the Purple Line Outcomes on Transportation (PLOT Study will exam pre- and post-Purple Line PT use, AT behaviors and attitudes and physical activity among Prince George’s County adults and youth. The PLOT Study will take advantage of this natural experiment in an area enduring significant racial/ethnic and gender-based overweight or obesity and physical inactivity disparities. While similar natural experiments on AT have been conducted in other U.S. cities, those studies lacked diverse and representative samples. To effectively evaluate these physical activity outcomes among this population, efforts will be used to recruit African American and Latino populations, the first and second most common racial/ethnic groups in Prince George’s County. Finally, the PLOT Study will also examine how contextual effects (e.g., neighborhood built environment impact PT, AT and physical activity.

  20. Power of two- and three-generation QTL mapping experiments in an outbred population containing full-sib or half-sib families.

    NARCIS (Netherlands)

    Beek, van der S.; Arendonk, van J.A.M.; Groen, A.F.

    1995-01-01

    QTL mapping experiments involve many animals to be genotyped and performance tested. Consequently, experimental designs need to be optimized to minimize the costs of data collection and genotyping. The present study has analyzed the power and efficiency of experiments with two or three-generation

  1. Urban Fault Lines in Shangri-La: Population and Economic Foundations of Inter-Ethnic Conflict in the Tibetan Areas of Western China

    NARCIS (Netherlands)

    A.M. Fischer (Andrew Martín)

    2004-01-01

    textabstractThis paper argues that contemporary experiences of social exclusion and interethnic conflict in the Tibetan areas of Western China are interrelated and revolve around three processes – population, growth and employment – all of which centre on the urban areas. In this setting, the

  2. Urban Fault Lines in Shangri-La: Population and economic foundations of interethnic conflict in the Tibetan areas of Western China

    NARCIS (Netherlands)

    A.M. Fischer (Andrew Martín)

    2004-01-01

    textabstractThis paper argues that contemporary experiences of social exclusion and interethnic conflict in the Tibetan areas of Western China are interrelated and revolve around three processes – population, growth and employment – all of which centre on the urban areas. In this setting, the

  3. Effects of seed mixture sowing with transgenic Bt rice and its parental line on the population dynamics of target stemborers and leafrollers, and non-target planthoppers.

    Science.gov (United States)

    Li, Zhuo; Li, Li-Kun; Liu, Bin; Wang, Long; Parajulee, Megha N; Chen, Fa-Jun

    2018-01-24

    The widespread planting of insect-resistant crops has caused a dramatic shift in agricultural landscapes, thus raising concerns about the potential impacts on both target and non-target pests. In this study, we examined the potential effects of intra-specific seed mixture sowing with transgenic Bt rice (Bt) and its parental non-transgenic line (Nt) (100% Bt rice [Bt 100 ], 5% Nt+95% Bt [Nt 05 Bt 95 ], 10% Nt+90% Bt [Nt 10 Bt 90 ], 20% Nt+80% Bt [Nt 20 Bt 80 ], 40% Nt+60% Bt [Nt 40 Bt 60 ] and 100% Nt rice [Nt 100 ]) on target and non-target pests in a 2-year field trial in southern China. The occurrence of target pests, Sesamia inferens, Chilo suppressalis and Cnaphalocrocis medinalis, decreased with the increased ratio of Bt rice, and the mixture ratios with more than 90% Bt rice (Bt 100 and Nt 05 Bt 95 ) significantly increased the pest suppression efficiency, with the lowest occurrences of non-target planthoppers, Nilaparvata lugens and Sogatella furcifera in Nt 100 and Nt 05 Bt 95 . Furthermore, there were no significant differences in 1000-grain dry weight and grain dry weight per 100 plants between Bt 100 and Nt 05 Bt 95 . Seed mixture sowing of Bt rice with ≤10% (especially 5%) of its parent line was sufficient to overcome potential compliance issues that exist with the use of block or structured refuge to provide most effective control of both target and non-target pests without compromising the grain yield. It is also expected that the strategy of seed mixture sowing with transgenic Bt rice and the non-transgenic parental line would provide rice yield stability while decreasing the insecticide use frequency in rice production. © 2018 Institute of Zoology, Chinese Academy of Sciences.

  4. Índice baseado em RFLPs para seleção de linhagens visando sintéticos de milho RFLP marker index for selection of inbred lines aimed at synthetic maize populations

    Directory of Open Access Journals (Sweden)

    Glauce Cristina Ricardo Rumin

    2001-06-01

    maize populations. It is based on field data and the RFLP genotypes of seed parents. Index usefulness was examined, considering its efficiency for generating synthetics with high QTL frequencies, in contrast with line selection based solely on topcross performance. Seed parents were genotyped for 157 RFLP marker loci with an average distance between loci of 15.30 cM. Sixty-eight S2 lines, stemming from an F2 population derived from a cross between two homozygous inbred lines, were topcrossed and evaluated in four locations in Iowa, USA, in 1996. From these 157 loci, 18 were identified as significantly associated with yield QTLs explaining 74.70 % of the genetic variance among topcross progenies. The proposed index included measures which are function of the per se line behaviour and the genetic complementarity between lines, and led to a diallel table homologue for all parental lines. These properties cannot be accomplished using only the topcross selection criterion. The index led to synthetic populations which are expected to be superior to the best synthetic population selected by topcross performance alone. However, this superiority is valid only for QTL regions covered by the markers used. This procedure allowed a useful monitoring of the genetic constitution of all possible synthetic populations.

  5. Functional capacity of XRCC1 protein variants identified in DNA repair-deficient Chinese hamster ovary cell lines and the human population

    DEFF Research Database (Denmark)

    Berquist, Brian R; Singh, Dharmendra Kumar; Fan, Jinshui

    2010-01-01

    XRCC1 operates as a scaffold protein in base excision repair, a pathway that copes with base and sugar damage in DNA. Studies using recombinant XRCC1 proteins revealed that: a C389Y substitution, responsible for the repair defects of the EM-C11 CHO cell line, caused protein instability; a V86R...... mutation abolished the interaction with POLbeta, but did not disrupt the interactions with PARP-1, LIG3alpha and PCNA; and an E98K substitution, identified in EM-C12, reduced protein integrity, marginally destabilized the POLbeta interaction, and slightly enhanced DNA binding. Two rare (P161L and Y576S...

  6. Dialelo entre linhagens de uma população de pepino do tipo 'Caipira' Diallel among lines of a 'Caipira' type cucumber population

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    Antonio Ismael Inácio Cardoso

    2006-06-01

    Full Text Available Este trabalho foi realizado para avaliar as capacidades geral e específica de combinação de seis linhagens de pepino 'Caipira', hibridizadas em um esquema dialélico, totalizando 15 híbridos experimentais (H-1 a H-15 possíveis (sem recíprocos. O delineamento foi em blocos ao acaso, com 23 tratamentos (6 linhagens, 15 híbridos experimentais e dois híbridos comerciais: 'Guarani' e 'Safira', quatro repetições e 5 plantas por parcela. Foram avaliadas as seguintes características: número e massa total de frutos por planta, número e massa de frutos comerciais por planta e taxa de frutos comerciais. O híbrido 'H-5' foi o que apresentou as maiores heteroses para produção de frutos (45 a 51%, com produção comercial (em número de frutos por planta superior a cinco linhagens e ao híbrido comercial 'Safira'. Tanto os efeitos aditivos como os não aditivos foram significativos para as características de produção de frutos (número e massa por planta, resultando em elevadas capacidades específicas de combinação para a maioria das combinações entre as linhagens. Das 75 estimativas de heterose obtidas, apenas três foram negativas.The objective of this work was to evaluate general and specific combining ability of six 'Caipira' cucumber lines, hybridized in a diallel cross, totalizing 15 experimental hybrids (H-1 to H-15, without reciprocals. The experimental design was randomized blocks with 23 treatments (6 lines, 15 experimental hybrids and two commercial hybrids: 'Safira' and 'Guarani', four replicates and 5 plants per plot. The following characteristics were evaluated: total fruit number and weight per plant, commercial fruit number and weight per plant and rate of commercial fruits. Hybrid H-5 showed the highest heterosis for fruit yield (45 to 51%, and had commercial yield (fruit number per plant superior to five lines and to 'Safira' hybrid. Additive and non additive effects were significant for fruit yield (number and weight

  7. Kinetic Line Voronoi Operations and Their Reversibility

    DEFF Research Database (Denmark)

    Mioc, Darka; Anton, François; Gold, Christopher

    2010-01-01

    In Geographic Information Systems the reversibility of map update operations has not been explored yet. In this paper we are using the Voronoi based Quad-edge data structure to define reversible map update operations. The reversibility of the map operations has been formalised at the lowest level...... mechanisms and dynamic map visualisations. In order to use the reversibility within the kinetic Voronoi diagram of points and open oriented line segments, we need to assure that reversing the map commands will produce exactly the changes in the map equivalent to the previous map states. To prove...... that reversing the map update operations produces the exact reverse changes, we show an isomorphism between the set of complex operations on the kinetic Voronoi diagram of points and open oriented line segments and the sets of numbers of new / deleted Voronoi regions induced by these operations, and its...

  8. Genetic linkage maps of chicken chromosomes 6, 7, 8, 11 and 13 from a Brazilian resource population Mapas de ligação dos cromossomos 6, 7, 8, 11 e 13 de uma população brasileira de galinha

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    Marcel Ambo

    2008-01-01

    Full Text Available A linkage map is essential not only for quantitative trait loci (QTL mapping, but also for the organization and location of genes along the chromosomes. The present study is part of a project whose major objective is, besides from construction the linkage maps, the whole genome scan for mapping QTL for performance traits in the Brazilian experimental chicken population. Linkage maps of chicken chromosomes 6 to 8, 11 and 13 were constructed based on this population. The population was developed from two generations of crossbreeding between a broiler and a layer line. Fifty-one microsatellite markers were tested, from which 28 were informative: 4, 8, 7, 4 and 5 for chromosomes 6, 7, 8, 11 and 13, respectively. A SNP located in the leptin receptor gene was included for chromosome 8. Ten parental, 8 F1 and 459 F2 chickens from five full-sib families were genotyped with these markers. The number of total informative meioses per locus varied from 232 to 862, and the number of phase-known informative meioses from 0 to 764. Marker orders in the chromosomes coincided with those of the chicken consensus map, except for markers ADL0147 and MCW0213, on chromosome 13, which were inverted. The reduced number of phase-known informative meioses for ADL0147 (150 may be pointed out as a possible cause for this inversion, apart from the relative short distance between the two markers involved in the inversion (10.5 cM.O mapa de ligação além de ser fundamental no mapeamento de locos de características quantitativas (QTLs é importante na organização e localização de genes distribuídos ao longo dos cromossomos. O presente estudo é parte de um trabalho cujo objetivo maior, é a análise de mapeamento de QTLs para características de desempenho no genoma de uma população experi