Science.gov

Sample records for nested association mapping

  1. Phenotypic assessments of peanut nested association mapping (NAM) populations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Nested association mapping (NAM) has been popular in recent years as a multi-parental mapping population due to the high-resolution trait mapping by combining the advantages of linkage analysis and association mapping. In peanut research community, two structured mapping populations were developed u...

  2. Phenotypic assessments of peanut nested association mapping (NAM) populations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Nested association mapping (NAM) is a valuable innovation and multi-parental mapping population strategy in peanut genetics which increases the power to map quantitative trait loci and assists in extending the gene pool of elite peanut lines. In the peanut research community, two structured mapping ...

  3. Nested association mapping of stem rust resistance in wheat using genotyping by sequencing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Nested association mapping is an approach to map trait loci in which families within populations are interconnected by a common parent. By implementing joint-linkage association analysis, this approach is able to map causative loci with higher power and resolution compared to biparental linkage mapp...

  4. Nested Association Mapping of Stem Rust Resistance in Wheat Using Genotyping by Sequencing.

    PubMed

    Bajgain, Prabin; Rouse, Matthew N; Tsilo, Toi J; Macharia, Godwin K; Bhavani, Sridhar; Jin, Yue; Anderson, James A

    2016-01-01

    We combined the recently developed genotyping by sequencing (GBS) method with joint mapping (also known as nested association mapping) to dissect and understand the genetic architecture controlling stem rust resistance in wheat (Triticum aestivum). Ten stem rust resistant wheat varieties were crossed to the susceptible line LMPG-6 to generate F6 recombinant inbred lines. The recombinant inbred line populations were phenotyped in Kenya, South Africa, and St. Paul, Minnesota, USA. By joint mapping of the 10 populations, we identified 59 minor and medium-effect QTL (explained phenotypic variance range of 1% - 20%) on 20 chromosomes that contributed towards adult plant resistance to North American Pgt races as well as the highly virulent Ug99 race group. Fifteen of the 59 QTL were detected in multiple environments. No epistatic relationship was detected among the QTL. While these numerous small- to medium-effect QTL are shared among the families, the founder parents were found to have different allelic effects for the QTL. Fourteen QTL identified by joint mapping were also detected in single-population mapping. As these QTL were mapped using SNP markers with known locations on the physical chromosomes, the genomic regions identified with QTL could be explored more in depth to discover candidate genes for stem rust resistance. The use of GBS-derived de novo SNPs in mapping resistance to stem rust shown in this study could be used as a model to conduct similar marker-trait association studies in other plant species. PMID:27186883

  5. Nested Association Mapping of Stem Rust Resistance in Wheat Using Genotyping by Sequencing

    PubMed Central

    Rouse, Matthew N.; Tsilo, Toi J.; Macharia, Godwin K.; Bhavani, Sridhar; Jin, Yue; Anderson, James A.

    2016-01-01

    We combined the recently developed genotyping by sequencing (GBS) method with joint mapping (also known as nested association mapping) to dissect and understand the genetic architecture controlling stem rust resistance in wheat (Triticum aestivum). Ten stem rust resistant wheat varieties were crossed to the susceptible line LMPG-6 to generate F6 recombinant inbred lines. The recombinant inbred line populations were phenotyped in Kenya, South Africa, and St. Paul, Minnesota, USA. By joint mapping of the 10 populations, we identified 59 minor and medium-effect QTL (explained phenotypic variance range of 1% – 20%) on 20 chromosomes that contributed towards adult plant resistance to North American Pgt races as well as the highly virulent Ug99 race group. Fifteen of the 59 QTL were detected in multiple environments. No epistatic relationship was detected among the QTL. While these numerous small- to medium-effect QTL are shared among the families, the founder parents were found to have different allelic effects for the QTL. Fourteen QTL identified by joint mapping were also detected in single-population mapping. As these QTL were mapped using SNP markers with known locations on the physical chromosomes, the genomic regions identified with QTL could be explored more in depth to discover candidate genes for stem rust resistance. The use of GBS-derived de novo SNPs in mapping resistance to stem rust shown in this study could be used as a model to conduct similar marker-trait association studies in other plant species. PMID:27186883

  6. Nested Association Mapping of Stem Rust Resistance in Wheat Using Genotyping by Sequencing.

    PubMed

    Bajgain, Prabin; Rouse, Matthew N; Tsilo, Toi J; Macharia, Godwin K; Bhavani, Sridhar; Jin, Yue; Anderson, James A

    2016-01-01

    We combined the recently developed genotyping by sequencing (GBS) method with joint mapping (also known as nested association mapping) to dissect and understand the genetic architecture controlling stem rust resistance in wheat (Triticum aestivum). Ten stem rust resistant wheat varieties were crossed to the susceptible line LMPG-6 to generate F6 recombinant inbred lines. The recombinant inbred line populations were phenotyped in Kenya, South Africa, and St. Paul, Minnesota, USA. By joint mapping of the 10 populations, we identified 59 minor and medium-effect QTL (explained phenotypic variance range of 1% - 20%) on 20 chromosomes that contributed towards adult plant resistance to North American Pgt races as well as the highly virulent Ug99 race group. Fifteen of the 59 QTL were detected in multiple environments. No epistatic relationship was detected among the QTL. While these numerous small- to medium-effect QTL are shared among the families, the founder parents were found to have different allelic effects for the QTL. Fourteen QTL identified by joint mapping were also detected in single-population mapping. As these QTL were mapped using SNP markers with known locations on the physical chromosomes, the genomic regions identified with QTL could be explored more in depth to discover candidate genes for stem rust resistance. The use of GBS-derived de novo SNPs in mapping resistance to stem rust shown in this study could be used as a model to conduct similar marker-trait association studies in other plant species.

  7. Elementary maps on nest algebras

    NASA Astrophysics Data System (ADS)

    Li, Pengtong

    2006-08-01

    Let , be algebras and let , be maps. An elementary map of is an ordered pair (M,M*) such that for all , . In this paper, the general form of surjective elementary maps on standard subalgebras of nest algebras is described. In particular, such maps are automatically additive.

  8. Genomic dissection of plant development and its impact on thousand grain weight in barley through nested association mapping

    PubMed Central

    Maurer, Andreas; Draba, Vera; Pillen, Klaus

    2016-01-01

    Flowering time is a key agronomic trait that plays an important role in crop yield. There is growing interest in dissecting the developmental subphases of flowering to better understand and fine-tune plant development and maximize yield. To do this, we used the wild barley nested association mapping (NAM) population HEB-25, comprising 1420 BC1S3 lines, to map quantitative trait loci (QTLs) controlling five developmental traits, plant height, and thousand grain weight. Genome-wide association studies (GWAS) enabled us to locate a total of 89 QTLs that genetically regulate the seven investigated traits. Several exotic QTL alleles proved to be highly effective and potentially useful in barley breeding. For instance, thousand grain weight was increased by 4.5g and flowering time was reduced by 9.3 days by substituting Barke elite QTL alleles for exotic QTL alleles at the denso/sdw1 and the Ppd-H1 loci, respectively. We showed that the exotic allele at the semi-dwarf locus denso/sdw1 can be used to increase grain weight since it uncouples the negative correlation between shoot elongation and the ripening phase. Our study demonstrates that nested association mapping of HEB-25 can help unravel the genetic regulation of plant development and yield formation in barley. Moreover, since we detected numerous useful exotic QTL alleles in HEB-25, we conclude that the introgression of these wild barley alleles into the elite barley gene pool may enable developmental phases to be specifically fine-tuned in order to maximize thousand grain weight and, potentially, yield in the long term. PMID:26936829

  9. Genomic dissection of plant development and its impact on thousand grain weight in barley through nested association mapping.

    PubMed

    Maurer, Andreas; Draba, Vera; Pillen, Klaus

    2016-04-01

    Flowering time is a key agronomic trait that plays an important role in crop yield. There is growing interest in dissecting the developmental subphases of flowering to better understand and fine-tune plant development and maximize yield. To do this, we used the wild barley nested association mapping (NAM) population HEB-25, comprising 1420 BC1S3 lines, to map quantitative trait loci (QTLs) controlling five developmental traits, plant height, and thousand grain weight. Genome-wide association studies (GWAS) enabled us to locate a total of 89 QTLs that genetically regulate the seven investigated traits. Several exotic QTL alleles proved to be highly effective and potentially useful in barley breeding. For instance, thousand grain weight was increased by 4.5 g and flowering time was reduced by 9.3 days by substituting Barke elite QTL alleles for exotic QTL alleles at the denso/sdw1 and the Ppd-H1 loci, respectively. We showed that the exotic allele at the semi-dwarf locus denso/sdw1 can be used to increase grain weight since it uncouples the negative correlation between shoot elongation and the ripening phase. Our study demonstrates that nested association mapping of HEB-25 can help unravel the genetic regulation of plant development and yield formation in barley. Moreover, since we detected numerous useful exotic QTL alleles in HEB-25, we conclude that the introgression of these wild barley alleles into the elite barley gene pool may enable developmental phases to be specifically fine-tuned in order to maximize thousand grain weight and, potentially, yield in the long term.

  10. Compositional assessments of key maize populations: B73 hybrids of the nested association mapping founder lines and diverse landrace inbred lines

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The present study provides an assessment of compositional diversity in maize B73 hybrids derived from both the nested association mapping (NAM) founder lines and from a geographically diverse collection of landrace accessions from North and South America. The NAM founders represent a key population...

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

    PubMed

    Saade, Stephanie; Maurer, Andreas; Shahid, Mohammed; Oakey, Helena; Schmöckel, Sandra M; Negrão, Sónia; Pillen, Klaus; Tester, Mark

    2016-01-01

    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.

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

    PubMed

    Saade, Stephanie; Maurer, Andreas; Shahid, Mohammed; Oakey, Helena; Schmöckel, Sandra M; Negrão, Sónia; Pillen, Klaus; Tester, Mark

    2016-01-01

    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. PMID:27585856

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

    PubMed Central

    Saade, Stephanie; Maurer, Andreas; Shahid, Mohammed; Oakey, Helena; Schmöckel, Sandra M.; Negrão, Sónia; Pillen, Klaus; Tester, Mark

    2016-01-01

    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. PMID:27585856

  14. Genetic Vulnerability and the Relationship of Commercial Germplasms of Maize in Brazil with the Nested Association Mapping Parents

    PubMed Central

    Fritsche Neto, Roberto; Granato, Ítalo Stefanine Correia; Sant’Ana, Gustavo César; Morais, Pedro Patric Pinho; Borém, Aluízio

    2016-01-01

    A few breeding companies dominate the maize (Zea mays L.) hybrid market in Brazil: Monsanto® (35%), DuPont Pioneer® (30%), Dow Agrosciences® (15%), Syngenta® (10%) and Helix Sementes (4%). Therefore, it is important to monitor the genetic diversity in commercial germplasms as breeding practices, registration and marketing of new cultivars can lead to a significant reduction of the genetic diversity. Reduced genetic variation may lead to crop vulnerabilities, food insecurity and limited genetic gains following selection. The aim of this study was to evaluate the genetic vulnerability risk by examining the relationship between the commercial Brazilian maize germplasms and the Nested Association Mapping (NAM) Parents. For this purpose, we used the commercial hybrids with the largest market share in Brazil and the NAM parents. The hybrids were genotyped for 768 single nucleotide polymorphisms (SNPs), using the Illumina Goldengate® platform. The NAM parent genomic data, comprising 1,536 SNPs for each line, were obtained from the Panzea data bank. The population structure, genetic diversity and the correlation between allele frequencies were analyzed. Based on the estimated effective population size and genetic variability, it was found that there is a low risk of genetic vulnerability in the commercial Brazilian maize germplasms. However, the genetic diversity is lower than those found in the NAM parents. Furthermore, the Brazilian germplasms presented no close relations with most NAM parents, except B73. This indicates that B73, or its heterotic group (Iowa Stiff Stalk Synthetic), contributed to the development of the commercial Brazilian germplasms. PMID:27780247

  15. Development and Genetic Characterization of an Advanced Backcross-Nested Association Mapping (AB-NAM) Population of Wild × Cultivated Barley.

    PubMed

    Nice, Liana M; Steffenson, Brian J; Brown-Guedira, Gina L; Akhunov, Eduard D; Liu, Chaochih; Kono, Thomas J Y; Morrell, Peter L; Blake, Thomas K; Horsley, Richard D; Smith, Kevin P; Muehlbauer, Gary J

    2016-07-01

    The ability to access alleles from unadapted germplasm collections is a long-standing problem for geneticists and breeders. Here we developed, characterized, and demonstrated the utility of a wild barley advanced backcross-nested association mapping (AB-NAM) population. We developed this population by backcrossing 25 wild barley accessions to the six-rowed malting barley cultivar Rasmusson. The 25 wild barley parents were selected from the 318 accession Wild Barley Diversity Collection (WBDC) to maximize allelic diversity. The resulting 796 BC2F4:6 lines were genotyped with 384 SNP markers, and an additional 4022 SNPs and 263,531 sequence variants were imputed onto the population using 9K iSelect SNP genotypes and exome capture sequence of the parents, respectively. On average, 96% of each wild parent was introgressed into the Rasmusson background, and the population exhibited low population structure. While linkage disequilibrium (LD) decay (r(2) = 0.2) was lowest in the WBDC (0.36 cM), the AB-NAM (9.2 cM) exhibited more rapid LD decay than comparable advanced backcross (28.6 cM) and recombinant inbred line (32.3 cM) populations. Three qualitative traits: glossy spike, glossy sheath, and black hull color were mapped with high resolution to loci corresponding to known barley mutants for these traits. Additionally, a total of 10 QTL were identified for grain protein content. The combination of low LD, negligible population structure, and high diversity in an adapted background make the AB-NAM an important tool for high-resolution gene mapping and discovery of novel allelic variation using wild barley germplasm.

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

    PubMed

    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

  17. A Cladistic Analysis of Phenotypic Associations with Haplotypes Inferred from Restriction Endonuclease Mapping. IV. Nested Analyses with Cladogram Uncertainty and Recombination

    PubMed Central

    Templeton, A. R.; Sing, C. F.

    1993-01-01

    We previously developed an analytical strategy based on cladistic theory to identify subsets of haplotypes that are associated with significant phenotypic deviations. Our initial approach was limited to segments of DNA in which little recombination occurs. In such cases, a cladogram can be constructed from the restriction site data to estimate the evolutionary steps that interrelate the observed haplotypes to one another. The cladogram is then used to define a nested statistical design for identifying mutational steps associated with significant phenotypic deviations. The central assumption behind this strategy is that a mutation responsible for a particular phenotypic effect is embedded within the evolutionary history that is represented by the cladogram. The power of this approach depends on the accuracy of the cladogram in portraying the evolutionary history of the DNA region. This accuracy can be diminished both by recombination and by uncertainty in the estimated cladogram topology. In a previous paper, we presented an algorithm for estimating the set of likely cladograms and recombination events. In this paper we present an algorithm for defining a nested statistical design under cladogram uncertainty and recombination. Given the nested design, phenotypic associations can be examined using either a nested analysis of variance (for haploids or homozygous strains) or permutation testing (for outcrossed, diploid gene regions). In this paper we also extend this analytical strategy to include categorical phenotypes in addition to quantitative phenotypes. Some worked examples are presented using Drosophila data sets. These examples illustrate that having some recombination may actually enhance the biological inferences that may derived from a cladistic analysis. In particular, recombination can be used to assign a physical localization to a given subregion for mutations responsible for significant phenotypic effects. PMID:8100789

  18. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. IV. Nested analyses with cladogram uncertainty and recombination.

    PubMed

    Templeton, A R; Sing, C F

    1993-06-01

    We previously developed an analytical strategy based on cladistic theory to identify subsets of haplotypes that are associated with significant phenotypic deviations. Our initial approach was limited to segments of DNA in which little recombination occurs. In such cases, a cladogram can be constructed from the restriction site data to estimate the evolutionary steps that interrelate the observed haplotypes to one another. The cladogram is then used to define a nested statistical design for identifying mutational steps associated with significant phenotypic deviations. The central assumption behind this strategy is that a mutation responsible for a particular phenotypic effect is embedded within the evolutionary history that is represented by the cladogram. The power of this approach depends on the accuracy of the cladogram in portraying the evolutionary history of the DNA region. This accuracy can be diminished both by recombination and by uncertainty in the estimated cladogram topology. In a previous paper, we presented an algorithm for estimating the set of likely claodgrams and recombination events. In this paper we present an algorithm for defining a nested statistical design under cladogram uncertainty and recombination. Given the nested design, phenotypic associations can be examined using either a nested analysis of variance (for haploids or homozygous strains) or permutation testing (for outcrossed, diploid gene regions). In this paper we also extend this analytical strategy to include categorical phenotypes in addition to quantitative phenotypes. Some worked examples are presented using Drosophila data sets. These examples illustrate that having some recombination may actually enhance the biological inferences that may derived from a cladistic analysis. In particular, recombination can be used to assign a physical localization to a given subregion for mutations responsible for significant phenotypic effects.

  19. Mapping risk for nest predation on a barrier island

    USGS Publications Warehouse

    Hackney, Amanda D.; Baldwin, Robert F.; Jodice, Patrick G.

    2013-01-01

    Barrier islands and coastal beach systems provide nesting habitat for marine and estuarine turtles. Densely settled coastal areas may subsidize nest predators. Our purpose was to inform conservation by providing a greater understanding of habitat-based risk factors for nest predation, for an estuarine turtle. We expected that habitat conditions at predated nests would differ from random locations at two spatial extents. We developed and validated an island-wide model for the distribution of predated Diamondback terrapin nests using locations of 198 predated nests collected during exhaustive searches at Fisherman Island National Wildlife Refuge, USA. We used aerial photographs to identify all areas of possible nesting habitat and searched each and surrounding environments for nests, collecting location and random-point microhabitat data. We built models for the probability of finding a predated nest using an equal number of random points and validated them with a reserve set (N = 67). Five variables in 9 a priori models were used and the best selected model (AIC weight 0.98) reflected positive associations with sand patches near marshes and roadways. Model validation had an average capture rate of predated nests of 84.14 % (26.17–97.38 %, Q1 77.53 %, median 88.07 %, Q3 95.08 %). Microhabitat selection results suggest that nests placed at the edges of sand patches adjacent to upland shrub/forest and marsh systems are vulnerable to predation. Forests and marshes provide cover and alternative resources for predators and roadways provide access; a suggestion is to focus nest protection efforts on the edges of dunes, near dense vegetation and roads.

  20. Metabolomic Assessment of Key Maize Resources: GC-MS and NMR Profiling of Grain from B73 Hybrids of the Nested Association Mapping (NAM) Founders and of Geographically Diverse Landraces.

    PubMed

    Venkatesh, Tyamagondlu V; Chassy, Alexander W; Fiehn, Oliver; Flint-Garcia, Sherry; Zeng, Qin; Skogerson, Kirsten; Harrigan, George G

    2016-03-16

    The present study expands metabolomic assessments of maize beyond commercial lines to include two sets of hybrids used extensively in the scientific community. One set included hybrids derived from the nested association mapping (NAM) founder lines, a collection of 25 inbreds selected on the basis of genetic diversity and used to investigate the genetic basis of complex plant traits. A second set included 24 hybrids derived from a collection of landraces representative of native diversity from North and South America that may serve as a source of new alleles for improving modern maize hybrids. Metabolomic analysis of grain harvested from these hybrids utilized gas chromatography-time-of-flight mass spectrometry (GC-TOF-MS) and (1)H nuclear magnetic resonance spectroscopy ((1)H NMR) techniques. Results highlighted extensive metabolomic variation in grain from both hybrid sets, but also demonstrated that, within each hybrid set, subpopulations could be differentiated in a pattern consistent with the known genetic and compositional variation of these lines. Correlation analysis did not indicate a strong association of the metabolomic data with grain nutrient composition, although some metabolites did show moderately strong correlations with agronomic features such as plant and ear height. Overall, this study provides insights into the extensive metabolomic diversity associated with conventional maize germplasm. PMID:26923484

  1. Mapping Sleeping Bees within Their Nest: Spatial and Temporal Analysis of Worker Honey Bee Sleep

    PubMed Central

    Klein, Barrett Anthony; Stiegler, Martin; Klein, Arno; Tautz, Jürgen

    2014-01-01

    Patterns of behavior within societies have long been visualized and interpreted using maps. Mapping the occurrence of sleep across individuals within a society could offer clues as to functional aspects of sleep. In spite of this, a detailed spatial analysis of sleep has never been conducted on an invertebrate society. We introduce the concept of mapping sleep across an insect society, and provide an empirical example, mapping sleep patterns within colonies of European honey bees (Apis mellifera L.). Honey bees face variables such as temperature and position of resources within their colony's nest that may impact their sleep. We mapped sleep behavior and temperature of worker bees and produced maps of their nest's comb contents as the colony grew and contents changed. By following marked bees, we discovered that individuals slept in many locations, but bees of different worker castes slept in different areas of the nest relative to position of the brood and surrounding temperature. Older worker bees generally slept outside cells, closer to the perimeter of the nest, in colder regions, and away from uncapped brood. Younger worker bees generally slept inside cells and closer to the center of the nest, and spent more time asleep than awake when surrounded by uncapped brood. The average surface temperature of sleeping foragers was lower than the surface temperature of their surroundings, offering a possible indicator of sleep for this caste. We propose mechanisms that could generate caste-dependent sleep patterns and discuss functional significance of these patterns. PMID:25029445

  2. Mapping sleeping bees within their nest: spatial and temporal analysis of worker honey bee sleep.

    PubMed

    Klein, Barrett Anthony; Stiegler, Martin; Klein, Arno; Tautz, Jürgen

    2014-01-01

    Patterns of behavior within societies have long been visualized and interpreted using maps. Mapping the occurrence of sleep across individuals within a society could offer clues as to functional aspects of sleep. In spite of this, a detailed spatial analysis of sleep has never been conducted on an invertebrate society. We introduce the concept of mapping sleep across an insect society, and provide an empirical example, mapping sleep patterns within colonies of European honey bees (Apis mellifera L.). Honey bees face variables such as temperature and position of resources within their colony's nest that may impact their sleep. We mapped sleep behavior and temperature of worker bees and produced maps of their nest's comb contents as the colony grew and contents changed. By following marked bees, we discovered that individuals slept in many locations, but bees of different worker castes slept in different areas of the nest relative to position of the brood and surrounding temperature. Older worker bees generally slept outside cells, closer to the perimeter of the nest, in colder regions, and away from uncapped brood. Younger worker bees generally slept inside cells and closer to the center of the nest, and spent more time asleep than awake when surrounded by uncapped brood. The average surface temperature of sleeping foragers was lower than the surface temperature of their surroundings, offering a possible indicator of sleep for this caste. We propose mechanisms that could generate caste-dependent sleep patterns and discuss functional significance of these patterns. PMID:25029445

  3. Mapping sleeping bees within their nest: spatial and temporal analysis of worker honey bee sleep.

    PubMed

    Klein, Barrett Anthony; Stiegler, Martin; Klein, Arno; Tautz, Jürgen

    2014-01-01

    Patterns of behavior within societies have long been visualized and interpreted using maps. Mapping the occurrence of sleep across individuals within a society could offer clues as to functional aspects of sleep. In spite of this, a detailed spatial analysis of sleep has never been conducted on an invertebrate society. We introduce the concept of mapping sleep across an insect society, and provide an empirical example, mapping sleep patterns within colonies of European honey bees (Apis mellifera L.). Honey bees face variables such as temperature and position of resources within their colony's nest that may impact their sleep. We mapped sleep behavior and temperature of worker bees and produced maps of their nest's comb contents as the colony grew and contents changed. By following marked bees, we discovered that individuals slept in many locations, but bees of different worker castes slept in different areas of the nest relative to position of the brood and surrounding temperature. Older worker bees generally slept outside cells, closer to the perimeter of the nest, in colder regions, and away from uncapped brood. Younger worker bees generally slept inside cells and closer to the center of the nest, and spent more time asleep than awake when surrounded by uncapped brood. The average surface temperature of sleeping foragers was lower than the surface temperature of their surroundings, offering a possible indicator of sleep for this caste. We propose mechanisms that could generate caste-dependent sleep patterns and discuss functional significance of these patterns.

  4. Mapping nested loop algorithms into multidimensional systolic arrays

    SciTech Connect

    Lee, P.Z. ); Kedem, Z.M. )

    1990-01-01

    This paper is concerned with transforming depth p-nested for loop algorithms into q-dimensional systolic VLSI arrays where 1 {le} q {le} p {minus} 1. Previously there existed complete characterizations of correct transformations only for the cases when q = p {minus} 1 or q = 1. The authors fill in this gap by giving formal necessary and sufficient conditions for correct transformation of a p-nested loop algorithm into a q-dimensional systolic array for any q, 1 {le} q {le} p {minus} 1. They also provide practical methods to derive optimal or suboptimal systolic array implementations. They apply the techniques developed by us to the automatic design of special purpose and programmable systolic arrays. The author's results also contribute towards automatic compilation onto more general purpose programmable arrays. Synthesis of linear and planar systolic array implementations for a three-dimensional cube-graph algorithm and a reindexed Warshall-Floyd pathfinding algorithm is used to illustrate our method.

  5. Is it safe to nest near conspicuous neighbours? Spatial patterns in predation risk associated with the density of American Golden-Plover nests.

    PubMed

    Giroux, Marie-Andrée; Trottier-Paquet, Myriam; Bêty, Joël; Lamarre, Vincent; Lecomte, Nicolas

    2016-01-01

    Predation is one of the main factors explaining nesting mortality in most bird species. Birds can avoid nest predation or reduce predation pressure by breeding at higher latitude, showing anti-predator behaviour, selecting nest sites protected from predators, and nesting in association with protective species. American Golden-Plovers (Pluvialis dominica) defend their territory by using various warning and distraction behaviours displayed at varying levels of intensity (hereafter "conspicuous behaviour"), as well as more aggressive behaviours such as aerial attacks, but only in some populations. Such antipredator behaviour has the potential to repel predators and thus benefit the neighbouring nests by decreasing their predation risk. Yet, conspicuous behaviour could also attract predators by signalling the presence of a nest. To test for the existence of a protective effect associated with the conspicuous antipredator behaviour of American Golden-Plovers, we studied the influence of proximity to plover nests on predation risk of artificial nests on Igloolik Island (Nunavut, Canada) in July 2014. We predicted that the predation risk of artificial nests would decrease with proximity to and density of plover nests. We monitored 18 plover nests and set 35 artificial nests at 30, 50, 100, 200, and 500 m from seven of those plover nests. We found that the predation risk of artificial nests increases with the density of active plover nests. We also found a significant negative effect of the distance to the nearest active protector nest on predation risk of artificial nests. Understanding how the composition and structure of shorebird communities generate spatial patterns in predation risks represents a key step to better understand the importance of these species of conservation concern in tundra food webs. PMID:27602257

  6. Is it safe to nest near conspicuous neighbours? Spatial patterns in predation risk associated with the density of American Golden-Plover nests

    PubMed Central

    Trottier-Paquet, Myriam; Bêty, Joël; Lamarre, Vincent; Lecomte, Nicolas

    2016-01-01

    Predation is one of the main factors explaining nesting mortality in most bird species. Birds can avoid nest predation or reduce predation pressure by breeding at higher latitude, showing anti-predator behaviour, selecting nest sites protected from predators, and nesting in association with protective species. American Golden-Plovers (Pluvialis dominica) defend their territory by using various warning and distraction behaviours displayed at varying levels of intensity (hereafter “conspicuous behaviour”), as well as more aggressive behaviours such as aerial attacks, but only in some populations. Such antipredator behaviour has the potential to repel predators and thus benefit the neighbouring nests by decreasing their predation risk. Yet, conspicuous behaviour could also attract predators by signalling the presence of a nest. To test for the existence of a protective effect associated with the conspicuous antipredator behaviour of American Golden-Plovers, we studied the influence of proximity to plover nests on predation risk of artificial nests on Igloolik Island (Nunavut, Canada) in July 2014. We predicted that the predation risk of artificial nests would decrease with proximity to and density of plover nests. We monitored 18 plover nests and set 35 artificial nests at 30, 50, 100, 200, and 500 m from seven of those plover nests. We found that the predation risk of artificial nests increases with the density of active plover nests. We also found a significant negative effect of the distance to the nearest active protector nest on predation risk of artificial nests. Understanding how the composition and structure of shorebird communities generate spatial patterns in predation risks represents a key step to better understand the importance of these species of conservation concern in tundra food webs. PMID:27602257

  7. Is it safe to nest near conspicuous neighbours? Spatial patterns in predation risk associated with the density of American Golden-Plover nests

    PubMed Central

    Trottier-Paquet, Myriam; Bêty, Joël; Lamarre, Vincent; Lecomte, Nicolas

    2016-01-01

    Predation is one of the main factors explaining nesting mortality in most bird species. Birds can avoid nest predation or reduce predation pressure by breeding at higher latitude, showing anti-predator behaviour, selecting nest sites protected from predators, and nesting in association with protective species. American Golden-Plovers (Pluvialis dominica) defend their territory by using various warning and distraction behaviours displayed at varying levels of intensity (hereafter “conspicuous behaviour”), as well as more aggressive behaviours such as aerial attacks, but only in some populations. Such antipredator behaviour has the potential to repel predators and thus benefit the neighbouring nests by decreasing their predation risk. Yet, conspicuous behaviour could also attract predators by signalling the presence of a nest. To test for the existence of a protective effect associated with the conspicuous antipredator behaviour of American Golden-Plovers, we studied the influence of proximity to plover nests on predation risk of artificial nests on Igloolik Island (Nunavut, Canada) in July 2014. We predicted that the predation risk of artificial nests would decrease with proximity to and density of plover nests. We monitored 18 plover nests and set 35 artificial nests at 30, 50, 100, 200, and 500 m from seven of those plover nests. We found that the predation risk of artificial nests increases with the density of active plover nests. We also found a significant negative effect of the distance to the nearest active protector nest on predation risk of artificial nests. Understanding how the composition and structure of shorebird communities generate spatial patterns in predation risks represents a key step to better understand the importance of these species of conservation concern in tundra food webs.

  8. Is it safe to nest near conspicuous neighbours? Spatial patterns in predation risk associated with the density of American Golden-Plover nests.

    PubMed

    Giroux, Marie-Andrée; Trottier-Paquet, Myriam; Bêty, Joël; Lamarre, Vincent; Lecomte, Nicolas

    2016-01-01

    Predation is one of the main factors explaining nesting mortality in most bird species. Birds can avoid nest predation or reduce predation pressure by breeding at higher latitude, showing anti-predator behaviour, selecting nest sites protected from predators, and nesting in association with protective species. American Golden-Plovers (Pluvialis dominica) defend their territory by using various warning and distraction behaviours displayed at varying levels of intensity (hereafter "conspicuous behaviour"), as well as more aggressive behaviours such as aerial attacks, but only in some populations. Such antipredator behaviour has the potential to repel predators and thus benefit the neighbouring nests by decreasing their predation risk. Yet, conspicuous behaviour could also attract predators by signalling the presence of a nest. To test for the existence of a protective effect associated with the conspicuous antipredator behaviour of American Golden-Plovers, we studied the influence of proximity to plover nests on predation risk of artificial nests on Igloolik Island (Nunavut, Canada) in July 2014. We predicted that the predation risk of artificial nests would decrease with proximity to and density of plover nests. We monitored 18 plover nests and set 35 artificial nests at 30, 50, 100, 200, and 500 m from seven of those plover nests. We found that the predation risk of artificial nests increases with the density of active plover nests. We also found a significant negative effect of the distance to the nearest active protector nest on predation risk of artificial nests. Understanding how the composition and structure of shorebird communities generate spatial patterns in predation risks represents a key step to better understand the importance of these species of conservation concern in tundra food webs.

  9. Colony mapping: A new technique for monitoring crevice-nesting seabirds

    USGS Publications Warehouse

    Renner, H.M.; Renner, M.; Reynolds, J.H.; Harping, A.M.A.; Jones, I.L.; Irons, D.B.; Byrd, G.V.

    2006-01-01

    Monitoring populations of auklets and other crevice-nesting seabirds remains problematic, although numerous methods have been attempted since the mid-1960s. Anecdotal evidence suggests several large auklet colonies have recently decreased in both abundance and extent, concurrently with vegetation encroachment and succession. Quantifying changes in the geographical extent of auklet colonies may be a useful alternative to monitoring population size directly. We propose a standardized method for colony mapping using a randomized systematic grid survey with two components: a simple presence/absence survey and an auklet evidence density survey. A quantitative auklet evidence density index was derived from the frequency of droppings and feathers. This new method was used to map the colony on St. George Island in the southeastern Bering Sea and results were compared to previous colony mapping efforts. Auklet presence was detected in 62 of 201 grid cells (each grid cell = 2500 m2) by sampling a randomly placed 16 m2 plot in each cell; estimated colony area = 155 000 m2. The auklet evidence density index varied by two orders of magnitude across the colony and was strongly correlated with means of replicated counts of birds socializing on the colony surface. Quantitatively mapping all large auklet colonies is logistically feasible using this method and would provide an important baseline for monitoring colony status. Regularly monitoring select colonies using this method may be the best means of detecting changes in distribution and population size of crevice-nesting seabirds. ?? The Cooper Ornithological Society 2006.

  10. Fitness costs associated with building and maintaining the burying beetle’s carrion nest

    PubMed Central

    De Gasperin, Ornela; Duarte, Ana; Troscianko, Jolyon; Kilner, Rebecca M.

    2016-01-01

    It is well-known that features of animal nest architecture can be explained by fitness benefits gained by the offspring housed within. Here we focus on the little-tested suggestion that the fitness costs associated with building and maintaining a nest should additionally account for aspects of its architecture. Burying beetles prepare an edible nest for their young from a small vertebrate carcass, by ripping off any fur or feathers and rolling the flesh into a rounded ball. We found evidence that only larger beetles are able to construct rounder carcass nests, and that rounder carcass nests are associated with lower maintenance costs. Offspring success, however, was not explained by nest roundness. Our experiment thus provides rare support for the suggestion that construction and maintenance costs are key to understanding animal architecture. PMID:27734965

  11. Fuzzy associative conjuncted maps network.

    PubMed

    Goh, Hanlin; Lim, Joo-Hwee; Quek, Chai

    2009-08-01

    The fuzzy associative conjuncted maps (FASCOM) is a fuzzy neural network that associates data of nonlinearly related inputs and outputs. In the network, each input or output dimension is represented by a feature map that is partitioned into fuzzy or crisp sets. These fuzzy sets are then conjuncted to form antecedents and consequences, which are subsequently associated to form if-then rules. The associative memory is encoded through an offline batch mode learning process consisting of three consecutive phases. The initial unsupervised membership function initialization phase takes inspiration from the organization of sensory maps in our brains by allocating membership functions based on uniform information density. Next, supervised Hebbian learning encodes synaptic weights between input and output nodes. Finally, a supervised error reduction phase fine-tunes the network, which allows for the discovery of the varying levels of influence of each input dimension across an output feature space in the encoded memory. In the series of experiments, we show that each phase in the learning process contributes significantly to the final accuracy of prediction. Further experiments using both toy problems and real-world data demonstrate significant superiority in terms of accuracy of nonlinear estimation when benchmarked against other prominent architectures and exhibit the network's suitability to perform analysis and prediction on real-world applications, such as traffic density prediction as shown in this paper.

  12. Genetic Properties of the Maize Nested Association Mapping Population

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Maize is one of the world’s most diverse species, and this variation can be used to understand the molecular basis of phenotypic variation and to improve agricultural efficiency and sustainability. To access this genetic variation, 25 diverse inbred maize lines were crossed to the B73 reference lin...

  13. Lesser prairie-chicken nest site selection, microclimate, and nest survival in association with vegetation response to a grassland restoration program

    USGS Publications Warehouse

    Boal, Clint W.; Grisham, Blake A.; Haukos, David A.; Zavaleta, Jennifer C.; Dixon, Charles

    2014-01-01

    Climate models predict that the region of the Great Plains Landscape Conservation Cooperative (GPLCC) will experience increased maximum and minimum temperatures, reduced frequency but greater intensity of precipitation events, and earlier springs. These climate changes along with different landscape management techniques may influence the persistence of the lesser prairie-chicken (Tympanuchus pallidicinctus), a candidate for protection under the Endangered Species Act and a priority species under the GPLCC, in positive or negative ways. The objectives of this study were to conduct (1) a literature review of lesser prairie-chicken nesting phenology and ecology, (2) an analysis of thermal aspects of lesser prairie-chicken nest microclimate data, and (3) an analysis of nest site selection, nest survival, and vegetation response to 10 years of tebuthiuron and/or grazing treatments. We found few reports in the literature containing useful data on the nesting phenology of lesser prairie-chickens; therefore, managers must rely on short-term observations and measurements of parameters that provide some predictive insight into climate impacts on nesting ecology. Our field studies showed that prairie-chickens on nests were able to maintain relatively consistent average nest temperature of 31 °C and nest humidities of 56.8 percent whereas average external temperatures (20.3–35.0 °C) and humidities (35.2–74.9 percent) varied widely throughout the 24 hour (hr) cycle. Grazing and herbicide treatments within our experimental areas were designed to be less intensive than in common practice. We determined nest locations by radio-tagging hen lesser prairie-chickens captured at leks, which are display grounds at which male lesser prairie-chickens aggregate and attempt to attract a female for mating. Because nest locations selected by hen lesser prairie-chicken are strongly associated with the lek at which they were captured, we assessed nesting habitat use on the basis of hens

  14. Detection of diisocyanates in nesting material associated with mortality in pigeon chicks.

    PubMed

    Mukai, Motoko; Woods, Leslie W; Stump, Samuel; Ebel, Joseph G; Levitt, Ariana S; Frey, Margaret W; Smith, Jeanne; Uzal, Francisco A; Poppenga, Robert H; Puschner, Birgit

    2014-03-01

    Diisocyanates, commonly used in the production of polyurethane foams, paints, elastomers, varnishes, and coatings, are considered among the most hazardous inhalation toxicants. The present report describes 2 unusual cases of mortality in pigeon chicks associated with nesting material contaminated by diisocyanates. Case 1 was submitted by a racing pigeon breeder who had lost all the hatchlings (n = 125) following replacement of the nesting material with a different lot. All adult birds appeared healthy, and hatchability was not significantly affected, but hatchlings became lethargic and dyspneic after a day of hatch. At necropsy, dark wet lungs were found in the hatchlings. Case 2 was submitted by a show-roller pigeon breeder. In this case, the owner reported lower hatchability, and all hatchlings (approximately 100) died within 2 days of hatching with clinical signs similar to the first case. Necropsy did not reveal any significant findings. For both cases, nesting materials were screened for toxic compounds using gas chromatography-mass spectrometry. Toluene-2,4-diisocyanate (approximately 190-290 ppm) and 4,4'-methylene diphenyl diisocyanate (unquantified) were detected in the nesting pads. While there is very limited information on toxicosis in birds, there are reports of inhalant exposure of diisocyanates causing pulmonary edema and death in various mammalian species. Although cause-effect relationship of mortality and the nesting material was not established in the present cases, the presence of toxic compounds in the nesting materials is a cause for concern. Further investigation is needed to determine the prevalence and toxicity of diisocyanates-contaminated nesting material in avian species.

  15. Inter-nesting habitat-use patterns of loggerhead sea turtles: Enhancing satellite tracking with benthic mapping

    USGS Publications Warehouse

    Hart, Kristen M.; Zawada, David G.; Fujisaki, Ikuko; Lidz, Barbara H.

    2010-01-01

    The loggerhead sea turtle Caretta caretta faces declining nest numbers and bycatches from commercial longline fishing in the southeastern USA. Understanding spatial and temporal habitat-use patterns of these turtles, especially reproductive females in the neritic zone, is critical for guiding management decisions. To assess marine turtle habitat use within the Dry Tortugas National Park (DRTO), we used satellite telemetry to identify core-use areas for 7 loggerhead females inter-nesting and tracked in 2008 and 2009. This effort represents the first tracking of DRTO loggerheads, a distinct subpopulation that is 1 of 7 recently proposed for upgrading from threatened to endangered under the US Endangered Species Act. We also used a rapid, high-resolution, digital imaging system to map benthic habitats in turtle core-use areas (i.e. 50% kernel density zones). Loggerhead females were seasonal residents of DRTO for 19 to 51 d, and individual inter-nesting habitats were located within 1.9 km (2008) and 2.3 km (2009) of the nesting beach and tagging site. The core area common to all tagged turtles was 4.2 km2 in size and spanned a depth range of 7.6 to 11.5 m. Mapping results revealed the diversity and distributions of benthic cover available in the core-use area, as well as a heavily used corridor to/from the nesting beach. This combined tagging-mapping approach shows potential for planning and improving the effectiveness of marine protected areas and for developing spatially explicit conservation plans.

  16. Ulyxes, a new Australopapuan mite genus associated with arboreal nests (Acari: Laelapidae).

    PubMed

    Shaw, Matthew D

    2014-01-01

    As part of a survey of mammal and bird nests, new species, new male stages, and some feeding observations have been collected from what was formerly called the Androlaelaps ulysses group. As many features of this group are consistently different from Androlaelaps, and also from Haemolaelaps where it was formerly placed, this group is here elevated to Ulyxes new genus, and U. autolycus, U. euryclea, and U. theoclymenus are described as new species. This genus has a broad range of feeding behaviour spanning intranasal parasitism, nidicolous parasitism, and at least one species is a nidicolous predator. Its host range is broad; two new species are shown here to cohabit with parrots while most remaining species associate with mammals. In contrast to the variation in feeding behaviour, Ulyxes spp are associated with a narrow range of nest types, being confined to arboreal nests, usually tree hollows (rarely fallen logs), and on the parrot or mammal hosts that use them. Ulyxes spp show a remarkable variability in male cheliceral development, which assorts according to feeding behaviour. There is a strong contrast between male chelicerae of predatory and parasitic species that has not been previously observed in such a compact dermanyssine genus. Previously male cheliceral morphology was thought to be conservative enough to provide diagnostic characters at suprageneric rank. For systematics, these findings complicate previous attempts to recognise male mouthparts as reliable features marking higher-level natural groups that include dermanyssoid vertebrate parasites. For evolutionary studies, this may be relevant in seeking examples of transitions to, or away from, parasitism. PMID:25544446

  17. Ulyxes, a new Australopapuan mite genus associated with arboreal nests (Acari: Laelapidae).

    PubMed

    Shaw, Matthew D

    2014-10-24

    As part of a survey of mammal and bird nests, new species, new male stages, and some feeding observations have been collected from what was formerly called the Androlaelaps ulysses group. As many features of this group are consistently different from Androlaelaps, and also from Haemolaelaps where it was formerly placed, this group is here elevated to Ulyxes new genus, and U. autolycus, U. euryclea, and U. theoclymenus are described as new species. This genus has a broad range of feeding behaviour spanning intranasal parasitism, nidicolous parasitism, and at least one species is a nidicolous predator. Its host range is broad; two new species are shown here to cohabit with parrots while most remaining species associate with mammals. In contrast to the variation in feeding behaviour, Ulyxes spp are associated with a narrow range of nest types, being confined to arboreal nests, usually tree hollows (rarely fallen logs), and on the parrot or mammal hosts that use them. Ulyxes spp show a remarkable variability in male cheliceral development, which assorts according to feeding behaviour. There is a strong contrast between male chelicerae of predatory and parasitic species that has not been previously observed in such a compact dermanyssine genus. Previously male cheliceral morphology was thought to be conservative enough to provide diagnostic characters at suprageneric rank. For systematics, these findings complicate previous attempts to recognise male mouthparts as reliable features marking higher-level natural groups that include dermanyssoid vertebrate parasites. For evolutionary studies, this may be relevant in seeking examples of transitions to, or away from, parasitism.

  18. Topographica: Building and Analyzing Map-Level Simulations from Python, C/C++, MATLAB, NEST, or NEURON Components.

    PubMed

    Bednar, James A

    2009-01-01

    Many neural regions are arranged into two-dimensional topographic maps, such as the retinotopic maps in mammalian visual cortex. Computational simulations have led to valuable insights about how cortical topography develops and functions, but further progress has been hindered by the lack of appropriate tools. It has been particularly difficult to bridge across levels of detail, because simulators are typically geared to a specific level, while interfacing between simulators has been a major technical challenge. In this paper, we show that the Python-based Topographica simulator makes it straightforward to build systems that cross levels of analysis, as well as providing a common framework for evaluating and comparing models implemented in other simulators. These results rely on the general-purpose abstractions around which Topographica is designed, along with the Python interfaces becoming available for many simulators. In particular, we present a detailed, general-purpose example of how to wrap an external spiking PyNN/NEST simulation as a Topographica component using only a dozen lines of Python code, making it possible to use any of the extensive input presentation, analysis, and plotting tools of Topographica. Additional examples show how to interface easily with models in other types of simulators. Researchers simulating topographic maps externally should consider using Topographica's analysis tools (such as preference map, receptive field, or tuning curve measurement) to compare results consistently, and for connecting models at different levels. This seamless interoperability will help neuroscientists and computational scientists to work together to understand how neurons in topographic maps organize and operate. PMID:19352443

  19. Branchial-like cysts of the thyroid associated with solid cell nests.

    PubMed

    Michal, Michal; Mukensnabl, Petr; Kazakov, Dmitry V

    2006-03-01

    Presented herein is the case of a 65-year-old man with a 20 year history of thyroid hypofunction. On sonography a cystic lesion 4 x 4 x 5 cm in largest diameter was found, replacing most of the right lobe of the thyroid gland. Microscopically, the lesion was composed of labyrinth-like cystic structures (LCS) lined by a few layers of benign-appearing squamous cells and filled by mucinous material. Adjacent to the cyst walls were discontinuous patches of a lymphoid tissue, composed of haloed centrocyte-like cells or germinal centers mostly depleted of germinal cells. Additionally, there were numerous squamous cell nests equivalent to solid cell nests (SCN), all of which were surrounded by a similar-looking lymphoid tissue. Rare SCN were thus cystically changed and contained a small amount of mucus. The SCN communicated with the LCS: the former represented the most distal outpouchings of the latter. The epithelial structures were surrounded by a loose collagenous adipocytic stroma with plump fibroblasts, which resembled the stroma often seen in lateral neck cysts associated with structures such as cartilage, accessory salivary gland tissues, cysts and accessory thyroid and thymus. Immunohistochemically, all lesional elements were negative for calcitonin and thyroglobulin. The results of the paper suggest that branchial cleft-like cyst have an origin in the ultimobranchial body.

  20. A Nested Case-Control Study of Association between Metabolome and Hypertension Risk

    PubMed Central

    Hao, Yongchen; Wang, Ying; Xi, Lu; Li, Guoqi; Zhao, Fan; Qi, Yue; Liu, Jing; Zhao, Dong

    2016-01-01

    We aimed to explore novel small metabolites that associated with hypertension risk in a population-based nested case-control study. Among 460 individuals with optimal blood pressure (<120/80 mmHg) at baseline, 55 progressed to hypertension during 5 years of follow-up. Twenty-nine cases of incident hypertension and 29 controls, matched for age, sex, and baseline systolic blood pressure, were included in this study. Serum metabolites were measured by gas chromatography-tandem mass spectrometry. t-test and logistic regression analysis were applied to investigate the association between metabolites and incident hypertension. Among the 241 metabolites identified in this study, baseline levels of 26 metabolites were significantly different between hypertension and control groups. After adjusting for body mass index, smoking, and drinking, 16 out of the 26 metabolites were still associated with hypertension risk including four amino acids. Amino acids were negatively associated with risk of future hypertension, with odds ratio (OR) ranging from 0.33 to 0.53. Two of these amino acids were essential amino acids including threonine and phenylalanine. Higher level of lyxose, a fermentation product of gut microbes, was associated with higher risk of hypertension. Our study identified multiple metabolites that associated with hypertension risk. These findings implied that low amino acid levels and gut microbiome might play an important role in the pathogenesis of hypertension. PMID:27119083

  1. A Nested Case-Control Study of Association between Metabolome and Hypertension Risk.

    PubMed

    Hao, Yongchen; Wang, Ying; Xi, Lu; Li, Guoqi; Zhao, Fan; Qi, Yue; Liu, Jing; Zhao, Dong

    2016-01-01

    We aimed to explore novel small metabolites that associated with hypertension risk in a population-based nested case-control study. Among 460 individuals with optimal blood pressure (<120/80 mmHg) at baseline, 55 progressed to hypertension during 5 years of follow-up. Twenty-nine cases of incident hypertension and 29 controls, matched for age, sex, and baseline systolic blood pressure, were included in this study. Serum metabolites were measured by gas chromatography-tandem mass spectrometry. t-test and logistic regression analysis were applied to investigate the association between metabolites and incident hypertension. Among the 241 metabolites identified in this study, baseline levels of 26 metabolites were significantly different between hypertension and control groups. After adjusting for body mass index, smoking, and drinking, 16 out of the 26 metabolites were still associated with hypertension risk including four amino acids. Amino acids were negatively associated with risk of future hypertension, with odds ratio (OR) ranging from 0.33 to 0.53. Two of these amino acids were essential amino acids including threonine and phenylalanine. Higher level of lyxose, a fermentation product of gut microbes, was associated with higher risk of hypertension. Our study identified multiple metabolites that associated with hypertension risk. These findings implied that low amino acid levels and gut microbiome might play an important role in the pathogenesis of hypertension. PMID:27119083

  2. Land cover associations of nesting territories of three sympatric buteos in shortgrass prairie

    USGS Publications Warehouse

    McConnell, S.; O'Connell, T. J.; Leslie, David M.

    2008-01-01

    Three species of Buteo hawks nest sympatrically in the southern Great Plains of the United States. Dietary overlap among them is broad and we tested the hypothesis these species partition their breeding habitat spatially. We compared land cover and topography around 224 nests of the three species breeding in shortgrass prairie in 2004 and 2005. Red-tailed Hawks (Buteo jamaicensis) nested almost exclusively in riparian timber surrounded by prairie (95% prairie land cover around nests) and disproportionately used areas with greater topographic relief within prairie landscapes. Swainson's Hawks (B. swainsoni) commonly nested in low-relief areas dominated by small-grain production agriculture but generally used habitats in proportion to availability. Most nest sites of Ferruginous Hawks (B. regalis) were in prairie (78% prairie land cover around nests), but some were in areas that were at least partially agricultural. Ferruginous Hawks had at least two times more sand sagebrush (Artemisia filifolia) around their nests than their two congeners. We conclude that sympatric breeding Buteos on the southern Great Plains spatially partitioned nest sites according to subtle differences in land cover and topography.

  3. Breeding ecology and nesting habitat associations of five marsh bird species in western New York

    USGS Publications Warehouse

    Lor, S.; Malecki, R.A.

    2006-01-01

    Nesting habitats and nest success of five species of marsh birds were studied during 1997 and 1998 at the Iroquois National Wildlife Refuge (NWR) and the adjacent Oak Orchard and Tonawanda State Wildlife Management Areas (WMA) located in western New York. Nest searches located 18 American Bittern (Botaurus lentiginosus), 117 Least Bittern (Ixobrychus exilis), 189 Pied-billed Grebe (Podilymbus podiceps), 23 Sora (Porzana carolina), and 72 Virginia Rail (Rallus limicola) nests. Average nest densities in 1998, our best nest searching year, ranged from 0.01/ha for Soras (N = 8) to 0.28/ha for Pied-billed Grebes (N = 160). Mayfield nest success estimates for Least Bittern were 80% (N = 16) in 1997 and 46% (N = 37) in 1998. Nest success estimates were 72% (N = 55) for Pied-billed Grebe, 43% (N = 6) for Sora, and 38% (N = 20) for Virginia Rail. Nests of all five species were located in ???70% emergent vegetation with a mean water depth of 24-56 cm and an average vegetation height that ranged from 69-133 cm. Logistic regression models were developed for each species using habitat variables at nest and random site locations. Each model was ranked with Akaike's Information Criterion for small sample size (AICc). In general, our best models indicated that increased emergent vegetation and horizontal cover with shallow water depths improved the odds of encountering marsh bird nests in the wetlands of western New York. We suggest that managing wetlands as a complex, at different stages of succession, would best benefit marsh bird species.

  4. Factors associated with excessive bleeding in cardiopulmonary bypass patients: a nested case-control study

    PubMed Central

    Jimenez Rivera, Juan J; Iribarren, Jose L; Raya, Jose M; Nassar, Ibrahim; Lorente, Leonardo; Perez, Rosalia; Brouard, Maitane; Lorenzo, Jose M; Garrido, Pilar; Barrios, Ysamar; Diaz, Maribel; Alarco, Blas; Martinez, Rafael; Mora, Maria L

    2007-01-01

    Introduction Excessive bleeding (EB) after cardiopulmonary bypass (CPB) may lead to increased mortality, morbidity, transfusion requirements and re-intervention. Less than 50% of patients undergoing re-intervention exhibit surgical sources of bleeding. We studied clinical and genetic factors associated with EB. Methods We performed a nested case-control study of 26 patients who did not receive antifibrinolytic prophylaxis. Variables were collected preoperatively, at intensive care unit (ICU) admission, at 4 and 24 hours post-CPB. EB was defined as 24-hour blood loss of >1 l post-CPB. Associations of EB with genetic, demographic, and clinical factors were analyzed, using SPSS-12.2 for statistical purposes. Results EB incidence was 50%, associated with body mass index (BMI)< 26.4 (25–28) Kg/m2, (P = 0.03), lower preoperative levels of plasminogen activator inhibitor-1 (PAI-1) (P = 0.01), lower body temperature during CPB (P = 0.037) and at ICU admission (P = 0.029), and internal mammary artery graft (P = 0.03) in bypass surgery. We found a significant association between EB and 5G homozygotes for PAI-1, after adjusting for BMI (F = 6.07; P = 0.02) and temperature during CPB (F = 8.84; P = 0.007). EB patients showed higher consumption of complement, coagulation, fibrinolysis and hemoderivatives, with significantly lower leptin levels at all postoperative time points (P = 0.01, P < 0.01 and P < 0.01). Conclusion Excessive postoperative bleeding in CPB patients was associated with demographics, particularly less pronounced BMI, and surgical factors together with serine protease activation. PMID:17425777

  5. Factors associated with duck nest success in the prairie pothole region of Canada

    USGS Publications Warehouse

    Greenwood, R.J.; Sargeant, A.B.; Johnson, D.H.; Cowardin, L.; Shaffer, T.L.

    1995-01-01

    Populations of some dabbling ducks have declined sharply in recent decades and information is needed to understand reasons for this. During 1982-85, we studied duck nesting for 1-4 years in 17 1.6 by 16.0-km, high-density duck areas in the Prairie Pothole Region (PPR) of Canada, 9 in parkland and 8 in prairie. We estimated nest-initiation dates, habitat preferences, nest success, and nest fates for mallards (Anas platyrhynchos), gadwalls (A. strepera), blue-winged teals (A. discors), northern shovelers (A. clypeata), and northern pintails (A. acuta). We also examined the relation of mallard production to geographic and temporal variation in wetlands, breeding populations, nesting effort, and hatch rate.Average periods of nest initiation were similar for mallards and northern pintails, and nearly twice as long as those of gadwalls, blue-winged teals, and northern shovelers. Median date of nest initiation was related to presence of wet wetlands (contained visible standing water), spring precipitation, and May temperature. Length of initiation period was related to presence of wet wetlands and precipitation in May, June temperature, and nest success; it was negatively related overall to drought that prevailed over much of Prairie Canada during the study, especially in 1984.Mallards, gadwalls, and northern pintails nested most often in brush in native grassland, blue-winged teals in road rights-of-way, and northern shovelers in hayfields and small (<2 ha) untilled tracts of upland habitat (hereafter called Odd area). Among 8 habitat classes that composed all suitable nesting habitat of each study area, nest success estimates averaged 25% in Woodland, 19% in Brush, 18% in Hayland, 16% in Wetland, 15% in Grass, 11% in Odd area, 8% in Right-of-way, and 2% in Cropland. We detected no significant difference in nest success among species: mallard (11%), gadwall (14%), blue-winged teal (15%), northern shoveler (12%), and northern pintail (7%). Annual nest success (pooled by

  6. Serum interleukin-6 associated with hepatocellular carcinoma risk: a nested case-control study.

    PubMed

    Ohishi, Waka; Cologne, John B; Fujiwara, Saeko; Suzuki, Gen; Hayashi, Tomonori; Niwa, Yasuharu; Akahoshi, Masazumi; Ueda, Keiko; Tsuge, Masataka; Chayama, Kazuaki

    2014-01-01

    Inflammatory markers have been associated with increased risk of several cancers, including colon, lung, breast and liver, but the evidence is inconsistent. We conducted a nested case-control study in the longitudinal cohort of atomic-bomb survivors. The study included 224 hepatocellular carcinoma (HCC) cases and 644 controls individually matched to cases on gender, age, city and time and method of serum storage, and countermatched on radiation dose. We measured C-reactive protein (CRP) and interleukin (IL)-6 using stored sera obtained within 6 years before HCC diagnosis from 188 HCC cases and 605 controls with adequate volumes of donated blood. Analyses with adjustment for hepatitis virus infection, alcohol consumption, smoking habit, body mass index (BMI) and radiation dose showed that relative risk (RR) of HCC [95% confidence interval (CI)] in the highest tertile of CRP levels was 1.94 (0.72-5.51) compared to the lowest tertile (p = 0.20). RR of HCC (95% CI) in the highest tertile of IL-6 levels was 5.12 (1.54-20.1) compared to the lowest tertile (p = 0.007). Among subjects with BMI > 25.0 kg/m(2) , a stronger association was found between a 1-standard deviation (SD) increase in log IL-6 and HCC risk compared to subjects in the middle quintile of BMI (21.3-22.9 kg/m(2) ), resulting in adjusted RR (95% CI) of 3.09 (1.78-5.81; p = 0.015). The results indicate that higher serum levels of IL-6 are associated with increased HCC risk, independently of hepatitis virus infection, lifestyle-related factors and radiation exposure. The association is especially pronounced among subjects with obesity. PMID:23784949

  7. Are interstitial lung abnormalities associated with COPD? A nested case–control study

    PubMed Central

    Bozzetti, Francesca; Paladini, Ilaria; Rabaiotti, Enrico; Franceschini, Alessandro; Alfieri, Veronica; Chetta, Alfredo; Crisafulli, Ernesto; Silva, Mario; Pastorino, Ugo; Sverzellati, Nicola

    2016-01-01

    Purpose In this study, we tested the association between COPD and interstitial lung abnormality (ILA), notably in relation to the presence of computed tomography (CT) signs of lung fibrosis. Patients and methods COPD cases were selected from participants undergoing lung cancer screening (Multicentric Italian Lung Detection trial) for airflow obstruction (n=311/2,303, 13.5%) and 146 consecutive patients with clinical COPD. In all, 457 COPD cases were selected and classified according to the stages of Global Initiative for Chronic Obstructive Lung Disease. A nested matching (case:control = 1:2) according to age, sex, and smoking history was operated between each COPD case and two control subjects from Multicentric Italian Lung Detection trial without airflow obstruction. Low-dose CT scans of COPD cases and controls were reviewed for the presence of ILA, which were classified into definite or indeterminate according to the presence of signs of lung fibrosis. Results The frequency of definite ILA was similar between COPD cases and controls (P=0.2), independent of the presence of signs of lung fibrosis (P=0.07). Combined definite and indeterminate ILA was homogeneously distributed across Global Initiative for Chronic Obstructive Lung Disease stages (P=0.6). Definite ILA was directly associated with current smoker status (odds ratio [OR] 4.05, 95% confidence interval [CI]: 2.2–7.4) and increasing pack-years (OR 1.01, 95% CI: 1–1.02). Subjects with any fibrotic ILA were more likely to be older (OR 1.17, 95% CI: 1.10–1.25) and male (OR 8.58, 95% CI: 1.58–68.9). Conclusion There was no association between COPD and definite ILA. However, low-dose CT signs of lung fibrosis were also observed in COPD, and their clinical relevance is yet to be determined. PMID:27307724

  8. Nested PCR detection of abalone shriveling syndrome-associated virus in China.

    PubMed

    Jiang, Jing-Zhe; Liang, Ya-Yu; Luo, Li-Juan; Guo, Zhi-Xun; Zhuang, Jun; Liu, Guang-Feng; Su, You-Lu; Wang, Jiang-Yong

    2012-09-01

    Haliotis diversicolor (small abalone) is an economic seafood found off the Southern coast of China. Since 1999, the cultured abalone yields in China have been affected severely by continual outbreaks of a fatal epidemic disease caused by abalone shriveling syndrome associated virus (AbSV), a double-stranded DNA virus. Although the pathogenicity and genome of AbSV have been ascertained, the epidemiology of AbSV infection remains to be investigated. In the present study, four pairs of AbSV-specific primers were designed on the basis of open reading frame (ORF)24 and ORF25 sequences in the AbSV genome. Two nested PCR detection methods were established by optimization of the annealing temperatures of primers. The results showed that the specificity of primers for AbSV detection could not be interfered with by the host genome and other aquaculture species or viruses. The detection limits of the two methods were about 10 copies of recombinant plasmid containing AbSV genes in 20μL reaction mixture. The results of detection of the AbSV epidemic showed that AbSV was still present in juvenile abalones in some farms along the Southern coast of China (Fujian and Guangdong).

  9. Associations with fracture in patients with diabetes: a nested case–control study

    PubMed Central

    Starup-Linde, Jakob; Gregersen, Søren; Vestergaard, Peter

    2016-01-01

    Objectives Diabetes mellitus is associated with an increased risk of fractures, which is not fully explained by bone mineral density and common risk factors. The aim of this study is to investigate the association of medication and biochemical markers on the risk of fracture in a diabetes population. Design and setting A nested case–control study was conducted based on Danish diabetes patients from The Danish National Hospital Discharge Registry. Participants The cases of the study were diabetes patients with a fracture (n=24 349), and controls were diabetes patients with no fracture (n=132 349). A total of 2627 diabetes patients were available for an analysis of patient characteristics, comorbidities, biochemical parameters and drug usage. Results Age (OR=1.02, 95% CI 1.01 to 1.04), diabetes duration (OR=1.06, 95% CI 1.02 to 1.09), a diagnosis of previous fracture (OR=2.20, 95% CI 1.55 to 3.11), an alcohol-related diagnosis (OR=2.94, 95% CI 1.76 to 4.91), total cholesterol level (OR=2.50, 95% CI 1.20 to 5.21) and the usage of antiepileptics (OR=2.12, 95% CI 1.39 to 3.59) all increased the odds of fracture. Low-density lipoprotein cholesterol levels decreased the odds of fracture (OR =0.34, 95% CI 0.16 to 0.74), where the level of 3.04–5.96 mmol/L was optimal with regard to fracture risk. Conclusions Low-density lipoprotein cholesterol may improve our understanding of fractures in diabetes patients, and it may be added to current fracture risk models in diabetes patients. PMID:26873048

  10. Lessons from Dwarf8 on the Strengths and Weaknesses of Structured Association Mapping

    PubMed Central

    Larsson, Sara J.; Lipka, Alexander E.; Buckler, Edward S.

    2013-01-01

    The strengths of association mapping lie in its resolution and allelic richness, but spurious associations arising from historical relationships and selection patterns need to be accounted for in statistical analyses. Here we reanalyze one of the first generation structured association mapping studies of the Dwarf8 (d8) locus with flowering time in maize using the full range of new mapping populations, statistical approaches, and haplotype maps. Because this trait was highly correlated with population structure, we found that basic structured association methods overestimate phenotypic effects in the region, while mixed model approaches perform substantially better. Combined with analysis of the maize nested association mapping population (a multi-family crossing design), it is concluded that most, if not all, of the QTL effects at the general location of the d8 locus are from rare extended haplotypes that include other linked QTLs and that d8 is unlikely to be involved in controlling flowering time in maize. Previous independent studies have shown evidence for selection at the d8 locus. Based on the evidence of population bottleneck, selection patterns, and haplotype structure observed in the region, we suggest that multiple traits may be strongly correlated with population structure and that selection on these traits has influenced segregation patterns in the region. Overall, this study provides insight into how modern association and linkage mapping, combined with haplotype analysis, can produce results that are more robust. PMID:23437002

  11. Assessing exotic plant species invasions and associated soil characteristics: A case study in eastern Rocky Mountain National Park, Colorado, USA, using the pixel nested plot design

    USGS Publications Warehouse

    Kalkhan, M.A.; Stafford, E.J.; Woodly, P.J.; Stohlgren, T.J.

    2007-01-01

    Rocky Mountain National Park (RMNP), Colorado, USA, contains a diversity of plant species. However, many exotic plant species have become established, potentially impacting the structure and function of native plant communities. Our goal was to quantify patterns of exotic plant species in relation to native plant species, soil characteristics, and other abiotic factors that may indicate or predict their establishment and success. Our research approach for field data collection was based on a field plot design called the pixel nested plot. The pixel nested plot provides a link to multi-phase and multi-scale spatial modeling-mapping techniques that can be used to estimate total species richness and patterns of plant diversity at finer landscape scales. Within the eastern region of RMNP, in an area of approximately 35,000 ha, we established a total of 60 pixel nested plots in 9 vegetation types. We used canonical correspondence analysis (CCA) and multiple linear regressions to quantify relationships between soil characteristics and native and exotic plant species richness and cover. We also used linear correlation, spatial autocorrelation and cross correlation statistics to test for the spatial patterns of variables of interest. CCA showed that exotic species were significantly (P < 0.05) associated with photosynthetically active radiation (r = 0.55), soil nitrogen (r = 0.58) and bare ground (r = -0.66). Pearson's correlation statistic showed significant linear relationships between exotic species, organic carbon, soil nitrogen, and bare ground. While spatial autocorrelations indicated that our 60 pixel nested plots were spatially independent, the cross correlation statistics indicated that exotic plant species were spatially associated with bare ground, in general, exotic plant species were most abundant in areas of high native species richness. This indicates that resource managers should focus on the protection of relatively rare native rich sites with little

  12. Drought and cooler temperatures are associated with higher nest survival in Mountain Plovers

    USGS Publications Warehouse

    Dreitz, V.J.; Conrey, R.Y.; Skagen, S.K.

    2012-01-01

    Native grasslands have been altered to a greater extent than any other biome in North America. The habitats and resources needed to support breeding performance of grassland birds endemic to prairie ecosystems are currently threatened by land management practices and impending climate change. Climate models for the Great Plains prairie region predict a future of hotter and drier summers with strong multiyear droughts and more frequent and severe precipitation events. We examined how fluctuations in weather conditions in eastern Colorado influenced nest survival of an avian species that has experienced recent population declines, the Mountain Plover (Charadrius montanus). Nest survival averaged 27.2% over a 7-yr period (n = 936 nests) and declined as the breeding season progressed. Nest survival was favored by dry conditions and cooler temperatures. Projected changes in regional precipitation patterns will likely influence nest survival, with positive influences of predicted declines in summer rainfall yet negative effects of more intense rain events. The interplay of climate change and land use practices within prairie ecosystems may result in Mountain Plovers shifting their distribution, changing local abundance, and adjusting fecundity to adapt to their changing environment.

  13. {open_quotes}Feature{close_quotes} mapping of the HLA-C linked DNA region: Construction by sequencing from nested deletions

    SciTech Connect

    Krishnan, B.R.; Chaplin, D.D. |

    1994-09-01

    The HLA complex located on chromosome 6p spans {approximately}4 Mb and is gene dense. To enable systematic analysis of less well-characterized portions of HLA, we are defining significant {open_quotes}features{close_quotes} of these DNA regions: locations of putative genes (prediction of exons by GRAIL analysis) and Alu elements, regions with homology to the database, and regions of evolutionarily conserved DNA sequence. Initially, we cloned a 35 kb DNA segment adjacent to HLA-C into a transposon {gamma}{delta}-based cosmid vector designed for generating nested deletions in vivo. Over 70 informative nested deletions were obtained and sequenced by fluorescent-automated technology. Islands of DNA sequences were obtained and used to construct a feature map of the 35 kb HLA segment. Our data (i) defined the organization of the previously identified keratinocyte-specific S gene, (ii) generated the DNA sequence of two evolutionarily conserved DNA segments, and (iii) located otherwise undefined putative exons and Alu elements. The construction of such feature maps of large DNA segments using the nested deletion-sequencing approach provides an efficient means to identify DNA segments meriting systematic and detailed analysis.

  14. Nesting Instincts.

    ERIC Educational Resources Information Center

    Greenman, Geri

    2003-01-01

    Describes an art project where beginning drawing students used values and chiaroscuro techniques to draw bird nests. Explains how the students observed the nest that was displayed in the art classroom. Discusses the steps involved in creating the artworks. (CMK)

  15. Sharing mates and nest boxes is associated with female "friendship" in European starlings, Sturnus vulgaris.

    PubMed

    Henry, Laurence; Bourguet, Cécile; Coulon, Marion; Aubry, Christine; Hausberger, Martine

    2013-02-01

    Breeding decisions in birds involve both mate and nest choice, and there is increasing evidence that social influences may modulate individual choices. Female preferences may be affected by other females' preferences and mutual choice cannot always be excluded, which makes the whole pattern more complex than assumed by most sexual selection models. Social transmission may be facilitated by particular social bonds, therefore prebreeding social networks may influence later mate choices. The other case where females share mate or resources is polygyny, generally viewed to only benefit males. If mutual benefits may arise then mechanisms should evolve to reduce the reproductive cost for females such as to reduce the cost of aggression by sharing their mate with a preferred same-sex social partner. We tested the hypothesis that females' mating decisions may be influenced by the prebreeding social network and that social partner relations established prior to breeding may share decisions (mate/sites) in a facultatively polygynous species, the European starling. Two experiments were designed to test the relative importance of male or nest by following the whole dynamics of the breeding cycle from the prebreeding period until mate and nest selection. In both cases socially isolated females tended to be excluded from breeding, while prebreeding social partners tended to share mates and to nest in close proximity, mate copying leading in some case to polygyny. The final pattern resulted both from female "likes and dislikes" and male preferences for some females. Aggressive interactions between females were rare. Vocal sharing between females may have been a clue for males as to the degree of social integration of these females. PMID:23106801

  16. Conflation and integration of archived geologic maps and associated uncertainties

    USGS Publications Warehouse

    Shoberg, Thomas G.

    2016-01-01

    Old, archived geologic maps are often available with little or no associated metadata. This creates special problems in terms of extracting their data to use with a modern database. This research focuses on some problems and uncertainties associated with conflating older geologic maps in regions where modern geologic maps are, as yet, non-existent as well as vertically integrating the conflated maps with layers of modern GIS data (in this case, The National Map of the U.S. Geological Survey). Ste. Genevieve County, Missouri was chosen as the test area. It is covered by six archived geologic maps constructed in the years between 1928 and 1994. Conflating these maps results in a map that is internally consistent with these six maps, is digitally integrated with hydrography, elevation and orthoimagery data, and has a 95% confidence interval useful for further data set integration.

  17. Microbial Infections Are Associated with Embryo Mortality in Arctic-Nesting Geese

    PubMed Central

    Hansen, Cristina M.; Meixell, Brandt W.; Van Hemert, Caroline; Hare, Rebekah F.

    2015-01-01

    To address the role of bacterial infection in hatching failure of wild geese, we monitored embryo development in a breeding population of Greater white-fronted geese (Anser albifrons) on the Arctic Coastal Plain of Alaska. During 2013, we observed mortality of normally developing embryos and collected 36 addled eggs for analysis. We also collected 17 infertile eggs for comparison. Using standard culture methods and gene sequencing to identify bacteria within collected eggs, we identified a potentially novel species of Neisseria in 33 eggs, Macrococcus caseolyticus in 6 eggs, and Streptococcus uberis and Rothia nasimurium in 4 eggs each. We detected seven other bacterial species at lower frequencies. Sequences of the 16S rRNA genes from the Neisseria isolates most closely matched sequences from N. animaloris and N. canis (96 to 97% identity), but phylogenetic analysis suggested substantial genetic differentiation between egg isolates and known Neisseria species. Although definitive sources of the bacteria remain unknown, we detected Neisseria DNA from swabs of eggshells, nest contents, and cloacae of nesting females. To assess the pathogenicity of bacteria identified in contents of addled eggs, we inoculated isolates of Neisseria, Macrococcus, Streptococcus, and Rothia at various concentrations into developing chicken eggs. Seven-day mortality rates varied from 70 to 100%, depending on the bacterial species and inoculation dose. Our results suggest that bacterial infections are a source of embryo mortality in wild geese in the Arctic. PMID:26048928

  18. Microbial infections are associated with embryo mortality in Arctic-nesting geese.

    USGS Publications Warehouse

    Hansen, Cristina M.; Meixell, Brandt W.; Van Hemert, Caroline R.; Hare, Rebekah F.; Hueffer, Karsten

    2015-01-01

    To address the role of bacterial infection in hatching failure of wild geese, we monitored embryo development in a breeding population of Greater white-fronted geese (Anser albifrons) on the Arctic Coastal Plain of Alaska. During 2013, we observed mortality of normally developing embryos and collected 36 addled eggs for analysis. We also collected 17 infertile eggs for comparison. Using standard culture methods and gene sequencing to identify bacteria within collected eggs, we identified a potentially novel species of Neisseria in 33 eggs, Macrococcus caseolyticus in 6 eggs, and Streptococcus uberis and Rothia nasimurium in 4 eggs each. We detected seven other bacterial species at lower frequencies. Sequences of the 16S rRNA genes from the Neisseria isolates most closely matched sequences from N. animaloris and N. canis (96 to 97% identity), but phylogenetic analysis suggested substantial genetic differentiation between egg isolates and known Neisseria species. Although definitive sources of the bacteria remain unknown, we detected Neisseria DNA from swabs of eggshells, nest contents, and cloacae of nesting females. To assess the pathogenicity of bacteria identified in contents of addled eggs, we inoculated isolates of Neisseria, Macrococcus, Streptococcus, and Rothia at various concentrations into developing chicken eggs. Seven-day mortality rates varied from 70 to 100%, depending on the bacterial species and inoculation dose. Our results suggest that bacterial infections are a source of embryo mortality in wild geese in the Arctic.    

  19. Ensemble experiments using a nested LETKF system to reproduce intense vortices associated with tornadoes of 6 May 2012 in Japan

    NASA Astrophysics Data System (ADS)

    Seko, Hiromu; Kunii, Masaru; Yokota, Sho; Tsuyuki, Tadashi; Miyoshi, Takemasa

    2015-12-01

    Experiments simulating intense vortices associated with tornadoes that occurred on 6 May 2012 on the Kanto Plain, Japan, were performed with a nested local ensemble transform Kalman filter (LETKF) system. Intense vortices were reproduced by downscale experiments with a 12-member ensemble in which the initial conditions were obtained from the nested LETKF system analyses. The downscale experiments successfully generated intense vortices in three regions similar to the observed vortices, whereas only one tornado was reproduced by a deterministic forecast. The intense vorticity of the strongest tornado, which was observed in the southernmost region, was successfully reproduced by 10 of the 12 ensemble members. An examination of the results of the ensemble downscale experiments showed that the duration of intense vorticities tended to be longer when the vertical shear of the horizontal wind was larger and the lower airflow was more humid. Overall, the study results show that ensemble forecasts have the following merits: (1) probabilistic forecasts of the outbreak of intense vortices associated with tornadoes are possible; (2) the miss rate of outbreaks should decrease; and (3) environmental factors favoring outbreaks can be obtained by comparing the multiple possible scenarios of the ensemble forecasts.

  20. Triangular Nests!

    ERIC Educational Resources Information Center

    Powell, R. I.

    2002-01-01

    Shows how integer-sided triangles can be nested, each nest having a single enclosing isosceles triangle. Brings to light what can be seen as a relatively simple generalization of Pythagoras' theorem, a result that should be readily accessible to many secondary school pupils. (Author/KHR)

  1. Marsh nesting by mallards

    USGS Publications Warehouse

    Krapu, G.L.; Talent, L.G.; Dwyer, T.J.

    1979-01-01

    Nest-site selection by mallard (Anas platyrhynchos) hens was studied on a 52-km2, privately owned area in the Missouri Coteau of south-central North Dakota during 1974-77. Sixty-six percent of 53 nests initiated by radio-marked and unmarked hens were in wetlands in dense stands of emergent vegetation and usually within 50 m of the wetland edge. These findings and other sources of information suggest that significant numbers of mallards breeding in the Prairie Pothole Region nest in marsh habitat. Potential factors contributing to mallard use of marsh habitat for nesting purposes are discussed. Management considerations associated with marsh nesting by mallards are described and research needs are identified.

  2. Complete Mapping of a Cystine Knot and Nested Disulfides of Recombinant Human Arylsulfatase A by Multi-Enzyme Digestion and LC-MS Analysis Using CID and ETD

    NASA Astrophysics Data System (ADS)

    Ni, Wenqin; Lin, Melanie; Salinas, Paul; Savickas, Philip; Wu, Shiaw-Lin; Karger, Barry L.

    2013-01-01

    Cystine knots or nested disulfides are structurally difficult to characterize, despite current technological advances in peptide mapping with high-resolution liquid chromatography coupled with mass spectrometry (LC-MS). In the case of recombinant human arylsulfatase A (rhASA), there is one cystine knot at the C-terminal, a pair of nested disulfides at the middle, and two out of three unpaired cysteines in the N-terminal region. The statuses of these cysteines are critical structure attributes for rhASA function and stability that requires precise examination. We used a unique approach to determine the status and linkage of each cysteine in rhASA, which was comprised of multi-enzyme digestion strategies (from Lys-C, trypsin, Asp-N, pepsin, and PNGase F) and multi-fragmentation methods in mass spectrometry using electron transfer dissociation (ETD), collision induced dissociation (CID), and CID with MS3 (after ETD). In addition to generating desired lengths of enzymatic peptides for effective fragmentation, the digestion pH was optimized to minimize the disulfide scrambling. The disulfide linkages, including the cystine knot and a pair of nested cysteines, unpaired cysteines, and the post-translational modification of a cysteine to formylglycine, were all determined. In the assignment, the disulfide linkages were Cys138-Cys154, Cys143-Cys150, Cys282-Cys396, Cys470-Cys482, Cys471-Cys484, and Cys475-Cys481. For the unpaired cysteines, Cys20 and Cys276 were free cysteines, and Cys51 was largely converted to formylglycine (>70 %). A successful methodology has been developed, which can be routinely used to determine these difficult-to-resolve disulfide linkages, ensuring drug function and stability.

  3. Association between Use of Oral Anti-Diabetic Drugs and the Risk of Sepsis: A Nested Case-Control Study

    PubMed Central

    Shih, Chia-Jen; Wu, Yueh-Lin; Chao, Pei-Wen; Kuo, Shu-Chen; Yang, Chih-Yu; Li, Szu-Yuan; Ou, Shuo-Ming; Chen, Yung-Tai

    2015-01-01

    Although oral antidiabetic drugs (OADs) have been associated with immunomodulation in preclinical studies, little is still known about the association between the use of OADs and the risk of sepsis. Using a cohort of patients, extracted from Taiwan’s National Health Insurance Research Database, with type 2 diabetes who were newly diagnosed between 2010 and 2012 and treated with OADs, we conducted a nested case-control study involving 43,015 cases (patients who were first hospitalized for sepsis) and 43,015 matched controls. Compared with non-use, metformin use was associated with a decreased risk of developing sepsis (adjusted odds ratio [OR] 0.80, 95% confidence interval [CI] 0.77–0.83, P < 0.001), but meglitinide (adjusted OR 1.32, 95% CI 1.25–1.40, P < 0.001) use was associated with the increased risk of developing sepsis. The risk for development of sepsis was also lower among current (adjusted OR 0.87, 95% CI 0.78–0.96) and recent (adjusted OR 0.83, 95% CI 0.73–0.94) thiazolidinedione users. Current or recent sulfonylurea use and dipeptidyl peptidase-4 inhibitor use were not significantly associated with the development of sepsis. Our results highlight the need to consider the potential pleiotropic effect of OADs against sepsis in addition to the lowering of blood glucose. PMID:26463557

  4. Different axes of environmental variation explain the presence versus extent of cooperative nest founding associations in Polistes paper wasps

    PubMed Central

    Sheehan, Michael J; Botero, Carlos A; Hendry, Tory A; Sedio, Brian E; Jandt, Jennifer M.; Weiner, Susan; Toth, Amy L; Tibbetts, Elizabeth A

    2015-01-01

    Ecological constraints on independent breeding are recognized as major drivers of cooperative breeding across diverse lineages. How the prevalence and degree of cooperative breeding relates to ecological variation remains unresolved. Using a large dataset on cooperative nesting in Polistes wasps we demonstrate that different aspects of cooperative breeding are likely to be driven by different aspects of climate. Whether or not a species forms cooperative groups is associated with greater short-term temperature fluctuations. In contrast, the number of cooperative foundresses increases in more benign environments with warmer, wetter conditions. The same dataset reveals that intraspecific responses to climate variation do not mirror genus-wide trends and instead are highly heterogeneous among species. Collectively these data suggest that the ecological drivers that lead to the origin or loss of cooperation are different from those that influence the extent of its expression within populations. PMID:26248800

  5. Different axes of environmental variation explain the presence vs. extent of cooperative nest founding associations in Polistes paper wasps.

    PubMed

    Sheehan, Michael J; Botero, Carlos A; Hendry, Tory A; Sedio, Brian E; Jandt, Jennifer M; Weiner, Susan; Toth, Amy L; Tibbetts, Elizabeth A

    2015-10-01

    Ecological constraints on independent breeding are recognised as major drivers of cooperative breeding across diverse lineages. How the prevalence and degree of cooperative breeding relates to ecological variation remains unresolved. Using a large data set of cooperative nesting in Polistes wasps we demonstrate that different aspects of cooperative breeding are likely to be driven by different aspects of climate. Whether or not a species forms cooperative groups is associated with greater short-term temperature fluctuations. In contrast, the number of cooperative foundresses increases in more benign environments with warmer, wetter conditions. The same data set reveals that intraspecific responses to climate variation do not mirror genus-wide trends and instead are highly heterogeneous among species. Collectively these data suggest that the ecological drivers that lead to the origin or loss of cooperation are different from those that influence the extent of its expression within populations.

  6. Nested Cohort

    Cancer.gov

    NestedCohort is an R software package for fitting Kaplan-Meier and Cox Models to estimate standardized survival and attributable risks for studies where covariates of interest are observed on only a sample of the cohort.

  7. Sandflies (Diptera: Psychodidae) associated with opossum nests at urban sites in southeastern Brazil: a risk factor for urban and periurban zoonotic Leishmania transmission?

    PubMed

    Cutolo, Andre Antonio; Teodoro, Anna Karollina Menezes; Ovallos, Fredy Galvis; Allegretti, Silmara Marques; Galati, Eunice Aparecida Bianchi

    2014-06-01

    Sandflies associated with opossum nests are reported for the first time in the yards of residences located in the urban area of the municipality of Monte Mor, situated in the metropolitan region of Campinas, state of São Paulo, Brazil. Eleven specimens of Evandromyia cortelezzii and one of Evandromyia lenti were captured in two Didelphis albiventris nests. Ev. cortelezzii is considered a secondary vector species for the transmission of Leishmania (Viannia) braziliensis and Leishmania (Leishmania) infantum in the Neotropics. This association may contribute to the introduction, establishment and maintenance of urban and periurban zoonotic transmission outbreaks of Leishmania and should therefore be investigated further.

  8. Blood fatty acid patterns are associated with prostate cancer risk in a prospective nested case-control study

    PubMed Central

    Yang, Meng; Ayuningtyas, Azalea; Kenfield, Stacey A.; Sesso, Howard D.; Campos, Hannia; Ma, Jing; Stampfer1, Meir J.; Chavarro, Jorge E.

    2016-01-01

    Background Circulating fatty acids are highly correlated with each other and analyzing fatty acid patterns could better capture their interactions and their relation to prostate cancer. We aimed to assess the associations between data-derived blood fatty acid patterns and prostate cancer risk. Methods We conducted a nested case-control study in the Physicians’ Health Study. Fatty acids levels were measured in whole blood samples of 476 cases and their matched controls by age and smoking status. Fatty acid patterns were identified using principal component analysis. Conditional logistic regression was used to estimate odds ratio (OR) and 95% confidence interval (CI). Results Two patterns explaining 40.9% of total variation in blood fatty acid levels were identified. Pattern 1, which mainly reflects polyunsaturated fatty acid metabolism, was suggestively positively related to prostate cancer risk (ORquintile 5 vs. quintile 1=1.37, 95%CI=0.91–2.05, Ptrend=0.07). Pattern 2, which largely reflects de novo lipogenesis, was significantly associated with higher prostate cancer risk (ORquintile5 vs quintile1=1.63, 95%CI=1.04–2.55, Ptrend=0.02). This association was similar across tumor stage, grade, clinical aggressiveness categories and follow-up time. Conclusion The two patterns of fatty acids we identified were consistent with known interactions between fatty acid intake and metabolism. A pattern suggestive of higher activity in the de novo lipogenesis pathway was related to higher risk of prostate cancer. PMID:27488836

  9. Disentangling the Association between Statins, Cholesterol, and Colorectal Cancer: A Nested Case-Control Study

    PubMed Central

    Mamtani, Ronac; Lewis, James D.; Scott, Frank I.; Ahmad, Tariq; Goldberg, David S.; Datta, Jashodeep; Yang, Yu-Xiao; Boursi, Ben

    2016-01-01

    Background Several prior studies have found an association between statin use and reduced risk of colorectal cancer. We hypothesized that these findings may be due to systematic bias and examined the independent association of colorectal cancer risk with statin use, serum cholesterol, and change in cholesterol concentration. Methods and Findings 22,163 colorectal cancer cases and 86,538 matched controls between 1995 and 2013 were identified within The Health Improvement Network (THIN) a population-representative database. Conditional logistic regression models estimated colorectal cancer risk with statin use, serum total cholesterol (mmol/L), and change in total cholesterol level. We confirmed a decreased risk of colorectal cancer with statin use (long-term: odds ratio [OR], 0.95; 95% confidence interval [CI], 0.91–0.99; short-term: OR, 0.92; 95% CI, 0.85–0.99). However, to assess whether the observed association may result from indication bias, a subgroup analysis was conducted among patients prescribed a statin. In this subgroup (n = 5,102 cases, n = 19,032 controls), 3.1% of case subjects and 3.1% of controls discontinued therapy. The risk of colorectal cancer was not significantly different among those who continued statin therapy and those who discontinued (OR, 0.98; 95% CI, 0.79–1.22). Increased serum cholesterol was independently associated with decreased risk of colorectal cancer (OR, 0.89 per mmol/L increase; 95% CI, 0.87–0.91); the association was only present if serum cholesterol was measured near the cancer diagnosis (<6 mo: OR, 0.76; 95% CI, 0.47–0.61; >24 mo: OR, 0.98; 95% CI, 0.93–1.03). Decreases in serum total cholesterol >1 mmol/L ≥1 year prior to cancer diagnosis were associated with subsequent colorectal cancer (statin users: OR, 1.25; 95 CI%, 1.03–1.53; nonusers: OR, 2.36; 95 CI%, 1.78–3.12). As an observational study, limitations included incomplete data and residual confounding. Conclusions Although the risk of colorectal

  10. Association between prediagnostic biomarkers of inflammation and endothelial function and cancer risk: a nested case-control study.

    PubMed

    Touvier, Mathilde; Fezeu, Léopold; Ahluwalia, Namanjeet; Julia, Chantal; Charnaux, Nathalie; Sutton, Angela; Méjean, Caroline; Latino-Martel, Paule; Hercberg, Serge; Galan, Pilar; Czernichow, Sébastien

    2013-01-01

    Experimental and prevalent case-control studies suggest an association between biomarkers of inflammation, endothelial function, and adiposity and cancer risk, but results from prospective studies have been limited. The authors' objective was to prospectively examine the relations between these biomarkers and cancer risk. A nested case-control study was designed within the Supplémentation en Vitamines et Minéraux Antioxydants (SU.VI.MAX) Study, a nationwide French cohort study, to include all first primary incident cancers diagnosed between 1994 and 2007 (n = 512). Cases were matched with randomly selected controls (n = 1,024) on sex, age (in 2-year strata), body mass index (weight (kg)/height (m)(2); <25 vs. ≥25), and SU.VI.MAX intervention group. Conditional logistic regression was used to study the associations between prediagnostic levels of high-sensitivity C-reactive protein (hs-CRP), adiponectin, leptin, soluble intercellular adhesion molecule 1 (sICAM-1), soluble vascular cell adhesion molecule 1, soluble E-selectin, and monocyte chemoattractant protein 1 and cancer risk. All statistical tests were 2-sided. Plasma sICAM-1 level was positively associated with breast cancer risk (for quartile 4 vs. quartile 1, multivariate odds ratio (OR) = 1.86, 95% confidence interval (CI): 1.06, 3.26; P(trend) = 0.048). Plasma hs-CRP level was positively associated with prostate cancer risk (for quartile 4 vs. quartile 1, multivariate OR = 3.04, 95% CI: 1.28, 7.23; P(trend) = 0.03). These results suggest that prediagnostic hs-CRP and sICAM-1 levels are associated with increased prostate and breast cancer risk, respectively. PMID:23171880

  11. Association Between Prediagnostic Biomarkers of Inflammation and Endothelial Function and Cancer Risk: A Nested Case-Control Study

    PubMed Central

    Touvier, Mathilde; Fezeu, Léopold; Ahluwalia, Namanjeet; Julia, Chantal; Charnaux, Nathalie; Sutton, Angela; Méjean, Caroline; Latino-Martel, Paule; Hercberg, Serge; Galan, Pilar; Czernichow, Sébastien

    2013-01-01

    Experimental and prevalent case-control studies suggest an association between biomarkers of inflammation, endothelial function, and adiposity and cancer risk, but results from prospective studies have been limited. The authors’ objective was to prospectively examine the relations between these biomarkers and cancer risk. A nested case-control study was designed within the Supplémentation en Vitamines et Minéraux Antioxydants (SU.VI.MAX) Study, a nationwide French cohort study, to include all first primary incident cancers diagnosed between 1994 and 2007 (n = 512). Cases were matched with randomly selected controls (n = 1,024) on sex, age (in 2-year strata), body mass index (weight (kg)/height (m)2; <25 vs. ≥25), and SU.VI.MAX intervention group. Conditional logistic regression was used to study the associations between prediagnostic levels of high-sensitivity C-reactive protein (hs-CRP), adiponectin, leptin, soluble intercellular adhesion molecule 1 (sICAM-1), soluble vascular cell adhesion molecule 1, soluble E-selectin, and monocyte chemoattractant protein 1 and cancer risk. All statistical tests were 2-sided. Plasma sICAM-1 level was positively associated with breast cancer risk (for quartile 4 vs. quartile 1, multivariate odds ratio (OR) = 1.86, 95% confidence interval (CI): 1.06, 3.26; Ptrend = 0.048). Plasma hs-CRP level was positively associated with prostate cancer risk (for quartile 4 vs. quartile 1, multivariate OR = 3.04, 95% CI: 1.28, 7.23; Ptrend = 0.03). These results suggest that prediagnostic hs-CRP and sICAM-1 levels are associated with increased prostate and breast cancer risk, respectively. PMID:23171880

  12. Phenotyping of Association Mapping Panel of Sugarcane and Related Grasses

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genus Saccharum is an important species that is used for sugar and fuel. A diversity panel of Saccharum and related genera was created in Canal Point, FL to investigate important traits and later associate them with molecular markers for association mapping. The plants were transferred from the ...

  13. A highly sensitive single-tube nested PCR assay for the detection of Pineapple mealybug wilt associated virus-2 (PMWaV-2)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    An assay was developed for the detection of Pineapple mealybug wilt associated virus-2 (PMWaV-2), an important factor in the etiology of mealybug wilt of pineapple. The assay combines reverse transcription of RNA isolated from pineapple with a specific and very sensitive, single, closed-tube nested ...

  14. Fuel traps: mapping stability via water association.

    SciTech Connect

    Rempe, Susan L.; Clawson, Jacalyn S.; Greathouse, Jeffery A.; Alam, Todd M; Leung, Kevin; Varma, Sameer; Sabo, Dubravko; Martin, Marcus Gary; Cygan, Randall Timothy

    2007-03-01

    Hydrogen storage is a key enabling technology required for attaining a hydrogen-based economy. Fundamental research can reveal the underlying principles controlling hydrogen uptake and release by storage materials, and also aid in characterizing and designing novel storage materials. New ideas for hydrogen storage materials come from exploiting the properties of hydrophobic hydration, which refers to water s ability to stabilize, by its mode of association, specific structures under specific conditions. Although hydrogen was always considered too small to support the formation of solid clathrate hydrate structures, exciting new experiments show that water traps hydrogen molecules at conditions of low temperatures and moderate pressures. Hydrogen release is accomplished by simple warming. While these experiments lend credibility to the idea that water could form an environmentally attractive alternative storage compound for hydrogen fuel, which would advance our nation s goals of attaining a hydrogen-based economy, much work is yet required to understand and realize the full potential of clathrate hydrates for hydrogen storage. Here we undertake theoretical studies of hydrogen in water to establish a firm foundation for predictive work on clathrate hydrate H{sub 2} storage capabilities. Using molecular simulation and statistical mechanical theories based in part on quantum mechanical descriptions of molecular interactions, we characterize the interactions between hydrogen and liquid water in terms of structural and thermodynamic properties. In the process we validate classical force field models of hydrogen in water and discover new features of hydrophobic hydration that impact problems in both energy technology and biology. Finally, we predict hydrogen occupancy in the small and large cages of hydrogen clathrate hydrates, a property unresolved by previous experimental and theoretical work.

  15. MAP3: characterization of a novel microtubule-associated protein

    PubMed Central

    1985-01-01

    Using monoclonal antibodies we have characterized a brain protein that copurifies with microtubules. We identify it as a microtubule- associated protein (MAP) by the following criteria: it copolymerizes with tubulin through repeated cycles of microtubule assembly in vitro; it is not associated with any brain subcellular fraction other than microtubules; in double-label immunofluorescence experiments antibodies against this protein stain the same fibrous elements in cultured cells as are stained by antitubulin; and this fibrous staining pattern is dispersed when cytoplasmic microtubules are disrupted by colchicine. Because it is distinct from previously described MAPs we designate this novel species MAP3. The MAP3 protein consists of a closely spaced pair of polypeptides on SDS gels, Mr 180,000, which are present in both glial (glioma C6) and neuronal (neuroblastoma B104) cell lines. In brain the MAP3 antigen is present in both neurons and glia. In nerve cells its distribution is strikingly restricted: anti-MAP3 staining is detectable only in neurofilament-rich axons. It is not, however, a component of isolated brain intermediate filaments. PMID:3968174

  16. Association Mapping of Main Tomato Fruit Sugars and Organic Acids

    PubMed Central

    Zhao, Jiantao; Xu, Yao; Ding, Qin; Huang, Xinli; Zhang, Yating; Zou, Zhirong; Li, Mingjun; Cui, Lu; Zhang, Jing

    2016-01-01

    Association mapping has been widely used to map the significant associated loci responsible for natural variation in complex traits and are valuable for crop improvement. Sugars and organic acids are the most important metabolites in tomato fruits. We used a collection of 174 tomato accessions composed of Solanum lycopersicum (123 accessions) and S. lycopersicum var cerasiforme (51 accessions) to detect significantly associated loci controlling the variation of main sugars and organic acids. The accessions were genotyped with 182 SSRs spreading over the tomato genome. Association mapping was conducted on the main sugars and organic acids detected by gas chromatography-mass spectrometer (GC-MS) over 2 years using the mixed linear model (MLM). We detected a total of 58 significantly associated loci (P < 0.001) for the 17 sugars and organic acids, including fructose, glucose, sucrose, citric acid, malic acid. These results not only co-localized with several reported QTLs, including fru9.1/PV, suc9.1/PV, ca2.1/HS, ca3.1/PV, ca4.1/PV, and ca8.1/PV, but also provided a list of candidate significantly associated loci to be functionally validated. These significantly associated loci could be used for deciphering the genetic architecture of tomato fruit sugars and organic acids and for tomato quality breeding. PMID:27617019

  17. Association Mapping of Main Tomato Fruit Sugars and Organic Acids.

    PubMed

    Zhao, Jiantao; Xu, Yao; Ding, Qin; Huang, Xinli; Zhang, Yating; Zou, Zhirong; Li, Mingjun; Cui, Lu; Zhang, Jing

    2016-01-01

    Association mapping has been widely used to map the significant associated loci responsible for natural variation in complex traits and are valuable for crop improvement. Sugars and organic acids are the most important metabolites in tomato fruits. We used a collection of 174 tomato accessions composed of Solanum lycopersicum (123 accessions) and S. lycopersicum var cerasiforme (51 accessions) to detect significantly associated loci controlling the variation of main sugars and organic acids. The accessions were genotyped with 182 SSRs spreading over the tomato genome. Association mapping was conducted on the main sugars and organic acids detected by gas chromatography-mass spectrometer (GC-MS) over 2 years using the mixed linear model (MLM). We detected a total of 58 significantly associated loci (P < 0.001) for the 17 sugars and organic acids, including fructose, glucose, sucrose, citric acid, malic acid. These results not only co-localized with several reported QTLs, including fru9.1/PV, suc9.1/PV, ca2.1/HS, ca3.1/PV, ca4.1/PV, and ca8.1/PV, but also provided a list of candidate significantly associated loci to be functionally validated. These significantly associated loci could be used for deciphering the genetic architecture of tomato fruit sugars and organic acids and for tomato quality breeding.

  18. Association Mapping of Main Tomato Fruit Sugars and Organic Acids.

    PubMed

    Zhao, Jiantao; Xu, Yao; Ding, Qin; Huang, Xinli; Zhang, Yating; Zou, Zhirong; Li, Mingjun; Cui, Lu; Zhang, Jing

    2016-01-01

    Association mapping has been widely used to map the significant associated loci responsible for natural variation in complex traits and are valuable for crop improvement. Sugars and organic acids are the most important metabolites in tomato fruits. We used a collection of 174 tomato accessions composed of Solanum lycopersicum (123 accessions) and S. lycopersicum var cerasiforme (51 accessions) to detect significantly associated loci controlling the variation of main sugars and organic acids. The accessions were genotyped with 182 SSRs spreading over the tomato genome. Association mapping was conducted on the main sugars and organic acids detected by gas chromatography-mass spectrometer (GC-MS) over 2 years using the mixed linear model (MLM). We detected a total of 58 significantly associated loci (P < 0.001) for the 17 sugars and organic acids, including fructose, glucose, sucrose, citric acid, malic acid. These results not only co-localized with several reported QTLs, including fru9.1/PV, suc9.1/PV, ca2.1/HS, ca3.1/PV, ca4.1/PV, and ca8.1/PV, but also provided a list of candidate significantly associated loci to be functionally validated. These significantly associated loci could be used for deciphering the genetic architecture of tomato fruit sugars and organic acids and for tomato quality breeding. PMID:27617019

  19. Association Mapping of Main Tomato Fruit Sugars and Organic Acids

    PubMed Central

    Zhao, Jiantao; Xu, Yao; Ding, Qin; Huang, Xinli; Zhang, Yating; Zou, Zhirong; Li, Mingjun; Cui, Lu; Zhang, Jing

    2016-01-01

    Association mapping has been widely used to map the significant associated loci responsible for natural variation in complex traits and are valuable for crop improvement. Sugars and organic acids are the most important metabolites in tomato fruits. We used a collection of 174 tomato accessions composed of Solanum lycopersicum (123 accessions) and S. lycopersicum var cerasiforme (51 accessions) to detect significantly associated loci controlling the variation of main sugars and organic acids. The accessions were genotyped with 182 SSRs spreading over the tomato genome. Association mapping was conducted on the main sugars and organic acids detected by gas chromatography-mass spectrometer (GC-MS) over 2 years using the mixed linear model (MLM). We detected a total of 58 significantly associated loci (P < 0.001) for the 17 sugars and organic acids, including fructose, glucose, sucrose, citric acid, malic acid. These results not only co-localized with several reported QTLs, including fru9.1/PV, suc9.1/PV, ca2.1/HS, ca3.1/PV, ca4.1/PV, and ca8.1/PV, but also provided a list of candidate significantly associated loci to be functionally validated. These significantly associated loci could be used for deciphering the genetic architecture of tomato fruit sugars and organic acids and for tomato quality breeding.

  20. Association Mapping of Leaf Rust Response in Durum Wheat

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Resistance to leaf rust (Puccinia triticina Eriks.) is a main objective for durum wheat (Triticum durum Desf.) breeding.Association mapping on germplasm collections is now being used as an additional approach for the discovery and validation of major genes/QTLs. In this study, a collection of 164 el...

  1. Association mapping of leaf traits in spinach (Spinacia oleracea L.)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Spinach (Spinacia oleracea L.) is an important leafy vegetable crop grown world-wide. Leaf traits, surface texture (smooth vs. savoy or semi-savoy), petiole color (green vs. purple), and edge shape (serrate vs. entire) are important for spinach. Association mapping of the three traits were conducted...

  2. Simultaneous spawning by female stream goby Rhinogobius sp. and the association with brood cannibalism by nesting males.

    PubMed

    Ito, S; Iwao, H; Sakata, J; Inoue, M; Omori, K; Yanagisawa, Y

    2016-09-01

    A laboratory experiment was conducted by varying the undersurface area of nesting substratum and the number of females in an experimental tank to elucidate the determinants of the mating pattern in the stream goby, Rhinogobius sp. cross-band type. Males with larger nests tended to attract two or more females to their nest in a tank. Moreover, males spawned simultaneously with multiple females and entire brood cannibalism by males was rarely observed under a female-biased sex ratio. When males spawned with a single female with low fecundity, however, entire brood cannibalism occurred at a high frequency, suggesting that a male guarding a nest with fewer eggs consumes the brood. Therefore, spawning behaviour of females that leads to a large egg mass would decrease the risk of entire brood cannibalism. In this species, simultaneous spawning by multiple females in a nest serves as a female counter-measure against entire brood cannibalism. These results suggest that a conflict of interest between the sexes through brood cannibalism is a major determinant of simultaneous spawning. PMID:27325563

  3. Optimizing nest survival and female survival: Consequences of nest site selection for Canada Geese

    USGS Publications Warehouse

    Miller, David A.; Grand, J.B.; Fondell, T.F.; Anthony, R.M.

    2007-01-01

    We examined the relationship between attributes of nest sites used by Canada Geese (Branta canadensis) in the Copper River Delta, Alaska, and patterns in nest and female survival. We aimed to determine whether nest site attributes related to nest and female survival differed and whether nest site attributes related to nest survival changed within and among years. Nest site attributes that we examined included vegetation at and surrounding the nest, as well as associations with other nesting birds. Optimal nest site characteristics were different depending on whether nest survival or female survival was examined. Prior to 25 May, the odds of daily survival for nests in tall shrubs and on islands were 2.92 and 2.26 times greater, respectively, than for nests in short shrub sites. Bald Eagles (Halieaeetus leucocephalus) are the major predator during the early breeding season and their behavior was likely important in determining this pattern. After 25 May, when eagle predation is limited due to the availability of alternative prey, no differences in nest survival among the nest site types were found. In addition, nest survival was positively related to the density of other Canada Goose nests near the nest site. Although the number of detected mortalities for females was relatively low, a clear pattern was found, with mortality three times more likely at nest sites dominated by high shrub density within 50 m than at open sites dominated by low shrub density. The negative relationship of nest concealment and adult survival is consistent with that found in other studies of ground-nesting birds. Physical barriers that limited access to nest sites by predators and sites that allowed for early detection of predators were important characteristics of nest site quality for Canada Geese and nest site quality shifted within seasons, likely as a result of shifting predator-prey interactions.

  4. C*-algebras associated with reversible extensions of logistic maps

    NASA Astrophysics Data System (ADS)

    Kwaśniewski, Bartosz K.

    2012-10-01

    The construction of reversible extensions of dynamical systems presented in a previous paper by the author and A.V. Lebedev is enhanced, so that it applies to arbitrary mappings (not necessarily with open range). It is based on calculating the maximal ideal space of C*-algebras that extends endomorphisms to partial automorphisms via partial isometric representations, and involves a new set of 'parameters' (the role of parameters is played by chosen sets or ideals). As model examples, we give a thorough description of reversible extensions of logistic maps and a classification of systems associated with compression of unitaries generating homeomorphisms of the circle. Bibliography: 34 titles.

  5. C*-algebras associated with reversible extensions of logistic maps

    SciTech Connect

    Kwasniewski, Bartosz K

    2012-10-31

    The construction of reversible extensions of dynamical systems presented in a previous paper by the author and A.V. Lebedev is enhanced, so that it applies to arbitrary mappings (not necessarily with open range). It is based on calculating the maximal ideal space of C*-algebras that extends endomorphisms to partial automorphisms via partial isometric representations, and involves a new set of 'parameters' (the role of parameters is played by chosen sets or ideals). As model examples, we give a thorough description of reversible extensions of logistic maps and a classification of systems associated with compression of unitaries generating homeomorphisms of the circle. Bibliography: 34 titles.

  6. Analysis and prediction of lightning strike distributions associated with synoptic map types over Florida

    SciTech Connect

    Reap, R.M.

    1994-08-01

    The temporal and spatial distributions of lightning activity associated with specific synoptic regimes of low-level wind flow were analyzed as part of an experiment to develop improved statistical thunderstorm forecasts for Florida. The synoptic regimes were identified by means of a linear correlation technique that was used to perform pattern classification or `map typing` of 18- and 30-h sea level pressure forecasts from the National Meteorological Center`s Nested Grid Model (NGM). Lightning location data for the 1987-90 warm seasons were subsequently analyzed on a 12-km grid to determine the thunderstorm distribution for each of the predetermined map types. The analysis revealed organized coastal maxima in lightning activity related to land-sea-breeze convergence zones that form in direct response to the low-level wind flow. Surface effects were also indicated by the persistent minima in lightning activity over Lake Okeechobee and by the lightning maxima found in regions with shoreline curvature favoring localized convergence. Experimental thunderstorm probability equations for Florida were subsequently developed from climatological lightning frequencies and NGM forecast fields. The lightning frequencies were combined with the K stability index to form interactive predictors that take into account the temporal and spatial variations in lightning occurrence for each map type but modulate the climatology in response to the daily large-scale synoptic situation. The statistical forecast equations were developed for each map type in an attempt to simulate the effects of small-scale processes, such as land-sea-breeze convergence zones, on the subsequent development of peninsular-scale convection.

  7. VARIABILITY IN SOILS AND VEGETATION ASSOCIATED WITH HARVESTER ANT (POGONOMYRMEX RUGOSUS) NESTS ON A CHIHUAHUAN DESERT WATERSHED

    EPA Science Inventory

    The effects of harvester ant (Pogonomyrmex rugosus) nests on the density and cover of spring annual plants and on soil characteristics were measured at three locations characterized by different soils and dominant vegetation on a desert watershed. There were few differences in ve...

  8. Nesting Behavior is Associated with VIP Expression and VIP-Fos Colocalization in a Network-Wide Manner

    PubMed Central

    Kingsbury, Marcy A.; Jan, Namratha; Klatt, James D.; Goodson, James L.

    2015-01-01

    Many species, including humans, engage in a series of behaviors that are preparatory to the arrival of offspring. Such "nesting behaviors" are of obvious importance, but relevant neuroendocrine mechanisms remain little studied. We here focus on the potential roles of vasoactive intestinal polypeptide (VIP) in the performance of appetitive and consummatory nesting behaviors in male and female zebra finches (Taeniopygia guttata). Using combined immunocytochemistry for Fos and in situ hybridization for VIP, we now show that many VIP cell groups show increased transcriptional activity in response to nest building in male and female zebra finches. Particularly strong data come from the preoptic area (medial preoptic area and medial preoptic nucleus), where VIP-Fos co-expression correlates positively with three different measures of nesting behavior, as does the number of VIP-expressing cells. Remarkably, we find that VIP mRNA and/or VIP-Fos co-expression is correlated with nesting behavior in virtually every brain area that we examined, including the medial amygdala (anterior and posterior), medial bed nucleus of the stria terminalis, medial preoptic area, medial preoptic nucleus, anterior hypothalamus, ventromedial hypothalamus, periaqueductal gray complex (central gray and nucleus intercollicularis), and ventral tegmental area. Near-significant effects are also obtained in the tuberoinfundibular hypothalamus. Although most correlations are positive, negative correlations are observed for the VIP cell group of the anterior hypothalamus, a population that selectively promotes aggression, and also the periaqueductal gray complex. These data demonstrate a network-wide relationship between peptide production and social behavior that is, to our knowledge, unparalleled by other peptidergic modulators. PMID:25573700

  9. Candidate Gene Association Mapping of Arabidopsis Flowering Time

    PubMed Central

    Ehrenreich, Ian M.; Hanzawa, Yoshie; Chou, Lucy; Roe, Judith L.; Kover, Paula X.; Purugganan, Michael D.

    2009-01-01

    The pathways responsible for flowering time in Arabidopsis thaliana comprise one of the best characterized genetic networks in plants. We harness this extensive molecular genetic knowledge to identify potential flowering time quantitative trait genes (QTGs) through candidate gene association mapping using 51 flowering time loci. We genotyped common single nucleotide polymorphisms (SNPs) at these genes in 275 A. thaliana accessions that were also phenotyped for flowering time and rosette leaf number in long and short days. Using structured association techniques, we find that haplotype-tagging SNPs in 27 flowering time genes show significant associations in various trait/environment combinations. After correction for multiple testing, between 2 and 10 genes remain significantly associated with flowering time, with CO arguably possessing the most promising associations. We also genotyped a subset of these flowering time gene SNPs in an independent recombinant inbred line population derived from the intercrossing of 19 accessions. Approximately one-third of significant polymorphisms that were associated with flowering time in the accessions and genotyped in the outbred population were replicated in both mapping populations, including SNPs at the CO, FLC, VIN3, PHYD, and GA1 loci, and coding region deletions at the FRI gene. We conservatively estimate that ∼4–14% of known flowering time genes may harbor common alleles that contribute to natural variation in this life history trait. PMID:19581446

  10. Association mapping in sunflower for sclerotinia head rot resistance

    PubMed Central

    2012-01-01

    Background Sclerotinia Head Rot (SHR) is one of the most damaging diseases of sunflower in Europe, Argentina, and USA, causing average yield reductions of 10 to 20 %, but leading to total production loss under favorable environmental conditions for the pathogen. Association Mapping (AM) is a promising choice for Quantitative Trait Locus (QTL) mapping, as it detects relationships between phenotypic variation and gene polymorphisms in existing germplasm without development of mapping populations. This article reports the identification of QTL for resistance to SHR based on candidate gene AM. Results A collection of 94 sunflower inbred lines were tested for SHR under field conditions using assisted inoculation with the fungal pathogen Sclerotinia sclerotiorum. Given that no biological mechanisms or biochemical pathways have been clearly identified for SHR, 43 candidate genes were selected based on previous transcript profiling studies in sunflower and Brassica napus infected with S. sclerotiorum. Associations among SHR incidence and haplotype polymorphisms in 16 candidate genes were tested using Mixed Linear Models (MLM) that account for population structure and kinship relationships. This approach allowed detection of a significant association between the candidate gene HaRIC_B and SHR incidence (P < 0.01), accounting for a SHR incidence reduction of about 20 %. Conclusions These results suggest that AM will be useful in dissecting other complex traits in sunflower, thus providing a valuable tool to assist in crop breeding. PMID:22708963

  11. Mapping asthma-associated variants in admixed populations

    PubMed Central

    Mersha, Tesfaye B.

    2015-01-01

    Admixed populations arise when two or more previously isolated populations interbreed. Mapping asthma susceptibility loci in an admixed population using admixture mapping (AM) involves screening the genome of individuals of mixed ancestry for chromosomal regions that have a higher frequency of alleles from a parental population with higher asthma risk as compared with parental population with lower asthma risk. AM takes advantage of the admixture created in populations of mixed ancestry to identify genomic regions where an association exists between genetic ancestry and asthma (in contrast to between the genotype of the marker and asthma). The theory behind AM is that chromosomal segments of affected individuals contain a significantly higher-than-average proportion of alleles from the high-risk parental population and thus are more likely to harbor disease–associated loci. Criteria to evaluate the applicability of AM as a gene mapping approach include: (1) the prevalence of the disease differences in ancestral populations from which the admixed population was formed; (2) a measurable difference in disease-causing alleles between the parental populations; (3) reduced linkage disequilibrium (LD) between unlinked loci across chromosomes and strong LD between neighboring loci; (4) a set of markers with noticeable allele-frequency differences between parental populations that contributes to the admixed population (single nucleotide polymorphisms (SNPs) are the markers of choice because they are abundant, stable, relatively cheap to genotype, and informative with regard to the LD structure of chromosomal segments); and (5) there is an understanding of the extent of segmental chromosomal admixtures and their interactions with environmental factors. Although genome-wide association studies have contributed greatly to our understanding of the genetic components of asthma, the large and increasing degree of admixture in populations across the world create many challenges

  12. Map syndrome (MYH Associated Polyposis) colorectal cancer, etiopathological connections

    PubMed Central

    Ion, D; Stoian, RV; Serban, MB

    2011-01-01

    The case presented raised our scientific curiosity and it is worthy of being brought in front of the medical audience because of several reasons presented below. Presently, there are 3 hereditary syndromes that have a demonstrated etiological relationship with the colorectal cancer: Familiar Adenomatous Polyposis (FAP syndrome), HNPCC syndrome (Hereditary Nonpoliposis Colorectal Cancer) and MAP syndrome. Discovered only in 2002, the MAP syndrome (MYH associated polyposis) is the first hereditary syndrome that has autosomal recessive transmission. The APC gene can be mutated in several ways during the colonic oncogenesis: congenital in the FAP syndrome, somatic in sporadic colorectal cancers and secondary to the MYH gene inactivation in MAP syndrome. MAP phenotype is similar to the FAP phenotype because of the somatic mutations to the APC gene. Colonic polyposis is lower than FAP syndrome and appeared later, in the 40's and 50's. Colorectal cancers are frequent and discovered in the same moment as the colonic polyposis. Patients are diagnosed mostly in cancer stages. Colonoscopy shows polyps disseminated around the entire colic frame. Treatment in these cases is total rectocolectomy with ileoanal anastomosis. When working in a general emergency surgery clinic, physicians are often faced with colorectal cancers in different evolutive stages, and mostly they are faced with their complications. PMID:21505584

  13. Association mapping for kernel phytosterol content in almond

    PubMed Central

    Font i Forcada, Carolina; Velasco, Leonardo; Socias i Company, Rafel; Fernández i Martí, Ángel

    2015-01-01

    Almond kernels are a rich source of phytosterols, which are important compounds for human nutrition. The genetic control of phytosterol content has not yet been documented in almond. Association mapping (AM), also known as linkage disequilibrium (LD), was applied to an almond germplasm collection in order to provide new insight into the genetic control of total and individual sterol contents in kernels. Population structure analysis grouped the accessions into two principal groups, the Mediterranean and the non-Mediterranean. There was a strong subpopulation structure with LD decaying with increasing genetic distance, resulting in lower levels of LD between more distant markers. A significant impact of population structure on LD in the almond cultivar groups was observed. The mean r2-value for all intra-chromosomal loci pairs was 0.040, whereas, the r2 for the inter-chromosomal loci pairs was 0.036. For analysis of association between the markers and phenotypic traits five models were tested. The mixed linear model (MLM) approach using co-ancestry values from population structure and kinship estimates (K model) as covariates identified a maximum of 13 significant associations. Most of the associations found appeared to map within the interval where many candidate genes involved in the sterol biosynthesis pathway are predicted in the peach genome. These findings provide a valuable foundation for quality gene identification and molecular marker assisted breeding in almond. PMID:26217374

  14. Association mapping of spot blotch resistance in wild barley

    PubMed Central

    Roy, Joy K.; Smith, Kevin P.; Muehlbauer, Gary J.; Chao, Shiaoman; Close, Timothy J.

    2010-01-01

    Spot blotch, caused by Cochliobolus sativus, is an important foliar disease of barley. The disease has been controlled for over 40 years through the deployment of cultivars with durable resistance derived from the line NDB112. Pathotypes of C. sativus with virulence for the NDB112 resistance have been detected in Canada; thus, many commercial cultivars are vulnerable to spot blotch epidemics. To increase the diversity of spot blotch resistance in cultivated barley, we evaluated 318 diverse wild barley accessions comprising the Wild Barley Diversity Collection (WBDC) for reaction to C. sativus at the seedling stage and utilized an association mapping (AM) approach to identify and map resistance loci. A high frequency of resistance was found in the WBDC as 95% (302/318) of the accessions exhibited low infection responses. The WBDC was genotyped with 558 Diversity Array Technology (DArT®) and 2,878 single nucleotide polymorphism (SNP) markers and subjected to structure analysis before running the AM procedure. Thirteen QTL for spot blotch resistance were identified with DArT and SNP markers. These QTL were found on chromosomes 1H, 2H, 3H, 5H, and 7H and explained from 2.3 to 3.9% of the phenotypic variance. Nearly half of the identified QTL mapped to chromosome bins where spot blotch resistance loci were previously reported, offering some validation for the AM approach. The other QTL mapped to unique genomic regions and may represent new spot blotch resistance loci. This study demonstrates that AM is an effective technique for identifying and mapping QTL for disease resistance in a wild crop progenitor. Electronic supplementary material The online version of this article (doi:10.1007/s11032-010-9402-8) contains supplementary material, which is available to authorized users. PMID:20694035

  15. SNP-based association mapping of Arachnomelia in Fleckvieh cattle.

    PubMed

    Seichter, D; Russ, I; Förster, M; Medugorac, I

    2011-10-01

    Bovine arachnomelia is an inherited congenital disorder with malformation mainly of the limbs, the vertebral column and the skull, following a monogenic autosomal recessive heredity. Despite almost identical pathological findings, arachnomelia has previously been mapped to bovine chromosome 23 and 5 in Fleckvieh and Braunvieh respectively. Therefore, this disorder may be an example of locus heterogeneity in cattle. This study aimed to refine the candidate region to allow positional cloning and sequence analyses of candidate genes in Fleckvieh cattle. For that purpose, a case-control association mapping design was set up with a case group of 16 pre-selected affected individuals and a control group of 50 unrelated animals. The subset of affected animals was selected from a total of 129 pathologically confirmed cases due to the occurrence of recombination(s) within a 14.5 cM candidate interval previously mapped to chromosome 23. Six linked microsatellites currently used for indirect gene testing in Fleckvieh were analysed for this purpose. In all selected cases, a genome-wide scan using 44 473 informative SNPs revealed shared segments of homozygosity at 15 adjacent SNPs on chromosome 23. Additional haplotype analysis of 37 carrier bulls confirmed the localization of the arachnomelia locus to a region of 927 kb (13.622-14.549 Mb) containing molybdenum cofactor biosynthesis protein 1 gene, the most likely candidate gene for arachnomelia in Fleckvieh. The number of recombinant haplotypes observed in cases was more than doubled compared with the number of expected recombinations. This remarkably increased mapping resolution and thus illustrates the benefit of pre-selection in association studies.

  16. Habitat associations of marbled murrelets during the nesting season in nearshore waters along the Washington to California coast

    NASA Astrophysics Data System (ADS)

    Raphael, Martin G.; Shirk, Andrew J.; Falxa, Gary A.; Pearson, Scott F.

    2015-06-01

    The marbled murrelet (Brachyramphus marmoratus) is a seabird in the family Alcidae that forages in nearshore waters of the Pacific Northwest, and nests in adjacent older-forest conifers within 80 km offshore. The species is of conservation concern due to habitat loss and declining numbers, and is listed as Threatened in British Columbia, Canada and in the United States portion of its range south of Canada. Recent monitoring in the United States indicated that murrelet numbers continued to decline there, especially in the waters of Washington State. To better understand this decline, and to inform conservation planning for the species, we evaluated how terrestrial and marine factors influence the distribution and abundance of the murrelet in coastal waters, including whether at-sea hotspots of murrelet abundance exist. Murrelet at-sea abundance and distribution were determined by surveys conducted annually from 2000 to 2012 in coastal waters from the United States-Canada border south to San Francisco Bay. We summarized mean and variance of murrelet density at the scale of 5-km segments of coastal waters throughout this area. We used a boosted regression tree analysis to investigate the contributions of a suite of marine and terrestrial attributes to at-sea murrelet abundance in each segment. We observed several regional hotspots of higher murrelet abundance at sea. Terrestrial attributes made the strongest contribution, especially the amount and cohesiveness of suitable nesting habitat in proximity to each segment, whereas marine attributes explained less of the spatial and temporal variations in murrelet abundance. At-sea hotspots of murrelet abundance therefore reflect not only suitable marine foraging habitat but primarily the proximity of suitable inland nesting habitat.

  17. Mapping quantitative trait loci associated with barley net blotch resistance.

    PubMed

    Grewal, T S; Rossnagel, B G; Pozniak, C J; Scoles, G J

    2008-02-01

    Net blotch of barley, caused by Pyrenophora teres Drechs., is an important foliar disease worldwide. Deployment of resistant cultivars is the most economic and eco-friendly control method. This report describes mapping of quantitative trait loci (QTL) associated with net blotch resistance in a doubled-haploid (DH) barley population using diversity arrays technology (DArT) markers. One hundred and fifty DH lines from the cross CDC Dolly (susceptible)/TR251 (resistant) were screened as seedlings in controlled environments with net-form net blotch (NFNB) isolates WRS858 and WRS1607 and spot-form net blotch (SFNB) isolate WRS857. The population was also screened at the adult-plant stage for NFNB resistance in the field in 2005 and 2006. A high-density genetic linkage map of 90 DH lines was constructed using 457 DArT and 11 SSR markers. A major NFNB seedling resistance QTL, designated QRpt6, was mapped to chromosome 6H for isolates WRS858 and WRS1607. QRpt6 was associated with adult-plant resistance in the 2005 and 2006 field trials. Additional QTL for NFNB seedling resistance to the more virulent isolate WRS858 were identified on chromosomes 2H, 4H, and 5H. A seedling resistance QTL (QRpts4) for the SFNB isolate WRS857 was detected on chromosome 4H as was a significant QTL (QRpt7) on chromosome 7H. Three QTL (QRpt6, QRpts4, QRpt7) were associated with resistance to both net blotch forms and lines with one or more of these demonstrated improved resistance. Simple sequence repeat (SSR) markers tightly linked to QRpt6 and QRpts4 were identified and validated in an unrelated barley population. The major 6H QTL, QRpt6, may provide adequate NFNB field resistance in western Canada and could be routinely selected for using molecular markers in a practical breeding program. PMID:18071668

  18. A Cladistic Analysis of Phenotype Associations with Haplotypes Inferred from Restriction Endonuclease Mapping. II. the Analysis of Natural Populations

    PubMed Central

    Templeton, A. R.; Sing, C. F.; Kessling, A.; Humphries, S.

    1988-01-01

    Genes that code for products involved in the physiology of a phenotype are logical candidates for explaining interindividual variation in that phenotype. We present a methodology for discovering associations between genetic variation at such candidate loci (assayed through restriction endonuclease mapping) with phenotypic variation at the population level. We confine our analyses to DNA regions in which recombination is very rare. In this case, the genetic variation at the candiate locus can be organized into a cladogram that represents the evolutionary relationships between the observed haplotypes. Any mutation causing a significant phenotypic effect should be imbedded within the same historical structure defined by the cladogram. We showed, in the first paper of this series, how to use the cladogram to define a nested analysis of variance (NANOVA) that was very efficient at detecting and localizing phenotypically important mutations. However, the NANOVA of haplotype effects could only be applied to populations of homozygous genotypes. In this paper, we apply the quantitative genetic concept of average excess to evaluate the phenotypic effect of a haplotype or group of haplotypes stratified and contrasted according to the nested design defined by the cladogram. We also show how a permutational procedure can be used to make statistical inferences about the nested average excess values in populations containing heterozygous as well as homozygous genotypes. We provide two worked examples that investigate associations between genetic variation at or near the Alcohol dehydrogenase (Adh) locus and Adh activity in Drosophila melanogaster, and associations between genetic variation at or near some apolipoprotein loci and various lipid phenotypes in a human population. PMID:3147219

  19. Association mapping in forest trees and fruit crops.

    PubMed

    Khan, M Awais; Korban, Schuyler S

    2012-06-01

    Association mapping (AM), also known as linkage disequilibrium (LD) mapping, is a viable approach to overcome limitations of pedigree-based quantitative trait loci (QTL) mapping. In AM, genotypic and phenotypic correlations are investigated in unrelated individuals. Unlike QTL mapping, AM takes advantage of both LD and historical recombination present within the gene pool of an organism, thus utilizing a broader reference population. In plants, AM has been used in model species with available genomic resources. Pursuing AM in tree species requires both genotyping and phenotyping of large populations with unique architectures. Recently, genome sequences and genomic resources for forest and fruit crops have become available. Due to abundance of single nucleotide polymorphisms (SNPs) within a genome, along with availability of high-throughput resequencing methods, SNPs can be effectively used for genotyping trees. In addition to DNA polymorphisms, copy number variations (CNVs) in the form of deletions, duplications, and insertions also play major roles in control of expression of phenotypic traits. Thus, CNVs could provide yet another valuable resource, beyond those of microsatellite and SNP variations, for pursuing genomic studies. As genome-wide SNP data are generated from high-throughput sequencing efforts, these could be readily reanalysed to identify CNVs, and subsequently used for AM studies. However, forest and fruit crops possess unique architectural and biological features that ought to be taken into consideration when collecting genotyping and phenotyping data, as these will also dictate which AM strategies should be pursued. These unique features as well as their impact on undertaking AM studies are outlined and discussed.

  20. Deletion mapping of genetic regions associated with apomixis in Hieracium.

    PubMed

    Catanach, Andrew S; Erasmuson, Sylvia K; Podivinsky, Ellen; Jordan, Brian R; Bicknell, Ross

    2006-12-01

    Although apomixis has been quoted as a technology with the potential to deliver benefits similar in scale to those achieved with the Green Revolution, very little is currently known of the genetic mechanisms that control this trait in plants. To address this issue, we developed Hieracium, a genus of daisies native to Eurasia and North America, as a genetic model to study apomixis. In a molecular mapping study, we defined the number of genetic loci involved in apomixis, and we explored dominance and linkage relationships between these loci. To avoid difficulties often encountered with inheritance studies of apomicts, we based our mapping effort on the use of deletion mutagenesis, coupled with amplified fragment length polymorphism (AFLP) as a genomic fingerprinting tool. The results indicate that apomixis in Hieracium caespitosum is controlled at two principal loci, one of which regulates events associated with the avoidance of meiosis (apomeiosis) and the other, an unlinked locus that controls events associated with the avoidance of fertilization (parthenogenesis). AFLP bands identified as central to both loci were isolated, sequenced, and used to develop sequence-characterized amplified region (SCAR) markers. The validity of the AFLP markers was verified by using a segregating population generated by hybridization. The validity of the SCAR markers was verified by their pattern of presence/absence in specific mutants. The mutants, markers, and genetic data derived from this work are now being used to isolate genes controlling apomixis in this system.

  1. Deletion mapping of genetic regions associated with apomixis in Hieracium.

    PubMed

    Catanach, Andrew S; Erasmuson, Sylvia K; Podivinsky, Ellen; Jordan, Brian R; Bicknell, Ross

    2006-12-01

    Although apomixis has been quoted as a technology with the potential to deliver benefits similar in scale to those achieved with the Green Revolution, very little is currently known of the genetic mechanisms that control this trait in plants. To address this issue, we developed Hieracium, a genus of daisies native to Eurasia and North America, as a genetic model to study apomixis. In a molecular mapping study, we defined the number of genetic loci involved in apomixis, and we explored dominance and linkage relationships between these loci. To avoid difficulties often encountered with inheritance studies of apomicts, we based our mapping effort on the use of deletion mutagenesis, coupled with amplified fragment length polymorphism (AFLP) as a genomic fingerprinting tool. The results indicate that apomixis in Hieracium caespitosum is controlled at two principal loci, one of which regulates events associated with the avoidance of meiosis (apomeiosis) and the other, an unlinked locus that controls events associated with the avoidance of fertilization (parthenogenesis). AFLP bands identified as central to both loci were isolated, sequenced, and used to develop sequence-characterized amplified region (SCAR) markers. The validity of the AFLP markers was verified by using a segregating population generated by hybridization. The validity of the SCAR markers was verified by their pattern of presence/absence in specific mutants. The mutants, markers, and genetic data derived from this work are now being used to isolate genes controlling apomixis in this system. PMID:17047034

  2. Nest Material Shapes Eggs Bacterial Environment.

    PubMed

    Ruiz-Castellano, Cristina; Tomás, Gustavo; Ruiz-Rodríguez, Magdalena; Martín-Gálvez, David; Soler, Juan José

    2016-01-01

    Selective pressures imposed by pathogenic microorganisms to embryos have selected in hosts for a battery of antimicrobial lines of defenses that includes physical and chemical barriers. Due to the antimicrobial properties of volatile compounds of green plants and of chemicals of feather degrading bacteria, the use of aromatic plants and feathers for nest building has been suggested as one of these barriers. However, experimental evidence suggesting such effects is scarce in the literature. During two consecutive years, we explored experimentally the effects of these nest materials on loads of different groups of bacteria (mesophilic bacteria, Enterobacteriaceae, Staphylococcus and Enterococcus) of eggshells in nests of spotless starlings (Sturnus unicolor) at the beginning and at the end of the incubation period. This was also explored in artificial nests without incubation activity. We also experimentally increased bacterial density of eggs in natural and artificial nests and explored the effects of nest lining treatments on eggshell bacterial load. Support for the hypothetical antimicrobial function of nest materials was mainly detected for the year and location with larger average values of eggshell bacterial density. The beneficial effects of feathers and plants were more easily detected in artificial nests with no incubation activity, suggesting an active role of incubation against bacterial colonization of eggshells. Pigmented and unpigmented feathers reduced eggshell bacterial load in starling nests and artificial nest boxes. Results from artificial nests allowed us to discuss and discard alternative scenarios explaining the detected association, particularly those related to the possible sexual role of feathers and aromatic plants in starling nests. All these results considered together confirm the antimicrobial functionality mainly of feathers but also of plants used as nest materials, and highlight the importance of temporally and geographically

  3. Nest Material Shapes Eggs Bacterial Environment

    PubMed Central

    Ruiz-Castellano, Cristina; Tomás, Gustavo; Ruiz-Rodríguez, Magdalena; Martín-Gálvez, David; Soler, Juan José

    2016-01-01

    Selective pressures imposed by pathogenic microorganisms to embryos have selected in hosts for a battery of antimicrobial lines of defenses that includes physical and chemical barriers. Due to the antimicrobial properties of volatile compounds of green plants and of chemicals of feather degrading bacteria, the use of aromatic plants and feathers for nest building has been suggested as one of these barriers. However, experimental evidence suggesting such effects is scarce in the literature. During two consecutive years, we explored experimentally the effects of these nest materials on loads of different groups of bacteria (mesophilic bacteria, Enterobacteriaceae, Staphylococcus and Enterococcus) of eggshells in nests of spotless starlings (Sturnus unicolor) at the beginning and at the end of the incubation period. This was also explored in artificial nests without incubation activity. We also experimentally increased bacterial density of eggs in natural and artificial nests and explored the effects of nest lining treatments on eggshell bacterial load. Support for the hypothetical antimicrobial function of nest materials was mainly detected for the year and location with larger average values of eggshell bacterial density. The beneficial effects of feathers and plants were more easily detected in artificial nests with no incubation activity, suggesting an active role of incubation against bacterial colonization of eggshells. Pigmented and unpigmented feathers reduced eggshell bacterial load in starling nests and artificial nest boxes. Results from artificial nests allowed us to discuss and discard alternative scenarios explaining the detected association, particularly those related to the possible sexual role of feathers and aromatic plants in starling nests. All these results considered together confirm the antimicrobial functionality mainly of feathers but also of plants used as nest materials, and highlight the importance of temporally and geographically

  4. Waterbird nest-site selection is influenced by neighboring nests and island topography

    USGS Publications Warehouse

    Hartman, Christopher; Ackerman, Josh; Takekawa, John Y.; Herzog, Mark

    2016-01-01

    Avian nest-site selection is influenced by factors operating across multiple spatial scales. Identifying preferred physical characteristics (e.g., topography, vegetation structure) can inform managers to improve nesting habitat suitability. However, social factors (e.g., attraction, territoriality, competition) can complicate understanding physical characteristics preferred by nesting birds. We simultaneously evaluated the physical characteristics and social factors influencing selection of island nest sites by colonial-nesting American avocets (Recurvirostra americana) and Forster's terns (Sterna forsteri) at 2 spatial scales in San Francisco Bay, 2011–2012. At the larger island plot (1 m2) scale, we used real-time kinematics to produce detailed topographies of nesting islands and map the distribution of nests. Nesting probability was greatest in island plots between 0.5 m and 1.5 m above the water surface, at distances <10 m from the water's edge, and of moderately steep (avocets) or flat (terns) slopes. Further, avocet and tern nesting probability increased as the number of nests initiated in adjacent plots increased up to a peak of 11–12 tern nests, and then decreased thereafter. Yet, avocets were less likely to nest in plots adjacent to plots with nesting avocets, suggesting an influence of intra-specific territoriality. At the smaller microhabitat scale, or the area immediately surrounding the nest, we compared topography, vegetation, and distance to nearest nest between nest sites and paired random sites. Topography had little influence on selection of the nest microhabitat. Instead, nest sites were more likely to have vegetation present, and greater cover, than random sites. Finally, avocet, and to a lesser extent tern, nest sites were closer to other active conspecific or heterospecific nests than random sites, indicating that social attraction played a role in selection of nest microhabitat. Our results demonstrate key differences in nest

  5. Behavior of Puerto Rican parrots during failed nesting attempts

    USGS Publications Warehouse

    Wilson, K.A.; Wilson, M.H.; Field, R.

    1997-01-01

    We compared patterns of nesting behavior of four pairs of Puerto Rican Parrots (Amazona vittata) that experienced failed nesting attempts to behavior of four pairs of parrots that experienced no substantial nest problems and successfully fledged young without management intervention. Only changes in female parrots' behavior were clearly associated with nest failure. During incubation, decreases in nest attendance, increases in duration of recesses, and increases in frequency of nest entries by female parrots were associated with imminent abandonment of nests. During early chick rearing, similar behavior was associated with the loss of broods. Low nest attendance and long recesses by female parrots during incubation were also associated with successful hatching of eggs followed by death of young several days later. The behavior patterns and changes in Puerto Rican Parrot nesting behavior described in this paper may alert biologists to nest problems that might be mitigated by management intervention.

  6. Association mapping of soybean seed germination under salt stress.

    PubMed

    Kan, Guizhen; Zhang, Wei; Yang, Wenming; Ma, Deyuan; Zhang, Dan; Hao, Derong; Hu, Zhenbin; Yu, Deyue

    2015-12-01

    Soil salinity is a serious threat to agriculture sustainability worldwide. Seed germination is a critical phase that ensures the successful establishment and productivity of soybeans in saline soils. However, little information is available regarding soybean salt tolerance at the germination stage. The objective of this study was to identify the genetic mechanisms of soybean seed germination under salt stress. One natural population consisting of 191 soybean landraces was used in this study. Soybean seeds produced in four environments were used to evaluate the salt tolerance at their germination stage. Using 1142 single-nucleotide polymorphisms (SNPs), the molecular markers associated with salt tolerance were detected by genome-wide association analysis. Eight SNP-trait associations and 13 suggestive SNP-trait associations were identified using a mixed linear model and the TASSEL 4.0 software. Eight SNPs or suggestive SNPs were co-associated with two salt tolerance indices, namely (1) the ratio of the germination index under salt conditions to the germination index under no-salt conditions (ST-GI) and (2) the ratio of the germination rate under salt conditions to the germination rate under no-salt conditions (ST-GR). One SNP (BARC-021347-04042) was significantly associated with these two traits (ST-GI and ST-GR). In addition, nine possible candidate genes were located in or near the genetic region where the above markers were mapped. Of these, five genes, Glyma08g12400.1, Glyma08g09730.1, Glyma18g47140.1, Glyma09g00460.1, and Glyma09g00490.3, were verified in response to salt stress at the germination stage. The SNPs detected could facilitate a better understanding of the genetic basis of soybean salt tolerance at the germination stage, and the marker BARC-021347-04042 could contribute to future breeding for soybean salt tolerance by marker-assisted selection.

  7. The association between component malalignment and post-operative pain following navigation-assisted total knee arthroplasty: results of a cohort/nested case-control study.

    PubMed

    Czurda, Thomas; Fennema, Peter; Baumgartner, Martin; Ritschl, Peter

    2010-07-01

    Previous studies have noted an adverse relationship between implant malalignment during total knee arthroplasty (TKA) and post-operative pain. Although some evidence exists indicating that computer-assisted surgical navigation for TKA can improve the accuracy of component alignment, its impact on clinical outcomes is currently unknown. The dual goals of the present cohort/nested case-control study were to (1) compare self-reported responses to the Western Ontario-McMaster Osteoarthritis Index (WOMAC) questionnaire between computer-assisted TKA (123 patients) using the imageless PiGalileo navigation system and conventional TKA (207 patients) [cohort analysis], and (2) to investigate a potential association between malalignment and post-operative pain in 19 painful knees and 19 asymptomatic knees obtained from the cohort analysis using matched sampling [nested case-control study]. In the cohort analysis, a relevant but non-significant (P = 0.06) difference in the occurrence of chronic pain was observed between the navigated (12%) and conventional arms (20%). Median post-operative WOMAC pain score was 100 (range, 50-100) in the conventional group and 100 (range, 65-100) in the navigated group. However, the Mann-Whitney test revealed a significant difference in favor of the navigated group (P = 0.01). In the nested case-control analysis, radiological outcomes and computer tomography (CT) measurements of femoral rotation were compared between the groups. The CT rotation measurements yielded evidence of a relationship between post-operative pain and incorrect rotational alignment of the femoral component of more than 3 degrees (OR: 7; 95% CI: 1.2-42; P = .033). In conclusion, there was no clinical benefit to computer-assisted navigation; however, a statistically significant relationship was observed between incorrect rotational alignment of the femoral component and symptoms of post-operative pain following TKA.

  8. Exploring Potential of Pearl Millet Germplasm Association Panel for Association Mapping of Drought Tolerance Traits

    PubMed Central

    Sehgal, Deepmala; Skot, Leif; Singh, Richa; Srivastava, Rakesh Kumar; Das, Sankar Prasad; Taunk, Jyoti; Sharma, Parbodh C.; Pal, Ram; Raj, Bhasker; Hash, Charles T.; Yadav, Rattan S.

    2015-01-01

    A pearl millet inbred germplasm association panel (PMiGAP) comprising 250 inbred lines, representative of cultivated germplasm from Africa and Asia, elite improved open-pollinated cultivars, hybrid parental inbreds and inbred mapping population parents, was recently established. This study presents the first report of genetic diversity in PMiGAP and its exploitation for association mapping of drought tolerance traits. For diversity and genetic structure analysis, PMiGAP was genotyped with 37 SSR and CISP markers representing all seven linkage groups. For association analysis, it was phenotyped for yield and yield components and morpho-physiological traits under both well-watered and drought conditions, and genotyped with SNPs and InDels from seventeen genes underlying a major validated drought tolerance (DT) QTL. The average gene diversity in PMiGAP was 0.54. The STRUCTURE analysis revealed six subpopulations within PMiGAP. Significant associations were obtained for 22 SNPs and 3 InDels from 13 genes under different treatments. Seven SNPs associations from 5 genes were common under irrigated and one of the drought stress treatments. Most significantly, an important SNP in putative acetyl CoA carboxylase gene showed constitutive association with grain yield, grain harvest index and panicle yield under all treatments. An InDel in putative chlorophyll a/b binding protein gene was significantly associated with both stay-green and grain yield traits under drought stress. This can be used as a functional marker for selecting high yielding genotypes with ‘stay green’ phenotype under drought stress. The present study identified useful marker-trait associations of important agronomics traits under irrigated and drought stress conditions with genes underlying a major validated DT-QTL in pearl millet. Results suggest that PMiGAP is a useful panel for association mapping. Expression patterns of genes also shed light on some physiological mechanisms underlying pearl millet

  9. Exploring potential of pearl millet germplasm association panel for association mapping of drought tolerance traits.

    PubMed

    Sehgal, Deepmala; Skot, Leif; Singh, Richa; Srivastava, Rakesh Kumar; Das, Sankar Prasad; Taunk, Jyoti; Sharma, Parbodh C; Pal, Ram; Raj, Bhasker; Hash, Charles T; Yadav, Rattan S

    2015-01-01

    A pearl millet inbred germplasm association panel (PMiGAP) comprising 250 inbred lines, representative of cultivated germplasm from Africa and Asia, elite improved open-pollinated cultivars, hybrid parental inbreds and inbred mapping population parents, was recently established. This study presents the first report of genetic diversity in PMiGAP and its exploitation for association mapping of drought tolerance traits. For diversity and genetic structure analysis, PMiGAP was genotyped with 37 SSR and CISP markers representing all seven linkage groups. For association analysis, it was phenotyped for yield and yield components and morpho-physiological traits under both well-watered and drought conditions, and genotyped with SNPs and InDels from seventeen genes underlying a major validated drought tolerance (DT) QTL. The average gene diversity in PMiGAP was 0.54. The STRUCTURE analysis revealed six subpopulations within PMiGAP. Significant associations were obtained for 22 SNPs and 3 InDels from 13 genes under different treatments. Seven SNPs associations from 5 genes were common under irrigated and one of the drought stress treatments. Most significantly, an important SNP in putative acetyl CoA carboxylase gene showed constitutive association with grain yield, grain harvest index and panicle yield under all treatments. An InDel in putative chlorophyll a/b binding protein gene was significantly associated with both stay-green and grain yield traits under drought stress. This can be used as a functional marker for selecting high yielding genotypes with 'stay green' phenotype under drought stress. The present study identified useful marker-trait associations of important agronomics traits under irrigated and drought stress conditions with genes underlying a major validated DT-QTL in pearl millet. Results suggest that PMiGAP is a useful panel for association mapping. Expression patterns of genes also shed light on some physiological mechanisms underlying pearl millet

  10. Nest predation risk influences a cavity-nesting passerine during the post-hatching care period.

    PubMed

    Yoon, Jongmin; Kim, Byung-Su; Joo, Eun-Jin; Park, Shi-Ryong

    2016-01-01

    Some nest predators visually assess parental activities to locate a prey nest, whereas parents modify fitness-related traits to reduce the probability of nest predation, and/or nestlings fledge early to escape the risky nest environment. Here, we experimentally tested if the parental and fledging behaviours of oriental tits (Parus minor) that bred in the nest-box varied with cavity conditions associated with nest predation risk during the nestling period. The entrance of experimental nest-boxes was enlarged to create a long-term risk soon after clutch competition. A short-term risk, using simulated playbacks with a coexisting control bird and avian nest predator sound, was simultaneously applied to the nest-boxes whether or not the long-term risk existed. We found that the parents reduced their hourly feeding trips, and the nestlings fledged early with the long-term risk, although the nest mortality of the two nest-box types was low and did not differ. While this study presents a portion of prey-predator interactions with the associated uncertainties, our results highlight that the entrance size of cavities for small hole-nesting birds may play an important role in determining their fitness-related traits depending upon the degree of perceived risk of nest predation. PMID:27553176

  11. Nest predation risk influences a cavity-nesting passerine during the post-hatching care period

    PubMed Central

    Yoon, Jongmin; Kim, Byung-Su; Joo, Eun-Jin; Park, Shi-Ryong

    2016-01-01

    Some nest predators visually assess parental activities to locate a prey nest, whereas parents modify fitness-related traits to reduce the probability of nest predation, and/or nestlings fledge early to escape the risky nest environment. Here, we experimentally tested if the parental and fledging behaviours of oriental tits (Parus minor) that bred in the nest-box varied with cavity conditions associated with nest predation risk during the nestling period. The entrance of experimental nest-boxes was enlarged to create a long-term risk soon after clutch competition. A short-term risk, using simulated playbacks with a coexisting control bird and avian nest predator sound, was simultaneously applied to the nest-boxes whether or not the long-term risk existed. We found that the parents reduced their hourly feeding trips, and the nestlings fledged early with the long-term risk, although the nest mortality of the two nest-box types was low and did not differ. While this study presents a portion of prey–predator interactions with the associated uncertainties, our results highlight that the entrance size of cavities for small hole-nesting birds may play an important role in determining their fitness-related traits depending upon the degree of perceived risk of nest predation. PMID:27553176

  12. Florida Harvester Ant Nest Architecture, Nest Relocation and Soil Carbon Dioxide Gradients

    PubMed Central

    Tschinkel, Walter R.

    2013-01-01

    Colonies of the Florida harvester ant, Pogonomyrmex badius, excavate species-typical subterranean nests up the 3 m deep with characteristic vertical distribution of chamber area/shape, spacing between levels and vertical arrangement of the ants by age and brood stage. Colonies excavate and occupy a new nest about once a year, and doing so requires that they have information about the depth below ground. Careful excavation and mapping of vacated and new nests revealed that there was no significant difference between the old and new nests in any measure of nest size, shape or arrangement. Colonies essentially built a replicate of the just-vacated nest (although details differed), and they did so in less than a week. The reason for nest relocation is not apparent. Tschinkel noted that the vertical distribution of chamber area, worker age and brood type was strongly correlated to the soil carbon dioxide gradient, and proposed that this gradient serves as a template for nest excavation and vertical distribution. To test this hypothesis, the carbon dioxide gradient of colonies that were just beginning to excavate a new nest was eliminated by boring 6 vent holes around the forming nest, allowing the soil CO2 to diffuse into the atmosphere and eliminating the gradient. Sadly, neither the nest architecture nor the vertical ant distribution of vented nests differed from either unvented control or from their own vacated nest. In a stronger test, workers excavated a new nest under a reversed carbon dioxide gradient (high concentration near the surface, low below). Even under these conditions, the new and old nests did not differ significantly, showing that the soil carbon dioxide gradient does not serve as a template for nest construction or vertical worker distribution. The possible importance of soil CO2 gradients for soil-dwelling animals is discussed. PMID:23555829

  13. Florida harvester ant nest architecture, nest relocation and soil carbon dioxide gradients.

    PubMed

    Tschinkel, Walter R

    2013-01-01

    Colonies of the Florida harvester ant, Pogonomyrmex badius, excavate species-typical subterranean nests up the 3 m deep with characteristic vertical distribution of chamber area/shape, spacing between levels and vertical arrangement of the ants by age and brood stage. Colonies excavate and occupy a new nest about once a year, and doing so requires that they have information about the depth below ground. Careful excavation and mapping of vacated and new nests revealed that there was no significant difference between the old and new nests in any measure of nest size, shape or arrangement. Colonies essentially built a replicate of the just-vacated nest (although details differed), and they did so in less than a week. The reason for nest relocation is not apparent. Tschinkel noted that the vertical distribution of chamber area, worker age and brood type was strongly correlated to the soil carbon dioxide gradient, and proposed that this gradient serves as a template for nest excavation and vertical distribution. To test this hypothesis, the carbon dioxide gradient of colonies that were just beginning to excavate a new nest was eliminated by boring 6 vent holes around the forming nest, allowing the soil CO2 to diffuse into the atmosphere and eliminating the gradient. Sadly, neither the nest architecture nor the vertical ant distribution of vented nests differed from either unvented control or from their own vacated nest. In a stronger test, workers excavated a new nest under a reversed carbon dioxide gradient (high concentration near the surface, low below). Even under these conditions, the new and old nests did not differ significantly, showing that the soil carbon dioxide gradient does not serve as a template for nest construction or vertical worker distribution. The possible importance of soil CO2 gradients for soil-dwelling animals is discussed.

  14. Finding genome-transcriptome-phenome association with structured association mapping and visualization in GenAMap.

    PubMed

    Curtis, Ross E; Yin, Junming; Kinnaird, Peter; Xing, Eric P

    2012-01-01

    Despite the success of genome-wide association studies in detecting novel disease variants, we are still far from a complete understanding of the mechanisms through which variants cause disease. Most of previous studies have considered only genome-phenome associations. However, the integration of transcriptome data may help further elucidate the mechanisms through which genetic mutations lead to disease and uncover potential pathways to target for treatment. We present a novel structured association mapping strategy for finding genome-transcriptome-phenome associations when SNP, gene-expression, and phenotype data are available for the same cohort. We do so via a two-step procedure where genome-transcriptome associations are identified by GFlasso, a sparse regression technique presented previously. Transcriptome-phenome associations are then found by a novel proposed method called gGFlasso, which leverages structure inherent in the genes and phenotypic traits. Due to the complex nature of three-way association results, visualization tools can aid in the discovery of causal SNPs and regulatory mechanisms affecting diseases. Using wellgrounded visualization techniques, we have designed new visualizations that filter through large three-way association results to detect interesting SNPs and associated genes and traits. The two-step GFlasso-gGFlasso algorithmic approach and new visualizations are integrated into GenAMap, a visual analytics system for structured association mapping. Results on simulated datasets show that our approach has the potential to increase the sensitivity and specificity of association studies, compared to existing procedures that do not exploit the full structural information of the data. We report results from an analysis on a publically available mouse dataset, showing that identified SNP-gene-trait associations are compatible with known biology.

  15. Identification of Environmental Factors Associated with Inflammatory Bowel Disease in a Southwestern Highland Region of China: A Nested Case-Control Study

    PubMed Central

    Tang, Yuan; Nan, Qiong; Liu, Yan; Yang, Gang; Dong, Xiangqian; Huang, Qi; Xia, Shuxian; Wang, Kunhua; Miao, Yinglei

    2016-01-01

    Background The aim of this study was to examine environmental factors associated with inflammatory bowel disease (IBD) in Yunnan Province, a southwestern highland region of China. Methods In this nested case-control study, newly diagnosed ulcerative colitis (UC) cases in 2 cities in Yunnan Province and Crohn’s disease (CD) cases in 16 cities in Yunnan Province were recruited between 2008 and 2013. Controls were matched by geography, sex and age at a ratio of 1:4. Data were collected using the designed questionnaire. Conditional logistic regression models were used to estimate adjusted odds ratios (ORs). Results A total of 678 UC and 102 CD cases were recruited. For UC, various factors were associated with an increased risk of developing UC: dietary habits, including frequent irregular meal times; consumption of fried foods, salty foods and frozen dinners; childhood factors, including intestinal infectious diseases and frequent use of antibiotics; and other factors, such as mental labor, high work stress, use of non-aspirin non-steroidal anti-inflammatory drugs and allergies (OR > 1, p < 0.05). Other factors showed a protective effect: such as consumption of fruits, current smoking, physical activity, and drinking tea (OR < 1, p < 0.05). For CD, appendectomy and irregular meal times increased the disease risk (OR >1, p < 0.05), whereas physical activity may have reduced this risk (OR < 1, p < 0.05). Conclusions This study is the first nested case-control study to analyze the association between environmental factors and IBD onset in a southwestern highland region of China. Certain dietary habits, lifestyles, allergies and childhood factors may play important roles in IBD, particularly UC. PMID:27070313

  16. Mapping

    ERIC Educational Resources Information Center

    Kinney, Douglas M.; McIntosh, Willard L.

    1978-01-01

    Geologic mapping in the United States increased by about one-quarter in the past year. Examinations of mapping trends were in the following categories: (1) Mapping at scales of 1:100, 000; (2) Metric-scale base maps; (3) International mapping, and (4) Planetary mapping. (MA)

  17. Testing ecological and behavioral correlates of nest predation

    USGS Publications Warehouse

    Fontaine, J.J.; Martel, M.; Markland, H.M.; Niklison, Alina M.; Decker, Karie L.; Martin, T.E.

    2007-01-01

    Variation in nest predation rates among bird species are assumed to reflect differences in risk that are specific to particular nest sites. Theoretical and empirical studies suggest that parental care behaviors can evolve in response to nest predation risk and thereby differ among ecological conditions that vary in inherent risk. However, parental care also can influence predation risk. Separating the effects of nest predation risk inherent to a nest site from the risk imposed by parental strategies is needed to understand the evolution of parental care. Here we identify correlations between risks inherent to nest sites, and risk associated with parental care behaviors, and use an artificial nest experiment to assess site-specific differences in nest predation risk across nesting guilds and between habitats that differed in nest predator abundance. We found a strong correlation between parental care behaviors and inherent differences in nest predation risk, but despite the absence of parental care at artificial nests, patterns of nest predation risk were similar for real and artificial nests both across nesting guilds and between predator treatments. Thus, we show for the first time that inherent risk of nest predation varies with nesting guild and predator abundance independent of parental care. ?? Oikos.

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

    PubMed

    Sahana, Goutam; Guldbrandtsen, Bernt; Janss, Luc; Lund, Mogens S

    2010-07-01

    Association mapping methods were compared using a simulation with a complex pedigree structure. The pedigree was simulated while keeping the present Danish Holstein population pedigree in view. A total of 15 quantitative trait loci (QTL) with varying effect sizes (10%, 5% and 2% of total genetic variance) were simulated. We compared the single-marker test, haplotype-based analysis, mixed model approach, and Bayesian analysis. The methods were compared for power, precision of location estimates, and type I error rates. Results found the best performance in a Bayesian method that included genetic background effects and simultaneously fitted all single-nucleotide polymorphisms (SNPs) with a variable selection method. A mixed model analysis that fitted genetic background effects and tested one SNP at a time performed nearly as well as the Bayesian method. For the Bayesian method, it proved necessary 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.

  19. The relationship between parental genetic or phenotypic divergence and progeny variation in the maize nested association mapping population

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The choice of populations for quantitative genetics experiments impacts inferences about genetic architecture and prospective selection gains. Plant breeding and quantitative genetics studies are often conducted in one or a few among many possible biparental families. Trait genotypic variation withi...

  20. Connecting Spatial Memories of Two Nested Spaces

    ERIC Educational Resources Information Center

    Zhang, Hui; Mou, Weimin; McNamara, Timothy P.; Wang, Lin

    2014-01-01

    Four experiments investigated the manner in which people use spatial reference directions to organize spatial memories of 2 conceptually nested layouts. Participants learned directions of 8 remote cities centered to Beijing or Edmonton, where the experiments occurred, using a map or using direct pointing. The map and the environment were aligned,…

  1. Beyond Smoking Prevalence: Exploring the Variability of Associations between Neighborhood Exposures across Two Nested Spatial Units and Two-Year Smoking Trajectory among Young Adults.

    PubMed

    Ghenadenik, Adrian E; Frohlich, Katherine L; Gauvin, Lise

    2016-01-06

    Young adults have the highest prevalence of smoking amongst all age groups. Significant uptake occurs after high school age. Although neighborhood exposures have been found to be associated with smoking behavior, research on neighborhood exposures and the smoking trajectories among young adults, and on the role of geographic scale in shaping findings, is scarce. We examined associations between neighborhood exposures across two nested, increasingly large spatial units and smoking trajectory over two years among young adults living in Montreal, Canada. A sample of 2093 participants aged 18-25 years from the Interdisciplinary Study of Inequalities in Smoking (ISIS) was surveyed. The dependent variable was self-reported smoking trajectory over the course of two years. Residential addresses, data on presence of tobacco retail outlets, and the presence of smoking accommodation facilities were coded and linked to spatial units. Three-level multinomial models were used to examine associations. The likelihood of being a smoker for 2+ years was significantly greater among those living in larger spatial unit neighborhoods that had a greater presence of smoking accommodation. This association was not statistically significant at the smaller spatial units. Our findings highlight the importance of studying young adults' smoking trajectories in addition to static smoking outcomes, and point to the relevance of considering spatial scale in studies of neighborhoods and smoking.

  2. Beyond Smoking Prevalence: Exploring the Variability of Associations between Neighborhood Exposures across Two Nested Spatial Units and Two-Year Smoking Trajectory among Young Adults

    PubMed Central

    Ghenadenik, Adrian E.; Frohlich, Katherine L.; Gauvin, Lise

    2016-01-01

    Young adults have the highest prevalence of smoking amongst all age groups. Significant uptake occurs after high school age. Although neighborhood exposures have been found to be associated with smoking behavior, research on neighborhood exposures and the smoking trajectories among young adults, and on the role of geographic scale in shaping findings, is scarce. We examined associations between neighborhood exposures across two nested, increasingly large spatial units and smoking trajectory over two years among young adults living in Montreal, Canada. A sample of 2093 participants aged 18–25 years from the Interdisciplinary Study of Inequalities in Smoking (ISIS) was surveyed. The dependent variable was self-reported smoking trajectory over the course of two years. Residential addresses, data on presence of tobacco retail outlets, and the presence of smoking accommodation facilities were coded and linked to spatial units. Three-level multinomial models were used to examine associations. The likelihood of being a smoker for 2+ years was significantly greater among those living in larger spatial unit neighborhoods that had a greater presence of smoking accommodation. This association was not statistically significant at the smaller spatial units. Our findings highlight the importance of studying young adults’ smoking trajectories in addition to static smoking outcomes, and point to the relevance of considering spatial scale in studies of neighborhoods and smoking. PMID:26751461

  3. Identification of Genetic Loci Associated with Quality Traits in Almond via Association Mapping

    PubMed Central

    Font i Forcada, Carolina; Oraguzie, Nnadozie; Reyes-Chin-Wo, Sebastian; Espiau, Maria Teresa; Socias i Company, Rafael; Fernández i Martí, Angel

    2015-01-01

    To design an appropriate association study, we need to understand population structure and the structure of linkage disequilibrium within and among populations as well as in different regions of the genome in an organism. In this study, we have used a total of 98 almond accessions, from five continents located and maintained at the Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA; Spain), and 40 microsatellite markers. Population structure analysis performed in ‘Structure’ grouped the accessions into two principal groups; the Mediterranean (Western-Europe) and the non-Mediterranean, with K = 3, being the best fit for our data. There was a strong subpopulation structure with linkage disequilibrium decaying with increasing genetic distance resulting in lower levels of linkage disequilibrium between more distant markers. A significant impact of population structure on linkage disequilibrium in the almond cultivar groups was observed. The mean r2 value for all intra-chromosomal loci pairs was 0.040, whereas, the r2 for the inter-chromosomal loci pairs was 0.036. For analysis of association between the markers and phenotypic traits, five models comprising both general linear models and mixed linear models were selected to test the marker trait associations. The mixed linear model (MLM) approach using co-ancestry values from population structure and kinship estimates (K model) as covariates identified a maximum of 16 significant associations for chemical traits and 12 for physical traits. This study reports for the first time the use of association mapping for determining marker-locus trait associations in a world-wide almond germplasm collection. It is likely that association mapping will have the most immediate and largest impact on the tier of crops such as almond with the greatest economic value. PMID:26111146

  4. Identification of Genetic Loci Associated with Quality Traits in Almond via Association Mapping.

    PubMed

    Font i Forcada, Carolina; Oraguzie, Nnadozie; Reyes-Chin-Wo, Sebastian; Espiau, Maria Teresa; Socias i Company, Rafael; Fernández i Martí, Angel

    2015-01-01

    To design an appropriate association study, we need to understand population structure and the structure of linkage disequilibrium within and among populations as well as in different regions of the genome in an organism. In this study, we have used a total of 98 almond accessions, from five continents located and maintained at the Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA; Spain), and 40 microsatellite markers. Population structure analysis performed in 'Structure' grouped the accessions into two principal groups; the Mediterranean (Western-Europe) and the non-Mediterranean, with K = 3, being the best fit for our data. There was a strong subpopulation structure with linkage disequilibrium decaying with increasing genetic distance resulting in lower levels of linkage disequilibrium between more distant markers. A significant impact of population structure on linkage disequilibrium in the almond cultivar groups was observed. The mean r2 value for all intra-chromosomal loci pairs was 0.040, whereas, the r2 for the inter-chromosomal loci pairs was 0.036. For analysis of association between the markers and phenotypic traits, five models comprising both general linear models and mixed linear models were selected to test the marker trait associations. The mixed linear model (MLM) approach using co-ancestry values from population structure and kinship estimates (K model) as covariates identified a maximum of 16 significant associations for chemical traits and 12 for physical traits. This study reports for the first time the use of association mapping for determining marker-locus trait associations in a world-wide almond germplasm collection. It is likely that association mapping will have the most immediate and largest impact on the tier of crops such as almond with the greatest economic value.

  5. Prospective Associations between Plasma Saturated, Monounsaturated and Polyunsaturated Fatty Acids and Overall and Breast Cancer Risk – Modulation by Antioxidants: A Nested Case-Control Study

    PubMed Central

    Pouchieu, Camille; Chajès, Véronique; Laporte, François; Kesse-Guyot, Emmanuelle; Galan, Pilar; Hercberg, Serge; Latino-Martel, Paule; Touvier, Mathilde

    2014-01-01

    Background Mechanistic data suggest that different types of fatty acids play a role in carcinogenesis and that antioxidants may modulate this relationship but epidemiologic evidence is lacking. Our aim was to investigate the association between plasma saturated, monounsaturated and polyunsaturated fatty acids (SFAs, MUFAs and PUFAs) and overall and breast cancer risk and to evaluate the potential modulatory effect of an antioxidant supplementation on these relationships. Methods A nested case-control study included all first incident cancer cases diagnosed in the SU.VI.MAX study between 1994 and 2002 (n = 250 cases, one matched control/case). Participants to the SU.VI.MAX randomized controlled trial received either vitamin/mineral antioxidants or placebo during this intervention period. Baseline fatty acid composition of plasma total lipids was measured by gas chromatography. Conditional logistic regression was performed overall and stratified by intervention group. Results Dihomo-γ-linolenic acid (Ptrend = 0.002), the dihomo-γ-linolenic/linoleic acids ratio (Ptrend = 0.001), mead acid (Ptrend = 0.0004), and palmitoleic acid (Ptrend = 0.02) were inversely associated with overall cancer risk. The arachidonic/dihomo-γ-linolenic acids ratio (Ptrend = 0.02) and linoleic acid (Ptrend = 0.02) were directly associated with overall cancer risk. Similar results were observed for breast cancer specifically. In stratified analyses, associations were only observed in the placebo group. Notably, total PUFAs were directly associated with overall (Ptrend = 0.02) and breast cancer risk in the placebo group only. Conclusion Specific SFAs, MUFAs and PUFAs were prospectively differentially associated with cancer risk. In addition, this study suggests that antioxidants may modulate these associations by counteracting the potential effects of these fatty acids on carcinogenesis. PMID:24587366

  6. Detection of Australian gill-associated virus (GAV) and lymphoid organ virus (LOV) of Penaeus monodon by RT-nested PCR.

    PubMed

    Cowley, J A; Dimmock, C M; Spann, K M; Walker, P J

    2000-02-01

    A highly sensitive test based on reverse transcription followed by nested polymerase chain reaction (RT-nPCR) was developed to detect the Australian yellow-head-like viruses, gill-associated virus (GAV) and lymphoid organ virus (LOV) of Penaeus monodon. The RT-nPCR detected viral RNA in as little as 10 fg lymphoid organ total RNA isolated from GAV-infected P. monodon. Amplification of serial dilutions of a GAV cDNA clone showed that the nested PCR was sufficiently sensitive to detect a single genome equivalent using a DNA template. The specificity and sensitivity of the RT-nPCR was also demonstrated using experimentally infected P. (Marsupenaeus) japonicus, where GAV sequences could be amplified from lymphoid organ and haemocyte RNA as early as 6 h post infection (p.i.), and from gills by 24 h p.i. In contrast, transmission electron microscopy (TEM) identified nucleocapsids and virions in lymphoid organ cells and haemocytes from Days 3 and 6 p.i., respectively, while there was no evidence of infection in gill cells at any time. The practical application of the RT-nPCR was demonstrated by screening healthy wild-caught P. monodon broodstock. The high prevalence (>98%) of broodstock that were positive by RT-nPCR suggests that LOV is endemic in northern Queensland. In addition, results with lymphoid organ, gill and haemocyte RNA suggest that small gill biopsies may be best suited to the non-sacrificial testing of valuable broodstock. The speed and sensitivity of the RT-nPCR make it a useful adjunct to TEM for diagnosing LOV/GAV infection of P. monodon, with the additional benefit that screening of gill biopsies may facilitate selection of LOV-free broodstock.

  7. PyMultiNest: Python interface for MultiNest

    NASA Astrophysics Data System (ADS)

    Buchner, Johannes

    2016-06-01

    PyMultiNest provides programmatic access to MultiNest (ascl:1109.006) and PyCuba, integration existing Python code (numpy, scipy), and enables writing Prior & LogLikelihood functions in Python. PyMultiNest can plot and visualize MultiNest's progress and allows easy plotting, visualization and summarization of MultiNest results. The plotting can be run on existing MultiNest output, and when not using PyMultiNest for running MultiNest.

  8. Association between serum uric acid levels and cardiovascular risk among university workers from the State of Mexico: a nested case–control study

    PubMed Central

    2013-01-01

    Background Recent evidence suggests that serum uric acid (SUA) can be an inexpensive and easy-to-obtain indicator of cardiovascular risk (CR). This is especially important in developing countries with high prevalence of cardiovascular disease. We examined the association between SUA levels and 10-year global CR among university workers from the State of Mexico, Mexico. Methods A case–control study nested within a cohort was conducted between 2004 and 2006. Anthropometric measures, lifestyle variables, family background and CR factors were assessed. The analysis estimated odds ratios using conditional logistic regression. Results The study included 319 cases with CR and 638 controls. Subjects in the upper tertile of SUA had 48.0% higher odds of having an elevated CR than those in the lower tertile (OR = 1.48, 95% CI: 1.04 - 2.10) in the crude analysis, but the association was non-significant when adjusting for other covariates. Among physically inactive individuals, being in the third tertile of SUA doubled the odds of high CR, compared with those who perform physical activity three or more hours per week being in the first tertile of SUA (OR = 2.35, 95% CI: 1.24 - 4.45). Conclusion Serum concentration of uric acid is associated with 10-year global CR among individuals with high levels of physical inactivity. PMID:23631758

  9. Inhaled Corticosteroids Use Is Not Associated With an Increased Risk of Pregnancy-Induced Hypertension and Gestational Diabetes Mellitus: Two Nested Case-Control Studies.

    PubMed

    Lee, Chang-Hoon; Kim, Jimin; Jang, Eun Jin; Lee, Joon-Ho; Kim, Yun Jung; Choi, Seongmi; Kim, Deog Kyeom; Yim, Jae-Joon; Yoon, Ho Il

    2016-05-01

    There have been concerns that systemic corticosteroid use is associated with pregnancy-induced hypertension (PIH) and diabetes mellitus. However, the relationship between inhaled corticosteroids (ICSs) and the risk of PIH has not been fully examined, and there was no study investigating the association between ICS use and the development of gestational diabetes mellitus (GDM). The aims of the study are to determine whether the use of ICSs during pregnancy increases the risk of PIH and GDM in women.We conducted 2 nested case-control studies utilizing the nationwide insurance claims database of the Health Insurance Review and Assessment Service (Seoul, Republic of Korea), in which 1,306,281 pregnant women who delivered between January 1, 2009 and December 31, 2011 were included. Among them, PIH cases and GDM cases were identified and matched controls were included. Conditional logistic regression analyses adjusted by other concomitant drugs use during and before pregnancy and confounding covariates including comorbidities were performed.Total 43,908 PIH cases and 219,534 controls, and 34,190 GDM cases and 170,934 control subjects were identified. When other concomitant drugs use during pregnancy was adjusted, ICS use was associated with an increased rate of PIH (adjusted odds ratio, 1.40 [95% CI, 1.05-1.87]). ICS medication possession ratios and cumulative doses were associated with an increased risk of PIH. However, the statistical significance was not found in other models. In both unadjusted and adjusted multivariable models, ICSs use was not associated with increase in the risk of GDM.ICSs use is not associated with an increased risk of PIH and GDM. PMID:27258493

  10. Genome-wide association mapping in plants exemplified for root growth in Arabidopsis thaliana.

    PubMed

    Slovak, Radka; Göschl, Christian; Seren, Ümit; Busch, Wolfgang

    2015-01-01

    Genome-wide association (GWA) mapping is a powerful technique to address the molecular basis of genotype to phenotype relationships and to map regulators of biological processes. This chapter presents a protocol for genome-wide association mapping in Arabidopsis thaliana using the user-friendly internet application GWAPP, and provides a specific protocol for acquiring root trait data suitable for GWA studies using the semi-automated, high-throughput phenotyping pipeline BRAT for early root growth.

  11. The association of polymorphisms in hormone metabolism pathway genes, menopausal hormone therapy, and breast cancer risk: a nested case-control study in the California Teachers Study cohort

    PubMed Central

    2011-01-01

    Introduction The female sex steroids estrogen and progesterone are important in breast cancer etiology. It therefore seems plausible that variation in genes involved in metabolism of these hormones may affect breast cancer risk, and that these associations may vary depending on menopausal status and use of hormone therapy. Methods We conducted a nested case-control study of breast cancer in the California Teachers Study cohort. We analyzed 317 tagging single nucleotide polymorphisms (SNPs) in 24 hormone pathway genes in 2746 non-Hispanic white women: 1351 cases and 1395 controls. Odds ratios (ORs) and 95% confidence intervals (CIs) were estimated by fitting conditional logistic regression models using all women or subgroups of women defined by menopausal status and hormone therapy use. P values were adjusted for multiple correlated tests (PACT). Results The strongest associations were observed for SNPs in SLCO1B1, a solute carrier organic anion transporter gene, which transports estradiol-17β-glucuronide and estrone-3-sulfate from the blood into hepatocytes. Ten of 38 tagging SNPs of SLCO1B1 showed significant associations with postmenopausal breast cancer risk; 5 SNPs (rs11045777, rs11045773, rs16923519, rs4149057, rs11045884) remained statistically significant after adjusting for multiple testing within this gene (PACT = 0.019-0.046). In postmenopausal women who were using combined estrogen-progestin therapy (EPT) at cohort enrollment, the OR of breast cancer was 2.31 (95% CI = 1.47-3.62) per minor allele of rs4149013 in SLCO1B1 (P = 0.0003; within-gene PACT = 0.002; overall PACT = 0.023). SNPs in other hormone pathway genes evaluated in this study were not associated with breast cancer risk in premenopausal or postmenopausal women. Conclusions We found evidence that genetic variation in SLCO1B1 is associated with breast cancer risk in postmenopausal women, particularly among those using EPT. PMID:21457551

  12. Association between traffic-related air pollution and asthma in preschool children in a national Japanese nested case–control study

    PubMed Central

    Hasunuma, Hideki; Sato, Tosiya; Iwata, Tsutomu; Kohno, Yoichi; Nitta, Hiroshi; Odajima, Hiroshi; Ohara, Toshimasa; Omori, Takashi; Ono, Masaji; Yamazaki, Shin; Shima, Masayuki

    2016-01-01

    Objectives There has been little study on the effect of traffic-related air pollution on the incidence and persistence of asthma in preschool children. We evaluated the association of exposure to traffic-related air pollution with the incidence/persistence of asthma during the first 3 years of life using a population-based study. Methods A baseline survey was conducted in 1½-year-old children (n=63 266). A follow-up survey at 3 years of age (n=43 343) identified new-onset asthma cases (n=853) and persistence of asthma (n=214). In the prevalence/persistence study, the outdoor concentrations of nitrogen oxides (NOx) and elemental carbon (EC) at home during the first 1½ years of life were estimated by a dispersion model. In the nested case–control study, which regarded incidence of asthma as cases, the personal exposure levels were estimated by dispersion model including time-activity pattern. Results There was no statistically significant association between the incidence of asthma between age 1½ and 3 years and personal exposure levels to NOx nor EC. However, the persistence of asthmatic symptoms (between 1½ and 3 years) was significantly associated with outdoor concentrations of NOx. ORs for the persistence of asthmatic symptoms were 6.02 (95% CI 1.51 to 23.92) for the comparison between the upper 5th and lower 25th centiles of NOx. Conclusions While no statistically significant association was observed for the incidence of asthma, the persistence of asthmatic symptoms in preschool children was significantly associated with traffic-related air pollution. This supports its importance as a risk factor in childhood airway disease. PMID:26916696

  13. Multi-trait association mapping in sugar beet (Beta vulgaris L.).

    PubMed

    Stich, Benjamin; Piepho, Hans-Peter; Schulz, Britta; Melchinger, Albrecht E

    2008-10-01

    Association mapping promises to overcome the limitations of linkage mapping methods. The main objective of this study was to examine the applicability of multivariate association mapping with an empirical data set of sugar beet. A total of 111 diploid sugar beet inbreds was selected from the seed parent heterotic pool to represent a broad diversity with respect to sugar content (SC). The inbreds were genotyped with 26 simple sequence repeat markers chosen according to their map positions in proximity to previously identified quantitative trait loci for SC. For SC and beet yield (BY), the genotypic variances were highly significant (P < 0.01). Based on the global test of the bivariate mixed-model approach, four markers were significantly associated with SC, BY, or both at a false discovery rate of 0.025. All four markers were significantly (P < 0.05) associated with BY but only two with SC. The identification of markers associated with SC, BY, or both indicated that association mapping can be successfully applied in a sugar beet breeding context for detection of marker-phenotype associations. Furthermore, based on our results multivariate association mapping can be recommended as a promising tool to discriminate with a high mapping resolution between pleiotropy and linkage as reasons for co-localization of marker-phenotype associations for different traits.

  14. Polymorphisms of IL-1beta, IL-1Ra, and TNF-alpha genes: a nested case-control study of their association with risk for stroke.

    PubMed

    Cvetkovic, Jasmina Trifunovic; Wiklund, Per Gunnar; Ahmed, Ejaz; Weinehall, Lars; Hallmans, Göran; Lefvert, Ann Kari

    2005-01-01

    Certain alleles of cytokine genes interleukin-1 beta (IL-1beta), interleukin-1 receptor antagonist (IL-1Ra), and tumor necrosis factor alpha (TNF-alpha) are correlated with increased production of the proteins. The aim of this study was to investigate polymorphisms of these genes and their possible correlation with the development of stroke. This matched case-control study was nested within the population-based Västerbotten Intervention Program (VIP) cohort and the Northern Sweden World Health Organization MONICA (Multinational Monitoring of Trends and Determinants in Cardiovascular Diseases) cohort, based on individuals who were free from cardiovascular events when the cohorts were established. After an average period of 34.1 months, 113 individuals developed stroke and to each case 2 individuals not suffering from cardiovascular events were matched to serve as controls. Polymerase chain reaction amplification was used to analyze genetic polymorphisms. There was no association between polymorphic sites of the IL-1beta and IL-1Ra genes and stroke. Carriage of haplotype A2+IL-1beta/A2+IL-1Ra was significantly increased in normotensive cases (23.1%) compared with normotensive controls (8.9%) (odds ratio [OR] = 3.07; P = .045). In hypertensive male cases, there was an association between the A1A1 genotype of TNF-alpha and risk of stroke (OR = 2.46; P = .034). Our findings indicate an association between allele A1 of the TNF-alpha NcoI polymorphism and stroke in hypertensive male cases, as well as an association between haplotype A2+IL-1beta/A2+IL-1Ra and stroke in normotensive cases.

  15. Mapping and candidate genes associated with saccharification yield in sorghum

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Sorghum [Sorghum bicolor (L.) Moench] is a potentially high-yielding hardy energy crop to produce lignocellulosic biofuels. Saccharification is a process by which hydrolytic enzymes break down lignocellulosic materials to fermentable sugars for biofuel production. Mapping and identifying genes und...

  16. The association of high-sensitivity c-reactive protein and other biomarkers with cardiovascular disease in patients treated for HIV: a nested case–control study

    PubMed Central

    2013-01-01

    Background Elevated high-sensitivity C-reactive protein (hsCRP) increases the risk of cardiovascular disease (CVD) in the general population, but its role as a predictive marker in HIV-positive patients remains unclear. Aim of the study was to evaluate whether hsCRP or other biomarkers are independent predictors of CVD risk in HIV-infected patients. Methods Retrospective, nested case–control study. HIV-positive men and women (35–69 years of age) receiving combination antiretroviral therapy (cART) were included. Cases (n = 35) had a major CVD event. Controls (n = 74) free from CVD events for at least 5 years from starting ART were matched on diabetes and smoking. HsCRP, D-dimer, P-selectin, interleukin-6 (IL-6), tissue plasminogen activator, plasminogen activator inhibitor-1 levels were measured. Results High hsCRP was associated with CVD risk, independently of traditional cardiovascular risk factors, HIV replication and the type of ART received at the time of sampling (adjusted odds ratio 8.00 [1.23-51.94] comparing >3.3 mg/L with <0.9 mg/L; P = 0.03). Higher IL-6 and P-selectin levels were also independently associated with increased CVD risk, although the association was weaker than for hsCRP. Higher total cholesterol and lower HDL cholesterol increased CVD risk, independent of hsCRP. Conclusion hsCRP may be a useful additional biomarker to predict CVD risk in HIV-infected patients receiving cART. PMID:24004495

  17. Impact of Circulating Vitamin D Binding Protein Levels on the Association Between 25-Hydroxyvitamin D and Pancreatic Cancer Risk: A Nested Case-Control Study

    PubMed Central

    Weinstein, Stephanie J.; Stolzenberg-Solomon, Rachael Z.; Kopp, William; Rager, Helen; Virtamo, Jarmo; Albanes, Demetrius

    2012-01-01

    High concentrations of circulating 25-hydroxyvitamin D [25(OH)D] have been associated with elevated pancreatic cancer risk. As this is contrary to an expected inverse association between vitamin D status and cancer, we examined whether vitamin D binding protein (DBP), the primary carrier of vitamin D compounds in circulation, plays a role in this relationship. Prediagnostic serum DBP and 25(OH)D were studied in relation to risk of pancreatic cancer in a nested case-control study of 234 pancreatic cancer cases and 234 controls in the Alpha-Tocopherol, Beta-Carotene Cancer Prevention Study of Finnish men. Odds ratios (OR) and 95% confidence intervals (CI) were estimated using logistic regression, and statistical tests were two-sided. We found that DBP and 25(OH)D were correlated (r=0.27; p<0.0001), and DBP was inversely associated with pancreatic cancer risk (OR=0.66, 95% CI=0.39–1.12, for the highest vs. lowest quartile; p-trend=0.02). Importantly, this association appeared to have a threshold between quartiles 2–4 and quartile 1, and was primarily evident among men with concurrent high 25(OH)D concentrations (OR=0.33, 95% CI=0.16–0.70 for highest vs. lowest quartile; p-trend=0.002), with no association in men with lower serum 25(OH)D (OR=1.28, 95% CI=0.62–2.61 for highest vs. lowest quartile, p-trend 0.63, p-interaction= 0.01). Men with higher 25(OH)D concentrations and serum DBP below the median showed greatly elevated risk of pancreatic cancer (OR=5.01, 95% CI 2.33–10.78, for highest vs. lowest quartile; p-trend < 0.0001), while risk was weakly inversely associated with serum 25(OH)D when DBP concentrations were higher (p-interaction = 0.001). Taken together, our findings indicate that higher DBP concentrations may sequester more 25(OH)D and reduce free 25(OH)D bioavailability. Simultaneous examination of DBP and 25(OH)D may be important in determining the association of vitamin D with cancer risk. PMID:22232734

  18. Association between Mycoplasma genitalium infection and HIV acquisition among female sex workers in Uganda: evidence from a nested case–control study

    PubMed Central

    Vandepitte, Judith; Weiss, Helen A; Bukenya, Justine; Kyakuwa, Nassim; Muller, Etienne; Buvé, Anne; Van der Stuyft, Patrick; Hayes, Richard J; Grosskurth, Heiner

    2014-01-01

    Objectives Cross-sectional studies have shown a strong association between Mycoplasma genitalium and HIV infections. We previously reported that in a cohort of female sex workers in Uganda, M genitalium infection at baseline was associated with HIV seroconversion. Here we examine the temporal association between the M genitalium infection status shortly before HIV seroconversion and HIV acquisition. Methods A nested case-control study was conducted within a cohort of women at high risk for HIV in Kampala. Cases were those of women acquiring HIV within 2 years of enrolment. For each of the 42 cases, 3 controls were selected from women HIV negative at the visit when the corresponding case first tested HIV seropositive. The association between HIV acquisition and M genitalium infection immediately prior to HIV testing was analysed using conditional logistic regression. Results There was weak evidence of an association between M genitalium infection and HIV acquisition overall (crude OR=1.57; 95% CI 0.67 to 3.72, aOR=2.28: 95% CI 0.81 to 6.47). However, time of M genitalium testing affected the association (p value for effect-modification=0.004). For 29 case-control sets with endocervical samples tested 3 months prior to the first HIV-positive result, M genitalium infection increased the risk of HIV acquisition (crude OR=3.09; 95% CI 1.06 to 9.05, aOR=7.19; 95% CI 1.68 to 30.77), whereas there was little evidence of an association among the 13 case-control sets with samples tested at an earlier visit (crude OR=0.30: 95% CI 0.04 to 2.51; aOR=0.34; 95% CI 0.02 to 5.94). Conclusions Our study showed evidence of a temporal relationship between M genitalium infection and HIV acquisition that suggests that M genitalium infection may be a co-factor in the acquisition of HIV infection. PMID:24687129

  19. Nested PCR approach for detection and typing of epidermodysplasia verruciformis-associated human papillomavirus types in cutaneous cancers from renal transplant recipients.

    PubMed Central

    Berkhout, R J; Tieben, L M; Smits, H L; Bavinck, J N; Vermeer, B J; ter Schegget, J

    1995-01-01

    The epidermodysplasia verruciformis (EV)-associated human papillomaviruses (HPVs) constitute a group of HPV genotypes isolated mostly from the cutaneous lesions of patients with the genetic disorder of EV. Broad-spectrum detection of EV HPVs in cutaneous lesions of non-EV patients was previously difficult because no EV HPV consensus PCR was available. We describe a nested PCR that enables the detection of all known EV HPV types at relatively low-copy-number levels. The deduced sequences of a 92-amino-acid stretch of the L1 open reading frames of all types are shown for convenient typing. The technique proved very valuable in viral studies of skin cancers from renal transplant recipients. A high prevalence (81%) of EV HPV types was found in skin cancer biopsies. A wide spectrum of EV HPV types that differed from HPV-5 and -8 was found to be involved. The technique also proved useful in detecting potentially novel EV HPV types in skin cancers. The relationship of these new types to known HPV types is demonstrated by phylogenetic tree analysis. PMID:7751378

  20. Frequent Dental Scaling Is Associated with a Reduced Risk of Periprosthetic Infection following Total Knee Arthroplasty: A Nationwide Population-Based Nested Case-Control Study

    PubMed Central

    Tai, Ta-Wei; Lin, Tzu-Chieh; Ho, Chia-Jung; Kao Yang, Yea-Huei; Yang, Chyun-Yu

    2016-01-01

    Oral bacteremia has been presumed to be an important risk factor for total knee arthroplasty (TKA) infection. We aimed to investigate whether dental scaling could reduce the risk of TKA infection. A nested case-control study was conducted to compare 1,291 TKA patients who underwent resection arthroplasty for infected TKA and 5,004 matched controls without infection in the TKA cohort of Taiwan’s National Health Insurance Research Database (NHIRD). The frequency of dental scaling was analyzed. Multiple conditional logistic regression was used to assess the frequency of dental scaling and the risk of TKA infection. The percentage of patients who received dental scaling was higher in the control group than in the TKA infection group. The risk for TKA infection was 20% lower for patients who received dental scaling at least once within a 3-year period than for patients who never received dental scaling. Moreover, the risk of TKA infection was reduced by 31% among patients who underwent more frequent dental scaling (5–6 times within 3 years). Frequent and regular dental scaling is associated with a reduced risk of TKA infection. PMID:27336912

  1. Frequent Dental Scaling Is Associated with a Reduced Risk of Periprosthetic Infection following Total Knee Arthroplasty: A Nationwide Population-Based Nested Case-Control Study.

    PubMed

    Tai, Ta-Wei; Lin, Tzu-Chieh; Ho, Chia-Jung; Kao Yang, Yea-Huei; Yang, Chyun-Yu

    2016-01-01

    Oral bacteremia has been presumed to be an important risk factor for total knee arthroplasty (TKA) infection. We aimed to investigate whether dental scaling could reduce the risk of TKA infection. A nested case-control study was conducted to compare 1,291 TKA patients who underwent resection arthroplasty for infected TKA and 5,004 matched controls without infection in the TKA cohort of Taiwan's National Health Insurance Research Database (NHIRD). The frequency of dental scaling was analyzed. Multiple conditional logistic regression was used to assess the frequency of dental scaling and the risk of TKA infection. The percentage of patients who received dental scaling was higher in the control group than in the TKA infection group. The risk for TKA infection was 20% lower for patients who received dental scaling at least once within a 3-year period than for patients who never received dental scaling. Moreover, the risk of TKA infection was reduced by 31% among patients who underwent more frequent dental scaling (5-6 times within 3 years). Frequent and regular dental scaling is associated with a reduced risk of TKA infection. PMID:27336912

  2. A Cladistic Analysis of Phenotypic Associations with Haplotypes Inferred from Restriction Endonuclease Mapping and DNA Sequence Data. III. Cladogram Estimation

    PubMed Central

    Templeton, A. R.; Crandall, K. A.; Sing, C. F.

    1992-01-01

    We previously developed a cladistic approach to identify subsets of haplotypes defined by restriction endonuclease mapping or DNA sequencing that are associated with significant phenotypic deviations. Our approach was limited to segments of DNA in which little recombination occurs. In such cases, a cladogram can be constructed from the restriction site or sequence data that represents the evolutionary steps that interrelate the observed haplotypes. The cladogram is used to define a nested statistical design to identify mutational steps associated with significant phenotypic deviations. The central assumption behind this strategy is that any undetected mutation causing a phenotypic effect is embedded within the same evolutionary history that is represented by the cladogram. The power of this approach depends upon the confidence one has in the particular cladogram used to draw inferences. In this paper, we present a strategy for estimating the set of cladograms that are consistent with a particular sample of either restriction site or nucleotide sequence data and that includes the possibility of recombination. We first evaluate the limits of parsimony in constructing cladograms. Once these limits have been determined, we construct the set of parsimonious and nonparsimonious cladograms that is consistent with these limits. Our estimation procedure also identifies haplotypes that are candidates for being products of recombination. If recombination is extensive, our algorithm subdivides the DNA region into two or more subsections, each having little or no internal recombination. We apply this estimation procedure to three data sets to illustrate varying degrees of cladogram ambiguity and recombination. PMID:1385266

  3. Mapping.

    ERIC Educational Resources Information Center

    Kinney, Douglas M.; McIntosh, Willard L.

    1979-01-01

    The area of geological mapping in the United States in 1978 increased greatly over that reported in 1977; state geological maps were added for California, Idaho, Nevada, and Alaska last year. (Author/BB)

  4. Systemic Lupus Erythematosus is Associated with Uranium Exposure in a Community Living Near a Uranium Processing Plant: A Nested Case-Control Study

    PubMed Central

    Lu-Fritts, Pai-Yue; Kottyan, Leah C.; James, Judith A.; Xie, Changchung; Buckholz, Jeanette M.; Pinney, Susan M.; Harley, John B.

    2014-01-01

    Objective Explore the hypothesis that cases of SLE will be found more frequently in community members with high prior uranium exposure in the Fernald Community Cohort (FCC). Methods A nested case control study was performed. The FCC is a volunteer population that lived near a uranium ore processing plant in Fernald, Ohio, USA during plant operation and members were monitored for 18 years. Uranium plant workers were excluded. SLE cases were identified using American College of Rheumatology classification criteria, laboratory testing, and medical record review. Each case was matched to four age-, race-, and sex-matched controls. Sera from potential cases and controls were screened for autoantibodies. Cumulative uranium particulate exposure was calculated using a dosimetry model. Logistic regression with covariates was used to calculate odds ratios (OR) with 95% confidence intervals (CI). Results The FCC includes 4,187 individuals with background uranium exposure, 1,273 with moderate exposure, and 2,756 with higher exposure. SLE was confirmed in 23 of 31 individuals with a lupus ICD9 code, and in 2 of 43 other individuals prescribed hydroxychloroquine. The female:male ratio was 5.25:1. Of the 25 SLE cases, 12 were in the higher exposure group. SLE was associated with higher uranium exposure (OR 3.92, 95% CI 1.131-13.588, p = 0.031). Conclusion High uranium exposure is associated with SLE relative to matched controls in this sample of uranium exposed individuals. Potential explanations for this relationship include possible autoimmune or estrogen effects of uranium, somatic mutation, epigenetic effects, or effects of some other unidentified accompanying exposure. PMID:25103365

  5. Nested Neural Networks

    NASA Technical Reports Server (NTRS)

    Baram, Yoram

    1992-01-01

    Report presents analysis of nested neural networks, consisting of interconnected subnetworks. Analysis based on simplified mathematical models more appropriate for artificial electronic neural networks, partly applicable to biological neural networks. Nested structure allows for retrieval of individual subpatterns. Requires fewer wires and connection devices than fully connected networks, and allows for local reconstruction of damaged subnetworks without rewiring entire network.

  6. Mapping of yellow mosaic virus (YMV) resistance in soybean (Glycine max L. Merr.) through association mapping approach.

    PubMed

    Kumar, Bhupender; Talukdar, Akshay; Verma, Khushbu; Bala, Indu; Harish, G D; Gowda, Sarmrat; Lal, S K; Sapra, R L; Singh, K P

    2015-02-01

    Yellow Mosaic Virus (YMV) is a serious disease of soybean. Resistance to YMV was mapped in 180 soybean genotypes through association mapping approach using 121 simple sequence repeats (SSR) and four resistance gene analogue (RGA)-based markers. The association mapping population (AMP) (96 genotypes) and confirmation population (CP) (84 genotypes) was tested for resistance to YMV at hot-spot consecutively for 3 years (2007-2009). The genotypes exhibited significant variability for YMV resistance (P < 0.01). Molecular genotyping and population structure analysis with 'admixture' co-ancestry model detected seven optimal sub-populations in the AMP. Linkage disequilibrium (LD) between the markers extended up to 35 and 10 cM with r2 > 0.15, and >0.25, respectively. The 4 RGA-based markers showed no association with YMV resistance. Two SSR markers, Satt301 and GMHSP179 on chromosome 17 were found to be in significant LD with YMV resistance. Contingency Chi-square test confirmed the association (P < 0.01) and the utility of the markers was validated in the CP. It would pave the way for marker assisted selection for YMV resistance in soybean. This is the first report of its kind in soybean.

  7. Attention Deficit/Hyperactivity Disorder and Childhood Autism in Association with Prenatal Exposure to Perfluoroalkyl Substances: A Nested Case–Control Study in the Danish National Birth Cohort

    PubMed Central

    Liew, Zeyan; Ritz, Beate; von Ehrenstein, Ondine S.; Bech, Bodil Hammer; Nohr, Ellen Aagaard; Fei, Chunyuan; Bossi, Rossana; Henriksen, Tine Brink; Bonefeld-Jørgensen, Eva Cecilie

    2014-01-01

    , Bossi R, Henriksen TB, Bonefeld-Jørgensen EC, Olsen J. 2015. Attention deficit/hyperactivity disorder and childhood autism in association with prenatal exposure to perfluoroalkyl substances: a nested case–control study in the Danish National Birth Cohort. Environ Health Perspect 123:367–373; http://dx.doi.org/10.1289/ehp.1408412 PMID:25616253

  8. Associating mapping of stigma characteristics using the USDA rice core collection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A mini-core from the USDA rice core collection was phenotyped for nine traits of stigma and spikelet and genotyped with 109 DNA markers. Marker-trait association mapping was used to identify the regions associated with the nine traits. Resulting associations were adjusted using false discovery rate ...

  9. GWAS and admixture mapping identify different asthma-associated loci in Latinos: The GALA II Study

    PubMed Central

    Galanter, Joshua M; Gignoux, Christopher R; Torgerson, Dara G; Roth, Lindsey A; Eng, Celeste; Oh, Sam S; Nguyen, Elizabeth A; Drake, Katherine A; Huntsman, Scott; Hu, Donglei; Sen, Saunak; Davis, Adam; Farber, Harold J.; Avila, Pedro C.; Brigino-Buenaventura, Emerita; LeNoir, Michael A.; Meade, Kelley; Serebrisky, Denise; Borrell, Luisa N; Rodríguez-Cintrón, William; Estrada, Andres Moreno; Mendoza, Karla Sandoval; Winkler, Cheryl A.; Klitz, William; Romieu, Isabelle; London, Stephanie J.; Gilliland, Frank; Martinez, Fernando; Bustamante, Carlos; Williams, L Keoki; Kumar, Rajesh; Rodríguez-Santana, José R.; Burchard, and Esteban G.

    2013-01-01

    Background Asthma is a complex disease with both genetic and environmental causes. Genome-wide association studies of asthma have mostly involved European populations and replication of positive associations has been inconsistent. Objective To identify asthma-associated genes in a large Latino population with genome-wide association analysis and admixture mapping. Methods Latino children with asthma (n = 1,893) and healthy controls (n = 1,881) were recruited from five sites in the United States: Puerto Rico, New York, Chicago, Houston, and the San Francisco Bay Area. Subjects were genotyped on an Affymetrix World Array IV chip. We performed genome-wide association and admixture mapping to identify asthma-associated loci. Results We identified a significant association between ancestry and asthma at 6p21 (lowest p-value: rs2523924, p < 5 × 10−6). This association replicates in a meta-analysis of the EVE Asthma Consortium (p = 0.01). Fine mapping of the region in this study and the EVE Asthma Consortium suggests an association between PSORS1C1 and asthma. We confirmed the strong allelic association between the 17q21 asthma in Latinos (IKZF3, lowest p-value: rs90792, OR: 0.67, 95% CI 0.61 – 0.75, p = 6 × 10−13) and replicated associations in several genes that had previously been associated with asthma in genome-wide association studies. Conclusions Admixture mapping and genome-wide association are complementary techniques that provide evidence for multiple asthma-associated loci in Latinos. Admixture mapping identifies a novel locus on 6p21 that replicates in a meta-analysis of several Latino populations, while genome-wide association confirms the previously identified locus on 17q21. PMID:24406073

  10. Association mapping of leaf traits, flowering time, and phytate content in Brassica rapa.

    PubMed

    Zhao, Jianjun; Paulo, Maria-João; Jamar, Diaan; Lou, Ping; van Eeuwijk, Fred; Bonnema, Guusje; Vreugdenhil, Dick; Koornneef, Maarten

    2007-10-01

    Association mapping was used to investigate the genetic basis of variation within Brassica rapa, which is an important vegetable and oil crop. We analyzed the variation of phytate and phosphate levels in seeds and leaves and additional developmental and morphological traits in a set of diverse B. rapa accessions and tested association of these traits with AFLP markers. The analysis of population structure revealed four subgroups in the population. Trait values differed between these subgroups, thus defining associations between population structure and trait values, even for traits such as phytate and phosphate levels. Marker-trait associations were investigated both with and without taking population structure into account. One hundred and seventy markers were found to be associated with the observed traits without correction for population structure. Association analysis with correction for population structure led to the identification of 27 markers, 6 of which had known map positions; 3 of these were confirmed in additional QTL mapping studies.

  11. Communal nesting and kinship in degus (Octodon degus)

    NASA Astrophysics Data System (ADS)

    Ebensperger, Luis A.; Hurtado, María José; Soto-Gamboa, Mauricio; Lacey, Eileen A.; Chang, Ann T.

    Communal nesting is a fundamental component of many animal societies. Because the fitness consequences of this behavior vary with the relatedness among nest mates, understanding the kin structure of communally nesting groups is critical to understanding why such groups form. Observations of captive degus (Octodon degus) indicate that multiple females nest together, even when supplied with several nest boxes. To determine whether free-living degus also engage in communal nesting, we used radiotelemetry to monitor spatial relationships among adult females in a population of O. degus in central Chile. These analyses revealed that females formed stable associations of > 2-4 individuals, all of whom shared the same nest site at night. During the daytime, spatial overlap and frequency of social interactions were greatest among co-nesting females, suggesting that nesting associations represent distinct social units. To assess kinship among co-nesting females, we examined genotypic variation in our study animals at six microsatellite loci. These analyses indicated that mean pairwise relatedness among members of a nesting association (r=0.25) was significantly greater than that among randomly selected females (r=-0.03). Thus, communally nesting groups of degus are composed of female kin, making it possible for indirect as well as direct fitness benefits to contribute to sociality in this species.

  12. Association mapping for phenological, morphological, and quality traits in canola quality winter rapeseed (Brassica napus L.).

    PubMed

    Honsdorf, Nora; Becker, Heiko C; Ecke, Wolfgang

    2010-11-01

    QTL mapping by association analysis has recently gained interest in plant breeding research as an alternative to QTL mapping in segregating populations from biparental crosses. In a first experiment on whole-genome association analysis in rapeseed, 684 mapped AFLP markers were tested for association with 14 traits in a set of 84 canola quality winter rapeseed cultivars. For association analysis a general linear model was used. By testing significance of marker-trait associations against a false discovery rate of 0.2, between 1 and 34 associated markers were found for 10 of the 14 traits. Taking into account linkage disequilibrium between the significant markers, these markers represent between 1 and 22 putative QTL for the respective traits. The minimum phenotypic variance explained by the QTL for the different traits ranged from 15% to 53%. A subset of 27 markers were significantly associated with two or more traits. These markers were predominantly shared between traits that were significantly correlated at the phenotypic level. The results show clearly that in rapeseed, QTL mapping by association analysis is a viable alternative to QTL mapping in segregating populations.

  13. Characterization of microbial associations with methanotrophic archaea and sulfate-reducing bacteria through statistical comparison of nested Magneto-FISH enrichments

    DOE PAGES

    Trembath-Reichert, Elizabeth; Case, David H.; Orphan, Victoria J.

    2016-04-18

    Methane seep systems along continental margins host diverse and dynamic microbial assemblages, sustained in large part through the microbially mediated process of sulfate-coupled Anaerobic Oxidation of Methane (AOM). This methanotrophic metabolism has been linked to consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). These two groups are the focus of numerous studies; however, less is known about the wide diversity of other seep associated microorganisms. We selected a hierarchical set of FISH probes targeting a range ofDeltaproteobacteriadiversity. Using the Magneto-FISH enrichment technique, we then magnetically captured CARD-FISH hybridized cells and their physically associated microorganisms from a methane seepmore » sediment incubation. DNA from nested Magneto-FISH experiments was analyzed using Illumina tag 16S rRNA gene sequencing (iTag). Enrichment success and potential bias with iTag was evaluated in the context of full-length 16S rRNA gene clone libraries, CARD-FISH, functional gene clone libraries, and iTag mock communities. We determined commonly used Earth Microbiome Project (EMP) iTAG primers introduced bias in some common methane seep microbial taxa that reduced the ability to directly compare OTU relative abundances within a sample, but comparison of relative abundances between samples (in nearly all cases) and whole community-based analyses were robust. The iTag dataset was subjected to statistical co-occurrence measures of the most abundant OTUs to determine which taxa in this dataset were most correlated across all samples. In addition, many non-canonical microbial partnerships were statistically significant in our co-occurrence network analysis, most of which were not recovered with conventional clone library sequencing, demonstrating the utility of combining Magneto-FISH and iTag sequencing methods for hypothesis generation of associations within complex microbial communities. Network analysis pointed

  14. Characterization of microbial associations with methanotrophic archaea and sulfate-reducing bacteria through statistical comparison of nested Magneto-FISH enrichments.

    PubMed

    Trembath-Reichert, Elizabeth; Case, David H; Orphan, Victoria J

    2016-01-01

    Methane seep systems along continental margins host diverse and dynamic microbial assemblages, sustained in large part through the microbially mediated process of sulfate-coupled Anaerobic Oxidation of Methane (AOM). This methanotrophic metabolism has been linked to consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). These two groups are the focus of numerous studies; however, less is known about the wide diversity of other seep associated microorganisms. We selected a hierarchical set of FISH probes targeting a range of Deltaproteobacteria diversity. Using the Magneto-FISH enrichment technique, we then magnetically captured CARD-FISH hybridized cells and their physically associated microorganisms from a methane seep sediment incubation. DNA from nested Magneto-FISH experiments was analyzed using Illumina tag 16S rRNA gene sequencing (iTag). Enrichment success and potential bias with iTag was evaluated in the context of full-length 16S rRNA gene clone libraries, CARD-FISH, functional gene clone libraries, and iTag mock communities. We determined commonly used Earth Microbiome Project (EMP) iTAG primers introduced bias in some common methane seep microbial taxa that reduced the ability to directly compare OTU relative abundances within a sample, but comparison of relative abundances between samples (in nearly all cases) and whole community-based analyses were robust. The iTag dataset was subjected to statistical co-occurrence measures of the most abundant OTUs to determine which taxa in this dataset were most correlated across all samples. Many non-canonical microbial partnerships were statistically significant in our co-occurrence network analysis, most of which were not recovered with conventional clone library sequencing, demonstrating the utility of combining Magneto-FISH and iTag sequencing methods for hypothesis generation of associations within complex microbial communities. Network analysis pointed to many co

  15. Characterization of microbial associations with methanotrophic archaea and sulfate-reducing bacteria through statistical comparison of nested Magneto-FISH enrichments.

    PubMed

    Trembath-Reichert, Elizabeth; Case, David H; Orphan, Victoria J

    2016-01-01

    Methane seep systems along continental margins host diverse and dynamic microbial assemblages, sustained in large part through the microbially mediated process of sulfate-coupled Anaerobic Oxidation of Methane (AOM). This methanotrophic metabolism has been linked to consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). These two groups are the focus of numerous studies; however, less is known about the wide diversity of other seep associated microorganisms. We selected a hierarchical set of FISH probes targeting a range of Deltaproteobacteria diversity. Using the Magneto-FISH enrichment technique, we then magnetically captured CARD-FISH hybridized cells and their physically associated microorganisms from a methane seep sediment incubation. DNA from nested Magneto-FISH experiments was analyzed using Illumina tag 16S rRNA gene sequencing (iTag). Enrichment success and potential bias with iTag was evaluated in the context of full-length 16S rRNA gene clone libraries, CARD-FISH, functional gene clone libraries, and iTag mock communities. We determined commonly used Earth Microbiome Project (EMP) iTAG primers introduced bias in some common methane seep microbial taxa that reduced the ability to directly compare OTU relative abundances within a sample, but comparison of relative abundances between samples (in nearly all cases) and whole community-based analyses were robust. The iTag dataset was subjected to statistical co-occurrence measures of the most abundant OTUs to determine which taxa in this dataset were most correlated across all samples. Many non-canonical microbial partnerships were statistically significant in our co-occurrence network analysis, most of which were not recovered with conventional clone library sequencing, demonstrating the utility of combining Magneto-FISH and iTag sequencing methods for hypothesis generation of associations within complex microbial communities. Network analysis pointed to many co

  16. Characterization of microbial associations with methanotrophic archaea and sulfate-reducing bacteria through statistical comparison of nested Magneto-FISH enrichments

    PubMed Central

    Case, David H.

    2016-01-01

    Methane seep systems along continental margins host diverse and dynamic microbial assemblages, sustained in large part through the microbially mediated process of sulfate-coupled Anaerobic Oxidation of Methane (AOM). This methanotrophic metabolism has been linked to consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). These two groups are the focus of numerous studies; however, less is known about the wide diversity of other seep associated microorganisms. We selected a hierarchical set of FISH probes targeting a range of Deltaproteobacteria diversity. Using the Magneto-FISH enrichment technique, we then magnetically captured CARD-FISH hybridized cells and their physically associated microorganisms from a methane seep sediment incubation. DNA from nested Magneto-FISH experiments was analyzed using Illumina tag 16S rRNA gene sequencing (iTag). Enrichment success and potential bias with iTag was evaluated in the context of full-length 16S rRNA gene clone libraries, CARD-FISH, functional gene clone libraries, and iTag mock communities. We determined commonly used Earth Microbiome Project (EMP) iTAG primers introduced bias in some common methane seep microbial taxa that reduced the ability to directly compare OTU relative abundances within a sample, but comparison of relative abundances between samples (in nearly all cases) and whole community-based analyses were robust. The iTag dataset was subjected to statistical co-occurrence measures of the most abundant OTUs to determine which taxa in this dataset were most correlated across all samples. Many non-canonical microbial partnerships were statistically significant in our co-occurrence network analysis, most of which were not recovered with conventional clone library sequencing, demonstrating the utility of combining Magneto-FISH and iTag sequencing methods for hypothesis generation of associations within complex microbial communities. Network analysis pointed to many co

  17. Nested neural networks

    NASA Technical Reports Server (NTRS)

    Baram, Yoram

    1988-01-01

    Nested neural networks, consisting of small interconnected subnetworks, allow for the storage and retrieval of neural state patterns of different sizes. The subnetworks are naturally categorized by layers of corresponding to spatial frequencies in the pattern field. The storage capacity and the error correction capability of the subnetworks generally increase with the degree of connectivity between layers (the nesting degree). Storage of only few subpatterns in each subnetworks results in a vast storage capacity of patterns and subpatterns in the nested network, maintaining high stability and error correction capability.

  18. Nested sampling with demons

    NASA Astrophysics Data System (ADS)

    Habeck, Michael

    2015-01-01

    This article looks at Skilling's nested sampling from a physical perspective and interprets it as a microcanonical demon algorithm. Using key quantities of statistical physics we investigate the performance of nested sampling on complex systems such as Ising, Potts and protein models. We show that releasing multiple demons helps to smooth the truncated prior and eases sampling from it because the demons keep the particle off the constraint boundary. For continuous systems it is straightforward to extend this approach and formulate a phase space version of nested sampling that benefits from correlated explorations guided by Hamiltonian dynamics.

  19. Joint QTL linkage mapping for multiple-cross mating design sharing one common parent

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Nested association mapping (NAM) is a novel genetic mating design that combines the advantages of linkage analysis and association mapping. This design provides opportunities to study the inheritance of complex traits, but also requires more advanced statistical methods. In this paper, we present th...

  20. Association mapping for pre-harvest sprouting resistance in white winter wheat.

    PubMed

    Kulwal, Pawan; Ishikawa, Goro; Benscher, David; Feng, Zongyun; Yu, Long-Xi; Jadhav, Ashok; Mehetre, Subhash; Sorrells, Mark E

    2012-08-01

    Association mapping identified quantitative trait loci (QTLs) and the markers linked to pre-harvest sprouting (PHS) resistance in an elite association mapping panel of white winter wheat comprising 198 genotypes. A total of 1,166 marker loci including DArT and SSR markers representing all 21 chromosomes of wheat were used in the analysis. General and mixed linear models were used to analyze PHS data collected over 4 years. Association analysis identified eight QTLs linked with 13 markers mapped on seven chromosomes. A QTL was detected on each arm of chromosome 2B and one each on chromosome arms 1BS, 2DS, 4AL, 6DL, 7BS and 7DS. All except the QTL on 7BS are located in a location similar to previous reports and, if verified, the QTL on 7BS is likely to be novel. Principal components and the kinship matrix were used to account for the presence of population structure but had only a minor effect on the results. Although, none of the QTLs was highly significant across all environments, a QTL on the long arm of chromosome 4A was detected in three different environments and also using the best linear unbiased predictions over years. Although previous reports have identified this as a major QTL, its effects were minor in our biparental mapping populations. The results of this study highlight the benefits of association mapping and the value of using elite material in association mapping for plant breeding programs. PMID:22547141

  1. Scale considerations in monitoring greater sage-grouse ( Centrocercus urophasianus) vegetation structure and habitat suitability within nesting habitat in western Wyoming

    NASA Astrophysics Data System (ADS)

    Zabihi Afratakhti, Khodabakhsh

    Disturbance of nesting habitat associated with energy development has contributed to population declines of greater sage-grouse (Centrocercus urophasianus) in western Wyoming. Greater sage-grouse, rely on sagebrush ecosystems during all of their life stages. Specific criteria for suitable nesting habitat for the species includes both amount and distribution of sagebrush and herbaceous cover. Loss of suitable sagebrush habitat makes the identification of remaining suitable habitat critical for long-term management of the species. This research documents spatial patterns of vegetation structure within greater sage-grouse nesting habitat to compare shrub configuration (shrub patchiness) between nest and random non-nest locations at very fine scales. Additionally, we examine the applicability of gap intercept techniques to quantify shrub structural characteristics (shrub height and patchiness). Finally, the suitability of nesting habitats was mapped using biophysical features and anthropogenic disturbances at fine to broad scales. Spatial vegetation patterns vary with scale, and spatial homogeneity of sagebrush stands declines with increasing shrub height. Canopy gap intercept techniques reliably quantify composition, configuration, and height of shrub cover. The proportion of shrub cover and non-shrub gaps can be used as a compositional attribute that characterizes nesting habitat at the broad scale (across kilometers). In addition, variation in gap sizes within shrub cover, or shrub patchiness is a habitat characteristic that differentiates nesting and non-nest habitat at fine scales. Shrub cover-to-gap proportion, shrub spatial configuration, and mean shrub heights are important vegetative traits that characterize sage-grouse nesting habitat. At broad scales, habitat suitability for nesting is related to both anthropogenic disturbances and the suitability of biophysical features (e.g., slope, aspect, vegetation type and composition). Information about habitat

  2. Spatial distribution, risk factors and haemato-biochemical alterations associated with Theileria equi infected equids of Punjab (India) diagnosed by indirect ELISA and nested PCR.

    PubMed

    Sumbria, Deepak; Singla, L D; Kumar, Sanjay; Sharma, Amrita; Dahiya, Rajesh K; Setia, Raj

    2016-03-01

    Equine piroplasmosis is a febrile, tick-borne disease of equids predominately caused by obligatory intra-erythrocytic protozoa Theileria equi in the Indian sub-continent. A cross-sectional study was carried out on 464 equids (426 horses and 38 donkeys/mules) in Punjab, India to assess the level of exposure to equine piroplasmosis by 18S rRNA gene nested polymerase chain reaction (nPCR) and equine merozoite antigen-2 (EMA2) indirect-ELISA (enzyme linked immunosorbent assay), to investigate risk factors and haemato-biochemical alterations associated with the infection. The endemicity of the disease was confirmed by positive PCR amplification in 21.77% and positive antibody titers in 49.78% equid samples. There was a fair agreement between these two diagnostic techniques (Kappa coefficient=0.326). The spatial distribution analysis revealed an increasing trend of T. equi prevalence from north-eastern to south-western region of Punjab by both the techniques correspondingly, which proffered a direct relation with temperature and inverse with humidity variables. The relatively prominent risk factor associated with sero-positivity was the presence of other domestic animals in the herd, while the propensity of finding a positive PCR amplification was higher in donkeys/mules, animal kept at unorganised farm or those used for commercial purposes as compared to their counterparts. There was a significant increase in globulins, gamma glutamyl-transferase, total bilirubin, direct bilirubin, indirect bilirubin, glucose levels and decrease in total erythrocyte count, haemoglobin, packed cell volume by animals, which were revealed positive by nPCR (may or may not positive by indirect-ELISA) and increase in creatinine, total bilirubin, direct bilirubin, glucose and decrease in total erythrocytes count by animals, which were revealed positive by indirect-ELISA (alone). To our knowledge, this study, for the first time, brings out a comprehensive report on the status on spatial

  3. A Large National Cohort Study of the Association between Bisphosphonates and Osteonecrosis of the Jaw in Patients with Osteoporosis: A Nested Case-control Study.

    PubMed

    Kwon, J-W; Park, E-J; Jung, S-Y; Sohn, H S; Ryu, H; Suh, H S

    2015-09-01

    The purpose of this study was to examine the association between bisphosphonate exposure and osteonecrosis of the jaw (ONJ) in Korean patients with osteoporosis. A nested case-control study was performed using the claims database during 2002 to 2010 provided by the National Health Insurance Service. We identified a cohort of individuals with diagnosis of osteoporosis during 2002 to 2010. Cases and controls were identified during 2004 to 2010, and the date of potential cases of ONJ was defined as the index date. Bisphosphonate exposure was evaluated during 2 y prior to the index date. The association between bisphosphonate exposure and ONJ was tested by performing a conditional logistic regression analysis for matched data, and odds ratios (ORs) with 95% confidence intervals (CIs) were presented. Subjects were classified as nonuser, recent user, past user, or continuous user, depending on the prescription of bisphosphonates in 2 periods (1 to 2 y and 0 to 1 y prior to the index date). Continuous users were defined as patients who were exposed to bisphosphonate in both periods. We also examined the impact of bisphosphonate medication compliance by measuring the cumulative duration of exposure (CDE) on the risk of ONJ. A total of 212 cases with ONJ and 2,120 controls matched by sex, age, income level, and insurance type were identified among 109,787 patients with osteoporosis out of 1,025,340 enrollees in the sample cohort. The odds of having ONJ after adjusting for patient comorbidities significantly increased in continuous users of bisphosphonates (OR, 3.9; 95% CI, 2.4 to 6.2) compared to nonusers. Increased odds of ONJ were observed as CDE increased. The adjusted OR in patients with 1.5 y < CDE ≤ 2 y prior to the index date was 7.8 (95% CI, 4.0 to 15.5) versus nonusers. Our study results support significantly increased occurrences of potential ONJ in patients with osteoporosis who were exposed to bisphosphonates compared to those without exposure. PMID:26001708

  4. Mapping Gene Associations in Human Mitochondria using Clinical Disease Phenotypes

    PubMed Central

    Scharfe, Curt; Lu, Henry Horng-Shing; Neuenburg, Jutta K.; Allen, Edward A.; Li, Guan-Cheng; Klopstock, Thomas; Cowan, Tina M.; Enns, Gregory M.; Davis, Ronald W.

    2009-01-01

    Nuclear genes encode most mitochondrial proteins, and their mutations cause diverse and debilitating clinical disorders. To date, 1,200 of these mitochondrial genes have been recorded, while no standardized catalog exists of the associated clinical phenotypes. Such a catalog would be useful to develop methods to analyze human phenotypic data, to determine genotype-phenotype relations among many genes and diseases, and to support the clinical diagnosis of mitochondrial disorders. Here we establish a clinical phenotype catalog of 174 mitochondrial disease genes and study associations of diseases and genes. Phenotypic features such as clinical signs and symptoms were manually annotated from full-text medical articles and classified based on the hierarchical MeSH ontology. This classification of phenotypic features of each gene allowed for the comparison of diseases between different genes. In turn, we were then able to measure the phenotypic associations of disease genes for which we calculated a quantitative value that is based on their shared phenotypic features. The results showed that genes sharing more similar phenotypes have a stronger tendency for functional interactions, proving the usefulness of phenotype similarity values in disease gene network analysis. We then constructed a functional network of mitochondrial genes and discovered a higher connectivity for non-disease than for disease genes, and a tendency of disease genes to interact with each other. Utilizing these differences, we propose 168 candidate genes that resemble the characteristic interaction patterns of mitochondrial disease genes. Through their network associations, the candidates are further prioritized for the study of specific disorders such as optic neuropathies and Parkinson disease. Most mitochondrial disease phenotypes involve several clinical categories including neurologic, metabolic, and gastrointestinal disorders, which might indicate the effects of gene defects within the

  5. Application of Association Mapping to Understanding the Genetic Diversity of Plant Germplasm Resources

    PubMed Central

    Abdurakhmonov, Ibrokhim Y.; Abdukarimov, Abdusattor

    2008-01-01

    Compared to the conventional linkage mapping, linkage disequilibrium (LD)-mapping, using the nonrandom associations of loci in haplotypes, is a powerful high-resolution mapping tool for complex quantitative traits. The recent advances in the development of unbiased association mapping approaches for plant population with their successful applications in dissecting a number of simple to complex traits in many crop species demonstrate a flourish of the approach as a “powerful gene tagging” tool for crops in the plant genomics era of 21st century. The goal of this review is to provide nonexpert readers of crop breeding community with (1) the basic concept, merits, and simple description of existing methodologies for an association mapping with the recent improvements for plant populations, and (2) the details of some of pioneer and recent studies on association mapping in various crop species to demonstrate the feasibility, success, problems, and future perspectives of the efforts in plants. This should be helpful for interested readers of international plant research community as a guideline for the basic understanding, choosing the appropriate methods, and its application. PMID:18551188

  6. Admixture mapping identifies a quantitative trait locus associated with FEV1/FVC in the COPDGene Study.

    PubMed

    Parker, Margaret M; Foreman, Marilyn G; Abel, Haley J; Mathias, Rasika A; Hetmanski, Jacqueline B; Crapo, James D; Silverman, Edwin K; Beaty, Terri H

    2014-11-01

    African Americans are admixed with genetic contributions from European and African ancestral populations. Admixture mapping leverages this information to map genes influencing differential disease risk across populations. We performed admixture and association mapping in 3,300 African American current or former smokers from the COPDGene Study. We analyzed estimated local ancestry and SNP genotype information to identify regions associated with FEV1 /FVC, the ratio of forced expiratory volume in one second to forced vital capacity, measured by spirometry performed after bronchodilator administration. Global African ancestry inversely associated with FEV1 /FVC (P = 0.035). Genome-wide admixture analysis, controlling for age, gender, body mass index, current smoking status, pack-years smoked, and four principal components summarizing the genetic background of African Americans in the COPDGene Study, identified a region on chromosome 12q14.1 associated with FEV1 /FVC (P = 2.1 × 10(-6) ) when regressed on local ancestry. Allelic association in this region of chromosome 12 identified an intronic variant in FAM19A2 (rs348644) as associated with FEV1 /FVC (P = 1.76 × 10(-6) ). By combining admixture and association mapping, a marker on chromosome 12q14.1 was identified as being associated with reduced FEV1 /FVC ratio among African Americans in the COPDGene Study.

  7. Association between cattle herd Mycobacterium avium subsp. paratuberculosis (MAP) infection and infection of a hare population.

    PubMed

    Salgado, Miguel; Monti, Gustavo; Sevilla, Iker; Manning, Elizabeth

    2014-10-01

    Paratuberculosis has long been considered a disease of domestic and wild ruminants only. The known host range of Mycobacterium avium subsp. paratuberculosis (MAP) was recently extended to include non-ruminant wildlife species believed to be exposed to spillover of MAP from infected domestic cattle herds. The aim of the present study was to assess the association between cattle herd MAP infection pressure level and the infection level of a hare population in two dairy farms of southern Chile. Fifty hares from a herd A and 42 hares from herd B were captured and sampled for MAP culture. The results showed a statistically significant association between the cattle herds' infection prevalence and the hare infection prevalence.

  8. Nesting habitat and reproductive success of southwestern riparian birds

    USGS Publications Warehouse

    Powell, B.F.; Steidl, R.J.

    2000-01-01

    Vegetation structure and floristic composition strongly influence the structure of bird communities. To assess the influence of vegetation and other environmental characteristics on songbirds, we quantified nest-site characteristics and reproductive success of a riparian songbird community in Arizona. Although we found interspecific variation in characteristics associated with nest sites, we identified two suites of species that chose sites with similar characteristics. These 'nest groups' were explained largely by nest height and characteristics of nest trees. Overall, nest success was low for songbirds in this community, and averaged 23%. The most common cause of nest failure was predation (81%), although brood parasitism by Brown-headed Cowbirds (Molothrus ater) was highest at nests of Bell's Vireos (Vireo bellii) (29%). No vegetation or environmental features were associated with the likelihood of cowbird parasitism for any species; nest success for Bell's Vireos was negatively associated with the amount of netleaf hackberry (Celtis reticulata) in the understory. Arizona sycamore (Platanus wrightii) and netleaf hackberry trees contained 41% and 17% of all nests, respectively, and therefore provide critically important nesting substrates for birds in this rare yet diverse vegetation community.

  9. Association of folate-pathway gene polymorphisms with the risk of prostate cancer: a population-based nested case-control study, systematic review, and meta-analysis.

    PubMed

    Collin, Simon M; Metcalfe, Chris; Zuccolo, Luisa; Lewis, Sarah J; Chen, Lina; Cox, Angela; Davis, Michael; Lane, J Athene; Donovan, Jenny; Smith, George Davey; Neal, David E; Hamdy, Freddie C; Gudmundsson, Julius; Sulem, Patrick; Rafnar, Thorunn; Benediktsdottir, Kristrun R; Eeles, Rosalind A; Guy, Michelle; Kote-Jarai, Zsofia; Morrison, Jonathan; Al Olama, Ali Amin; Stefansson, Kari; Easton, Douglas F; Martin, Richard M

    2009-09-01

    Folate-pathway gene polymorphisms have been implicated in several cancers and investigated inconclusively in relation to prostate cancer. We conducted a systematic review, which identified nine case-control studies (eight included, one excluded). We also included data from four genome-wide association studies and from a case-control study nested within the UK population-based Prostate Testing for Cancer and Treatment study. We investigated by meta-analysis the effects of eight polymorphisms: MTHFR C677T (rs1801133; 12 studies; 10,745 cases; 40,158 controls), MTHFR A1298C (rs1801131; 5 studies; 3,176 cases; 4,829 controls), MTR A2756G (rs1805087; 8 studies; 7,810 cases; 37,543 controls), MTRR A66G (rs1801394; 4 studies; 3,032 cases; 4,515 controls), MTHFD1 G1958A (rs2236225; 6 studies; 7,493 cases; 36,941 controls), SLC19A1/RFC1 G80A (rs1051266; 4 studies; 6,222 cases; 35,821 controls), SHMT1 C1420T (rs1979277; 2 studies; 2,689 cases; 4,110 controls), and FOLH1 T1561C (rs202676; 5 studies; 6,314 cases; 35,190 controls). The majority (10 of 13) of eligible studies had 100% Caucasian subjects; only one study had <90% Caucasian subjects. We found weak evidence of dominant effects of two alleles: MTR 2756A>G [random effects pooled odds ratio, 1.06 (1.00-1.12); P = 0.06 (P = 0.59 for heterogeneity across studies)] and SHMT1 1420C>T [random effects pooled odds ratio, 1.11 (1.00-1.22); P = 0.05 (P = 0.38 for heterogeneity across studies)]. We found no effect of MTHFR 677C>T or any of the other alleles in dominant, recessive or additive models, or in comparing a/a versus A/A homozygous. Neither did we find any difference in effects on advanced or localized cancers. Our meta-analysis suggests that known common folate-pathway single nucleotide polymorphisms do not have significant effects on susceptibility to prostate cancer. PMID:19706844

  10. Size matters: nest colonization patterns for twig-nesting ants.

    PubMed

    Jiménez-Soto, Estelí; Philpott, Stacy M

    2015-08-01

    Understanding the drivers of ant diversity and co-occurrence in agroecosystems is fundamental because ants participate in interactions that influence agroecosystem processes. Multiple local and regional factors influence ant community assembly.We examined local factors that influence the structure of a twig-nesting ant community in a coffee system in Mexico using an experimental approach. We investigated whether twig characteristics (nest entrance size and diversity of nest entrance sizes) and nest strata (canopy shade tree or coffee shrub) affected occupation, species richness, and community composition of twig-nesting ants and whether frequency of occupation of ant species varied with particular nest entrance sizes or strata.We conducted our study in a shaded coffee farm in Chiapas, Mexico, between March and June 2012. We studied ant nest colonization by placing artificial nests (bamboo twigs) on coffee shrubs and shade trees either in diverse or uniform treatments. We also examined whether differences in vegetation (no. of trees, canopy cover and coffee density) influenced nest colonization.We found 33 ant species occupying 73% of nests placed. Nest colonization did not differ with nest strata or size. Mean species richness of colonizing ants was significantly higher in the diverse nest size entrance treatment, but did not differ with nest strata. Community composition differed between strata and also between the diverse and uniform size treatments on coffee shrubs, but not on shade trees. Some individual ant species were more frequently found in certain nest strata and in nests with certain entrance sizes.Our results indicate that twig-nesting ants are nest-site limited, quickly occupy artificial nests of many sizes, and that trees or shrubs with twigs of a diversity of entrance sizes likely support higher ant species richness. Further, individual ant species more frequently occupy nests with different sized entrances promoting ant richness on individual coffee

  11. Size matters: nest colonization patterns for twig-nesting ants

    PubMed Central

    Jiménez-Soto, Estelí; Philpott, Stacy M

    2015-01-01

    Understanding the drivers of ant diversity and co-occurrence in agroecosystems is fundamental because ants participate in interactions that influence agroecosystem processes. Multiple local and regional factors influence ant community assembly. We examined local factors that influence the structure of a twig-nesting ant community in a coffee system in Mexico using an experimental approach. We investigated whether twig characteristics (nest entrance size and diversity of nest entrance sizes) and nest strata (canopy shade tree or coffee shrub) affected occupation, species richness, and community composition of twig-nesting ants and whether frequency of occupation of ant species varied with particular nest entrance sizes or strata. We conducted our study in a shaded coffee farm in Chiapas, Mexico, between March and June 2012. We studied ant nest colonization by placing artificial nests (bamboo twigs) on coffee shrubs and shade trees either in diverse or uniform treatments. We also examined whether differences in vegetation (no. of trees, canopy cover and coffee density) influenced nest colonization. We found 33 ant species occupying 73% of nests placed. Nest colonization did not differ with nest strata or size. Mean species richness of colonizing ants was significantly higher in the diverse nest size entrance treatment, but did not differ with nest strata. Community composition differed between strata and also between the diverse and uniform size treatments on coffee shrubs, but not on shade trees. Some individual ant species were more frequently found in certain nest strata and in nests with certain entrance sizes. Our results indicate that twig-nesting ants are nest-site limited, quickly occupy artificial nests of many sizes, and that trees or shrubs with twigs of a diversity of entrance sizes likely support higher ant species richness. Further, individual ant species more frequently occupy nests with different sized entrances promoting ant richness on individual

  12. Allelic association patterns for a dense SNP map.

    PubMed

    Weir, B S; Hill, W G; Cardon, L R

    2004-12-01

    A dense set of 5,000 SNPs on a 10-Mb region of human chromosome 20 has been typed on samples of African Americans, East Asians, and United Kingdom Caucasians. There are departures from Hardy-Weinberg equilibrium beyond the level at which markers are often discarded because of possible genotyping errors. The observation that markers showing such departures are often close together on the chromosome confirms the result that Hardy-Weinberg tests at two loci are correlated to an extent that depends on the linkage disequilibrium between those two markers. Linkage disequilibrium can be described by the composite linkage disequilibrium coefficient, the parameter that determines the behavior of case-control allelic tests of association. A useful preliminary investigation of datasets of this type is provided by counting the numbers of distinct multi-locus genotypes in windows of a few markers.

  13. Single-nucleotide-polymorphism-based association mapping of dog stereotypes.

    PubMed

    Jones, Paul; Chase, Kevin; Martin, Alan; Davern, Pluis; Ostrander, Elaine A; Lark, Karl G

    2008-06-01

    Phenotypic stereotypes are traits, often polygenic, that have been stringently selected to conform to specific criteria. In dogs, Canis familiaris, stereotypes result from breed standards set for conformation, performance (behaviors), etc. As a consequence, phenotypic values measured on a few individuals are representative of the breed stereotype. We used DNA samples isolated from 148 dog breeds to associate SNP markers with breed stereotypes. Using size as a trait to test the method, we identified six significant quantitative trait loci (QTL) on five chromosomes that include candidate genes appropriate to regulation of size (e.g., IGF1, IGF2BP2 SMAD2, etc.). Analysis of other morphological stereotypes, also under extreme selection, identified many additional significant loci. Less well-documented data for behavioral stereotypes tentatively identified loci for herding, pointing, boldness, and trainability. Four significant loci were identified for longevity, a breed characteristic not under direct selection, but inversely correlated with breed size. The strengths and limitations of the approach are discussed as well as its potential to identify loci regulating the within-breed incidence of specific polygenic diseases. PMID:18505865

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

    PubMed

    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.

  15. Superposition Enhanced Nested Sampling

    NASA Astrophysics Data System (ADS)

    Martiniani, Stefano; Stevenson, Jacob D.; Wales, David J.; Frenkel, Daan

    2014-07-01

    The theoretical analysis of many problems in physics, astronomy, and applied mathematics requires an efficient numerical exploration of multimodal parameter spaces that exhibit broken ergodicity. Monte Carlo methods are widely used to deal with these classes of problems, but such simulations suffer from a ubiquitous sampling problem: The probability of sampling a particular state is proportional to its entropic weight. Devising an algorithm capable of sampling efficiently the full phase space is a long-standing problem. Here, we report a new hybrid method for the exploration of multimodal parameter spaces exhibiting broken ergodicity. Superposition enhanced nested sampling combines the strengths of global optimization with the unbiased or athermal sampling of nested sampling, greatly enhancing its efficiency with no additional parameters. We report extensive tests of this new approach for atomic clusters that are known to have energy landscapes for which conventional sampling schemes suffer from broken ergodicity. We also introduce a novel parallelization algorithm for nested sampling.

  16. Serenbe Nest Cottages

    SciTech Connect

    Butler, T.; Curtis, O.; Kim, E.; Roberts, S.; Stephenson, R.

    2012-12-01

    As part of the NAHB Research Center Industry Partnership, Southface partnered with Martin Dodson Builders and the Serenbe community on the construction of a new test home in the suburbs of Atlanta, GA in the mixed humid climate zone. The most recent subdivision within the Serenbe community, the Nest, will contain 15 small footprint cottage style homes, and Southface has selected Lot Nine, as the test home for this study. This Nest subdivision serves as a project showcase for both the builder partner and the Serenbe community as a whole. The planning and design incorporated into the Nest cottages will be implemented in each home within the subdivision. These homes addresses Building America Savings targets and serve as a basis of design for other homes Martin Dodson plans to build within the Serenbe community.

  17. Serenbe Nest Cottages

    SciTech Connect

    Butler, T.; Curtis, O.; Kim, E.; Roberts, S.; Stephenson, R.

    2012-12-01

    As part of the NAHB Research Center Industry Partnership, Southface partnered with Martin Dodson Builders and the Serenbe community on the construction of a new test home in the suburbs of Atlanta, GA, in the mixed humid climate zone. The most recent subdivision within the Serenbe community, the Nest, will contain 15 small footprint cottage-style homes, and Southface has selected Lot Nine, as the test home for this study. This Nest subdivision serves as a project showcase for both the builder partner and the Serenbe community as a whole. The planning and design incorporated into the Nest cottages will be implemented in each home within the subdivision. These homes addresses Building America savings targets and serve as a basis of design for other homes Martin Dodson plans to build within the Serenbe community.

  18. Risky business: Site selection by Acadian Flycatchers under threat of nest predation and brood parasitism

    USGS Publications Warehouse

    HazIer, K.R.; Cooper, R.J.; Twedt, D.J.

    2006-01-01

    Habitat quality is determined not only by habitat structure and the availability of resources, but also by competitors, cooperators, predators, and parasites. We hypothesized that, for passerines, minimizing risk from avian nest predators and brood parasites is an important factor in selecting a breeding site. Through the early part of two breeding seasons, we spot-mapped locations of Acadian Flycatchers (Empidonax virescens, territory selectors), Red-bellied Woodpeckers (Melanerpes carolinus, nest predators) and Brown-headed Cowbirds (Molothrus ater, brood parasites) in a 56-ha study area within an extensive bottomland hardwood forest. We were thereby able to determine the order of flycatcher territory settlement and nest initiation in relation to risk of predation and parasitism, while accounting for habitat structure. Male settlement was influenced by both habitat structure and risk avoidance. However, risk trom woodpeckers was relatively more important in the first season and risk from cowbirds in the second, evidently due to differences in the relative abundance of predator and brood-parasite in each year. For male flycatchers, settlement choices appear to be flexible in the face of changing 'risk landscapes.' For females, habitat structure was the most important predictor of nest site selection. Even so, there was evidence that females avoided cowbirds. Surprisingly, nest site selection was positively associated with woodpecker abundance in the first season when woodpeckers were present in greater numbers. Possible explanations for this contradictory result are discussed.

  19. Risk Factor Associated with Negative Spouse HIV Seroconversion among Sero-Different Couples: A Nested Case-Control Retrospective Survey Study in 30 Counties in Rural China

    PubMed Central

    Tang, Houlin; Wu, Zunyou; Mao, Yurong; Cepeda, Javier; Morano, Jamie

    2016-01-01

    Background Antiretroviral therapy (ART) and condom use have been proven to reduce the risk of sexual transmission of human immunodeficiency virus (HIV) among HIV sero-different couples, but its full implementation remains a challenge. This study aims to assess HIV seroconversion rate of HIV-negative spouse and its associated risk factors among HIV sero-different couples in rural China. Methods An open cohort of HIV sero-different couples enrolled in 30 counties in China between October 1, 2010, and September 30, 2012, and followed-up to December 31, 2012, was constructed retrospectively. A nested case-control study of risk factors of HIV seroconversion among sero-different couples was conducted in April and May of 2013, based on the open cohort. Sero-different couples with the HIV-negative spouse seroconverting at least 3 months after the previous negative diagnosis during cohort observation period were labeled as “case couples”. The “control couples” were selected randomly from the same cohort that did not have the HIV-negative spouse seroconversion during the same period. The “case couples” and “control couples” were matched on gender, age, and region of residence. Sexual behaviors among HIV sero-different couples before and after the index spouses notifying their HIV infection status to their HIV-negative spouses were collected via face-to-face interview. Univariate and multivariate logistic regression models were used to assess factors associated with HIV seroconversion among HIV sero-different couples. Results Of 4481 HIV sero-different couples, a total of 53 seroconversions were observed within 5218 person-years of follow-up. The incidence rate was 1.02 (95%CI: 0.76–1.33) per 100 person-years. Forty “case couples” confirmed HIV-negative spouse seroconversions infected via marital sexual transmission, were matched to 80 “control couples”. Of the 120 couples, 81(67.5%) were receiving ART, and 70 (58.3%) reported consistently used

  20. History and future of the Multidisciplinary Association for Psychedelic Studies (MAPS).

    PubMed

    Emerson, Amy; Ponté, Linnae; Jerome, Lisa; Doblin, Rick

    2014-01-01

    This article describes the teenage vision of the founder of the Multidisciplinary Association for Psychedelic Studies (MAPS) that humanity's future would be aided by the therapeutic and spiritual potential of psychedelic substances. The article traces the trajectory of MAPS from inception in 1986 to its present, noting future goals with respect to research, outreach, and harm reduction. MAPS was created as a non-profit psychedelic pharmaceutical company in response to the 1985 scheduling of 3,4-methylenedioxymethamphetamine (MDMA). Overcoming many hurdles, MAPS developed the first double-blind, placebo-controlled trial of MDMA-assisted psychotherapy for posttraumatic stress disorder (PTSD) and plans for FDA prescription approval in 2021. MAPS' program of research expanded to include a trial of lysergic acid diethylamide (LSD)-assisted psychotherapy for anxiety when facing life-threatening illness, observational studies of ibogaine in the treatment of addiction, and studies of MDMA for social anxiety in people with autism spectrum disorders. MAPS meets the challenges of drug development through a clinical research team led by a former Novartis drug development professional experienced in the conduct, monitoring, and analysis of clinical trials. MAPS' harm-reduction efforts are intended to avoid backlash and build a post-prohibition world by assisting non-medical users to transform difficult psychedelic experiences into opportunities for growth.

  1. History and future of the Multidisciplinary Association for Psychedelic Studies (MAPS).

    PubMed

    Emerson, Amy; Ponté, Linnae; Jerome, Lisa; Doblin, Rick

    2014-01-01

    This article describes the teenage vision of the founder of the Multidisciplinary Association for Psychedelic Studies (MAPS) that humanity's future would be aided by the therapeutic and spiritual potential of psychedelic substances. The article traces the trajectory of MAPS from inception in 1986 to its present, noting future goals with respect to research, outreach, and harm reduction. MAPS was created as a non-profit psychedelic pharmaceutical company in response to the 1985 scheduling of 3,4-methylenedioxymethamphetamine (MDMA). Overcoming many hurdles, MAPS developed the first double-blind, placebo-controlled trial of MDMA-assisted psychotherapy for posttraumatic stress disorder (PTSD) and plans for FDA prescription approval in 2021. MAPS' program of research expanded to include a trial of lysergic acid diethylamide (LSD)-assisted psychotherapy for anxiety when facing life-threatening illness, observational studies of ibogaine in the treatment of addiction, and studies of MDMA for social anxiety in people with autism spectrum disorders. MAPS meets the challenges of drug development through a clinical research team led by a former Novartis drug development professional experienced in the conduct, monitoring, and analysis of clinical trials. MAPS' harm-reduction efforts are intended to avoid backlash and build a post-prohibition world by assisting non-medical users to transform difficult psychedelic experiences into opportunities for growth. PMID:24830183

  2. Variation in nesting behavior of eight species of spider mites, Stigmaeopsis having sociality

    NASA Astrophysics Data System (ADS)

    Saito, Yutaka; Zhang, Yan-Xuan; Mori, Kotaro; Ito, Katsura; Sato, Yukie; Chittenden, Anthony R.; Lin, Jian-Zhen; Chae, Younghae; Sakagami, Takane; Sahara, Ken

    2016-10-01

    Nesting behavior is considered to be an important element of social living in animals. The spider mites belonging to the genus Stigmaeopsis spend their lives within nests produced from silk threads. Several of these species show cooperative sociality, while the others are subsocial. In order to identify the origins of this social behavior, comparisons of nest sizes, nesting behaviors (making nests continuously or separately), and their associated traits (fecal deposition patterns) were made for eight cogeneric Stigmaeopsis species showing various levels of social development. All of these species inhabit bamboo plants (Poaceae). We initially addressed the proximate factor of nest size variation. The variation in nest size of the eight species corresponded well with the variation in dorsal seta sc1 length, suggesting that nest size variation among species may have a genetic basis. The time spent within a nest (nest duration) increased with nest size on the respective host plants. Nest arrangement patterns varied among species showing different sized nests: Large nest builders continuously extended their nests, while middle and small nest-building species built new separate nests, which resulted in different social interaction times among species, and is thought to be closely related to social development. Fecal deposition behaviors also varied among Stigmaeopsis species, suggesting diversity in anti-predatory adaptations. Finally, we discuss how the variation in sociality observed within this genus is likely the result of nest size variation that initially evolved as anti-predator strategies.

  3. Population structure and association mapping of yield contributing agronomic traits in foxtail millet.

    PubMed

    Gupta, Sarika; Kumari, Kajal; Muthamilarasan, Mehanathan; Parida, Swarup Kumar; Prasad, Manoj

    2014-06-01

    Association analyses accounting for population structure and relative kinship identified eight SSR markers ( p < 0.01) showing significant association ( R (2) = 18 %) with nine agronomic traits in foxtail millet. Association mapping is an efficient tool for identifying genes regulating complex traits. Although association mapping using genomic simple sequence repeat (SSR) markers has been successfully demonstrated in many agronomically important crops, very few reports are available on marker-trait association analysis in foxtail millet. In the present study, 184 foxtail millet accessions from diverse geographical locations were genotyped using 50 SSR markers representing the nine chromosomes of foxtail millet. The genetic diversity within these accessions was examined using a genetic distance-based and a general model-based clustering method. The model-based analysis using 50 SSR markers identified an underlying population structure comprising five sub-populations which corresponded well with distance-based groupings. The phenotyping of plants was carried out in the field for three consecutive years for 20 yield contributing agronomic traits. The linkage disequilibrium analysis considering population structure and relative kinship identified eight SSR markers (p < 0.01) on different chromosomes showing significant association (R (2) = 18 %) with nine agronomic traits. Four of these markers were associated with multiple traits. The integration of genetic and physical map information of eight SSR markers with their functional annotation revealed strong association of two markers encoding for phospholipid acyltransferase and ubiquitin carboxyl-terminal hydrolase located on the same chromosome (5) with flag leaf width and grain yield, respectively. Our findings on association mapping is the first report on Indian foxtail millet germplasm and this could be effectively applied in foxtail millet breeding to further uncover marker-trait associations with a large number of

  4. Effects of nest density, location, and timing on breeding success of Caspian Terns

    USGS Publications Warehouse

    Antolos, M.; Roby, D.D.; Lyons, Donald E.; Anderson, S.K.; Collis, K.

    2006-01-01

    One of the proposed benefits of colonial nesting in birds is the protection afforded against avian predators. This advantage may be counter-balanced by the negative effects of intraspecific aggression on breeding success. Effects of nest density, nest location within the colony, and timing of nest initiation on productivity of Caspian Terns (Sterna caspia) were investigated on Crescent Island in the mid-Columbia River, Washington, USA. In the absence of intense nest predation at the Crescent Island tern colony, it was hypothesized that nest density would be negatively associated with productivity. A rangefinder was used to determine spatial distribution of Caspian Tern nests, and these data used to calculate nest characteristics (nest density, nearest neighbor distance, and distance to colony edge) for a randomly-selected subset of nests monitored for nest chronology and productivity. Productivity did not differ between nests in high- and low-density areas of the colony, and was positively associated with earlier nest initiation. Early nests were more productive, were located in areas of higher nest density, and were further from the colony edge than late nests. The strong effect of timing may have been attributable to seasonal declines in prey resources for terns at this site. Our results suggest that Caspian Terns nesting at the highest densities observed in this study did not incur immediate reproductive costs, despite increased potential for encounters between chicks and aggressive conspecific adults.

  5. Association mapping in multiple segregating populations of sugar beet (Beta vulgaris L.).

    PubMed

    Stich, Benjamin; Melchinger, Albrecht E; Heckenberger, Martin; Möhring, Jens; Schechert, Axel; Piepho, Hans-Peter

    2008-11-01

    Association mapping in multiple segregating populations (AMMSP) combines high power to detect QTL in genome-wide approaches of linkage mapping with high mapping resolution of association mapping. The main objectives of this study were to (1) examine the applicability of AMMSP in a plant breeding context based on segregating populations of various size of sugar beet (Beta vulgaris L.), (2) compare different biometric approaches for AMMSP, and (3) detect markers with significant main effect across locations for nine traits in sugar beet. We used 768 F(n) (n = 2, 3, 4) sugar beet genotypes which were randomly derived from 19 crosses among diploid elite sugar beet clones. For all nine traits, the genotypic and genotype x location interaction variances were highly significant (P < 0.01). Using a one-step AMMSP approach, the total number of significant (P < 0.05) marker-phenotype associations was 44. The identification of genome regions associated with the traits under consideration indicated that not only segregating populations derived from crosses of parental genotypes in a systematic manner could be used for AMMSP but also populations routinely derived in plant breeding programs from multiple, related crosses. Furthermore, our results suggest that data sets, whose size does not permit analysis by the one-step AMMSP approach, might be analyzed using the two-step approach based on adjusted entry means for each location without losing too much power for detection of marker-phenotype associations.

  6. Density-dependent nest predation in waterfowl: the relative importance of nest density versus nest dispersion

    USGS Publications Warehouse

    Ackerman, Joshua T.; Ringelman, KM; Eadie, J.M.

    2012-01-01

    When nest predation levels are very high or very low, the absolute range of observable nest success is constrained (a floor/ceiling effect), and it may be more difficult to detect density-dependent nest predation. Density-dependent nest predation may be more detectable in years with moderate predation rates, simply because there can be a greater absolute difference in nest success between sites. To test this, we replicated a predation experiment 10 years after the original study, using both natural and artificial nests, comparing a year when overall rates of nest predation were high (2000) to a year with moderate nest predation (2010). We found no evidence for density-dependent predation on artificial nests in either year, indicating that nest predation is not density-dependent at the spatial scale of our experimental replicates (1-ha patches). Using nearest-neighbor distances as a measure of nest dispersion, we also found little evidence for “dispersion-dependent” predation on artificial nests. However, when we tested for dispersion-dependent predation using natural nests, we found that nest survival increased with shorter nearest-neighbor distances, and that neighboring nests were more likely to share the same nest fate than non-adjacent nests. Thus, at small spatial scales, density-dependence appears to operate in the opposite direction as predicted: closer nearest neighbors are more likely to be successful. We suggest that local nest dispersion, rather than larger-scale measures of nest density per se, may play a more important role in density-dependent nest predation.

  7. International association for the study of lung cancer map, Wang lymph node map and rapid on-site evaluation in transbronchial needle aspiration

    PubMed Central

    Liu, Qing-Hua; Arias, Sixto

    2016-01-01

    The invaluable role of transbronchial needle aspiration (TBNA) in the diagnosis and staging of mediastinal adenopathy and lung cancer has been well established. Different lymph nodes regional nomenclatures and maps had been described over the years. The international association for the study of lung cancer (IASLC) and Wang’s maps complement each other benefiting patients with lung cancer. In this article we briefly reviewed the roles of IALSC, Wang’s maps and ROSE in TBNA. PMID:27747023

  8. Epigenome-wide association of DNA methylation markers in peripheral blood from Indian Asians and Europeans with incident type 2 diabetes: a nested case-control study

    PubMed Central

    Wahl, Simone; Elliott, Hannah R; Rota, Federica; Scott, William R; Zhang, Weihua; Tan, Sian-Tsung; Campanella, Gianluca; Chadeau-Hyam, Marc; Yengo, Loic; Richmond, Rebecca C; Adamowicz-Brice, Martyna; Afzal, Uzma; Bozaoglu, Kiymet; Mok, Zuan Yu; Ng, Hong Kiat; Pattou, François; Prokisch, Holger; Rozario, Michelle Ann; Tarantini, Letizia; Abbott, James; Ala-Korpela, Mika; Albetti, Benedetta; Ammerpohl, Ole; Bertazzi, Pier Alberto; Blancher, Christine; Caiazzo, Robert; Danesh, John; Gaunt, Tom R; de Lusignan, Simon; Gieger, Christian; Illig, Thomas; Jha, Sujeet; Jones, Simon; Jowett, Jeremy; Kangas, Antti J; Kasturiratne, Anuradhani; Kato, Norihiro; Kotea, Navaratnam; Kowlessur, Sudhir; Pitkäniemi, Janne; Punjabi, Prakash; Saleheen, Danish; Schafmayer, Clemens; Soininen, Pasi; Tai, E-Shyong; Thorand, Barbara; Tuomilehto, Jaakko; Wickremasinghe, Ananda Rajitha; Kyrtopoulos, Soterios A; Aitman, Timothy J; Herder, Christian; Hampe, Jochen; Cauchi, Stéphane; Relton, Caroline L; Froguel, Philippe; Soong, Richie; Vineis, Paolo

    2016-01-01

    Summary Background Indian Asians, who make up a quarter of the world’s population, are at high risk of developing type 2 diabetes. We investigated whether DNA methylation is associated with future type 2 diabetes incidence in Indian Asians and whether differences in methylation patterns between Indian Asians and Europeans are associated with, and could be used to predict, differences in the magnitude of risk of developing type 2 diabetes. Methods We did a nested case-control study of DNA methylation in Indian Asians and Europeans with incident type 2 diabetes who were identified from the 8-year follow-up of 25 372 participants in the London Life Sciences Prospective Population (LOLIPOP) study. Patients were recruited between May 1, 2002, and Sept 12, 2008. We did epigenome-wide association analysis using samples from Indian Asians with incident type 2 diabetes and age-matched and sex-matched Indian Asian controls, followed by replication testing of top-ranking signals in Europeans. For both discovery and replication, DNA methylation was measured in the baseline blood sample, which was collected before the onset of type 2 diabetes. Epigenome-wide significance was set at p<1 × 10−7. We compared methylation levels between Indian Asian and European controls without type 2 diabetes at baseline to estimate the potential contribution of DNA methylation to increased risk of future type 2 diabetes incidence among Indian Asians. Findings 1608 (11·9%) of 13 535 Indian Asians and 306 (4·3%) of 7066 Europeans developed type 2 diabetes over a mean of 8·5 years (SD 1·8) of follow-up. The age-adjusted and sex-adjusted incidence of type 2 diabetes was 3·1 times (95% CI 2·8–3·6; p<0·0001) higher among Indian Asians than among Europeans, and remained 2·5 times (2·1–2·9; p<0·0001) higher after adjustment for adiposity, physical activity, family history of type 2 diabetes, and baseline glycaemic measures. The mean absolute difference in methylation level between

  9. Puerto Rican parrot (Amazona vittata) reproductive behavior: a guideline for management of active nests

    USGS Publications Warehouse

    Wilson, K.A.

    1993-01-01

    One explanation for the failure of intensively monitored Puerto Rican Parrot nests is that observers may lack the information needed to evaluate pair behavior and to recognize behaviors indicative of nest problems. I examined the behavior of Puerto Rican Parrots during eight non-problematic and six problematic nesting attempts to 1) describe behavior of pairs that experienced no notable nest problems and 2) to identify and describe behaviors associated with nest problems. I examined nest attendance, duration of attentive periods, and frequency of nest visits for both males and females, and duration of periods away from the nest for females only. Adult behavior during incubation and early chick rearing at non-problematic nests was well-defined. Females spent an average of 93.2 to 97.3% of the observation period in their nests during incubation and generally left their nests for average periods of 5 to 12 min. Female nest attendance generally declined and recesses became longer as chick rearing progressed. Males rarely entered their nests during incubation, but they generally established a regular pattern of nest visits within seven to 10 days of hatching of their young. In some cases, incidents of human disturbance to nest pairs during incubation and early chick rearing were associated with sudden changes in behavior. The key indicator of nest problems (abandonment during incubation or loss of young) was unexpected declines in female nest attendance. Declines were often accompanied by unexpected increases in female recesses or frequency of female nest visits, and sometimes by increases in male nest visits. Abandonment of nests during incubation was associated with repeated incidents of potentially disturbing activities (e.g., nest inspections). Deaths of embryos and young were associated with behaviors that allowed increased cooling of embryos.

  10. Nest-site selection in the acorn woodpecker

    USGS Publications Warehouse

    Hooge, P.N.; Stanback, M.T.; Koenig, W.D.

    1999-01-01

    Acorn Woodpeckers (Melanerpes formicivorus) at Hastings Reservation in central California prefer to nest in dead limbs in large, dead valley oaks (Quercus lobata) and California sycamores (Platanus racemosa) that are also frequently used as acorn storage trees. Based on 232 nest cavities used over an 18-year period, we tested whether preferred or modal nest-site characters were associated with increased reproductive success (the 'nest-site quality' hypothesis). We also examined whether more successful nests were likely to experience more favorable microclimatic conditions or to be less accessible to terrestrial predators. We found only equivocal support for the nest-site quality hypothesis: only 1 of 5 preferred characters and 2 of 10 characters exhibiting a clear modality were correlated with higher reproductive success. All three characteristics of nests known or likely to be associated with a more favorable microclimate, and two of five characteristics likely to render nests less accessible to predators, were correlated with higher reproductive success: These results suggest that nest cavities in this population are built in part to take advantage of favorable microclimatic conditions and, to a lesser extent, to reduce access to predators. However, despite benefits of particular nest characteristics, birds frequently nested in apparently suboptimal cavities. We also found a significant relationship between mean group size and the history of occupancy of particular territories and the probability of nest cavities being built in microclimatically favorable live limbs, suggesting that larger groups residing on more stable territories were better able to construct nests with optimal characteristics. This indicates that there may be demographic, as well as ecological, constraints on nest-site selection in this primary cavity nester.

  11. Variability in nest survival rates and implications to nesting studies

    USGS Publications Warehouse

    Klett, A.T.; Johnson, D.H.

    1982-01-01

    We used four reasonably large samples (83-213) of Mallard (Anas platyrhynchos) and Blue-winged Teal (A. discors) nests on an interstate highway right-of-way in southcentral North Dakota to evaluate potential biases in hatch-rate estimates. Twelve consecutive, weekly searches for nests were conducted with a cable-chain drag in 1976 and 1977. Nests were revisited at weekly intervals. Four methods were used to estimate hatch rates for the four data sets: the Traditional Method, the Mayfield Method, and two modifications of the Mayfield Method that are sometimes appropriate when daily mortality rates of nests are not constant. Hatch rates and the average age of nests at discovery declined as the interval between searches decreased, suggesting that mortality rates were not constant in our samples. An analysis of variance indicated that daily mortality rates varied with the age of nests in all four samples. Mortality was generally highest during the early laying period, moderately high during the late laying period, and lowest during incubation. We speculate that this relationship of mortality to nest age might be due to the presence of hens at nests or to differences in the vulnerability of nest sites to predation. A modification of the Mayfield Method that accounts for age-related variation in nest mortality was most appropriate for our samples. We suggest methods for conducting nesting studies and estimating nest success for species possessing similar nesting habits.

  12. Feathering Your Nest

    ERIC Educational Resources Information Center

    Nabors, Martha L.; Edwards, Linda Carol; Decker, Suzanne

    2010-01-01

    The first-grade classroom was like a natural history museum. Bird nests of every shape and size lay on top of bookshelves that lined two walls. Methods students, who were visiting the classroom in preparation for the science lessons they would teach there, were immediately inspired by the collection. They used the collection as a springboard for…

  13. A pooling-based approach to mapping genetic variants associated with DNA methylation.

    PubMed

    Kaplow, Irene M; MacIsaac, Julia L; Mah, Sarah M; McEwen, Lisa M; Kobor, Michael S; Fraser, Hunter B

    2015-06-01

    DNA methylation is an epigenetic modification that plays a key role in gene regulation. Previous studies have investigated its genetic basis by mapping genetic variants that are associated with DNA methylation at specific sites, but these have been limited to microarrays that cover <2% of the genome and cannot account for allele-specific methylation (ASM). Other studies have performed whole-genome bisulfite sequencing on a few individuals, but these lack statistical power to identify variants associated with DNA methylation. We present a novel approach in which bisulfite-treated DNA from many individuals is sequenced together in a single pool, resulting in a truly genome-wide map of DNA methylation. Compared to methods that do not account for ASM, our approach increases statistical power to detect associations while sharply reducing cost, effort, and experimental variability. As a proof of concept, we generated deep sequencing data from a pool of 60 human cell lines; we evaluated almost twice as many CpGs as the largest microarray studies and identified more than 2000 genetic variants associated with DNA methylation. We found that these variants are highly enriched for associations with chromatin accessibility and CTCF binding but are less likely to be associated with traits indirectly linked to DNA, such as gene expression and disease phenotypes. In summary, our approach allows genome-wide mapping of genetic variants associated with DNA methylation in any tissue of any species, without the need for individual-level genotype or methylation data.

  14. Breeding Phenology of Birds: Mechanisms Underlying Seasonal Declines in the Risk of Nest Predation

    PubMed Central

    Borgmann, Kathi L.; Conway, Courtney J.; Morrison, Michael L.

    2013-01-01

    Seasonal declines in avian clutch size are well documented, but seasonal variation in other reproductive parameters has received less attention. For example, the probability of complete brood mortality typically explains much of the variation in reproductive success and often varies seasonally, but we know little about the underlying cause of that variation. This oversight is surprising given that nest predation influences many other life-history traits and varies throughout the breeding season in many songbirds. To determine the underlying causes of observed seasonal decreases in risk of nest predation, we modeled nest predation of Dusky Flycatchers (Empidonax oberholseri) in northern California as a function of foliage phenology, energetic demand, developmental stage, conspecific nest density, food availability for nest predators, and nest predator abundance. Seasonal variation in the risk of nest predation was not associated with seasonal changes in energetic demand, conspecific nest density, or predator abundance. Instead, seasonal variation in the risk of nest predation was associated with foliage density (early, but not late, in the breeding season) and seasonal changes in food available to nest predators. Supplemental food provided to nest predators resulted in a numerical response by nest predators, increasing the risk of nest predation at nests that were near supplemental feeders. Our results suggest that seasonal changes in foliage density and factors associated with changes in food availability for nest predators are important drivers of temporal patterns in risk of avian nest predation. PMID:23776566

  15. Bee species-specific nesting material attracts a generalist parasitoid: implications for co-occurring bees in nest box enhancements.

    PubMed

    Macivor, J Scott; Salehi, Baharak

    2014-08-01

    Artificial nests (e.g., nest boxes) for bees are increasingly being used to contribute to nesting habitat enhancement for bees that use preexisting cavities to provision brood. They usually incorporate additional nesting materials that vary by species. Cavity-nesting bees are susceptible to brood parasitoids that recognize their host(s) using visual and chemical cues. Understanding the range of cues that attract parasitoids to bee nests, including human-made analogues, is important if we wish to control parasitism and increase the potential value of artificial nests as habitat-enhancement strategies. In this study, we investigated the cues associated with the orientation of the generalist brood parasitoid Monodontomerus obscurus Westwood (Hymenoptera: Torymidae) to the nests of a common cavity-nesting resin bee Megachile campanulae (Robertson) (Megachilidae). The parasitoids were reared from previously infested M. campanulae brood cells and placed into choice trials where they were presented with pairs of different nest material cues. Among different materials tested, we found that Mo. obscurus was most attracted to fresh resin collected directly from Pinus strobus trees followed by previously used resin collected from the bee nest. The parasitoid also attacked other bee species in the same nest boxes, including those that do not use resin for nesting. Our findings suggest that M. campanulae could act as a magnet, drawing parasites away from other bee hosts co-occurring in nest boxes, or, as an attractant of Mo. obscurus to nest boxes, increasing attacks on co-occurring host bee species, potentially undermining bee diversity enhancement initiatives. PMID:24959997

  16. Association mapping of fruit, seed and disease resistance traits in Theobroma cacao L

    Technology Transfer Automated Retrieval System (TEKTRAN)

    An association mapping approach was employed to find markers for color, size, girth and mass of fruits; seed number and butterfat content; and resistance to black pod and witches’ broom diseases in cacao (Theobroma cacao L.). Ninety-five microsatellites (SSRs) and 775 single nucleotide polymorphisms...

  17. Genome-wide association mapping of partial resistance to Aphanomyces euteiches in pea

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genome-wide association mapping has recently emerged as a valuable approach to refine genetic basis of polygenic resistance to plant diseases, which are increasingly used in integrated strategies for durable crop protection. Aphanomyces euteiches is a soil borne pathogen of pea and other legumes wor...

  18. Use of a General Graph-Drawing Algorithm in the Construction of Association Maps.

    ERIC Educational Resources Information Center

    Craven, Timothy C.

    1992-01-01

    Describes research that investigated a method of automatically generating concept association maps that could be useful to abstractors. The use of word stems as concept surrogates, cooccurrence to define concept links, and a general-purpose graph-drawing algorithm is described; and results of evaluation of two link selection methods are reported.…

  19. Allelic analysis of sheath blight resistance with association mapping in rice

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Sheath blight is one of the most devastating diseases world-wide in rice. For the first time, we adopted association mapping to identify quantitative trait loci for sheath blight resistance from the USDA rice mini-core collection. The phenotyping was conducted with a newly developed micro-chamber me...

  20. Association mapping of agronomic and quality traits in USDA pea single-plant collection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Association mapping is an efficient approach for the identification of the molecular basis of agronomic traits in crop plants. For this purpose in pea (Pisum sativum L.), we genotyped and phenotyped individual lines of the single-plant derived core collection of the USDA pea single-plant (PSP) colle...

  1. Buteo Nesting Ecology: Evaluating Nesting of Swainson's Hawks in the Northern Great Plains.

    PubMed

    Inselman, Will M; Datta, Shubham; Jenks, Jonathan A; Jensen, Kent C; Grovenburg, Troy W

    2015-01-01

    Swainson's hawks (Buteo swainsoni) are long-distance migratory raptors that nest primarily in isolated trees located in areas of high grassland density. In recent years, anthropogenic conversion of grassland habitat has raised concerns about the status of the breeding population in the northern Great Plains. In 2013, we initiated a study to investigate the influence of extrinsic factors influencing Swainson's hawk nesting ecology in north-central South Dakota and south-central North Dakota. Using ground and aerial surveys, we located and monitored nesting Swainson's hawk pairs: 73 in 2013 and 120 in 2014. We documented 98 successful breeding attempts that fledged 163 chicks; 1.52 and 1.72 fledglings per successful nest in 2013 and 2014, respectively. We used Program MARK to evaluate the influence of land cover on nest survival. The top model, SDist2Farm+%Hay, indicated that nest survival (fledging at least one chick) decreased as nests were located farther from farm sites and as the percent of hay cover increased within 1200-m of the nest site (34.4%; 95% CI = 27.6%-42.3%). We used logistic regression analysis to evaluate the influence of landscape variables on nest-site selection; Swainson's hawks selected for nest sites located closer to roads. We suggest that tree belts associated with farm sites, whether occupied or not, provide critical breeding sites for Swainson's hawks. Additionally, poor breeding success may be related to the late migratory behavior of this species which requires them to occupy marginal habitat due to other raptors occupying the most suitable habitat prior to Swainson's hawks arriving to the breeding grounds. PMID:26327440

  2. Buteo Nesting Ecology: Evaluating Nesting of Swainson's Hawks in the Northern Great Plains.

    PubMed

    Inselman, Will M; Datta, Shubham; Jenks, Jonathan A; Jensen, Kent C; Grovenburg, Troy W

    2015-01-01

    Swainson's hawks (Buteo swainsoni) are long-distance migratory raptors that nest primarily in isolated trees located in areas of high grassland density. In recent years, anthropogenic conversion of grassland habitat has raised concerns about the status of the breeding population in the northern Great Plains. In 2013, we initiated a study to investigate the influence of extrinsic factors influencing Swainson's hawk nesting ecology in north-central South Dakota and south-central North Dakota. Using ground and aerial surveys, we located and monitored nesting Swainson's hawk pairs: 73 in 2013 and 120 in 2014. We documented 98 successful breeding attempts that fledged 163 chicks; 1.52 and 1.72 fledglings per successful nest in 2013 and 2014, respectively. We used Program MARK to evaluate the influence of land cover on nest survival. The top model, SDist2Farm+%Hay, indicated that nest survival (fledging at least one chick) decreased as nests were located farther from farm sites and as the percent of hay cover increased within 1200-m of the nest site (34.4%; 95% CI = 27.6%-42.3%). We used logistic regression analysis to evaluate the influence of landscape variables on nest-site selection; Swainson's hawks selected for nest sites located closer to roads. We suggest that tree belts associated with farm sites, whether occupied or not, provide critical breeding sites for Swainson's hawks. Additionally, poor breeding success may be related to the late migratory behavior of this species which requires them to occupy marginal habitat due to other raptors occupying the most suitable habitat prior to Swainson's hawks arriving to the breeding grounds.

  3. Buteo Nesting Ecology: Evaluating Nesting of Swainson’s Hawks in the Northern Great Plains

    PubMed Central

    Inselman, Will M.; Datta, Shubham; Jenks, Jonathan A.; Jensen, Kent C.; Grovenburg, Troy W.

    2015-01-01

    Swainson’s hawks (Buteo swainsoni) are long-distance migratory raptors that nest primarily in isolated trees located in areas of high grassland density. In recent years, anthropogenic conversion of grassland habitat has raised concerns about the status of the breeding population in the northern Great Plains. In 2013, we initiated a study to investigate the influence of extrinsic factors influencing Swainson’s hawk nesting ecology in north-central South Dakota and south-central North Dakota. Using ground and aerial surveys, we located and monitored nesting Swainson’s hawk pairs: 73 in 2013 and 120 in 2014. We documented 98 successful breeding attempts that fledged 163 chicks; 1.52 and 1.72 fledglings per successful nest in 2013 and 2014, respectively. We used Program MARK to evaluate the influence of land cover on nest survival. The top model, SDist2Farm+%Hay, indicated that nest survival (fledging at least one chick) decreased as nests were located farther from farm sites and as the percent of hay cover increased within 1200-m of the nest site (34.4%; 95% CI = 27.6%–42.3%). We used logistic regression analysis to evaluate the influence of landscape variables on nest-site selection; Swainson’s hawks selected for nest sites located closer to roads. We suggest that tree belts associated with farm sites, whether occupied or not, provide critical breeding sites for Swainson’s hawks. Additionally, poor breeding success may be related to the late migratory behavior of this species which requires them to occupy marginal habitat due to other raptors occupying the most suitable habitat prior to Swainson’s hawks arriving to the breeding grounds. PMID:26327440

  4. A review of the ectoparasitic mites (Acari: Dermanyssoidea) associated with birds and their nests in Slovakia, with notes on identification of some species.

    PubMed

    Mašán, Peter; Fenďa, Peter; Krištofík, Ján; Halliday, Bruce

    2014-12-05

    We review the parasitic mites of the superfamily Dermanyssoidea found in the nests of Slovakian domestic and wild birds (and a few mammals), compiled from new data and literature sources. Three mite genera are included, namely Dermanyssus Dugès (Dermanyssidae), Ornithonyssus Sambon and Pellonyssus Clark & Yunker (Macronyssidae), in which we recognised nine reliably documented species. Pellonyssus is represented by one species, Dermanyssus by five species, and Ornithonyssus by three species. We compiled information on the ecological requirements and host preferences of these mite species, including data on geographic distribution, altitudinal distribution, and occurrence in different habitats and nest types. An identification key to the species occurring in Slovakia is provided, together with taxonomic remarks on the identification and external morphology of some selected species. Parasitic mites have been reported from 119 taxa of Slovakian vertebrates (including man), of which 108 belong to 17 orders of birds. Dermanyssus americanus Ewing and Ornithonyssus bursa (Berlese) are reported from Slovakia for the first time. Examination of older voucher material collected in Slovakia revealed many misidentified specimens: the name Dermanyssus hirundinis (Hermann) has been widely used for misidentified specimens of Dermanyssus carpathicus Zeman; D. americanus was confused with D. hirundinis; while O. bursa has been confused with Ornithonyssus sylviarum (Canestrini & Fanzago). Slovakia is the second country in Europe with known occurrence of the genus Pellonyssus. 

  5. Landsat evaluation of trumpeter swan historical nesting sites in Yellowstone National Park

    NASA Astrophysics Data System (ADS)

    Cockrell, Laura Elizabeth

    The trumpeter swan (Cygnus buccinator) has historically nested in the Greater Yellowstone Ecosystem of Montana, Idaho, and Wyoming. Declines in habitat quality may be limiting the growth of the Tri-State Flock. The purpose of this study was to map historical nesting areas for trumpeter swans in Yellowstone National Park (YNP) and evaluate Landsat images for changes to habitat. Historical nesting sites were evaluated through image classification and Normalized Difference Vegetation Index (NDVI) and compared to field conditions. Swan nesting records were analyzed in comparison to drought index and human visitation rates to determine if these factors may contribute to the decline of trumpeter swans nesting in YNP. Vegetation type and water quality were evaluated at 36 wetlands identified as historical nesting locations. Potamogetonaceae was the largest family represented in plant samples and had the highest frequency of occurrence in samples. There was no significant difference in whether swans were present or absent in wetlands with regards to water quality parameters tested or physical parameters identified. There was an association between certain drought index values and the number of cygnets fledged and the number of territories occupied by swan pairs. I was unsuccessful in using image classification to define pixel characteristics common among historical nesting territories of swans in YNP based on 5 Landsat images from 1975, 1979, 1990, 1999, and 2005. I was also unable to distinguish aquatic plant species composition, emergent and submergent plants, open water versus aquatic vegetation, wetland classification, or swan preference using image classification. No relationship was found in a regression model of NDVI values and swan pair occupancy or number of swans fledged, with the exception of a weak, positive relationship between pair occupancy and positive NDVI values, and a strong, positive relationship between swan fledge rates and positive NDVI values

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

    PubMed Central

    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

  7. Nest-site characteristics and linear abundance of cliff-nesting American kestrels on San Clemente Island, California

    USGS Publications Warehouse

    Sullivan, Brian L.; Kershner, Eric L.; Finn, S.P.; Condon, Anne M.; Cooper, Douglass M.; Garcelon, David K.

    2003-01-01

    American Kestrels( Falco sparverius) are typically secondary-cavity nesters, and use of natural cliff cavities for nest sites is less-commonly reported. On San Clemente Island (SCI), California, however, American Kestrels nest primarily on cliffs in major canyons(93%), to a lesser extent on seacliffs(4%), as well as in man-made structures (3%). We located and mapped 99 American Kestrel territories on SCI, and recorded 11 nest-site characteristics at 40 cliff nests during 2001-02. Nest cliffs were typically fractured igneous rock with mean height of 16.1 m +_ 1.8 SE. Mean slope of nest cliffs was vertical (x=91 degrees). Nest cliffs and cavities were significantly oriented to the southeast, away from the prevailing wind direction(NW). In eight canyons, where we believe that we found all occupied American Kestrel territories, the mean linear abundance was 2.1 pairs/km, greater than most published estimates. Contrary to most previous studies, no American Kestrels nested in tree cavities despite their presence in SCI canyons. The absence of cavity-excavating breeding birds from the island likely restricts kestrels to nesting in naturally-formed cavities and man-made structures.

  8. Association Mapping for Fruit, Plant and Leaf Morphology Traits in Eggplant.

    PubMed

    Portis, Ezio; Cericola, Fabio; Barchi, Lorenzo; Toppino, Laura; Acciarri, Nazzareno; Pulcini, Laura; Sala, Tea; Lanteri, Sergio; Rotino, Giuseppe Leonardo

    2015-01-01

    An eggplant (Solanum melongena) association panel of 191 accessions, comprising a mixture of breeding lines, old varieties and landrace selections was SNP genotyped and phenotyped for key breeding fruit and plant traits at two locations over two seasons. A genome-wide association (GWA) analysis was performed using the mixed linear model, which takes into account both a kinship matrix and the sub-population membership of the accessions. Overall, 194 phenotype/genotype associations were uncovered, relating to 30 of the 33 measured traits. These associations involved 79 SNP loci mapping to 39 distinct chromosomal regions distributed over all 12 eggplant chromosomes. A comparison of the map positions of these SNPs with those of loci derived from conventional linkage mapping showed that GWA analysis both validated many of the known controlling loci and detected a large number of new marker/trait associations. Exploiting established syntenic relationships between eggplant chromosomes and those of tomato and pepper recognized orthologous regions in ten eggplant chromosomes harbouring genes influencing breeders' traits.

  9. Association Mapping for Fruit, Plant and Leaf Morphology Traits in Eggplant.

    PubMed

    Portis, Ezio; Cericola, Fabio; Barchi, Lorenzo; Toppino, Laura; Acciarri, Nazzareno; Pulcini, Laura; Sala, Tea; Lanteri, Sergio; Rotino, Giuseppe Leonardo

    2015-01-01

    An eggplant (Solanum melongena) association panel of 191 accessions, comprising a mixture of breeding lines, old varieties and landrace selections was SNP genotyped and phenotyped for key breeding fruit and plant traits at two locations over two seasons. A genome-wide association (GWA) analysis was performed using the mixed linear model, which takes into account both a kinship matrix and the sub-population membership of the accessions. Overall, 194 phenotype/genotype associations were uncovered, relating to 30 of the 33 measured traits. These associations involved 79 SNP loci mapping to 39 distinct chromosomal regions distributed over all 12 eggplant chromosomes. A comparison of the map positions of these SNPs with those of loci derived from conventional linkage mapping showed that GWA analysis both validated many of the known controlling loci and detected a large number of new marker/trait associations. Exploiting established syntenic relationships between eggplant chromosomes and those of tomato and pepper recognized orthologous regions in ten eggplant chromosomes harbouring genes influencing breeders' traits. PMID:26284782

  10. Association Mapping for Fruit, Plant and Leaf Morphology Traits in Eggplant

    PubMed Central

    Portis, Ezio; Cericola, Fabio; Barchi, Lorenzo; Toppino, Laura; Acciarri, Nazzareno; Pulcini, Laura; Sala, Tea; Lanteri, Sergio; Rotino, Giuseppe Leonardo

    2015-01-01

    An eggplant (Solanum melongena) association panel of 191 accessions, comprising a mixture of breeding lines, old varieties and landrace selections was SNP genotyped and phenotyped for key breeding fruit and plant traits at two locations over two seasons. A genome-wide association (GWA) analysis was performed using the mixed linear model, which takes into account both a kinship matrix and the sub-population membership of the accessions. Overall, 194 phenotype/genotype associations were uncovered, relating to 30 of the 33 measured traits. These associations involved 79 SNP loci mapping to 39 distinct chromosomal regions distributed over all 12 eggplant chromosomes. A comparison of the map positions of these SNPs with those of loci derived from conventional linkage mapping showed that GWA analysis both validated many of the known controlling loci and detected a large number of new marker/trait associations. Exploiting established syntenic relationships between eggplant chromosomes and those of tomato and pepper recognized orthologous regions in ten eggplant chromosomes harbouring genes influencing breeders’ traits. PMID:26284782

  11. Allelic analysis of sheath blight resistance with association mapping in rice.

    PubMed

    Jia, Limeng; Yan, Wengui; Zhu, Chengsong; Agrama, Hesham A; Jackson, Aaron; Yeater, Kathleen; Li, Xiaobai; Huang, Bihu; Hu, Biaolin; McClung, Anna; Wu, Dianxing

    2012-01-01

    Sheath blight (ShB) caused by the soil-borne pathogen Rhizoctonia solani is one of the most devastating diseases in rice world-wide. Global attention has focused on examining individual mapping populations for quantitative trait loci (QTLs) for ShB resistance, but to date no study has taken advantage of association mapping to examine hundreds of lines for potentially novel QTLs. Our objective was to identify ShB QTLs via association mapping in rice using 217 sub-core entries from the USDA rice core collection, which were phenotyped with a micro-chamber screening method and genotyped with 155 genome-wide markers. Structure analysis divided the mapping panel into five groups, and model comparison revealed that PCA5 with genomic control was the best model for association mapping of ShB. Ten marker loci on seven chromosomes were significantly associated with response to the ShB pathogen. Among multiple alleles in each identified loci, the allele contributing the greatest effect to ShB resistance was named the putative resistant allele. Among 217 entries, entry GSOR 310389 contained the most putative resistant alleles, eight out of ten. The number of putative resistant alleles presented in an entry was highly and significantly correlated with the decrease of ShB rating (r = -0.535) or the increase of ShB resistance. Majority of the resistant entries that contained a large number of the putative resistant alleles belonged to indica, which is consistent with a general observation that most ShB resistant accessions are of indica origin. These findings demonstrate the potential to improve breeding efficiency by using marker-assisted selection to pyramid putative resistant alleles from various loci in a cultivar for enhanced ShB resistance in rice.

  12. Nested Hierarchical Dirichlet Processes.

    PubMed

    Paisley, John; Wang, Chong; Blei, David M; Jordan, Michael I

    2015-02-01

    We develop a nested hierarchical Dirichlet process (nHDP) for hierarchical topic modeling. The nHDP generalizes the nested Chinese restaurant process (nCRP) to allow each word to follow its own path to a topic node according to a per-document distribution over the paths on a shared tree. This alleviates the rigid, single-path formulation assumed by the nCRP, allowing documents to easily express complex thematic borrowings. We derive a stochastic variational inference algorithm for the model, which enables efficient inference for massive collections of text documents. We demonstrate our algorithm on 1.8 million documents from The New York Times and 2.7 million documents from Wikipedia. PMID:26353240

  13. Testing Nested Distributions

    NASA Astrophysics Data System (ADS)

    Economou, P.

    2010-09-01

    A number of criteria, test statistics and diagnostic plots have been developed in order to test the adapted distribution assumption. Usually, a simpler distribution is tested against a more complicated one (by adding an extra parameter), which include the first distribution as a special case (nested distributions). A characteristic example of such cases is the Burr XII distribution which can be obtained under the proportional hazards frailty model by assuming a Weibull baseline function and a Gamma frailty distribution with mean frailty equal to 1 and variance equal to θ. In this work, two new easy to construct and to interpret tests, a diagnostic plot and an asymptotic test, are presented in order to test nested distributions. The asymptotic test is based on the approximation of the difference of the two estimated nested distribution functions using the first two terms of the Taylor's expansion while the diagnostic plot is constructed using the exact difference of the two fitted distribution functions. Simulation results, using data sets with and without censored observations, demonstrate that the proposed tests perform, in most of the cases, better than other test statistics such as the LR and the Wald.

  14. Identification of genetic loci associated with fire blight resistance in Malus through combined use of QTL and association mapping.

    PubMed

    Khan, M Awais; Zhao, Youfu Frank; Korban, Schuyler S

    2013-07-01

    Fire blight, incited by the enterobacterium Erwinia amylovora, is a destructive disease of Rosaceae, particularly of apples and pears. There are reports on the molecular mechanisms underlying E. amylovora pathogenesis and how the host activates its resistance mechanism. The host's resistance mechanism is quantitatively controlled, although some major genes might also be involved. Thus far, quantitative trait loci (QTL) mapping and differential expression studies have been used to elucidate those genes and/or genomic regions underlying quantitative resistance present in the apple genome. In this study, an effort is undertaken to dissect the genetic basis of fire blight resistance in apple using both QTL and genome-wide association mapping. On the basis of an F1 pedigree of 'Coop 16' × 'Coop 17' and a genome-wide association study (GWAS) mapping population of Malus accessions (species, old and new cultivars and selections), new QTLs and associations have been identified. A total of three QTLs for resistance to fire blight, with above 95% significant logarithm of odds threshold value of 2.5, have been identified on linkage groups (LGs) 02, 06, and 15 of the apple genome with phenotypic variation explained values of 14.7, 20.1 and 17.4, respectively. Although elevated P-values with signals for marker-trait associations are observed for some LGs, these are not found to be significant. However, a total of 34 significant associations, with P-values ≥0.02, have been detected including 8 for lesion length at 7 days following inoculation (PL1), 14 for lesion length at 14 days following inoculation (PL2), and 12 for shoot length. PMID:23627651

  15. Identification of genetic loci associated with fire blight resistance in Malus through combined use of QTL and association mapping.

    PubMed

    Khan, M Awais; Zhao, Youfu Frank; Korban, Schuyler S

    2013-07-01

    Fire blight, incited by the enterobacterium Erwinia amylovora, is a destructive disease of Rosaceae, particularly of apples and pears. There are reports on the molecular mechanisms underlying E. amylovora pathogenesis and how the host activates its resistance mechanism. The host's resistance mechanism is quantitatively controlled, although some major genes might also be involved. Thus far, quantitative trait loci (QTL) mapping and differential expression studies have been used to elucidate those genes and/or genomic regions underlying quantitative resistance present in the apple genome. In this study, an effort is undertaken to dissect the genetic basis of fire blight resistance in apple using both QTL and genome-wide association mapping. On the basis of an F1 pedigree of 'Coop 16' × 'Coop 17' and a genome-wide association study (GWAS) mapping population of Malus accessions (species, old and new cultivars and selections), new QTLs and associations have been identified. A total of three QTLs for resistance to fire blight, with above 95% significant logarithm of odds threshold value of 2.5, have been identified on linkage groups (LGs) 02, 06, and 15 of the apple genome with phenotypic variation explained values of 14.7, 20.1 and 17.4, respectively. Although elevated P-values with signals for marker-trait associations are observed for some LGs, these are not found to be significant. However, a total of 34 significant associations, with P-values ≥0.02, have been detected including 8 for lesion length at 7 days following inoculation (PL1), 14 for lesion length at 14 days following inoculation (PL2), and 12 for shoot length.

  16. PyNEST: A Convenient Interface to the NEST Simulator.

    PubMed

    Eppler, Jochen Martin; Helias, Moritz; Muller, Eilif; Diesmann, Markus; Gewaltig, Marc-Oliver

    2008-01-01

    The neural simulation tool NEST (http://www.nest-initiative.org) is a simulator for heterogeneous networks of point neurons or neurons with a small number of compartments. It aims at simulations of large neural systems with more than 10(4) neurons and 10(7) to 10(9) synapses. NEST is implemented in C++ and can be used on a large range of architectures from single-core laptops over multi-core desktop computers to super-computers with thousands of processor cores. Python (http://www.python.org) is a modern programming language that has recently received considerable attention in Computational Neuroscience. Python is easy to learn and has many extension modules for scientific computing (e.g. http://www.scipy.org). In this contribution we describe PyNEST, the new user interface to NEST. PyNEST combines NEST's efficient simulation kernel with the simplicity and flexibility of Python. Compared to NEST's native simulation language SLI, PyNEST makes it easier to set up simulations, generate stimuli, and analyze simulation results. We describe how PyNEST connects NEST and Python and how it is implemented. With a number of examples, we illustrate how it is used. PMID:19198667

  17. Retrospective study of central nervous system lesions and association with Parelaphostrongylus species by histology and specific nested polymerase chain reaction in domestic camelids and wild ungulates.

    PubMed

    Dobey, Carrie L; Grunenwald, Caroline; Newman, Shelley J; Muller, Lisa; Gerhold, Richard W

    2014-11-01

    Formalin-fixed, paraffin-embedded tissues from elk (Cervus elaphus), goats, and camelids with case histories and lesions suggestive of Parelaphostrongylus tenuis were examined by histology to characterize lesions that could aid in definitively diagnosing P. tenuis infection. Additionally, sections of paraffin-embedded tissue were used in a nested polymerase chain reaction (nPCR) using Parelaphostrongylus-specific primers to determine how PCR results corresponded with histological findings. Histological changes in brain and spinal cord consisted of linear tracks of hemorrhage; tracks or perivascular accumulations of hemosiderin-laden macrophages; acute foci of axonal degeneration and/or linear glial scars; and perivascular, parenchymal, or meningeal accumulations of eosinophils and/or lymphocytes and plasma cells. Of the 43 samples with histologic lesions consistent with neural larval migrans, 19 were PCR positive; however, only 8 were confirmed Parelaphostrongylus by DNA sequencing. Additionally, 1 goat was identified with a protostrongylid that had a 97% identity to both Parelaphostrongylus odocoilei and a protostrongylid nematode from pampas deer (Ozotoceros bezoarticus celer) from Argentina. None of the histologic lesions individually or in combination correlated statistically to positive molecular tests for the nematode. The results indicate that it is possible to extract Parelaphostrongylus DNA from formalin-fixed, paraffin-embedded tissue, but extended fixation presumably can cause DNA crosslinking. Nested PCR provides another diagnostic tool to identify the cause of neurologic disease in camelids and elk with histologic lesions consistent with neural larval migrans. Furthermore, potential novel protostrongylid DNA was detected from a goat with lesions consistent with P. tenuis infection, suggesting that other neurotropic Parelaphostrongylus species may occur locally.

  18. Linkage disequilibrium based association mapping of fiber quality traits in G. hirsutum L. variety germplasm.

    PubMed

    Abdurakhmonov, Ibrokhim Y; Saha, Sukumar; Jenkins, Jonnie N; Buriev, Zabardast T; Shermatov, Shukhrat E; Scheffler, Brain E; Pepper, Alan E; Yu, John Z; Kohel, Russell J; Abdukarimov, Abdusattor

    2009-07-01

    Cotton is the world's leading cash crop, but it lags behind other major crops for marker-assisted breeding due to limited polymorphisms and a genetic bottleneck through historic domestication. This underlies a need for characterization, tagging, and utilization of existing natural polymorphisms in cotton germplasm collections. Here we report genetic diversity, population characteristics, the extent of linkage disequilibrium (LD), and association mapping of fiber quality traits using 202 microsatellite marker primer pairs in 335 G. hirsutum germplasm grown in two diverse environments, Uzbekistan and Mexico. At the significance threshold (r (2) >or= 0.1), a genome-wide average of LD extended up to genetic distance of 25 cM in assayed cotton variety accessions. Genome wide LD at r (2) >or= 0.2 was reduced to approximately 5-6 cM, providing evidence of the potential for association mapping of agronomically important traits in cotton. Results suggest linkage, selection, inbreeding, population stratification, and genetic drift as the potential LD-generating factors in cotton. In two environments, an average of ~20 SSR markers was associated with each main fiber quality traits using a unified mixed liner model (MLM) incorporating population structure and kinship. These MLM-derived significant associations were confirmed in general linear model and structured association test, accounting for population structure and permutation-based multiple testing. Several common markers, showing the significant associations in both Uzbekistan and Mexican environments, were determined. Between 7 and 43% of the MLM-derived significant associations were supported by a minimum Bayes factor at 'moderate to strong' and 'strong to very strong' evidence levels, suggesting their usefulness for marker-assisted breeding programs and overall effectiveness of association mapping using cotton germplasm resources. PMID:19067183

  19. Why wasp foundresses change nests: relatedness, dominance, and nest quality.

    PubMed

    Seppä, Perttu; Queller, David C; Strassmann, Joan E

    2012-01-01

    The costs and benefits of different social options are best understood when individuals can be followed as they make different choices, something that can be difficult in social insects. In this detailed study, we follow overwintered females of the social wasp Polistes carolina through different nesting strategies in a stratified habitat where nest site quality varies with proximity to a foraging area, and genetic relatedness among females is known. Females may initiate nests, join nests temporarily or permanently, or abandon nests. Females can become helpers or egglayers, effectively workers or queens. What they actually do can be predicted by a combination of ecological and relatedness factors. Advantages through increased lifetime success of individuals and nests drives foundresses of the social wasp Polistes from solitary to social nest founding. We studied reproductive options of spring foundresses of P. carolina by monitoring individually-marked wasps and assessing reproductive success of each foundress by using DNA microsatellites. We examined what behavioral decisions foundresses make after relaxing a strong ecological constraint, shortage of nesting sites. We also look at the reproductive consequences of different behaviors. As in other Polistes, the most successful strategy for a foundress was to initiate a nest as early as possible and then accept others as subordinates. A common feature for many P. carolina foundresses was, however, that they reassessed their reproductive options by actively monitoring other nests at the field site and sometimes moving permanently to new nests should that offer better (inclusive) fitness prospects compared to their original nests. A clear motivation for moving to new nests was high genetic relatedness; by the end of the foundress period all females were on nests with full sisters.

  20. Design of a Brassica rapa core collection for association mapping studies.

    PubMed

    Zhao, Jianjun; Artemyeva, Anna; Del Carpio, Dunia Pino; Basnet, Ram Kumar; Zhang, Ningwen; Gao, Jie; Li, Fei; Bucher, Johan; Wang, Xiaowu; Visser, Richard G F; Bonnema, Guusje

    2010-11-01

    A Brassica rapa collection of 239 accessions, based on two core collections representing different morphotypes from different geographical origins, is presented and its use for association mapping is illustrated for flowering time. We analyzed phenotypic variation of leaf and seed pod traits, plant architecture, and flowering time using data collected from three field experiments and evaluated the genetic diversity with a set of SSR markers. The Wageningen University and Research Centre (WUR) and the Vavilov Research Institute of Plant Industry (VIR) core collections had similar representations of most morphotypes, as illustrated by the phenotypic and genetic variation within these groups. The analysis of population structure revealed five subgroups in the collection, whereas previous studies of the WUR core collection indicated four subgroups; the fifth group identified consisted mainly of oil accessions from the VIR core collection, winter oils from Pakistan, and a number of other types. A very small group of summer oils is described, that is not related to other oil accessions. A candidate gene approach was chosen for association mapping of flowering time with a BrFLC1 biallelic CAPS marker and a BrFLC2 multiallelic SSR marker. The two markers were significantly associated with flowering time, but their effects were confined to certain morphotypes and (or) alleles. Based on these results, we discuss the optimal design for an association mapping population and the need to fix the heterogeneous accessions to facilitate phenotyping and genotyping.

  1. Design of a Brassica rapa core collection for association mapping studies.

    PubMed

    Zhao, Jianjun; Artemyeva, Anna; Del Carpio, Dunia Pino; Basnet, Ram Kumar; Zhang, Ningwen; Gao, Jie; Li, Fei; Bucher, Johan; Wang, Xiaowu; Visser, Richard G F; Bonnema, Guusje

    2010-11-01

    A Brassica rapa collection of 239 accessions, based on two core collections representing different morphotypes from different geographical origins, is presented and its use for association mapping is illustrated for flowering time. We analyzed phenotypic variation of leaf and seed pod traits, plant architecture, and flowering time using data collected from three field experiments and evaluated the genetic diversity with a set of SSR markers. The Wageningen University and Research Centre (WUR) and the Vavilov Research Institute of Plant Industry (VIR) core collections had similar representations of most morphotypes, as illustrated by the phenotypic and genetic variation within these groups. The analysis of population structure revealed five subgroups in the collection, whereas previous studies of the WUR core collection indicated four subgroups; the fifth group identified consisted mainly of oil accessions from the VIR core collection, winter oils from Pakistan, and a number of other types. A very small group of summer oils is described, that is not related to other oil accessions. A candidate gene approach was chosen for association mapping of flowering time with a BrFLC1 biallelic CAPS marker and a BrFLC2 multiallelic SSR marker. The two markers were significantly associated with flowering time, but their effects were confined to certain morphotypes and (or) alleles. Based on these results, we discuss the optimal design for an association mapping population and the need to fix the heterogeneous accessions to facilitate phenotyping and genotyping. PMID:21076504

  2. Association Mapping and Validation of QTLs for Flour Yield in the Soft Winter Wheat Variety Kitahonami

    PubMed Central

    Ishikawa, Goro; Nakamura, Kazuhiro; Ito, Hiroyuki; Saito, Mika; Sato, Mikako; Jinno, Hironobu; Yoshimura, Yasuhiro; Nishimura, Tsutomu; Maejima, Hidekazu; Uehara, Yasushi; Kobayashi, Fuminori; Nakamura, Toshiki

    2014-01-01

    The winter wheat variety Kitahonami shows a superior flour yield in comparison to other Japanese soft wheat varieties. To map the quantitative trait loci (QTL) associated with this trait, association mapping was performed using a panel of lines from Kitahonami’s pedigree, along with leading Japanese varieties and advanced breeding lines. Using a mixed linear model corrected for kernel types and familial relatedness, 62 marker-trait associations for flour yield were identified and classified into 21 QTLs. In eighteen of these, Kitahonami alleles showed positive effects. Pedigree analysis demonstrated that a continuous pyramiding of QTLs had occurred throughout the breeding history of Kitahonami. Linkage analyses using three sets of doubled haploid populations from crosses in which Kitahonami was used as a parent were performed, leading to the validation of five of the eight QTLs tested. Among these, QTLs on chromosomes 3B and 7A showed highly significant and consistent effects across the three populations. This study shows that pedigree-based association mapping using breeding materials can be a useful method for QTL identification at the early stages of breeding programs. PMID:25360619

  3. Avian nest success in midwestern forests fragmented by agriculture

    USGS Publications Warehouse

    Knutson, M.G.; Niemi, G.J.; Newton, W.E.; Friberg, M.A.

    2004-01-01

    We studied how forest-bird nest success varied by landscape context from 1996 to 1998 in an agricultural region of southeastern Minnesota, southwestern Wisconsin, and northeastern Iowa. Nest success was 48% for all nests, 82% for cavity-nesting species, and 42% for cup-nesting species. Mayfield-adjusted nest success for five common species ranged from 23% for the American Redstart (Setophaga ruticilla) to 43% for the Eastern Wood-Pewee (Contopus virens). Nest success was lowest for open-cup nesters, species that reject Brown-headed Cowbird (Molothrus ater) eggs, species that nest near forest edges, and Neo-tropical migrants. The proportion of forest core area in a 5-km radius around the plot had a weakly negative relationship with daily survival rate of nests for all species pooled and for medium or high canopy nesters, species associated with interior and edge habitats, open-cup nesters, and nests located between 75 and 199 m from an edge. The proportion of forest core area was positively related to daily survival rate only for ground and low nesters. Our findings are in contrast to a number of studies from the eastern United States reporting strong positive associations between forest area and nesting success. Supported models of habitat associations changed with the spatial scale of analysis and included variables not often considered in studies of forest birds, including the proportion of water, shrubs, and grasslands in the landscape. Forest area may not be a strong indicator of nest success in landscapes where all the available forests are fragmented.

  4. Phenotypic diversity and association mapping for fruit quality traits in cultivated tomato and related species.

    PubMed

    Xu, Jiaxin; Ranc, Nicolas; Muños, Stéphane; Rolland, Sophie; Bouchet, Jean-Paul; Desplat, Nelly; Le Paslier, Marie-Christine; Liang, Yan; Brunel, Dominique; Causse, Mathilde

    2013-03-01

    Association mapping has been proposed as an efficient approach to assist in the identification of the molecular basis of agronomical traits in plants. For this purpose, we analyzed the phenotypic and genetic diversity of a large collection of tomato accessions including 44 heirloom and vintage cultivars (Solanum lycopersicum), 127 S. lycopersicum var. cerasiforme (cherry tomato) and 17 Solanum pimpinellifolium accessions. The accessions were genotyped using a SNPlex™ assay of 192 SNPs, among which 121 were informative for subsequent analysis. Linkage disequilibrium (LD) of pairwise loci and population structure were analyzed, and the association analysis between SNP genotypes and ten fruit quality traits was performed using a mixed linear model. High level of LD was found in the collection at the whole genome level. It was lower when considering only the 127 S. lycopersicum var. cerasiforme accessions. Genetic structure analysis showed that the population was structured into two main groups, corresponding to cultivated and wild types and many intermediates. The number of associations detected per trait varied, according to the way the structure was taken into account, with 0-41 associations detected per trait in the whole collection and a maximum of four associations in the S. lycopersicum var. cerasiforme accessions. A total of 40 associations (30 %) were co-localized with previously identified quantitative trait loci. This study thus showed the potential and limits of using association mapping in tomato populations. PMID:23124430

  5. Island characteristics within wetlands influence waterbird nest success and abundance

    USGS Publications Warehouse

    Hartman, Christopher; Ackerman, Josh; Herzog, Mark

    2016-01-01

    Coastal waterbird populations are threatened by habitat loss and degradation from urban and agricultural development and forecasted sea level rise associated with climate change. Remaining wetlands often must be managed to ensure that waterbird habitat needs, and other ecosystem functions, are met. For many waterbirds, the availability of island nesting habitat is important for conserving breeding populations. We used linear mixed models to investigate the influence of pond and island landscape characteristics on nest abundance and nest success of American avocets (Recurvirostra americana), black-necked stilts (Himantopus mexicanus), and Forster's terns (Sterna forsteri) in San Francisco Bay, California, USA, based on a 9-year dataset that included >9,000 nests. Nest abundance and nest success were greatest within ponds and on individual islands located either <1 km or >4 km from San Francisco Bay. Further, nest abundance was greater within ponds with relatively few islands, and on linear-shaped, highly elongated islands compared to more rounded islands. Nest success was greater on islands located away from the nearest surrounding pond levee. Compared to more rounded islands, linear islands contained more near-water habitat preferred by many nesting waterbirds. Islands located away from pond levees may provide greater protection from terrestrial egg and chick predators. Our results indicate that creating and maintaining a few, relatively small, highly elongated and narrow islands away from mainland levees, in as many wetland ponds as possible would be effective at providing waterbirds with preferred nesting habitat.

  6. The light chains of microtubule-associated proteins MAP1A and MAP1B interact with α1-syntrophin in the central and peripheral nervous system.

    PubMed

    Fuhrmann-Stroissnigg, Heike; Noiges, Rainer; Descovich, Luise; Fischer, Irmgard; Albrecht, Douglas E; Nothias, Fatiha; Froehner, Stanley C; Propst, Friedrich

    2012-01-01

    Microtubule-associated proteins of the MAP1 family (MAP1A, MAP1B, and MAP1S) share, among other features, a highly conserved COOH-terminal domain approximately 125 amino acids in length. We conducted a yeast 2-hybrid screen to search for proteins interacting with this domain and identified α1-syntrophin, a member of a multigene family of adapter proteins involved in signal transduction. We further demonstrate that the interaction between the conserved COOH-terminal 125-amino acid domain (which is located in the light chains of MAP1A, MAP1B, and MAP1S) and α1-syntrophin is direct and occurs through the pleckstrin homology domain 2 (PH2) and the postsynaptic density protein 95/disk large/zonula occludens-1 protein homology domain (PDZ) of α1-syntrophin. We confirmed the interaction of MAP1B and α1-syntrophin by co-localization of the two proteins in transfected cells and by co-immunoprecipitation experiments from mouse brain. In addition, we show that MAP1B and α1-syntrophin partially co-localize in Schwann cells of the murine sciatic nerve during postnatal development and in the adult. However, intracellular localization of α1-syntrophin and other Schwann cell proteins such as ezrin and dystrophin-related protein 2 (DRP2) and the localization of the axonal node of Ranvier-associated protein Caspr1/paranodin were not affected in MAP1B null mice. Our findings add to a growing body of evidence that classical MAPs are likely to be involved in signal transduction not only by directly modulating microtubule function, but also through their interaction with signal transduction proteins. PMID:23152929

  7. The Light Chains of Microtubule-Associated Proteins MAP1A and MAP1B Interact with α1-Syntrophin in the Central and Peripheral Nervous System

    PubMed Central

    Descovich, Luise; Fischer, Irmgard; Albrecht, Douglas E.; Nothias, Fatiha; Froehner, Stanley C.; Propst, Friedrich

    2012-01-01

    Microtubule-associated proteins of the MAP1 family (MAP1A, MAP1B, and MAP1S) share, among other features, a highly conserved COOH-terminal domain approximately 125 amino acids in length. We conducted a yeast 2-hybrid screen to search for proteins interacting with this domain and identified α1-syntrophin, a member of a multigene family of adapter proteins involved in signal transduction. We further demonstrate that the interaction between the conserved COOH-terminal 125-amino acid domain (which is located in the light chains of MAP1A, MAP1B, and MAP1S) and α1-syntrophin is direct and occurs through the pleckstrin homology domain 2 (PH2) and the postsynaptic density protein 95/disk large/zonula occludens-1 protein homology domain (PDZ) of α1-syntrophin. We confirmed the interaction of MAP1B and α1-syntrophin by co-localization of the two proteins in transfected cells and by co-immunoprecipitation experiments from mouse brain. In addition, we show that MAP1B and α1-syntrophin partially co-localize in Schwann cells of the murine sciatic nerve during postnatal development and in the adult. However, intracellular localization of α1-syntrophin and other Schwann cell proteins such as ezrin and dystrophin-related protein 2 (DRP2) and the localization of the axonal node of Ranvier-associated protein Caspr1/paranodin were not affected in MAP1B null mice. Our findings add to a growing body of evidence that classical MAPs are likely to be involved in signal transduction not only by directly modulating microtubule function, but also through their interaction with signal transduction proteins. PMID:23152929

  8. Genome-wide Association Study and Admixture Mapping Reveal New Loci Associated with Total IgE Levels in Latinos

    PubMed Central

    Pino-Yanes, Maria; Gignoux, Christopher R.; Galanter, Joshua M.; Levin, Albert M.; Campbell, Catarina D.; Eng, Celeste; Huntsman, Scott; Nishimura, Katherine K.; Gourraud, Pierre-Antoine; Mohajeri, Kiana; O'Roak, Brian J.; Hu, Donglei; Mathias, Rasika A.; Nguyen, Elizabeth A.; Roth, Lindsey A.; Padhukasahasram, Badri; Moreno-Estrada, Andres; Sandoval, Karla; Winkler, Cheryl A.; Lurmann, Fred; Davis, Adam; Farber, Harold J.; Meade, Kelley; Avila, Pedro C.; Serebrisky, Denise; Chapela, Rocio; Ford, Jean G.; Lenoir, Michael A.; Thyne, Shannon M.; Brigino-Buenaventura, Emerita; Borrell, Luisa N.; Rodriguez-Cintron, William; Sen, Saunak; Kumar, Rajesh; Rodriguez-Santana, Jose R.; Bustamante, Carlos D.; Martinez, Fernando D.; Raby, Benjamin A.; Weiss, Scott T.; Nicolae, Dan L.; Ober, Carole; Meyers, Deborah A.; Bleecker, Eugene R.; Mack, Steven J.; Hernandez, Ryan D.; Eichler, Evan E.; Barnes, Kathleen C.; Williams, L. Keoki; Torgerson, Dara G.; Burchard, Esteban G.

    2014-01-01

    Background Immunoglobulin E (IgE) is a key mediator of allergic inflammation and is frequently elevated in allergic disorders. Objective To identify genetic variants associated with IgE levels in Latinos. Methods We performed a genome-wide association study (GWAS) and admixture mapping of total IgE levels in 3,334 Latinos from the Genes-environments & Admixture in Latino Americans (GALA II) study. Replication was evaluated in 454 Latinos, 1,564 European Americans, and 3,187 African Americans from independent studies. Results We confirmed associations of six genes identified by previous GWAS and identified a novel genome-wide significant association of a polymorphism in ZNF365 with total IgE (rs200076616, p=2.3x10−8). We next identified four admixture mapping peaks (6p21.32-p22.1, 13p22-31, 14q23.2, and 22q13.1) where local African, European, and/or Native American ancestry was significantly associated with IgE levels. The most significant peak was 6p21.32-p22.1, where Native American ancestry was associated with lower levels of IgE (p=4.95x10−8). All but 22q13.1 were replicated in an independent sample of Latinos, and two of the peaks were replicated in African Americans (6p21.32-p22.1 and 14q23.2). Fine mapping of 6p21.32-p22.1 identified six genome-wide significant single nucleotide polymorphisms in Latinos, two of which replicated in European Americans. Another SNP was peak-wide significant within 14q23.2 in African Americans (rs1741099, p=3.7x10−6), and replicated in non-African American samples (p=0.011). Conclusion We confirmed genetic associations at six genes, and identified novel associations within ZNF365, HLA-DQA1, and 14q23.2. Our results highlight the importance of studying diverse, multi-ethnic populations to uncover novel loci associated with total IgE levels. PMID:25488688

  9. Mutations in the Microtubule-Associated Protein 1A (Map1a) Gene Cause Purkinje Cell Degeneration

    PubMed Central

    Liu, Ye; Lee, Jeong Woong

    2015-01-01

    The structural microtubule-associated proteins (MAPs) are critical for the organization of neuronal microtubules (MTs). Microtubule-associated protein 1A (MAP1A) is one of the most abundantly expressed MAPs in the mammalian brain. However, its in vivo function remains largely unknown. Here we describe a spontaneous mouse mutation, nm2719, which causes tremors, ataxia, and loss of cerebellar Purkinje neurons in aged homozygous mice. The nm2719 mutation disrupts the Map1a gene. We show that targeted deletion of mouse Map1a gene leads to similar neurodegenerative defects. Before neuron death, Map1a mutant Purkinje cells exhibited abnormal focal swellings of dendritic shafts and disruptions in axon initial segment (AIS) morphology. Furthermore, the MT network was reduced in the somatodendritic and AIS compartments, and both the heavy and light chains of MAP1B, another brain-enriched MAP, was aberrantly distributed in the soma and dendrites of mutant Purkinje cells. MAP1A has been reported to bind to the membrane-associated guanylate kinase (MAGUK) scaffolding proteins, as well as to MTs. Indeed, PSD-93, the MAGUK specifically enriched in Purkinje cells, was reduced in Map1a−/− Purkinje cells. These results demonstrate that MAP1A functions to maintain both the neuronal MT network and the level of PSD-93 in neurons of the mammalian brain. PMID:25788676

  10. Percolation in insect nest networks: Evidence for optimal wiring

    NASA Astrophysics Data System (ADS)

    Valverde, Sergi; Corominas-Murtra, Bernat; Perna, Andrea; Kuntz, Pascale; Theraulaz, Guy; Solé, Ricard V.

    2009-06-01

    Optimization has been shown to be a driving force for the evolution of some biological structures, such as neural maps in the brain or transport networks. Here we show that insect networks also display characteristic traits of optimality. By using a graph representation of the chamber organization of termite nests and a disordered lattice model, it is found that these spatial nests are close to a percolation threshold. This suggests that termites build efficient systems of galleries spanning most of the nest volume at low cost. The evolutionary consequences are outlined.

  11. A new bee species that excavates sandstone nests.

    PubMed

    Orr, Michael C; Griswold, Terry; Pitts, James P; Parker, Frank D

    2016-09-12

    Humanity has long been fascinated by animals with apparently unfavorable lifestyles [1]. Nesting habits are especially important because they can limit where organisms live, thereby driving population, community, and even ecosystem dynamics [2]. The question arises, then, why bees nest in active termite mounds [3] or on the rim of degassing volcanoes, seemingly preferring such hardship [4]. Here, we present a new bee species that excavates sandstone nests, Anthophora (Anthophoroides) pueblo Orr (described in Supplemental Information, published with this article online), despite the challenges already inherent to desert life. Ultimately, the benefits of nesting in sandstone appear to outweigh the associated costs in this system. PMID:27623257

  12. A new bee species that excavates sandstone nests.

    PubMed

    Orr, Michael C; Griswold, Terry; Pitts, James P; Parker, Frank D

    2016-09-12

    Humanity has long been fascinated by animals with apparently unfavorable lifestyles [1]. Nesting habits are especially important because they can limit where organisms live, thereby driving population, community, and even ecosystem dynamics [2]. The question arises, then, why bees nest in active termite mounds [3] or on the rim of degassing volcanoes, seemingly preferring such hardship [4]. Here, we present a new bee species that excavates sandstone nests, Anthophora (Anthophoroides) pueblo Orr (described in Supplemental Information, published with this article online), despite the challenges already inherent to desert life. Ultimately, the benefits of nesting in sandstone appear to outweigh the associated costs in this system.

  13. Nests with numerous SOX10 and MiTF-positive cells in lichenoid inflammation: pseudomelanocytic nests or authentic melanocytic proliferation?

    PubMed

    Silva, Claudine Yap; Goldberg, Lynne J; Mahalingam, Meera; Bhawan, Jag; Wolpowitz, Deon

    2011-10-01

    Pseudomelanocytic nests in the setting of lichenoid inflammation can mimic atypical melanocytic proliferations. Both melanocytic and cytokeratin immunohistochemical stains may be utilized to differentiate these entities. Unlike true melanocytic nests, pseudomelanocytic nests contain Melanoma Antigen Recognized by T-cells 1 (MART-1)/ Melan-A-positive cells and cells positive for pan-cytokeratins, CD3 and/or CD68. Recently, rare (1-2 cells/nest) microphthalmia- associated transcription factor (MiTF)-positive cells were also reported in pseudomelanocytic nests. We present a 48-year-old man with a 2 × 3 cm violaceous to hyperpigmented, non-blanching, polygonal patch on the neck. Histopathology showed focal epidermal atrophy, irregularly distributed junctional nests and a lichenoid infiltrate with colloid bodies. Immunoperoxidase studies revealed occasional pan-cytokeratin and MART-1/Melan-A-positive staining in nests as well as focal S-100 protein-positive cells. Importantly, the majority of nests showed numerous cells positive for MiTF and SOX10 (>2 cells/nest and some the majority of cells). This combined staining pattern confounds the above-described immunohistochemical distinction between pseudo and true melanocytic nests. Clinically felt to represent unilateral lichen planus pigmentosus/erythema dyschromicum perstans and not malignant melanoma in situ, this lesion highlights the importance of clinicopathologic correlation and suggests either a new melanocytic entity or a novel pattern of benign melanocytic reorganization in a subset of lichenoid dermatitides.

  14. Nest-site selection and success of mottled ducks on agricultural lands in southwest Louisiana

    USGS Publications Warehouse

    Durham, R.S.; Afton, A.D.

    2003-01-01

    Listing of the mottled duck (Anas fulvigula maculosa) as a priority species in the Gulf Coast Joint Venture of the North American Waterfowl Management Plan, coupled with recent declines of rice (Oryza sativa) acreage, led us to investigate the nesting ecology of this species on agricultural lands in southwest Louisiana. We examined nest-site selection at macro- and microhabitat levels, nest success, causes of nest failures, and habitat features influencing nest success. We found that female mottled ducks preferred to nest in permanent pastures with knolls (53% of nests) and idle fields (22% of nests). Vegetation height was greater at nests than at random points within the same macrohabitat patch. Successful nests were associated with greater numbers of plant species, located farther from water, and associated with higher vegetation density values than were unsuccessful nests. We determined that mammalian predators caused most nest failures (77% of 52 unsuccessful nests). Our results suggest that nest success of mottled ducks on agricultural lands in southwest Louisiana could be improved by 1) locating large permanent pastures and idle fields near rice fields and other available wetlands, 2) managing plant communities in these upland areas to favor dense stands of perennial bunch grasses, tall composites, dewberry (Rubus trivialis), and other native grasses and forbs, and 3) managing cattle-stocking rates and the duration and timing of grazing to promote tall, dense stands of these plant taxa during the nesting season (March-June).

  15. Identification and validation of functional markers in a global rice collection by association mapping.

    PubMed

    Jahani, Mojtaba; Nematzadeh, Ghorbanali; Dolatabadi, Behnaz; Hashemi, Sayyed Hamidreza; Mohammadi-Nejad, Ghasem

    2014-06-01

    Recent results indicate that marker-assisted selection is an effective approach to reduce the cost and to improve the efficacy and accuracy of selection in plant breeding. This study was conducted to identify and validate molecular markers linked to important breeding traits by association mapping. The association was evaluated between 81 molecular markers (STS, SSR, Indel, CAPS, and PCR-based SNP) and 15 morphological traits in a global panel of 100 rice (Oryza sativa) accessions. The population structure analysis identified three main subpopulations. Obvious kinship relationships were also detected between the rice accessions. Association analysis was performed based on the mixed linear model by considering population structure and family relatedness. In addition, the false discovery rate method was used to correct the multiple testing. A total of 47 marker-trait associations were identified, including 22 markers for 14 traits. Among all, the polymorphism at the loci DDR-GL was highly associated with grain characters (grain length, grain width, and length/width ratio). In addition, marker RM3148 was responsible for five important traits simultaneously. Results demonstrated that such informative markers can be very useful for rice breeding programs using marker-assisted selection. Moreover, the diverse populations of rice accessions are a valuable resource for association mapping of morphological traits.

  16. Fine-Mapping of Common Genetic Variants Associated with Colorectal Tumor Risk Identified Potential Functional Variants.

    PubMed

    Du, Mengmeng; Jiao, Shuo; Bien, Stephanie A; Gala, Manish; Abecasis, Goncalo; Bezieau, Stephane; Brenner, Hermann; Butterbach, Katja; Caan, Bette J; Carlson, Christopher S; Casey, Graham; Chang-Claude, Jenny; Conti, David V; Curtis, Keith R; Duggan, David; Gallinger, Steven; Haile, Robert W; Harrison, Tabitha A; Hayes, Richard B; Hoffmeister, Michael; Hopper, John L; Hudson, Thomas J; Jenkins, Mark A; Küry, Sébastien; Le Marchand, Loic; Leal, Suzanne M; Newcomb, Polly A; Nickerson, Deborah A; Potter, John D; Schoen, Robert E; Schumacher, Fredrick R; Seminara, Daniela; Slattery, Martha L; Hsu, Li; Chan, Andrew T; White, Emily; Berndt, Sonja I; Peters, Ulrike

    2016-01-01

    Genome-wide association studies (GWAS) have identified many common single nucleotide polymorphisms (SNPs) associated with colorectal cancer risk. These SNPs may tag correlated variants with biological importance. Fine-mapping around GWAS loci can facilitate detection of functional candidates and additional independent risk variants. We analyzed 11,900 cases and 14,311 controls in the Genetics and Epidemiology of Colorectal Cancer Consortium and the Colon Cancer Family Registry. To fine-map genomic regions containing all known common risk variants, we imputed high-density genetic data from the 1000 Genomes Project. We tested single-variant associations with colorectal tumor risk for all variants spanning genomic regions 250-kb upstream or downstream of 31 GWAS-identified SNPs (index SNPs). We queried the University of California, Santa Cruz Genome Browser to examine evidence for biological function. Index SNPs did not show the strongest association signals with colorectal tumor risk in their respective genomic regions. Bioinformatics analysis of SNPs showing smaller P-values in each region revealed 21 functional candidates in 12 loci (5q31.1, 8q24, 11q13.4, 11q23, 12p13.32, 12q24.21, 14q22.2, 15q13, 18q21, 19q13.1, 20p12.3, and 20q13.33). We did not observe evidence of additional independent association signals in GWAS-identified regions. Our results support the utility of integrating data from comprehensive fine-mapping with expanding publicly available genomic databases to help clarify GWAS associations and identify functional candidates that warrant more onerous laboratory follow-up. Such efforts may aid the eventual discovery of disease-causing variant(s).

  17. Association Mapping for Aluminum Tolerance in a Core Collection of Rice Landraces

    PubMed Central

    Zhang, Peng; Zhong, Kaizhen; Tong, Hanhua; Shahid, Muhammad Qasim; Li, Jinquan

    2016-01-01

    Trivalent aluminum (Al3+) has drastic effect on the rice production in acidic soils. Elite genes for aluminum (Al) tolerance might exist in rice landraces. Therefore, the purpose of this research is to mine the elite genes within rice landraces. Association mapping for Al tolerance traits [i.e., relative root elongation (RRE)] was performed by using a core collection of 150 accessions of rice landraces (i.e., Ting’s rice core collection). Our results showed that the Ting’s rice core collection possessed a wide-range of phenotypic variation for Al tolerance, and the index of Al tolerance (RRE) was ranged from 0.22 to 0.89. Moreover, the groups with different origins and compositions of indica and japonica rice showed different degrees of tolerance to varying levels of Al. These rice landraces were further screened with 274 simple sequence repeat markers, and association mapping was performed using a mixed linear model approach. The mapping results showed that a total of 23 significant (P < 0.05) trait–marker associations were detected for Al tolerance. Of these, three associations (13%) were identical to the quantitative trait loci reported previously, and other 20 associations were reported for the first time in this study. The proportion of phenotypic variance (R2) explained by 23 significant associations ranged from 5.03 to 20.03% for Al tolerance. We detected several elite alleles for Al tolerance based on multiple comparisons of allelic effects, which could be used to develop Al tolerant rice cultivars through marker-assisted breeding. PMID:27757115

  18. Fine-Mapping of Common Genetic Variants Associated with Colorectal Tumor Risk Identified Potential Functional Variants.

    PubMed

    Du, Mengmeng; Jiao, Shuo; Bien, Stephanie A; Gala, Manish; Abecasis, Goncalo; Bezieau, Stephane; Brenner, Hermann; Butterbach, Katja; Caan, Bette J; Carlson, Christopher S; Casey, Graham; Chang-Claude, Jenny; Conti, David V; Curtis, Keith R; Duggan, David; Gallinger, Steven; Haile, Robert W; Harrison, Tabitha A; Hayes, Richard B; Hoffmeister, Michael; Hopper, John L; Hudson, Thomas J; Jenkins, Mark A; Küry, Sébastien; Le Marchand, Loic; Leal, Suzanne M; Newcomb, Polly A; Nickerson, Deborah A; Potter, John D; Schoen, Robert E; Schumacher, Fredrick R; Seminara, Daniela; Slattery, Martha L; Hsu, Li; Chan, Andrew T; White, Emily; Berndt, Sonja I; Peters, Ulrike

    2016-01-01

    Genome-wide association studies (GWAS) have identified many common single nucleotide polymorphisms (SNPs) associated with colorectal cancer risk. These SNPs may tag correlated variants with biological importance. Fine-mapping around GWAS loci can facilitate detection of functional candidates and additional independent risk variants. We analyzed 11,900 cases and 14,311 controls in the Genetics and Epidemiology of Colorectal Cancer Consortium and the Colon Cancer Family Registry. To fine-map genomic regions containing all known common risk variants, we imputed high-density genetic data from the 1000 Genomes Project. We tested single-variant associations with colorectal tumor risk for all variants spanning genomic regions 250-kb upstream or downstream of 31 GWAS-identified SNPs (index SNPs). We queried the University of California, Santa Cruz Genome Browser to examine evidence for biological function. Index SNPs did not show the strongest association signals with colorectal tumor risk in their respective genomic regions. Bioinformatics analysis of SNPs showing smaller P-values in each region revealed 21 functional candidates in 12 loci (5q31.1, 8q24, 11q13.4, 11q23, 12p13.32, 12q24.21, 14q22.2, 15q13, 18q21, 19q13.1, 20p12.3, and 20q13.33). We did not observe evidence of additional independent association signals in GWAS-identified regions. Our results support the utility of integrating data from comprehensive fine-mapping with expanding publicly available genomic databases to help clarify GWAS associations and identify functional candidates that warrant more onerous laboratory follow-up. Such efforts may aid the eventual discovery of disease-causing variant(s). PMID:27379672

  19. Genome-Wide Association Mapping of Root Traits in a Japonica Rice Panel

    PubMed Central

    Courtois, Brigitte; Audebert, Alain; Dardou, Audrey; Roques, Sandrine; Ghneim- Herrera, Thaura; Droc, Gaëtan; Frouin, Julien; Rouan, Lauriane; Gozé, Eric; Kilian, Andrzej; Ahmadi, Nourollah; Dingkuhn, Michael

    2013-01-01

    Rice is a crop prone to drought stress in upland and rainfed lowland ecosystems. A deep root system is recognized as the best drought avoidance mechanism. Genome-wide association mapping offers higher resolution for locating quantitative trait loci (QTLs) than QTL mapping in biparental populations. We performed an association mapping study for root traits using a panel of 167 japonica accessions, mostly of tropical origin. The panel was genotyped at an average density of one marker per 22.5 kb using genotyping by sequencing technology. The linkage disequilibrium in the panel was high (r2>0.6, on average, for 20 kb mean distances between markers). The plants were grown in transparent 50 cm × 20 cm × 2 cm Plexiglas nailboard sandwiches filled with 1.5 mm glass beads through which a nutrient solution was circulated. Root system architecture and biomass traits were measured in 30-day-old plants. The panel showed a moderate to high diversity in the various traits, particularly for deep (below 30 cm depth) root mass and the number of deep roots. Association analyses were conducted using a mixed model involving both population structure and kinship to control for false positives. Nineteen associations were significant at P<1e-05, and 78 were significant at P<1e-04. The greatest numbers of significant associations were detected for deep root mass and the number of deep roots, whereas no significant associations were found for total root biomass or deep root proportion. Because several QTLs for different traits were co-localized, 51 unique loci were detected; several co-localized with meta-QTLs for root traits, but none co-localized with rice genes known to be involved in root growth. Several likely candidate genes were found in close proximity to these loci. Additional work is necessary to assess whether these markers are relevant in other backgrounds and whether the genes identified are robust candidates. PMID:24223758

  20. Fine-Mapping of Common Genetic Variants Associated with Colorectal Tumor Risk Identified Potential Functional Variants

    PubMed Central

    Gala, Manish; Abecasis, Goncalo; Bezieau, Stephane; Brenner, Hermann; Butterbach, Katja; Caan, Bette J.; Carlson, Christopher S.; Casey, Graham; Chang-Claude, Jenny; Conti, David V.; Curtis, Keith R.; Duggan, David; Gallinger, Steven; Haile, Robert W.; Harrison, Tabitha A.; Hayes, Richard B.; Hoffmeister, Michael; Hopper, John L.; Hudson, Thomas J.; Jenkins, Mark A.; Küry, Sébastien; Le Marchand, Loic; Leal, Suzanne M.; Newcomb, Polly A.; Nickerson, Deborah A.; Potter, John D.; Schoen, Robert E.; Schumacher, Fredrick R.; Seminara, Daniela; Slattery, Martha L.; Hsu, Li; Chan, Andrew T.; White, Emily; Berndt, Sonja I.; Peters, Ulrike

    2016-01-01

    Genome-wide association studies (GWAS) have identified many common single nucleotide polymorphisms (SNPs) associated with colorectal cancer risk. These SNPs may tag correlated variants with biological importance. Fine-mapping around GWAS loci can facilitate detection of functional candidates and additional independent risk variants. We analyzed 11,900 cases and 14,311 controls in the Genetics and Epidemiology of Colorectal Cancer Consortium and the Colon Cancer Family Registry. To fine-map genomic regions containing all known common risk variants, we imputed high-density genetic data from the 1000 Genomes Project. We tested single-variant associations with colorectal tumor risk for all variants spanning genomic regions 250-kb upstream or downstream of 31 GWAS-identified SNPs (index SNPs). We queried the University of California, Santa Cruz Genome Browser to examine evidence for biological function. Index SNPs did not show the strongest association signals with colorectal tumor risk in their respective genomic regions. Bioinformatics analysis of SNPs showing smaller P-values in each region revealed 21 functional candidates in 12 loci (5q31.1, 8q24, 11q13.4, 11q23, 12p13.32, 12q24.21, 14q22.2, 15q13, 18q21, 19q13.1, 20p12.3, and 20q13.33). We did not observe evidence of additional independent association signals in GWAS-identified regions. Our results support the utility of integrating data from comprehensive fine-mapping with expanding publicly available genomic databases to help clarify GWAS associations and identify functional candidates that warrant more onerous laboratory follow-up. Such efforts may aid the eventual discovery of disease-causing variant(s). PMID:27379672

  1. EAGLES NEST WILDERNESS, COLORADO.

    USGS Publications Warehouse

    Tweto, Ogden; Williams, Frank E.

    1984-01-01

    On the basis of a geologic and mineral survey, a primitive area that constitutes the nucleus of the Eagles Nest Wilderness, Colorado was appraised to offer little promise for the occurrence of mineral or energy resources. Among the additional areas later incorporated in the wilderness, only a strip near a major fault west and northwest of Frisco and Dillon is classed as having probable mineral-resource potential. If mineral deposits exist, they probably are of the silver-lead-zinc or fluorspar types.

  2. Where to nest? Ecological determinants of chimpanzee nest abundance and distribution at the habitat and tree species scale.

    PubMed

    Carvalho, Joana S; Meyer, Christoph F J; Vicente, Luis; Marques, Tiago A

    2015-02-01

    Conversion of forests to anthropogenic land-uses increasingly subjects chimpanzee populations to habitat changes and concomitant alterations in the plant resources available to them for nesting and feeding. Based on nest count surveys conducted during the dry season, we investigated nest tree species selection and the effect of vegetation attributes on nest abundance of the western chimpanzee, Pan troglodytes verus, at Lagoas de Cufada Natural Park (LCNP), Guinea-Bissau, a forest-savannah mosaic widely disturbed by humans. Further, we assessed patterns of nest height distribution to determine support for the anti-predator hypothesis. A zero-altered generalized linear mixed model showed that nest abundance was negatively related to floristic diversity (exponential form of the Shannon index) and positively with the availability of smaller-sized trees, reflecting characteristics of dense-canopy forest. A positive correlation between nest abundance and floristic richness (number of plant species) and composition indicated that species-rich open habitats are also important in nest site selection. Restricting this analysis to feeding trees, nest abundance was again positively associated with the availability of smaller-sized trees, further supporting the preference for nesting in food tree species from dense forest. Nest tree species selection was non-random, and oil palms were used at a much lower proportion (10%) than previously reported from other study sites in forest-savannah mosaics. While this study suggests that human disturbance may underlie the exclusive arboreal nesting at LCNP, better quantitative data are needed to determine to what extent the construction of elevated nests is in fact a response to predators able to climb trees. Given the importance of LCNP as refuge for Pan t. verus our findings can improve conservation decisions for the management of this important umbrella species as well as its remaining suitable habitats. PMID:25224379

  3. Nest-size and colony characteristics of wading birds in selected Atlantic Coast colonies

    USGS Publications Warehouse

    Beaver, D.L.; Osborn, R.G.; Custer, T.W.

    1980-01-01

    Nests of 5 species of wading birds were identified and marked during the breeding season at 6 locations from Massachusetts to North Carolina. At the end of the breeding season 12 characteristics of nest-site location were measured. Nest locations were mapped to examine dispersion and nearest neighbor relationships. Multivariate analyses were used to describe and compare sites and species.....We found that variations in nest-sites between colonies were greater than between species; colonies differed mainly in the variety and size of vegetation; birds preferred to nest in vegetation that offered relatively stable nest-sites; and the dispersion of nests in the colonies was related to vegetative patterns. The interaction of these factors with the number of bird species and the abundance of birds in the colony seemed to determine whether nest-sites were stratified, segregated or randomly distributed.

  4. The Effect of the Empty Nest on the Morale of Mexican American and White Women.

    ERIC Educational Resources Information Center

    Bremer, Teresa H.; Ragan, Pauline K.

    The empty nest has been thought to be associated with low morale among women. The emphasis on the mother role among Mexican American families may result in a stronger negative association between low morale and the empty nest among Mexican American women than among white women. This study tests two hypotheses: first, that the empty nest is…

  5. Confirmation and Fine Mapping of a Major QTL for Aflatoxin Resistance in Maize Using a Combination of Linkage and Association Mapping.

    PubMed

    Zhang, Yu; Cui, Min; Zhang, Jimin; Zhang, Lei; Li, Chenliu; Kan, Xin; Sun, Qian; Deng, Dexiang; Yin, Zhitong

    2016-01-01

    Maize grain contamination with aflatoxin from Aspergillus flavus (A. flavus) is a serious health hazard to animals and humans. To map the quantitative trait loci (QTLs) associated with resistance to A. flavus, we employed a powerful approach that differs from previous methods in one important way: it combines the advantages of the genome-wide association analysis (GWAS) and traditional linkage mapping analysis. Linkage mapping was performed using 228 recombinant inbred lines (RILs), and a highly significant QTL that affected aflatoxin accumulation, qAA8, was mapped. This QTL spanned approximately 7 centi-Morgan (cM) on chromosome 8. The confidence interval was too large for positional cloning of the causal gene. To refine this QTL, GWAS was performed with 558,629 single nucleotide polymorphisms (SNPs) in an association population comprising 437 maize inbred lines. Twenty-five significantly associated SNPs were identified, most of which co-localised with qAA8 and explained 6.7% to 26.8% of the phenotypic variation observed. Based on the rapid linkage disequilibrium (LD) and the high density of SNPs in the association population, qAA8 was further localised to a smaller genomic region of approximately 1500 bp. A high-resolution map of the qAA8 region will be useful towards a marker-assisted selection (MAS) of A. flavus resistance and a characterisation of the causal gene. PMID:27598199

  6. Confirmation and Fine Mapping of a Major QTL for Aflatoxin Resistance in Maize Using a Combination of Linkage and Association Mapping.

    PubMed

    Zhang, Yu; Cui, Min; Zhang, Jimin; Zhang, Lei; Li, Chenliu; Kan, Xin; Sun, Qian; Deng, Dexiang; Yin, Zhitong

    2016-09-02

    Maize grain contamination with aflatoxin from Aspergillus flavus (A. flavus) is a serious health hazard to animals and humans. To map the quantitative trait loci (QTLs) associated with resistance to A. flavus, we employed a powerful approach that differs from previous methods in one important way: it combines the advantages of the genome-wide association analysis (GWAS) and traditional linkage mapping analysis. Linkage mapping was performed using 228 recombinant inbred lines (RILs), and a highly significant QTL that affected aflatoxin accumulation, qAA8, was mapped. This QTL spanned approximately 7 centi-Morgan (cM) on chromosome 8. The confidence interval was too large for positional cloning of the causal gene. To refine this QTL, GWAS was performed with 558,629 single nucleotide polymorphisms (SNPs) in an association population comprising 437 maize inbred lines. Twenty-five significantly associated SNPs were identified, most of which co-localised with qAA8 and explained 6.7% to 26.8% of the phenotypic variation observed. Based on the rapid linkage disequilibrium (LD) and the high density of SNPs in the association population, qAA8 was further localised to a smaller genomic region of approximately 1500 bp. A high-resolution map of the qAA8 region will be useful towards a marker-assisted selection (MAS) of A. flavus resistance and a characterisation of the causal gene.

  7. Confirmation and Fine Mapping of a Major QTL for Aflatoxin Resistance in Maize Using a Combination of Linkage and Association Mapping

    PubMed Central

    Zhang, Yu; Cui, Min; Zhang, Jimin; Zhang, Lei; Li, Chenliu; Kan, Xin; Sun, Qian; Deng, Dexiang; Yin, Zhitong

    2016-01-01

    Maize grain contamination with aflatoxin from Aspergillus flavus (A. flavus) is a serious health hazard to animals and humans. To map the quantitative trait loci (QTLs) associated with resistance to A. flavus, we employed a powerful approach that differs from previous methods in one important way: it combines the advantages of the genome-wide association analysis (GWAS) and traditional linkage mapping analysis. Linkage mapping was performed using 228 recombinant inbred lines (RILs), and a highly significant QTL that affected aflatoxin accumulation, qAA8, was mapped. This QTL spanned approximately 7 centi-Morgan (cM) on chromosome 8. The confidence interval was too large for positional cloning of the causal gene. To refine this QTL, GWAS was performed with 558,629 single nucleotide polymorphisms (SNPs) in an association population comprising 437 maize inbred lines. Twenty-five significantly associated SNPs were identified, most of which co-localised with qAA8 and explained 6.7% to 26.8% of the phenotypic variation observed. Based on the rapid linkage disequilibrium (LD) and the high density of SNPs in the association population, qAA8 was further localised to a smaller genomic region of approximately 1500 bp. A high-resolution map of the qAA8 region will be useful towards a marker-assisted selection (MAS) of A. flavus resistance and a characterisation of the causal gene. PMID:27598199

  8. Landscape distribution of food and nesting sites affect larval diet and nest size, but not abundance of Osmia bicornis.

    PubMed

    Coudrain, Valérie; Rittiner, Sarah; Herzog, Felix; Tinner, Willy; Entling, Martin H

    2016-10-01

    Habitat fragmentation is a major threat for beneficial organisms and the ecosystem services they provide. Multiple-habitat users such as wild bees depend on both nesting and foraging habitat. Thus, they may be affected by the fragmentation of at least two habitat types. We investigated the effects of landscape-scale amount of and patch isolation from both nesting habitat (woody plants) and foraging habitat (specific pollen sources) on the abundance and diet of Osmia bicornis L. Trap-nests of O. bicornis were studied in 30 agricultural landscapes of the Swiss Plateau. Nesting and foraging habitats were mapped in a radius of 500 m around the sites. Pollen composition of larval diet changed as isolation to the main pollen source, Ranunculus, increased, suggesting that O. bicornis adapted its foraging strategy in function of the nest proximity to main pollen sources. Abundance of O. bicornis was neither related to isolation or amount of nesting habitat nor to isolation or abundance of food plants. Surprisingly, nests of O. bicornis contained fewer larvae in sites at forest edge compared to isolated sites, possibly due to higher parasitism risk. This study indicates that O. bicornis can nest in a variety of situations by compensating scarcity of its main larval food by exploiting alternative food sources.

  9. Landscape distribution of food and nesting sites affect larval diet and nest size, but not abundance of Osmia bicornis.

    PubMed

    Coudrain, Valérie; Rittiner, Sarah; Herzog, Felix; Tinner, Willy; Entling, Martin H

    2016-10-01

    Habitat fragmentation is a major threat for beneficial organisms and the ecosystem services they provide. Multiple-habitat users such as wild bees depend on both nesting and foraging habitat. Thus, they may be affected by the fragmentation of at least two habitat types. We investigated the effects of landscape-scale amount of and patch isolation from both nesting habitat (woody plants) and foraging habitat (specific pollen sources) on the abundance and diet of Osmia bicornis L. Trap-nests of O. bicornis were studied in 30 agricultural landscapes of the Swiss Plateau. Nesting and foraging habitats were mapped in a radius of 500 m around the sites. Pollen composition of larval diet changed as isolation to the main pollen source, Ranunculus, increased, suggesting that O. bicornis adapted its foraging strategy in function of the nest proximity to main pollen sources. Abundance of O. bicornis was neither related to isolation or amount of nesting habitat nor to isolation or abundance of food plants. Surprisingly, nests of O. bicornis contained fewer larvae in sites at forest edge compared to isolated sites, possibly due to higher parasitism risk. This study indicates that O. bicornis can nest in a variety of situations by compensating scarcity of its main larval food by exploiting alternative food sources. PMID:25973721

  10. Association mapping and marker-assisted selection of the lettuce dieback resistance gene Tvr1

    PubMed Central

    2009-01-01

    Background Lettuce (Lactuca saliva L.) is susceptible to dieback, a soilborne disease caused by two viruses from the family Tombusviridae. Susceptibility to dieback is widespread in romaine and leaf-type lettuce, while modern iceberg cultivars are resistant to this disease. Resistance in iceberg cultivars is conferred by Tvr1 - a single, dominant gene that provides durable resistance. This study describes fine mapping of the resistance gene, analysis of nucleotide polymorphism and linkage disequilibrium in the Tvr1 region, and development of molecular markers for marker-assisted selection. Results A combination of classical linkage mapping and association mapping allowed us to pinpoint the location of the Tvr1 resistance gene on chromosomal linkage group 2. Nine molecular markers, based on expressed sequence tags (EST), were closely linked to Tvr1 in the mapping population, developed from crosses between resistant (Salinas and Salinas 88) and susceptible (Valmaine) cultivars. Sequencing of these markers from a set of 68 cultivars revealed a relatively high level of nucleotide polymorphism (θ = 6.7 × 10-3) and extensive linkage disequilibrium (r2 = 0.124 at 8 cM) in this region. However, the extent of linkage disequilibrium was affected by population structure and the values were substantially larger when the analysis was performed only for romaine (r2 = 0.247) and crisphead (r2 = 0.345) accessions. The association mapping approach revealed that one of the nine markers (Cntg10192) in the Tvr1 region matched exactly with resistant and susceptible phenotypes when tested on a set of 200 L. sativa accessions from all horticultural types of lettuce. The marker-trait association was also confirmed on two accessions of Lactuca serriola - a wild relative of cultivated lettuce. The combination of three single-nucleotide polymorphisms (SNPs) at the Cntg10192 marker identified four haplotypes. Three of the haplotypes were associated with resistance and one of them was always

  11. Microtubule-associated protein 2 (MAP2) associates with the NMDA receptor and is spatially redistributed within rat hippocampal neurons after oxygen-glucose deprivation.

    PubMed

    Buddle, Michele; Eberhardt, Eric; Ciminello, Lauren H; Levin, Tal; Wing, Richard; DiPasquale, Kathleen; Raley-Susman, Kathleen M

    2003-07-18

    MAP2 (microtubule-associated protein 2) is a cytoskeletal phosphoprotein that regulates the dynamic assembly characteristics of microtubules and appears to provide scaffolding for organelle distribution into the dendrites and for the localization of signal transduction apparatus in dendrites, particularly near spines. MAP2 is degraded after ischemia and other metabolic insults, but the time course and initial triggers of that breakdown are not fully understood. This study determined that MAP2 resides in a complex with the NMDA receptor, suggesting that spatially localized changes may be important in the mechanism of MAP2 redistribution and breakdown after oxygen-glucose deprivation (OGD). Using OGD in the adult rat hippocampal slice as a model system, this study demonstrated that MAP2 breakdown occurs very early after OGD, with the first statistical decrease in MAP2 levels within the first 30 min after the insult. There is a dramatic redistribution of MAP2 to the somata of pyramidal neurons, particularly neurons at the CA1-subiculum border. Free radicals and nitric oxide are not involved in the damage to MAP2. NMDA-receptor activation plays a prominent role in the MAP2 breakdown. In direct response to NMDA receptor activation, calcium influx, likely through the receptor ion channel complex, as well as release of calcium from the mitochondria through activation of the 2Na(+)-Ca(2+) exchanger of mitochondria, triggers MAP2 degradation. The proteolysis of MAP2 is limited by endogenous calpain activity, likely via the spatial access of calpain to MAP2.

  12. Fine mapping of the celiac disease-associated LPP locus reveals a potential functional variant

    PubMed Central

    Almeida, Rodrigo; Ricaño-Ponce, Isis; Kumar, Vinod; Deelen, Patrick; Szperl, Agata; Trynka, Gosia; Gutierrez-Achury, Javier; Kanterakis, Alexandros; Westra, Harm-Jan; Franke, Lude; Swertz, Morris A.; Platteel, Mathieu; Bilbao, Jose Ramon; Barisani, Donatella; Greco, Luigi; Mearin, Luisa; Wolters, Victorien M.; Mulder, Chris; Mazzilli, Maria Cristina; Sood, Ajit; Cukrowska, Bozena; Núñez, Concepción; Pratesi, Riccardo; Withoff, Sebo; Wijmenga, Cisca

    2014-01-01

    Using the Immunochip for genotyping, we identified 39 non-human leukocyte antigen (non-HLA) loci associated to celiac disease (CeD), an immune-mediated disease with a worldwide frequency of ∼1%. The most significant non-HLA signal mapped to the intronic region of 70 kb in the LPP gene. Our aim was to fine map and identify possible functional variants in the LPP locus. We performed a meta-analysis in a cohort of 25 169 individuals from six different populations previously genotyped using Immunochip. Imputation using data from the Genome of the Netherlands and 1000 Genomes projects, followed by meta-analysis, confirmed the strong association signal on the LPP locus (rs2030519, P = 1.79 × 10−49), without any novel associations. The conditional analysis on this top SNP-indicated association to a single common haplotype. By performing haplotype analyses in each population separately, as well as in a combined group of the four populations that reach the significant threshold after correction (P < 0.008), we narrowed down the CeD-associated region from 70 to 2.8 kb (P = 1.35 × 10−44). By intersecting regulatory data from the ENCODE project, we found a functional SNP, rs4686484 (P = 3.12 × 10−49), that maps to several B-cell enhancer elements and a highly conserved region. This SNP was also predicted to change the binding motif of the transcription factors IRF4, IRF11, Nkx2.7 and Nkx2.9, suggesting its role in transcriptional regulation. We later found significantly low levels of LPP mRNA in CeD biopsies compared with controls, thus our results suggest that rs4686484 is the functional variant in this locus, while LPP expression is decreased in CeD. PMID:24334606

  13. Neste plans three projects

    SciTech Connect

    Not Available

    1993-02-03

    Neste Chemicals (Helsinki) is discussing three joint ventures with local authorities in China, says Mikko Haapavaara, v.p./Asia. The projects should help the Finnish producer to increase sales in Asia by a considerable amount by 2000, he says. The plan involves production of polyethylene (PE), unsaturated polyester resins and PE compounding-all core operations. Sites have not been selected, but Shanghai is the favored location for the PE operations. The company is also looking at a site in the south, near Hong Kong, and at locations near Beijing. The PE plant would need to be near an ethylene unit, says Haapavaara. The PE resin plant would be designed to produce about 150,000 m.t./year and would cost about No. 150 million. A part of the output would need to be exported to take care of the financing, the company says. A feasibility study now under way with the potential Chinese partners should be completed by the end of March. The plant would use Neste's linear low-density PE process, proved in a world-scale plant at Beringen, Belgium. The compounding units would produce specialty PE material for the wire and cable and pipe industry. The company is a joint venture partner in a propane dehydrogenation/polypropylene (PP) plant and a minority partner in a Qualipoly, the 20,000 m.t./year unsaturated polyester resin producer.

  14. Microtubule-associated protein 9 (Map9/Asap) is required for the early steps of zebrafish development

    PubMed Central

    Fontenille, Laura; Rouquier, Sylvie; Lutfalla, Georges; Giorgi, Dominique

    2014-01-01

    Microtubules are structural components of the cell cytoskeleton and key factors for mitosis and ciliogenesis in eukaryotes. The regulation of MT dynamics requires non-motor MAPs. We previously showed that, in human cells in culture, MAP9 (also named ASAP) is involved in MT dynamics and is essential for mitotic spindle formation and mitosis progression. Indeed, misexpression of MAP9 leads to severe mitotic defects and cell death. Here, we investigated the in vivo role of map9 during zebrafish development. Map9 is expressed mainly as a maternal gene. Within cells, Map9 is associated with the MT network of the mitotic spindle and with centrosomes. Morpholino-mediated depletion of map9 leads to early development arrest before completion of epiboly. Map9 localizes to the MT array of the YSL. This MT network is destroyed in Map9-depleted embryos, and injection of anti-map9 morpholinos directly in the nascent YSL leads to arrest of epiboly/gastrulation. Finally, map9 knockdown deregulates the expression of genes involved in endodermal differentiation, dorso–ventral and left–right patterning, and other MT-based functions. At low morpholino doses, the surviving embryos show dramatic developmental defects, spindle and mitotic defects, and increased apoptosis. Our findings suggest that map9 is a crucial factor in early zebrafish development by regulating different MT-based processes. PMID:24553125

  15. A communication scheme for the distrubted execution of loop nests with while loops

    SciTech Connect

    Griebl, M.; Lengauer, C.

    1995-10-01

    The mathematical model for the parallelization, or {open_quotes}space-time mapping,{close_quotes} of loop nests is the polyhedron model. The presence of while loops in the nest complicates matters for two reasons: (1) the parallelized loop nest does not correspond to a polyhedron but instead to a subset that resembles a (multi-dimensional) comb and (2) it is not clear when the entire loop nest has terminated. We describe a communication scheme which can deal with both problems and which can be added to the parallel target loop nest by a compiler.

  16. Mapping of numerous disease-associated expression polymorphisms in primary peripheral blood CD4+ lymphocytes.

    PubMed

    Murphy, Amy; Chu, Jen-Hwa; Xu, Mousheng; Carey, Vincent J; Lazarus, Ross; Liu, Andy; Szefler, Stanley J; Strunk, Robert; Demuth, Karen; Castro, Mario; Hansel, Nadia N; Diette, Gregory B; Vonakis, Becky M; Adkinson, N Franklin; Klanderman, Barbara J; Senter-Sylvia, Jody; Ziniti, John; Lange, Christoph; Pastinen, Tomi; Raby, Benjamin A

    2010-12-01

    Genome-wide association studies of human gene expression promise to identify functional regulatory genetic variation that contributes to phenotypic diversity. However, it is unclear how useful this approach will be for the identification of disease-susceptibility variants. We generated gene expression profiles for 22 184 mRNA transcripts using RNA derived from peripheral blood CD4+ lymphocytes, and genome-wide genotype data for 516 512 autosomal markers in 200 subjects. We screened for cis-acting variants by testing variants mapping within 50 kb of expressed transcripts for association with transcript abundance using generalized linear models. Significant associations were identified for 1585 genes at a false discovery rate of 0.05 (corresponding to P-values ranging from 1 × 10(-91) to 7 × 10(-4)). Importantly, we identified evidence of regulatory variation for 119 previously mapped disease genes, including 24 examples where the variant with the strongest evidence of disease-association demonstrates strong association with specific transcript abundance. The prevalence of cis-acting variants among disease-associated genes was 63% higher than the genome-wide rate in our data set (P = 6.41 × 10(-6)), and although many of the implicated loci were associated with immune-related diseases (including asthma, connective tissue disorders and inflammatory bowel disease), associations with genes implicated in non-immune-related diseases including lipid profiles, anthropomorphic measurements, cancer and neurologic disease were also observed. Genetic variants that confer inter-individual differences in gene expression represent an important subset of variants that contribute to disease susceptibility. Population-based integrative genetic approaches can help identify such variation and enhance our understanding of the genetic basis of complex traits.

  17. Time-specific patterns of nest survival for ducks and passerines breeding in North Dakota

    USGS Publications Warehouse

    Shaffer, Terry L.; Grant, Todd A.

    2012-01-01

    In many bird species, survival can vary with the age of the nest, with the date a nest was initiated, or among years within the same nesting area. A literature review showed that patterns of survival vary in relation to nest age and date and are often contradictory. Inconsistencies could be a result of temporal variation in the environment or life-history differences among species. We examined patterns of nest survival in relation to nest age, date, and year for several duck and passerine species nesting at a single location in North Dakota during 1998–2003. We predicted that if environment shaped nest survival patterns, then temporal patterns in survival might be similar among three species of upland nesting ducks, and also among three species of grassland passerines nesting at the same site. We expected that survival patterns would differ between ducks and passerines because of relatively disparate life histories and differences in predators that prey on their nests. Nest survival was rarely constant among years, seasonally, or with age of the nest for species that we studied. As predicted, the pattern of survival was similar among duck species, driven mainly by differences in nest survival associated with nest initiation date. The pattern of survival also was similar among passerine species, but nest survival was more influenced by nest age than by date. Our findings suggest that some but not all variation in temporal patterns of nest survival in grassland birds reported in the literature can be explained on the basis of temporal environmental variation. Because patterns of survival were dissimilar among ducks and passerines, it is likely that mechanisms such as predation or brood parasitism have variable influences on productivity of ducks and passerines nesting in the same area. Our results indicate that biologists and managers should not assume that temporal environmental variations, especially factors that affect nest survival, act similarly on all

  18. Habitat fragmentation reduces nest survival in an Afrotropical bird community in a biodiversity hotspot

    USGS Publications Warehouse

    Newmark, W.D.; Stanley, T.R.

    2011-01-01

    Ecologists have long hypothesized that fragmentation of tropical landscapes reduces avian nest success. However, this hypothesis has not been rigorously assessed because of the difficulty of finding large numbers of well-hidden nests in tropical forests. Here we report that in the East Usambara Mountains in Tanzania, which are part of the Eastern Arc Mountains, a global biodiversity hotspot, that daily nest survival rate and nest success for seven of eight common understory bird species that we examined over a single breeding season were significantly lower in fragmented than in continuous forest, with the odds of nest failure for these seven species ranging from 1.9 to 196.8 times higher in fragmented than continuous forest. Cup-shaped nests were particularly vulnerable in fragments. We then examined over six breeding seasons and 14 study sites in a multivariable survival analysis the influence of landscape structure and nest location on daily nest survival for 13 common species representing 1,272 nests and four nest types (plate, cup, dome, and pouch). Across species and nest types, area, distance of nest to edge, and nest height had a dominant influence on daily nest survival, with area being positively related to nest survival and distance of nest to edge and nest height being both positively and negatively associated with daily nest survival. Our results indicate that multiple environmental factors contribute to reduce nest survival within a tropical understory bird community in a fragmented landscape and that maintaining large continuous forest is important for enhancing nest survival for Afrotropical understory birds.

  19. Habitat fragmentation reduces nest survival in an Afrotropical bird community in a biodiversity hotspot

    PubMed Central

    Newmark, William D.; Stanley, Thomas R.

    2011-01-01

    Ecologists have long hypothesized that fragmentation of tropical landscapes reduces avian nest success. However, this hypothesis has not been rigorously assessed because of the difficulty of finding large numbers of well-hidden nests in tropical forests. Here we report that in the East Usambara Mountains in Tanzania, which are part of the Eastern Arc Mountains, a global biodiversity hotspot, that daily nest survival rate and nest success for seven of eight common understory bird species that we examined over a single breeding season were significantly lower in fragmented than in continuous forest, with the odds of nest failure for these seven species ranging from 1.9 to 196.8 times higher in fragmented than continuous forest. Cup-shaped nests were particularly vulnerable in fragments. We then examined over six breeding seasons and 14 study sites in a multivariable survival analysis the influence of landscape structure and nest location on daily nest survival for 13 common species representing 1,272 nests and four nest types (plate, cup, dome, and pouch). Across species and nest types, area, distance of nest to edge, and nest height had a dominant influence on daily nest survival, with area being positively related to nest survival and distance of nest to edge and nest height being both positively and negatively associated with daily nest survival. Our results indicate that multiple environmental factors contribute to reduce nest survival within a tropical understory bird community in a fragmented landscape and that maintaining large continuous forest is important for enhancing nest survival for Afrotropical understory birds. PMID:21709237

  20. Association mapping of Septoria speckled leaf blotch resistance in U.S. barley breeding germplasm.

    PubMed

    Zhou, Hao; Steffenson, Brian J

    2013-06-01

    Septoria speckled leaf blotch (SSLB) is a sporadic but important disease of barley (Hordeum vulgare) in the Upper Midwest region of the United States and Prairie Provinces of Canada that is caused primarily by Septoria passerinii. Most of the widely grown cultivars in the region are susceptible to the disease. To identify and map SSLB resistance loci in U.S. barley breeding germplasm, we employed an association mapping approach using 3,840 breeding lines and cultivars and nearly 3,000 single-nucleotide polymorphism markers previously mapped to the seven barley chromosomes. SSLB infection responses (IRs) were assayed on seedling plants in the greenhouse using a 0-to-5 scale. From the analysis of four yearly panels consisting of 960 lines each, four quantitative trait loci (QTL) for SSLB resistance were identified: one on chromosome 1H (Rsp-qtl-H_12_31144), one on chromosome 3H (Rsp-qtl-3H_12_31488), and two on chromosome 6H (Rsp-qtl-6H_11_21032 and Rsp-qtl-6H_11_10064). Individual resistance QTL reduced the mean IR from 9 to 38% compared with lines lacking any resistance alleles. However, the combination of all four resistance QTL together reduced the mean IR by 83%. The markers found associated with these QTL will be valuable for programs utilizing marker-assisted selection for SSLB resistance.

  1. International association for the study of lung cancer (IASLC) lymph node map: radiologic review with CT illustration.

    PubMed

    El-Sherief, Ahmed H; Lau, Charles T; Wu, Carol C; Drake, Richard L; Abbott, Gerald F; Rice, Thomas W

    2014-10-01

    Accurate clinical or pretreatment stage classification of lung cancer leads to optimal treatment outcomes and improved prognostication. Such classification requires an accurate assessment of the clinical extent of regional lymph node metastasis. Consistent and reproducible regional lymph node designations facilitate reliable assessment of the clinical extent of regional lymph node metastasis. Regional lymph node maps, such as the Naruke lymph node map and the Mountain-Dresler modification of the American Thoracic Society lymph node map, were proposed for this purpose in the past. The most recent regional lymph node map to be published is the International Association for the Study of Lung Cancer (IASLC) lymph node map. The IASLC lymph node map supersedes all previous maps and should be used in tandem with the current seventh edition of the tumor, node, metastasis stage classification for lung cancer.

  2. Predators of Greater Sage-Grouse nests identified by video monitoring

    USGS Publications Warehouse

    Coates, P.S.; Connelly, J.W.; Delehanty, D.J.

    2008-01-01

    Nest predation is the primary cause of nest failure for Greater Sage-Grouse (Centrocercus urophasianus), but the identity of their nest predators is often uncertain. Confirming the identity of these predators may be useful in enhancing management strategies designed to increase nest success. From 2002 to 2005, we monitored 87 Greater Sage-Grouse nests (camera, N = 55; no camera, N = 32) in northeastern Nevada and south-central Idaho and identified predators at 17 nests, with Common Ravens (Corvus corax) preying on eggs at 10 nests and American badgers (Taxidea taxis) at seven. Rodents were frequently observed at grouse nests, but did not prey on grouse eggs. Because sign left by ravens and badgers was often indistinguishable following nest predation, identifying nest predators based on egg removal, the presence of egg shells, or other sign was not possible. Most predation occurred when females were on nests. Active nest defense by grouse was rare and always unsuccessful. Continuous video monitoring of Sage-Grouse nests permitted unambiguous identification of nest predators. Additional monitoring studies could help improve our understanding of the causes of Sage-Grouse nest failure in the face of land-use changes in the Intermountain West. ?? 2008 Association of Field Ornithologists.

  3. Association mapping of seedling resistance to spot form net blotch in a worldwide collection of barley.

    PubMed

    Tamang, Prabin; Neupane, Anjan; Mamidi, Sujan; Friesen, Timothy; Brueggeman, Robert

    2015-04-01

    Spot form net blotch (SFNB), caused by the necrotrophic fungal pathogen Pyrenophora teres f. maculata, is an important foliar disease of barley in major production regions around the world. Deployment of adequate host resistance is challenging because the virulence of P. teres f. maculata is highly variable and characterized minor-effect resistances are typically ineffective against the diverse pathogen populations. A world barley core collection consisting of 2,062 barley accessions of diverse origin and genotype were phenotyped at the seedling stage with four P. teres f. maculata isolates collected from the United States (FGO), New Zealand (NZKF2), Australia (SG1), and Denmark (DEN 2.6). Of the 2,062 barley accessions phenotyped, 1,480 were genotyped with the Illumina barley iSelect chip and passed the quality controls with 5,954 polymorphic markers used for further association mapping analysis. Genome-wide association mapping was utilized to identify and map resistance loci from the seedling disease response data and the single nucleotide polymorphism (SNP) marker data. The best among six different regression models was identified for each isolate and association analysis was performed separately for each. A total of 138 significant (-log10P value>3.0) marker-trait associations (MTA) were detected. Using a 5 cM cutoff, a total of 10, 8, 13, and 10 quantitative trait loci (QTL) associated with SFNB resistance were identified for the FGO, SG1, NZKF2, and DEN 2.6 isolates, respectively. Loci containing from 1 to 34 MTA were identified on all seven barley chromosomes with one locus at 66 to 69 cM on chromosome 2H common to all four isolates. Six distinct loci were identified by the association mapping (AM) analysis that corresponded to previously characterized SFNB resistance QTL identified by biparental population analysis (QRpt4, QRpt6, Rpt4, Rpt6, Rpt7, and a QTL on 4H that was not given a provisional gene or QTL nomenclature). The 21 putative novel loci

  4. Molecular diversity and association mapping of fiber quality traits in exotic G. hirsutum L. germplasm.

    PubMed

    Abdurakhmonov, I Y; Kohel, R J; Yu, J Z; Pepper, A E; Abdullaev, A A; Kushanov, F N; Salakhutdinov, I B; Buriev, Z T; Saha, S; Scheffler, B E; Jenkins, J N; Abdukarimov, A

    2008-12-01

    The narrow genetic base of cultivated cotton germplasm is hindering the cotton productivity worldwide. Although potential genetic diversity exists in Gossypium genus, it is largely 'underutilized' due to photoperiodism and the lack of innovative tools to overcome such challenges. The application of linkage disequilibrium (LD)-based association mapping is an alternative powerful molecular tool to dissect and exploit the natural genetic diversity conserved within cotton germplasm collections, greatly accelerating still 'lagging' cotton marker-assisted selection (MAS) programs. However, the extent of genome-wide linkage disequilibrium (LD) has not been determined in cotton. We report the extent of genome-wide LD and association mapping of fiber quality traits by using a 95 core set of microsatellite markers in a total of 285 exotic Gossypium hirsutum accessions, comprising of 208 landrace stocks and 77 photoperiodic variety accessions. We demonstrated the existence of useful genetic diversity within exotic cotton germplasm. In this germplasm set, 11-12% of SSR loci pairs revealed a significant LD. At the significance threshold (r(2)>/=0.1), a genome-wide average of LD declines within the genetic distance at <10 cM in the landrace stocks germplasm and >30 cM in variety germplasm. Genome wide LD at r(2)>/=0.2 was reduced on average to approximately 1-2 cM in the landrace stock germplasm and 6-8 cM in variety germplasm, providing evidence of the potential for association mapping of agronomically important traits in cotton. We observed significant population structure and relatedness in assayed germplasm. Consequently, the application of the mixed liner model (MLM), considering both kinship (K) and population structure (Q) detected between 6% and 13% of SSR markers associated with the main fiber quality traits in cotton. Our results highlight for the first time the feasibility and potential of association mapping, with consideration of the population structure and

  5. Diversity, differentiation, and linkage disequilibrium: prospects for association mapping in the malaria vector Anopheles arabiensis.

    PubMed

    Marsden, Clare Diana; Lee, Yoosook; Kreppel, Katharina; Weakley, Allison; Cornel, Anthony; Ferguson, Heather M; Eskin, Eleazar; Lanzaro, Gregory C

    2014-01-10

    Association mapping is a widely applied method for elucidating the genetic basis of phenotypic traits. However, factors such as linkage disequilibrium and levels of genetic diversity influence the power and resolution of this approach. Moreover, the presence of population subdivision among samples can result in spurious associations if not accounted for. As such, it is useful to have a detailed understanding of these factors before conducting association mapping experiments. Here we conducted whole-genome sequencing on 24 specimens of the malaria mosquito vector, Anopheles arabiensis, to further understanding of patterns of genetic diversity, population subdivision and linkage disequilibrium in this species. We found high levels of genetic diversity within the An. arabiensis genome, with ~800,000 high-confidence, single- nucleotide polymorphisms detected. However, levels of nucleotide diversity varied significantly both within and between chromosomes. We observed lower diversity on the X chromosome, within some inversions, and near centromeres. Population structure was absent at the local scale (Kilombero Valley, Tanzania) but detected between distant populations (Cameroon vs. Tanzania) where differentiation was largely restricted to certain autosomal chromosomal inversions such as 2Rb. Overall, linkage disequilibrium within An. arabiensis decayed very rapidly (within 200 bp) across all chromosomes. However, elevated linkage disequilibrium was observed within some inversions, suggesting that recombination is reduced in those regions. The overall low levels of linkage disequilibrium suggests that association studies in this taxon will be very challenging for all but variants of large effect, and will require large sample sizes.

  6. Association mapping of caffeine content with TCS1 in tea plant and its related species.

    PubMed

    Jin, Ji-Qiang; Yao, Ming-Zhe; Ma, Chun-Lei; Ma, Jian-Qiang; Chen, Liang

    2016-08-01

    Caffeine is the most abundant purine alkaloid in majority of tea plant and its related species. This purine alkaloid contributes to the important flavor and health attributes of tea. Tea caffeine synthase 1 (TCS1, EC 2.1.1.159/2.1.1.160) gene plays a crucial role in caffeine biosynthesis. The objective of this study was to investigate the genetic relationship between the TCS1 and caffeine content of tea plant and its related species using association mapping. We identified 87 single-nucleotide polymorphisms (SNPs, π = 0.00447) by resequencing the TCS1 locus of 44 tea accessions. Linkage disequilibrium (LD) analysis showed that LD did not extend over the entire gene (r(2) < 0.1, within 1000 bp). Two cleaved amplified polymorphism sequence (CAPS) markers were developed from sequence variations (SNP4318 and SNP6252). By association mapping, we identified SNP4318 associated with caffeine content in four environments, explaining 4.0%-7.7% of the phenotypic variance. We also validated the significant marker-trait associations in site-directed mutagenesis experiments. Examination of allelic variation and linkage disequilibrium by a candidate-gene-based approach can help to decipher the genetic basis of caffeine biosynthesis. Moreover, the SNP marker identified in this study can potentially be applied for future marker-assisted selection to improve tea quality.

  7. Equivalence of three score tests for association mapping of quantitative trait loci under selective genotyping.

    PubMed

    Tang, Yongqiang

    2010-07-01

    Huang and Lin ([2007] Am J Hum Genet 80:567-572) proposed a conditional-likelihood approach for mapping quantitative trait loci (QTL) under selective genotyping, and demonstrated via simulation that their model tends to be more powerful than the prospective linear regression. However, we show that the three score tests based on the conditional, prospective and retrospective likelihoods are numerically identical in testing association between a quantitative trait and a candidate locus. Two approximations are derived for calculating power and sample size for the score test. Compared to the random sampling, a single-tail selection generally reduces the power of the score test in mapping small effect QTLs. A two-tail selection generally enhances the QTL heritability; however, in small samples, the power of the test may actually decrease if the sample sizes are highly unbalanced in the upper and lower tails of the trait distribution. PMID:20552655

  8. Amyotrophic Lateral Sclerosis Genetic Studies: From Genome-wide Association Mapping to Genome Sequencing.

    PubMed

    He, Ji; Mangelsdorf, Marie; Fan, Dongsheng; Bartlett, Perry; Brown, Matthew A

    2015-12-01

    Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease of obscure etiology. Multiple genetic studies have been conducted to advance our understanding of the disease, employing a variety of techniques such as linkage mapping in families, to genome-wide association studies and sequencing based approaches such as whole exome sequencing and whole genome sequencing and a few epigenetic analyses. While major progress has been made, the majority of the genetic variation involved in ALS is yet to be undefined. The optimal study designs to investigate ALS depend on the genetic model for the disease, and it is likely that different approaches will be required to map genes involved in familial and sporadic disease. The potential approaches and their strengths and weaknesses are discussed.

  9. Association Mapping for Fiber-Related Traits and Digestibility in Alfalfa (Medicago sativa)

    PubMed Central

    Wang, Zan; Qiang, Haiping; Zhao, Haiming; Xu, Ruixuan; Zhang, Zhengli; Gao, Hongwen; Wang, Xuemin; Liu, Guibo; Zhang, Yingjun

    2016-01-01

    Association mapping is a powerful approach for exploring the molecular genetic basis of complex quantitative traits. An alfalfa (Medicago sativa) association panel comprised of 336 genotypes from 75 alfalfa accessions represented by four to eight genotypes for each accession. Each genotype was genotyped using 85 simple sequence repeat (SSR) markers and phenotyped for five fiber-related traits in four different environments. A model-based structure analysis was used to group all genotypes into two groups. Most of the genotypes have a low relative kinship (<0.3), suggesting population stratification not be an issue for association analysis. Generally, the Q + K model exhibited the best performance to eliminate the false associated positives. In total, 124 marker-trait associations were predicted (p < 0.005). Among these, eight associations were predicted in two environments repeatedly and 20 markers were predicted to be associated with multiple traits. These trait-associated markers will greatly help marker-assisted breeding programs to improve fiber-related quality traits in alfalfa. PMID:27047512

  10. Mapping of QTL Associated with Waterlogging Tolerance during the Seedling Stage in Maize

    PubMed Central

    Qiu, Fazhan; Zheng, Yonglian; Zhang, Zili; Xu, Shangzhong

    2007-01-01

    Background and Aims Soil waterlogging is a major environmental stress that suppresses maize (Zea mays) growth and yield. To identify quantitative trait loci (QTL) associated with waterlogging tolerance at the maize seedling stage, a F2 population consisting of 288 F2:3 lines was created from a cross between two maize genotypes, ‘HZ32’ (waterlogging-tolerant) and ‘K12’ (waterlogging-sensitive). Methods The F2 population was genotyped and a base-map of 1710·5 cM length was constructed with an average marker space of 11·5 cM based on 177 SSR (simple sequence repeat) markers. QTL associated with root length, root dry weight, plant height, shoot dry weight, total dry weight and waterlogging tolerance coefficient were identified via composite interval mapping (CIM) under waterlogging and control conditions in 2004 (EXP.1) and 2005 (EXP.2), respectively. Key Results and Conclusions Twenty-five and thirty-four QTL were detected in EXP.1 and EXP.2, respectively. The effects of each QTL were moderate, ranging from 3·9 to 37·3 %. Several major QTL determining shoot dry weight, root dry weight, total dry weight, plant height and their waterlogging tolerance coefficient each mapped on chromosomes 4 and 9. These QTL were detected consistently in both experiments. Secondary QTL influencing tolerance were also identified and located on chromosomes 1, 2, 3, 6, 7 and 10. These QTL were specific to particular traits or environments. Although the detected regions need to be mapped more precisely, the findings and QTL found in this study may provide useful information for marker-assisted selection (MAS) and further genetic studies on maize waterlogging tolerance. PMID:17470902

  11. MAPping the eukaryotic tree of life: structure, function, and evolution of the MAP215/Dis1 family of microtubule-associated proteins.

    PubMed

    Gard, David L; Becker, Bret E; Josh Romney, S

    2004-01-01

    The MAP215/Dis1 family of proteins is an evolutionarily ancient family of microtubule-associated proteins, with characterized members in all major kingdoms of eukaryotes, including fungi (Stu2 in S. cerevisiae, Dis1 and Alp14 in S. pombe), Dictyostelium (DdCP224), plants (Mor1 in A. thaliana and TMBP200 in N. tabaccum), and animals (Zyg9 in C. elegans, Msps in Drosophila, XMAP215 in Xenopus, and ch-TOG in humans). All MAP215/Dis1 proteins (with the exception of those in plants) localize to microtubule-organizing centers (MTOCs), including spindle pole bodies in yeast and centrosomes in animals, and all bind to microtubules in vitro and?or in vivo. Diverse roles in regulating microtubule assembly and organization have been proposed for individual family members, and a substantial body of evidence suggests that MAP215/Dis1-related proteins play critical roles in the assembly and function of the meiotic/mitotic spindles and/or cell division. An extensive search of public databases (including both EST and genome databases) identified partial sequences predicted to encode more than three dozen new members of the MAP215/Dis1 family, including putative MAP215/Dis1-related proteins in Giardia lamblia and four other protists, sixteen additional species of fungi, six plants, and twelve animals. The structure and function of MAP215/Dis1 proteins are discussed in relation to the evolution of this ancient family of microtubule-associated proteins.

  12. Inflatable nested toroid structure

    NASA Technical Reports Server (NTRS)

    Johnson, Christopher J. (Inventor); Raboin, Jasen L. (Inventor); Spexarth, Gary R. (Inventor)

    2011-01-01

    An inflatable structure comprises at least two generally toroidal, inflatable modules. When in a deployed mode, the first, inner module has a major diameter less than that of a second, outer module and is positioned within the inner circumference of the outer module such that the first module is nested circumferentially alongside the second module. The inflatable structure, in a non-deployed, non-inflated mode, is of compact configuration and adapted to be transported to a site of deployment. When deployed, the inflatable structure is of substantially increased interior volume. In one embodiment, access between the interior of the first module and the second module is provided by at least one port or structural pass-through. In another embodiment, the inflatable structure includes at least one additional generally toroidal module external of and circumferentially surrounding the second module.

  13. Using a Concept Mapping Tool with a Photograph Association Technique (CoMPAT) to Elicit Children's Ideas about Microbial Activity

    ERIC Educational Resources Information Center

    Byrne, Jenny; Grace, Marcus

    2010-01-01

    Concept mapping is a technique used to provide a visual representation of an individual's ideas about a concept or set of related concepts. This paper describes a concept mapping tool using a photograph association technique (CoMPAT) that is considered to be a novel way of eliciting children's ideas. What children at 11 years of age know about…

  14. Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa

    PubMed Central

    Zhao, Keyan; Tung, Chih-Wei; Eizenga, Georgia C.; Wright, Mark H.; Ali, M. Liakat; Price, Adam H.; Norton, Gareth J.; Islam, M. Rafiqul; Reynolds, Andy; Mezey, Jason; McClung, Anna M.; Bustamante, Carlos D.; McCouch, Susan R.

    2011-01-01

    Asian rice, Oryza sativa is a cultivated, inbreeding species that feeds over half of the world's population. Understanding the genetic basis of diverse physiological, developmental, and morphological traits provides the basis for improving yield, quality and sustainability of rice. Here we show the results of a genome-wide association study based on genotyping 44,100 SNP variants across 413 diverse accessions of O. sativa collected from 82 countries that were systematically phenotyped for 34 traits. Using cross-population-based mapping strategies, we identified dozens of common variants influencing numerous complex traits. Significant heterogeneity was observed in the genetic architecture associated with subpopulation structure and response to environment. This work establishes an open-source translational research platform for genome-wide association studies in rice that directly links molecular variation in genes and metabolic pathways with the germplasm resources needed to accelerate varietal development and crop improvement. PMID:21915109

  15. Developing Association Mapping in Polyploid Perennial Biofuel Grasses: Final Technical Report

    SciTech Connect

    Buckler, Edward S; Casler, Michael D; Cherney, Jerome H

    2012-01-20

    This project had six objectives, four of which have been completed: 1) Association panels of diverse populations and linkage populations for switchgrass and reed canarygrass (~1,000 clones each) were assembled and planted in two sites (Ithaca, NY and Arlington, WI); 2) Key biofeedstock characteristics were evaluated in these panels for three field seasons; 3) High density SNP markers were developed in switchgrass; and 4) Switchgrass association panels and linkage populations were genotyped. The remaining two original objectives will be met in the next year, as the analyses are completed and papers published: 5) Switchgrass population structure and germplasm diversity will be evaluated; and 6) Association mapping will be established and marker based breeding values estimated in switchgrass. We also completed a study of the chromosome-number variation found in switchgrass.

  16. Association mapping of genetic risk factors for chronic wasting disease in wild deer

    USGS Publications Warehouse

    Tomomi Matsumoto,; Samuel, Michael D.; Trent Bollinger,; Margo Pybus,; David W. Coltman,

    2013-01-01

    Chronic wasting disease (CWD) is a fatal transmissible spongiform encephalopathy affecting North American cervids. We assessed the feasibility of association mapping CWD genetic risk factors in wild white-tailed deer (Odocoileus virginianus) and mule deer (Odocoileus hemionus) using a panel of bovine microsatellite markers from three homologous deer linkage groups predicted to contain candidate genes. These markers had a low cross-species amplification rate (27.9%) and showed weak linkage disequilibrium (<1 cM). Markers near the prion protein and the neurofibromin 1 (NF1) genes were suggestively associated with CWD status in white-tailed deer (P = 0.006) and mule deer (P = 0.02), respectively. This is the first time an association between the NF1 region and CWD has been reported.

  17. Association mapping of genetic risk factors for chronic wasting disease in wild deer.

    PubMed

    Matsumoto, Tomomi; Samuel, Michael D; Bollinger, Trent; Pybus, Margo; Coltman, David W

    2013-02-01

    Chronic wasting disease (CWD) is a fatal transmissible spongiform encephalopathy affecting North American cervids. We assessed the feasibility of association mapping CWD genetic risk factors in wild white-tailed deer (Odocoileus virginianus) and mule deer (Odocoileus hemionus) using a panel of bovine microsatellite markers from three homologous deer linkage groups predicted to contain candidate genes. These markers had a low cross-species amplification rate (27.9%) and showed weak linkage disequilibrium (<1 cM). Markers near the prion protein and the neurofibromin 1 (NF1) genes were suggestively associated with CWD status in white-tailed deer (P = 0.006) and mule deer (P = 0.02), respectively. This is the first time an association between the NF1 region and CWD has been reported.

  18. Replication and fine mapping of asthma-associated loci in individuals of African ancestry.

    PubMed

    Kantor, David B; Palmer, Cameron D; Young, Taylor R; Meng, Yan; Gajdos, Zofia K; Lyon, Helen; Price, Alkes L; Pollack, Samuela; London, Stephanie J; Loehr, Laura R; Smith, Lewis J; Kumar, Rajesh; Jacobs, David R; Petrini, Marcy F; O'Connor, George T; White, Wendy B; Papanicolaou, George; Burkart, Kristin M; Heckbert, Susan R; Barr, R Graham; Hirschhorn, Joel N

    2013-09-01

    Asthma originates from genetic and environmental factors with about half the risk of disease attributable to heritable causes. Genome-wide association studies, mostly in populations of European ancestry, have identified numerous asthma-associated single nucleotide polymorphisms (SNPs). Studies in populations with diverse ancestries allow both for identification of robust associations that replicate across ethnic groups and for improved resolution of associated loci due to different patterns of linkage disequilibrium between ethnic groups. Here we report on an analysis of 745 African-American subjects with asthma and 3,238 African-American control subjects from the Candidate Gene Association Resource (CARe) Consortium, including analysis of SNPs imputed using 1,000 Genomes reference panels and adjustment for local ancestry. We show strong evidence that variation near RAD50/IL13, implicated in studies of European ancestry individuals, replicates in individuals largely of African ancestry. Fine mapping in African ancestry populations also refined the variants of interest for this association. We also provide strong or nominal evidence of replication at loci near ORMDL3/GSDMB, IL1RL1/IL18R1, and 10p14, all previously associated with asthma in European or Japanese populations, but not at the PYHIN1 locus previously reported in studies of African-American samples. These results improve the understanding of asthma genetics and further demonstrate the utility of genetic studies in populations other than those of largely European ancestry.

  19. Using Artificial Nests to Study Nest Predation in Birds

    ERIC Educational Resources Information Center

    Belthoff, James R.

    2005-01-01

    A simple and effective field exercise that demonstrates factors affecting predation on bird nests is described. With instructor guidance, students in high school biology or college-level biology, ecology, animal behavior, wildlife management or ornithology laboratory courses can collaborate to design field experiments related to nest depredation.

  20. Nesting habitat of the Tule Greater White-fronted Goose Anser albifrons elgasi

    USGS Publications Warehouse

    Densmore, R.V.; Ely, C.R.; Bollinger, K.S.; Kratzer, S.; Udevitz, M.S.; Fehringer, D.J.; Rothe, T.C.

    2006-01-01

    This paper presents the first information on the availability and use of nesting habitat by the rare Tule Greater White-fronted Goose Anser albifrons elgasi. The breeding range was sampled by marking geese with radio transmitters on wintering and moulting areas, and tracking them to nest sites in Alaska. Nesting habitat was described at the scales of ecoregion, wetland ecosystem (National Wetlands Inventory (NWI) maps), vegetation type within wetland (Alaska Vegetation Classification (AVC) maps based on satellite imagery), and nest site. Tule Greater White-fronted Goose nests were located in boreal forest wetlands in the upper Cook Inlet Basin ecoregion. Nesting Tule Greater White-fronted Geese selected NWT Palustrine Seasonally Flooded wetlands and used NWI Palustrine Saturated wetlands in proportion to availability. Within these wetlands, Tule Greater White-fronted Geese used Needleleaf Forest, Low Shrub and Herbaceous (mostly graminoid) AVC classes for nest sites in proportion to availability Most (93%) Tule Greater White-fronted Geese nested > 75 m from open water ponds or lakes, and many nested in wetlands with little or no open water. Tule Greater White-fronted Geese nest only in a small breeding area near the most human-impacted area of the state, and continued development may limit the use of suitable nesting habitat.

  1. Pregnancy Associated Plasma Protein-A and Placental Growth Factor in a Sub-Saharan African Population: A Nested Cross-Sectional Study

    PubMed Central

    Klipstein-Grobusch, Kerstin; Koster, Maria P. H.; Ramamoorthy, Dhivya; Antwi, Edward; Belmouden, Idder; Franx, Arie; Grobbee, Diederick E.; Schielen, Peter C. J. I.

    2016-01-01

    Background Baseline distributions of pregnancy disorders’ biomarkers PlGF and PAPP-A levels are primarily based on Western European populations of Caucasian ethnicity. Differences in PAPP-A and PlGF concentrations by ethnicity have been observed, with increased levels in Afro-Caribbean, East Asian, and South Asian women. Baseline concentrations of sub-Saharan African women have not been evaluated. Objectives To investigate PlGF and PAPP-A in a sub-Saharan African population and assess the performance of existing reference values of PAPP-A and PlGF. Methods A nested cross-sectional study was conducted in two public hospitals in Accra, Ghana. Out of the original 1010 women enrolled in the cohort, 398 participants were eligible for inclusion with a normotensive singleton gestation and serum samples taken between 56–97 days of pregnancy. PAPP-A and PlGF concentrations were measured with an automated immunoassay. Multiple of the median (MoM) values corrected for gestation and maternal weight for PAPP-A and PlGF were calculated using reference values of a Dutch perinatal screening laboratory based on over 10.000 samples, and PlGF manufacturer reference values, respectively. Results The PAPP-A median MoM was 2.34 (interquartile range (IQR) 1.24–3.97). Median PlGF MoM was 1.25 (IQR 0.95–1.80). Median MoM values for PAPP-A and PlGF tended to be slightly different for various Ghanaian ethnic subgroups. Conclusions PAPP-A and PlGF MoM values appear to be substantially higher in a sub-Saharan African population compared to the Caucasian or Afro-Caribbean MoM values previously reported. The difference suggests the need for a specific correction factor for this population to avoid underestimation of risk for fetal aneuploidies or placental disorders when using PAPP-A and PlGF MoM for screening purposes. PMID:27532602

  2. Genomewide association study of opioid dependence: multiple associations mapped to calcium and potassium pathways

    PubMed Central

    Gelernter, Joel; Kranzler, Henry R.; Sherva, Richard; Koesterer, Ryan; Almasy, Laura; Zhao, Hongyu; Farrer, Lindsay A.

    2013-01-01

    Background We report a GWAS of two populations, African- and European-American (AA, EA) for opioid dependence (OD) in three sets of subjects, to identify pathways, genes, and alleles important in OD risk. Methods Design employed three phases (based on separate sample collections). Phase 1 included our discovery GWAS dataset consisting of 5,697 subjects (58% AA) diagnosed with opioid and/or other substance dependence (SD), and controls. Subjects were genotyped using the Illumina OmniQuad microarray, yielding 890,000 SNPs suitable for analysis. Additional genotypes were imputed using the 1000 Genomes reference panel. Top-ranked findings were further evaluated in Phase 2 by incorporating information from the publicly available SAGE dataset, with GWAS data from 4,063 subjects (32% AA). In Phase 3, the most significant SNPs from Phase 2 were genotyped in 2,549 independent subjects (32% AA). Analyses were performed using case-control and ordinal trait designs. Results Most significant results emerged from the AA subgroup. Genomewide-significant associations (p<5.0×10−8) were observed with SNPs from multiple loci - KCNC1*rs60349741 most significant after combining results from datasets in every phase of the study. The most compelling results were obtained with genes involved in potassium signaling pathways (e.g., KCNC1, KCNG2, and KCNA4). Pathway analysis also implicated genes involved in calcium signaling and long-term potentiation. Conclusions This is the first study to identify risk variants for OD using GWAS. Our results strongly implicate risk pathways, provide insights into novel therapeutic and prevention strategies, and may provide biologically bridge OD and other non-SD psychiatric traits where similar pathways have been implicated. PMID:24143882

  3. Does nonrandom nest placement imply nonrandom nest predation? - A reply

    USGS Publications Warehouse

    Cooper, R.J.; Wilson, R.R.; Zenitsky, G.D.; Mullin, S.J.; Dececco, J.D.; Marshall, M.R.; Wolf, D.J.; Pomara, L.Y.

    1999-01-01

    In response to the critique by Schmidt and Whelan (Condor 101(4):916-920, 1999), we find that the relationship between nest success and tree selectivity is dependent upon inclusion or exclusion of particular tree species, whether or not years are pooled, and the selectivity index used. We question their use of point estimates of nest success with extremely high variances, defend our index, question the application of the Chesson (1983) index to our data, and explain the need to analyze years separately. Bottomland hardwood forest systems are extremely variable; hydroperiods alter the suitability of nesting substrates, availability of alternative food, and behavior of predators and their prey. Given these features, actively searching for Acadian Flycatcher (Empidonax virescens) nests is seldom an efficient predator foraging strategy. Therefore, these predation events are best described as random; nests are principally encountered opportunistically by generalist predators while searching for other prey.

  4. Sharp wave/ripple network oscillations and learning-associated hippocampal maps.

    PubMed

    Csicsvari, Jozsef; Dupret, David

    2014-02-01

    Sharp wave/ripple (SWR, 150-250 Hz) hippocampal events have long been postulated to be involved in memory consolidation. However, more recent work has investigated SWRs that occur during active waking behaviour: findings that suggest that SWRs may also play a role in cell assembly strengthening or spatial working memory. Do such theories of SWR function apply to animal learning? This review discusses how general theories linking SWRs to memory-related function may explain circuit mechanisms related to rodent spatial learning and to the associated stabilization of new cognitive maps.

  5. Case study: Mapping tsunami hazards associated with debris flow into a reservoir

    USGS Publications Warehouse

    Walder, J.S.; Watts, P.; Waythomas, C.F.

    2006-01-01

    Debris-flow generated impulse waves (tsunamis) pose hazards in lakes, especially those used for hydropower or recreation. We describe a method for assessing tsunami-related hazards for the case in which inundation by coherent water waves, rather than chaotic splashing, is of primary concern. The method involves an experimentally based initial condition (tsunami source) and a Boussinesq model for tsunami propagation and inundation. Model results are used to create hazard maps that offer guidance for emergency planners and responders. An example application explores tsunami hazards associated with potential debris flows entering Baker Lake, a reservoir on the flanks of the Mount Baker volcano in the northwestern United States. ?? 2006 ASCE.

  6. Generation of large-scale maps of science and associated indicators.

    SciTech Connect

    Klavans, Richard; Boyack, Kevin W.

    2005-12-01

    Over the past several years, techniques have been developed for clustering very large segments of the technical literature using sources such as Thomson ISI's Science Citation Index. The primary objective of this work has been to develop indicators of potential impact at the paper level to enhance planning and evaluation of research. These indicators can also be aggregated at different levels to enable profiling of departments, institutions, agencies, etc. Results of this work are presented as maps of science and technology with various overlays corresponding to the indicators associated with a particular search or question.

  7. Population structure analysis and association mapping of blast resistance in indica rice (Oryza sativa L.) landraces.

    PubMed

    Wu, Y Y; He, J B; Li, A H; Fang, N Y; He, W W; Dang, L L; Zeng, G Y; Huang, J; Bao, Y M; Zhang, H S

    2016-08-12

    Rice blast caused by Magnaporthe oryzae is one of the most devastating rice diseases worldwide. To understand the genetic diversity of indica landrace accessions and identify simple sequence repeat (SSR) markers that are associated with blast resistance, a population of 276 indica landraces from across the world was constructed. This population was then used to evaluate the blast-resistance phenotype through artificial inoculation under controlled conditions in 2012 and 2013. The genetic diversity and association of the population with resistance were analyzed by examining the phenotype for 160 SSR markers distributed on 12 rice chromosomes. The 276 accessions were classified into seven groups using model- and distance-based cluster analyses. Associations between SSR markers and blast resistance showed that 26 SSR markers were significantly associated with blast resistance in 2012 and 2013 (P < 0.01) and that the phenotypic variation ranged from 2.68 to 13.11%. Nineteen of the markers associated with blast resistance were located in regions where genes or quantitative trait loci (QTLs) have been previously reported, and seven were newly identified in this study. These results indicate that marker-trait association has potential advantages over classical linkage analysis and QTL mapping, and that these markers could be used for marker-assisted selection in rice blast-resistance-breeding programs.

  8. Population structure analysis and association mapping of blast resistance in indica rice (Oryza sativa L.) landraces.

    PubMed

    Wu, Y Y; He, J B; Li, A H; Fang, N Y; He, W W; Dang, L L; Zeng, G Y; Huang, J; Bao, Y M; Zhang, H S

    2016-01-01

    Rice blast caused by Magnaporthe oryzae is one of the most devastating rice diseases worldwide. To understand the genetic diversity of indica landrace accessions and identify simple sequence repeat (SSR) markers that are associated with blast resistance, a population of 276 indica landraces from across the world was constructed. This population was then used to evaluate the blast-resistance phenotype through artificial inoculation under controlled conditions in 2012 and 2013. The genetic diversity and association of the population with resistance were analyzed by examining the phenotype for 160 SSR markers distributed on 12 rice chromosomes. The 276 accessions were classified into seven groups using model- and distance-based cluster analyses. Associations between SSR markers and blast resistance showed that 26 SSR markers were significantly associated with blast resistance in 2012 and 2013 (P < 0.01) and that the phenotypic variation ranged from 2.68 to 13.11%. Nineteen of the markers associated with blast resistance were located in regions where genes or quantitative trait loci (QTLs) have been previously reported, and seven were newly identified in this study. These results indicate that marker-trait association has potential advantages over classical linkage analysis and QTL mapping, and that these markers could be used for marker-assisted selection in rice blast-resistance-breeding programs. PMID:27525942

  9. Hyperspectral Mapping of Iron-bearing Minerals Associated with Dry and Ephemeral Lakes

    NASA Astrophysics Data System (ADS)

    Farrand, W. H.; Bowen, B. B.

    2014-12-01

    This research project is utilizing data from the Hyperspectral Imager for the Coastal Ocean (HICO) on the International Space Station (ISS) to examine a set of playas and ephemeral lakes in Australia and in the southwestern United States. HICO collects hyperspectral data from 0.35 to 1.08 μm thus excluding the SWIR vibrational overtone region of clays and carbonates. We are assessing the utility of HICO for detecting iron-bearing minerals and materials associated with playas and mapping their fractional abundance outside of the playa boundaries. Sites being investigated include the clastics-dominated Railroad Valley and Lunar Lake playas of Nevada, the evaporite-dominated Bonneville Salt Flats, and the acid-saline Lake Tyrrell of northwest Victoria, Australia. HICO, and supporting airborne hyperspectral datasets (AVIRIS and HyMap), are being converted from at-sensor radiance to surface reflectance using the FLAASH radiance transfer-based atmospheric correction software. Fe-bearing minerals and materials are determined through a standardized endmember detection approach using the commercial ENVI software and mapped using a variety of approaches including linear spectral mixture analysis, constrained energy minimization, and spectral feature fitting. Interpretations of remote data are guided by field-based observations and mapping. We are using the remote sensing data to assess the surface state of the playa (wet vs. dry, soft vs. hard). These factors have bearing in that dusts stripped from playa surfaces can affect nearby human communities and agricultural fields. Playas are also used for recreation and sometimes as transportation corridors and their physical state has important bearing for those functions. Assessing the types of minerals present has relevance for their impact as wind-entrained particulates that could have adverse effects on the health of humans, crops, or livestock.

  10. Observations on the nesting biology of Andrena (Plastandrena) prunorum Cockerell in Washington State (Hymenoptera: Andrenidae)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Nesting and associated behaviors of Andrena (Plastandrena) prunorum Cockerell were studied at two sites in western Washington: a suburban lawn and a vacant lot. A maximum of five nests, usually well separated from one another, was found at a given site and year. Nest and cell structure at both sites...

  11. Genome-wide association mapping of acute lung injury in neonatal inbred mice

    PubMed Central

    Nichols, Jennifer L.; Gladwell, Wesley; Verhein, Kirsten C.; Cho, Hye-Youn; Wess, Jürgen; Suzuki, Oscar; Wiltshire, Tim; Kleeberger, Steven R.

    2014-01-01

    Reactive oxygen species (ROS) contribute to the pathogenesis of many acute and chronic pulmonary disorders, including bronchopulmonary dysplasia (BPD), a respiratory condition that affects preterm infants. However, the mechanisms of susceptibility to oxidant stress in neonatal lungs are not completely understood. We evaluated the role of genetic background in response to oxidant stress in the neonatal lung by exposing mice from 36 inbred strains to hyperoxia (95% O2) for 72 h after birth. Hyperoxia-induced lung injury was evaluated by using bronchoalveolar lavage fluid (BALF) analysis and pathology. Statistically significant interstrain variation was found for BALF inflammatory cells and protein (heritability estimates range: 33.6–55.7%). Genome-wide association mapping using injury phenotypes identified quantitative trait loci (QTLs) on chromosomes 1, 2, 4, 6, and 7. Comparative mapping of the chromosome 6 QTLs identified Chrm2 (cholinergic receptor, muscarinic 2, cardiac) as a candidate susceptibility gene, and mouse strains with a nonsynonymous coding single-nucleotide polymorphism (SNP) in Chrm2 that causes an amino acid substitution (P265L) had significantly reduced hyperoxia-induced inflammation compared to strains without the SNP. Further, hyperoxia-induced lung injury was significantly reduced in neonatal mice with targeted deletion of Chrm2, relative to wild-type controls. This study has important implications for understanding the mechanisms of oxidative lung injury in neonates.—Nichols, J. L., Gladwell, W., Verhein, K. C., Cho, H.-Y., Wess, J., Suzuki, O., Wiltshire, T., Kleeberger, S. R. Genome-wide association mapping of acute lung injury in neonatal inbred mice. PMID:24571919

  12. Mourning Dove nesting habitat and nest success in Central Missouri

    USGS Publications Warehouse

    Drobney, R.D.; Schulz, J.H.; Sheriff, S.L.; Fuemmeler, W.J.

    1998-01-01

    Previous Mourning Dove (Zenaida macroura) nesting studies conducted in areas containing a mixture of edge and continuous habitats have focused on edge habitats. Consequently, little is known about the potential contribution of continuous habitats to dove production. In this study we evaluated the relative importance of these two extensive habitat types by monitoring the habitat use and nest success of 59 radio-marked doves during 1990-1991 in central Missouri. Of 83 nests initiated by our marked sample, most (81.9%) were located in edge habitats. Although continuous habitats were selected less as nest sites, the proportion of successful nests did not differ significantly from that in edge habitats. Our data indicate that continuous habitats should not be considered marginal nesting habitat. If the intensity of use and nest success that we observed are representative regionally or nationally, continuous habitats could contribute substantially to annual Mourning Dove production because of the high availability of these habitats throughout much of the Mourning Dove breeding range.

  13. GWAPP: A Web Application for Genome-Wide Association Mapping in Arabidopsis[W][OA

    PubMed Central

    Seren, Ümit; Vilhjálmsson, Bjarni J.; Horton, Matthew W.; Meng, Dazhe; Forai, Petar; Huang, Yu S.; Long, Quan; Segura, Vincent; Nordborg, Magnus

    2012-01-01

    Arabidopsis thaliana is an important model organism for understanding the genetics and molecular biology of plants. Its highly selfing nature, small size, short generation time, small genome size, and wide geographic distribution make it an ideal model organism for understanding natural variation. Genome-wide association studies (GWAS) have proven a useful technique for identifying genetic loci responsible for natural variation in A. thaliana. Previously genotyped accessions (natural inbred lines) can be grown in replicate under different conditions and phenotyped for different traits. These important features greatly simplify association mapping of traits and allow for systematic dissection of the genetics of natural variation by the entire A. thaliana community. To facilitate this, we present GWAPP, an interactive Web-based application for conducting GWAS in A. thaliana. Using an efficient implementation of a linear mixed model, traits measured for a subset of 1386 publicly available ecotypes can be uploaded and mapped with a mixed model and other methods in just a couple of minutes. GWAPP features an extensive, interactive, and user-friendly interface that includes interactive Manhattan plots and linkage disequilibrium plots. It also facilitates exploratory data analysis by implementing features such as the inclusion of candidate polymorphisms in the model as cofactors. PMID:23277364

  14. Association mapping of starch physicochemical properties with starch biosynthesizing genes in waxy rice (Oryza sativa L.).

    PubMed

    Xu, Feifei; Zhang, Gan; Tong, Chuan; Sun, Xiao; Corke, Harold; Sun, Mei; Bao, Jinsong

    2013-10-23

    Waxy (glutinous) rice is widely used in traditional foods, and understanding the genetic bases of its diverse physicochemical properties will contribute to breeding of new waxy rice with unique qualities. The objective of this study was to investigate the genetic relationship between the starch biosynthesis related genes and the physicochemical properties of waxy rice using association mapping. A total of 36 molecular markers representing 18 genes were used to genotype 50 waxy rice accessions for which starch properties were previously available. Most of the starch properties differed between high and low gelatinization temperature (GT) groups, whereas most traits were similar between the low-GT indica rice and low-GT japonica rice, suggesting GT was the main determinant of the starch quality of waxy rice. Association mapping indicated that the starch properties of waxy rice were mainly controlled by starch synthase IIa (SSIIa or SSII-3, a major gene responsible for the gelatinization temperature) and SSI. It was found that gene-gene interactions were also important for the genetic control of starch properties of waxy rice. This study suggests that application of the functional SNPs of SSIIa in molecular breeding may facilitate quality improvement of waxy rice.

  15. Identification of a 34-kD polypeptide as a light chain of microtubule- associated protein-1 (MAP-1) and its association with a MAP-1 peptide that binds to microtubules

    PubMed Central

    1986-01-01

    We examined the association of a 34-kD light chain component to the heavy chains of MAP-1 using a monoclonal antibody that specifically binds the 34-kD component and labels neuronal microtubules in a specific and saturable manner. Immunoprecipitation of MAP-1 heavy chains together with the 34-kD component by the antibody indicates that the 34-kD polypeptide forms a complex with MAP-1 heavy chains. Both major isoforms of MAP-1 heavy chains (MAP-1A and MAP-1B) were found in the immunoprecipitate. Digestion of MAP-1 with alpha-chymotrypsin and analysis of the chymotryptic peptides reveals a 120-kD fragment of the MAP-1 heavy chain that binds to microtubules and is precipitable with the 34-kD light chain antibody, suggesting that the 34-kD light chain also binds to this domain of the molecule. Since microtubules that contain the 120-kD fragment lack the long lateral projections characteristic of microtubules with intact MAP-1, the 34-kD light chains may be localized at or near the microtubule surface. PMID:3512577

  16. Nest-site selection in individual loggerhead turtles and consequences for doomed-egg relocation.

    PubMed

    Pfaller, Joseph B; Limpus, Colin J; Bjorndal, Karen A

    2009-02-01

    Relocation of eggs is a common strategy for conservation of declining reptilian populations around the world. If individuals exhibit consistency in their nest-site selection and if nest-site selection is a heritable trait, relocating eggs deposited in vulnerable locations may impose artificial selection that would maintain traits favoring unsuccessful nest-site selection. Conversely, if most individuals scatter their nesting effort and individuals that consistently select unsuccessful nest sites are uncommon, then artificial selection would be less of a concern. During the 2005 nesting season of loggerhead turtles (Caretta caretta) at Mon Repos beach, Queensland, Australia, we measured the perpendicular distance from the original nest site to a stationary dune baseline for in situ (unrelocated) and relocated clutches of eggs. We observed the fate of in situ clutches and predicted what would have been the fate of relocated clutches if they had not been moved by mapping tidal inundation and storm erosion lines. In 2005 turtles deposited an average of 3.84 nests and did not consistently select nest sites at particular distances from the stationary dune baseline. Selection of unsuccessful nest sites was distributed across the nesting population; 80.3% of the turtles selected at least one unsuccessful nest site and when previous breeding seasons were included, 97% selected at least one unsuccessful nest site. Females with nesting experience selected more successful nest sites than females with little or no experience. Relocating eggs vulnerable to tidal inundation and erosion saves the progeny from a large percentage of the population and the progeny from individuals who may in subsequent years nest successfully. Our results suggest that doomed-egg relocation does not substantially distort the gene pool in the eastern Australian loggerhead stock and should not be abandoned as a strategy for the conservation of marine turtle populations.

  17. Unraveling the Complex Trait of Harvest Index with Association Mapping in Rice (Oryza sativa L.)

    PubMed Central

    Li, Xiaobai; Yan, Wengui; Agrama, Hesham; Jia, Limeng; Jackson, Aaron; Moldenhauer, Karen; Yeater, Kathleen; McClung, Anna; Wu, Dianxing

    2012-01-01

    Harvest index is a measure of success in partitioning assimilated photosynthate. An improvement of harvest index means an increase in the economic portion of the plant. Our objective was to identify genetic markers associated with harvest index traits using 203 O. sativa accessions. The phenotyping for 14 traits was conducted in both temperate (Arkansas) and subtropical (Texas) climates and the genotyping used 154 SSRs and an indel marker. Heading, plant height and weight, and panicle length had negative correlations, while seed set and grain weight/panicle had positive correlations with harvest index across both locations. Subsequent genetic diversity and population structure analyses identified five groups in this collection, which corresponded to their geographic origins. Model comparisons revealed that different dimensions of principal components analysis (PCA) affected harvest index traits for mapping accuracy, and kinship did not help. In total, 36 markers in Arkansas and 28 markers in Texas were identified to be significantly associated with harvest index traits. Seven and two markers were consistently associated with two or more harvest index correlated traits in Arkansas and Texas, respectively. Additionally, four markers were constitutively identified at both locations, while 32 and 24 markers were identified specifically in Arkansas and Texas, respectively. Allelic analysis of four constitutive markers demonstrated that allele 253 bp of RM431 had significantly greater effect on decreasing plant height, and 390 bp of RM24011 had the greatest effect on decreasing panicle length across both locations. Many of these identified markers are located either nearby or flanking the regions where the QTLs for harvest index have been reported. Thus, the results from this association mapping study complement and enrich the information from linkage-based QTL studies and will be the basis for improving harvest index directly and indirectly in rice. PMID:22291889

  18. Genome-wide mapping of IBD segments in an Ashkenazi PD cohort identifies associated haplotypes.

    PubMed

    Vacic, Vladimir; Ozelius, Laurie J; Clark, Lorraine N; Bar-Shira, Anat; Gana-Weisz, Mali; Gurevich, Tanya; Gusev, Alexander; Kedmi, Merav; Kenny, Eimear E; Liu, Xinmin; Mejia-Santana, Helen; Mirelman, Anat; Raymond, Deborah; Saunders-Pullman, Rachel; Desnick, Robert J; Atzmon, Gil; Burns, Edward R; Ostrer, Harry; Hakonarson, Hakon; Bergman, Aviv; Barzilai, Nir; Darvasi, Ariel; Peter, Inga; Guha, Saurav; Lencz, Todd; Giladi, Nir; Marder, Karen; Pe'er, Itsik; Bressman, Susan B; Orr-Urtreger, Avi

    2014-09-01

    The recent series of large genome-wide association studies in European and Japanese cohorts established that Parkinson disease (PD) has a substantial genetic component. To further investigate the genetic landscape of PD, we performed a genome-wide scan in the largest to date Ashkenazi Jewish cohort of 1130 Parkinson patients and 2611 pooled controls. Motivated by the reduced disease allele heterogeneity and a high degree of identical-by-descent (IBD) haplotype sharing in this founder population, we conducted a haplotype association study based on mapping of shared IBD segments. We observed significant haplotype association signals at three previously implicated Parkinson loci: LRRK2 (OR = 12.05, P = 1.23 × 10(-56)), MAPT (OR = 0.62, P = 1.78 × 10(-11)) and GBA (multiple distinct haplotypes, OR > 8.28, P = 1.13 × 10(-11) and OR = 2.50, P = 1.22 × 10(-9)). In addition, we identified a novel association signal on chr2q14.3 coming from a rare haplotype (OR = 22.58, P = 1.21 × 10(-10)) and replicated it in a secondary cohort of 306 Ashkenazi PD cases and 2583 controls. Our results highlight the power of our haplotype association method, particularly useful in studies of founder populations, and reaffirm the benefits of studying complex diseases in Ashkenazi Jewish cohorts. PMID:24842889

  19. Identification of Candidate Genes for Seed Glucosinolate Content Using Association Mapping in Brassica napus L.

    PubMed Central

    Qu, Cun-Min; Li, Shi-Meng; Duan, Xiu-Jian; Fan, Jin-Hua; Jia, Le-Dong; Zhao, Hui-Yan; Lu, Kun; Li, Jia-Na; Xu, Xin-Fu; Wang, Rui

    2015-01-01

    Rapeseed contains glucosinolates, a toxic group of sulfur-containing glucosides, which play critical roles in defense against herbivores and microbes. However, the presence of glucosinolates in rapeseed reduces the value of the meal as feed for livestock. We performed association mapping of seed glucosinolate (GS) content using the 60K Brassica Infinium single nucleotide polymorphism (SNP) array in 520 oilseed rape accessions. A total of 11 peak SNPs significantly associated with GS content were detected in growing seasons of 2013 and 2014 and were located on B. napus chromosomes A08, A09, C03, and C09, respectively. Two associated regions of GS content covered by these markers were further verified, and three B. napus homologous genes involved in the biosynthesis and accumulation of GS were identified. These genes were multigene family members and were distributed on different chromosomes. Moreover, two genes (BnGRT2 and BnMYB28) associated with GS content were validated by the qRT-PCR analysis of their expression profiles. The further identification and functionalization of these genes will provide useful insight into the mechanism underlying GS biosynthesis and allocation in B. napus, and the associated SNPs markers could be helpful for molecular maker-assisted breeding for low seed GS in B. napus. PMID:26593950

  20. Genetic and association mapping study of wheat agronomic traits under contrasting water regimes.

    PubMed

    Dodig, Dejan; Zoric, Miroslav; Kobiljski, Borislav; Savic, Jasna; Kandic, Vesna; Quarrie, Steve; Barnes, Jeremy

    2012-01-01

    Genetic analyses and association mapping were performed on a winter wheat core collection of 96 accessions sampled from a variety of geographic origins. Twenty-four agronomic traits were evaluated over 3 years under fully irrigated, rainfed and drought treatments. Grain yield was the most sensitive trait to water deficit and was highly correlated with above-ground biomass per plant and number of kernels per m(2). The germplasm was structured into four subpopulations. The association of 46 SSR loci distributed throughout the wheat genome with yield and agronomic traits was analyzed using a general linear model, where subpopulation information was used to control false-positive or spurious marker-trait associations (MTAs). A total of 26, 21 and 29 significant (P < 0.001) MTAs were identified in irrigated, rainfed and drought treatments, respectively. The marker effects ranged from 14.0 to 50.8%. Combined across all treatments, 34 significant (P < 0.001) MTAs were identified with nine markers, and R(2) ranged from 14.5 to 50.2%. Marker psp3200 (6DS) and particularly gwm484 (2DS) were associated with many significant MTAs in each treatment and explained the greatest proportion of phenotypic variation. Although we were not able to recognize any marker related to grain yield under drought stress, a number of MTAs associated with developmental and agronomic traits highly correlated with grain yield under drought were identified.

  1. Association mapping of stigma and spikelet characteristics in rice (Oryza sativa L.).

    PubMed

    Yan, Wen Gui; Li, Yong; Agrama, Hesham A; Luo, Dagang; Gao, Fangyuan; Lu, Xianjun; Ren, Guangjun

    2009-10-01

    Stigma and spikelet characteristics play an essential role in hybrid seed production. A mini-core of 90 accessions developed from USDA rice core collection was phenotyped in field grown for nine traits of stigma and spikelet and genotyped with 109 DNA markers, 108 SSRs plus an indel. Three major clusters were built upon Rogers' genetic distance, indicative of indicas, and temperate and tropical japonicas. A mixed linear model combining PC-matrix and K-matrix was adapted for mapping marker-trait associations. Resulting associations were adjusted using false discovery rate technique. We identified 34 marker-trait associations involving 22 SSR markers for eight traits. Four markers were associated with single stigma exsertion (SStgE), six with dual exsertion (DStgE) and five with total exsertion. RM5_Chr1 played major role indicative of high regression with not only DStgE but also SStgE. Four markers were associated with spikelet length, three with width and seven with L/W ratio. Numerous markers were co-associated with multiple traits that were phenotypically correlated, i.e. RM12521_Chr2 associated with all three correlated spikelet traits. The co-association should improve breeding efficiency because single marker could be used to assist breeding for multiple traits. Indica entry 1032 (cultivar 50638) and japonica entry 671 (cultivar Linia 84 Icar) with 80.65 and 75.17% of TStgE, respectively are recommended to breeder for improving stigma exsertion. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11032-009-9290-y) contains supplementary material, which is available to authorized users.

  2. Factors affecting Culicoides species composition and abundance in avian nests.

    PubMed

    Martínez-de la Puente, J; Merino, S; Tomás, G; Moreno, J; Morales, J; Lobato, E; Talavera, S; Sarto I Monteys, V

    2009-08-01

    Mechanisms affecting patterns of vector distribution among host individuals may influence the population and evolutionary dynamics of vectors, hosts and the parasites transmitted. We studied the role of different factors affecting the species composition and abundance of Culicoides found in nests of the blue tit (Cyanistes caeruleus). We identified 1531 females and 2 males of 7 different Culicoides species in nests, with C. simulator being the most abundant species, followed by C. kibunensis, C. festivipennis, C. segnis, C. truncorum, C. pictipennis and C. circumscriptus. We conducted a medicationxfumigation experiment randomly assigning bird's nests to different treatments, thereby generating groups of medicated and control pairs breeding in fumigated and control nests. Medicated pairs were injected with the anti-malarial drug Primaquine diluted in saline solution while control pairs were injected with saline solution. The fumigation treatment was carried out using insecticide solution or water for fumigated and control nests respectively. Brood size was the main factor associated with the abundance of biting midges probably because more nestlings may produce higher quantities of vector attractants. In addition, birds medicated against haemoparasites breeding in non-fumigated nests supported a higher abundance of C. festivipennis than the rest of the groups. Also, we found that the fumigation treatment reduced the abundance of engorged Culicoides in both medicated and control nests, thus indicating a reduction of feeding success produced by the insecticide. These results represent the first evidence for the role of different factors in affecting the Culicoides infracommunity in wild avian nests.

  3. Should I stay or should I go? Fitness costs and benefits of prolonged parent-offspring and sibling-sibling associations in an Arctic-nesting goose population.

    PubMed

    Weegman, Mitch D; Bearhop, Stuart; Hilton, Geoff M; Walsh, Alyn J; Weegman, Kaitlin M; Hodgson, David J; Fox, Anthony David

    2016-07-01

    Theory predicts persistence of long-term family relationships in vertebrates will occur until perceived fitness costs exceed benefits to either parents or offspring. We examined whether increased breeding probability and survival were associated with prolonged parent-offspring and sibling-sibling relationships in a long-lived Arctic migrant herbivore, the Greenland white-fronted goose (Anser albifrons flavirostris). Although offspring associated with parents for 1-13 years, 79 % of these associations lasted two or less years. Only 65 (9.9 %) of the 656 marked offspring bred once in their lifetime, and just 16 (2.4 %) bred twice or more. The probability of birds with siblings breeding successfully in a subsequent year was credibly greater than that of independent birds at ages 5, 6, and 7. Survival of offspring with parents was credibly greater than that of independent/nonbreeder birds at all possible ages (i.e., ages 2-7+). A cost-benefit matrix model utilizing breeding and survival probabilities showed that staying with family groups was favored over leaving until age 3, after which there were no credible differences between staying and leaving strategies until the oldest ages, when leaving family groups was favored. Thus, most birds in this study either departed family groups early (e.g., at age 2, when the "stay" strategy was favored) or as predicted by our cost-benefit model (i.e., at age 3). Although extended family associations are a feature of this population, we contend that the survival benefits are not sufficient enough to yield clear fitness benefits, and associations only persist because parents and offspring mutually benefit from their persistence. PMID:26995680

  4. Should I stay or should I go? Fitness costs and benefits of prolonged parent-offspring and sibling-sibling associations in an Arctic-nesting goose population.

    PubMed

    Weegman, Mitch D; Bearhop, Stuart; Hilton, Geoff M; Walsh, Alyn J; Weegman, Kaitlin M; Hodgson, David J; Fox, Anthony David

    2016-07-01

    Theory predicts persistence of long-term family relationships in vertebrates will occur until perceived fitness costs exceed benefits to either parents or offspring. We examined whether increased breeding probability and survival were associated with prolonged parent-offspring and sibling-sibling relationships in a long-lived Arctic migrant herbivore, the Greenland white-fronted goose (Anser albifrons flavirostris). Although offspring associated with parents for 1-13 years, 79 % of these associations lasted two or less years. Only 65 (9.9 %) of the 656 marked offspring bred once in their lifetime, and just 16 (2.4 %) bred twice or more. The probability of birds with siblings breeding successfully in a subsequent year was credibly greater than that of independent birds at ages 5, 6, and 7. Survival of offspring with parents was credibly greater than that of independent/nonbreeder birds at all possible ages (i.e., ages 2-7+). A cost-benefit matrix model utilizing breeding and survival probabilities showed that staying with family groups was favored over leaving until age 3, after which there were no credible differences between staying and leaving strategies until the oldest ages, when leaving family groups was favored. Thus, most birds in this study either departed family groups early (e.g., at age 2, when the "stay" strategy was favored) or as predicted by our cost-benefit model (i.e., at age 3). Although extended family associations are a feature of this population, we contend that the survival benefits are not sufficient enough to yield clear fitness benefits, and associations only persist because parents and offspring mutually benefit from their persistence.

  5. Admixture in Hispanic Americans: its impact on ITGAM association and implications for admixture mapping in SLE.

    PubMed

    Molineros, J E; Kim-Howard, X; Deshmukh, H; Jacob, C O; Harley, J B; Nath, S K

    2009-07-01

    Systemic Lupus Erythematosus (SLE) disproportionately affects minorities, such as Hispanic Americans (HA). Prevalence of SLE is 3-5 times higher in HA than in European-derived populations and have more active disease at the time of diagnosis, with more serious organ system involvement. HA is an admixed population, it is possible that there is an effect of admixture on the relative risk of the disease. This admixture can create substantial increase of linkage disequilibrium (LD) in both magnitude and range, which can provide a unique opportunity for admixture mapping. The main objectives of this study are to (a) estimate hidden population structure in HA individuals; (b) estimate individual ancestry proportions and its impact on SLE risk; (c) assess impact of admixture on ITGAM association, a recently identified SLE susceptibility gene; and (d) estimate power of admixture mapping in HA. Our dataset contained 1125 individuals, of whom 884 (657 SLE cases and 227 controls) were self-classified as HA. Using 107 unlinked ancestry informative markers (AIMs), we estimated hidden population structure and individual ancestry in HA. Out of 5671 possible pairwise LD, 54% were statistically significant, indicating recent population admixture. The best-fitted model for HA was a four-population model with average ancestry of European (48%), American-Indian (AI) (40%), African (8%) and a fourth population (4%) with unknown ancestry. We also identified significant higher risk associated with AI ancestry (odds ratio (OR)=4.84, P=0.0001, 95% CI (confidence interval)=2.14-10.95) on overall SLE. We showed that ITGAM is associated as a risk factor for SLE (OR=2.06, P=8.74 x 10(-5), 95% CI=1.44-2.97). This association is not affected by population substructure or admixture. We have shown that HA have great potential and are an appropriate population for admixture mapping. As expected, the case-only design is more powerful than case-control design, for any given admixture proportion or

  6. Predator identity influences the effect of habitat management on nest predation.

    PubMed

    Lyons, Timothy P; Miller, James R; Debinski, Diane M; Engle, David M

    2015-09-01

    Predation is the leading cause of nest failure for many passerines and considerable effort is devoted to identifying the habitat characteristics and management practices that influence nest loss. The habitat components associated with nest loss are strongly influenced by the ecology of nest predators and differ among predator species as a result. Nevertheless, there is a tendency to generalize about the effects of habitat features and management on nest failure without considering how resulting patterns are influenced by nest predators. We examined how predator-specific patterns of nest loss differed among predators and in response to grassland management with fire and grazing by cattle (Bos taurus). We used video cameras to monitor and identify predators at nests of the Grasshopper Sparrow (Ammodramus savannarum), a species of conservation concern throughout its range. We observed predation by 15 different species that differed in their response to management and the habitat characteristics associated with nests they preyed on. Losses to mammals and snakes were more likely at nests with greater amounts of litter cover and tall fescue (Schedonorus phoenix). Mammals were less likely to prey on nests surrounded by greater forb cover. Nest predation by snakes was lower in burned areas, whereas predation by mammals and Brown-headed Cowbirds (Molothrus ater) was unaffected by the use of fire. Neither vegetation density at the nest, nor landscape context was related to nest loss by any predator taxon. Although there were many similarities, we identified important differences in the species composing the nest predator community between our. study and other published research. These differences are likely to be responsible for geographic variation in the influence of habitat features and management actions on nest success. Our results demonstrate the need for natural resource managers to incorporate knowledge of local nest predators and their ecology when developing

  7. Association-heterogeneity mapping identifies an Asian-specific association of the GTF2I locus with rheumatoid arthritis

    PubMed Central

    Kim, Kwangwoo; Bang, So-Young; Ikari, Katsunori; Yoo, Dae Hyun; Cho, Soo-Kyung; Choi, Chan-Bum; Sung, Yoon-Kyoung; Kim, Tae-Hwan; Jun, Jae-Bum; Kang, Young Mo; Suh, Chang-Hee; Shim, Seung-Cheol; Lee, Shin-Seok; Lee, Jisoo; Chung, Won Tae; Kim, Seong-Kyu; Choe, Jung-Yoon; Momohara, Shigeki; Taniguchi, Atsuo; Yamanaka, Hisashi; Nath, Swapan K.; Lee, Hye-Soon; Bae, Sang-Cheol

    2016-01-01

    Considerable sharing of disease alleles among populations is well-characterized in autoimmune disorders (e.g., rheumatoid arthritis), but there are some exceptional loci showing heterogenic association among populations. Here we investigated genetic variants with distinct effects on the development of rheumatoid arthritis in Asian and European populations. Ancestry-related association heterogeneity was examined using Cochran’s homogeneity tests for the disease association data from large Asian (n = 14,465; 9,299 discovery subjects and 5,166 validation subjects; 4 collections) and European (n = 45,790; 11 collections) rheumatoid arthritis case-control cohorts with Immunochip and genome-wide SNP array data. We identified significant heterogeneity between the two ancestries for the common variants in the GTF2I locus (PHeterogeneity = 9.6 × 10−9 at rs73366469) and showed that this heterogeneity was due to an Asian-specific association effect (ORMeta = 1.37 and PMeta = 4.2 × 10−13 in Asians; ORMeta = 1.00 and PMeta = 1.00 in Europeans). Trans-ancestral comparison and bioinfomatics analysis revealed a plausibly causal or disease-variant-tagging SNP (rs117026326; in linkage disequilibrium with rs73366469), whose minor allele is common in Asians but rare in Europeans. In conclusion, we identified largest-ever effect on Asian rheumatoid arthritis across human non-HLA regions at GTF2I by heterogeneity mapping followed by replication studies, and pinpointed a possible causal variant. PMID:27272985

  8. Microtubule-associated proteins 1 (MAP1) promote human immunodeficiency virus type I (HIV-1) intracytoplasmic routing to the nucleus.

    PubMed

    Fernandez, Juliette; Portilho, Débora M; Danckaert, Anne; Munier, Sandie; Becker, Andreas; Roux, Pascal; Zambo, Anaba; Shorte, Spencer; Jacob, Yves; Vidalain, Pierre-Olivier; Charneau, Pierre; Clavel, François; Arhel, Nathalie J

    2015-02-20

    After cell entry, HIV undergoes rapid transport toward the nucleus using microtubules and microfilaments. Neither the cellular cytoplasmic components nor the viral proteins that interact to mediate transport have yet been identified. Using a yeast two-hybrid screen, we identified four cytoskeletal components as putative interaction partners for HIV-1 p24 capsid protein: MAP1A, MAP1S, CKAP1, and WIRE. Depletion of MAP1A/MAP1S in indicator cell lines and primary human macrophages led to a profound reduction in HIV-1 infectivity as a result of impaired retrograde trafficking, demonstrated by a characteristic accumulation of capsids away from the nuclear membrane, and an overall defect in nuclear import. MAP1A/MAP1S did not impact microtubule network integrity or cell morphology but contributed to microtubule stabilization, which was shown previously to facilitate infection. In addition, we found that MAP1 proteins interact with HIV-1 cores both in vitro and in infected cells and that interaction involves MAP1 light chain LC2. Depletion of MAP1 proteins reduced the association of HIV-1 capsids with both dynamic and stable microtubules, suggesting that MAP1 proteins help tether incoming viral capsids to the microtubular network, thus promoting cytoplasmic trafficking. This work shows for the first time that following entry into target cells, HIV-1 interacts with the cytoskeleton via its p24 capsid protein. Moreover, our results support a role for MAP1 proteins in promoting efficient retrograde trafficking of HIV-1 by stimulating the formation of stable microtubules and mediating the association of HIV-1 cores with microtubules.

  9. Microtubule-associated Proteins 1 (MAP1) Promote Human Immunodeficiency Virus Type I (HIV-1) Intracytoplasmic Routing to the Nucleus

    PubMed Central

    Fernandez, Juliette; Portilho, Débora M.; Danckaert, Anne; Munier, Sandie; Becker, Andreas; Roux, Pascal; Zambo, Anaba; Shorte, Spencer; Jacob, Yves; Vidalain, Pierre-Olivier; Charneau, Pierre; Clavel, François; Arhel, Nathalie J.

    2015-01-01

    After cell entry, HIV undergoes rapid transport toward the nucleus using microtubules and microfilaments. Neither the cellular cytoplasmic components nor the viral proteins that interact to mediate transport have yet been identified. Using a yeast two-hybrid screen, we identified four cytoskeletal components as putative interaction partners for HIV-1 p24 capsid protein: MAP1A, MAP1S, CKAP1, and WIRE. Depletion of MAP1A/MAP1S in indicator cell lines and primary human macrophages led to a profound reduction in HIV-1 infectivity as a result of impaired retrograde trafficking, demonstrated by a characteristic accumulation of capsids away from the nuclear membrane, and an overall defect in nuclear import. MAP1A/MAP1S did not impact microtubule network integrity or cell morphology but contributed to microtubule stabilization, which was shown previously to facilitate infection. In addition, we found that MAP1 proteins interact with HIV-1 cores both in vitro and in infected cells and that interaction involves MAP1 light chain LC2. Depletion of MAP1 proteins reduced the association of HIV-1 capsids with both dynamic and stable microtubules, suggesting that MAP1 proteins help tether incoming viral capsids to the microtubular network, thus promoting cytoplasmic trafficking. This work shows for the first time that following entry into target cells, HIV-1 interacts with the cytoskeleton via its p24 capsid protein. Moreover, our results support a role for MAP1 proteins in promoting efficient retrograde trafficking of HIV-1 by stimulating the formation of stable microtubules and mediating the association of HIV-1 cores with microtubules. PMID:25505242

  10. Desmoplastic nested spindle cell tumours and nested stromal epithelial tumours of the liver.

    PubMed

    Misra, Sunayana; Bihari, Chhagan

    2016-04-01

    Desmoplastic nested spindle cell tumour of liver (DNSTL), nested stromal-epithelial tumour (NSET) and calcifying nested stromal-epithelial tumour (CNSET) are recently described entities with similar morphology, immunohistochemistry and molecular genetics. These are rare entities with only three large case series described till date. These tumours commonly present in the paediatric age group. NSETs, in addition have been described to be associated with ectopic adrenocorticotropic hormone (ACTH) production and Cushingoid features. It is important to discuss this rare group of tumours with a low malignant potential as the most common radiological differential diagnosis is hepatoblastoma, which has a relatively poorer prognosis. Thus, a pathologist needs to keep this entity in mind, so as to offer a correct histological diagnosis.

  11. Screening of SSR markers associated with scale cover pattern and mapped to a genetic linkage map of common carp (Cyprinus carpio L.).

    PubMed

    Xiao, Tongqian; Lu, Cuiyun; Xu, Yulan; Li, Chao; Zheng, Xianhu; Cao, Dingchen; Cheng, Lei; Mahboob, Shahid; Sun, Xiaowen

    2015-05-01

    Fish scale is an attractive model in bone physiology research and is also a crucial character for breeding new varieties. Thus, it is important to identify loci in the genome associated with scale formation. In this study, 290 microsatellite markers in common carp (Cyprinus carpio L.) were selected and tested for their segregation in a full-sib mapping panel containing 96 individuals (population 1). Association analysis identified seven simple sequence repeats (SSRs) (HLJ2509, HLJ3227, HLJ3675, HLJ3766, HLJ3863, FGFR1, FGFR7) that showed significant correlation with scale cover pattern in population 1. When the seven SSRs were investigated in two other populations, seven and five SSRs were significantly correlated with scale cover pattern in population 2 (116 individuals) and population 3 (57 individuals), respectively. The exceptions were FGFR1 and HLJ3227. A genetic linkage map was constructed using the 290 SSRs and 241 SSRs were mapped into 47 linkage groups (LGs), with 2-15 markers per LG. The map spanned 2,241.7 cM, with LG sizes that varied from 1.1 to 124.9 cM. All seven markers associated with scale cover mapped into LG3. We considered that a gene cluster that affected the scale cover pattern possibly existed in LG3. By aligning the seven markers with the zebrafish (Danio rerio) genome, we identified six candidate genes (atoh1a, ptch1, bmp1a, fgfr1a, fgf17, wnt5a) that may be associated with scale formation. We propose that the seven markers could be used with marker-assisted selection to breed a new variety of common carp, and the six candidate genes could help in understanding the scale cover mechanism. PMID:25339596

  12. Screening of SSR markers associated with scale cover pattern and mapped to a genetic linkage map of common carp (Cyprinus carpio L.).

    PubMed

    Xiao, Tongqian; Lu, Cuiyun; Xu, Yulan; Li, Chao; Zheng, Xianhu; Cao, Dingchen; Cheng, Lei; Mahboob, Shahid; Sun, Xiaowen

    2015-05-01

    Fish scale is an attractive model in bone physiology research and is also a crucial character for breeding new varieties. Thus, it is important to identify loci in the genome associated with scale formation. In this study, 290 microsatellite markers in common carp (Cyprinus carpio L.) were selected and tested for their segregation in a full-sib mapping panel containing 96 individuals (population 1). Association analysis identified seven simple sequence repeats (SSRs) (HLJ2509, HLJ3227, HLJ3675, HLJ3766, HLJ3863, FGFR1, FGFR7) that showed significant correlation with scale cover pattern in population 1. When the seven SSRs were investigated in two other populations, seven and five SSRs were significantly correlated with scale cover pattern in population 2 (116 individuals) and population 3 (57 individuals), respectively. The exceptions were FGFR1 and HLJ3227. A genetic linkage map was constructed using the 290 SSRs and 241 SSRs were mapped into 47 linkage groups (LGs), with 2-15 markers per LG. The map spanned 2,241.7 cM, with LG sizes that varied from 1.1 to 124.9 cM. All seven markers associated with scale cover mapped into LG3. We considered that a gene cluster that affected the scale cover pattern possibly existed in LG3. By aligning the seven markers with the zebrafish (Danio rerio) genome, we identified six candidate genes (atoh1a, ptch1, bmp1a, fgfr1a, fgf17, wnt5a) that may be associated with scale formation. We propose that the seven markers could be used with marker-assisted selection to breed a new variety of common carp, and the six candidate genes could help in understanding the scale cover mechanism.

  13. Fine Mapping Major Histocompatibility Complex Associations in Psoriasis and Its Clinical Subtypes

    PubMed Central

    Okada, Yukinori; Han, Buhm; Tsoi, Lam C.; Stuart, Philip E.; Ellinghaus, Eva; Tejasvi, Trilokraj; Chandran, Vinod; Pellett, Fawnda; Pollock, Remy; Bowcock, Anne M.; Krueger, Gerald G.; Weichenthal, Michael; Voorhees, John J.; Rahman, Proton; Gregersen, Peter K.; Franke, Andre; Nair, Rajan P.; Abecasis, Gonçalo R.; Gladman, Dafna D.; Elder, James T.; de Bakker, Paul I.W.; Raychaudhuri, Soumya

    2014-01-01

    Psoriasis vulgaris (PsV) risk is strongly associated with variation within the major histocompatibility complex (MHC) region, but its genetic architecture has yet to be fully elucidated. Here, we conducted a large-scale fine-mapping study of PsV risk in the MHC region in 9,247 PsV-affected individuals and 13,589 controls of European descent by imputing class I and II human leukocyte antigen (HLA) genes from SNP genotype data. In addition, we imputed sequence variants for MICA, an MHC HLA-like gene that has been associated with PsV, to evaluate association at that locus as well. We observed that HLA-C∗06:02 demonstrated the lowest p value for overall PsV risk (p = 1.7 × 10−364). Stepwise analysis revealed multiple HLA-C∗06:02-independent risk variants in both class I and class II HLA genes for PsV susceptibility (HLA-C∗12:03, HLA-B amino acid positions 67 and 9, HLA-A amino acid position 95, and HLA-DQα1 amino acid position 53; p < 5.0 × 10−8), but no apparent risk conferred by MICA. We further evaluated risk of two major clinical subtypes of PsV, psoriatic arthritis (PsA; n = 3,038) and cutaneous psoriasis (PsC; n = 3,098). We found that risk heterogeneity between PsA and PsC might be driven by HLA-B amino acid position 45 (pomnibus = 2.2 × 10−11), indicating that different genetic factors underlie the overall risk of PsV and the risk of specific PsV subphenotypes. Our study illustrates the value of high-resolution HLA and MICA imputation for fine mapping causal variants in the MHC. PMID:25087609

  14. Time-Course Association Mapping of the Grain-Filling Rate in Rice (Oryza sativa L.)

    PubMed Central

    Liu, Erbao; Liu, Xiaoli; Zeng, Siyuan; Zhao, Kaiming; Zhu, Changfeng; Liu, Yang; Breria, Manamik Caleb; Zhang, Baojuan; Hong, Delin

    2015-01-01

    Detecting quantity trait locus (QTLs) and elite alleles that are associated with grain-filling rate (GFR) in rice is essential for promoting the utilization of hybrid japonica rice and improving rice yield. Ninety-five varieties including 58 landraces and 37 elite varieties from the core germplasm collection were genotyped with 263 simple sequence repeat (SSR) markers. The GFR of the 95 varieties was evaluated at five stages, 7, 14, 21, 28 and 35 days after flowering (DAF) both in 2011 and 2012. We found abundant phenotypic and genetic diversity in the studied population. A population structure analysis identified seven subpopulations. A linkage disequilibrium (LD) analysis indicated that the levels of LD ranged from 60.3 cM to 84.8 cM and artificial selection had enhanced the LD. A time-course association analysis detected 31 marker-GFR associations involving 24 SSR markers located on chromosomes 1, 2, 3, 4, 5, 6, 8, 9, 11 and 12 of rice at five stages. The elite alleles for high GFR at each stage were detected. Fifteen excellent parental combinations were predicted, and the best parental combination ‘Nannongjing62401×Laolaihong’ could theoretically increase 4.086 mg grain-1 d-1 at the five stages. Our results demonstrate that the time-course association mapping for GFR in rice could detect elite alleles at different filling stages and that these elite alleles could be used to improve the GFR via pyramiding breeding. PMID:25789629

  15. SNPs Selection using Gravitational Search Algorithm and Exhaustive Search for Association Mapping

    NASA Astrophysics Data System (ADS)

    Kusuma, W. A.; Hasibuan, L. S.; Istiadi, M. A.

    2016-01-01

    Single Nucleotide Polymorphisms (SNPs) are known having association to phenotipic variations. The study of linking SNPs to interest phenotype is refer to Association Mapping (AM), which is classified as a combinatorial problem. Exhaustive Search (ES) approach is able to be implemented to select targeted SNPs exactly since it evaluate all possible combinations of SNPs, but it is not efficient in terms of computer resources and computation time. Heuristic Search (HS) approach is an alternative to improve the performance of ES in those terms, but it still suffers high false positive SNPs in each combinations. Gravitational Search Algorithm (GSA) is a new HS algorithm that yields better performance than other nature inspired HS. This paper proposed a new method which combined GSA and ES to identify the most appropriate combination of SNPs linked to interest phenotype. Testing was conducted using dataset without epistasis and dataset with epistasis. Using dataset without epistasis with 7 targeted SNPs, the proposed method identified 7 SNPs - 6 True Positive (TP) SNPs and 1 False Positive (FP) SNP- with association value of 0.83. In addition, the proposed method could identified 3 SNPs- 2 TP SNP and 1 FP SNP with association value of 0.87 by using dataset with epistases and 5 targeted SNPs. The results showed that the method is robust in reducing redundant SNPs and identifying main markers.

  16. A spatial model of waterfowl nest site selection in grassland nesting cover

    NASA Astrophysics Data System (ADS)

    Pool, Duane Bruce

    Ducks Unlimited's (DU) mission statement is focused on providing for the annual lifecycle needs of migratory waterfowl. The largest impacts to the success and numbers of continental populations are determined by their activities on the breeding grounds. To model and therefore manage habitats and landscapes for ducks (Anas and Aythya spp.) it is necessary to understand several characteristics of their behavior. This research builds a model of nest site selection from nest probability based on remotely sensed data, presence data and minimum threshold theory. The methods used are applicable to other sensor platforms as well as other target species or phenomenon. Using data compression techniques, logistic regression, and spatial statistical functions (Ripley's k-function, a global k-function, and Multiple Response Permutation Procedure) we tested the observed point patterns and developed a point process model to predict nesting patterns. The application of this type of fine resolution database, validated by empirical data, will be more powerful than either classified remote sensing data or field level nest demographic data alone. In the largest of the five study sites, which was also the site with the greatest number of observations, the pattern of nests were significantly different from Poisson. The model developed to fit these data was tested using the other sites and the observed data on the other four sites were not shown to be significantly different from the model. The tests for spatial association showed some evidence negative association between Blue-winged Teal and Gadwall as well as between successful and unsuccessful nest. There is some evidence that a process of natural selection may exist and the future studies should be designed with this in mind. These data will be used as a baseline for future habitat manipulation and controlled experiments on the DU Goebel Ranch complex. The results of this and future studies will be used as the basis for DU strategic

  17. Parallelized nested sampling

    NASA Astrophysics Data System (ADS)

    Henderson, R. Wesley; Goggans, Paul M.

    2014-12-01

    One of the important advantages of nested sampling as an MCMC technique is its ability to draw representative samples from multimodal distributions and distributions with other degeneracies. This coverage is accomplished by maintaining a number of so-called live samples within a likelihood constraint. In usual practice, at each step, only the sample with the least likelihood is discarded from this set of live samples and replaced. In [1], Skilling shows that for a given number of live samples, discarding only one sample yields the highest precision in estimation of the log-evidence. However, if we increase the number of live samples, more samples can be discarded at once while still maintaining the same precision. For computer code running only serially, this modification would considerably increase the wall clock time necessary to reach convergence. However, if we use a computer with parallel processing capabilities, and we write our code to take advantage of this parallelism to replace multiple samples concurrently, the performance penalty can be eliminated entirely and possibly reversed. In this case, we must use the more general equation in [1] for computing the expectation of the shrinkage distribution: E [- log t]= (N r-r+1)-1+(Nr-r+2)-1+⋯+Nr-1, for shrinkage t with Nr live samples and r samples discarded at each iteration. The equation for the variance Var (- log t)= (N r-r+1)-2+(Nr-r+2)-2+⋯+Nr-2 is used to find the appropriate number of live samples Nr to use with r > 1 to match the variance achieved with N1 live samples and r = 1. In this paper, we show that by replacing multiple discarded samples in parallel, we are able to achieve a more thorough sampling of the constrained prior distribution, reduce runtime, and increase precision.

  18. Decoding the Formation of New Semantics: MVPA Investigation of Rapid Neocortical Plasticity during Associative Encoding through Fast Mapping

    PubMed Central

    Atir-Sharon, Tali; Gilboa, Asaf; Hazan, Hananel; Koilis, Ester; Manevitz, Larry M.

    2015-01-01

    Neocortical structures typically only support slow acquisition of declarative memory; however, learning through fast mapping may facilitate rapid learning-induced cortical plasticity and hippocampal-independent integration of novel associations into existing semantic networks. During fast mapping the meaning of new words and concepts is inferred, and durable novel associations are incidentally formed, a process thought to support early childhood's exuberant learning. The anterior temporal lobe, a cortical semantic memory hub, may critically support such learning. We investigated encoding of semantic associations through fast mapping using fMRI and multivoxel pattern analysis. Subsequent memory performance following fast mapping was more efficiently predicted using anterior temporal lobe than hippocampal voxels, while standard explicit encoding was best predicted by hippocampal activity. Searchlight algorithms revealed additional activity patterns that predicted successful fast mapping semantic learning located in lateral occipitotemporal and parietotemporal neocortex and ventrolateral prefrontal cortex. By contrast, successful explicit encoding could be classified by activity in medial and dorsolateral prefrontal and parahippocampal cortices. We propose that fast mapping promotes incidental rapid integration of new associations into existing neocortical semantic networks by activating related, nonoverlapping conceptual knowledge. In healthy adults, this is better captured by unique anterior and lateral temporal lobe activity patterns, while hippocampal involvement is less predictive of this kind of learning. PMID:26257961

  19. The Association Between Cervical Human Papillomavirus Infection and Subsequent HIV Acquisition in Tanzanian and Ugandan Women: A Nested Case-Control Study

    PubMed Central

    Gallagher, Katherine E.; Baisley, Kathy; Grosskurth, Heiner; Vallely, Andrew; Kapiga, Saidi; Vandepitte, Judith; Kamali, Anatoli; De Sanjosé, Silvia; Changalucha, John; Hayes, Richard; Watson-Jones, Deborah

    2016-01-01

    Objective This study was performed to analyze the associations between cervical human papillomavirus (HPV) infection and human immunodeficiency virus (HIV) acquisition, using cervical samples from previous studies in Tanzania and Uganda. Methods. A total of 161 adult women who acquired HIV infection during follow-up and 464 individually matched HIV-seronegative controls were selected from 5 cohorts of women working in bars and recreational facilities. Stored cervical samples were tested for 37 HPV genotypes, using a polymerase chain reaction assay (Roche Linear Array genotyping assay). Multivariate matched analysis using conditional logistic regression was performed to evaluate HPV infection, persistence, and clearance as predictors of HIV acquisition. Results. HIV seroconverters were significantly more likely than controls to frequently drink alcohol and to be infected with Chlamydia trachomatis, Neisseria gonorrhoeae, or herpes simplex virus type 2. There was no evidence of an association between HIV acquisition and any detectable HPV at the visit prior to HIV seroconversion (adjusted odds ratio, 1.02; 95% confidence interval, .66–1.57) or between HIV acquisition and persistent HPV infection (defined as 2 positive HPV genotype–specific test results at least 6 months apart), cleared HPV infection (defined as a positive HPV test result followed by negative HPV genotype–specific test result), or newly acquired HPV infection, compared with HPV-negative women. Conclusions. There was no evidence of association between HPV infection status and subsequent HIV acquisition. These results stand in contrast to other observational studies. PMID:26951818

  20. Foam nests provide context-dependent thermal insulation to embryos of three leptodactylid frogs.

    PubMed

    Méndez-Narváez, J; Flechas, S V; Amézquita, A

    2015-01-01

    The choice of adequate breeding habitat and its associated thermoregulatory conditions are thought to be important in the evolution of amphibian reproductive strategies. Among leptodactylid frogs, there is a terrestrial cline in the oviposition sites chosen to build foam nests for eggs. Although several functions have been attributed to foam nests, their role in temperature regulation for embryos is unclear. Here we tested the hypothesis that foam nests buffer embryos from variation in air temperature. We examined the degree of terrestrial nest sites in three species, finding a terrestrial cline of sites in terms of distance from water. We tested whether this nest-insulation effect varied among these species that differ in the degree of terrestrial nest sites and whether translocating nests impacted embryonic mortality. Our results demonstrate a negative effect of translocating aquatic nests to land, inferred from the highest hatching success in natural nests sites. All nests attenuated environmental thermal variation, but more terrestrial nests buffered embryos from a greater range of temperatures than did aquatic ones. Altogether, our data indicate that foam nests insulate embryos from daily temperature fluctuations among leptodactylid frogs with different degrees of terrestrial nests, which may well have contributed to the evolution of this reproductive strategy.

  1. Foam nests provide context-dependent thermal insulation to embryos of three leptodactylid frogs.

    PubMed

    Méndez-Narváez, J; Flechas, S V; Amézquita, A

    2015-01-01

    The choice of adequate breeding habitat and its associated thermoregulatory conditions are thought to be important in the evolution of amphibian reproductive strategies. Among leptodactylid frogs, there is a terrestrial cline in the oviposition sites chosen to build foam nests for eggs. Although several functions have been attributed to foam nests, their role in temperature regulation for embryos is unclear. Here we tested the hypothesis that foam nests buffer embryos from variation in air temperature. We examined the degree of terrestrial nest sites in three species, finding a terrestrial cline of sites in terms of distance from water. We tested whether this nest-insulation effect varied among these species that differ in the degree of terrestrial nest sites and whether translocating nests impacted embryonic mortality. Our results demonstrate a negative effect of translocating aquatic nests to land, inferred from the highest hatching success in natural nests sites. All nests attenuated environmental thermal variation, but more terrestrial nests buffered embryos from a greater range of temperatures than did aquatic ones. Altogether, our data indicate that foam nests insulate embryos from daily temperature fluctuations among leptodactylid frogs with different degrees of terrestrial nests, which may well have contributed to the evolution of this reproductive strategy. PMID:25860824

  2. Genome-wide association mapping of cadmium accumulation in different organs of barley.

    PubMed

    Wu, Dezhi; Sato, Kazuhiro; Ma, Jian Feng

    2015-11-01

    The threshold value of cadmium (Cd) concentration in grains of barley (Hordeum vulgare) is the lowest among cereal crops; however, it is poorly understood how Cd accumulation in barley grain is genetically controlled. We investigated genotypic variation in Cd accumulation of different organs in 100 accessions from a subset of the barley core collection using both hydroponic and Cd-contaminated soil culture. We also performed a genome-wide association (GWA) mapping for Cd accumulation in different organs. A large genotypic variation in the Cd concentration was found in all organs. There was a good correlation between shoot Cd of solution and soil culture, the shoot Cd and grain Cd, but no correlation between the root Cd and grain Cd. GWA mapping detected 9 quantitative trait loci (QTL) for root Cd, 21 for shoot Cd, 14 for root-to-shoot translocation and 15 for grain Cd. A common QTL for the shoot Cd and root-to-shoot translocation was found at 132.6 cM on chromosome 5H. Two major QTL for grain Cd were identified on chromosome 2H and chromosome 5H. The genetic variation in Cd accumulation and major QTL detected provide useful information helpful for cloning candidate genes for Cd accumulation and breeding low-Cd barley cultivars in future.

  3. Biallelic and Genome Wide Association Mapping of Germanium Tolerant Loci in Rice (Oryza sativa L.)

    PubMed Central

    Talukdar, Partha; Douglas, Alex; Price, Adam H.; Norton, Gareth J.

    2015-01-01

    Rice plants accumulate high concentrations of silicon. Silicon has been shown to be involved in plant growth, high yield, and mitigating biotic and abiotic stresses. However, it has been demonstrated that inorganic arsenic is taken up by rice through silicon transporters under anaerobic conditions, thus the ability to efficiently take up silicon may be considered either a positive or a negative trait in rice. Germanium is an analogue of silicon that produces brown lesions in shoots and leaves, and germanium toxicity has been used to identify mutants in silicon and arsenic transport. In this study, two different genetic mapping methods were performed to determine the loci involved in germanium sensitivity in rice. Genetic mapping in the biparental cross of Bala × Azucena (an F6 population) and a genome wide association (GWA) study with 350 accessions from the Rice Diversity Panel 1 were conducted using 15 μM of germanic acid. This identified a number of germanium sensitive loci: some co-localised with previously identified quantitative trait loci (QTL) for tissue silicon or arsenic concentration, none co-localised with Lsi1 or Lsi6, while one single nucleotide polymorphism (SNP) was detected within 200 kb of Lsi2 (these are genes known to transport silicon, whose identity was discovered using germanium toxicity). However, examining candidate genes that are within the genomic region of the loci detected above reveals genes homologous to both Lsi1 and Lsi2, as well as a number of other candidate genes, which are discussed. PMID:26356220

  4. Biallelic and Genome Wide Association Mapping of Germanium Tolerant Loci in Rice (Oryza sativa L.).

    PubMed

    Talukdar, Partha; Douglas, Alex; Price, Adam H; Norton, Gareth J

    2015-01-01

    Rice plants accumulate high concentrations of silicon. Silicon has been shown to be involved in plant growth, high yield, and mitigating biotic and abiotic stresses. However, it has been demonstrated that inorganic arsenic is taken up by rice through silicon transporters under anaerobic conditions, thus the ability to efficiently take up silicon may be considered either a positive or a negative trait in rice. Germanium is an analogue of silicon that produces brown lesions in shoots and leaves, and germanium toxicity has been used to identify mutants in silicon and arsenic transport. In this study, two different genetic mapping methods were performed to determine the loci involved in germanium sensitivity in rice. Genetic mapping in the biparental cross of Bala × Azucena (an F6 population) and a genome wide association (GWA) study with 350 accessions from the Rice Diversity Panel 1 were conducted using 15 μM of germanic acid. This identified a number of germanium sensitive loci: some co-localised with previously identified quantitative trait loci (QTL) for tissue silicon or arsenic concentration, none co-localised with Lsi1 or Lsi6, while one single nucleotide polymorphism (SNP) was detected within 200 kb of Lsi2 (these are genes known to transport silicon, whose identity was discovered using germanium toxicity). However, examining candidate genes that are within the genomic region of the loci detected above reveals genes homologous to both Lsi1 and Lsi2, as well as a number of other candidate genes, which are discussed.

  5. QTL Detection and Elite Alleles Mining for Stigma Traits in Oryza sativa by Association Mapping.

    PubMed

    Dang, Xiaojing; Liu, Erbao; Liang, Yinfeng; Liu, Qiangming; Breria, Caleb M; Hong, Delin

    2016-01-01

    Stigma traits are very important for hybrid seed production in Oryza sativa, which is a self-pollinated crop; however, the genetic mechanism controlling the traits is poorly understood. In this study, we investigated the phenotypic data of 227 accessions across 2 years and assessed their genotypic variation with 249 simple sequence repeat (SSR) markers. By combining phenotypic and genotypic data, a genome-wide association (GWA) map was generated. Large phenotypic variations in stigma length (STL), stigma brush-shaped part length (SBPL) and stigma non-brush-shaped part length (SNBPL) were found. Significant positive correlations were identified among stigma traits. In total, 2072 alleles were detected among 227 accessions, with an average of 8.3 alleles per SSR locus. GWA mapping detected 6 quantitative trait loci (QTLs) for the STL, 2 QTLs for the SBPL and 7 QTLs for the SNBPL. Eleven, 5, and 12 elite alleles were found for the STL, SBPL, and SNBPL, respectively. Optimal cross designs were predicted for improving the target traits. The detected genetic variation in stigma traits and QTLs provides helpful information for cloning candidate STL genes and breeding rice cultivars with longer STLs in the future. PMID:27555858

  6. QTL Detection and Elite Alleles Mining for Stigma Traits in Oryza sativa by Association Mapping

    PubMed Central

    Dang, Xiaojing; Liu, Erbao; Liang, Yinfeng; Liu, Qiangming; Breria, Caleb M.; Hong, Delin

    2016-01-01

    Stigma traits are very important for hybrid seed production in Oryza sativa, which is a self-pollinated crop; however, the genetic mechanism controlling the traits is poorly understood. In this study, we investigated the phenotypic data of 227 accessions across 2 years and assessed their genotypic variation with 249 simple sequence repeat (SSR) markers. By combining phenotypic and genotypic data, a genome-wide association (GWA) map was generated. Large phenotypic variations in stigma length (STL), stigma brush-shaped part length (SBPL) and stigma non-brush-shaped part length (SNBPL) were found. Significant positive correlations were identified among stigma traits. In total, 2072 alleles were detected among 227 accessions, with an average of 8.3 alleles per SSR locus. GWA mapping detected 6 quantitative trait loci (QTLs) for the STL, 2 QTLs for the SBPL and 7 QTLs for the SNBPL. Eleven, 5, and 12 elite alleles were found for the STL, SBPL, and SNBPL, respectively. Optimal cross designs were predicted for improving the target traits. The detected genetic variation in stigma traits and QTLs provides helpful information for cloning candidate STL genes and breeding rice cultivars with longer STLs in the future. PMID:27555858

  7. Genome-wide association mapping of cadmium accumulation in different organs of barley.

    PubMed

    Wu, Dezhi; Sato, Kazuhiro; Ma, Jian Feng

    2015-11-01

    The threshold value of cadmium (Cd) concentration in grains of barley (Hordeum vulgare) is the lowest among cereal crops; however, it is poorly understood how Cd accumulation in barley grain is genetically controlled. We investigated genotypic variation in Cd accumulation of different organs in 100 accessions from a subset of the barley core collection using both hydroponic and Cd-contaminated soil culture. We also performed a genome-wide association (GWA) mapping for Cd accumulation in different organs. A large genotypic variation in the Cd concentration was found in all organs. There was a good correlation between shoot Cd of solution and soil culture, the shoot Cd and grain Cd, but no correlation between the root Cd and grain Cd. GWA mapping detected 9 quantitative trait loci (QTL) for root Cd, 21 for shoot Cd, 14 for root-to-shoot translocation and 15 for grain Cd. A common QTL for the shoot Cd and root-to-shoot translocation was found at 132.6 cM on chromosome 5H. Two major QTL for grain Cd were identified on chromosome 2H and chromosome 5H. The genetic variation in Cd accumulation and major QTL detected provide useful information helpful for cloning candidate genes for Cd accumulation and breeding low-Cd barley cultivars in future. PMID:26061418

  8. Potential self-selection bias in a nested case-control study on indoor environmental factors and their association with asthma and allergic symptoms among pre-school children.

    PubMed

    Bornehag, Carl-Gustaf; Sundell, Jan; Sigsgaard, Torben; Janson, Staffan

    2006-01-01

    Selection bias means a systematic difference between the characteristics of selected and non-selected individuals in epidemiological studies. Such bias may be introduced if participants select themselves for a study. The present study aims at identifying differences in family characteristics, including health, building characteristics of the home, and socioeconomic factors between participating and non-participating families in a nested case-control study on asthma and allergy among children. Information was collected in a baseline questionnaire to the parents of 14,077 children aged 1-6 years in a first step. In a second step 2,156 of the children were invited to participate in a case-control study. Of these, 198 cases and 202 controls were finally selected. For identifying potential selection bias, information concerning all invited families in the case-control study was obtained from the baseline questionnaire. Results show that there are several possible biases due to self-selection involved in an extensive study on the impact of the home environment on asthma and allergy among children. Factors associated with participating were high socioeconomic status of the family, more health problems in the case families, and health-related lifestyle factors, such as non-smoking parents. The overall conclusion of this study is that there are selection biases involved in studies that need close cooperation with the families involved. One solution to this problem is stratification, i.e. investigating associations between exposures and health in the same socioeconomic strata. PMID:16990165

  9. The Genetic Architecture of Complex Traits in Teosinte (Zea mays ssp. parviglumis): New Evidence from Association Mapping

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Our previous association analyses showed that variation at major regulatory genes contributes to standing variation for complex traits in Balsas teosinte, the progenitor of maize. This study expands our previous association mapping effort in teosinte by testing 123 markers in 52 candidate genes for ...

  10. Genome-wide association mapping of milk production traits in Braunvieh cattle.

    PubMed

    Maxa, J; Neuditschko, M; Russ, I; Förster, M; Medugorac, I

    2012-09-01

    A whole-genome association study of milk production traits: milk yield, protein yield, fat yield, protein percentage, and fat percentage, was performed on the population of Braunvieh cattle. Five hundred and fifty-four progeny-tested bulls and 36,219 autosomal single nucleotide polymorphism (SNP) markers on 29 Bos taurus autosomes (BTA) were included in the analysis. A principal component analysis was conducted to adjust for the effect of population stratification in the analyzed data set. For the principal component analysis, genome-wide relationships between individuals were calculated. Three different criteria (Horn's test, Kaiser's criterion, and Jolliffe's criterion) were tested to determine the number of significant principal components. Estimation of putative associations between SNP and milk production traits was carried out using a linear regression model in R software (R Foundation for Statistical Computing, Vienna, Austria). Significant principal components, adjusting for population stratification separately for each criterion and family relationships and genotypes at individual SNP were included as fixed effects in the model. The inflation factor λ and quantile-quantile plots were calculated to compare how the different criteria deal with stratification in our mapping population. Based on the analyses on all of the aforementioned criteria, we can conclude that Jolliffe's criterion deals the best with population stratification. Furthermore, significance thresholds for a given genome-wide false discovery rate of 5% were estimated and used for specific traits. Three of the analyzed traits showed genome-wide significant association with SNP. Two SNP had an effect on milk yield on BTA4, 2 SNP affected fat yield on BTA14 and BTA23, and 1 SNP was associated with fat percent on BTA1. Single nucleotide polymorphisms identified in this study as associated with milk production traits will further contribute to the mapping of corresponding quantitative trait loci

  11. Olfactory response of megachilid bees, Osmia lignaria, Megachile rotundata, and M. pugnata, to individual cues from old nest cavities.

    PubMed

    Pitts-Singer, Theresa L

    2007-04-01

    The megachilid bees Osmia lignaria Say, Megachile rotundata (F.), and M. pugnata Say were tested for attraction to various components associated with their old nest cavities, or chemical extracts of these components, using a Y-tube olfactory response bioassay. Female bees of these species are known to nest in or near old nest cavities, implying that remnant nest components are important cues for bees looking for nest cavities. Significant results show that female bees were attracted to components that may provide species-specific cues or indicate conspecific nesting activity. Specifically, O. lignaria females showed attraction only to the female cocoon. M. rotundata females were attracted to intact nest cells, the fecal material on the outside of a cocoon, leaf pieces used as nest cell lining, and the extract of leaf pieces. M. pugnata females were attracted to the whole nest cell, the paper straw nesting material with attached cocoon, and feces. PMID:17445375

  12. Open access resources for genome-wide association mapping in rice.

    PubMed

    McCouch, Susan R; Wright, Mark H; Tung, Chih-Wei; Maron, Lyza G; McNally, Kenneth L; Fitzgerald, Melissa; Singh, Namrata; DeClerck, Genevieve; Agosto-Perez, Francisco; Korniliev, Pavel; Greenberg, Anthony J; Naredo, Ma Elizabeth B; Mercado, Sheila Mae Q; Harrington, Sandra E; Shi, Yuxin; Branchini, Darcy A; Kuser-Falcão, Paula R; Leung, Hei; Ebana, Kowaru; Yano, Masahiro; Eizenga, Georgia; McClung, Anna; Mezey, Jason

    2016-01-01

    Increasing food production is essential to meet the demands of a growing human population, with its rising income levels and nutritional expectations. To address the demand, plant breeders seek new sources of genetic variation to enhance the productivity, sustainability and resilience of crop varieties. Here we launch a high-resolution, open-access research platform to facilitate genome-wide association mapping in rice, a staple food crop. The platform provides an immortal collection of diverse germplasm, a high-density single-nucleotide polymorphism data set tailored for gene discovery, well-documented analytical strategies, and a suite of bioinformatics resources to facilitate biological interpretation. Using grain length, we demonstrate the power and resolution of our new high-density rice array, the accompanying genotypic data set, and an expanded diversity panel for detecting major and minor effect QTLs and subpopulation-specific alleles, with immediate implications for rice improvement. PMID:26842267

  13. Open access resources for genome-wide association mapping in rice

    PubMed Central

    McCouch, Susan R.; Wright, Mark H.; Tung, Chih-Wei; Maron, Lyza G.; McNally, Kenneth L.; Fitzgerald, Melissa; Singh, Namrata; DeClerck, Genevieve; Agosto-Perez, Francisco; Korniliev, Pavel; Greenberg, Anthony J.; Naredo, Ma. Elizabeth B.; Mercado, Sheila Mae Q.; Harrington, Sandra E.; Shi, Yuxin; Branchini, Darcy A.; Kuser-Falcão, Paula R.; Leung, Hei; Ebana, Kowaru; Yano, Masahiro; Eizenga, Georgia; McClung, Anna; Mezey, Jason

    2016-01-01

    Increasing food production is essential to meet the demands of a growing human population, with its rising income levels and nutritional expectations. To address the demand, plant breeders seek new sources of genetic variation to enhance the productivity, sustainability and resilience of crop varieties. Here we launch a high-resolution, open-access research platform to facilitate genome-wide association mapping in rice, a staple food crop. The platform provides an immortal collection of diverse germplasm, a high-density single-nucleotide polymorphism data set tailored for gene discovery, well-documented analytical strategies, and a suite of bioinformatics resources to facilitate biological interpretation. Using grain length, we demonstrate the power and resolution of our new high-density rice array, the accompanying genotypic data set, and an expanded diversity panel for detecting major and minor effect QTLs and subpopulation-specific alleles, with immediate implications for rice improvement. PMID:26842267

  14. Open access resources for genome-wide association mapping in rice.

    PubMed

    McCouch, Susan R; Wright, Mark H; Tung, Chih-Wei; Maron, Lyza G; McNally, Kenneth L; Fitzgerald, Melissa; Singh, Namrata; DeClerck, Genevieve; Agosto-Perez, Francisco; Korniliev, Pavel; Greenberg, Anthony J; Naredo, Ma Elizabeth B; Mercado, Sheila Mae Q; Harrington, Sandra E; Shi, Yuxin; Branchini, Darcy A; Kuser-Falcão, Paula R; Leung, Hei; Ebana, Kowaru; Yano, Masahiro; Eizenga, Georgia; McClung, Anna; Mezey, Jason

    2016-01-01

    Increasing food production is essential to meet the demands of a growing human population, with its rising income levels and nutritional expectations. To address the demand, plant breeders seek new sources of genetic variation to enhance the productivity, sustainability and resilience of crop varieties. Here we launch a high-resolution, open-access research platform to facilitate genome-wide association mapping in rice, a staple food crop. The platform provides an immortal collection of diverse germplasm, a high-density single-nucleotide polymorphism data set tailored for gene discovery, well-documented analytical strategies, and a suite of bioinformatics resources to facilitate biological interpretation. Using grain length, we demonstrate the power and resolution of our new high-density rice array, the accompanying genotypic data set, and an expanded diversity panel for detecting major and minor effect QTLs and subpopulation-specific alleles, with immediate implications for rice improvement.

  15. Chain mapping approach of Hamiltonian for FMO complex using associated, generalized and exceptional Jacobi polynomials

    NASA Astrophysics Data System (ADS)

    Mahdian, M.; Arjmandi, M. B.; Marahem, F.

    2016-06-01

    The excitation energy transfer (EET) in photosynthesis complex has been widely investigated in recent years. However, one of the main problems is simulation of this complex under realistic condition. In this paper by using the associated, generalized and exceptional Jacobi polynomials, firstly, we introduce the spectral density of Fenna-Matthews-Olson (FMO) complex. Afterward, we obtain a map that transforms the Hamiltonian of FMO complex as an open quantum system to a one-dimensional chain of oscillatory modes with only nearest neighbor interaction in which the system is coupled only to first mode of chain. The frequency and coupling strength of each mode can be analytically obtained from recurrence coefficient of mentioned orthogonal polynomials.

  16. Pre-nesting and nesting behavior of the Swainson's warbler

    USGS Publications Warehouse

    Meanley, B.

    1969-01-01

    The Swainson?s Warbler is one of the least known of southern birds. Although fairly common in some parts of its summer range, observations of its breeding biology have been made by very few persons. The present study was conducted mostly at Macon, Georgia; Pendleton Ferry, Arkansas; and Dismal Swamp, Virginia....In central Georgia and east-central Arkansas, Swainson?s Warblers usually arrive on their territories during the first two weeks in April. Territories in several localities ranged in size from 0.3 to 4.8 acres. A color-marked Arkansas male occupied the same territory for at least four months. Hostile encounters between territorial male Swainson?s Warblers usually take place along the boundary of adjacent territories. Paired males were more aggressive than unpaired males. Toward the end of an encounter one of the two males would usually perform a display in which the wing and tail feathers were spread and the tail vibrated. Following boundary encounters males drifted back onto their territories and usually sang unbroken courses of songs for several minutes.....During pre-nesting at Macon, a mated pair spent the day mostly on the ground within 20 feet of each other, often foragin g 3 to 4 feet apart. What may have been a form of courtship display, in which the male flew from a perch down to the female and either pecked her rump or pounced on her, occurred about three times each hour throughout the day. During this period the male sang less than at other times during the breeding season.....First nests are usually built by the first week in May. Although other investigators reported finding nests of this species outside of the defended territory, all nests that I have found were within the territory. The large, bulky nest of this species usually is placed 2-6 feet above the ground. It is built by the female from materials gathered close to the nest site; and takes two or three days to complete.....Three and occasionally four white eggs are laid. The female

  17. Association mapping of germinability and seedling vigor in sorghum under controlled low-temperature conditions.

    PubMed

    Upadhyaya, Hari D; Wang, Yi-Hong; Sastry, Dintyala V S S R; Dwivedi, Sangam L; Prasad, P V Vara; Burrell, A Millie; Klein, Robert R; Morris, Geoffrey P; Klein, Patricia E

    2016-02-01

    Sorghum is one of the world's most important food, feed, and fiber crops as well as a potential feedstock for lignocellulosic bioenergy. Early-season planting extends sorghum's growing season and increases yield in temperate regions. However, sorghum's sensitivity to low soil temperatures adversely impacts seed germination. In this study, we evaluated the 242 accessions of the ICRISAT sorghum mini core collection for seed germination and seedling vigor at 12 °C as a measure of cold tolerance. Genome-wide association analysis was performed with approximately 162,177 single nucleotide polymorphism markers. Only one marker locus (Locus 7-2) was significantly associated with low-temperature germination and none with vigor. The linkage of Locus 7-2 to low-temperature germination was supported by four lines of evidence: strong association in three independent experiments, co-localization with previously mapped cold tolerance quantitative trait loci (QTL) in sorghum, a candidate gene that increases cold tolerance and germination rate when its wheat homolog is overexpressed in tobacco, and its syntenic region in rice co-localized with two cold tolerance QTL in rice. This locus may be useful in developing tools for molecular breeding of sorghums with improved low-temperature germinability.

  18. Efficient network-guided multi-locus association mapping with graph cuts

    PubMed Central

    Azencott, Chloé-Agathe; Grimm, Dominik; Sugiyama, Mahito; Kawahara, Yoshinobu

    2013-01-01

    Motivation: As an increasing number of genome-wide association studies reveal the limitations of the attempt to explain phenotypic heritability by single genetic loci, there is a recent focus on associating complex phenotypes with sets of genetic loci. Although several methods for multi-locus mapping have been proposed, it is often unclear how to relate the detected loci to the growing knowledge about gene pathways and networks. The few methods that take biological pathways or networks into account are either restricted to investigating a limited number of predetermined sets of loci or do not scale to genome-wide settings. Results: We present SConES, a new efficient method to discover sets of genetic loci that are maximally associated with a phenotype while being connected in an underlying network. Our approach is based on a minimum cut reformulation of the problem of selecting features under sparsity and connectivity constraints, which can be solved exactly and rapidly. SConES outperforms state-of-the-art competitors in terms of runtime, scales to hundreds of thousands of genetic loci and exhibits higher power in detecting causal SNPs in simulation studies than other methods. On flowering time phenotypes and genotypes from Arabidopsis thaliana, SConES detects loci that enable accurate phenotype prediction and that are supported by the literature. Availability: Code is available at http://webdav.tuebingen.mpg.de/u/karsten/Forschung/scones/. Contact: chloe-agathe.azencott@tuebingen.mpg.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23812981

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

    PubMed Central

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

    2013-01-01

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

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

    PubMed

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

    2013-01-01

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

  1. The International Association for the Study of Lung Cancer Lymph Node Map: A Radiologic Atlas and Review.

    PubMed

    Kim, Jin Hwan; van Beek, Edwin Jr; Murchison, John T; Marin, Aleksander; Mirsadraee, Saeed

    2015-07-01

    Accurate lymph node staging of lung cancer is crucial in determining optimal treatment plans and predicting patient outcome. Currently used lymph node maps have been reconciled to the internationally accepted International Association for the Study of Lung Cancer (IASLC) map published in the seventh edition of TNM classification system of malignant tumours. This article provides computed tomographic illustrations of the IASLC nodal map, to facilitate its application in day-to-day clinical practice in order to increase the appropriate classification in lung cancer staging.

  2. Genome-wide association mapping of salinity tolerance in rice (Oryza sativa).

    PubMed

    Kumar, Vinod; Singh, Anshuman; Mithra, S V Amitha; Krishnamurthy, S L; Parida, Swarup K; Jain, Sourabh; Tiwari, Kapil K; Kumar, Pankaj; Rao, Atmakuri R; Sharma, S K; Khurana, Jitendra P; Singh, Nagendra K; Mohapatra, Trilochan

    2015-04-01

    Salinity tolerance in rice is highly desirable to sustain production in areas rendered saline due to various reasons. It is a complex quantitative trait having different components, which can be dissected effectively by genome-wide association study (GWAS). Here, we implemented GWAS to identify loci controlling salinity tolerance in rice. A custom-designed array based on 6,000 single nucleotide polymorphisms (SNPs) in as many stress-responsive genes, distributed at an average physical interval of <100 kb on 12 rice chromosomes, was used to genotype 220 rice accessions using Infinium high-throughput assay. Genetic association was analysed with 12 different traits recorded on these accessions under field conditions at reproductive stage. We identified 20 SNPs (loci) significantly associated with Na(+)/K(+) ratio, and 44 SNPs with other traits observed under stress condition. The loci identified for various salinity indices through GWAS explained 5-18% of the phenotypic variance. The region harbouring Saltol, a major quantitative trait loci (QTLs) on chromosome 1 in rice, which is known to control salinity tolerance at seedling stage, was detected as a major association with Na(+)/K(+) ratio measured at reproductive stage in our study. In addition to Saltol, we also found GWAS peaks representing new QTLs on chromosomes 4, 6 and 7. The current association mapping panel contained mostly indica accessions that can serve as source of novel salt tolerance genes and alleles. The gene-based SNP array used in this study was found cost-effective and efficient in unveiling genomic regions/candidate genes regulating salinity stress tolerance in rice.

  3. Gene map of large yellow croaker (Larimichthys crocea) provides insights into teleost genome evolution and conserved regions associated with growth.

    PubMed

    Xiao, Shijun; Wang, Panpan; Zhang, Yan; Fang, Lujing; Liu, Yang; Li, Jiong-Tang; Wang, Zhi-Yong

    2015-12-22

    The genetic map of a species is essential for its whole genome assembly and can be applied to the mapping of important traits. In this study, we performed RNA-seq for a family of large yellow croakers (Larimichthys crocea) and constructed a high-density genetic map. In this map, 24 linkage groups comprised 3,448 polymorphic SNP markers. Approximately 72.4% (2,495) of the markers were located in protein-coding regions. Comparison of the croaker genome with those of five model fish species revealed that the croaker genome structure was closer to that of the medaka than to the remaining four genomes. Because the medaka genome preserves the teleost ancestral karyotype, this result indicated that the croaker genome might also maintain the teleost ancestral genome structure. The analysis also revealed different genome rearrangements across teleosts. QTL mapping and association analysis consistently identified growth-related QTL regions and associated genes. Orthologs of the associated genes in other species were demonstrated to regulate development, indicating that these genes might regulate development and growth in croaker. This gene map will enable us to construct the croaker genome for comparative studies and to provide an important resource for selective breeding of croaker.

  4. Gene map of large yellow croaker (Larimichthys crocea) provides insights into teleost genome evolution and conserved regions associated with growth

    PubMed Central

    Xiao, Shijun; Wang, Panpan; Zhang, Yan; Fang, Lujing; Liu, Yang; Li, Jiong-Tang; Wang, Zhi-Yong

    2015-01-01

    The genetic map of a species is essential for its whole genome assembly and can be applied to the mapping of important traits. In this study, we performed RNA-seq for a family of large yellow croakers (Larimichthys crocea) and constructed a high-density genetic map. In this map, 24 linkage groups comprised 3,448 polymorphic SNP markers. Approximately 72.4% (2,495) of the markers were located in protein-coding regions. Comparison of the croaker genome with those of five model fish species revealed that the croaker genome structure was closer to that of the medaka than to the remaining four genomes. Because the medaka genome preserves the teleost ancestral karyotype, this result indicated that the croaker genome might also maintain the teleost ancestral genome structure. The analysis also revealed different genome rearrangements across teleosts. QTL mapping and association analysis consistently identified growth-related QTL regions and associated genes. Orthologs of the associated genes in other species were demonstrated to regulate development, indicating that these genes might regulate development and growth in croaker. This gene map will enable us to construct the croaker genome for comparative studies and to provide an important resource for selective breeding of croaker. PMID:26689832

  5. Power lines, roads, and avian nest survival: effects on predator identity and predation intensity

    PubMed Central

    DeGregorio, Brett A; Weatherhead, Patrick J; Sperry, Jinelle H

    2014-01-01

    1 Anthropogenic alteration of landscapes can affect avian nest success by influencing the abundance, distribution, and behavior of predators. Understanding avian nest predation risk necessitates understanding how landscapes affect predator distribution and behavior. 2 From a sample of 463 nests of 17 songbird species, we evaluated how landscape features (distance to forest edge, unpaved roads, and power lines) influenced daily nest survival. We also used video cameras to identify nest predators at 137 nest predation events and evaluated how landscape features influenced predator identity. Finally, we determined the abundance and distribution of several of the principal predators using surveys and radiotelemetry. 3 Distance to power lines was the best predictor of predator identity: predation by brown-headed cowbirds (Molothrus ater), corvids (Corvus sp. and Cyanocitta cristata), racers (Coluber constrictor), and coachwhips (Masticophis flagellum) increased with proximity to power lines, whereas predation by rat snakes (Elaphe obsoleta) and raptors decreased. In some cases, predator density may reliably indicate nest predation risk because racers, corvids, and cowbirds frequently used power line right-of-ways. 4 Of five bird species with enough nests to analyze individually, daily nest survival of only indigo buntings (Passerina cyanea) decreased with proximity to power lines, despite predation by most predators at our site being positively associated with power lines. For all nesting species combined, distance to unpaved road was the model that most influenced daily nest survival. This pattern is likely a consequence of rat snakes, the locally dominant nest predator (28% of predation events), rarely using power lines and associated areas. Instead, rat snakes were frequently associated with road edges, indicating that not all edges are functionally similar. 5 Our results suggest that interactions between predators and landscape features are likely to be specific to

  6. Host selection in the forest interior: cowbirds target ground-nesting species

    USGS Publications Warehouse

    Hahn, D.C.; Hatfield, J.S.

    2000-01-01

    We investigated patterns of cowbird host selection in a large (1300 ha), unfragmented forest in eastern New York in 1992-3 to determine whether cowbird parasitism rates can be attributed to species-specific traits or to other features associated with nest sites. Nest height was significantly associated with parasitism (P = 0.003) in this community of 23 species (n = 430 nests, 23% parasitized). Further analysis revealed that the difference in mean nest heights between parasitized and unparasitized nests was due to species identity, and within each species there was no difference in mean nest heights between parasitized and unparasitized nests. These results imply that during 1992-3 cowbirds in this forest specialized on species that have low nests and did not necessarily select low nests regardless of species. This was further supported by a negative association across all 23 species between mean nest height and parasitism rate (P = 0.03). Thus, although most of the forest-nesting species in this community experienced cowbird parasitism, there was a tendency for higher parasitism rates on low-nesting species such as the Ovenbird, Black-and-white Warbler, Louisiana Waterthrush, Veery, and Hermit Thrush. The Wood Thrush, a mid-range nester which is heavily parasitized in southern Illinois, experienced only 10% parasitism in our site and ranked 9th in parasitism rate, although it was the most abundant species in this forest in terms of the number of nests found. A long-term study is necessary to determine whether this cowbird population consistently parasitizes the ground-nesting species of this forest community more often than those nesting at higher levels or whether they periodically shift among hosts at different heights and in different habitats across the local landscape.

  7. Assessing microsatellite linkage disequilibrium in wild, cultivated, and mapping populations of Theobroma cacao L and its impact on association mapping

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Linkage disequilibrium (LD) is the nonrandom association of alleles and loci within sets of genetic data and when measured over the genomes of a species can provide important indications for how future association analyses should proceed. This information can be advantageous especially for slow-gro...

  8. Genome-Wide Association Mapping of Yield and Grain Quality Traits in Winter Wheat Genotypes

    PubMed Central

    Tadesse, W.; Ogbonnaya, F. C.; Jighly, A.; Sanchez-Garcia, M.; Sohail, Q.; Rajaram, S.; Baum, M.

    2015-01-01

    The main goal of this study was to investigate the genetic basis of yield and grain quality traits in winter wheat genotypes using association mapping approach, and identify linked molecular markers for marker assisted selection. A total of 120 elite facultative/winter wheat genotypes were evaluated for yield, quality and other agronomic traits under rain-fed and irrigated conditions for two years (2011–2012) at the Tel Hadya station of ICARDA, Syria. The same genotypes were genotyped using 3,051 Diversity Array Technologies (DArT) markers, of which 1,586 were of known chromosome positions. The grain yield performance of the genotypes was highly significant both in rain-fed and irrigated sites. Average yield of the genotypes ranged from 2295 to 4038 kg/ha and 4268 to 7102 kg/ha under rain-fed and irrigated conditions, respectively. Protein content and alveograph strength (W) ranged from 13.6–16.1% and 217.6–375 Jx10-4, respectively. DArT markers wPt731910 (3B), wPt4680 (4A), wPt3509 (5A), wPt8183 (6B), and wPt0298 (2D) were significantly associated with yield under rain-fed conditions. Under irrigated condition, tPt4125 on chromosome 2B was significantly associated with yield explaining about 13% of the variation. Markers wPt2607 and wPt1482 on 5B were highly associated with protein content and alveograph strength explaining 16 and 14% of the variations, respectively. The elite genotypes have been distributed to many countries using ICARDA’s International system for potential direct release and/or use as parents after local adaptation trials by the NARSs of respective countries. The QTLs identified in this study are recommended to be used for marker assisted selection after through validation using bi-parental populations. PMID:26496075

  9. Physical cognition: birds learn the structural efficacy of nest material.

    PubMed

    Bailey, Ida E; Morgan, Kate V; Bertin, Marion; Meddle, Simone L; Healy, Susan D

    2014-06-01

    It is generally assumed that birds' choice of structurally suitable materials for nest building is genetically predetermined. Here, we tested that assumption by investigating whether experience affected male zebra finches' (Taeniopygia guttata) choice of nest material. After a short period of building with relatively flexible string, birds preferred to build with stiffer string while those that had experienced a stiffer string were indifferent to string type. After building a complete nest with either string type, however, all birds increased their preference for stiff string. The stiffer string appeared to be the more effective building material as birds required fewer pieces of stiffer than flexible string to build a roofed nest. For birds that raised chicks successfully, there was no association between the material they used to build their nest and the type they subsequently preferred. Birds' material preference reflected neither the preference of their father nor of their siblings but juvenile experience of either string type increased their preference for stiffer string. Our results represent two important advances: (i) birds choose nest material based on the structural properties of the material; (ii) nest material preference is not entirely genetically predetermined as both the type and amount of experience influences birds' choices.

  10. Postfledging nest dependence period for bald eagles in Florida

    USGS Publications Warehouse

    Wood, P.B.; Collopy, M.W.; Sekerak, C.M.

    1998-01-01

    We studied the postfledging dependency period in bald eagles (Haliaeetus leucocephalus), a little studied but important period in the life cycle of avian species. Bald eagles in Florida had a postfledging dependency period of 4-11 weeks (15-22 weeks old). The length of the dependency period did not vary by year of study, sex, number of fledgings, timing of fledging, or hatch order (P > 0.05). Mean distance fledglings ranged from the nest increased with age, but they were observed in the nest or nest tree throughout the postfledging dependency period. Distance from the nest did not vary by sex, number of fledglings, or timing of fledging (P > 0.05). Over 80% of the fledgling observations were within 229 m of the nest. The boundary of the primary protection zone specified in the bald eagle habitat management guidelines for the southeastern United States is 229 m. Restrictions on human disturbance around nest sites should remain in place during the postfledging dependency period because of the close association of fledglings with the nest site. Restrictions also should be flexible because of the varying length of the dependency period.

  11. Genome Wide Association Mapping for the Tolerance to the Polyamine Oxidase Inhibitor Guazatine in Arabidopsis thaliana

    PubMed Central

    Atanasov, Kostadin E.; Barboza-Barquero, Luis; Tiburcio, Antonio F.; Alcázar, Rubén

    2016-01-01

    Guazatine is a potent inhibitor of polyamine oxidase (PAO) activity. In agriculture, guazatine is used as non-systemic contact fungicide efficient in the protection of cereals and citrus fruits against disease. The composition of guazatine is complex, mainly constituted by a mixture of synthetic guanidated polyamines (polyaminoguanidines). Here, we have studied the effects from exposure to guazatine in the weed Arabidopsis thaliana. We report that micromolar concentrations of guazatine are sufficient to inhibit growth of Arabidopsis seedlings and induce chlorosis, whereas germination is barely affected. We observed the occurrence of quantitative variation in the response to guazatine between 107 randomly chosen Arabidopsis accessions. This enabled us to undertake genome-wide association (GWA) mapping that identified a locus on chromosome one associated with guazatine tolerance. CHLOROPHYLLASE 1 (CLH1) within this locus was studied as candidate gene, together with its paralog (CLH2). The analysis of independent clh1-2, clh1-3, clh2-3, clh2-2, and double clh1-2 clh2-3 mutant alleles indicated that CLH1 and/or CLH2 loss-of-function or expression down-regulation promote guazatine tolerance in Arabidopsis. We report a natural mechanism by which Arabidopsis populations can overcome toxicity by the fungicide guazatine. PMID:27092150

  12. Development of exposome correlation globes to map out environment-wide associations.

    PubMed

    Patel, Chirag J; Manrai, Arjun K

    2015-01-01

    The environment plays a major role in influencing diseases and health. The phenomenon of environmental exposure is complex and humans are not exposed to one or a handful factors but potentially hundreds factors throughout their lives. The exposome, the totality of exposures encountered from birth, is hypothesized to consist of multiple inter-dependencies, or correlations, between individual exposures. These correlations may reflect how individuals are exposed. Currently, we lack methods to comprehensively identify robust and replicated correlations between environmental exposures of the exposome. Further, we have not mapped how exposures associated with disease identified by environment-wide association studies (EWAS) are correlated with other exposures. To this end, we implement methods to describe a first "exposome globe", a comprehensive display of replicated correlations between individual exposures of the exposome. First, we describe overall characteristics of the dense correlations between exposures, showing that we are able to replicate 2,656 correlations between individual exposures of 81,937 total considered (3%). We document the correlation within and between broad a priori defined categories of exposures (e.g., pollutants and nutrient exposures). We also demonstrate utility of the exposome globe to contextualize exposures found through two EWASs in type 2 diabetes and all-cause mortality, such as exposure clusters putatively related to smoking behaviors and persistent pollutant exposure. The exposome globe construct is a useful tool for the display and communication of the complex relationships between exposure factors and between exposure factors related to disease status.

  13. Mapping the Extracellular and Membrane Proteome Associated with the Vasculature and the Stroma in the Embryo*

    PubMed Central

    Soulet, Fabienne; Kilarski, Witold W.; Roux-Dalvai, Florence; Herbert, John M. J.; Sacewicz, Izabela; Mouton-Barbosa, Emmanuelle; Bicknell, Roy; Lalor, Patricia; Monsarrat, Bernard; Bikfalvi, Andreas

    2013-01-01

    In order to map the extracellular or membrane proteome associated with the vasculature and the stroma in an embryonic organism in vivo, we developed a biotinylation technique for chicken embryo and combined it with mass spectrometry and bioinformatic analysis. We also applied this procedure to implanted tumors growing on the chorioallantoic membrane or after the induction of granulation tissue. Membrane and extracellular matrix proteins were the most abundant components identified. Relative quantitative analysis revealed differential protein expression patterns in several tissues. Through a bioinformatic approach, we determined endothelial cell protein expression signatures, which allowed us to identify several proteins not yet reported to be associated with endothelial cells or the vasculature. This is the first study reported so far that applies in vivo biotinylation, in combination with robust label-free quantitative proteomics approaches and bioinformatic analysis, to an embryonic organism. It also provides the first description of the vascular and matrix proteome of the embryo that might constitute the starting point for further developments. PMID:23674615

  14. Genome Wide Association Mapping for the Tolerance to the Polyamine Oxidase Inhibitor Guazatine in Arabidopsis thaliana.

    PubMed

    Atanasov, Kostadin E; Barboza-Barquero, Luis; Tiburcio, Antonio F; Alcázar, Rubén

    2016-01-01

    Guazatine is a potent inhibitor of polyamine oxidase (PAO) activity. In agriculture, guazatine is used as non-systemic contact fungicide efficient in the protection of cereals and citrus fruits against disease. The composition of guazatine is complex, mainly constituted by a mixture of synthetic guanidated polyamines (polyaminoguanidines). Here, we have studied the effects from exposure to guazatine in the weed Arabidopsis thaliana. We report that micromolar concentrations of guazatine are sufficient to inhibit growth of Arabidopsis seedlings and induce chlorosis, whereas germination is barely affected. We observed the occurrence of quantitative variation in the response to guazatine between 107 randomly chosen Arabidopsis accessions. This enabled us to undertake genome-wide association (GWA) mapping that identified a locus on chromosome one associated with guazatine tolerance. CHLOROPHYLLASE 1 (CLH1) within this locus was studied as candidate gene, together with its paralog (CLH2). The analysis of independent clh1-2, clh1-3, clh2-3, clh2-2, and double clh1-2 clh2-3 mutant alleles indicated that CLH1 and/or CLH2 loss-of-function or expression down-regulation promote guazatine tolerance in Arabidopsis. We report a natural mechanism by which Arabidopsis populations can overcome toxicity by the fungicide guazatine. PMID:27092150

  15. Nest poaching in Neotropical parrots

    USGS Publications Warehouse

    Wright, T.F.; Toft, C.A.; Enkerlin-Hoeflich, E.; Gonzalez-Elizondo, J.; Albornoz, M.; Rodriguez-Ferraro, A.; Rojas-Suarez, F.; Sanz, V.; Trujillo, A.; Beissinger, S.R.; Berovides A., V.; Galvez A., X.; Brice, A.T.; Joyner, K.; Eberhard, J.; Gilardi, J.; Koenig, S.E.; Stoleson, S.; Martuscelli, P.; Meyers, J.M.; Renton, K.; Rodriguez, A.M.; Sosa-Asanza, A.C.; Vilella, F.J.; Wiley, J.W.

    2001-01-01

    Although the poaching of nestlings for the pet trade is thought to contribute to the decline of many species of parrots, its effects have been poorly demonstrated. We calculated rates of mortality due to nest poaching in 23 studies of Neotropical parrots, representing 4024 nesting attempts in 21 species and 14 countries. We also examined how poaching rates vary with geographic region, presence of active protection programs, conservation status and economic value of a species, and passage of the U.S. Wild Bird Conservation Act. The average poaching rate across all studies was 30% of all nests observed. Thirteen studies reported poaching rates of >20%, and four reported rates of >70%. Only six studies documented no nest poaching. Of these, four were conducted on islands in the Caribbean region, which had significantly lower poaching rates than the mainland Neotropics. The other two studies that showed no poaching were conducted on the two species with the lowest economic value in our sample (U.S. retail price). In four studies that allowed direct comparison between poaching at sites with active nest protection versus that at unprotected sites, poaching rates were significantly lower at protected sites, suggesting that active protection efforts can be effective in reducing nest poaching. In those studies conducted both before and after the passage of the U.S. Wild Bird Conservation Act, poaching rates were found to be significantly lower following its enactment than in the period before. This result supports the hypothesis that the legal and illegal parrot trades are positively related, rather than inversely related as has been suggested by avicultural interests. Overall, our study indicates that poaching of parrot nestlings for economic gain is a widespread and biologically significant source of nest mortality in Neotropical parrots.

  16. Comparative mapping of the constitutional and tumor-associated 11;22 translocations.

    PubMed Central

    Budarf, M; Sellinger, B; Griffin, C; Emanuel, B S

    1989-01-01

    The reciprocal t(11;22)(q23;q11) is the most common non-Robertsonian constitutional translocation in humans. The tumor-associated 11;22 rearrangement of Ewing sarcoma (ES) and peripheral neuroepithelioma (NE) is cytologically very similar to the 11;22 constitutional rearrangement. Using immunoglobulin light-chain constant region, ETS1 probes, and the technique of in situ hybridization, we previously were able to show that the constitutional and ES/NE breakpoints are different. As a first step toward isolating these translocation junctions and to further distinguish between them, we have made somatic cell hybrids. Cells from a constitutional 46,XX,inv(9),t(11;22) carrier and from an ES cell line with a t(11;22) were separately fused to a hypoxanthine-guanine phosphoribosyltransferase-deficient Chinese hamster cell line (RJK88). Resulting clones were screened with G-banding and Southern hybridization. Hybrid clones derived from the constitutional t(11;22) were established which contained the der(22) and both the der(22) and the der(11). Hybrid clones derived from the ES cell line containing the der(11) were isolated. Using the technique of Southern hybridization we have sublocalized the loci; ApoA1/C3, CD3D, ETS1, PBGD, THY1, D11S29, D11S34, and D11S147 to the region between the two breakpoints on chromosome 11 and V lambda I, V lambda VI, V lambda VII, and D22S10 to the region between the breakpoints on chromosome 22. Using anonymous DNA probes, we found that D22S9 and D22S24 map proximal to the constitutional breakpoint and that D22S15 and D22S32 map distal to the ES breakpoint on chromosome 22. Images Figure 1 Figure 2 Figure 5 PMID:2741943

  17. Epistatic association mapping for alkaline and salinity tolerance traits in the soybean germination stage.

    PubMed

    Zhang, Wen-Jie; Niu, Yuan; Bu, Su-Hong; Li, Meng; Feng, Jian-Ying; Zhang, Jin; Yang, Sheng-Xian; Odinga, Medrine Mmayi; Wei, Shi-Ping; Liu, Xiao-Feng; Zhang, Yuan-Ming

    2014-01-01

    Soil salinity and alkalinity are important abiotic components that frequently have critical effects on crop growth, productivity and quality. Developing soybean cultivars with high salt tolerance is recognized as an efficient way to maintain sustainable soybean production in a salt stress environment. However, the genetic mechanism of the tolerance must first be elucidated. In this study, 257 soybean cultivars with 135 SSR markers were used to perform epistatic association mapping for salt tolerance. Tolerance was evaluated by assessing the main root length (RL), the fresh and dry weights of roots (FWR and DWR), the biomass of seedlings (BS) and the length of hypocotyls (LH) of healthy seedlings after treatments with control, 100 mM NaCl or 10 mM Na2CO3 solutions for approximately one week under greenhouse conditions. A total of 83 QTL-by-environment (QE) interactions for salt tolerance index were detected: 24 for LR, 12 for FWR, 11 for DWR, 15 for LH and 21 for BS, as well as one epistatic QTL for FWR. Furthermore, 86 QE interactions for alkaline tolerance index were found: 17 for LR, 16 for FWR, 17 for DWR, 18 for LH and 18 for BS. A total of 77 QE interactions for the original trait indicator were detected: 17 for LR, 14 for FWR, 4 for DWR, 21 for LH and 21 for BS, as well as 3 epistatic QTL for BS. Small-effect QTL were frequently observed. Several soybean genes with homology to Arabidopsis thaliana and soybean salt tolerance genes were found in close proximity to the above QTL. Using the novel alleles of the QTL detected above, some elite parental combinations were designed, although these QTL need to be further confirmed. The above results provide a valuable foundation for fine mapping, cloning and molecular breeding by design for soybean alkaline and salt tolerance. PMID:24416275

  18. Incorporation of cigarette butts into nests reduces nest ectoparasite load in urban birds: new ingredients for an old recipe?

    PubMed Central

    Suárez-Rodríguez, Monserrat; López-Rull, Isabel; Macías Garcia, Constantino

    2013-01-01

    Birds are known to respond to nest-dwelling parasites by altering behaviours. Some bird species, for example, bring fresh plants to the nest, which contain volatile compounds that repel parasites. There is evidence that some birds living in cities incorporate cigarette butts into their nests, but the effect (if any) of this behaviour remains unclear. Butts from smoked cigarettes retain substantial amounts of nicotine and other compounds that may also act as arthropod repellents. We provide the first evidence that smoked cigarette butts may function as a parasite repellent in urban bird nests. The amount of cellulose acetate from butts in nests of two widely distributed urban birds was negatively associated with the number of nest-dwelling parasites. Moreover, when parasites were attracted to heat traps containing smoked or non-smoked cigarette butts, fewer parasites reached the former, presumably due to the presence of nicotine. Because urbanization changes the abundance and type of resources upon which birds depend, including nesting materials and plants involved in self-medication, our results are consistent with the view that urbanization imposes new challenges on birds that are dealt with using adaptations evolved elsewhere. PMID:23221874

  19. Incorporation of cigarette butts into nests reduces nest ectoparasite load in urban birds: new ingredients for an old recipe?

    PubMed

    Suárez-Rodríguez, Monserrat; López-Rull, Isabel; Garcia, Constantino Macías

    2013-02-23

    Birds are known to respond to nest-dwelling parasites by altering behaviours. Some bird species, for example, bring fresh plants to the nest, which contain volatile compounds that repel parasites. There is evidence that some birds living in cities incorporate cigarette butts into their nests, but the effect (if any) of this behaviour remains unclear. Butts from smoked cigarettes retain substantial amounts of nicotine and other compounds that may also act as arthropod repellents. We provide the first evidence that smoked cigarette butts may function as a parasite repellent in urban bird nests. The amount of cellulose acetate from butts in nests of two widely distributed urban birds was negatively associated with the number of nest-dwelling parasites. Moreover, when parasites were attracted to heat traps containing smoked or non-smoked cigarette butts, fewer parasites reached the former, presumably due to the presence of nicotine. Because urbanization changes the abundance and type of resources upon which birds depend, including nesting materials and plants involved in self-medication, our results are consistent with the view that urbanization imposes new challenges on birds that are dealt with using adaptations evolved elsewhere.

  20. Nesting biology of Lesser Canada Geese, Branta canadensis parvipes, along the Tanana River, Alaska

    USGS Publications Warehouse

    Ely, C.R.; Pearce, J.M.; Ruess, R.W.

    2008-01-01

    Lesser Canada Geese (Branta canadensis parvipes) are widespread throughout interior regions of Alaska and Canada, yet there have been no published studies documenting basic aspects of their nesting biology. We conducted a study to determine reproductive parameters of Lesser Canada Geese nesting along the Tanana River near the city of Fairbanks, in interior Alaska. Fieldwork was conducted in May of 2003, and consisted of locating nests along the riparian corridor between Fairbanks and Northpole, Alaska. Nests were found on gravel islands and shore habitats along the Tanana River, and were most commonly observed among driftwood logs associated with patches of alder (Alnus spp.) and willow (Salix spp.). Peak of nest initiation was 3-8 May, with a range from 27 April to 20 May; renesting was likely. Clutches ranged in size from 2 to 7 eggs and averaged 4.6 eggs. There was a negative correlation between clutch size and date of nest initiation. Egg size (X?? mass = 128 g) was similar to other medium-sized Canada Geese. A positive correlation between egg size and clutch size was likely related to female age. Nineteen of 28 nests (68%) were active when visited; nests located on islands with nesting Mew Gulls (Larus canus) were more likely to be active than nests located elsewhere. Evidence at nest sites implicated Bald Eagles (Haliaeetus leucocephalus) and Red Foxes (Vulpes vulpes) as nest predators.

  1. Brood parasitism among waterfowl nesting on islands and peninsulas in North Dakota

    USGS Publications Warehouse

    Lokemoen, J.T.

    1991-01-01

    During 1985 and 1986 I studied interspecific brood parasitism among seven species of waterfowl nesting on 36 islands and 24 peninsulas in central North Dakota. On islands, 40% of 178 nests were parasitized with an average of 4.3 parasitic eggs, and on peninsulas 2% of 275 nests were parasitized with an average of 2.2 parasitic eggs. Redheads (Aythya americana) were the primary parasite, adding eggs to 92% of all parasitized nests. Species nesting in open cover were parasitized at a higher rate than species nesting in dense cover. Nests with parasitic eggs had fewer host eggs and there was a negative association between the number of parasitic eggs and the success of host eggs. Parasitized nests had lower success, but additional parasitic eggs had no added influence on nest success. Interspecific brood parasitism had significant negative effects on dabbling ducks on islands but Lesser Scaup (Aythya affinis) were little affected. Even so, the number of young hatched per nest was much higher on islands because of the high loss of eggs to predators on the mainland. Parasitic eggs were deposited during the middle of the nesting season, but the peak of parasitic laying occurred before the peak of normal nesting.

  2. High-resolution genetic mapping of allelic variants associated with cell wall chemistry in Populus

    SciTech Connect

    Muchero, Wellington; Guo, Jianjun; Difazio, Stephen P.; Chen, Jay; Ranjan, Priya; Slavov, Gancho; Gunter, Lee E.; Jawdy, Sara; Bryan, Anthony C.; Sykes, Robert; Ziebell, Angela L.; Klapste, Jaroslav; Porth, Ilga; Skyba, Oleksandr; Unda, Faride; El-Kassaby, Yousry; Douglas, Carl; Mansfield, Shawn; Martin, Joel; Schackwitz, Wendy; Evans, Luke M.; Czarnecki, Olaf; Tuskan, Gerald A.

    2015-01-23

    We report the identification of six genetic loci and the allelic-variants associated with Populus cell wall phenotypes determined independently using pyrolysis Molecular Beam Mass Spectrometry (pyMBMS), saccharification assay and wet chemistry in two partially overlapping populations of P. trichocarpa genotypes sampled from multiple environments in the Pacific Northwest of North America. All 6 variants co-located with a quantitative trait locus (QTL) hotspot on chromosome XIV for lignin content, syringyl to guaiacyl (S/G) ratio, 5- and 6- carbon sugars identified in an interspecific P. trichocarpa x P. deltoides pseudo-backcross mapping pedigree. Genomic intervals containing an amino acid transporter, a MYB transcription factor, an angustifolia CtBP transcription factor, a copper transport protein ATOX1-related, a Ca2+ transporting ATPase and a protein kinase were identified within 5 QTL regions. Each interval contained single nucleotide polymorphisms (SNPs) that were significantly associated to cell-wall phenotypes, with associations exceeding the chromosome-wise Bonferroni-adjusted p-values in at least one environment. cDNA sequencing for allelic variants of 3 of the 6 genes identified polymorphisms leading to premature stop codons in the MYB transcription factor and protein kinase. On the other hand, variants of the Angustifolia CtBP transcription factor exhibited a polyglutamine (PolyQ) length polymorphism. Results from transient protoplast assays suggested that each of the polymorphisms conferred allelic differences in activation of cellulose, hemicelluloses and lignin pathway marker genes, with truncated and short PolyQ alleles exhibiting significantly reduced marker gene activation. Genes identified in this study represent novel targets for reducing cell wall recalcitrance for lignocellulosic biofuels production using plant biomass.

  3. High-resolution genetic mapping of allelic variants associated with cell wall chemistry in Populus

    DOE PAGES

    Muchero, Wellington; Guo, Jianjun; Difazio, Stephen P.; Chen, Jay; Ranjan, Priya; Slavov, Gancho; Gunter, Lee E.; Jawdy, Sara; Bryan, Anthony C.; Sykes, Robert; et al

    2015-01-23

    We report the identification of six genetic loci and the allelic-variants associated with Populus cell wall phenotypes determined independently using pyrolysis Molecular Beam Mass Spectrometry (pyMBMS), saccharification assay and wet chemistry in two partially overlapping populations of P. trichocarpa genotypes sampled from multiple environments in the Pacific Northwest of North America. All 6 variants co-located with a quantitative trait locus (QTL) hotspot on chromosome XIV for lignin content, syringyl to guaiacyl (S/G) ratio, 5- and 6- carbon sugars identified in an interspecific P. trichocarpa x P. deltoides pseudo-backcross mapping pedigree. Genomic intervals containing an amino acid transporter, a MYB transcriptionmore » factor, an angustifolia CtBP transcription factor, a copper transport protein ATOX1-related, a Ca2+ transporting ATPase and a protein kinase were identified within 5 QTL regions. Each interval contained single nucleotide polymorphisms (SNPs) that were significantly associated to cell-wall phenotypes, with associations exceeding the chromosome-wise Bonferroni-adjusted p-values in at least one environment. cDNA sequencing for allelic variants of 3 of the 6 genes identified polymorphisms leading to premature stop codons in the MYB transcription factor and protein kinase. On the other hand, variants of the Angustifolia CtBP transcription factor exhibited a polyglutamine (PolyQ) length polymorphism. Results from transient protoplast assays suggested that each of the polymorphisms conferred allelic differences in activation of cellulose, hemicelluloses and lignin pathway marker genes, with truncated and short PolyQ alleles exhibiting significantly reduced marker gene activation. Genes identified in this study represent novel targets for reducing cell wall recalcitrance for lignocellulosic biofuels production using plant biomass.« less

  4. Application of Selection Mapping to Identify Genomic Regions Associated with Dairy Production in Sheep

    PubMed Central

    Gutiérrez-Gil, Beatriz; Arranz, Juan Jose; Pong-Wong, Ricardo; García-Gámez, Elsa; Kijas, James; Wiener, Pamela

    2014-01-01

    In Europe, especially in Mediterranean areas, the sheep has been traditionally exploited as a dual purpose species, with income from both meat and milk. Modernization of husbandry methods and the establishment of breeding schemes focused on milk production have led to the development of “dairy breeds.” This study investigated selective sweeps specifically related to dairy production in sheep by searching for regions commonly identified in different European dairy breeds. With this aim, genotypes from 44,545 SNP markers covering the sheep autosomes were analysed in both European dairy and non-dairy sheep breeds using two approaches: (i) identification of genomic regions showing extreme genetic differentiation between each dairy breed and a closely related non-dairy breed, and (ii) identification of regions with reduced variation (heterozygosity) in the dairy breeds using two methods. Regions detected in at least two breeds (breed pairs) by the two approaches (genetic differentiation and at least one of the heterozygosity-based analyses) were labeled as core candidate convergence regions and further investigated for candidate genes. Following this approach six regions were detected. For some of them, strong candidate genes have been proposed (e.g. ABCG2, SPP1), whereas some other genes designated as candidates based on their association with sheep and cattle dairy traits (e.g. LALBA, DGAT1A) were not associated with a detectable sweep signal. Few of the identified regions were coincident with QTL previously reported in sheep, although many of them corresponded to orthologous regions in cattle where QTL for dairy traits have been identified. Due to the limited number of QTL studies reported in sheep compared with cattle, the results illustrate the potential value of selection mapping to identify genomic regions associated with dairy traits in sheep. PMID:24788864

  5. Mapping playa evaporite minerals and associated sediments in Death Valley, California, with multispectral thermal infrared images

    USGS Publications Warehouse

    Crowley, J.K.; Hook, S.J.

    1996-01-01

    Efflorescent salt crusts and associated sediments in Death Valley, California, were studied with remote-sensing data acquired by the NASA thermal infrared multispectral scanner (TIMS). Nine spectral classes that represent a variety of surface materials were distinguished, including several classes that reflect important aspects of the playa groundwater chemistry and hydrology. Evaporite crusts containing abundant thenardite (sodium sulfate) were mapped along the northern and eastern margins of the Cottonball Basin, areas where the inflow waters are rich in sodium. Gypsum (calcium sulfate) crusts were more common in the Badwater Basin, particularly near springs associated with calcic groundwaters along the western basin margin. Evaporite-rich crusts generally marked areas where groundwater is periodically near the surface and thus able to replenish the crusts though capillary evaporation. Detrital silicate minerals were prevalent in other parts of the salt pan where shallow groundwater does not affect the surface composition. The surface features in Death Valley change in response to climatic variations on several different timescales. For example, salt crusts on low-lying mudflats form and redissolve during seasonal-to-interannual cycles of wetting and desiccation. In contrast, recent flooding and erosion of rough-salt surfaces in Death Valley probably reflect increased regional precipitation spanning several decades. Remote-sensing observations of playas can provide a means for monitoring changes in evaporite facies and for better understanding the associated climatic processes. At present, such studies are limited by the availability of suitable airborne scanner data. However, with the launch of the Earth Observing System (EOS) AM-1 Platform in 1998, multispectral visible/near-infrared and thermal infrared remote-sensing data will become globally available. Copyright 1996 by the American Geophysical Union.

  6. Nest use is influenced by the positions of nests and drinkers in aviaries.

    PubMed

    Lentfer, T L; Gebhardt-Henrich, S G; Fröhlich, E K F; von Borell, E

    2013-06-01

    The influence of the nest location and the placement of nipple drinkers on nest use by laying hens in a commercial aviary was assessed. Twenty pens in a laying hen house were equipped with the same commercial aviary system, but the pens differed in the nest location and the placement of nipple drinkers. Nests were placed along the walls in 10 pens, and nipple drinkers were installed in front of the nests in 5 of these pens. The other 10 pens were equipped with nests placed on a tier within the aviary (integrated nests). Nipple drinkers were installed in front of the nests in 5 of these pens. A total of 225 Lohmann Selected Leghorns were housed per pen. The hens were offered 4 nests per pen: 2 facing the service corridor of the laying hen house and 2 facing the outdoor area. The numbers of nest eggs and mislaid eggs were counted daily per pen. At 25, 36, and 43 wk of age, the nest platforms were videotaped and the behavior of laying hens in front of the nests was analyzed. The nest location affected the stationary and locomotive behaviors in front of the nests. Hens in front of the integrated nests and the nests with drinkers displayed more stationary behaviors than hens in front of wall-placed nests or nests without drinkers. No difference in the number of nest eggs could be detected, but the integration of the nests inside the aviary led to a more even distribution of hens while nest searching. In the pens with wall-placed nests, significantly more hens laid eggs in the nests at the wall near the service corridor than at the wall near the outdoor area. Due to this imbalance, crowding in front of the preferred nests occurred and pushing and agonistic interactions on the nest platforms were significantly more frequent. Placement of nipple drinkers in front of nests had no effect on the number of eggs laid in those nests.

  7. Successful nesting behavior of Puerto Rican parrots

    USGS Publications Warehouse

    Wilson, K.A.; Field, R.; Wilson, M.H.

    1995-01-01

    We analyzed nesting behavior of five pairs of the endangered Puerto Rican Parrot (Amazona vittata) during eight successful nesting attempts. Each stage of the nesting cycle (egg laying, incubation, early chick rearing, and late chick rearing) was characterized by distinct trends or levels of behavior. During egg laying, female attentiveness to tile nest increased, and male attentiveness decreased. Throughout incubation and the first several days of early chick rearing, females were highly attentive to their nests, whereas males rarely entered the nest cavities. Female attentiveness then began to decline. Male attentiveness to the nest was sporadic until chicks were 10-12 days old. when all males began to enter their nests at least once each day. During late chick rearing, both male and female attentiveness were erratic and highly variable. Biologists may be able to use these results to identify nest problems and the need for management intervention when patterns of nest attentiveness deviate from the limits described in this study..

  8. Whole genome association mapping of plant height in winter wheat (Triticum aestivum L.).

    PubMed

    Zanke, Christine D; Ling, Jie; Plieske, Jörg; Kollers, Sonja; Ebmeyer, Erhard; Korzun, Viktor; Argillier, Odile; Stiewe, Gunther; Hinze, Maike; Neumann, Kerstin; Ganal, Martin W; Röder, Marion S

    2014-01-01

    The genetic architecture of plant height was investigated in a set of 358 recent European winter wheat varieties plus 14 spring wheat varieties based on field data in eight environments. Genotyping of diagnostic markers revealed the Rht-D1b mutant allele in 58% of the investigated varieties, while the Rht-B1b mutant was only present in 7% of the varieties. Rht-D1 was significantly associated with plant height by using a mixed linear model and employing a kinship matrix to correct for population stratification. Further genotyping data included 732 microsatellite markers, resulting in 770 loci, of which 635 markers were placed on the ITMI map plus a set of 7769 mapped SNP markers genotyped with the 90 k iSELECT chip. When Bonferroni correction was applied, a total of 153 significant marker-trait associations (MTAs) were observed for plant height and the SSR markers (-log10 (P-value) ≥ 4.82) and 280 (-log10 (P-value) ≥ 5.89) for the SNPs. Linear regression between the most effective markers and the BLUEs for plant height indicated additive effects for the MTAs of different chromosomal regions. Analysis of syntenic regions in the rice genome revealed closely linked rice genes related to gibberellin acid (GA) metabolism and perception, i.e. GA20 and GA2 oxidases orthologous to wheat chromosomes 1A, 2A, 3A, 3B, 5B, 5D and 7B, ent-kaurenoic acid oxidase orthologous to wheat chromosome 7A, ent-kaurene synthase on wheat chromosome 2B, as well as GA-receptors like DELLA genes orthologous to wheat chromosomes 4B, 4D and 7A and genes of the GID family orthologous to chromosomes 2B and 5B. The data indicated that besides the widely used GA-insensitive dwarfing genes Rht-B1 and Rht-D1 there is a wide spectrum of loci available that could be used for modulating plant height in variety development.

  9. Whole genome association mapping of plant height in winter wheat (Triticum aestivum L.).

    PubMed

    Zanke, Christine D; Ling, Jie; Plieske, Jörg; Kollers, Sonja; Ebmeyer, Erhard; Korzun, Viktor; Argillier, Odile; Stiewe, Gunther; Hinze, Maike; Neumann, Kerstin; Ganal, Martin W; Röder, Marion S

    2014-01-01

    The genetic architecture of plant height was investigated in a set of 358 recent European winter wheat varieties plus 14 spring wheat varieties based on field data in eight environments. Genotyping of diagnostic markers revealed the Rht-D1b mutant allele in 58% of the investigated varieties, while the Rht-B1b mutant was only present in 7% of the varieties. Rht-D1 was significantly associated with plant height by using a mixed linear model and employing a kinship matrix to correct for population stratification. Further genotyping data included 732 microsatellite markers, resulting in 770 loci, of which 635 markers were placed on the ITMI map plus a set of 7769 mapped SNP markers genotyped with the 90 k iSELECT chip. When Bonferroni correction was applied, a total of 153 significant marker-trait associations (MTAs) were observed for plant height and the SSR markers (-log10 (P-value) ≥ 4.82) and 280 (-log10 (P-value) ≥ 5.89) for the SNPs. Linear regression between the most effective markers and the BLUEs for plant height indicated additive effects for the MTAs of different chromosomal regions. Analysis of syntenic regions in the rice genome revealed closely linked rice genes related to gibberellin acid (GA) metabolism and perception, i.e. GA20 and GA2 oxidases orthologous to wheat chromosomes 1A, 2A, 3A, 3B, 5B, 5D and 7B, ent-kaurenoic acid oxidase orthologous to wheat chromosome 7A, ent-kaurene synthase on wheat chromosome 2B, as well as GA-receptors like DELLA genes orthologous to wheat chromosomes 4B, 4D and 7A and genes of the GID family orthologous to chromosomes 2B and 5B. The data indicated that besides the widely used GA-insensitive dwarfing genes Rht-B1 and Rht-D1 there is a wide spectrum of loci available that could be used for modulating plant height in variety development. PMID:25405621

  10. Construction of a high-density genetic map for grape using next generation restriction-site associated DNA sequencing

    PubMed Central

    2012-01-01

    Background Genetic mapping and QTL detection are powerful methodologies in plant improvement and breeding. Construction of a high-density and high-quality genetic map would be of great benefit in the production of superior grapes to meet human demand. High throughput and low cost of the recently developed next generation sequencing (NGS) technology have resulted in its wide application in genome research. Sequencing restriction-site associated DNA (RAD) might be an efficient strategy to simplify genotyping. Combining NGS with RAD has proven to be powerful for single nucleotide polymorphism (SNP) marker development. Results An F1 population of 100 individual plants was developed. In-silico digestion-site prediction was used to select an appropriate restriction enzyme for construction of a RAD sequencing library. Next generation RAD sequencing was applied to genotype the F1 population and its parents. Applying a cluster strategy for SNP modulation, a total of 1,814 high-quality SNP markers were developed: 1,121 of these were mapped to the female genetic map, 759 to the male map, and 1,646 to the integrated map. A comparison of the genetic maps to the published Vitis vinifera genome revealed both conservation and variations. Conclusions The applicability of next generation RAD sequencing for genotyping a grape F1 population was demonstrated, leading to the successful development of a genetic map with high density and quality using our designed SNP markers. Detailed analysis revealed that this newly developed genetic map can be used for a variety of genome investigations, such as QTL detection, sequence assembly and genome comparison. PMID:22908993

  11. Applying MetaMap to Medline for identifying novel associations in a large clinical dataset: a feasibility analysis

    PubMed Central

    Hanauer, David A; Saeed, Mohammed; Zheng, Kai; Mei, Qiaozhu; Shedden, Kerby; Aronson, Alan R; Ramakrishnan, Naren

    2014-01-01

    Objective We describe experiments designed to determine the feasibility of distinguishing known from novel associations based on a clinical dataset comprised of International Classification of Disease, V.9 (ICD-9) codes from 1.6 million patients by comparing them to associations of ICD-9 codes derived from 20.5 million Medline citations processed using MetaMap. Associations appearing only in the clinical dataset, but not in Medline citations, are potentially novel. Methods Pairwise associations of ICD-9 codes were independently identified in both the clinical and Medline datasets, which were then compared to quantify their degree of overlap. We also performed a manual review of a subset of the associations to validate how well MetaMap performed in identifying diagnoses mentioned in Medline citations that formed the basis of the Medline associations. Results The overlap of associations based on ICD-9 codes in the clinical and Medline datasets was low: only 6.6% of the 3.1 million associations found in the clinical dataset were also present in the Medline dataset. Further, a manual review of a subset of the associations that appeared in both datasets revealed that co-occurring diagnoses from Medline citations do not always represent clinically meaningful associations. Discussion Identifying novel associations derived from large clinical datasets remains challenging. Medline as a sole data source for existing knowledge may not be adequate to filter out widely known associations. Conclusions In this study, novel associations were not readily identified. Further improvements in accuracy and relevance for tools such as MetaMap are needed to realize their expected utility. PMID:24928177

  12. Evidence of territoriality and species interactions from spatial point-pattern analyses of subarctic-nesting geese.

    PubMed

    Reiter, Matthew E; Andersen, David E

    2013-01-01

    Quantifying spatial patterns of bird nests and nest fate provides insights into processes influencing a species' distribution. At Cape Churchill, Manitoba, Canada, recent declines in breeding Eastern Prairie Population Canada geese (Branta canadensis interior) has coincided with increasing populations of nesting lesser snow geese (Chen caerulescens caerulescens) and Ross's geese (Chen rossii). We conducted a spatial analysis of point patterns using Canada goose nest locations and nest fate, and lesser snow goose nest locations at two study areas in northern Manitoba with different densities and temporal durations of sympatric nesting Canada and lesser snow geese. Specifically, we assessed (1) whether Canada geese exhibited territoriality and at what scale and nest density; and (2) whether spatial patterns of Canada goose nest fate were associated with the density of nesting lesser snow geese as predicted by the protective-association hypothesis. Between 2001 and 2007, our data suggest that Canada geese were territorial at the scale of nearest neighbors, but were aggregated when considering overall density of conspecifics at slightly broader spatial scales. The spatial distribution of nest fates indicated that lesser snow goose nest proximity and density likely influence Canada goose nest fate. Our analyses of spatial point patterns suggested that continued changes in the distribution and abundance of breeding lesser snow geese on the Hudson Bay Lowlands may have impacts on the reproductive performance of Canada geese, and subsequently the spatial distribution of Canada goose nests. PMID:24312520

  13. Evidence of territoriality and species interactions from spatial point-pattern analyses of subarctic-nesting geese.

    PubMed

    Reiter, Matthew E; Andersen, David E

    2013-01-01

    Quantifying spatial patterns of bird nests and nest fate provides insights into processes influencing a species' distribution. At Cape Churchill, Manitoba, Canada, recent declines in breeding Eastern Prairie Population Canada geese (Branta canadensis interior) has coincided with increasing populations of nesting lesser snow geese (Chen caerulescens caerulescens) and Ross's geese (Chen rossii). We conducted a spatial analysis of point patterns using Canada goose nest locations and nest fate, and lesser snow goose nest locations at two study areas in northern Manitoba with different densities and temporal durations of sympatric nesting Canada and lesser snow geese. Specifically, we assessed (1) whether Canada geese exhibited territoriality and at what scale and nest density; and (2) whether spatial patterns of Canada goose nest fate were associated with the density of nesting lesser snow geese as predicted by the protective-association hypothesis. Between 2001 and 2007, our data suggest that Canada geese were territorial at the scale of nearest neighbors, but were aggregated when considering overall density of conspecifics at slightly broader spatial scales. The spatial distribution of nest fates indicated that lesser snow goose nest proximity and density likely influence Canada goose nest fate. Our analyses of spatial point patterns suggested that continued changes in the distribution and abundance of breeding lesser snow geese on the Hudson Bay Lowlands may have impacts on the reproductive performance of Canada geese, and subsequently the spatial distribution of Canada goose nests.

  14. Can selection on nest size from nest predation explain the latitudinal gradient in clutch size?

    USGS Publications Warehouse

    Biancucci, L.; Martin, T.E.

    2010-01-01

    1. Latitudinal variation in clutch sizes of birds is a well described, but poorly understood pattern. Many hypotheses have been proposed, but few have been experimentally tested, and none have been universally accepted by researchers. 2. The nest size hypothesis posits that higher nest predation in the tropics favours selection for smaller nests and thereby constrains clutch size by shrinking available space for eggs and/or nestlings in the nest. We tested this hypothesis with an experiment in a tropical forest and a comparative study between temperate and tropical field sites. 3. Specifically, we tested if: (i) predation increased with nest size; (ii) tropical birds had smaller nests controlled for body size; and (iii) clutch size was explained by nest size controlled for body size. 4. Experimental swapping of nests of different sizes showed that nest predation increased with nest size in the tropical site. Moreover, nest predation rates were higher in species with larger nests in both sites. However, nest size, corrected for body mass and phylogeny, did not differ between sites and was not related to clutch size between sites. 5. Hence, nest predation can exert selection on nest size as predicted by the hypothesis. Nest size increased with adult body mass, such that adult size might indirectly influence reproductive success through effects on nest size and nest predation risk. Ultimately, however, selection from nest predation on nest size does not explain the smaller clutch sizes typical of the tropics.

  15. Association Mapping for Important Agronomic Traits in Core Collection of Rice (Oryza sativa L.) with SSR Markers

    PubMed Central

    Zhang, Peng; Liu, Xiangdong; Tong, Hanhua; Lu, Yonggen; Li, Jinquan

    2014-01-01

    Mining elite genes within rice landraces is of importance for the improvement of cultivated rice. An association mapping for 12 agronomic traits was carried out using a core collection of rice consisting of 150 landraces (Panel 1) with 274 simple sequence repeat (SSR) markers, and the mapping results were further verified using a Chinese national rice micro-core collection (Panel 2) and a collection from a global molecular breeding program (Panel 3). Our results showed that (1) 76 significant (P<0.05) trait-marker associations were detected using mixed linear model (MLM) within Panel 1 in two years, among which 32% were identical with previously mapped QTLs, and 11 significant associations had >10% explained ratio of genetic variation; (2) A total of seven aforementioned trait-marker associations were verified within Panel 2 and 3 when using a general linear model (GLM) and 55 SSR markers of the 76 significant trait-marker associations. However, no significant trait-marker association was found to be identical within three panels when using the MLM model; (3) several desirable alleles of the loci which showed significant trait-marker associations were identified. The research provided important information for further mining these elite genes within rice landraces and using them for rice breeding. PMID:25360796

  16. Construction of High-Density Genetic Map in Barley through Restriction-Site Associated DNA Sequencing.

    PubMed

    Zhou, Gaofeng; Zhang, Qisen; Zhang, Xiao-Qi; Tan, Cong; Li, Chengdao

    2015-01-01

    Genetic maps in barley are usually constructed from a limited number of molecular markers such as SSR (simple sequence repeat) and DarT (diversity arrays technology). These markers must be first developed before being used for genotyping. Here, we introduce a new strategy based on sequencing progeny of a doubled haploid population from Baudin × AC Metcalfe to construct a genetic map in barley. About 13,547 polymorphic SNP tags with >93% calling rate were selected to construct the genetic map. A total of 12,998 SNP tags were anchored to seven linkage groups which spanned a cumulative 967.6 cM genetic distance. The high-density genetic map can be used for QTL mapping and the assembly of WGS and BAC contigs. The genetic map was evaluated for its effectiveness and efficiency in QTL mapping and candidate gene identification. A major QTL for plant height was mapped at 105.5 cM on chromosome 3H. This QTL with LOD value of 13.01 explained 44.5% of phenotypic variation. This strategy will enable rapid and efficient establishment of high-density genetic maps in other species. PMID:26182149

  17. Mapping turbulent diffusivity associated with oceanic internal lee waves offshore Costa Rica

    NASA Astrophysics Data System (ADS)

    Fortin, Will F. J.; Holbrook, W. Steven; Schmitt, Raymond W.

    2016-04-01

    Breaking internal waves play a primary role in maintaining the meridional overturning circulation. Oceanic lee waves are known to be a significant contributor to diapycnal mixing associated with internal wave dissipation, but direct measurement is difficult with standard oceanographic sampling methods due to the limited spatial extent of standing lee waves. Here, we present an analysis of oceanic internal lee waves observed offshore eastern Costa Rica using seismic imaging and estimate the turbulent diffusivity via a new seismic slope spectrum method that extracts diffusivities directly from seismic images, using tracked reflections only to scale diffusivity values. The result provides estimates of turbulent diffusivities throughout the water column at scales of a few hundred meters laterally and 10 m vertically. Synthetic tests demonstrate the method's ability to resolve turbulent structures and reproduce accurate diffusivities. A turbulence map of our seismic section in the western Caribbean shows elevated turbulent diffusivities near rough seafloor topography as well as in the mid-water column where observed lee wave propagation terminates. Mid-water column hotspots of turbulent diffusivity show levels 5 times higher than surrounding waters and 50 times greater than typical open-ocean diffusivities. This site has steady currents that make it an exceptionally accessible laboratory for the study of lee-wave generation, propagation, and decay.

  18. Developing a common bean core collection suitable for association mapping studies

    PubMed Central

    Perseguini, Juliana Morini Küpper Cardoso; Silva, Gliciane Micaele Borges; Rosa, João Ricardo Bachega Feijó; Gazaffi, Rodrigo; Marçal, Jéssica Fernanda; Carbonell, Sérgio Augusto Morais; Chiorato, Alisson Fernando; Zucchi, Maria Imaculada; Garcia, Antonio Augusto Franco; Benchimol-Reis, Luciana Lasry

    2015-01-01

    Because of the continuous introduction of germplasm from abroad, some collections have a high number of accessions, making it difficult to explore the genetic variability present in a germplasm bank for conservation and breeding purposes. Therefore, the aim of this study was to quantify and analyze the structure of genetic variability among 500 common bean accessions to construct a core collection. A total of 58 SSRs were used for this purpose. The polymorphism information content (PIC) in the 180 common bean accessions selected to compose the core collection ranged from 0.17 to 0.86, and the discriminatory power (DP) ranged from 0.21 to 0.90. The 500 accessions were clustered into 15 distinct groups and the 180 accessions into four distinct groups in the Structure analysis. According to analysis of molecular variance, the most divergent accessions comprised 97.2% of the observed genetic variability present within the base collection, confirming the efficiency of the selection criterion. The 180 selected accessions will be used for association mapping in future studies and could be potentially used by breeders to direct new crosses and generate elite cultivars that meet current and future global market needs. PMID:25983627

  19. Developing a common bean core collection suitable for association mapping studies.

    PubMed

    Perseguini, Juliana Morini Küpper Cardoso; Silva, Gliciane Micaele Borges; Rosa, João Ricardo Bachega Feijó; Gazaffi, Rodrigo; Marçal, Jéssica Fernanda; Carbonell, Sérgio Augusto Morais; Chiorato, Alisson Fernando; Zucchi, Maria Imaculada; Garcia, Antonio Augusto Franco; Benchimol-Reis, Luciana Lasry

    2015-03-01

    Because of the continuous introduction of germplasm from abroad, some collections have a high number of accessions, making it difficult to explore the genetic variability present in a germplasm bank for conservation and breeding purposes. Therefore, the aim of this study was to quantify and analyze the structure of genetic variability among 500 common bean accessions to construct a core collection. A total of 58 SSRs were used for this purpose. The polymorphism information content (PIC) in the 180 common bean accessions selected to compose the core collection ranged from 0.17 to 0.86, and the discriminatory power (DP) ranged from 0.21 to 0.90. The 500 accessions were clustered into 15 distinct groups and the 180 accessions into four distinct groups in the Structure analysis. According to analysis of molecular variance, the most divergent accessions comprised 97.2% of the observed genetic variability present within the base collection, confirming the efficiency of the selection criterion. The 180 selected accessions will be used for association mapping in future studies and could be potentially used by breeders to direct new crosses and generate elite cultivars that meet current and future global market needs.

  20. Association Mapping of Flowering Time QTLs and Insight into Their Contributions to Rapeseed Growth Habits

    PubMed Central

    Wang, Nian; Chen, Biyun; Xu, Kun; Gao, Guizhen; Li, Feng; Qiao, Jiangwei; Yan, Guixin; Li, Jun; Li, Hao; Wu, Xiaoming

    2016-01-01

    Plants have developed sophisticated systems to adapt to local conditions during evolution, domestication and natural or artificial selection. The selective pressures of these different growing conditions have caused significant genomic divergence within species. The flowering time trait is the most crucial factor because it helps plants to maintain sustainable development. Controlling flowering at appropriate times can also prevent plants from suffering from adverse growth conditions, such as drought, winter hardness, and disease. Hence, discovering the genome-wide genetic mechanisms that influence flowering time variations and understanding their contributions to adaptation should be a central goal of plant genetics and genomics. A global core collection panel with 448 inbred rapeseed lines was first planted in four independent environments, and their flowering time traits were evaluated. We then performed a genome-wide association mapping of flowering times with a 60 K SNP array for this core collection. With quality control and filtration, 20,342 SNP markers were ultimately used for further analyses. In total, 312 SNPs showed marker-trait associations in all four environments, and they were based on a threshold p-value of 4.06 × 10−4; the 40 QTLs showed significant association with flowering time variations. To explore flowering time QTLs and genes related to growth habits in rapeseed, selection signals related to divergent habits were screened at the genome-wide level and 117 genomic regions were found. Comparing locations of flowering time QTLs and genes with these selection regions revealed that 20 flowering time QTLs and 224 flowering time genes overlapped with 24 and 81 selected regions, respectively. Based on this study, a number of marker-trait associations and candidate genes for flowering time variations in rapeseed were revealed. Moreover, we also showed that both flowering time QTLs and genes play important roles in rapeseed growth habits. These

  1. High-Resolution Association Mapping of Quantitative Trait Loci: A Population-Based Approach

    PubMed Central

    Fan, Ruzong; Jung, Jeesun; Jin, Lei

    2006-01-01

    In this article, population-based regression models are proposed for high-resolution linkage disequilibrium mapping of quantitative trait loci (QTL). Two regression models, the “genotype effect model” and the “additive effect model,” are proposed to model the association between the markers and the trait locus. The marker can be either diallelic or multiallelic. If only one marker is used, the method is similar to a classical setting by Nielsen and Weir, and the additive effect model is equivalent to the haplotype trend regression (HTR) method by Zaykin et al. If two/multiple marker data with phase ambiguity are used in the analysis, the proposed models can be used to analyze the data directly. By analytical formulas, we show that the genotype effect model can be used to model the additive and dominance effects simultaneously; the additive effect model takes care of the additive effect only. On the basis of the two models, F-test statistics are proposed to test association between the QTL and markers. By a simulation study, we show that the two models have reasonable type I error rates for a data set of moderate sample size. The noncentrality parameter approximations of F-test statistics are derived to make power calculation and comparison. By a simulation study, it is found that the noncentrality parameter approximations of F-test statistics work very well. Using the noncentrality parameter approximations, we compare the power of the two models with that of the HTR. In addition, a simulation study is performed to make a comparison on the basis of the haplotype frequencies of 10 SNPs of angiotensin-1 converting enzyme (ACE) genes. PMID:16172503

  2. Association mapping of grain hardness, polyphenol oxidase, total phenolics, amylose content, and ß-glucan in US barley breeding germplasm

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A renewed interest in breeding barley specifically for food end-uses is being driven by increased consumer interest in healthier foods. We conducted association mapping on physicochemical properties of barley that play a role in food quality and processing including, grain hardness, polyphenol oxid...

  3. Detection and fine-mapping of SC7 resistance genes via linkage and association analysis in soybean.

    PubMed

    Yan, Honglang; Wang, Hui; Cheng, Hao; Hu, Zhenbin; Chu, Shanshan; Zhang, Guozheng; Yu, Deyue

    2015-08-01

    Soybean mosaic virus (SMV) disease is one of the most serious and broadly distributed soybean (Glycine max (L.) Merr.) diseases. Here, we combine the advantages of association and linkage analysis to identify and fine-map the soybean genes associated with resistance to SMV strain SC7. A set of 191 soybean accessions from different geographic origins and 184 recombinant inbred lines (RILs) derived from Kefeng No.1 (resistant) × Nannong 1138-2 (susceptible) were used in this study. The SC7 resistance genes were previously mapped to a 2.65 Mb region on chromosome 2 and a 380 kb region on chromosome 13. Among 19 single nucleotide polymorphisms (SNPs) detected via association analysis in the study, the SNP BARC-021625-04157 was located in the 2.65 Mb region, and the SNP BARC-041671-08065 was located near the 380 kb region; three genes harboring the SNPs were probably related to SC7 resistance. The resistance gene associated with BARC-021625-04157 was then fine-mapped to a region of approximately 158 kb on chromosome 2 using 184 RILs. Among the 15 genes within this region, one NBS-LRR type gene, one HSP40 gene and one serine carboxypeptidase-type gene might be candidate SC7 resistance genes. These results will be useful for map-based cloning and marker-assisted selection in soybean breeding programs.

  4. Mapping of quantitative trait loci associated with partial resistance to phytophthora sojae and flooding tolerance in soybean

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Phytophthora root rot (PRR) caused by Phytophthora sojae Kaufm. & Gerd. and flooding can limit growth and productivity, of soybean [Glycine max (L.) Merr.], especially on poorly drained soils. The primary objective of this research project was to map quantitative trait loci (QTL) associated with f...

  5. Genetic diversity for Russian wheat aphid resistance as determined by genome-wide association mapping and inheritance in progeny

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Russian wheat aphid (RWA) is an increasing problem on barley throughout the world. Genetic resistance has been identified and used to create barley germplasm and cultivars adapted to the US. Several mapping studies have been conducted to identify loci associated with resistance, but questions remain...

  6. Genetic structure, linkage disequilibrium and association mapping of Verticillium wilt resistance in elite cotton (Gossypium hirsutum L.) germplasm population.

    PubMed

    Zhao, Yunlei; Wang, Hongmei; Chen, Wei; Li, Yunhai

    2014-01-01

    Understanding the population structure and linkage disequilibrium in an association panel can effectively avoid spurious associations and improve the accuracy in association mapping. In this study, one hundred and fifty eight elite cotton (Gossypium hirsutum L.) germplasm from all over the world, which were genotyped with 212 whole genome-wide marker loci and phenotyped with an disease nursery and greenhouse screening method, were assayed for population structure, linkage disequilibrium, and association mapping of Verticillium wilt resistance. A total of 480 alleles ranging from 2 to 4 per locus were identified from all collections. Model-based analysis identified two groups (G1 and G2) and seven subgroups (G1a-c, G2a-d), and differentiation analysis showed that subgroup having a single origin or pedigree was apt to differentiate with those having a mixed origin. Only 8.12% linked marker pairs showed significant LD (P<0.001) in this association panel. The LD level for linked markers is significantly higher than that for unlinked markers, suggesting that physical linkage strongly influences LD in this panel, and LD level was elevated when the panel was classified into groups and subgroups. The LD decay analysis for several chromosomes showed that different chromosomes showed a notable change in LD decay distances for the same gene pool. Based on the disease nursery and greenhouse environment, 42 marker loci associated with Verticillium wilt resistance were identified through association mapping, which widely were distributed among 15 chromosomes. Among which 10 marker loci were found to be consistent with previously identified QTLs and 32 were new unreported marker loci, and QTL clusters for Verticillium wilt resistanc on Chr.16 were also proved in our study, which was consistent with the strong linkage in this chromosome. Our results would contribute to association mapping and supply the marker candidates for marker-assisted selection of Verticillium wilt

  7. The alcohol dehydrogenase gene is nested in the outspread locus of Drosophila melanogaster

    SciTech Connect

    McNabb, S.; Greig, S.; Davis, T.

    1996-06-01

    This report describes the structure and expression of the outspread (osp) gene of Drosophila melanogaster. Previous work showed that chromosomal breakpoints associated with mutations of the osp locus map to both sides of the alcohol dehydrogenase gene (Adh), suggesting that Adh and the adjacent gene Adh{sup r} are nested in osp. We extended a chromosomal walk and mapped additional osp mutations to define the maximum molecular limit of osp as 119 kb. We identified a 6-kb transcript that hybridizes to osp region DNA and is altered or absent in osp mutants. Accumulation of this RNA peaks during embryonic and pupal periods. The osp cDNAs comprise two distinct classes based on alternative splicing patterns. The 5{prime} end of the longest cDNA was extended by PCR amplification. When hybridized to the osp walk, the 5{prime} extension verifies that Adh and Adh{sup r} are nested in osp and shows that osp has a transcription unit of {ge}74 kb. In situ hybridization shows that osp is expressed both maternally and zygotically. In the ovary, osp is transcribed in nurse cells and localized in the oocyte. In embryos, expression is most abundant in the developing visceral and somatic musculature. 55 refs., 11 figs., 1 tab.

  8. Nest visits and capture events affect breeding success of Yellow-billed and Pacific loons

    USGS Publications Warehouse

    Uher-Koch, Brian D.; Schmutz, Joel A.; Wright, Kenneth G.

    2015-01-01

    Accurate estimates of breeding success are essential for understanding population dynamics and for managing populations. Unfortunately, research activities to collect these data can negatively impact the breeding success of the study species and bias estimates of breeding success. Despite the potential for negative impacts, few studies have documented the effect of capturing incubating adults on nest survival or compared nest survival following different capture methods. In this study we evaluate the impacts of investigator disturbance associated with captures and nest visits on nest survival of Yellow-billed Loons (Gavia adamsii) and Pacific Loons (Gavia pacifica) in the National Petroleum Reserve-Alaska (NPR-A), an area of conservation concern, in 2011–2013. In an effort to reduce capture-related nest failures, we developed a new suspended dive net technique to catch territorial aquatic birds while off their nests. We then compared nest survival following suspended dive net captures to bow-net trap captures of breeding adult loons. Daily nest survival following bow-net trap or suspended dive net capture was about 30% lower than when adults were not captured. The effect of captures on nest survival was similar between bow-net trap and suspended dive net capture methods. Nest visits without captures also negatively impacted nest survival, although less than captures. If not accounted for, nest visitation biased daily survival rates of nests downward 6%. Effects of investigator disturbance did not differ by species or between years. Our results suggest that any source of disturbance that displaces incubating adult loons could potentially reduce nest survival. To maximize breeding success, human disturbance factors should be limited near loon nests.

  9. Identification and Validation of Loci Governing Seed Coat Color by Combining Association Mapping and Bulk Segregation Analysis in Soybean

    PubMed Central

    Ma, Yansong; Tian, Long; Li, Xinxiu; Li, Ying-Hui; Guan, Rongxia; Guo, Yong; Qiu, Li-Juan

    2016-01-01

    Soybean seed coat exists in a range of colors from yellow, green, brown, black, to bicolor. Classical genetic analysis suggested that soybean seed color was a moderately complex trait controlled by multi-loci. However, only a couple of loci could be detected using a single biparental segregating population. In this study, a combination of association mapping and bulk segregation analysis was employed to identify genes/loci governing this trait in soybean. A total of 14 loci, including nine novel and five previously reported ones, were identified using 176,065 coding SNPs selected from entire SNP dataset among 56 soybean accessions. Four of these loci were confirmed and further mapped using a biparental population developed from the cross between ZP95-5383 (yellow seed color) and NY279 (brown seed color), in which different seed coat colors were further dissected into simple trait pairs (green/yellow, green/black, green/brown, yellow/black, yellow/brown, and black/brown) by continuously developing residual heterozygous lines. By genotyping entire F2 population using flanking markers located in fine-mapping regions, the genetic basis of seed coat color was fully dissected and these four loci could explain all variations of seed colors in this population. These findings will be useful for map-based cloning of genes as well as marker-assisted breeding in soybean. This work also provides an alternative strategy for systematically isolating genes controlling relative complex trait by association analysis followed by biparental mapping. PMID:27404272

  10. Bird's Nest View from a Dermatologist's Eye.

    PubMed

    Anisha, Sethi; Sukhjot, Kaur; Sunil, Gupta Kumar; Sandeep, Puri

    2016-01-01

    Plica neuropathica also known as "birds nest" is irreversible matting of hair seen in otherwise healthy individuals and is usually associated with use of ionic/herbal soaps, shampoos, parasitic infestations, psychiatric alterations, or neglect. Anagen effluvium is a known side effect of many immunosuppressive drugs. Rarely matting of hair has been reported following azathioprine. We report plica neuropathica in two chronically ill patients on immunosuppressive drugs, that is, azathioprine and methotrexate along with a review of literature of its etiological factors and pathogenesis. PMID:27127367

  11. Unusual raptor nests around the world

    USGS Publications Warehouse

    Ellis, D.H.; Craig, T.; Craig, E.; Postupalsky, S.; LaRue, C.T.; Nelson, R.W.; Anderson, D.W.; Henny, C.J.; Watson, J.; Millsap, B.A.; Dawson, J.W.; Cole, K.L.; Martin, E.M.; Margalida, A.; Kung, P.

    2009-01-01

    From surveys in many countries, we report raptors using unusual nesting materials (e.g., paper money, rags, metal, antlers, and large bones) and unusual nesting situations. For example, we documented nests of Steppe Eagles Aquila nipalensis and Upland Buzzards Buteo hemilasius on the ground beside well-traveled roads, Saker Falcon Falco cherrug eyries in attics and a cistern, and Osprey Pandion haliaetus nests on the masts of boats and on a suspended automobile. Other records include a Golden Eagle A. chrysaetos nest 7.0 m in height, believed to be the tallest nest ever described, and, for the same species, we report nesting in rudimentary nests. Some nest sites are within a few meters of known predators or competitors. These unusual observations may be important in revealing the plasticity of a species' behavioral repertoire. ?? 2009 The Raptor Research Foundation, Inc.

  12. Construction of High-Density Linkage Maps of Populus deltoides × P. simonii Using Restriction-Site Associated DNA Sequencing

    PubMed Central

    Tong, Chunfa; Li, Huogen; Wang, Ying; Li, Xuran; Ou, Jiajia; Wang, Deyuan; Xu, Houxi; Ma, Chao; Lang, Xianye; Liu, Guangxin; Zhang, Bo; Shi, Jisen

    2016-01-01

    Although numerous linkage maps have been constructed in the genus Populus, they are typically sparse and thus have limited applications due to low throughput of traditional molecular markers. Restriction-site associated DNA sequencing (RADSeq) technology allows us to identify a large number of single nucleotide polymorphisms (SNP) across genomes of many individuals in a fast and cost-effective way, and makes it possible to construct high-density genetic linkage maps. We performed RADSeq for 299 progeny and their two parents in an F1 hybrid population generated by crossing the female Populus deltoides ‘I-69’ and male Populus simonii ‘L3’. A total of 2,545 high quality SNP markers were obtained and two parent-specific linkage maps were constructed. The female genetic map contained 1601 SNPs and 20 linkage groups, spanning 4,249.12 cM of the genome with an average distance of 2.69 cM between adjacent markers, while the male map consisted of 940 SNPs and also 20 linkage groups with a total length of 3,816.24 cM and an average marker interval distance of 4.15 cM. Finally, our analysis revealed that synteny and collinearity are highly conserved between the parental linkage maps and the reference genome of P. trichocarpa. We demonstrated that RAD sequencing is a powerful technique capable of rapidly generating a large number of SNPs for constructing genetic maps in outbred forest trees. The high-quality linkage maps constructed here provided reliable genetic resources to facilitate locating quantitative trait loci (QTLs) that control growth and wood quality traits in the hybrid population. PMID:26964097

  13. Techniques for identifying predators of goose nests

    USGS Publications Warehouse

    Anthony, R.M.; Grand, J.B.; Fondell, T.F.; Miller, David A.

    2006-01-01

    We used cameras and artificial eggs to identify nest predators of dusky Canada goose Branta canadensis occidentalis nests during 1997-2000. Cameras were set up at 195 occupied goose nests and 60 artificial nests. We placed wooden eggs and domestic goose eggs that were emptied and then filled with wax or foam in an additional 263 natural goose nests to identify predators from marks in the artificial eggs. All techniques had limitations, but each correctly identified predators and estimated their relative importance. Nests with cameras had higher rates of abandonment than natural nests, especially during laying. Abandonment rates were reduced by deploying artificial eggs late in laying and reducing time at nests. Predation rates for nests with cameras were slightly lower than for nests without cameras. Wax-filled artificial eggs caused mortality of embryos in natural nests, but were better for identifying predator marks at artificial nests. Use of foam-filled artificial eggs in natural nests was the most cost effective means of monitoring nest predation. ?? Wildlife Biology (2006).

  14. Nested-Fermi-liquid theory

    SciTech Connect

    Virosztek, A.; Ruvalds, J. )

    1990-09-01

    The susceptibility and quasiparticle self-energy are found to exhibit anomalous behavior in nested-Fermi-liquid (NFL) systems that have nearly parallel sections of the Fermi surface. Electron-electron scattering yields damping much stronger than the conventional electron-gas result and predicts a linear temperature variation of the resistivity. The susceptibility {chi}{sub NFL}{sup {prime}{prime}}({bold q},{omega}) for nested fermions is calculated at {bold q}{approx equal}{bold Q}, where {bold Q} is a typical nesting wave vector. The NFL susceptibility is linear in frequency up to a crossover region near {omega}{approx equal}4{ital T} where a saturation to a constant value occurs. The above features, as well as various theoretical constraints, are highly sensitive to the strength of the electron-electron coupling and to the degree of nesting. The relevance of the NFL results to superconducting oxides is briefly examined, with emphasis on the resistivity and the photoemission data, which supports the calculated damping {Gamma}({omega}{gt}{ital T}){approx equal}{alpha}{omega} with an intermediate on-site Coulomb coupling.

  15. Nest success of northern bobwhite on managed and unmanaged landscapes in southeast Iowa

    USGS Publications Warehouse

    Potter, Lisa M.; Otis, David L.; Bogenschutz, Todd R.

    2011-01-01

    Range-wide declines in northern bobwhite populations (Colinus virginianus) have been attributed to concomitant loss of breeding habitat. Bobwhite management efforts to restore this habitat resource can be informed by empirical studies of associations between breeding success and multi-scale habitat attributes. We compared bobwhite nest success in 2 southern Iowa landscapes as a function of microhabitat and landscape composition. Lake Sugema Fish and Wildlife Area (LSWA) was managed to promote bobwhite recruitment, and Harrisburg Township (HT) was an adjacent landscape dominated by private agricultural production. Survival rate modeling based on telemetry data provided evidence for age-specific daily nest survival rate. Daily survival rates decreased as nest age increased, but the decline was more severe at HT. Nest survival at LSWA (S = 0.495, SE = 0.103) was nearly twice that on HT (S = 0.277, SE = 0.072). We found no evidence that habitat composition or spatial attributes within 210 m of a nest site significantly influenced nest success. Forb canopy at the nest site had a positive influence on nest success at HT but not at LSWA. We suggest nesting habitat with greater forb canopy cover will increase the opportunity for nesting success in landscapes with limited nesting habitat.

  16. Birds of the Hanford site: nest site selection

    SciTech Connect

    Rickard, W.H.; Fitzner, R.E.

    1983-03-01

    At least 62 species of birds regularly nest on the 1400 km/sup 2/ Hanford Site in the semi-arid interior of southcentral Washington. Birds showed nesting preferences for different kinds of vegetation, special natural landscape features and certain kinds of man-made structures. Vegetational nest site preferences were categorized as shrubsteppe, natural coppice, planted trees and cattail-reed marsh. The nonvegetational nest-site preferences were categorized as cliff, rock talus, riverine islands and industrial structures. Natural coppice vegetation was preferred by colorful passerine birds. Planted trees were selected by raptors, crows, ravens, herons and magpies. Shrubsteppe plant communities occupy most of the land area of the Hanford Site; only thirteen species of birds chose to nest in them. Nest-site selection by birds can be used for wildlife mitigation practices associated with the siting, construction and operation of energy related industries on the Hanford Site and in other undeveloped semi-arid regions in the western United States. 22 references, 5 figures, 2 tables.

  17. Plastic and the nest entanglement of urban and agricultural crows.

    PubMed

    Townsend, Andrea K; Barker, Christopher M

    2014-01-01

    Much attention has been paid to the impacts of plastics and other debris on marine organisms, but the effects of plastic on terrestrial organisms have been largely ignored. Detrimental effects of terrestrial plastic could be most pronounced in intensively human-modified landscapes (e.g., urban and agricultural areas), which are a source of much anthropogenic debris. Here, we examine the occurrence, types, landscape associations, and consequences of anthropogenic nest material in the American crow (Corvus brachyrhynchos), a North American species that breeds in both urban and agricultural landscapes. We monitored 195 nestlings in 106 nests across an urban and agricultural gradient in the Sacramento Valley, California, USA. We found that 85.2% of crow nests contained anthropogenic material, and 11 of 195 nestlings (5.6%) were entangled in their nests. The length of the material was greater in nests in agricultural territories than in urban territories, and the odds of entanglement increased 7.55 times for each meter of anthropogenic material in the nest. Fledging success was significantly lower for entangled than for unentangled nestlings. In all environments, particularly urban, agricultural, and marine, careful disposal of potential hazards (string, packing and hay bale twine, balloon ribbon, wire, fishing line) could reduce the occurrence of entanglement of nestling birds.

  18. Plastic and the Nest Entanglement of Urban and Agricultural Crows

    PubMed Central

    Townsend, Andrea K.; Barker, Christopher M.

    2014-01-01

    Much attention has been paid to the impacts of plastics and other debris on marine organisms, but the effects of plastic on terrestrial organisms have been largely ignored. Detrimental effects of terrestrial plastic could be most pronounced in intensively human-modified landscapes (e.g., urban and agricultural areas), which are a source of much anthropogenic debris. Here, we examine the occurrence, types, landscape associations, and consequences of anthropogenic nest material in the American crow (Corvus brachyrhynchos), a North American species that breeds in both urban and agricultural landscapes. We monitored 195 nestlings in 106 nests across an urban and agricultural gradient in the Sacramento Valley, California, USA. We found that 85.2% of crow nests contained anthropogenic material, and 11 of 195 nestlings (5.6%) were entangled in their nests. The length of the material was greater in nests in agricultural territories than in urban territories, and the odds of entanglement increased 7.55 times for each meter of anthropogenic material in the nest. Fledging success was significantly lower for entangled than for unentangled nestlings. In all environments, particularly urban, agricultural, and marine, careful disposal of potential hazards (string, packing and hay bale twine, balloon ribbon, wire, fishing line) could reduce the occurrence of entanglement of nestling birds. PMID:24498238

  19. Nest sanitation elicits egg discrimination in cuckoo hosts.

    PubMed

    Yang, Canchao; Chen, Min; Wang, Longwu; Liang, Wei; Møller, Anders Pape

    2015-11-01

    Nest sanitation is a nearly universal behavior in birds, while egg discrimination is a more specific adaptation that has evolved to counter brood parasitism. These two behaviors are closely related with nest sanitation being the ancestral behavior, and it has been hypothesized to constitute a preadaptation for egg discrimination. However, previous studies found little evidence to support this hypothesis. Here, we conducted an empirical test of the association between nest sanitation and egg discrimination in the barn swallow (Hirundo rustica) by inserting a single non-mimetic model egg or a non-mimetic model egg plus half a peanut shell into host nests. Compared to the rejection rate of single model eggs, barn swallows significantly increased egg rejection frequency if a half peanut shell was simultaneously introduced. Our result for the first time shows the impact of nest sanitation on egg discrimination and demonstrates that nest sanitation can elicit egg discrimination in hosts of brood parasites. This study provided evidence for nest sanitation being a preadaptation to egg discrimination by facilitating egg rejection, thereby significantly advancing our understanding of avian cognition of foreign objects. Furthermore, we suggest that egg discrimination behavior in many accepters and intermediate rejecters may be lost or diluted. Such egg discrimination can be elicited and restored after nest sanitation, implying a sensitive and rapid phenotypic response to increased risk of parasitism. Our study offers a novel perspective for investigating the role of so-called intermediate rejecter individuals or species in the long-term coevolutionary cycle between brood parasites and their hosts. PMID:26160343

  20. Nest sanitation elicits egg discrimination in cuckoo hosts.

    PubMed

    Yang, Canchao; Chen, Min; Wang, Longwu; Liang, Wei; Møller, Anders Pape

    2015-11-01

    Nest sanitation is a nearly universal behavior in birds, while egg discrimination is a more specific adaptation that has evolved to counter brood parasitism. These two behaviors are closely related with nest sanitation being the ancestral behavior, and it has been hypothesized to constitute a preadaptation for egg discrimination. However, previous studies found little evidence to support this hypothesis. Here, we conducted an empirical test of the association between nest sanitation and egg discrimination in the barn swallow (Hirundo rustica) by inserting a single non-mimetic model egg or a non-mimetic model egg plus half a peanut shell into host nests. Compared to the rejection rate of single model eggs, barn swallows significantly increased egg rejection frequency if a half peanut shell was simultaneously introduced. Our result for the first time shows the impact of nest sanitation on egg discrimination and demonstrates that nest sanitation can elicit egg discrimination in hosts of brood parasites. This study provided evidence for nest sanitation being a preadaptation to egg discrimination by facilitating egg rejection, thereby significantly advancing our understanding of avian cognition of foreign objects. Furthermore, we suggest that egg discrimination behavior in many accepters and intermediate rejecters may be lost or diluted. Such egg discrimination can be elicited and restored after nest sanitation, implying a sensitive and rapid phenotypic response to increased risk of parasitism. Our study offers a novel perspective for investigating the role of so-called intermediate rejecter individuals or species in the long-term coevolutionary cycle between brood parasites and their hosts.

  1. Ecology of a nesting red-shouldered hawk population

    USGS Publications Warehouse

    Stewart, R.E.

    1949-01-01

    An ecological study of a nesting Red-shouldered Hawk population was made over a 185 square mile area on the Coastal Plain of Maryland in 1947. The courting and nesting season extended from late February until late June.....During the nesting season a combination of fairly extensive flood-plain forest with adjacent clearings appears to meet the major ecological requirements of the Red-shouldered Hawk in this region. A total of 51 pairs was found in the study area, occupying about 42 square miles or 23% of the total area studied. The population density on the land that was suitable for this species was about 1 pair per .8 of a square mile, while the density for the entire study area would be only about 1 pair per 3.6 square miles.....Nests were spaced fairly evenly over most of the flood-plain forests, especially in areas where the width.of the flood plain was relatively constant. There was an inverse correlation between the width of the flood plain and the distances between nests in adjacent territories. The nests were all situated in fairly large trees and were from 28 feet to 77 feet above the ground, averaging 50. They were found in 14 different species of trees, all deciduous.....The Barred Owl and Red-shouldered Hawk were commonly associated together in the same lowland habitats. Other raptores were all largely restricted to upland habitats....The average number of young in 47 occupied nests following the hatching period was 2.7 with extremes of 1 and 4. Only 3 out of 52 nests (6%) were found deserted at this time....The food habits of nestling Red-shouldered Hawks are very diversified. They feed on many types of warm-blooded and cold-blooded vertebrates as well as invertebrates.

  2. Association mapping of complex diseases in linked regions: estimation of genetic effects and feasibility of testing rare variants.

    PubMed

    Wang, William Y S; Cordell, Heather J; Todd, John A

    2003-01-01

    Association mapping in linked regions is a current major approach for the identification of genes for complex diseases. Loci contributing to linkage, even with small values of sibling recurrence risk (lambda(s)), may be equivalent to substantial underlying genetic effects for association studies. For disease alleles with a frequency as low as 1%, highly reliable association studies (80% power for significance level alpha=10(-6)) require only 277, 781, and 1289 families or cases and controls for loci detected with lambda(s) of 1.5, 1.1, and 1.05, respectively, under a multiplicative genetic model. Under alternative models, provided epistatic effects are minor, larger achievable sample sizes will provide sufficient power to map almost any disease gene that may have initially contributed to linkage.

  3. Debris Flow Vulnerability Assessment in Urban Area Associated with Landslide Hazard Map : Application to Busan, Korea

    NASA Astrophysics Data System (ADS)

    Okjeong, Lee; Yoonkyung, Park; Mookwang, Sung; Sangdan, Kim

    2016-04-01

    In this presentation, an urban debris flow disaster vulnerability assessment methodology is suggested with major focus on urban social and economic aspect. The proposed methodology is developed based on the landslide hazard maps that Korean Forest Service has utilized to identify landslide source areas. Frist, debris flows are propagated to urban areas from such source areas by Flow-R model, and then urban vulnerability is evaluated by two categories; physical and socio-economic aspect. The physical vulnerability is associated to buildings that can be broken down by a landslide event directly. This study considers two popular building structure types, reinforced concrete frame and non-reinforced concretes frame, to evaluate the physically-based vulnerability. The socio-economic vulnerability is measured as a function of the resistant levels of the exposed people, the intensity and magnitude of indirect or intangible losses, and preparedness level of the local government. An indicator-based model is established to evaluate the life and indirect loss under urban debris flow disasters as well as the resilience ability against disasters. To illuminate the validity of the suggested methodology, physical and socio-economic vulnerability levels are investigated for Daejeon, Korea using the proposed approach. The results reveal that the higher population density areas under a weaker fiscal condition that are located at the downstream of mountainous areas are more vulnerable than the areas in opposite conditions. Key words: Debris flow disasters, Physical vulnerability, Socio-economic Vulnerability, Urban Acknowledgement This research was supported by a grant(13SCIPS04) from Smart Civil Infrastructure Research Program funded by Ministry of Land, Infrastructure and Transport(MOLIT) of Korea government and Korea Agency for Infrastructure Technology Advancement(KAIA).

  4. Genetic association between chromosome 8 microsatellite (MS8-134) and Werner syndrome (WRN): Chromosome microdissection and homozygosity mapping

    SciTech Connect

    Ye, Lin; Nakura, Jun; Mitsuda, Noriaki; Miki, Tetsuro

    1995-08-10

    Werner syndrome (WRN) is an autosomal recessive disorder characterized by premature aging that has been mapped to the short arm of chromosome 8, 8p11.2-p12. To refine the genetic map around the WRN region, we have isolated eight microsatellites for this region from a microdissection library. We typed members of Japanese families with WRN on the basis of homozygosity mapping analysis. There was no obligate recombination between the WRN locus and microsatellite clone, MS8-134 (D8S1055). The maximum lod score was 20.28 at {theta} = 0.00. Alleles for MS8-134 showed association with WRN in a case-control study (OR = 3.55, 95% CI 1.56-8.07, P < 0.01). Such microsatellites from a microdissection library of the definite chromosome region may be useful for positional cloning of the WRN gene. 23 refs., 1 figs., 1 tab.

  5. Identifying Kittlitz's Murrelet nesting habitat in North America at the landscape scale

    USGS Publications Warehouse

    Felis, Jonathan J.; Kissling, Michelle L.; Kaler, Robb S.A.; Kenney, Leah A.; Lawonn, Matthew J.

    2016-01-01

    The Kittlitz's Murrelet (Brachyramphus brevirostris) is a small, non-colonial seabird endemic to marine waters of Alaska and eastern Russia that may have experienced significant population decline in recent decades, in part because of low reproductive success and terrestrial threats. Although recent studies have shed new light on Kittlitz's Murrelet nesting habitat in a few discrete areas, the location and extent of suitable nesting habitat throughout most of its range remains unclear. Here, we have compiled all existing nest records and locations to identify landscape-scale parameters (distance to coast, elevation, slope, and land cover) that provide potential nesting habitat in four regions: northern Alaska, Aleutian Islands, Alaska Peninsula Mountains and Kodiak Island, and Pacific Coastal Mountains (including nearshore interior Canada). We produced a final map classifying 12% (70,411 km2) of the lands assessed as potential Kittlitz's Murrelet nesting habitat, with dense but distinct patches in northern Alaska and a more uninterrupted, narrow band extending across the Pacific Coastal Mountains, Alaska Peninsula Mountains, and Aleutian Islands. The extent of habitat-capable parameter values varied regionally, indicating that the Kittlitz's Murrelet may be able to use a variety of habitats for nesting, depending on availability. Future nesting habitat studies could employ spatially random sampling designs to allow for quantitatively robust modeling of nesting habitat and predictive extrapolation to areas where nests have not been located but likely exist.

  6. Deletions of Yq11 associated with short stature and the Turner syndrome. Tentative mapping of a region associated with specific Turner stigmata to proximal interval 5.

    SciTech Connect

    McElreavey, K.; Barbaux, S.; Vilain, E.

    1994-09-01

    Turner syndrome is a complex human phenotype, commonly associated with a 45,X karyotype. Mapping the Turner phenotype is difficult since hidden mosaicisms, partial monosomy and complex rearrangements are present in many affected individuals. In addition, attempts to map the genes involved to the X chromosome have failed to yield a consistent localisation. An alternative approach to map and identify Turner genes is to study XY individuals, with sex chromosome abnormalities, who present with or without characteristic Turner stigmata. We report the analysis of 4 individuals with terminal deletions of Yq. The individuals were azoospermic males without phenotypic abnormalities (2 cases) and azoospermic males presenting with a specific subset of Turner stigmata (2 cases). Breakpoints in each of the cytogenetically detectable Yq deletions were mapped by Southern analysis and Y chromosome-specific sequence tagged sites (STS). Correlation between the patients phenotypes and the extent of their deletion indicate a critical region associated with specific Turner stigmata (cubitus valgus, shield chest, short fourth metacarpals) and growth retardation at Yq at proximal interval 5. These data provide evidence that the somatic features of the Turner syndrome are most likely caused by haploinsufficiency of genes at several loci.

  7. Interhemispheric transfalcine approach and awake cortical mapping for resection of peri-atrial gliomas associated with the central lobule.

    PubMed

    Malekpour, Mahdi; Cohen-Gadol, Aaron A

    2015-02-01

    Medial posterior frontal and parietal gliomas extending to the peri-atrial region are difficult to reach surgically because of the working angle required to expose the lateral aspect of the tumor and the proximity of the tumor to the sensorimotor lobule; retraction of the sensorimotor cortex may lead to morbidity. The interhemispheric transfalcine approach is favorable and safe for resection of medial hemispheric tumors adjacent to the falx cerebri, but the literature on this approach is scarce. Awake cortical mapping using this operative route for tumors associated with the sensorimotor cortex has not been previously reported to our knowledge. We present the first case of a right medial posterior frontoparietal oligoastrocytoma that was resected through the interhemispheric transfalcine approach using awake cortical and subcortical mapping. Through a contralateral frontoparietal craniotomy, we excised a section of the falx and exposed the contralateral medial hemisphere. Cortical stimulation allowed localization of the supplementary motor cortex, and suprathreshold stimulation mapping excluded the primary motor cortex corresponding to the leg area. Gross total tumor resection was accomplished without any intraoperative or postoperative deficits. Awake cortical mapping using the contralateral transfalcine approach allows a "cross-court" operative route to map functional cortices and resect peri-atrial low-grade gliomas. This technique can minimize the otherwise necessary retraction on the ipsilateral hemisphere through an ipsilateral craniotomy.

  8. Nest marking behavior and chemical composition of olfactory cues involved in nest recognition in Megachile rotundata.

    PubMed

    Guédot, Christelle; Buckner, James S; Hagen, Marcia M; Bosch, Jordi; Kemp, William P; Pitts-Singer, Theresa L

    2013-08-01

    In-nest observations of the solitary bee, Megachile rotundata (F.), revealed that nesting females apply olfactory cues to nests for nest recognition. On their way in and out of the nest, females drag the abdomen along the entire length of the nest, and sometimes deposit fluid droplets from the tip of the abdomen. The removal of bee-marked sections of the nest resulted in hesitation and searching behavior by females, indicating the loss of olfactory cues used for nest recognition. Chemical analysis of female cuticles and the deposits inside marked nesting tubes revealed the presence of hydrocarbons, wax esters, fatty aldehydes, and fatty alcohol acetate esters. Chemical compositions were similar across tube samples, but proportionally different from cuticular extracts. These findings reveal the importance of lipids as chemical signals for nest recognition and suggest that the nest-marking cues are derived from a source in addition to, or other than, the female cuticle.

  9. Nest marking behavior and chemical composition of olfactory cues involved in nest recognition in Megachile rotundata.

    PubMed

    Guédot, Christelle; Buckner, James S; Hagen, Marcia M; Bosch, Jordi; Kemp, William P; Pitts-Singer, Theresa L

    2013-08-01

    In-nest observations of the solitary bee, Megachile rotundata (F.), revealed that nesting females apply olfactory cues to nests for nest recognition. On their way in and out of the nest, females drag the abdomen along the entire length of the nest, and sometimes deposit fluid droplets from the tip of the abdomen. The removal of bee-marked sections of the nest resulted in hesitation and searching behavior by females, indicating the loss of olfactory cues used for nest recognition. Chemical analysis of female cuticles and the deposits inside marked nesting tubes revealed the presence of hydrocarbons, wax esters, fatty aldehydes, and fatty alcohol acetate esters. Chemical compositions were similar across tube samples, but proportionally different from cuticular extracts. These findings reveal the importance of lipids as chemical signals for nest recognition and suggest that the nest-marking cues are derived from a source in addition to, or other than, the female cuticle. PMID:23905742

  10. Water level dynamics in wetlands and nesting success of Black Terns in Maine

    USGS Publications Warehouse

    Gilbert, A.T.; Servello, F.A.

    2005-01-01

    The Black Tern (Chlidonias niger) nests in freshwater wetlands that are prone to water level fluctuations, and nest losses to flooding are common. We examined temporal patterns in water levels at six sites with Black Tern colonies in Maine and determined probabilities of flood events and associated nest loss at Douglas Pond, the location of the largest breeding colony. Daily precipitation data from weather stations and water flow data from a flow gauge below Douglas Pond were obtained for 1960-1999. Information on nest losses from three floods at Douglas Pond in 1997-1999 were used to characterize small (6% nest loss), medium (56% nest loss) and large (94% nest loss) flood events, and we calculated probabilities of these three levels of flooding occurring at Douglas Pond using historic water levels data. Water levels generally decreased gradually during the nesting season at colony sites, except at Douglas Pond where water levels fluctuated substantially in response to rain events. Annual probabilities of small, medium, and large flood events were 68%, 35%, and 13% for nests initiated during 23 May-12 July, with similar probabilities for early (23 May-12 June) and late (13 June-12 July) periods. An index of potential nest loss indicated that medium floods at Douglas Pond had the greatest potential effect on nest success because they occurred relatively frequently and inundated large proportions of nests. Nest losses at other colonies were estimated to be approximately 30% of those at Douglas Pond. Nest losses to flooding appear to be common for the Black Tern in Maine and related to spring precipitation patterns, but ultimate effects on breeding productivity are uncertain.

  11. Population dynamics of adult fleas (Siphonaptera) on hosts and in nests of the California vole.

    PubMed

    Stark, Harold E

    2002-11-01

    Microtus californicus (Peale, 1848) were live trapped or retrapped 887 times, and fleas were collected over a 2.5-yr period in the San Francisco Watershed and Wildlife Refuge. Also, 179 M. californicus nests were collected monthly with observations to identify the environment of fleas. The ratio of the mean number of fleas per nest to the mean number collected on voles was 4.7:1 for Malaraeus telchinus (Rothschild, 1905), 13:1 for Hystrichopsylla occidentalis linsdalei Holland, 1957,9:1 for Atyphloceras multidentatus multidentatus (C. Fox, 1909), and 76:1 for Catallagia wymani (C. Fox, 1909). The proportion of each flea species per nest to those per host was not closely associated seasonally or spatially. The average nest contained 37.5% moisture content in relation to its total weight and ranged between 3 and 92%. No relationship was observed between relative humidity of air within nests and flea number, but a significant relationship existed between the moisture of nesting materials and flea number. Malaraeus telchinus and A. m. multidentatus were collected in greatest numbers from nests having 30-39% moisture content by weight, and H. o. linsdalei and C. wymani were most numerous in nests that had 40-49% moisture content. Catallagia wymani had the greatest tolerance for high moisture and was severely affected by lack of moisture and nearly absent in drier nests. No ectoparasites were collected from nests that had <12% moisture content, and nests with >50% moisture content had few fleas. A static concept of nest fleas and host fleas as suggested by averages and often used in literature is questionable. In seasonal comparison of populations of fleas on hosts and in nests, M. telchinus and H. o. linsdalei reversed so that more of the flea population was on the host than in the nest for a short time during fall. PMID:12495178

  12. Association between lesion location and language function in adult glioma using voxel-based lesion-symptom mapping

    PubMed Central

    Banerjee, Pia; Leu, Kevin; Harris, Robert J.; Cloughesy, Timothy F.; Lai, Albert; Nghiemphu, Phioanh L.; Pope, Whitney B.; Bookheimer, Susan Y.; Ellingson, Benjamin M.

    2015-01-01

    Background Management of language difficulties is an important aspect of clinical care for glioma patients, and accurately identifying the possible language deficits in patients based on lesion location would be beneficial to clinicians. To that end, we examined the relationship between lesion presence and language performance on tests of receptive language and expressive language using a highly specific voxel-based lesion–symptom mapping (VLSM) approach in glioma patients. Methods 98 adults with primary glioma, who were pre-surgical candidates, were administered seven neurocognitive tests within the domains of receptive language and expressive language. The association between language performance and lesion presence was examined using VLSM. Statistical parametric maps were created for each test, and composite maps for both receptive language and expressive language were created to display the significant voxels common to all tests within these language domains. Results We identified clusters of voxels with a significant relationship between lesion presence and language performance. All tasks were associated with several white matter pathways. The receptive language tasks were additionally all associated with regions primarily within the lateral temporal lobe and medial temporal lobe. In contrast, the expressive language tasks shared little overlap, despite each task being independently associated with large anatomic areas. Conclusions Our findings identify the key anatomic structures involved in language functioning in adult glioma patients using an innovative lesion analysis technique and suggest that expressive language abilities may be more task-dependent and distributed than receptive language abilities. PMID:26740915

  13. Association mapping and genetic dissection of nitrogen use efficiency-related traits in rice (Oryza sativa L.).

    PubMed

    Liu, Zhiyi; Zhu, Chengsong; Jiang, Yue; Tian, Yunlu; Yu, Jun; An, Hongzhou; Tang, Weijie; Sun, Juan; Tang, Jianpeng; Chen, Gaoming; Zhai, Huqu; Wang, Chunming; Wan, Jianmin

    2016-05-01

    The increases in the usage of nitrogen fertilizer result in deleterious impacts on the environment; thus, there is an urgent need to improve nitrogen use efficiency (NUE) in crops including rice (Oryza sativa L.). Attentions have focused on quantitative trait loci (QTL) mapping of NUE-related traits using single experimental population, but to date, very few studies have taken advantage of association mapping to examine hundreds of lines for identifying potentially novel QTLs in rice. Here, we conducted association analysis on NUE-related traits using a population containing 184 varieties, which were genotyped with 157 genome-wide simple sequence repeat (SSR) markers. We detected eight statistically significant marker loci associating with NUE-related traits, of which two QTLs at RM5639 and RM3628 harbored known NUE-related genes GS1;2 and AspAt3, respectively. At a novel NUE-related locus RM5748, we developed Kompetitive Allele Specific PCR (KASP) single nucleotide polymorphism (SNP) markers and searched for putative NUE-related genes which are close to the associated SNP marker. Based on a transcriptional map of N stress responses constructed by our lab, we evaluated expressions of the NUE-related genes in this region and validated their effect on NUE. Meanwhile, we analyzed NUE-related alleles of the eight loci that could be utilized in marker-assisted selection. Moreover, we estimated breeding values of all the varieties through genomic prediction approach that could be beneficial for rice NUE enhancement.

  14. Genome-wide association mapping in tomato (Solanum lycopersicum) is possible using genome admixture of Solanum lycopersicum var. cerasiforme.

    PubMed

    Ranc, Nicolas; Muños, Stephane; Xu, Jiaxin; Le Paslier, Marie-Christine; Chauveau, Aurélie; Bounon, Rémi; Rolland, Sophie; Bouchet, Jean-Paul; Brunel, Dominique; Causse, Mathilde

    2012-08-01

    Genome-wide association mapping is an efficient way to identify quantitative trait loci controlling the variation of phenotypes, but the approach suffers severe limitations when one is studying inbred crops like cultivated tomato (Solanum lycopersicum). Such crops exhibit low rates of molecular polymorphism and high linkage disequilibrium, which reduces mapping resolution. The cherry type tomato (S. lycopersicum var. cerasiforme) genome has been described as an admixture between the cultivated tomato and its wild ancestor, S. pimpinellifolium. We have thus taken advantage of the properties of this admixture to improve the resolution of association mapping in tomato. As a proof of concept, we sequenced 81 DNA fragments distributed on chromosome 2 at different distances in a core collection of 90 tomato accessions, including mostly cherry type tomato accessions. The 81 Sequence Tag Sites revealed 352 SNPs and indels. Molecular diversity was greatest for S. pimpinellifolium accessions, intermediate for S. l. cerasiforme accessions, and lowest for the cultivated group. We assessed the structure of molecular polymorphism and the extent of linkage disequilibrium over genetic and physical distances. Linkage disequilibrium decreased under r(2) = 0.3 within 1 cM, and minimal estimated value (r(2) = 0.13) was reached within 20 kb over the physical regions studied. Associations between polymorphisms and fruit weight, locule number, and soluble solid content were detected. Several candidate genes and quantitative trait loci previously identified were validated and new associations detected. This study shows the advantages of using a collection of S. l. cerasiforme accessions to overcome the low resolution of association mapping in tomato. PMID:22908034

  15. Nest predation increases with parental activity: Separating nest site and parental activity effects

    USGS Publications Warehouse

    Martin, T.E.; Scott, J.; Menge, C.

    2000-01-01

    Alexander Skutch hypothesized that increased parental activity can increase the risk of nest predation. We tested this hypothesis using ten open-nesting bird species in Arizona, USA. Parental activity was greater during the nestling than incubation stage because parents visited the nest frequently to feed their young during the nestling stage. However, nest predation did not generally increase with parental activity between nesting stages across the ten study species. Previous investigators have found similar results. We tested whether nest site effects might yield higher predation during incubation because the most obvious sites are depredated most rapidly. We conducted experiments using nest sites from the previous year to remove parental activity. Our results showed that nest sites have highly repeatable effects on nest predation risk; poor nest sites incurred rapid predation and caused predation rates to be greater during the incubation than nestling stage. This pattern also was exhibited in a bird species with similar (i.e. controlled) parental activity between nesting stages. Once nest site effects are taken into account, nest predation shows a strong proximate increase with parental activity during the nestling stage within and across species. Parental activity and nest sites exert antagonistic influences on current estimates of nest predation between nesting stages and both must be considered in order to understand current patterns of nest predation, which is an important source of natural selection.

  16. Decoration Increases the Conspicuousness of Raptor Nests

    PubMed Central

    Canal, David; Mulero-Pázmány, Margarita; Negro, Juan José; Sergio, Fabrizio

    2016-01-01

    Avian nests are frequently concealed or camouflaged, but a number of species builds noticeable nests or use conspicuous materials for nest decoration. In most cases, nest decoration has a role in mate choice or provides thermoregulatory or antiparasitic benefits. In territorial species however, decorations may serve additional or complementary functions, such as extended phenotypic signaling of nest-site occupancy and social status to potential intruders. The latter may benefit both signaler and receiver by minimizing the risk of aggressive interactions, especially in organisms with dangerous weaponry. Support for this hypothesis was recently found in a population of black kites (Milvus migrans), a territorial raptor that decorates its nest with white artificial materials. However, the crucial assumption that nest decorations increased nest-site visibility to conspecifics was not assessed, a key aspect given that black kite nests may be well concealed within the canopy. Here, we used an unmanned aircraft system to take pictures of black kite nests, with and without an experimentally placed decoration, from different altitudes and distances simulating the perspective of a flying and approaching, prospecting intruder. The pictures were shown to human volunteers through a standardized routine to determine whether detection rates varied according the nest decoration status and distance. Decorated nests consistently showed a higher detection frequency and a lower detection-latency, compared to undecorated versions of the same nests. Our results confirm that nest decoration in this species may act as a signaling medium that enhances nest visibility for aerial receivers, even at large distances. This finding complements previous work on this communication system, which showed that nest decoration was a threat informing trespassing conspecifics on the social dominance, territory quality and fighting capabilities of the signaler. PMID:27455066

  17. Decoration Increases the Conspicuousness of Raptor Nests.

    PubMed

    Canal, David; Mulero-Pázmány, Margarita; Negro, Juan José; Sergio, Fabrizio

    2016-01-01

    Avian nests are frequently concealed or camouflaged, but a number of species builds noticeable nests or use conspicuous materials for nest decoration. In most cases, nest decoration has a role in mate choice or provides thermoregulatory or antiparasitic benefits. In territorial species however, decorations may serve additional or complementary functions, such as extended phenotypic signaling of nest-site occupancy and social status to potential intruders. The latter may benefit both signaler and receiver by minimizing the risk of aggressive interactions, especially in organisms with dangerous weaponry. Support for this hypothesis was recently found in a population of black kites (Milvus migrans), a territorial raptor that decorates its nest with white artificial materials. However, the crucial assumption that nest decorations increased nest-site visibility to conspecifics was not assessed, a key aspect given that black kite nests may be well concealed within the canopy. Here, we used an unmanned aircraft system to take pictures of black kite nests, with and without an experimentally placed decoration, from different altitudes and distances simulating the perspective of a flying and approaching, prospecting intruder. The pictures were shown to human volunteers through a standardized routine to determine whether detection rates varied according the nest decoration status and distance. Decorated nests consistently showed a higher detection frequency and a lower detection-latency, compared to undecorated versions of the same nests. Our results confirm that nest decoration in this species may act as a signaling medium that enhances nest visibility for aerial receivers, even at large distances. This finding complements previous work on this communication system, which showed that nest decoration was a threat informing trespassing conspecifics on the social dominance, territory quality and fighting capabilities of the signaler. PMID:27455066

  18. Decoration Increases the Conspicuousness of Raptor Nests.

    PubMed

    Canal, David; Mulero-Pázmány, Margarita; Negro, Juan José; Sergio, Fabrizio

    2016-01-01

    Avian nests are frequently concealed or camouflaged, but a number of species builds noticeable nests or use conspicuous materials for nest decoration. In most cases, nest decoration has a role in mate choice or provides thermoregulatory or antiparasitic benefits. In territorial species however, decorations may serve additional or complementary functions, such as extended phenotypic signaling of nest-site occupancy and social status to potential intruders. The latter may benefit both signaler and receiver by minimizing the risk of aggressive interactions, especially in organisms with dangerous weaponry. Support for this hypothesis was recently found in a population of black kites (Milvus migrans), a territorial raptor that decorates its nest with white artificial materials. However, the crucial assumption that nest decorations increased nest-site visibility to conspecifics was not assessed, a key aspect given that black kite nests may be well concealed within the canopy. Here, we used an unmanned aircraft system to take pictures of black kite nests, with and without an experimentally placed decoration, from different altitudes and distances simulating the perspective of a flying and approaching, prospecting intruder. The pictures were shown to human volunteers through a standardized routine to determine whether detection rates varied according the nest decoration status and distance. Decorated nests consistently showed a higher detection frequency and a lower detection-latency, compared to undecorated versions of the same nests. Our results confirm that nest decoration in this species may act as a signaling medium that enhances nest visibility for aerial receivers, even at large distances. This finding complements previous work on this communication system, which showed that nest decoration was a threat informing trespassing conspecifics on the social dominance, territory quality and fighting capabilities of the signaler.

  19. QTLs Associated with Agronomic Traits in the Cutler × AC Barrie Spring Wheat Mapping Population Using Single Nucleotide Polymorphic Markers

    PubMed Central

    Perez-Lara, Enid; Semagn, Kassa; Chen, Hua; Iqbal, Muhammad; N’Diaye, Amidou; Kamran, Atif; Navabi, Alireza; Pozniak, Curtis; Spaner, Dean

    2016-01-01

    We recently reported three earliness per se quantitative trait loci (QTL) associated with flowering and maturity in a recombinant inbred lines (RILs) population derived from a cross between the spring wheat (Triticum aestivum L.) cultivars ‘Cutler’ and ‘AC Barrie’ using 488 microsatellite and diversity arrays technology (DArT) markers. Here, we present QTLs associated with flowering time, maturity, plant height, and grain yield using high density single nucleotide polymorphic (SNP) markers in the same population. A mapping population of 158 RILs and the two parents were evaluated at five environments for flowering, maturity, plant height and grain yield under field conditions, at two greenhouse environments for flowering, and genotyped with a subset of 1809 SNPs out of the 90K SNP array and 2 functional markers (Ppd-D1 and Rht-D1). Using composite interval mapping on the combined phenotype data across all environments, we identified a total of 19 QTLs associated with flowering time in greenhouse (5), and field (6) conditions, maturity (5), grain yield (2) and plant height (1). We mapped these QTLs on 8 chromosomes and they individually explained between 6.3 and 37.8% of the phenotypic variation. Four of the 19 QTLs were associated with multiple traits, including a QTL on 2D associated with flowering, maturity and grain yield; two QTLs on 4A and 7A associated with flowering and maturity, and another QTL on 4D associated with maturity and plant height. However, only the QTLs on both 2D and 4D had major effects, and they mapped adjacent to well-known photoperiod response Ppd-D1 and height reducing Rht-D1 genes, respectively. The QTL on 2D reduced flowering and maturity time up to 5 days with a yield penalty of 436 kg ha-1, while the QTL on 4D reduced plant height by 13 cm, but increased maturity by 2 days. The high density SNPs allowed us to map eight moderate effect, two major effect, and nine minor effect QTLs that were not identified in our previous study

  20. QTLs Associated with Agronomic Traits in the Cutler × AC Barrie Spring Wheat Mapping Population Using Single Nucleotide Polymorphic Markers.

    PubMed

    Perez-Lara, Enid; Semagn, Kassa; Chen, Hua; Iqbal, Muhammad; N'Diaye, Amidou; Kamran, Atif; Navabi, Alireza; Pozniak, Curtis; Spaner, Dean

    2016-01-01

    We recently reported three earliness per se quantitative trait loci (QTL) associated with flowering and maturity in a recombinant inbred lines (RILs) population derived from a cross between the spring wheat (Triticum aestivum L.) cultivars 'Cutler' and 'AC Barrie' using 488 microsatellite and diversity arrays technology (DArT) markers. Here, we present QTLs associated with flowering time, maturity, plant height, and grain yield using high density single nucleotide polymorphic (SNP) markers in the same population. A mapping population of 158 RILs and the two parents were evaluated at five environments for flowering, maturity, plant height and grain yield under field conditions, at two greenhouse environments for flowering, and genotyped with a subset of 1809 SNPs out of the 90K SNP array and 2 functional markers (Ppd-D1 and Rht-D1). Using composite interval mapping on the combined phenotype data across all environments, we identified a total of 19 QTLs associated with flowering time in greenhouse (5), and field (6) conditions, maturity (5), grain yield (2) and plant height (1). We mapped these QTLs on 8 chromosomes and they individually explained between 6.3 and 37.8% of the phenotypic variation. Four of the 19 QTLs were associated with multiple traits, including a QTL on 2D associated with flowering, maturity and grain yield; two QTLs on 4A and 7A associated with flowering and maturity, and another QTL on 4D associated with maturity and plant height. However, only the QTLs on both 2D and 4D had major effects, and they mapped adjacent to well-known photoperiod response Ppd-D1 and height reducing Rht-D1 genes, respectively. The QTL on 2D reduced flowering and maturity time up to 5 days with a yield penalty of 436 kg ha-1, while the QTL on 4D reduced plant height by 13 cm, but increased maturity by 2 days. The high density SNPs allowed us to map eight moderate effect, two major effect, and nine minor effect QTLs that were not identified in our previous study using

  1. Woodcock nesting habitat in northern Wisconsin

    USGS Publications Warehouse

    Gregg, L.E.; Hale, J.B.

    1977-01-01

    Of 32 woodcock nests studied in northern Wisconsin, 29 were in forest stands dominated by aspen, and 3 were in northern hardwoods. Well-drained, upland nest sites near the brushy edges of poorly stocked poletimber stands were apparently preferred. More than 30 woody plant species were found at the 32 nest sites. Hazel was the most important shrub species noted.

  2. Nesting behavior of the poo-uli

    USGS Publications Warehouse

    Kepler, C.B.; Pratt, T.K.; Ecton, A.M.; Engilis, A.; Fluetsch, K.M.

    1996-01-01

    We describe two sequential nestings of a pair of Poo-uli (Melamprosops phaeosoma), a Hawaiian honeycreeper nearing extinction. Similarities to nesting of most other honeycreepers included: nest site in ohia lehua (Metrosideros polymorpha Gaud.) canopy; breeding in March through June; monogamous breeding system with the putative male helping build the nest, feeding the putative female throughout each nesting event, and feeding the chicks, but not incubating or brooding; and complete nest sanitation. Notable differences were the paucity of songs and calls by the parents and inclusion of snails in the diet of nestlings. Clutch size was probably two eggs for both nests. High winds, rain, or both influenced parental behavior: the female stayed longer on the nest and took shorter recesses in poor weather. Weather did not affect rates at which the male fed the female on the nest; however, the feeding rate increased from the egg to the chick stage probably because food was passed on to the chicks. At nest #2, parents fed young chicks (<14 days old) more often in good than in poor weather; data were insufficient for old chicks. Weather is usually poor throughout the year in the relictual range of the Poo-uli and is likely to impact nesting success. The first nest failed in poor weather. The second fledged a single young 21 days old. Diet of nestlings appeared to consist of a higher proportion of insect larvae than that of older birds, which are reported to eat mostly snails.

  3. Teaching Ecological Concepts with Mud Dauber Nests.

    ERIC Educational Resources Information Center

    Matthews, Robert W.; Matthews, Janice R.

    1999-01-01

    Contends that mud dauber nests--which are widely available, safe, inexpensive, and easy to use--offer a novel and highly motivating way to teach ecological concepts to life science students at many grade levels. Presents background information for teachers, details classroom-tested methods for nest dissection, provides keys to nest contents, and…

  4. Eleven X chromosome breakpoints associated with premature ovarian failure (POF) map to a 15-Mb YAC contig spanning Xq21.

    PubMed

    Sala, C; Arrigo, G; Torri, G; Martinazzi, F; Riva, P; Larizza, L; Philippe, C; Jonveaux, P; Sloan, F; Labella, T; Toniolo, D

    1997-02-15

    Eleven balanced X-autosome translocations associated with premature ovarian failure (POF) were mapped to a YAC contig spanning most of Xq21 and constructed between the DXS223 and DXS1171 loci. The contig corresponds to a genomic region of about 15 Mb and contains the whole X-Y homologous region. The most proximal and most distal breakpoints associated with POF were mapped 15 Mb apart. The remaining breakpoints were localized along this large region, in the X-specific and in the X-Y homologous region. Four of the YACs contained two breakpoints in the same or in flanking STS intervals. Our results confirm the cytological findings and suggest that a minimum number of eight different genes in Xq21 may be involved with ovary development. Interruption of such loci could be the cause of POF.

  5. Information content in genome-wide scans: concordance between patterns of genetic differentiation and linkage mapping associations

    PubMed Central

    2011-01-01

    Background Scanning the genome with high density SNP markers has become a standard approach for identifying regions of the genome showing substantial between-population genetic differentiation, and thus evidence of diversifying selection. Such regions may contain genes of large phenotypic effect. However, few studies have attempted to address the power or efficacy of such an approach. Results In this study, the patterns of allele frequency differences between two cattle breeds based on the Bovine HapMap study were compared with statistical evidence for QTL based on a linkage mapping study of an experimental population formed by a cross between the same breeds. Concordance between the two datasets was seen for chromosomes carrying QTL with strong statistical support, such as BTA5 and BTA18, which carry genes associated with coat color. For these chromosomes, there was a correspondence between the strength of the QTL signal along the chromosome and the degree of genetic differentiation between breeds. However, such an association was not seen in a broader comparison that also included chromosomes carrying QTL with lower significance levels. In addition, other chromosomal regions with substantial QTL effects did not include markers showing extreme between-breed genetic differentiation. Furthermore, the overall consistency between the two studies was weak, with low genome-wide correlation between the statistical values obtained in the linkage mapping study and between-breed genetic differentiation from the HapMap study. Conclusions These results suggest that genomic diversity scans are capable of detecting regions associated with qualitative traits but may be limited in their power to detect regions associated with quantitative phenotypic differences between populations, which may depend on the marker resolution of the study and the level of LD in the populations under investigation. PMID:21269469

  6. Nesting ecology of Greater Sandhill Cranes (Grus canadensis tabida) in riparian and palustrine wetlands of eastern Idaho

    USGS Publications Warehouse

    McWethy, D.B.; Austin, J.E.

    2009-01-01

    Little information exists on breeding Greater Sandhill Cranes (Grus canadensis tabida) in riparian wetlands of the Intermountain West. We examined the nesting ecology of Sandhill Cranes associated with riparian and palustrine wetlands in the Henry's Fork Watershed in eastern Idaho in 2003. We located 36 active crane nests, 19 in riparian wetlands and 17 in palustrine wetlands. Nesting sites were dominated by rushes (Juncus spp.), sedges (Carex spp.), Broad-leaved Cattail (Typha latifolia) and willow (Salix spp.), and adjacent foraging areas were primarily composed of sagebrush (Artemisia spp.), cinquefoil (Potentilla spp.),Rabbitbrush (Ericameria bloomeri) bunch grasses, upland forbs, Quaking Aspen (Populus tremuloides) and cottonwood (Populus spp.). Mean water depth surrounding nests was 23 cm (SD = 22). A majority of nests (61%) were surrounded by vegetation between 3060 cm, 23% by vegetation 60 cm in height. We were able to determine the fate of 29 nests, of which 20 were successful (69%). Daily nest survival was 0.986 (95% LCI 0.963, UCI 0.995), equivalent to a Mayfield nest success of 0.654 (95% LCI 0.324, UCI 0.853). Model selection favored models with the covariates vegetation type, vegetation height, and water depth. Nest survival increased with increasing water depth surrounding nest sites. Mean water depth was higher around successful nests (30 cm, SD = 21) than unsuccessful nests (15 cm, SD 22). Further research is needed to evaluate the relative contribution of cranes nesting in palustrine and riparian wetlands distributed widely across the Intermountain West.

  7. Controlling false positives in the mapping of epistatic QTL.

    PubMed

    Wei, W-H; Knott, S; Haley, C S; de Koning, D-J

    2010-04-01

    This study addresses the poorly explored issue of the control of false positive rate (FPR) in the mapping of pair-wise epistatic quantitative trait loci (QTL). A nested test framework was developed to (1) allow pre-identified QTL to be used directly to detect epistasis in one-dimensional genome scans, (2) to detect novel epistatic QTL pairs in two-dimensional genome scans and (3) to derive genome-wide thresholds through permutation and handle multiple testing. We used large-scale simulations to evaluate the performance of both the one- and two-dimensional approaches in mapping different forms and levels of epistasis and to generate profiles of FPR, power and accuracy to inform epistasis mapping studies. We showed that the nested test framework and genome-wide thresholds were essential to control FPR at the 5% level. The one-dimensional approach was generally more powerful than the two-dimensional approach in detecting QTL-associated epistasis and identified nearly all epistatic pairs detected from the two-dimensional approach. However, only the two-dimensional approach could detect epistatic QTL with weak main effects. Combining the two approaches allowed effective mapping of different forms of epistasis, whereas using the nested test framework kept the FPR under control. This approach provides a good search engine for high-throughput epistasis analyses.

  8. Statistical epistasis between candidate gene alleles for complex tuber traits in an association mapping population of tetraploid potato.

    PubMed

    Li, Li; Paulo, Maria-João; van Eeuwijk, Fred; Gebhardt, Christiane

    2010-11-01

    Association mapping using DNA-based markers is a novel tool in plant genetics for the analysis of complex traits. Potato tuber yield, starch content, starch yield and chip color are complex traits of agronomic relevance, for which carbohydrate metabolism plays an important role. At the functional level, the genes and biochemical pathways involved in carbohydrate metabolism are among the best studied in plants. Quantitative traits such as tuber starch and sugar content are therefore models for association genetics in potato based on candidate genes. In an association mapping experiment conducted with a population of 243 tetraploid potato varieties and breeding clones, we previously identified associations between individual candidate gene alleles and tuber starch content, starch yield and chip quality. In the present paper, we tested 190 DNA markers at 36 loci scored in the same association mapping population for pairwise statistical epistatic interactions. Fifty marker pairs were associated mainly with tuber starch content and/or starch yield, at a cut-off value of q ≤ 0.20 for the experiment-wide false discovery rate (FDR). Thirteen marker pairs had an FDR of q ≤ 0.10. Alleles at loci encoding ribulose-bisphosphate carboxylase/oxygenase activase (Rca), sucrose phosphate synthase (Sps) and vacuolar invertase (Pain1) were most frequently involved in statistical epistatic interactions. The largest effect on tuber starch content and starch yield was observed for the paired alleles Pain1-8c and Rca-1a, explaining 9 and 10% of the total variance, respectively. The combination of these two alleles increased the means of tuber starch content and starch yield. Biological models to explain the observed statistical epistatic interactions are discussed.

  9. Consequences of least tern (Sternula antillarum) microhabitat nest-site selection on natural and mechanically constructed sandbars in the Missouri River

    USGS Publications Warehouse

    Stucker, Jennifer H.; Buhl, Deborah A.; Sherfy, Mark H.

    2013-01-01

    Nest-habitat selection in colonial species has rarely been assessed at multiple spatial scales to evaluate its fitness consequences. Management for the federally endangered U.S. Interior population of Least Terns (Sternula antillarum) has focused on maintenance of breeding habitats, including mechanical construction of sandbars from dredged material. Least Terns are attracted to large areas of unvegetated substrate, yet small-scale habitat features are thought to trigger selection for nesting. We evaluated nest-scale habitat selection to determine (1) whether selection differs between constructed and natural sandbars and (2) the subsequent consequences of habitat selection on nest success. During 2006–2008, we examined 869 Least Tern nest sites on constructed and natural sandbars in the Missouri River for evidence of microhabitat selection at the nest in relation to habitat within the surrounding 3-m area. Least Tern nest sites had coarser and larger substrate materials at the nest, more debris, and less vegetation than the surrounding area. Nests in constructed habitats had a greater percentage of coarse substrates and less vegetation or debris than nests in naturally created habitats. Apparent nest success was 1.8× greater on constructed than on natural sandbars. Nest success was best predicted by models with two spatial scales of predictors, including substrates (nest) and vegetation and debris (nest or surrounding area). Our results indicate that Least Terns select nest microhabitat characteristics that are associated with wind- and water-scoured habitats, and that nest success increases when these habitats are selected.

  10. Identification of associated SSR markers for yield component and fiber quality traits based on frame map and Upland cotton collections.

    PubMed

    Qin, Hongde; Chen, Min; Yi, Xianda; Bie, Shu; Zhang, Cheng; Zhang, Youchang; Lan, Jiayang; Meng, Yanyan; Yuan, Youlu; Jiao, Chunhai

    2015-01-01

    Detecting QTLs (quantitative trait loci) that enhance cotton yield and fiber quality traits and accelerate breeding has been the focus of many cotton breeders. In the present study, 359 SSR (simple sequence repeat) markers were used for the association mapping of 241 Upland cotton collections. A total of 333 markers, representing 733 polymorphic loci, were detected. The average linkage disequilibrium (LD) decay distances were 8.58 cM (r2 > 0.1) and 5.76 cM (r2 > 0.2). 241 collections were arranged into two subgroups using STRUCTURE software. Mixed linear modeling (MLM) methods (with population structure (Q) and relative kinship matrix (K)) were applied to analyze four phenotypic datasets obtained from four environments (two different locations and two years). Forty-six markers associated with the number of bolls per plant (NB), boll weight (BW), lint percentage (LP), fiber length (FL), fiber strength (FS) and fiber micornaire value (FM) were repeatedly detected in at least two environments. Of 46 associated markers, 32 were identified as new association markers, and 14 had been previously reported in the literature. Nine association markers were near QTLs (at a distance of less than 1-2 LD decay on the reference map) that had been previously described. These results provide new useful markers for marker-assisted selection in breeding programs and new insights for understanding the genetic basis of Upland cotton yields and fiber quality traits at the whole-genome level.

  11. Quantitative trait loci for rice blast resistance detected in a local rice breeding population by genome-wide association mapping.

    PubMed

    Shinada, Hiroshi; Yamamoto, Toshio; Sato, Hirokazu; Yamamoto, Eiji; Hori, Kiyosumi; Yonemaru, Junichi; Sato, Takashi; Fujino, Kenji

    2015-12-01

    Plant breeding programs aim to develop cultivars with high adaptability to the specific conditions in a local region. As a result, unique genes and gene combinations have been accumulated in local elite breeding populations during the long history of plant breeding. Genetic analyses on such genes and combinations may be useful for developing new cultivars with more-desirable agronomic traits. Here, we attempted to detect quantitative trait loci (QTL) for rice blast resistance (BR) using a local breeding rice population from Hokkaido, Japan. Using genotyping data on single nucleotide polymorphisms and simple sequence repeat markers distributed throughout the whole genomic region, we detected genetic regions associated with phenotypic variation in BR by a genome-wide association mapping study (GWAS). An additional association analysis using other breeding cultivars verified the effect and inheritance of the associated region. Furthermore, the existence of a gene for BR in the associated region was confirmed by QTL mapping. The results from these studies enabled us to estimate potential of the Hokkaido rice population as a gene pool for improving BR. The results of this study could be useful for developing novel cultivars with vigorous BR in rice breeding programs.

  12. Historical versus contemporary climate forcing on the annual nesting variability of loggerhead sea turtles in the Northwest Atlantic Ocean.

    PubMed

    Arendt, Michael D; Schwenter, Jeffrey A; Witherington, Blair E; Meylan, Anne B; Saba, Vincent S

    2013-01-01

    A recent analysis suggested that historical climate forcing on the oceanic habitat of neonate sea turtles explained two-thirds of interannual variability in contemporary loggerhead (Caretta caretta) sea turtle nest counts in Florida, where nearly 90% of all nesting by this species in the Northwest Atlantic Ocean occurs. Here, we show that associations between annual nest counts and climate conditions decades prior to nest counts and those conditions one year prior to nest counts were not significantly different. Examination of annual nest count and climate data revealed that statistical artifacts influenced the reported 31-year lag association with nest counts. The projected importance of age 31 neophytes to annual nest counts between 2020 and 2043 was modeled using observed nest counts between 1989 and 2012. Assuming consistent survival rates among cohorts for a 5% population growth trajectory and that one third of the mature female population nests annually, the 41% decline in annual nest counts observed during 1998-2007 was not projected for 2029-2038. This finding suggests that annual nest count trends are more influenced by remigrants than neophytes. Projections under the 5% population growth scenario also suggest that the Peninsular Recovery Unit could attain the demographic recovery criteria of 106,100 annual nests by 2027 if nest counts in 2019 are at least comparable to 2012. Because the first year of life represents only 4% of the time elapsed through age 31, cumulative survival at sea across decades explains most cohort variability, and thus, remigrant population size. Pursuant to the U.S. Endangered Species Act, staggered implementation of protection measures for all loggerhead life stages has taken place since the 1970s. We suggest that the 1998-2007 nesting decline represented a lagged perturbation response to historical anthropogenic impacts, and that subsequent nest count increases since 2008 reflect a potential recovery response. PMID:24339901

  13. Historical versus Contemporary Climate Forcing on the Annual Nesting Variability of Loggerhead Sea Turtles in the Northwest Atlantic Ocean

    PubMed Central

    Arendt, Michael D.; Schwenter, Jeffrey A.; Witherington, Blair E.; Meylan, Anne B.; Saba, Vincent S.

    2013-01-01

    A recent analysis suggested that historical climate forcing on the oceanic habitat of neonate sea turtles explained two-thirds of interannual variability in contemporary loggerhead (Caretta caretta) sea turtle nest counts in Florida, where nearly 90% of all nesting by this species in the Northwest Atlantic Ocean occurs. Here, we show that associations between annual nest counts and climate conditions decades prior to nest counts and those conditions one year prior to nest counts were not significantly different. Examination of annual nest count and climate data revealed that statistical artifacts influenced the reported 31-year lag association with nest counts. The projected importance of age 31 neophytes to annual nest counts between 2020 and 2043 was modeled using observed nest counts between 1989 and 2012. Assuming consistent survival rates among cohorts for a 5% population growth trajectory and that one third of the mature female population nests annually, the 41% decline in annual nest counts observed during 1998–2007 was not projected for 2029–2038. This finding suggests that annual nest count trends are more influenced by remigrants than neophytes. Projections under the 5% population growth scenario also suggest that the Peninsular Recovery Unit could attain the demographic recovery criteria of 106,100 annual nests by 2027 if nest counts in 2019 are at least comparable to 2012. Because the first year of life represents only 4% of the time elapsed through age 31, cumulative survival at sea across decades explains most cohort variability, and thus, remigrant population size. Pursuant to the U.S. Endangered Species Act, staggered implementation of protection measures for all loggerhead life stages has taken place since the 1970s. We suggest that the 1998–2007 nesting decline represented a lagged perturbation response to historical anthropogenic impacts, and that subsequent nest count increases since 2008 reflect a potential recovery response. PMID

  14. Nest Predation Deviates from Nest Predator Abundance in an Ecologically Trapped Bird.

    PubMed

    Hollander, Franck A; Van Dyck, Hans; San Martin, Gilles; Titeux, Nicolas

    2015-01-01

    In human-modified environments, ecological traps may result from a preference for low-quality habitat where survival or reproductive success is lower than in high-quality habitat. It has often been shown that low reproductive success for birds in preferred habitat types was due to higher nest predator abundance. However, between-habitat differences in nest predation may only weakly correlate with differences in nest predator abundance. An ecological trap is at work in a farmland bird (Lanius collurio) that recently expanded its breeding habitat into open areas in plantation forests. This passerine bird shows a strong preference for forest habitat, but it has a higher nest success in farmland. We tested whether higher abundance of nest predators in the preferred habitat or, alternatively, a decoupling of nest predator abundance and nest predation explained this observed pattern of maladaptive habitat selection. More than 90% of brood failures were attributed to nest predation. Nest predator abundance was more than 50% higher in farmland, but nest predation was 17% higher in forest. Differences between nest predation on actual shrike nests and on artificial nests suggested that parent shrikes may facilitate nest disclosure for predators in forest more than they do in farmland. The level of caution by parent shrikes when visiting their nest during a simulated nest predator intrusion was the same in the two habitats, but nest concealment was considerably lower in forest, which contributes to explaining the higher nest predation in this habitat. We conclude that a decoupling of nest predator abundance and nest predation may create ecological traps in human-modified environments.

  15. Nest Predation Deviates from Nest Predator Abundance in an Ecologically Trapped Bird

    PubMed Central

    Hollander, Franck A.; Van Dyck, Hans; San Martin, Gilles; Titeux, Nicolas

    2015-01-01

    In human-modified environments, ecological traps may result from a preference for low-quality habitat where survival or reproductive success is lower than in high-quality habitat. It has often been shown that low reproductive success for birds in preferred habitat types was due to higher nest predator abundance. However, between-habitat differences in nest predation may only weakly correlate with differences in nest predator abundance. An ecological trap is at work in a farmland bird (Lanius collurio) that recently expanded its breeding habitat into open areas in plantation forests. This passerine bird shows a strong preference for forest habitat, but it has a higher nest success in farmland. We tested whether higher abundance of nest predators in the preferred habitat or, alternatively, a decoupling of nest predator abundance and nest predation explained this observed pattern of maladaptive habitat selection. More than 90% of brood failures were attributed to nest predation. Nest predator abundance was more than 50% higher in farmland, but nest predation was 17% higher in forest. Differences between nest predation on actual shrike nests and on artificial nests suggested that parent shrikes may facilitate nest disclosure for predators in forest more than they do in farmland. The level of caution by parent shrikes when visiting their nest during a simulated nest predator intrusion was the same in the two habitats, but nest concealment was considerably lower in forest, which contributes to explaining the higher nest predation in this habitat. We conclude that a decoupling of nest predator abundance and nest predation may create ecological traps in human-modified environments. PMID:26624619

  16. Age-specific productivity and nest site characteristics of Cooper's hawks (Accipiter cooperii)

    USGS Publications Warehouse

    Moore, K.R.; Henny, C.J.

    1984-01-01

    Nesting Cooper's Hawks (Accipiter cooperii) were studied in northeastern Oregon. Second-year (SY) males did not breed, but 22 percent of the breeding females were SY's. Mean clutch size (P = 0.012) and mean number of young fledged per pair that laid eggs (P < 0.10) were lower for SY females than for adult (after second year [ASY}) females; however, an equal percentage of the eggs (excluding a collected sample egg) yielded fledged young for each age class. Stepwise discriminant analysis suggested differences in structural characteristics of the nest site habitat for ASY and SY females, i.e., SY female nest sites were associated with younger successional stages than ASY female nest sites. Nests of both age groups were built in trees with high crown volume, but ASY females utilized mistletoe (Arceuthobium sp.) for nest structures more frequently (P < 0.01) than SY females.

  17. Breeding biology and nesting success of palila

    USGS Publications Warehouse

    Pletschet, S.M.; Kelly, J.F.

    1990-01-01

    We studied the breeding biology of Palila (Loxioides bailleui ) at 85 nests from 20 April to 14 September 1988. Eggs were laid over a 139-day period and incubation averaged 16.6 days. The female incubated 85.2% of daylight hours and males fed incubating females. Modal clutch size was 2 (x super(-) = 2.0) and an average of 1.4 nestlings fledged per successful nest. Nestlings were in the nest an average of 25.3 days. Both females and males fed nestlings with the rate of feeding decreasing as the nestlings grew older. Palila nesting success was 25%, reduced primarily by hatching failure and depredation of nestlings. Hatching failure, due to inviable eggs or desertion, occurred in 41% of nests with eggs (55% of nest mortality). Egg depredation was rare (5% of nest mortality). Inbreeding and low food availability are postulated as the major causes for poor hatching success.

  18. Identification and Verification of QTL Associated with Frost Tolerance Using Linkage Mapping and GWAS in Winter Faba Bean.

    PubMed

    Sallam, Ahmed; Arbaoui, Mustapha; El-Esawi, Mohamed; Abshire, Nathan; Martsch, Regina

    2016-01-01

    Frost stress is one of the abiotic stresses that causes a significant reduction in winter faba bean yield in Europe. The main objective of this work is to genetically improve frost tolerance in winter faba bean by identifying and validating QTL associated with frost tolerance to be used in marker-assisted selection (MAS). Two different genetic backgrounds were used: a biparental population (BPP) consisting of 101 inbred lines, and 189 genotypes from single seed descent (SSD) from the Gottingen Winter bean Population (GWBP). All experiments were conducted in a frost growth chamber under controlled conditions. Both populations were genotyped using the same set of 189 SNP markers. Visual scoring for frost stress symptoms was used to define frost tolerance in both populations. In addition, leaf fatty acid composition (FAC) and proline content were analyzed in BPP as physiological traits. QTL mapping (for BPP) and genome wide association studies (for GWBP) were performed to detect QTL associated with frost tolerance. High genetic variation between genotypes, and repeatability estimates, were found for all traits. QTL mapping and GWAS identified new putative QTL associated with promising frost tolerance and related traits. A set of 54 SNP markers common in both genetic backgrounds showed a high genetic diversity with polymorphic information content (PIC) ranging from 0.31 to 0.37 and gene diversity ranging from 0.39 to 0.50. This indicates that these markers may be polymorphic for many faba bean populations. Five SNP markers showed a significant marker-trait association with frost tolerance and related traits in both populations. Moreover, synteny analysis between Medicago truncatula (a model legume) and faba bean genomes was performed to identify candidate genes for these markers. Collinearity was evaluated between the faba bean genetic map constructed in this study and the faba bean consensus map, resulting in identifying possible genomic regions in faba bean which may

  19. Identification and Verification of QTL Associated with Frost Tolerance Using Linkage Mapping and GWAS in Winter Faba Bean

    PubMed Central

    Sallam, Ahmed; Arbaoui, Mustapha; El-Esawi, Mohamed; Abshire, Nathan; Martsch, Regina

    2016-01-01

    Frost stress is one of the abiotic stresses that causes a significant reduction in winter faba bean yield in Europe. The main objective of this work is to genetically improve frost tolerance in winter faba bean by identifying and validating QTL associated with frost tolerance to be used in marker-assisted selection (MAS). Two different genetic backgrounds were used: a biparental population (BPP) consisting of 101 inbred lines, and 189 genotypes from single seed descent (SSD) from the Gottingen Winter bean Population (GWBP). All experiments were conducted in a frost growth chamber under controlled conditions. Both populations were genotyped using the same set of 189 SNP markers. Visual scoring for frost stress symptoms was used to define frost tolerance in both populations. In addition, leaf fatty acid composition (FAC) and proline content were analyzed in BPP as physiological traits. QTL mapping (for BPP) and genome wide association studies (for GWBP) were performed to detect QTL associated with frost tolerance. High genetic variation between genotypes, and repeatability estimates, were found for all traits. QTL mapping and GWAS identified new putative QTL associated with promising frost tolerance and related traits. A set of 54 SNP markers common in both genetic backgrounds showed a high genetic diversity with polymorphic information content (PIC) ranging from 0.31 to 0.37 and gene diversity ranging from 0.39 to 0.50. This indicates that these markers may be polymorphic for many faba bean populations. Five SNP markers showed a significant marker-trait association with frost tolerance and related traits in both populations. Moreover, synteny analysis between Medicago truncatula (a model legume) and faba bean genomes was performed to identify candidate genes for these markers. Collinearity was evaluated between the faba bean genetic map constructed in this study and the faba bean consensus map, resulting in identifying possible genomic regions in faba bean which may

  20. Identification and Verification of QTL Associated with Frost Tolerance Using Linkage Mapping and GWAS in Winter Faba Bean.

    PubMed

    Sallam, Ahmed; Arbaoui, Mustapha; El-Esawi, Mohamed; Abshire, Nathan; Martsch, Regina

    2016-01-01

    Frost stress is one of the abiotic stresses that causes a significant reduction in winter faba bean yield in Europe. The main objective of this work is to genetically improve frost tolerance in winter faba bean by identifying and validating QTL associated with frost tolerance to be used in marker-assisted selection (MAS). Two different genetic backgrounds were used: a biparental population (BPP) consisting of 101 inbred lines, and 189 genotypes from single seed descent (SSD) from the Gottingen Winter bean Population (GWBP). All experiments were conducted in a frost growth chamber under controlled conditions. Both populations were genotyped using the same set of 189 SNP markers. Visual scoring for frost stress symptoms was used to define frost tolerance in both populations. In addition, leaf fatty acid composition (FAC) and proline content were analyzed in BPP as physiological traits. QTL mapping (for BPP) and genome wide association studies (for GWBP) were performed to detect QTL associated with frost tolerance. High genetic variation between genotypes, and repeatability estimates, were found for all traits. QTL mapping and GWAS identified new putative QTL associated with promising frost tolerance and related traits. A set of 54 SNP markers common in both genetic backgrounds showed a high genetic diversity with polymorphic information content (PIC) ranging from 0.31 to 0.37 and gene diversity ranging from 0.39 to 0.50. This indicates that these markers may be polymorphic for many faba bean populations. Five SNP markers showed a significant marker-trait association with frost tolerance and related traits in both populations. Moreover, synteny analysis between Medicago truncatula (a model legume) and faba bean genomes was performed to identify candidate genes for these markers. Collinearity was evaluated between the faba bean genetic map constructed in this study and the faba bean consensus map, resulting in identifying possible genomic regions in faba bean which may

  1. Waterbird nest density and nest survival in rice fields of southwestern Louisiana

    USGS Publications Warehouse

    Pierluissi, S.; King, Sammy L.; Kaller, Michael D.

    2010-01-01

    Rice fields in southwestern Louisiana provide breeding habitat for several waterbird species; however, little is known about nest density, nest survival and the importance of landscape context of rice fields in determining breeding activity. In 2004, 42 rice fields were searched for nests, and 40 were searched in 2005. Land uses surrounding rice fields, including irrigation canals, trees, crawfish ponds, rice, fallow and soybean fields, were examined to determine influence on nest density and survival. Nest densities were 13.5-16.0 nests/km2 for Purple Gallinules (Porphyrio martinica), 3.0-13.7 nests/km2 for Fulvous Whistling Ducks (Dendrocygna bicolor), 2.6-2.8 nests/km2 for Common Moorhens (Gallinula chloropus), 0.3-0.92 nests/km2 for Least Bitterns (Ixobrychus exilisi) and 0-0.6 nests/km2 for Mottled Ducks (Anas fulvigula). Nest survival was 52-79% for Purple Gallinules and 39-43% for Fulvous Whistling Ducks. Apparent nest success of Common Moorhens was 73-75%, 83% for Least Bitterns and 33% for Mottled Ducks. Purple Gallinule and Common Moorhen nest densities were highest in fields with a larger proportion of irrigation canals surrounding rice fields. Purple Gallinule nest densities were greater in fields devoid of trees and landscapes dominated by rice fields and pasture, rather than landscapes containing soybean fields and residential areas. Fulvous Whistling Duck nest densities were higher in agriculturally-dominated landscapes with few trees.

  2. Home improvement: C57BL/6J mice given more naturalistic nesting materials build better nests.

    PubMed

    Hess, Sarah E; Rohr, Stephanie; Dufour, Brett D; Gaskill, Brianna N; Pajor, Edmond A; Garner, Joseph P

    2008-11-01

    Environmental enrichment of laboratory mice can improve the quality of research, but debate arises over the means of enrichment and its ability to be used in a sterile environment. One important form of enrichment is nesting material. Mice in the wild build dome-shaped, complex, multilayered nests, but this behavior is not seen in the laboratory, perhaps due to inappropriate nesting material rather than the nest-building ability of the mice. Here we focus on the use of naturalistic nesting materials to test whether they improve nest quality through the use of a 'naturalistic nest score' system; we also focus on materials that can be sterilized and easily used in existing housing systems. We first determined whether C57BL/6J mice build naturalistic nests when given shredded paper strips. We then compared these shredded paper strips with other commonly used nesting enrichments (facial tissues and compressed cotton squares). Nests were scored for 6 d. We found that the shredded paper strips allowed the mice to build higher quality nests than those built with any of the other materials. Nests built with tissues were of intermediate quality, and nests built with compressed cotton squares were of poor quality, similar to those built by the control group. These results suggest that C57BL/6J mice given appropriate nesting materials can build nests similar to those built by their wild counterparts.

  3. Dependency of microtubule-associated proteins (MAPs) for tubulin stability and assembly; use of estramus