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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) 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 ...

  2. GENOME-WIDE COMPLEX TRAIT DISSECTION THROUGH NESTED ASSOCIATION MAPPING

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We investigated the genetic and statistical properties of the nested association mapping (NAM) design currently being implemented in maize (26 diverse founders and 5000 distinct immortal genotypes), which simultaneously exploits the advantages of both linkage analysis and association mapping. We de...

  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. Genetic Architecture of Maize Kernel Quality in the Nested Association Mapping (NAM) Population

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Many studies have been conducted to identify genes (quantitative trait loci; QTL) underlying kernel quality traits. However, these studies were limited to analyzing two parents at once and often resulted in low resolution mapping of QTL. The maize nested association mapping (NAM) population is a r...

  5. Maize Phenomics: Massively Parallel Phenotyping of the Nested Association Mapping Population

    Technology Transfer Automated Retrieval System (TEKTRAN)

    How does the tremendous genetic variation within maize cause the phenotypic diversity displayed in this species? A goal of the Maize Diversity Project is the development of the genetic resources and methods to answer this question. We created a Nested Association Mapping (NAM) population consisting ...

  6. Genome-wide association of carbon and nitrogen metabolism in the maize nested association mapping population.

    PubMed

    Zhang, Nengyi; Gibon, Yves; Wallace, Jason G; Lepak, Nicholas; Li, Pinghua; Dedow, Lauren; Chen, Charles; So, Yoon-Sup; Kremling, Karl; Bradbury, Peter J; Brutnell, Thomas; Stitt, Mark; Buckler, Edward S

    2015-06-01

    Carbon (C) and nitrogen (N) metabolism are critical to plant growth and development and are at the basis of crop yield and adaptation. We performed high-throughput metabolite analyses on over 12,000 samples from the nested association mapping population to identify genetic variation in C and N metabolism in maize (Zea mays ssp. mays). All samples were grown in the same field and used to identify natural variation controlling the levels of 12 key C and N metabolites, namely chlorophyll a, chlorophyll b, fructose, fumarate, glucose, glutamate, malate, nitrate, starch, sucrose, total amino acids, and total protein, along with the first two principal components derived from them. Our genome-wide association results frequently identified hits with single-gene resolution. In addition to expected genes such as invertases, natural variation was identified in key C4 metabolism genes, including carbonic anhydrases and a malate transporter. Unlike several prior maize studies, extensive pleiotropy was found for C and N metabolites. This integration of field-derived metabolite data with powerful mapping and genomics resources allows for the dissection of key metabolic pathways, providing avenues for future genetic improvement. PMID:25918116

  7. Limits on the reproducibility of marker associations with southern leaf blight resistance in the maize nested association mapping population

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A previous study reported a comprehensive quantitative trait locus (QTL) and genome wide association study (GWAS) of southern leaf blight (SLB) resistance in the maize Nested Association Mapping (NAM) panel. Since that time, the genomic resources available for such analyses have improved substantial...

  8. 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

  9. Genome-Wide Association of Carbon and Nitrogen Metabolism in the Maize Nested Association Mapping Population1[OPEN

    PubMed Central

    Zhang, Nengyi; Gibon, Yves; Chen, Charles; So, Yoon-Sup; Kremling, Karl; Bradbury, Peter J.; Brutnell, Thomas; Stitt, Mark

    2015-01-01

    Carbon (C) and nitrogen (N) metabolism are critical to plant growth and development and are at the basis of crop yield and adaptation. We performed high-throughput metabolite analyses on over 12,000 samples from the nested association mapping population to identify genetic variation in C and N metabolism in maize (Zea mays ssp. mays). All samples were grown in the same field and used to identify natural variation controlling the levels of 12 key C and N metabolites, namely chlorophyll a, chlorophyll b, fructose, fumarate, glucose, glutamate, malate, nitrate, starch, sucrose, total amino acids, and total protein, along with the first two principal components derived from them. Our genome-wide association results frequently identified hits with single-gene resolution. In addition to expected genes such as invertases, natural variation was identified in key C4 metabolism genes, including carbonic anhydrases and a malate transporter. Unlike several prior maize studies, extensive pleiotropy was found for C and N metabolites. This integration of field-derived metabolite data with powerful mapping and genomics resources allows for the dissection of key metabolic pathways, providing avenues for future genetic improvement. PMID:25918116

  10. 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

  11. 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...

  12. 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

  13. 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

  14. 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. PMID:27182953

  15. Resistance to Gray Leaf Spot of Maize: Genetic Architecture and Mechanisms Elucidated through Nested Association Mapping and Near-Isogenic Line Analysis

    PubMed Central

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

    2015-01-01

    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

  16. 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.

  17. Joint multiple family QTL analysis predicts within-family variation better than single family analysis of the maize nested association mapping population

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Quantitative trait loci (QTL) mapping has been used to dissect the genetic architecture of a trait and predict phenotypes for marker-assisted selection. Many QTL mapping studies in plants have been limited to one biparental family population. Joint analysis of multiple biparental families offers an ...

  18. 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

  19. Association mapping in cacao

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Association mapping is becoming important in perennial crops because it is a better alternative to the classical QTL's mapping approaches. The development of large breeding populations (F2, backcrosses and recombinant inbred populations) is a requirement of QTL's discovery; however, this process req...

  20. 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

  1. 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

  2. Woodpigeons nesting in association with hobby falcons: advantages and choice rules.

    PubMed

    Bogliani; Sergio; Tavecchia

    1999-01-01

    Many bird species nest in close association with other bolder and more aggressive birds which provide protection against nest predators. The woodpigeons, Columba palumbus, that nest in poplar plantations in Northern Italy are found almost exclusively clumped around hobby, Falco subbuteo, nests. Woodpigeons settle in the area and build their nests after the hobby has started nesting. We carried out experiments with dummy nests and observations on woodpigeon nests. Dummy woodpigeon nests placed near a hobby's nest suffered less depredation by hooded crows, Corvus corone cornix, than those placed far from it. A logistic regression analysis showed that three variables, hobby nesting stage, distance from the hobby's nest and the hobby's aggressiveness, influenced the probability of nest predation. The degree of protection varied during the hobby's nesting period and was highest when chicks were in the nest. The hobby's aggressiveness against intruders varied both between and within individuals during different nesting phases. The predation rate of dummy nests associated with the falcon was negatively correlated with the aggressiveness score of the hobby during the 6 days of dummy nest exposure. Observations on real nests showed that woodpigeons selected hobbies that had a high fledging success, and a more vigorous defensive behaviour. Clues that would allow woodpigeons to choose the best protector may be early nesting by the hobby and its aggressiveness. Hobbies preyed on adult woodpigeons, but the risk incurred by the woodpigeons was low compared with the very high risk of nest predation in this area. Copyright 1999 The Association for the Study of Animal Behaviour. PMID:10053079

  3. 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.

  4. 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

  5. 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

  6. 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.

  7. Ionomics of the Maize Nested Association Mapping Panel

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Heterogeneity in the elemental composition of soils is among the major causes of plant stress worldwide. In order to adapt to these conditions, plants frequently alter their elemental content. We employed mineral nutrient and trace element profiling in diverse maize germplasm, to examine the connect...

  8. 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...

  9. 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

  10. Association mapping in structured populations.

    PubMed

    Pritchard, J K; Stephens, M; Rosenberg, N A; Donnelly, P

    2000-07-01

    The use, in association studies, of the forthcoming dense genomewide collection of single-nucleotide polymorphisms (SNPs) has been heralded as a potential breakthrough in the study of the genetic basis of common complex disorders. A serious problem with association mapping is that population structure can lead to spurious associations between a candidate marker and a phenotype. One common solution has been to abandon case-control studies in favor of family-based tests of association, such as the transmission/disequilibrium test (TDT), but this comes at a considerable cost in the need to collect DNA from close relatives of affected individuals. In this article we describe a novel, statistically valid, method for case-control association studies in structured populations. Our method uses a set of unlinked genetic markers to infer details of population structure, and to estimate the ancestry of sampled individuals, before using this information to test for associations within subpopulations. It provides power comparable with the TDT in many settings and may substantially outperform it if there are conflicting associations in different subpopulations. PMID:10827107

  11. 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.

  12. An example of association mapping in Cacao.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Association mapping and genomic selection have become important methodologies in perennial crop breeding improvement programs for accelerating breeding efforts and increasing the efficiency of selection. They are good alternatives to the classical Quantitative Trait Loci (QTL) mapping approach.The ...

  13. 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

  14. 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

  15. A recursive approach to the O(n) model on random maps via nested loops

    NASA Astrophysics Data System (ADS)

    Borot, G.; Bouttier, J.; Guitter, E.

    2012-02-01

    We consider the O(n) loop model on tetravalent maps and show how to rephrase it into a model of bipartite maps without loops. This follows from a combinatorial decomposition that consists in cutting the O(n) model configurations along their loops so that each elementary piece is a map that may have arbitrary even face degrees. In the induced statistics, these maps are drawn according to a Boltzmann distribution whose parameters (the face weights) are determined by a fixed point condition. In particular, we show that the dense and dilute critical points of the O(n) model correspond to bipartite maps with large faces (i.e. whose degree distribution has a fat tail). The re-expression of the fixed point condition in terms of linear integral equations allows us to explore the phase diagram of the model. In particular, we determine this phase diagram exactly for the simplest version of the model where the loops are ‘rigid’. Several generalizations of the model are discussed.

  16. 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.

  17. Association Mapping for Enhancing Maize Genetic Improvement

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Association mapping through linkage disequilibrium (LD) analysis is a powerful tool for the dissection of complex agronomic traits and for the identification of alleles that can contribute to the enhancement of a target trait. With the developments of high throughput genotyping techniques and advanc...

  18. 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

  19. 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

  20. 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

  1. Comparison of biometrical models for joint linkage association mapping

    PubMed Central

    Würschum, T; Liu, W; Gowda, M; Maurer, H P; Fischer, S; Schechert, A; Reif, J C

    2012-01-01

    Joint linkage association mapping (JLAM) combines the advantages of linkage mapping and association mapping, and is a powerful tool to dissect the genetic architecture of complex traits. The main goal of this study was to use a cross-validation strategy, resample model averaging and empirical data analyses to compare seven different biometrical models for JLAM with regard to the correction for population structure and the quantitative trait loci (QTL) detection power. Three linear models and four linear mixed models with different approaches to control for population stratification were evaluated. Models A, B and C were linear models with either cofactors (Model-A), or cofactors and a population effect (Model-B), or a model in which the cofactors and the single-nucleotide polymorphism effect were modeled as nested within population (Model-C). The mixed models, D, E, F and G, included a random population effect (Model-D), or a random population effect with defined variance structure (Model-E), a kinship matrix defining the degree of relatedness among the genotypes (Model-F), or a kinship matrix and principal coordinates (Model-G). The tested models were conceptually different and were also found to differ in terms of power to detect QTL. Model-B with the cofactors and a population effect, effectively controlled population structure and possessed a high predictive power. The varying allele substitution effects in different populations suggest as a promising strategy for JLAM to use Model-B for the detection of QTL and then to estimate their effects by applying Model-C. PMID:21878984

  2. 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

  3. Genetic architecture of maize kernel composition in the nested association mapping and inbred association panels

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The maize kernel plays a critical role in feeding humans and livestock around the world and in a wide array of industrial applications. An understanding of the regulation of kernel starch, protein, and oil is needed in order to manipulate composition to meet future needs. We conducted quantitative...

  4. 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

  5. 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.

  6. Aluminum tolerance association mapping in triticale

    PubMed Central

    2012-01-01

    Background Crop production practices and industrialization processes result in increasing acidification of arable soils. At lower pH levels (below 5.0), aluminum (Al) remains in a cationic form that is toxic to plants, reducing growth and yield. The effect of aluminum on agronomic performance is particularly important in cereals like wheat, which has promoted the development of programs directed towards selection of tolerant forms. Even in intermediately tolerant cereals (i.e., triticale), the decrease in yield may be significant. In triticale, Al tolerance seems to be influenced by both wheat and rye genomes. However, little is known about the precise chromosomal location of tolerance-related genes, and whether wheat or rye genomes are crucial for the expression of that trait in the hybrid. Results A mapping population consisting of 232 advanced breeding triticale forms was developed and phenotyped for Al tolerance using physiological tests. AFLP, SSR and DArT marker platforms were applied to obtain a sufficiently large set of molecular markers (over 3000). Associations between the markers and the trait were tested using General (GLM) and Multiple (MLM) Linear Models, as well as the Statistical Machine Learning (SML) approach. The chromosomal locations of candidate markers were verified based on known assignments of SSRs and DArTs or by using genetic maps of rye and triticale. Two candidate markers on chromosome 3R and 9, 15 and 11 on chromosomes 4R, 6R and 7R, respectively, were identified. The r2 values were between 0.066 and 0.220 in most cases, indicating a good fit of the data, with better results obtained with the GML than the MLM approach. Several QTLs on rye chromosomes appeared to be involved in the phenotypic expression of the trait, suggesting that rye genome factors are predominantly responsible for Al tolerance in triticale. Conclusions The Diversity Arrays Technology was applied successfully to association mapping studies performed on triticale

  7. 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)

  8. {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.

  9. Comparison of Mixed-Model Approaches for Association Mapping

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Association-mapping methods promise to overcome the limitations of linkage-mapping methods. The main objectives of this study were to (i) evaluate various methods for association mapping in the autogamous species wheat using an empirical data set, (ii) determine a marker-based kinship matrix using a...

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

    PubMed

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

    2015-08-15

    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

  11. 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

  12. 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.

  13. 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.    

  14. 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.

  15. Mapping to molecular resolution in the T to H-2 region of the mouse genome with a nested set of meiotic recombinants.

    PubMed Central

    King, T R; Dove, W F; Herrmann, B; Moser, A R; Shedlovsky, A

    1989-01-01

    We describe a meiotic fine-structure mapping strategy for achieving molecular access to developmental mutations in the mouse. The induction of lethal point mutations with the potent germ-line mutagen N-ethyl-N-nitrosourea has been reported. One lethal mutation of prime interest is an allele at the quaking locus on chromosome 17. To map this mutation, quaking(lethal-1), we have intercrossed hybrid mice that carry distinct alleles at many classical and DNA marker loci on proximal chromosome 17. From this cross we have obtained 337 animals recombinant in the T to H-2 region. This number of crossovers provides a mapping resolution in the size range of single mammalian genes if recombinational hot spots are absent. DNA samples obtained from these recombinant animals can be used retrospectively to map any restriction fragment length polymorphism in the region. This set of DNA samples has been used to map the molecular marker D17RP17 just distal of quaking(lethal-1). With the nested set of crossover DNA samples and appropriate cloning techniques, this tightly linked marker can be used to clone the quaking locus. Images PMID:2911572

  16. 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)

  17. 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.

  18. Gastroenteritis outbreaks associated with Norwalk-like viruses and their investigation by nested RT-PCR

    PubMed Central

    O'Neill, Hugh J; McCaughey, Conall; Wyatt, Dorothy E; Mitchell, Frederick; Coyle, Peter V

    2001-01-01

    Background Norwalk-like viruses are the most common cause of gastroenteritis outbreaks and sporadic cases of vomiting and diarrhoea. In healthy individuals infection is often mild and short-lived but in debilitated patients infection can be severe. It is essential that the virus laboratory can offer a sensitive and specific test, delivered in a timely manner. Methods We have developed a nested reverse transcriptase PCR based on published primers against the RNA polymerase gene and after comparison with electronmicroscopy used the assay to investigate 31 outbreaks of gastroenteritis. These were in diverse situations including nursing homes, small district hospitals, large general hospitals, a ferry ship, hotels, restaurants and staff canteens. Results A positive diagnosis was made in 30/31 outbreaks investigated giving an overall outbreak positive detection rate of 97%. At an individual patient level there was a positive diagnostic rate of 11.5% in a large hospital environment to 100% in smaller outbreak situations. The average patient positive rate was 34%. In addition we investigated 532 control faecal specimens from adults. Of these 530 were negative and 2 were repeatedly positive. Conclusions It is essential that insensitive electronmicroscopy is replaced with the more sensitive reverse transcription PCR assays. These tests should be made available "on call" at weekends and public holidays. It is also important that outbreaks of NLV infection are monitored using sensitive RT-PCR assays so that the laboratory information can be used in ascertaining the spread and duration of the outbreak PMID:11511325

  19. Association mapping of fiber quality traits in Gossypium arboreum accessions.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Application of association mapping to germplasm resources has a potential to revolutionize plant genetics. Information about the genome distribution of linkage disequilibrium (LD) is of fundamental importance for association mapping. In addition, genetic diversity is desirable for long-term crop imp...

  20. Community resources and strategies for association mapping in sorghum

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Association mapping is a powerful strategy for identifying genes underlying quantitative traits in plants. We have assembled and characterized genetic and phenotypic diversity of a sorghum panel suitable for association mapping, comprised of 377 accessions representing all major cultivated races (t...

  1. 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.

  2. 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

  3. 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.

  4. Genome-wide nested association mapping of quantitative resistance to northern leaf blight in maize

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Quantitative resistance to plant pathogens, controlled by multiple loci of small effect, is important for food production, food security, and food safety but is poorly understood. To gain insights into the genetic architecture of quantitative resistance in maize, we evaluated a 5,000 inbred-line ne...

  5. 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. PMID:24789554

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

    PubMed Central

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

    2014-01-01

    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. PMID:24789554

  7. 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

  8. Status and Prospects of Association Mapping in Plants

    Technology Transfer Automated Retrieval System (TEKTRAN)

    There is tremendous interest in using association mapping to identify genes responsible for quantitative variation of complex traits with agricultural and evolutionary importance. Recent advances in genomic technology, impetus to exploit natural diversity, and development of robust statistical analy...

  9. 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

  10. 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

  11. Association Between Recent Use of Proton Pump Inhibitors and Nontyphoid Salmonellosis: A Nested Case-Control Study

    PubMed Central

    Wu, Hau-Hsin; Chen, Yung-Tai; Shih, Chia-Jen; Lee, Yi-Tzu; Kuo, Shu-Chen; Chen, Te-Li

    2014-01-01

    Background. The association between proton pump inhibitors (PPIs) and nontyphoid salmonellosis (NTS) continues to be debated. The current study was designed to determine the association between use of oral PPIs and the diagnosis of NTS. Methods. The Taiwan National Health Insurance Research Database from 2000 to 2010 was searched for cases of NTS, defined by the International Classification of Disease, Ninth revision, Clinical Modification. A nested case-control study in hospitalized population was conducted using 4 controls for each case patient (14 736 case patients and 58 944 controls), matched for age, month and year of entry, Charlson comorbidity index score, and well-known predisposing factors for NTS, including autoimmune diseases, acquired immunodeficiency syndrome, diabetes, cirrhosis, transplantation, gastrointestinal operations or diseases, and malignancies. Results. Persons with NTS had a higher rate of using oral PPIs within the prior year (adjusted odds ratio [OR], 2.09; 95% confidence interval [CI], 1.95–2.24; P < .001). The association was greatest for current PPI use (adjusted OR, 5.39; 95% CI, 4.79–6.06; P < .001). Although use of H2-receptor antagonists (adjusted OR, 1.84; 95% CI, 1.71–1.98), antibiotics (5.21; 4.81–5.64), steroids (3.18; 2.99–3.39), and nonsteroidal anti-inflammatory drugs (2.37; 2.26–2.48) within the 30 days were also associated with NTS, the linkage between PPI use and NTS remained significant in the subgroup without these medications. Conclusions. The use of oral PPIs was associated with the occurrence of NTS. The risk waned with time after discontinuation. PMID:25091310

  12. 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 ...

  13. Efficient control of population structure in model organism association mapping.

    PubMed

    Kang, Hyun Min; Zaitlen, Noah A; Wade, Claire M; Kirby, Andrew; Heckerman, David; Daly, Mark J; Eskin, Eleazar

    2008-03-01

    Genomewide association mapping in model organisms such as inbred mouse strains is a promising approach for the identification of risk factors related to human diseases. However, genetic association studies in inbred model organisms are confronted by the problem of complex population structure among strains. This induces inflated false positive rates, which cannot be corrected using standard approaches applied in human association studies such as genomic control or structured association. Recent studies demonstrated that mixed models successfully correct for the genetic relatedness in association mapping in maize and Arabidopsis panel data sets. However, the currently available mixed-model methods suffer from computational inefficiency. In this article, we propose a new method, efficient mixed-model association (EMMA), which corrects for population structure and genetic relatedness in model organism association mapping. Our method takes advantage of the specific nature of the optimization problem in applying mixed models for association mapping, which allows us to substantially increase the computational speed and reliability of the results. We applied EMMA to in silico whole-genome association mapping of inbred mouse strains involving hundreds of thousands of SNPs, in addition to Arabidopsis and maize data sets. We also performed extensive simulation studies to estimate the statistical power of EMMA under various SNP effects, varying degrees of population structure, and differing numbers of multiple measurements per strain. Despite the limited power of inbred mouse association mapping due to the limited number of available inbred strains, we are able to identify significantly associated SNPs, which fall into known QTL or genes identified through previous studies while avoiding an inflation of false positives. An R package implementation and webserver of our EMMA method are publicly available. PMID:18385116

  14. Associated factors for treatment delay in pulmonary tuberculosis in HIV-infected individuals: a nested case-control study

    PubMed Central

    2012-01-01

    Background The delay in initiating treatment for tuberculosis (TB) in HIV-infected individuals may lead to the development of a more severe form of the disease, with higher rates of morbidity, mortality and transmissibility. The aim of the present study was to estimate the time interval between the onset of symptoms and initiating treatment for TB in HIV-infected individuals, and to identify the factors associated to this delay. Methods A nested case-control study was undertaken within a cohort of HIV-infected individuals, attended at two HIV referral centers, in the state of Pernambuco, Brazil. Delay in initiating treatment for TB was defined as the period of time, in days, which was greater than the median value between the onset of cough and initiating treatment for TB. The study analyzed biological, clinical, socioeconomic, and lifestyle factors as well as those related to HIV and TB infection, potentially associated to delay. The odds ratios were estimated with the respective confidence intervals and p-values. Results From a cohort of 2365 HIV-infected adults, 274 presented pulmonary TB and of these, 242 participated in the study. Patients were already attending 2 health services at the time they developed a cough (period range: 1 – 552 days), with a median value of 41 days. Factors associated to delay were: systemic symptoms asthenia, chest pain, use of illicit drugs and sputum smear-negative. Conclusion The present study indirectly showed the difficulty of diagnosing TB in HIV-infected individuals and indicated the need for a better assessment of asthenia and chest pain as factors that may be present in co-infected patients. It is also necessary to discuss the role played by negative sputum smear results in diagnosing TB/HIV co-infection as well as the need to assess the best approach for drug users with TB/HIV. PMID:22958583

  15. Evaluation of concept mapping in an associate degree nursing program.

    PubMed

    Abel, Willie Mae; Freeze, Martha

    2006-09-01

    The purpose of this project was to evaluate concept mapping as a clinical teaching-learning activity that reflects critical thinking by promoting identification of nonlinear relationships among the components of the nursing process. The sample involved 28 associate degree nursing students from one graduating class. Students completed one map each in the second and fourth semesters and two maps in the fifth semester, for a total of four concept maps. The students' learning activity was to create a concept map on a blank sheet of paper describing the clients' physiological and psychosocial needs and nursing care and the relationships among concepts. As students progressed through the curriculum, there was a steady increase in the mean scores and the average number of cross-links in their concept maps. Cross-links indicated students' ability to use nonlinear thinking to identify relationships among concepts. The results of this study support the use of concept maps as an effective teaching-learning activity and support concept mapping as an evidence-based nursing education strategy. PMID:17002082

  16. 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.

  17. 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

  18. 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.

  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. PMID:27617019

  20. 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

  1. 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...

  2. 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...

  3. 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

  4. Nesting behavior is associated with VIP expression and VIP-Fos colocalization in a network-wide manner.

    PubMed

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

    2015-03-01

    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

  5. 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.

  6. 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.

  7. Mapping a disease locus by allelic association

    PubMed Central

    Collins, A.; Morton, N. E.

    1998-01-01

    Allelic association provides a means to map disease genes that, in a dense map of polymorphic markers, has considerably higher resolution than linkage methods. We describe here a composite likelihood estimate of location for a disease gene against a high-resolution marker map by using allele frequencies at linked loci. Data may be family-based, as in the transmission disequilibrium test, or from a case-control study. χ2 tests, logarithm of odds, standard errors, and information weights are provided. The method is illustrated by analysis of published cystic fibrosis haplotypes, in which ΔF508 is more accurately localized than by other association studies. This differs from current approaches by adopting a more general Malecot model for isolation by distance, where distance here is between marker and disease locus, allowance for errors in the map and model, and freedom from assumptions about demography, systematic pressures, and the ratio of physical to genetic distance. When these assumptions are introduced the number of generations since the original mutation may be estimated, but this is not required to determine location and its standard error, so that evidence from allelic association may be efficiently combined with linkage evidence to identify a region for positional cloning of a disease gene. PMID:9465087

  8. 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.

  9. Joint MAP bias estimation and data association: simulations

    NASA Astrophysics Data System (ADS)

    Danford, Scott; Kragel, Bret; Poore, Aubrey

    2007-09-01

    The problem of joint maximum a posteriori (MAP) bias estimation and data association belongs to a class of nonconvex mixed integer nonlinear programming problems. These problems are difficult to solve due to both the combinatorial nature of the problem and the nonconvexity of the objective function or constraints. Algorithms for this class of problems have been developed in a companion paper of the authors. This paper presents simulations that compare the "all-pairs" heuristic, the k-best heuristic, and a partial A*-based branch and bound algorithm. The combination of the latter two algorithms is an excellent candidate for use in a realtime system. For an optimal algorithm that also computes the k-best solutions of the joint MAP bias estimation problem and data association problem, we investigate a branch and bound framework that employs either a depth-first algorithm or an A*-search procedure. In addition, we demonstrate the improvements due to a new gating procedure.

  10. 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

  11. 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

  12. 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

  13. 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.

  14. 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

  15. 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

  16. 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

  17. 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

  18. Association Mapping and the Genomic Consequences of Selection in Sunflower

    PubMed Central

    Mandel, Jennifer R.; Nambeesan, Savithri; Bowers, John E.; Marek, Laura F.; Ebert, Daniel; Rieseberg, Loren H.; Knapp, Steven J.; Burke, John M.

    2013-01-01

    The combination of large-scale population genomic analyses and trait-based mapping approaches has the potential to provide novel insights into the evolutionary history and genome organization of crop plants. Here, we describe the detailed genotypic and phenotypic analysis of a sunflower (Helianthus annuus L.) association mapping population that captures nearly 90% of the allelic diversity present within the cultivated sunflower germplasm collection. We used these data to characterize overall patterns of genomic diversity and to perform association analyses on plant architecture (i.e., branching) and flowering time, successfully identifying numerous associations underlying these agronomically and evolutionarily important traits. Overall, we found variable levels of linkage disequilibrium (LD) across the genome. In general, islands of elevated LD correspond to genomic regions underlying traits that are known to have been targeted by selection during the evolution of cultivated sunflower. In many cases, these regions also showed significantly elevated levels of differentiation between the two major sunflower breeding groups, consistent with the occurrence of divergence due to strong selection. One of these regions, which harbors a major branching locus, spans a surprisingly long genetic interval (ca. 25 cM), indicating the occurrence of an extended selective sweep in an otherwise recombinogenic interval. PMID:23555290

  19. 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.

  20. Linear models for joint association and linkage QTL mapping

    PubMed Central

    2009-01-01

    Background Populational linkage disequilibrium and within-family linkage are commonly used for QTL mapping and marker assisted selection. The combination of both results in more robust and accurate locations of the QTL, but models proposed so far have been either single marker, complex in practice or well fit to a particular family structure. Results We herein present linear model theory to come up with additive effects of the QTL alleles in any member of a general pedigree, conditional to observed markers and pedigree, accounting for possible linkage disequilibrium among QTLs and markers. The model is based on association analysis in the founders; further, the additive effect of the QTLs transmitted to the descendants is a weighted (by the probabilities of transmission) average of the substitution effects of founders' haplotypes. The model allows for non-complete linkage disequilibrium QTL-markers in the founders. Two submodels are presented: a simple and easy to implement Haley-Knott type regression for half-sib families, and a general mixed (variance component) model for general pedigrees. The model can use information from all markers. The performance of the regression method is compared by simulation with a more complex IBD method by Meuwissen and Goddard. Numerical examples are provided. Conclusion The linear model theory provides a useful framework for QTL mapping with dense marker maps. Results show similar accuracies but a bias of the IBD method towards the center of the region. Computations for the linear regression model are extremely simple, in contrast with IBD methods. Extensions of the model to genomic selection and multi-QTL mapping are straightforward. PMID:19788745

  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. Antidepressants in association with reducing risk of oral cancer occurrence: a nationwide population-based cohort and nested case-control studies

    PubMed Central

    Chung, Chia-Min; Kuo, Tzer-Min; Chiang, Shang-Lun; Wang, Zhi-Hong; Hung, Chung-Chieh; Lane, Hsien-Yuan; Liu, Chiu-Shong; Ko, Ying-Chin

    2016-01-01

    Objectives Several studies suggested that antidepressant use may increase or decrease the risk of cancer occurrence, depending on specific cancer types. The possible carcinogenic effect of antidepressants has received substantial attention; however, evidence remains inconclusive. Here we investigated associations between the use of antidepressants and occurrences of oral cancer (OC). Methods Two million samples were randomly collected from the National Health Insurance Research Database in Taiwan, which covers 98% of the total population (23 million). All patients from2000 to 2009 were followed up. We identified 5103 patients newly diagnosed with OC after antidepressants use in addition to 20,412 non-OC matched subjects and 95,452 unmatched non-OC subjects. Results In nested case control analysis, factors associating with OC, including age [OR = 1.02; 95% confidence interval (CI) = 1.01–1.03) and male (OR = 5.30; 95% CI = 4.92–5.70) were independently associated with increased risk of OC. Based on the functions of antidepressants, antidepressants treatment medications were further classified to investigate risk of OC. Selective serotonin reuptake inhibitors (OR = 0.61; 95% CI = 0.53–0.70) and tricyclic antidepressants (OR = 0.57; 95% CI = 0.52–0.63) were associated with reduced risk of OC. The risk of developing OC among subjects taking antidepressants was less than 26% [hazard ratio (HR) =0.74; 95% CI = 0.68–0.81] in prospective cohort study. The effect of a cumulative duration and dose was a significantly reduced risk of OC. Conclusions The association between antidepressant use and decreasing OC risk were demonstrated by both prospective and nested case–control studies. PMID:26840257

  3. 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

  4. 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

  5. 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. PMID:23555829

  6. 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

  7. Joint MAP bias estimation and data association: algorithms

    NASA Astrophysics Data System (ADS)

    Danford, Scott; Kragel, Bret; Poore, Aubrey

    2007-09-01

    The problem of joint maximum a posteriori (MAP) bias estimation and data association belongs to a class of nonconvex mixed integer nonlinear programming problems. These problems are difficult to solve due to both the combinatorial nature of the problem and the nonconvexity of the objective function or constraints. A specific problem that has received some attention in the tracking literature is that of the target object map problem in which one tries match a set of tracks as observed by two different sensors in the presence of biases, which are modeled here as a translation between the track states. The general framework also applies to problems in which the costs are general nonlinear functions of the biases. The goal of this paper is to present a class of algorithms based on the branch and bound framework and the "all-pairs" and k-best heuristics that provide a good initial upper bound for a branch and bound algorithm. These heuristics can be used as part of a real-time algorithm or as part of an "anytime algorithm" within the branch and bound framework. In addition, we consider both the A*-search and depth-first search procedures as well as several efficiency improvements such as gating. While this paper focuses on the algorithms, a second paper will focus on simulations.

  8. 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

  9. 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

  10. 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

  11. 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.

  12. 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

  13. 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,…

  14. 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...

  15. 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

  16. 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.

  17. 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

  18. 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

  19. A Comparison of Association Methods for Cytotoxicity Mapping in Pharmacogenomics

    PubMed Central

    Brown, Chad; Havener, Tammy M.; Everitt, Lorraine; McLeod, Howard; Motsinger-Reif, Alison A.

    2011-01-01

    Cytotoxicity assays of immortalized lymphoblastoid cell lines (LCLs) represent a promising new in vitro approach in pharmacogenomics research. However, previous studies employing LCLs in gene mapping have used simple association methods, which may not adequately capture the true differences in non-linear response profiles between genotypes. Two common approaches summarize each dose-response curve with either the IC50 or the slope parameter estimates from a hill slope fit and treat these estimates as the response in a linear model. The current study investigates these two methods, as well as four novel methods, and compares their power to detect differences between the response profiles of genotypes under a variety of different alternatives. The four novel methods include two methods that summarize each dose-response by its area under the curve, one method based off of an analysis of variance (ANOVA) design, and one method that compares hill slope fits for all individuals of each genotype. The power of each method was found to depend not only on the choice of alternative, but also on the choice for the set of dosages used in cytotoxicity measurements. The ANOVA-based method was found to be the most robust across alternatives and dosage sets for power in detecting differences between genotypes. PMID:22303380

  20. 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

  1. Genome-wide Association Mapping of Fusarium Head Blight Resistance in Contemporary Barley Breeding Germplasm

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Utilization of quantitative trait loci (QTL) identified in bi-parental mapping populations has had limited success for complex quantitative traits. The use of association mapping in contemporary breeding germplasm may lead to more effective marker strategies for crop improvement. To map Fusarium he...

  2. 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

  3. 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

  4. Non-Microtubular Localizations of Microtubule-Associated Protein 6 (MAP6)

    PubMed Central

    Gory-Fauré, Sylvie; Windscheid, Vanessa; Brocard, Jacques; Montessuit, Sylvie; Tsutsumi, Ryouhei; Denarier, Eric; Fukata, Yuko; Bosc, Christophe; Delaroche, Julie; Collomb, Nora; Fukata, Masaki; Martinou, Jean-Claude; Pernet-Gallay, Karin; Andrieux, Annie

    2014-01-01

    MAP6 proteins (MAP6s), which include MAP6-N (also called Stable Tubule Only Polypeptide, or STOP) and MAP6d1 (MAP6 domain-containing protein 1, also called STOP-Like protein 21 kD, or SL21), bind to and stabilize microtubules. MAP6 deletion in mice severely alters integrated brain functions and is associated with synaptic defects, suggesting that MAP6s may also have alternative cellular roles. MAP6s reportedly associate with the Golgi apparatus through palmitoylation of their N-terminal domain, and specific isoforms have been shown to bind actin. Here, we use heterologous systems to investigate several biochemical properties of MAP6 proteins. We demonstrate that the three N-terminal cysteines of MAP6d1 are palmitoylated by a subset of DHHC-type palmitoylating enzymes. Analysis of the subcellular localization of palmitoylated MAP6d1, including electron microscopic analysis, reveals possible localization to the Golgi and the plasma membrane but no association with the endoplasmic reticulum. Moreover, we observed localization of MAP6d1 to mitochondria, which requires the N-terminus of the protein but does not require palmitoylation. We show that endogenous MAP6d1 localized at mitochondria in mature mice neurons as well as at the outer membrane and in the intermembrane space of purified mouse mitochondria. Last, we found that MAP6d1 can multimerize via a microtubule-binding module. Interestingly, most of these properties of MAP6d1 are shared by MAP6-N. Together, these results describe several properties of MAP6 proteins, including their intercellular localization and multimerization activity, which may be relevant to neuronal differentiation and synaptic functions. PMID:25526643

  5. Incremental Reduction in Risk of Death Associated With Use of Guideline-Recommended Therapies in Patients With Heart Failure: A Nested Case-Control Analysis of IMPROVE HF

    PubMed Central

    Fonarow, Gregg C.; Albert, Nancy M.; Curtis, Anne B.; Gheorghiade, Mihai; Liu, Yang; Mehra, Mandeep R.; O'Connor, Christopher M.; Reynolds, Dwight; Walsh, Mary N.; Yancy, Clyde W.

    2012-01-01

    Background Several therapies are guideline-recommended to reduce mortality in patients with heart failure (HF) and reduced left ventricular ejection fraction, but the incremental clinical effectiveness of these therapies has not been well studied. We aimed to evaluate the individual and incremental benefits of guideline-recommended HF therapies associated with 24-month survival. Methods and Results We performed a nested case-control study of HF patients enrolled in IMPROVE HF. Cases were patients who died within 24 months and controls were patients who survived to 24 months, propensity-matched 1:2 for multiple prognostic variables. Logistic regression was performed, and the attributable mortality risk from incomplete application of each evidence-based therapy among eligible patients was calculated. A total of 1376 cases and 2752 matched controls were identified. β-Blocker and cardiac resynchronization therapy were associated with the greatest 24-month survival benefit (adjusted odds ratio for death 0.42, 95% confidence interval (CI), 0.34–0.52; and 0.44, 95% CI, 0.29–0.67, respectively). Angiotensin-converting enzyme inhibitors/angiotensin receptor blockers, implantable cardioverter-defibrillators, anticoagulation for atrial fibrillation, and HF education were also associated with benefit, whereas aldosterone antagonist use was not. Incremental benefits were observed with each successive therapy, plateauing once any 4 to 5 therapies were provided (adjusted odds ratio 0.31, 95% CI, 0.23–0.42 for 5 or more versus 0/1, P<0.0001). Conclusions Individual, with a single exception, and incremental use of guideline-recommended therapies was associated with survival benefit, with a potential plateau at 4 to 5 therapies. These data provide further rationale to implement guideline-recommended HF therapies in the absence of contraindications to patients with HF and reduced left ventricular ejection fraction. (J Am Heart Assoc. 2012;1:16-26.) PMID:23130115

  6. Genetic analysis and characterization of a new maize association mapping panel for quantitative trait loci dissesction

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Association mapping based on linkage disequilibrium provides a promising method to identify genes responsible for quantitative variation underlying complex traits. Presented here is a maize association mapping panel consisting of 155 diverse (mainly temperate inbred lines) suitable for marker-trait ...

  7. 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

  8. 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

  9. 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

  10. 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.

  11. 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

  12. Association of Serum Magnesium Level with Odds of Prediabetes and Diabetes in a Southern Chinese Population: a Prospective Nested Case-Control Study.

    PubMed

    Fang, Chenchen; Wang, Xuebao; Wu, Wenjun; Gu, Xuejiang; Ye, Tingting; Deng, Huihui; Wang, Xianqin; Shen, Feixia

    2016-08-01

    Although emerging clinical evidence supports that magnesium deficiency is a risk factor for the development of type 2 diabetes, there are sparse studies concerning the dynamic change of serum magnesium with the risk of diabetes and its early stages. In this nested case-control study, we performed a 75-g oral glucose tolerance test or a standardized steamed bread meal test in 178 subjects with incident glucose metabolism impairment (33 with type 2 diabetes and 145 with prediabetes) and 178 matched controls at baseline and at 3-year follow-up and determined the associations between baseline serum magnesium levels as well as changes in serum magnesium levels at follow-up and odds of prediabetes and diabetes. After adjusting for potential confounders, the odds ratios of risk for prediabetes and type 2 diabetes in the highest quartile of serum magnesium levels were 0.22 (95 % confidence intervals [CI] 0.10-0.49; p for trend <0.001) and 0.02 (95 % CI 0.00-0.29; p for trend = 0.009), respectively, as compared with the lowest quartile. In addition, a significant decline in the serum magnesium level was detected in type 2 diabetes cases (p = 0.015) at 3 years as compared with at baseline. These results suggest that a low magnesium level is an independent risk factor for prediabetes and type 2 diabetes, and that the reduction of serum magnesium is associated with type 2 diabetes in a southern Chinese population. PMID:26706038

  13. Porcine NAMPT gene: search for polymorphism, mapping and association studies

    Technology Transfer Automated Retrieval System (TEKTRAN)

    NAMPT encodes for an enzyme catalysing the rate-limiting step in NAD biosynthesis. The extracellular form of the enzyme is known as adipokine visfatin. We detected SNP AM999341:g.669T>C in intron 9 and SNP FN392209:g.358A>G in the promoter of the gene. RH mapping linked the gene to microsatellite SW...

  14. 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...

  15. Association mapping: critical considerations shift from genotyping to experimental design

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The goal of many plant scientists’ research is to explain natural phenotypic variation in terms of simple changes in DNA sequence. Traditionally, linkage mapping has been the most commonly employed method to reach this goal: experimental crosses are made to generate a family with known relatedness ...

  16. Microtubule-associated proteins: a monoclonal antibody to MAP2 binds to differentiated neurons.

    PubMed

    Izant, J G; McIntosh, J R

    1980-08-01

    Hybridomas that secret IgG reacting specifically with the brain microtubule-associated protein MAP2 have been prepared with speen cells from BALB/c mice hyperimmunized with high molecular weight neurotubule-associated proteins. Immunofluorecence microscopy using dual fluorochrome labeling of tubulin and MAP2 antigens revealed identical patterns of interphase fiber networks in cells from explants of newborn mouse brain. The anti-MAP2 antibody did not stain primary mouse kidney cells or CHO, 3T3, HeLa, or PtK1 cell lines. Immunoprecipitation and antibody gel staining techniques failed to demonstrate any crossreacting antigen in these cells. MAP2 antigen was not seen in association with the mitotic spindle in any of the cells examined. Radioimmunoassay showed species crossreactivity of the anti-MAP2 antibody with mammalian but not avian neural cell extracts. Glial cells and some neuroblastoma cell lines did not appear to contain MAP2. However, in the B104 rat neuroblastoma cell line the MAP2 antigen appeared to be associated with the cytoskeleton concomitant with differentiation induced by dibutyryl cyclic AMP. In disagreement with most previously published reports, our data suggest that MAP2 is found only in differentiated neuronal cells and raises the possibility that MAP2 is involved in neuronal differentiation or neuron-specific processes. PMID:7001466

  17. 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

  18. 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

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

    DOE PAGESBeta

    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

  20. 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

  1. 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.

  2. 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.

  3. Association mapping of four important traits using the USDA rice mini-core collection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Classical quantitative trait loci (QTL) mapping in diploids reveals only a slice of the genetic architecture for a trait because only two alleles that differ between the two parental lines segregate. Association mapping provides an effective method to identify QTL that have effects across a broad sp...

  4. 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)

  5. Do chimpanzees build comfortable nests?

    PubMed

    Stewart, Fiona A; Pruetz, Jill D; Hansell, Mike H

    2007-08-01

    Nests built by wild chimpanzees (Pan troglodytes verus) were studied at the Fongoli research site in southeastern Senegal from January 2004-May 2004 to investigate the role of comfort in nest building behavior by relating measures of nest comfort and building effort. Nest comfort across zones of the nest surface were compared with construction effort for 25 nests. Several variables of nest comfort were assessed: (1) physical discomfort, (2) visible discomfort, and (3) softness. Physical discomfort was used as a representative measure of nest discomfort. Building effort was measured by (1) construction force, (2) complexity, and (3) added material. Spearman rank correlations compared Effort and Comfort measures for both whole nests and central versus edge zones. The results show that construction force and complexity do not influence comfort of the nest as a whole. Greater Construction force correlates with more nest edge discomfort, yet the central area shows no difference. More complex nests do result in a more comfortable central area in the nest. Nests built with greater force may result in more discomfort, whereas complexity may allow chimpanzees to maintain comfort in a central area for sleep. Chimpanzees may place additional leaves or twigs over hard branches, protruding from the nest surface after construction, to increase comfort of the central nest area. Functions of chimpanzee nest building are likely to be several, but these results suggest comfort is a factor in nest building behavior. PMID:17358021

  6. High-resolution mapping of gene expression using association in an outbred mouse stock.

    PubMed

    Ghazalpour, Anatole; Doss, Sudheer; Kang, Hyun; Farber, Charles; Wen, Ping-Zi; Brozell, Alec; Castellanos, Ruth; Eskin, Eleazar; Smith, Desmond J; Drake, Thomas A; Lusis, Aldons J

    2008-01-01

    Quantitative trait locus (QTL) analysis is a powerful tool for mapping genes for complex traits in mice, but its utility is limited by poor resolution. A promising mapping approach is association analysis in outbred stocks or different inbred strains. As a proof of concept for the association approach, we applied whole-genome association analysis to hepatic gene expression traits in an outbred mouse population, the MF1 stock, and replicated expression QTL (eQTL) identified in previous studies of F2 intercross mice. We found that the mapping resolution of these eQTL was significantly greater in the outbred population. Through an example, we also showed how this precise mapping can be used to resolve previously identified loci (in intercross studies), which affect many different transcript levels (known as eQTL "hotspots"), into distinct regions. Our results also highlight the importance of correcting for population structure in whole-genome association studies in the outbred stock. PMID:18688273

  7. 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

  8. 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

  9. Increased body mass index may be associated with greater risk of end-stage renal disease in whites compared to blacks: A nested case–control study

    PubMed Central

    Akwo, Elvis, A.; Cavanaugh, Kerri, L.; Ikizler, Talat, Alp; Blot, William, J.; Lipworth, Loren

    2016-01-01

    Background The relationship between body mass index (BMI) and end-stage renal disease (ESRD) may differ between blacks and whites due to underlying metabolic differences. Methods We conducted a nested case-control study of 631 incident ESRD cases and 1,897 matched controls within the Southern Community Cohort Study. Current weight, height, and weight at age 21 were reported at enrollment. Occurrence of ESRD was ascertained by linkage with the United States Renal Data System. With normal BMI (18.5–24.9 kg/m2) as reference, conditional logistic regression was used to calculate adjusted odds ratios (OR) and corresponding 95% confidence intervals (CI) for ESRD across other BMI categories by race. In subsequent analysis, BMI at age 21 was modeled using restricted cubic splines with 5 knots. Predicted probabilities of incident ESRD were computed from the multivariable logistic models and plotted against BMI at age 21. Results Among blacks, odds of ESRD were significantly increased among those who were overweight (OR: 1.41; 95%CI: 1.09, 1.83) or obese (OR: 2.56; 95%CI: 1.88, 3.47) at age 21. Among whites, the association between ESRD and BMI at age 21 was more pronounced, with corresponding ORs of 2.13 (95%CI: 0.92, 4.93) and 7.46 (95%CI: 2.90, 19.21; p-interaction 0.05). Only among whites was high BMI at enrollment associated with ESRD risk; OR for BMI≥40 kg/m2, was 3.31 (95%CI: 1.08, 10.12). The plot of the predicted probabilities of incident ESRD vs BMI at age 21 showed a monotonic increase in the probability of ESRD after a BMI cutoff ≈ 25Kg/m2 in both whites and blacks but the slope of the curve for whites appeared greater. Conclusions Our results suggest racial differences in the relationship between BMI, both in early adulthood and middle age, and ESRD. These findings warrant further research into understanding the underlying metabolic differences that may explain these differences.

  10. 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

  11. Association Mapping in Turkish Olive Cultivars Revealed Significant Markers Related to Some Important Agronomic Traits.

    PubMed

    Kaya, Hilal Betul; Cetin, Oznur; Kaya, Hulya Sozer; Sahin, Mustafa; Sefer, Filiz; Tanyolac, Bahattin

    2016-08-01

    Olive (Olea europaea L.) is one of the most important fruit trees especially in the Mediterranean countries due to high consumption of table olive and olive oil. In olive breeding, the phenotypic traits associated to fruit are the key factors that determine productivity. Association mapping has been used in some tree species and a lot of crop plant species, and here, we perform an initial effort to detect marker-trait associations in olive tree. In the current study, a total of 96 olive genotypes, including both oil and table olive genotypes from Turkish Olive GenBank Resources, were used to examine marker-trait associations. For olive genotyping, SNP, AFLP, and SSR marker data were selected from previously published study and association analysis was performed between these markers and 5 yield-related traits. Three different approaches were used to check for false-positive results in association tests, and association results obtained from these models were compared. Using the model utilizing both population structure and relative kinship, eleven associations were significant with FDR ≤ 0.05. The largest number of significant associations was detected for fruit weight and stone weight. Our results suggested that association mapping could be an effective approach for identifying marker-trait associations in olive genotypes, without the development of mapping populations. This study shows for the first time the use of association mapping for identifying molecular markers linked to important traits in olive tree. PMID:27209034

  12. 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

  13. Fine scale association mapping of disease loci using simplex families.

    PubMed

    Morris, A P; Whittaker, J C

    2000-05-01

    We present a new method for the fine scale mapping of disease loci based on samples of simplex families, each containing an affected child. The method is based on a generalisation of a single locus allele transmission model to multiple marker loci. The model is developed under the assumption of a single ancestral mutation and allows for the calculation of posterior probabilities that each allele at a particular marker was present on the founder chromosome. We illustrate the method using simulated family data for cystic fibrosis and Huntingtons disease, for which the locations of mutations in the disease genes are now known. For both diseases, our new method provides good estimates of the location of the mutations. PMID:11246474

  14. The plant cytoskeleton: recent advances in the study of the plant microtubule-associated proteins MAP-65, MAP-190 and the Xenopus MAP215-like protein, MOR1.

    PubMed

    Hussey, Patrick J; Hawkins, Timothy J; Igarashi, Hisako; Kaloriti, Despina; Smertenko, Andrei

    2002-12-01

    The microtubule cytoskeleton is a dynamic filamentous structure involved in many key processes in plant cell morphogenesis including nuclear and cell division, deposition of cell wall, cell expansion, organelle movement and secretion. The principal microtubule protein is tubulin, which associates to form the wall of the tubule. In addition, various associated proteins bind microtubules either to anchor, cross-link or regulate the microtubule network within cells. Biochemical, molecular biological and genetic approaches are being successfully used to identify these microtubule-associated proteins (MAPs) in plants, and we describe recent progress on three of these proteins. PMID:12516862

  15. 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...

  16. 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.

  17. 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

  18. 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

  19. 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

  20. Blocking the association of HDAC4 with MAP1S accelerates autophagy clearance of mutant Huntingtin

    PubMed Central

    Yue, Fei; Li, Wenjiao; Zou, Jing; Chen, Qi; Xu, Guibin; Huang, Hai; Xu, Zhen; Zhang, Sheng; Gallinari, Paola; Wang, Fen; McKeehan, Wallace L.; Liu, Leyuan

    2015-01-01

    Autophagy controls and executes the turnover of abnormally aggregated proteins. MAP1S interacts with the autophagy marker LC3 and positively regulates autophagy flux. HDAC4 associates with the aggregation-prone mutant huntingtin protein (mHTT) that causes Huntington's disease, and colocalizes with it in cytosolic inclusions. It was suggested HDAC4 interacts with MAP1S in a yeast two-hybrid screening. Here, we found that MAP1S interacts with HDAC4 via a HDAC4-binding domain (HBD). HDAC4 destabilizes MAP1S, suppresses autophagy flux and promotes the accumulation of mHTT aggregates. This occurs by an increase in the deacetylation of the acetylated MAP1S. Either suppression of HDAC4 with siRNA or overexpression of the MAP1S HBD leads to stabilization of MAP1S, activation of autophagy flux and clearance of mHTT aggregates. Therefore, specific interruption of the HDAC4-MAP1S interaction with short peptides or small molecules to enhance autophagy flux may relieve the toxicity of mHTT associated with Huntington's disease and improve symptoms of HD patients. PMID:26540094

  1. Examination of woodcock nest sites in central Pennsylvania

    USGS Publications Warehouse

    Coon, R.A.; Williams, B.K.; Lindzey, J.S.; George, J.L.

    1982-01-01

    Evidence is given to support Iow selectivity in choice of nest sites by woodcock (Philohela minor). Habitat characteristics measured at 30 woodcock nest sites were compared with non-nest control sites in Huntingdon County, central Pennsylvania. Mean nest density per year was 1/4.8 ha within the 54-ha study area. Of 14 characteristics measured, higher shrub-stem density at nests was the only variable significantly different (P 0.05) between habitat characteristics at nests and controls. A computed discriminant function also indicated little distinction between nests and controls. Spatial distribution of nests for each of the three years did not depart significantly (P :> 0.05) from a random distribution. Although evidence is given for little overall selectivity, greater shrub-stem density at nests and associations related in part to 'edge' habitat may be important in the location of substantial numbers of woodcock nests. The mean distance from nest site to nearest tree (1.0 ? 1.1 m) and to nearest shrub (22.8 ? 17.8 cm) was significantly less (P < 0.01) than for control areas. Additional research on woodcock nest-site selection may lead to enhanced woodcock production in a variety of habitats.

  2. Geographically weighted Poisson regression for disease association mapping.

    PubMed

    Nakaya, T; Fotheringham, A S; Brunsdon, C; Charlton, M

    2005-09-15

    This paper describes geographically weighted Poisson regression (GWPR) and its semi-parametric variant as a new statistical tool for analysing disease maps arising from spatially non-stationary processes. The method is a type of conditional kernel regression which uses a spatial weighting function to estimate spatial variations in Poisson regression parameters. It enables us to draw surfaces of local parameter estimates which depict spatial variations in the relationships between disease rates and socio-economic characteristics. The method therefore can be used to test the general assumption made, often without question, in the global modelling of spatial data that the processes being modelled are stationary over space. Equally, it can be used to identify parts of the study region in which 'interesting' relationships might be occurring and where further investigation might be warranted. Such exceptions can easily be missed in traditional global modelling and therefore GWPR provides disease analysts with an important new set of statistical tools. We demonstrate the GWPR approach applied to a data set of working-age deaths in the Tokyo metropolitan area, Japan. The results indicate that there are significant spatial variations (that is, variation beyond that expected from random sampling) in the relationships between working-age mortality and occupational segregation and between working-age mortality and unemployment throughout the Tokyo metropolitan area and that, consequently, the application of traditional 'global' models would yield misleading results. PMID:16118814

  3. 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

  4. 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.

  5. 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.

  6. 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.

  7. TASSEL: Software for Association Mapping of Complex Traits in Diverse Samples

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The association mapping of complex traits is becoming the method of choice in plant and animal genetics. In most samples, researchers have to deal with both population and family structure. TASSEL (Trait Analysis by aSSociation, Evolution and Linkage) implements general linear model and mixed line...

  8. 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.

  9. 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. PMID:25030465

  10. Ground-nesting by the chimpanzees of the Nimba Mountains, Guinea: environmentally or socially determined?

    PubMed

    Koops, Kathelijne; Humle, Tatyana; Sterck, Elisabeth H M; Matsuzawa, Tetsuro

    2007-04-01

    The chimpanzees (Pan troglodytes verus) of the Nimba Mountains, Guinea, West Africa, commonly make both elaborate ("night") and simple ("day") nests on the ground. In this study we investigated which factors might influence ground-nesting in this population, and tested two ecological hypotheses: 1) climatic conditions, such as high wind speeds at high altitudes, may deter chimpanzees from nesting in trees; and 2) a lack of appropriate arboreal nesting opportunities may drive the chimpanzees to nest on the ground. In addition to testing these two hypotheses, we explored whether ground-nesting is a sex-linked behavior. Data were collected monthly between August 2003 and May 2004 along transects and ad libitum. To identify the sex of ground-nesting individuals, we used DNA extracted from hair samples. The results showed that the occurrence and distribution of ground nests were not affected by climatic conditions or a lack of appropriate nest trees. Support was found for the notion that ground-nesting is a sex-linked behavior, as males were responsible for building all of the elaborate ground nests and most of the simple ground nests sampled. Elaborate ground nests occurred mostly in nest groups associated with tree nests, whereas simple ground nests usually occurred without tree nests in their vicinity. These results suggest that ground-nesting may be socially, rather than ecologically, determined. PMID:17146789

  11. Eggs, nests, and nesting behavior of akiapolaau (Drepanidinae)

    USGS Publications Warehouse

    Banko, P.C.; Williams, J.

    1993-01-01

    We describe the fifth verified nest and first verified egg of the Akiapolaau (Hemignathus munroi), an endangered Hawaiian honeycreeper. We dispute the validity of Bryan?s (1905a) description of three eggs and two nests of the Akiapolaau. Eggs that he attributed to this species were much smaller than ours, and his nest descriptions did not match the only nest apparently belonging to the Akiapolaau in the B. P. Bishop Museum in Honolulu, where Bryan worked. Twigs and bark were distinctively combined in the nest that we examined. We compare eggs and nests of the Akiapolaau with those of other Hawaiian honeycreepers.

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

    PubMed

    Ringelman, Kevin M; Eadie, John M; Ackerman, Joshua T

    2012-07-01

    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. PMID:22179311

  13. 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.

  14. 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.

  15. 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

  16. 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…

  17. 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.

  18. 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

  19. Rapid and robust association mapping of expression quantitative trait loci.

    PubMed

    Lam, Alex C; Schouten, Michael; Aulchenko, Yurii S; Haley, Chris S; de Koning, Dirk-Jan

    2007-01-01

    We applied a simple and efficient two-step method to analyze a family-based association study of gene expression quantitative trait loci (eQTL) in a mixed model framework. This two-step method produces very similar results to the full mixed model method, with our method being significantly faster than the full model. Using the Genetic Analysis Workshop 15 (GAW15) Problem 1 data, we demonstrated the value of data filtering for reducing the number of tests and controlling the number of false positives. Specifically, we showed that removing non-expressed genes by filtering on expression variability effectively reduced the number of tests by nearly 50%. Furthermore, we demonstrated that filtering on genotype counts substantially reduced spurious detection. Finally, we restricted our analysis to the markers and transcripts that were closely located. We found five times more signals in close proximity (cis-) to transcripts than in our genome-wide analysis. Our results suggest that careful pre-filtering and partitioning of data are crucial for controlling false positives and allowing detection of genuine effects in genetic analysis of gene expression. PMID:18466488

  20. 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

  1. Fiber Tracking Cylinder Nesting

    SciTech Connect

    Stredde, H.; /Fermilab

    1999-03-30

    The fiber tracker consists of 8 concentric carbon fiber cylinders of varying diameters, from 399mm to 1032.2mm and two different lengths. 1.66 and 2.52 meters. Each completed cylinder is covered over the entire o.d. with scintillating fiber ribbons with a connector on each ribbon. These ribbons are axial (parallel to the beam line) at one end and stereo (at 3 deg. to the beam line) at the other. The ribbon connectors have dowel pins which are used to match with the connectors on the wave guide ribbons. These dowel pins are also used during the nesting operation, locating and positioning measurements. The nesting operation is the insertion of one cylinder into another, aligning them with one another and fastening them together into a homogeneous assembly. For ease of assembly. the nesting operation is accomplished working from largest diameter to smallest. Although the completed assembly of all 8 cylinders glued and bolted together is very stiff. individual cylinders are relatively flexible. Therefore. during this operation, No.8 must be supported in a manner which maintains its integrity and yet allows the insertion of No.7. This is accomplished by essentially building a set of dummy end plates which replicate a No.9 cylinder. These end plates are mounted on a wheeled cart that becomes the nesting cart. Provisions for a protective cover fastened to these rings has been made and will be incorporated in finished product. These covers can be easily removed for access to No.8 and/or the connection of No.8 to No.9. Another wheeled cart, transfer cart, is used to push a completed cylinder into the cylinder(s) already mounted in the nesting cart.

  2. High-Density Genotypes of Inbred Mouse Strains: Improved Power and Precision of Association Mapping

    PubMed Central

    Rau, Christoph D.; Parks, Brian; Wang, Yibin; Eskin, Eleazar; Simecek, Petr; Churchill, Gary A.; Lusis, Aldons J.

    2015-01-01

    Human genome-wide association studies have identified thousands of loci associated with disease phenotypes. Genome-wide association studies also have become feasible using rodent models and these have some important advantages over human studies, including controlled environment, access to tissues for molecular profiling, reproducible genotypes, and a wide array of techniques for experimental validation. Association mapping with common mouse inbred strains generally requires 100 or more strains to achieve sufficient power and mapping resolution; in contrast, sample sizes for human studies typically are one or more orders of magnitude greater than this. To enable well-powered studies in mice, we have generated high-density genotypes for ∼175 inbred strains of mice using the Mouse Diversity Array. These new data increase marker density by 1.9-fold, have reduced missing data rates, and provide more accurate identification of heterozygous regions compared with previous genotype data. We report the discovery of new loci from previously reported association mapping studies using the new genotype data. The data are freely available for download, and Web-based tools provide easy access for association mapping and viewing of the underlying intensity data for individual loci. PMID:26224782

  3. [Genetic diversity of arbuscular mycorrhizal fungi associated with four Alnus species in Changbai Mountains: a nested PCR-rFLP analysis].

    PubMed

    Dong, Tian; Zhang, Huiwen; Zhang, Yue; He, Xingyuan

    2006-10-01

    In this paper, the colonization of arbuscular mycorrhizal fungi (AMF) on the root samples of 4 Alnus species in Changbai Mountains was investigated by using nested PCR-RFLP technique, and the PCR results were tested by restriction endonuclease analysis method. The results revealed that the uncultured AMF had a high genetic diversity, and the colonization had a trend from promiscuity to specialization. The AMF from Alnus mandshuica showed the greatest specialization to the host, and Glomus was the dominant colonizer of A. mandshuica. The AMF from A. sibirica var. hirsuta, A. sibirica, and A. tinctoria showed promiscuity, and host had more significant effects on the colonization of AMF than altitude. PMID:17209372

  4. 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

  5. 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

  6. Cell Based Associations: A procedure for considering scarce and mixed mineral occurrences in predictive mapping

    NASA Astrophysics Data System (ADS)

    Tourlière, Bruno; Pakyuz-Charrier, Evren; Cassard, Daniel; Barbanson, Luc; Gumiaux, Charles

    2015-05-01

    Cell Based Association is an innovative mineral favorability procedure designed to answer special needs of the mining industry in data wise critical situations where usual favorability methods may not yield satisfactory results. Those situations relate to input data quality (e.g. clustered points, mixed and scarce data, approximate location) or some assumptions that are considered unreasonable (e.g. map areas relevance, conditional independence). The principle of CBA consists in replacing polygons of geological units with a square cell grid (hence the 'cell-based'). Each cell contains a range of units ('association') that are binary coded in terms of their presence (1) or absence (0) within study area. The loss of resolution inherent to this procedure is compensated by the enriched information contained in each cell owing to the notion of (lithological) association. Lithological associations are considered as binary spectra and as such are classified using Ascendant Hierarchical Clustering (AHC) thus obtaining a synthetic map of lithological associations. The prospectivity map shows as favourable the cells of the same AHC classes that the ones including mineral occurrences. It was observed that CBA can distinguish between different ore deposit varieties from a blended mineral occurrences data set. CBA can theoretically include any spatialized data (e.g. geophysics, structural data) as an extra variable to specify classification and narrow favourable areas. Doing so would make it an independent favorability mapping procedure and is still under development. Cell size in a grid is a critical parameter of the procedure; it must be compatible with the looked-for phenomena and should have a sufficient lithological variability. In addition to its use for producing favorability maps, a CBA-derived map could help in understanding the background information contained in geological maps. CBA can also be applied to other fields, such as agriculture and urban planning

  7. 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

  8. Linkage Disequilibrium and Genome-Wide Association Mapping in Tetraploid Wheat (Triticum turgidum L.)

    PubMed Central

    Laidò, Giovanni; Marone, Daniela; Russo, Maria A.; Colecchia, Salvatore A.; Mastrangelo, Anna M.; De Vita, Pasquale; Papa, Roberto

    2014-01-01

    Association mapping is a powerful tool for the identification of quantitative trait loci through the exploitation of the differential decay of linkage disequilibrium (LD) between marker loci and genes of interest in natural and domesticated populations. Using a sample of 230 tetraploid wheat lines (Triticum turgidum ssp), which included naked and hulled accessions, we analysed the pattern of LD considering 26 simple sequence repeats and 970 mostly mapped diversity array technology loci. In addition, to validate the potential for association mapping in durum wheat, we evaluated the same genotypes for plant height, heading date, protein content, and thousand-kernel weight. Molecular and phenotypic data were used to: (i) investigate the genetic and phenotypic diversity; (ii) study the dynamics of LD across the durum wheat genome, by investigating the patterns of LD decay; and (iii) test the potential of our panel to identify marker–trait associations through the analysis of four quantitative traits of major agronomic importance. Moreover, we compared and validated the association mapping results with outlier detection analysis based on population divergence. Overall, in tetraploid wheat, the pattern of LD is extremely population dependent and is related to the domestication and breeding history of durum wheat. Comparing our data with several other studies in wheat, we confirm the position of many major genes and quantitative trait loci for the traits considered. Finally, the analysis of the selection signature represents a very useful complement to validate marker–trait associations. PMID:24759998

  9. 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

  10. 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

  11. 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.

  12. PyNEST: A Convenient Interface to the NEST Simulator

    PubMed Central

    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 104 neurons and 107 to 109 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

  13. 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

  14. 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...

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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. Linkage disequilibrium (LD)-mapping using nonrandom associations of loci in haplotypes is a powerful high-r...

  16. High-Resolution Mapping of Gene Expression Using Association in an Outbred Mouse Stock

    PubMed Central

    Ghazalpour, Anatole; Doss, Sudheer; Kang, Hyun; Farber, Charles; Wen, Ping-Zi; Brozell, Alec; Castellanos, Ruth; Eskin, Eleazar; Smith, Desmond J.; Drake, Thomas A.; Lusis, Aldons J.

    2008-01-01

    Quantitative trait locus (QTL) analysis is a powerful tool for mapping genes for complex traits in mice, but its utility is limited by poor resolution. A promising mapping approach is association analysis in outbred stocks or different inbred strains. As a proof of concept for the association approach, we applied whole-genome association analysis to hepatic gene expression traits in an outbred mouse population, the MF1 stock, and replicated expression QTL (eQTL) identified in previous studies of F2 intercross mice. We found that the mapping resolution of these eQTL was significantly greater in the outbred population. Through an example, we also showed how this precise mapping can be used to resolve previously identified loci (in intercross studies), which affect many different transcript levels (known as eQTL “hotspots”), into distinct regions. Our results also highlight the importance of correcting for population structure in whole-genome association studies in the outbred stock. PMID:18688273

  17. Simulation appraisal of the adequacy of numbers of background markers for relationship estimation in association mapping

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The number of background markers and sample size are two common issues that need to be addressed in many association mapping studies. Our objectives were (1) to investigate the robustness of genetic relatedness estimates based on different numbers of background markers via model testing and variance...

  18. 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.

  19. 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.

  20. 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

  1. Gene-Based Single Nucleotide Polymorphism Markers for Genetic and Association Mapping in Common Bean

    PubMed Central

    2012-01-01

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

  2. 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.

  3. The HapMap and Genome-Wide Association Studies in Diagnosis and Therapy*

    PubMed Central

    Manolio, Teri A.; Collins, Francis S.

    2009-01-01

    The International HapMap Project produced a genome-wide database of human genetic variation for use in genetic association studies of common diseases. The initial output of these studies has been overwhelming, with over 150 risk loci identified in studies of more than 60 common diseases and traits. These associations have suggested previously unsuspected etiologic pathways for common diseases that will be of use in identifying new therapeutic targets and developing targeted interventions based on genetically defined risk. Here we examine the development and application of the HapMap to genome-wide association (GWA) studies; present and future technologies for GWA research; current major efforts in GWA studies; successes and limitations of the GWA approach in identifying polymorphisms related to complex diseases; data release and privacy polices; use of these findings by clinicians, the public, and academic physicians; and sources of ongoing authoritative information on this rapidly evolving field. PMID:19630580

  4. Association mapping of disease loci, by use of a pooled DNA genomic screen.

    PubMed Central

    Barcellos, L F; Klitz, W; Field, L L; Tobias, R; Bowcock, A M; Wilson, R; Nelson, M P; Nagatomi, J; Thomson, G

    1997-01-01

    Genomic screening to map disease loci by association requires automation, pooling of DNA samples, and 3,000-6,000 highly polymorphic, evenly spaced microsatellite markers. Case-control samples can be used in an initial screen, followed by family-based data to confirm marker associations. Association mapping is relevant to genetic studies of complex diseases in which linkage analysis may be less effective and to cases in which multigenerational data are difficult to obtain, including rare or late-onset conditions and infectious diseases. The method can also be used effectively to follow up and confirm regions identified in linkage studies or to investigate candidate disease loci. Study designs can incorporate disease heterogeneity and interaction effects by appropriate subdivision of samples before screening. Here we report use of pooled DNA amplifications-the accurate determination of marker-disease associations for both case-control and nuclear family-based data-including application of correction methods for stutter artifact and preferential amplification. These issues, combined with a discussion of both statistical power and experimental design to define the necessary requirements for detecting of disease loci while virtually eliminating false positives, suggest the feasibility and efficiency of association mapping using pooled DNA screening. PMID:9326338

  5. 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

  6. 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

  7. Nest and nest site characterisitcs of some ground-nesting, non-passerine birds of northern grasslands

    USGS Publications Warehouse

    Kantrud, H.A.; Higgins, K.F.

    1992-01-01

    We summarized biological and ecologic characteristics of 2490 nests of 16 species of upland-nesting, non-passerine birds of northern grasslands found during 1963 through 1991. Nest initiation and hatch dates, clutch sizes, nest fates, causes of failure, success rates of nests among major habitat types and land uses, and vegetation measurements at nest sites are analyzed.

  8. 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. PMID:22427867

  9. Nested subcritical flows within supercritical systems

    NASA Technical Reports Server (NTRS)

    Hendricks, R. C.; Braun, M. J.; Wheeler, R. L., III; Mullen, R. L.

    1985-01-01

    In supercritical systems the design inlet and outlet pressures are maintained above the thermaodynamic critical pressure P sub C. Designers rely on this simple rule of thumb to circumvent problems associated with a subcritical pressure regime nested within the supercritical pressure system along with the uncertainties in heat transfer, fluid mechanics, and thermophysical property variations. The simple rule of thumb is adequate in many low-power designs but is inadequate for high-performance turbomachines and linear systems, where nested two-phase regions can exist. Examples for a free-jet expansion with backpressure greater than P sub C and a rotor (bearing) with ambient pressure greater than P sub C illustrate the existence of subcritical pressure regimes nested within supercritical systems.

  10. 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

  11. Constraints on nest site selection: a comparison of predator and flood avoidance in four species of marsh-nesting birds (genera: Catoptrophorus, Larus, Rallus, and Sterna).

    PubMed

    Storey, A E; Montevecchi, W A; Andrews, H F; Sims, N

    1988-03-01

    Nest site characteristics associated with flood and predator avoidance were compared for four nonpasserine species of marsh-nesting birds: clapper rails, willets, laughing gulls, and common terns. Species with short nests, willets and terns, minimized flood damage by nesting on higher ground than did gulls and rails that build tall nests. Species with dispersed, cryptic nests had taller surrounding grass than did open-nesting colonial species. Total nest height was similar for species with tall nests and for terns whose short nests were elevated by placement on mats of dead Spartina grass. Willets had lower nest heights than the other species, probably because the inverse relation between grass height and ground height in the salt marsh makes it difficult for willets to find sites with high enough ground for flood avoidance while still retaining high enough grass for nest crypticity. Ground height for common terns and grass height for gulls and rails appear to be cues used in nest site selection. Nests of each species in which these characteristics were maximized were more successful in a major tidal flood. Laughing gulls and clapper rails appear to be more specialized salt marsh nesters than the other two species. PMID:3365941

  12. 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

  13. 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

  14. 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.

  15. Nest site 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 spp. of wading birds [Egretta thula, Plegadis falcinellus, Florida caerulea, casmerodius albus and Hydranassa tricolor] were identified and marked during the breeding season at 6 locations from Maccachusetts [USA] to North Carolina [USA]. 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 analysis were used to describe and compare sites and species. 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 determined whether nest sites were stratified, segregated or randomly distributed.

  16. 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

  17. 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

  18. 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.

  19. 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

  20. 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.

  1. Association mapping of disease resistance traits in rainbow trout using restriction site associated DNA sequencing.

    PubMed

    Campbell, Nathan R; LaPatra, Scott E; Overturf, Ken; Towner, Richard; Narum, Shawn R

    2014-12-01

    Recent advances in genotyping-by-sequencing have enabled genome-wide association studies in nonmodel species including those in aquaculture programs. As with other aquaculture species, rainbow trout and steelhead (Oncorhynchus mykiss) are susceptible to disease and outbreaks can lead to significant losses. Fish culturists have therefore been pursuing strategies to prevent losses to common pathogens such as Flavobacterium psychrophilum (the etiological agent for bacterial cold water disease [CWD]) and infectious hematopoietic necrosis virus (IHNV) by adjusting feed formulations, vaccine development, and selective breeding. However, discovery of genetic markers linked to disease resistance offers the potential to use marker-assisted selection to increase resistance and reduce outbreaks. For this study we sampled juvenile fish from 40 families from 2-yr classes that either survived or died after controlled exposure to either CWD or IHNV. Restriction site-associated DNA sequencing produced 4661 polymorphic single-nucleotide polymorphism loci after strict filtering. Genotypes from individual survivors and mortalities were then used to test for association between disease resistance and genotype at each locus using the program TASSEL. After we accounted for kinship and stratification of the samples, tests revealed 12 single-nucleotide polymorphism markers that were highly associated with resistance to CWD and 19 markers associated with resistance to IHNV. These markers are candidates for further investigation and are expected to be useful for marker assisted selection in future broodstock selection for various aquaculture programs. PMID:25354781

  2. Association Mapping of Disease Resistance Traits in Rainbow Trout Using Restriction Site Associated DNA Sequencing

    PubMed Central

    Campbell, Nathan R.; LaPatra, Scott E.; Overturf, Ken; Towner, Richard; Narum, Shawn R.

    2014-01-01

    Recent advances in genotyping-by-sequencing have enabled genome-wide association studies in nonmodel species including those in aquaculture programs. As with other aquaculture species, rainbow trout and steelhead (Oncorhynchus mykiss) are susceptible to disease and outbreaks can lead to significant losses. Fish culturists have therefore been pursuing strategies to prevent losses to common pathogens such as Flavobacterium psychrophilum (the etiological agent for bacterial cold water disease [CWD]) and infectious hematopoietic necrosis virus (IHNV) by adjusting feed formulations, vaccine development, and selective breeding. However, discovery of genetic markers linked to disease resistance offers the potential to use marker-assisted selection to increase resistance and reduce outbreaks. For this study we sampled juvenile fish from 40 families from 2-yr classes that either survived or died after controlled exposure to either CWD or IHNV. Restriction site−associated DNA sequencing produced 4661 polymorphic single-nucleotide polymorphism loci after strict filtering. Genotypes from individual survivors and mortalities were then used to test for association between disease resistance and genotype at each locus using the program TASSEL. After we accounted for kinship and stratification of the samples, tests revealed 12 single-nucleotide polymorphism markers that were highly associated with resistance to CWD and 19 markers associated with resistance to IHNV. These markers are candidates for further investigation and are expected to be useful for marker assisted selection in future broodstock selection for various aquaculture programs. PMID:25354781

  3. 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.

  4. 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.

  5. 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

  6. 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

  7. 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

  8. Adeno-Associated Viral Vectors for Mapping, Monitoring, and Manipulating Neural Circuits

    PubMed Central

    Betley, J. Nicholas

    2011-01-01

    Abstract Understanding the structure and function of neural circuits is central is neuroscience research. To address the associated questions, new genetically encoded tools have been developed for mapping, monitoring, and manipulating neurons. Essential to implementation of these tools is their selective delivery to defined neuronal populations in the brain. This has been facilitated by recent improvements in cell type–specific transgene expression using recombinant adeno-associated viral vectors. Here, we highlight these developments and discuss areas for improvement that could further expand capabilities for neural circuit analysis. PMID:21319997

  9. 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.

  10. 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.

  11. 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

  12. 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

  13. Linkage and Association Mapping of Arabidopsis thaliana Flowering Time in Nature

    PubMed Central

    Brachi, Benjamin; Faure, Nathalie; Horton, Matt; Flahauw, Emilie; Vazquez, Adeline; Nordborg, Magnus; Bergelson, Joy; Cuguen, Joel; Roux, Fabrice

    2010-01-01

    Flowering time is a key life-history trait in the plant life cycle. Most studies to unravel the genetics of flowering time in Arabidopsis thaliana have been performed under greenhouse conditions. Here, we describe a study about the genetics of flowering time that differs from previous studies in two important ways: first, we measure flowering time in a more complex and ecologically realistic environment; and, second, we combine the advantages of genome-wide association (GWA) and traditional linkage (QTL) mapping. Our experiments involved phenotyping nearly 20,000 plants over 2 winters under field conditions, including 184 worldwide natural accessions genotyped for 216,509 SNPs and 4,366 RILs derived from 13 independent crosses chosen to maximize genetic and phenotypic diversity. Based on a photothermal time model, the flowering time variation scored in our field experiment was poorly correlated with the flowering time variation previously obtained under greenhouse conditions, reinforcing previous demonstrations of the importance of genotype by environment interactions in A. thaliana and the need to study adaptive variation under natural conditions. The use of 4,366 RILs provides great power for dissecting the genetic architecture of flowering time in A. thaliana under our specific field conditions. We describe more than 60 additive QTLs, all with relatively small to medium effects and organized in 5 major clusters. We show that QTL mapping increases our power to distinguish true from false associations in GWA mapping. QTL mapping also permits the identification of false negatives, that is, causative SNPs that are lost when applying GWA methods that control for population structure. Major genes underpinning flowering time in the greenhouse were not associated with flowering time in this study. Instead, we found a prevalence of genes involved in the regulation of the plant circadian clock. Furthermore, we identified new genomic regions lacking obvious candidate genes

  14. An associative model of adaptive inference for learning word-referent mappings.

    PubMed

    Kachergis, George; Yu, Chen; Shiffrin, Richard M

    2012-04-01

    People can learn word-referent pairs over a short series of individually ambiguous situations containing multiple words and referents (Yu & Smith, 2007, Cognition 106: 1558-1568). Cross-situational statistical learning relies on the repeated co-occurrence of words with their intended referents, but simple co-occurrence counts cannot explain the findings. Mutual exclusivity (ME: an assumption of one-to-one mappings) can reduce ambiguity by leveraging prior experience to restrict the number of word-referent pairings considered but can also block learning of non-one-to-one mappings. The present study first trained learners on one-to-one mappings with varying numbers of repetitions. In late training, a new set of word-referent pairs were introduced alongside pretrained pairs; each pretrained pair consistently appeared with a new pair. Results indicate that (1) learners quickly infer new pairs in late training on the basis of their knowledge of pretrained pairs, exhibiting ME; and (2) learners also adaptively relax the ME bias and learn two-to-two mappings involving both pretrained and new words and objects. We present an associative model that accounts for both results using competing familiarity and uncertainty biases. PMID:22215466

  15. 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.

  16. 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

  17. 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

  18. 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.

  19. Tessellation and Lyubich-Minsky laminations associated with quadratic maps, II

    NASA Astrophysics Data System (ADS)

    Kawahira, Tomoki

    According to an analogy to quasi-Fuchsian groups, we investigate the topological and combinatorial structures of Lyubich and Minsky's affine and hyperbolic 3 -laminations associated with hyperbolic and parabolic quadratic maps. We begin by showing that hyperbolic rational maps in the same hyperbolic component have quasi-isometrically the same 3 -laminations. This gives a good reason to regard the main cardioid of the Mandelbrot set as an analogue of the Bers slices in the quasi-Fuchsian space. Then we describe the topological and combinatorial changes of laminations associated with hyperbolic-to-parabolic degenerations (and parabolic-to-hyperbolic bifurcations) of quadratic maps. For example, the differences between the structures of the quotient 3 -laminations of Douady's rabbit, the Cauliflower, and z mapsto z2 are described. The descriptions employ a new method of tessellation inside the filled Julia set introduced in Part I [Ergodic Theory Dynam. Systems 29 (2009), no. 2] that works like external rays outside the Julia set.

  20. 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

  1. 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. PMID:27116373

  2. 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

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

    PubMed

    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

  4. 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

  5. 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.

  6. 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...

  7. 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.

  8. 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.

  9. 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…

  10. Developing a Vulnerability Mapping Methodology: Applying the Water-Associated Disease Index to Dengue in Malaysia

    PubMed Central

    Dickin, Sarah K.; Schuster-Wallace, Corinne J.; Elliott, Susan J.

    2013-01-01

    The Water-associated Disease Index (WADI) was developed to identify and visualize vulnerability to different water-associated diseases by integrating a range of social and biophysical determinants in map format. In this study vulnerability is used to encompass conditions of exposure, susceptibility, and differential coping capacity to a water-associated health hazard. By assessing these conditions, the tool is designed to provide stakeholders with an integrated and long-term understanding of subnational vulnerabilities to water-associated disease and contribute to intervention strategies to reduce the burden of illness. The objective of this paper is to describe and validate the WADI tool by applying it to dengue. A systemic ecohealth framework that considers links between people, the environment and health was applied to identify secondary datasets, populating the index with components including climate conditions, land cover, education status and water use practices. Data were aggregated to create composite indicators of exposure and of susceptibility in a Geographic Information System (GIS). These indicators were weighted by their contribution to dengue vulnerability, and the output consisted of an overall index visualized in map format. The WADI was validated in this Malaysia case study, demonstrating a significant association with dengue rates at a sub-national level, and illustrating a range of factors that drive vulnerability to the disease within the country. The index output indicated high vulnerability to dengue in urban areas, especially in the capital Kuala Lumpur and surrounding region. However, in other regions, vulnerability to dengue varied throughout the year due to the influence of seasonal climate conditions, such as monsoon patterns. The WADI tool complements early warning models for water-associated disease by providing upstream information for planning prevention and control approaches, which increasingly require a comprehensive and

  11. R2* mapping for brain iron: associations with cognition in normal aging.

    PubMed

    Ghadery, Christine; Pirpamer, Lukas; Hofer, Edith; Langkammer, Christian; Petrovic, Katja; Loitfelder, Marisa; Schwingenschuh, Petra; Seiler, Stephan; Duering, Marco; Jouvent, Eric; Schmidt, Helena; Fazekas, Franz; Mangin, Jean-Francois; Chabriat, Hugues; Dichgans, Martin; Ropele, Stefan; Schmidt, Reinhold

    2015-02-01

    Brain iron accumulates during aging and has been associated with neurodegenerative disorders including Alzheimer's disease. Magnetic resonance (MR)-based R2* mapping enables the in vivo detection of iron content in brain tissue. We investigated if during normal brain aging iron load relates to cognitive impairment in region-specific patterns in a community-dwelling cohort of 336 healthy, middle aged, and older adults from the Austrian Stroke Prevention Family Study. MR imaging and R2* mapping in the basal ganglia and neocortex were done at 3T. Comprehensive neuropsychological testing assessed memory, executive function, and psychomotor speed. We found the highest iron concentration in the globus pallidus, and pallidal and putaminal iron was significantly and inversely associated with cognitive performance in all cognitive domains, except memory. These associations were iron load dependent. Vascular brain lesions and brain volume did not mediate the relationship between iron and cognitive performance. We conclude that higher R2*-determined iron in the basal ganglia correlates with cognitive impairment during brain aging independent of concomitant brain abnormalities. The prognostic significance of this finding needs to be determined. PMID:25443291

  12. 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.

  13. 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.

  14. 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

  15. 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

  16. 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

  17. Admixture mapping and subsequent fine-mapping suggests a biologically relevant and novel association on chromosome 11 for type 2 diabetes in African Americans.

    PubMed

    Jeff, Janina M; Armstrong, Loren L; Ritchie, Marylyn D; Denny, Joshua C; Kho, Abel N; Basford, Melissa A; Wolf, Wendy A; Pacheco, Jennifer A; Li, Rongling; Chisholm, Rex L; Roden, Dan M; Hayes, M Geoffrey; Crawford, Dana C

    2014-01-01

    Type 2 diabetes (T2D) is a complex metabolic disease that disproportionately affects African Americans. Genome-wide association studies (GWAS) have identified several loci that contribute to T2D in European Americans, but few studies have been performed in admixed populations. We first performed a GWAS of 1,563 African Americans from the Vanderbilt Genome-Electronic Records Project and Northwestern University NUgene Project as part of the electronic Medical Records and Genomics (eMERGE) network. We successfully replicate an association in TCF7L2, previously identified by GWAS in this African American dataset. We were unable to identify novel associations at p<5.0×10(-8) by GWAS. Using admixture mapping as an alternative method for discovery, we performed a genome-wide admixture scan that suggests multiple candidate genes associated with T2D. One finding, TCIRG1, is a T-cell immune regulator expressed in the pancreas and liver that has not been previously implicated for T2D. We performed subsequent fine-mapping to further assess the association between TCIRG1 and T2D in >5,000 African Americans. We identified 13 independent associations between TCIRG1, CHKA, and ALDH3B1 genes on chromosome 11 and T2D. Our results suggest a novel region on chromosome 11 identified by admixture mapping is associated with T2D in African Americans. PMID:24595071

  18. Maize genetic diversity and association mapping using transposable element insertion polymorphisms.

    PubMed

    Zerjal, Tatiana; Rousselet, Agnès; Mhiri, Corinne; Combes, Valérie; Madur, Delphine; Grandbastien, Marie-Angèle; Charcosset, Alain; Tenaillon, Maud I

    2012-05-01

    Transposable elements are the major component of the maize genome and presumably highly polymorphic yet they have not been used in population genetics and association analyses. Using the Transposon Display method, we isolated and converted into PCR-based markers 33 Miniature Inverted Repeat Transposable Elements (MITE) polymorphic insertions. These polymorphisms were genotyped on a population-based sample of 26 American landraces for a total of 322 plants. Genetic diversity was high and partitioned within and among landraces. The genetic groups identified using Bayesian clustering were in agreement with published data based on SNPs and SSRs, indicating that MITE polymorphisms reflect maize genetic history. To explore the contribution of MITEs to phenotypic variation, we undertook an association mapping approach in a panel of 367 maize lines phenotyped for 26 traits. We found a highly significant association between the marker ZmV1-9, on chromosome 1, and male flowering time. The variance explained by this association is consistent with a flowering delay of +123 degree-days. This MITE insertion is located at only 289 nucleotides from the 3' end of a Cytochrome P450-like gene, a region that was never identified in previous association mapping or QTL surveys. Interestingly, we found (i) a non-synonymous mutation located in the exon 2 of the gene in strong linkage disequilibrium with the MITE polymorphism, and (ii) a perfect sequence homology between the MITE sequence and a maize siRNA that could therefore potentially interfere with the expression of the Cytochrome P450-like gene. Those two observations among others offer exciting perspectives to validate functionally the role of this region on phenotypic variation. PMID:22350086

  19. CADYRI, a dynamic mapping tool of human risk associated with flooding in urban areas

    NASA Astrophysics Data System (ADS)

    Tanguy, M.; Chokmani, K.; Bernier, M.; Poulin, J.

    2013-12-01

    When a flood affects an urban area, the managers and services responsible for public safety need precise and real time information on the localization of the flooded areas, on the submersion heights in those areas, but also on the vulnerability of people exposed to this hazard. Such information is essential for an effective crisis management. Despite a growing interest in this topic over the last 15 years, the development of flood risk assessment tools mainly focused on quantitative modeling of the monetary damages caused by floods to residential buildings or to critical infrastructures. Little attention was paid to the vulnerability of people exposed to flooding but also to the effects of the failure or destruction of critical infrastructures and residential building on people health and security during the disaster. Moreover, these models do not integrate the dynamic features of the flood (extent, submersion heights) and the evolution of human vulnerability in the same mapping tool. Thus, an accurate and precise evaluation of human risk induced by urban flooding is hardly feasible using such models. This study presents CADYRI, a dynamic mapping tool of human risk associated with flooding in urban areas, which fills the actual needs in terms of flood risk evaluation and management. This innovative tool integrates a methodology of flood hazard mapping that simulates, for a given discharge, the associated water level, and subsequently determines the extent of the flooded area and the submersion heights at each point of the flooded area, using a DEM. The dynamics of human vulnerability is then mapped at the household level, according to the characteristics of the flood hazard. Three key components of human vulnerability have been identified and are integrated to CADYRI: 1, the intrinsic vulnerability of the population, estimated by specific socio-economic indicators; 2, the vulnerability of buildings, assessed by their structural features; 3, the vulnerability of

  20. 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.

  1. 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

  2. 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

  3. No association between exposure to perfluorinated compounds and congenital cryptorchidism: a nested case-control study among 215 boys from Denmark and Finland.

    PubMed

    Vesterholm Jensen, Dorte; Christensen, Jeppe; Virtanen, Helena E; Skakkebæk, Niels E; Main, Katharina M; Toppari, Jorma; Veje, Christine W; Andersson, Anna-Maria; Nielsen, Flemming; Grandjean, Philippe; Jensen, Tina Kold

    2014-01-01

    Geographical differences in the occurrence of diseases in male reproductive organs, including malformation in reproductive tract, between Denmark and Finland have been reported. The reason for these differences is unknown, but differences in exposure to chemicals with endocrine-disrupting abilities have been suggested. Among these chemicals are perfluoro-alkylated substances (PFASs), a group of water- and grease-repellent chemicals used in outdoor clothes, cookware, food packaging, and textiles. In this study, we, therefore, investigated differences in PFAS exposure levels between Denmark and Finland and the association between cord blood PFAS levels and congenital cryptorchidism. Boys from a joint ongoing prospective birth cohort study were included. We analyzed PFAS levels in cord blood serum samples collected from 29 Danish boys with congenital cryptorchidism, 30 healthy Danish matched controls recruited from 1997 to 2001, 30 Finnish cases, and 78 Finnish healthy matched controls recruited from 1997 to 1999. Additionally, 48 Finnish cases recruited from 2000 to 2002 were included. Perfluorooctanoic acid (PFOA) and perfluorooctanesulfonic acid (PFOS) were detected in all the 215 Danish and Finnish cord blood samples with significantly higher levels being observed in the Danish samples (medians: PFOA, 2.6 ng/ml and PFOS, 9.1 ng/ml) than in the Finnish samples (medians: PFOA, 2.1 ng/ml and PFOS, 5.2 ng/ml). We found no associations between cord blood PFOA and PFOS levels and congenital cryptorchidism after adjustment for confounders. Our data indicate that women in Denmark and Finland are generally exposed to PFOA and PFOS but there are differences in exposure levels between countries. We found no statistically significant association between cord blood PFOA and PFOS levels and congenital cryptorchidism; however, our study was small and larger studies are warranted. PMID:24218628

  4. Association mapping of common bacterial blight resistance QTL in Ontario bean breeding populations

    PubMed Central

    2011-01-01

    Background Common bacterial blight (CBB), incited by Xanthomonas axonopodis pv. phaseoli (Xap), is a major yield-limiting factor of common bean (Phaseolus vulgaris L.) production around the world. Host resistance is practically the most effective and environmentally-sound approach to control CBB. Unlike conventional QTL discovery strategies, in which bi-parental populations (F2, RIL, or DH) need to be developed, association mapping-based strategies can use plant breeding populations to synchronize QTL discovery and cultivar development. Results A population of 469 dry bean lines of different market classes representing plant materials routinely developed in a bean breeding program were used. Of them, 395 lines were evaluated for CBB resistance at 14 and 21 DAI (Days After Inoculation) in the summer of 2009 in an artificially inoculated CBB nursery in south-western Ontario. All lines were genotyped using 132 SNPs (Single Nucleotide Polymorphisms) evenly distributed across the genome. Of the 132 SNPs, 26 SNPs had more than 20% missing data, 12 SNPs were monomorphic, and 17 SNPs had a MAF (Minor Allelic Frequency) of less than 0.20, therefore only 75 SNPs were used for association study, based on one SNP per locus. The best possible population structure was to assign 36% and 64% of the lines into Andean and Mesoamerican subgroups, respectively. Kinship analysis also revealed complex familial relationships among all lines, which corresponds with the known pedigree history. MLM (Mixed Linear Model) analysis, including population structure and kinship, was used to discover marker-trait associations. Eighteen and 22 markers were significantly associated with CBB rating at 14 and 21 DAI, respectively. Fourteen markers were significant for both dates and the markers UBC420, SU91, g321, g471, and g796 were highly significant (p ≤ 0.001). Furthermore, 12 significant SNP markers were co-localized with or close to the CBB-QTLs identified previously in bi-parental QTL mapping

  5. 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

  6. 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

  7. Trans-ethnic genome-wide association studies: advantages and challenges of mapping in diverse populations.

    PubMed

    Li, Yun R; Keating, Brendan J

    2014-01-01

    Genome-wide association studies (GWASs) are the method most often used by geneticists to interrogate the human genome, and they provide a cost-effective way to identify the genetic variants underpinning complex traits and diseases. Most initial GWASs have focused on genetically homogeneous cohorts from European populations given the limited availability of ethnic minority samples and so as to limit population stratification effects. Transethnic studies have been invaluable in explaining the heritability of common quantitative traits, such as height, and in examining the genetic architecture of complex diseases, such as type 2 diabetes. They provide an opportunity for large-scale signal replication in independent populations and for cross-population meta-analyses to boost statistical power. In addition, transethnic GWASs enable prioritization of candidate genes, fine-mapping of functional variants, and potentially identification of SNPs associated with disease risk in admixed populations, by taking advantage of natural differences in genomic linkage disequilibrium across ethnically diverse populations. Recent efforts to assess the biological function of variants identified by GWAS have highlighted the need for large-scale replication, meta-analyses and fine-mapping across worldwide populations of ethnically diverse genetic ancestries. Here, we review recent advances and new approaches that are important to consider when performing, designing or interpreting transethnic GWASs, and we highlight existing challenges, such as the limited ability to handle heterogeneity in linkage disequilibrium across populations and limitations in dissecting complex architectures, such as those found in recently admixed populations. PMID:25473427

  8. 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

  9. Genomic regions underlying agronomic traits in linseed (Linum usitatissimum L.) as revealed by association mapping.

    PubMed

    Soto-Cerda, Braulio J; Duguid, Scott; Booker, Helen; Rowland, Gordon; Diederichsen, Axel; Cloutier, Sylvie

    2014-01-01

    The extreme climate of the Canadian Prairies poses a major challenge to improve yield. Although it is possible to breed for yield per se, focusing on yield-related traits could be advantageous because of their simpler genetic architecture. The Canadian flax core collection of 390 accessions was genotyped with 464 simple sequence repeat markers, and phenotypic data for nine agronomic traits including yield, bolls per area, 1,000 seed weight, seeds per boll, start of flowering, end of flowering, plant height, plant branching, and lodging collected from up to eight environments was used for association mapping. Based on a mixed model (principal component analysis (PCA) + kinship matrix (K)), 12 significant marker-trait associations for six agronomic traits were identified. Most of the associations were stable across environments as revealed by multivariate analyses. Statistical simulation for five markers associated with 1000 seed weight indicated that the favorable alleles have additive effects. None of the modern cultivars carried the five favorable alleles and the maximum number of four observed in any accessions was mostly in breeding lines. Our results confirmed the complex genetic architecture of yield-related traits and the inherent difficulties associated with their identification while illustrating the potential for improvement through marker-assisted selection. PMID:24138336

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

    PubMed

    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

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

    PubMed Central

    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

    2014-01-01

    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

  12. 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

  13. Influence of quantity of litter on nest box selection and nesting behaviour of domestic hens.

    PubMed

    Petherick, J C; Seawright, E; Waddington, D

    1993-12-01

    1. Twenty two hens (Gallus gallus domesticus) were given a free choice, for egg laying, between 4 nest boxes containing different quantities of wood shavings (litter): 3180 cm3 (large), 1060 cm3 (medium), 350 cm3 (small) and none (zero). 2. There was considerable individual variation in the quantity of litter selected for egg laying, but 17 hens laid 50% or more of their eggs in a single litter quantity. Hens selected the large quantity in preference to the small and zero. More searching, nest selection and nesting behaviours tended to be directed to the boxes with the largest quantities and also to the quantities that the hens finally selected for egg laying. 3. In a second experiment, the hens from experiment 1 which showed a preference for litter, and a further 22 naïve hens were given a choice of three nest boxes containing no litter and one containing one of 6 quantities. Over 30 trials there were 5 replicates using each of the three quantities used in experiment 1 plus 115 cm3, 40 cm3 and 10 cm3. 4. There was a wide range in the proportion of trials in which hens selected litter; for experienced hens the range was 0.43 to 0.97, but only two naïve hens were within this range, all others being between 0 and 0.43. 5. The pattern of choosing litter quantities was comparable but at different levels of preference in experienced and naïve hens and a contour map was derived enabling predictions to be made of the probability of a particular quantity being chosen. 6. The variability of individual responses suggest that no single type of nest box system can cater for the requirements of all hens. PMID:8156424

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

    PubMed

    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

  15. 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

  16. 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

  17. 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.

  18. 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

  19. 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

  20. Fine mapping major histocompatibility complex associations in psoriasis and its clinical subtypes.

    PubMed

    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

    2014-08-01

    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

  1. Association of Rheumatoid Arthritis and Hepatitis B Infection: A Nationwide Nested Case-Control Study From 1999 to 2009 in Taiwan.

    PubMed

    Hsu, Ching-Sheng; Lang, Hui-Chu; Huang, Kuang-Yung; Lin, Hans Hsienhong; Chen, Chien-Lin

    2016-05-01

    Rheumatoid arthritis (RA) is a disorder with altered immunologic function and increased risks of infection, while the association between HBV and RA remains largely unknown.To determine the prevalence and risk of HBV infection in patients with RA, 2 cohort datasets were sourced from Taiwan's National Health Insurance Research Database to capture National Health Insurance claims data between 1999 and 2009. One set was a specially requested RA subject's dataset extracted from the whole 23 million beneficiaries, and a total of 38,969 aged ≧18 years RA subjects were identified (RA cohort). The other one was a randomly selected 1 million patients' longitudinal dataset, and from which an additional 701,476 aged ≧18 years non-RA subjects were identified (non-RA cohort). An epidemiological approach was used to compare the prevalence and risk for HBV infection between RA and non-RA subjects.During the followed interval between 1999 and 2009, 3260 in RA cohort and 63,588 in non-RA cohort had a diagnosis of HBV infection. The annual age- and sex-standardized prevalence of HBV infection in the RA cohort was generally higher than that in the non-RA cohort. The RA patients had a higher HBV period prevalence than did the non-RA subjects (RA vs. non-RA = 69.9 vs. 60.1 cases per 1000 subjects). Compared with the non-RA cohort, the RA cohort had an increased risk of HBV infection after adjustment for potential prognostic factors (1.13, 95% CIs: 1.08-1.17).RA patients are characterized by an increased risk of HBV infection than non-RA subjects. PMID:27149469

  2. Power lines, roads, and avian nest survival: effects on predator identity and predation intensity.

    PubMed

    DeGregorio, Brett A; Weatherhead, Patrick J; Sperry, Jinelle H

    2014-05-01

    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

  3. 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

  4. 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.

  5. 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.

  6. Physical cognition: birds learn the structural efficacy of nest material

    PubMed Central

    Bailey, Ida E.; Morgan, Kate V.; Bertin, Marion; Meddle, Simone L.; Healy, Susan D.

    2014-01-01

    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. PMID:24741011

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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.

  13. 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 ...

  14. Association mapping of yield candidate gene homologs in a diverse collection of pea (Pisum sativum L.) lines

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Association mapping, based on linkage disequilibrium (LD), is used increasingly to describe associations between allelic variation and phenotype. Yield is a key economic trait for most field crops, including pea (Pisum sativum L.). Recent reports in plant systems have identified candidate genes fo...

  15. 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

  16. 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

  17. In-depth mapping of human testicular and epididymal proteins and their functional association with spermatozoa

    PubMed Central

    LIU, XUEXIA; LIU, FUJUN

    2015-01-01

    The mammalian testis and epididymis are responsible for spermatozoa production and maturation, which contributes to male fertility. Predominantly expressed proteins in the testis and epididymis were suggested to be involved in the key functions or pathways in spermatogenesis and sperm maturation. To further investigate these proteins and their associations with sperm, large protein profiles of human testis and epididymis were mapped. Predominantly-expressed testicular (173) and epididymal (244) secreted proteins were further screened and functionally characterized. Differential expression levels of solute carrier family 2 (facilitated glucose transporter), member 3, solute carrier family 25 (carnitine/acylcarnitine translocase), member 20, WAP-type four-disulfide core domain protein 8 and prostate and testis expressed 1 were validated using western blot and immunohistochemical analyses. The results may provide novel insight into the understanding of testicular and epididymal physiology and function, and facilitate sperm maturation research. PMID:25760095

  18. 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.

  19. Effects of agricultural burning on nesting waterfowl

    USGS Publications Warehouse

    Fritzell, E.K.

    1975-01-01

    Agricultural burning in an intensively farmed region within Manitoba's pothole district is shown to affect the nesting activities of ground-nesting ducks. All species, except Blue-winged Teal (Anas discors), preferred unburned nest cover, although success was higher in burned areas, where predators may have exerted less influence. Attitudes of farmers, burning chronology, and nest destruction by fires are also reported.

  20. Admixture Mapping Provides Evidence of Association of the VNN1 Gene with Hypertension

    PubMed Central

    Zhu, Xiaofeng; Cooper, Richard S.

    2007-01-01

    Migration patterns in modern societies have created the opportunity to use population admixture as a strategy to identify susceptibility genes. To implement this strategy, we genotyped a highly informative ancestry marker panel of 2270 single nucleotide polymorphisms in a random population sample of African Americans (N = 1743), European Americans (N = 1000) and Mexican Americans (N = 581). We then examined the evidence for over-transmission of specific loci to cases from one of the two ancestral populations. Hypertension cases and controls were defined based on standard clinical criteria. Both case-only and case-control analyses were performed among African Americans. With the genome-wide markers we replicated the findings identified in our previous admixture mapping study on chromosomes 6 and 21 [1]. For case-control analysis we then genotyped 51 missense SNPs in 36 genes spaced across an 18.3 Mb region. Further analyses demonstrated that the missense SNP rs2272996 (or N131S) in the VNN1 gene was significantly associated with hypertension in African Americans and the association was replicated in Mexican Americans; a non-significant opposite association was observed in European Americans. This SNP also accounted for most of the evidence observed in the admixture analysis on chromosome 6. Despite these encouraging results, susceptibility loci for hypertension have been exceptionally difficult to localize and confirmation by independent studies will be necessary to establish these findings. PMID:18043751

  1. 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

  2. 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. PMID:26758024

  3. Genetic association mapping based on discordant sib pairs: the discordant-alleles test.

    PubMed

    Boehnke, M; Langefeld, C D

    1998-04-01

    Family-based tests of association provide the opportunity to test for an association between a disease and a genetic marker. Such tests avoid false-positive results produced by population stratification, so that evidence for association may be interpreted as evidence for linkage or causation. Several methods that use family-based controls have been proposed, including the haplotype relative risk, the transmission-disequilibrium test, and affected family-based controls. However, because these methods require genotypes on affected individuals and their parents, they are not ideally suited to the study of late-onset diseases. In this paper, we develop several family-based tests of association that use discordant sib pairs (DSPs) in which one sib is affected with a disease and the other sib is not. These tests are based on statistics that compare counts of alleles or genotypes or that test for symmetry in tables of alleles or genotypes. We describe the use of a permutation framework to assess the significance of these statistics. These DSP-based tests provide the same general advantages as parent-offspring trio-based tests, while being applicable to essentially any disease; they may also be tailored to particular hypotheses regarding the genetic model. We compare the statistical properties of our DSP-based tests by computer simulation and illustrate their use with an application to Alzheimer disease and the apolipoprotein E polymorphism. Our results suggest that the discordant-alleles test, which compares the numbers of nonmatching alleles in DSPs, is the most powerful of the tests we considered, for a wide class of disease models and marker types. Finally, we discuss advantages and disadvantages of the DSP design for genetic association mapping. PMID:9529345

  4. Genome-wide association mapping of salinity tolerance in rice (Oryza sativa)

    PubMed Central

    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

    2015-01-01

    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. PMID:25627243

  5. 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.

  6. 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.

  7. 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

  8. 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

  9. The International Association for the Study of Lung Cancer Lymph Node Map: A Radiologic Atlas and Review

    PubMed Central

    van Beek, Edwin JR; Murchison, John T; Marin, Aleksander; Mirsadraee, Saeed

    2015-01-01

    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. PMID:26175770

  10. 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..

  11. 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

  12. Social status-dependent nest choice of territorial males under reproductive parasitism in a Lake Tanganyika cichlid Telmatochromis vittatus.

    PubMed

    Ota, K; Kohda, M

    2011-03-01

    Field and laboratory studies were conducted to examine how territorial males of a Lake Tanganyika cichlid Telmatochromis vittatus balance the conflicting demands on nest choice between occupying large nests with more females and avoiding reproductive parasitism (nest piracy, which is adopted by the largest males in the population). Pirates less frequently intruded the nests farther from neighbours, perhaps due to the costs associated with travelling between nests. The field experiment showed that territorial male T. vittatus sacrificed the fitness benefits that large nests offer and instead prioritized occupying the nests farther from neighbours on which fewer pirates intruded. The field observations suggested that they adopt different strategies for nest choice according to their relative competitive ability to pirates; the large territorial males, who are size-matched to pirates and can defend their nests against them, compete for larger nests among the more-isolated nests, whereas subordinate territorial males, which are smaller than pirates and thus inferior to them, compete for the more-isolated nests among the less-isolated nests. These findings suggest that the territorial male T. vittatus chooses the more-isolated nests to avoid pirate males at the expense of occupying large nests. PMID:21366567

  13. The structure of gallery networks in the nests of termite Cubitermes spp. revealed by X-ray tomography

    NASA Astrophysics Data System (ADS)

    Perna, Andrea; Jost, Christian; Couturier, Etienne; Valverde, Sergi; Douady, Stéphane; Theraulaz, Guy

    2008-09-01

    Recent studies have introduced computer tomography (CT) as a tool for the visualisation and characterisation of insect architectures. Here, we use CT to map the three-dimensional networks of galleries inside Cubitermes nests in order to analyse them with tools from graph theory. The structure of these networks indicates that connections inside the nest are rearranged during the whole nest life. The functional analysis reveals that the final network topology represents an excellent compromise between efficient connectivity inside the nest and defence against attacking predators. We further discuss and illustrate the usefulness of CT to disentangle environmental and specific influences on nest architecture.

  14. 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...

  15. 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.

  16. 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

  17. From Association Mapping to Marker-Assisted Selection: Experimental Design and Application.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The most common method for mapping genes in cultivated plant species is genetic linkage mapping. This approach involves generating populations derived from single crosses and estimating the recombination frequencies between marker loci and the genes of interest. However, such mapping populations sam...

  18. POLYCHORD: nested sampling for cosmology

    NASA Astrophysics Data System (ADS)

    Handley, W. J.; Hobson, M. P.; Lasenby, A. N.

    2015-06-01

    POLYCHORD is a novel nested sampling algorithm tailored for high-dimensional parameter spaces. In addition, it can fully exploit a hierarchy of parameter speeds such as is found in COSMOMC and CAMB. It utilizes slice sampling at each iteration to sample within the hard likelihood constraint of nested sampling. It can identify and evolve separate modes of a posterior semi-independently and is parallelized using OPENMPI. POLYCHORD is available for download at http://ccpforge.cse.rl.ac.uk/gf/project/polychord/.

  19. 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

  20. 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

  1. 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

  2. FISH Mapping of De Novo Apparently Balanced Chromosome Rearrangements Identifies Characteristics Associated with Phenotypic Abnormality

    PubMed Central

    Fantes, J.A.; Boland, E.; Ramsay, J.; Donnai, D.; Splitt, M.; Goodship, J.A.; Stewart, H.; Whiteford, M.; Gautier, P.; Harewood, L.; Holloway, S.; Sharkey, F.; Maher, E.; van Heyningen, V.; Clayton-Smith, J.; Fitzpatrick, D.R.; Black, G.C.M.

    2008-01-01

    We report fluorescence in situ hybridization (FISH) mapping of 152, mostly de novo, apparently balanced chromosomal rearrangement (ABCR) breakpoints in 76 individuals, 30 of whom had no obvious phenotypic abnormality (control group) and 46 of whom had an associated disease (case group). The aim of this study was to identify breakpoint characteristics that could discriminate between these groups and which might be of predictive value in de novo ABCR (DN-ABCR) cases detected antenatally. We found no difference in the proportion of breakpoints that interrupted a gene, although in three cases, direct interruption or deletion of known autosomal-dominant or X-linked recessive Mendelian disease genes was diagnostic. The only significant predictor of phenotypic abnormality in the group as a whole was the localization of one or both breakpoints to an R-positive (G-negative) band with estimated predictive values of 0.69 (95% CL 0.54–0.81) and 0.90 (95% CL 0.60–0.98), respectively. R-positive bands are known to contain more genes and have a higher guanine-cytosine (GC) content than do G-positive (R-negative) bands; however, whether a gene was interrupted by the breakpoint or the GC content in the 200kB around the breakpoint had no discriminant ability. Our results suggest that the large-scale genomic context of the breakpoint has prognostic utility and that the pathological mechanism of mapping to an R-band cannot be accounted for by direct gene inactivation. PMID:18374296

  3. Tomographic mapping of a coastal upwelling and the associated diurnal internal tides in Hiroshima Bay, Japan

    NASA Astrophysics Data System (ADS)

    Zhang, Chuanzheng; Kaneko, Arata; Zhu, Xiao-Hua; Gohda, Noriaki

    2015-06-01

    Temperature variations caused by a typhoon were measured in the northern part of Hiroshima Bay by four coastal acoustic tomography (CAT) systems. The horizontal distributions of depth-averaged temperature from 0 to 8 m were mapped at 10 min intervals between the 11 and 25 September 2013. The horizontal distributions of a coastal upwelling and the associated diurnal internal tides were reconstructed well by regularized inversion based on the grid segmented method, using one-way travel time data along five successful sound transmission lines. Station-to-station ranges were corrected in such a way that sound speed (determined from one-way travel time data) was equal to sound speed calculated from a couple of CTD (conductivity-temperature-depth) data sets on each transmission line. In addition, all station positions were adjusted to make focal points at the geographical positions of the transducers. The corrections increased the accuracy of temperature measurements to make temperature errors as small as 0.073-0.079°C. The high accuracy made it possible to map the temperature structure with a variation range of less than 0.5°C. An upwelling grew from 16 to 17 September, due to a typhoon-derived northerly wind. The diurnal internal tide resonated with the semidiurnal external tide, which was pronounced after the upwelling decayed (18 September), around the time the spring tide occurred. The upwelling and mixing fractions were formulated. These fractions increased continuously as the upwelling grew. Complete mixing was observed during the upwelling's mature phase.

  4. 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

  5. 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.

  6. Cloning, characterization, and mapping of human homolog of mouse T-cell death-associated gene.

    PubMed

    Kyaw, H; Zeng, Z; Su, K; Fan, P; Shell, B K; Carter, K C; Li, Y

    1998-06-01

    To establish immunologic autotolerance, self-reactive immature thymocytes are eliminated by negative selection during T-cell development in the thymus. Self-reactive clones undergo apoptosis after stimulation via the T-cell receptor (TCR). The process of cell selection is determined by the dedication of the TCR for tolerogenic antigen/major histocompatibility complex. We have cloned a novel human gene that is highly homologous in the transmembrane and G protein-coupling domains to mouse T-cell death-associated gene 8 (TDAG8). The gene, human TDAG8 (hTDAG8), which belongs to the G protein-couple receptor superfamily, encodes a protein of 337 amino acids. An expressed sequence tag (EST) corresponding to hTDAG8 was identified from a human thyroid cDNA library and subsequently used to isolate a full-length genomic clone. Northern blot analysis revealed that the hTDAG8 gene is expressed predominantly in lymphoid tissues, including peripheral blood leukocytes, spleen, lymph nodes, and thymus. Stably transfected mammalian CHO cells were generated, and heterologous expression of hTDAG8 was confirmed by Northern blot analysis. Fluorescent in situ hybridization (FISH) revealed that hTDAG8 maps to human chromosome 14q31-32.1, a region in which abnormalities associated with human T-cell lymphoma or leukemia are found. Taken together, these data implicate the hTDAG8 gene in T-cell-associated diseases in humans, but its actual physiological and pathological role in the human immune system needs further investigation. PMID:9655242

  7. High-resolution genetic mapping of allelic variants associated with cell wall chemistry in Populus

    DOE PAGESBeta

    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

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. 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.

  14. 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. PMID:24498238

  15. 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

  16. 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.

  17. 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

  18. 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

  19. MUTYH-associated polyposis (MAP), the syndrome implicating base excision repair in inherited predisposition to colorectal tumors

    PubMed Central

    Venesio, Tiziana; Balsamo, Antonella; D'Agostino, Vito G.; Ranzani, Guglielmina N.

    2012-01-01

    In 2002, Al-Tassan and co-workers described for the first time a recessive form of inherited polyposis associated with germline mutations of MUTYH, a gene encoding a base excision repair (BER) protein that counteracts the DNA damage induced by the oxidative stress. MUTYH-associated polyposis (MAP) is now a well-defined cancer susceptibility syndrome, showing peculiar molecular features that characterize disease progression. However, some aspects of MAP, including diagnostic criteria, genotype-phenotype correlations, pathogenicity of variants, as well as relationships between BER and other DNA repair pathways, are still poorly understood. A deeper knowledge of the MUTYH expression pattern is likely to refine our understanding of the protein role and, finally, to improve guidances for identifying and handling MAP patients. PMID:22876359

  20. 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.

  1. Genetic dissection of heterosis using epistatic association mapping in a partial NCII mating design

    PubMed Central

    Wen, Jia; Zhao, Xinwang; Wu, Guorong; Xiang, Dan; Liu, Qing; Bu, Su-Hong; Yi, Can; Song, Qijian; Dunwell, Jim M.; Tu, Jinxing; Zhang, Tianzhen; Zhang, Yuan-Ming

    2015-01-01

    Heterosis refers to the phenomenon in which an F1 hybrid exhibits enhanced growth or agronomic performance. However, previous theoretical studies on heterosis have been based on bi-parental segregating populations instead of F1 hybrids. To understand the genetic basis of heterosis, here we used a subset of F1 hybrids, named a partial North Carolina II design, to perform association mapping for dependent variables: original trait value, general combining ability (GCA), specific combining ability (SCA) and mid-parental heterosis (MPH). Our models jointly fitted all the additive, dominance and epistatic effects. The analyses resulted in several important findings: 1) Main components are additive and additive-by-additive effects for GCA and dominance-related effects for SCA and MPH, and additive-by-dominant effect for MPH was partly identified as additive effect; 2) the ranking of factors affecting heterosis was dominance > dominance-by-dominance > over-dominance > complete dominance; and 3) increasing the proportion of F1 hybrids in the population could significantly increase the power to detect dominance-related effects, and slightly reduce the power to detect additive and additive-by-additive effects. Analyses of cotton and rapeseed datasets showed that more additive-by-additive QTL were detected from GCA than from trait phenotype, and fewer QTL were from MPH than from other dependent variables. PMID:26679476

  2. 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

  3. 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

  4. Genome-wide association and fine mapping of genetic loci predisposing to colon carcinogenesis in mice.

    PubMed

    Liu, Pengyuan; Lu, Yan; Liu, Hongbo; Wen, Weidong; Jia, Dongmei; Wang, Yian; You, Ming

    2012-01-01

    To identify the genetic determinants of colon tumorigenesis, 268 male mice from 33 inbred strains derived from different genealogies were treated with azoxymethane (AOM; 10 mg/kg) once a week for six weeks to induce colon tumors. Tumors were localized exclusively within the distal colon in each of the strains examined. Inbred mouse strains exhibit a large variability in genetic susceptibility to AOM-induced colon tumorigenesis. The mean colon tumor multiplicity ranged from 0 to 38.6 (mean = 6.5 ± 8.6) and tumor volume ranged from 0 to 706.5 mm(3) (mean = 87.4 ± 181.9) at 24 weeks after the first dose of AOM. AOM-induced colon tumor phenotypes are highly heritable in inbred mice, and 68.8% and 71.3% of total phenotypic variation in colon tumor multiplicity and tumor volume, respectively, are attributable to strain-dependent genetic background. Using 97,854 single-nucleotide polymorphisms, we carried out a genome-wide association study (GWAS) of AOM-induced colon tumorigenesis and identified a novel susceptibility locus on chromosome 15 (rs32359607, P = 6.31 × 10(-6)). Subsequent fine mapping confirmed five (Scc3, Scc2, Scc12, Scc8, and Ccs1) of 16 linkage regions previously found to be associated with colon tumor susceptibility. These five loci were refined to less than 1 Mb genomic regions of interest. Major candidates in these loci are Sema5a, Fmn2, Grem2, Fap, Gsg1l, Xpo6, Rabep2, Eif3c, Unc5d, and Gpr65. In particular, the refined Scc3 locus shows high concordance with the human GWAS locus that underlies hereditary mixed polyposis syndrome. These findings increase our understanding of the complex genetics of colon tumorigenesis, and provide important insights into the pathways of colorectal cancer development and might ultimately lead to more effective individually targeted cancer prevention strategies. PMID:22127497

  5. Whole genome association mapping of grain shape variation among Oryza sativa L. germplasms based on elliptic Fourier analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Although grain shape is an important cereal breeding target, it has been evaluated using simple measurements, e.g. the length : width ratio. We used elliptic Fourier analysis to evaluate grain shape variation and conducted whole genome association mapping of grain shape using a germplasm collectio...

  6. 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...

  7. 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...

  8. 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...

  9. Structural basis for the association of MAP6 protein with microtubules and its regulation by calmodulin.

    PubMed

    Lefèvre, Julien; Savarin, Philippe; Gans, Pierre; Hamon, Loïc; Clément, Marie-Jeanne; David, Marie-Odile; Bosc, Christophe; Andrieux, Annie; Curmi, Patrick A

    2013-08-23

    Microtubules are highly dynamic αβ-tubulin polymers. In vitro and in living cells, microtubules are most often cold- and nocodazole-sensitive. When present, the MAP6/STOP family of proteins protects microtubules from cold- and nocodazole-induced depolymerization but the molecular and structure determinants by which these proteins stabilize microtubules remain under debate. We show here that a short protein fragment from MAP6-N, which encompasses its Mn1 and Mn2 modules (MAP6(90-177)), recapitulates the function of the full-length MAP6-N protein toward microtubules, i.e. its ability to stabilize microtubules in vitro and in cultured cells in ice-cold conditions or in the presence of nocodazole. We further show for the first time, using biochemical assays and NMR spectroscopy, that these effects result from the binding of MAP6(90-177) to microtubules with a 1:1 MAP6(90-177):tubulin heterodimer stoichiometry. NMR data demonstrate that the binding of MAP6(90-177) to microtubules involve its two Mn modules but that a single one is also able to interact with microtubules in a closely similar manner. This suggests that the Mn modules represent each a full microtubule binding domain and that MAP6 proteins may stabilize microtubules by bridging tubulin heterodimers from adjacent protofilaments or within a protofilament. Finally, we demonstrate that Ca(2+)-calmodulin competes with microtubules for MAP6(90-177) binding and that the binding mode of MAP6(90-177) to microtubules and Ca(2+)-calmodulin involves a common stretch of amino acid residues on the MAP6(90-177) side. This result accounts for the regulation of microtubule stability in cold condition by Ca(2+)-calmodulin. PMID:23831686

  10. 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.

  11. Assessment of hydrothermal processes associated with Proterozoic mineral systems in Finland using self-organizing maps.

    NASA Astrophysics Data System (ADS)

    Lerssi, J.; Sorjonen-Ward, P.; Fraser, S. J.; Ruotsalainen, A.

    2009-04-01

    reflection on the significance of clustering allows progressive refinement and enhancement of subtle differences, leading to delineation of specific areas whose attributes correspond closely to those associated with known mineralization. In the Hammaslahti test area, there appears to be good agreement between the results of the SiroSOM evaluation with areas currently targeted as prospective on the basis of a priori geological knowledge. [1] Kohonen, T., (2001): Self-Organizing Maps. 3rd Extended Edition, Springer Series in Information Sciences, Vol. 30, Springer, Berlin, Heidelberg, New York, 1995,1997, 2001.

  12. Visualizing Science by Citation Mapping.

    ERIC Educational Resources Information Center

    Small, Henry

    1999-01-01

    Discusses science mapping in the general context of information visualization and reviews attempts to construct maps of science using citation data, focusing on the use of co-citation clusters. Reports new work on a dataset of 36,00 documents using simplified methods for ordination and nesting maps hierarchically. Also discusses virtual-reality…

  13. 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

  14. 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

  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. Nest predation increases with parental activity: separating nest site and parental activity effects.

    PubMed Central

    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. PMID:11413645

  17. 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

  18. 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

  19. 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

  20. Nesting behavior of the poo-uli

    USGS Publications Warehouse

    Kepler, C.B.; Pratt, T.K.; Ecton, A.M.; Engilis, A., Jr.; 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.

  1. 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…

  2. NESTED GRID MESOSCALE ATMOSPHERIC CHEMISTRY MODEL

    EPA Science Inventory

    A nested grid version of the Regional Acid Deposition Model (RADM) has been developed. he horizontal grid interval size of the nested model is 3 times smaller than that of RADM (80/3 km 26.7 km). herefore the nested model is better able to simulate mesoscale atmospheric processes...

  3. Supramolecular nesting of cyclic polymers

    NASA Astrophysics Data System (ADS)

    Kondratuk, Dmitry V.; Perdigão, Luís M. A.; Esmail, Ayad M. S.; O'Shea, James N.; Beton, Peter H.; Anderson, Harry L.

    2015-04-01

    Advances in template-directed synthesis make it possible to create artificial molecules with protein-like dimensions, directly from simple components. These synthetic macromolecules have a proclivity for self-organization that is reminiscent of biopolymers. Here, we report the synthesis of monodisperse cyclic porphyrin polymers, with diameters of up to 21 nm (750 C-C bonds). The ratio of the intrinsic viscosities for cyclic and linear topologies is 0.72, indicating that these polymers behave as almost ideal flexible chains in solution. When deposited on gold surfaces, the cyclic polymers display a new mode of two-dimensional supramolecular organization, combining encapsulation and nesting; one nanoring adopts a near-circular conformation, thus allowing a second nanoring to be captured within its perimeter, in a tightly folded conformation. Scanning tunnelling microscopy reveals that nesting occurs in combination with stacking when nanorings are deposited under vacuum, whereas when they are deposited directly from solution under ambient conditions there is stacking or nesting, but not a combination of both.

  4. Nested Variant of Urothelial Carcinoma

    PubMed Central

    Venyo, Anthony Kodzo-Grey

    2014-01-01

    Background. Nested variant of urothelial carcinoma was added to the WHO's classification in 2004. Aims. To review the literature on nested variant of urothelial carcinoma. Results. About 200 cases of the tumour have been reported so far and it has the ensuing morphological features: large numbers of small confluent irregular nests of bland-appearing, closely packed, haphazardly arranged, and poorly defined urothelial cells infiltrating the lamina propria and the muscularis propria. The tumour has a bland histomorphologic appearance, has an aggressive biological behaviour, and has at times been misdiagnosed as a benign lesion which had led to a significant delay in the establishment of the correct diagnosis and contributing to the advanced stage of the disease. Immunohistochemically, the tumour shares some characteristic features with high-risk conventional urothelial carcinomas such as high proliferation index and loss of p27 expression. However, p53, bcl-2, or EGF-r immunoreactivity is not frequently seen. The tumour must be differentiated from a number of proliferative lesions of the urothelium. Conclusions. Correct and early diagnosis of this tumour is essential to provide early curative treatment to avoid diagnosis at an advanced stage. A multicentre trial is required to identify treatment options that would improve the outcome of this tumour. PMID:24587796

  5. Proteomic profile of edible bird's nest proteins.

    PubMed

    Liu, Xiaoqing; Lai, Xintian; Zhang, Shiwei; Huang, Xiuli; Lan, Quanxue; Li, Yun; Li, Bifang; Chen, Wei; Zhang, Qinlei; Hong, Dezhi; Yang, Guowu

    2012-12-26

    Edible bird's nest (EBN) is made of the swiftlets' saliva, which has attracted rather more attention owing to its nutritious and medical properties. Although protein constitutes the main composition and plays an important role in EBN, few studies have focused on the proteomic profile of EBN. The purpose of this study was to produce a proteomic map and clarify common EBN proteins. Liquid-phase isoelectric focusing (LIEF) was combined with two-dimensional electrophoresis (2-DE) for comprehensive analysis of EBN proteins. From 20 to 100 protein spots were detected on 2-DE maps of EBN samples from 15 different sources. The proteins were mainly distributed in four taxa (A, B, C, and D) according to their molecular mass. Taxa A and D both contained common proteins and proteins that may be considered another characteristic of EBN. Taxon A was identified using MALDI-TOF-TOF/MS and found to be homologous to acidic mammalian chitinase-like ( Meleagris gallopavo ), which is in glycosyl hydrolase family 18. PMID:23214475

  6. Mouse Genome-Wide Association Mapping Needs Linkage Analysis to Avoid False-Positive Loci

    PubMed Central

    Manenti, Giacomo; Galvan, Antonella; Pettinicchio, Angela; Trincucci, Gaia; Spada, Elena; Zolin, Anna; Milani, Silvano; Gonzalez-Neira, Anna; Dragani, Tommaso A.

    2009-01-01

    We carried out genome-wide association (GWA) studies in inbred mouse strains characterized for their lung tumor susceptibility phenotypes (spontaneous or urethane-induced) with panels of 12,959 (13K) or 138,793 (140K) single-nucleotide polymorphisms (SNPs). Above the statistical thresholds, we detected only SNP rs3681853 on Chromosome 5, two SNPs in the pulmonary adenoma susceptibility 1 (Pas1) locus, and SNP rs4174648 on Chromosome 16 for spontaneous tumor incidence, urethane-induced tumor incidence, and urethane-induced tumor multiplicity, respectively, with the 13K SNP panel, but only the Pas1 locus with the 140K SNP panel. Haplotype analysis carried out in the latter panel detected four additional loci. Loci reported in previous GWA studies failed to replicate. Genome-wide genetic linkage analysis in urethane-treated (BALB/c×C3H/He)F2, (BALB/c×SWR/J)F2, and (A/J×C3H/He)F2 mice showed that Pas1, but none of the other loci detected previously or herein by GWA, had a significant effect. The Lasc1 gene, identified by GWA as a functional element (Nat. Genet., 38:888–95, 2006), showed no genetic effects in the two independent intercross mouse populations containing both alleles, nor was it expressed in mouse normal lung or lung tumors. Our results indicate that GWA studies in mouse inbred strains can suffer a high rate of false-positive results and that such an approach should be used in conjunction with classical linkage mapping in genetic crosses. PMID:19132132

  7. Genetic Analysis of Cold Tolerance at the Germination and Booting Stages in Rice by Association Mapping

    PubMed Central

    Zhang, Dongling; Li, Jinjie; Xiong, Haiyan; Yu, Jianping; Li, Jilong; Rashid, Muhammad Abdul Rehman; Li, Gangling; Ma, Xiaoding; Cao, Guilan; Han, Longzhi; Li, Zichao

    2015-01-01

    Low temperature affects the rice plants at all stages of growth. It can cause severe seedling injury and male sterility resulting in severe yield losses. Using a mini core collection of 174 Chinese rice accessions and 273 SSR markers we investigated cold tolerance at the germination and booting stages, as well as the underlying genetic bases, by association mapping. Two distinct populations, corresponding to subspecies indica and japonica showed evident differences in cold tolerance and its genetic basis. Both subspecies were sensitive to cold stress at both growth stages. However, japonica was more tolerant than indica at all stages as measured by seedling survival and seed setting. There was a low correlation in cold tolerance between the germination and booting stages. Fifty one quantitative trait loci (QTLs) for cold tolerance were dispersed across all 12 chromosomes; 22 detected at the germination stage and 33 at the booting stage. Eight QTLs were identified by at least two of four measures. About 46% of the QTLs represented new loci. The only QTL shared between indica and japonica for the same measure was qLTSSvR6-2 for SSvR. This implied a complicated mechanism of old tolerance between the two subspecies. According to the relative genotypic effect (RGE) of each genotype for each QTL, we detected 18 positive genotypes and 21 negative genotypes in indica, and 19 positive genotypes and 24 negative genotypes in japonica. In general, the negative effects were much stronger than the positive effects in both subspecies. Markers for QTL with positive effects in one subspecies were shown to be effective for selection of cold tolerance in that subspecies, but not in the other subspecies. QTL with strong negative effects on cold tolerance should be avoided during MAS breeding so as to not cancel the effect of favorable QTL at other loci. PMID:25790128

  8. 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).

  9. 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.

  10. Reduced density and nest survival of ground-nesting songbirds relative to earthworm invasions in northern hardwood forests.

    PubMed

    Loss, Scott R; Blair, Robert B

    2011-10-01

    European earthworms (Lumbricus spp.) are spreading into previously earthworm-free forests in the United States and Canada and causing substantial changes, including homogenization of soil structure, removal of the litter layer, and reduction in arthropod abundance and species richness of understory plants. Whether these changes affect songbirds that nest and forage on the forest floor is unknown. In stands with and without earthworms in the Chequamegon-Nicolet National Forest, Wisconsin (U.S.A.), we surveyed for, monitored nests of, and measured attributes of habitat of Ovenbirds (Seiurus aurocapillus) and Hermit Thrushes (Catharus guttatus), both ground-dwelling songbirds, and we sampled earthworms at survey points and nests. Bird surveys indicated significantly lower densities of Ovenbirds and Hermit Thrushes in relation to Lumbricus invasions at survey point and stand extents (3.1 and 15-20 ha, respectively). Modeling of Ovenbird nest survival (i.e., the probability that nestlings successfully fledge) indicated that lower survival probabilities were associated with increased sedge cover and decreased litter depth, factors that are related to Lumbricus invasions, possibly due to reduced nest concealment or arthropod abundance. Our findings provide compelling evidence that earthworm invasions may be associated with local declines of forest songbird populations. PMID:21797927

  11. The genetics of winterhardiness in barley: Perspectives from genome-wide association mapping

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Winterhardiness is a complex trait that involves low temperature (LT) tolerance, vernalization sensitivity and photoperiod sensitivity. Quantitative trait loci (QTL) for these traits were first identified using biparental mapping populations; candidate genes for all loci have since been identified a...

  12. 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.

  13. Functionally Relevant Microsatellite Markers From Chickpea Transcription Factor Genes for Efficient Genotyping Applications and Trait Association Mapping

    PubMed Central

    Kujur, Alice; Bajaj, Deepak; Saxena, Maneesha S.; Tripathi, Shailesh; Upadhyaya, Hari D.; Gowda, C.L.L.; Singh, Sube; Jain, Mukesh; Tyagi, Akhilesh K.; Parida, Swarup K.

    2013-01-01

    We developed 1108 transcription factor gene-derived microsatellite (TFGMS) and 161 transcription factor functional domain-associated microsatellite (TFFDMS) markers from 707 TFs of chickpea. The robust amplification efficiency (96.5%) and high intra-specific polymorphic potential (34%) detected by markers suggest their immense utilities in efficient large-scale genotyping applications, including construction of both physical and functional transcript maps and understanding population structure. Candidate gene-based association analysis revealed strong genetic association of TFFDMS markers with three major seed and pod traits. Further, TFGMS markers in the 5′ untranslated regions of TF genes showing differential expression during seed development had higher trait association potential. The significance of TFFDMS markers was demonstrated by correlating their allelic variation with amino acid sequence expansion/contraction in the functional domain and alteration of secondary protein structure encoded by genes. The seed weight-associated markers were validated through traditional bi-parental genetic mapping. The determination of gene-specific linkage disequilibrium (LD) patterns in desi and kabuli based on single nucleotide polymorphism-microsatellite marker haplotypes revealed extended LD decay, enhanced LD resolution and trait association potential of genes. The evolutionary history of a strong seed-size/weight-associated TF based on natural variation and haplotype sharing among desi, kabuli and wild unravelled useful information having implication for seed-size trait evolution during chickpea domestication. PMID:23633531

  14. 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

  15. 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.

  16. 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

  17. Fine mapping and association analysis of a quantitative trait locus for milk production traits on Bos taurus autosome 4.

    PubMed

    Rincón, G; Islas-Trejo, A; Casellas, J; Ronin, Y; Soller, M; Lipkin, E; Medrano, J F

    2009-02-01

    To fine map a quantitative trait locus (QTL) affecting milk production traits previously associated with microsatellite RM188, we implemented an interval mapping analysis by using microsatellite markers in a large Israeli Holstein half-sib sire family, and linkage disequilibrium (LD) mapping in a large set of US Holstein bulls. Interval mapping located the target QTL to the near vicinity of RM188. For the LD mapping, we identified 42 single nucleotide polymorphisms (SNP) in 15 genes in a 12-Mb region on bovine chromosome 4. A total of 24 tag SNP were genotyped in 882 bulls belonging to the University of California Davis archival collection of Holstein bull DNA samples with predicted transmitted ability phenotypes. Marker-to-marker LD analysis revealed 2 LD blocks, with intrablock r(2) values of 0.10 and 0.46, respectively; outside the blocks, r(2) values ranged from 0.002 to 0.23. A standard additive/dominance model using the generalized linear model procedure of SAS and the regression module of HelixTree software were used to test marker-trait associations. Single nucleotide polymorphism 9 on ARL4A, SNP10 on XR_027435.1, SNP12 on ETV1, SNP21 on SNX13, and SNP24 were significantly associated with milk production traits. We propose the interval encompassing ARL4A and SNX13 genes as a candidate region in bovine chromosome 4 for a concordant QTL related to milk protein traits in dairy cattle. Functional studies are needed to confirm this result. PMID:19164688

  18. 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

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. 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

  5. Plants use macronutrients accumulated in leaf-cutting ant nests

    PubMed Central

    da S.L Sternberg, Leonel; Pinzon, Maria Camila; Moreira, Marcelo Z; Moutinho, Paulo; Rojas, Enith I; Herre, Edward Allen

    2006-01-01

    Leaf-cutting ants (Atta spp.) are known for their extensive defoliation in neo-tropical forests and savannahs. Debate about the costs and benefits of their activities has been largely dominated by their detrimental effects on agriculture and agroforestry. However, the large accumulation of nutrients and changes in soil properties near their nests might benefit plants growing near them. Here, we test whether trees use nutrients that accumulate in debris piles near, or refuse chambers within, leaf-cutting ant nests. At two tropical sites (a moist tropical forest site in Panama and a savannah site in Brazil), we fed leaves labelled with the stable isotope 15N to two species of leaf-cutting ants (Atta colombica and Atta laevigata) and traced the stable isotope label in plants surrounding the two nests. Thus, we show that plants in both sites access resources associated with Atta nests. In addition, leaf tissue of trees near the nests labelled with 15N had significantly higher calcium concentrations than those of distal, unlabelled conspecifics. It has been documented that calcium is a limiting macronutrient in tropical forests and savannahs. Atta may thus play an important ecological role through their long-distance transport, redistribution and concentration of critical macronutrients. PMID:17164194

  6. Nested-cone transformer antenna

    DOEpatents

    Ekdahl, Carl A.

    1991-01-01

    A plurality of conical transmission lines are concentrically nested to form n output antenna for pulsed-power, radio-frequency, and microwave sources. The diverging conical conductors enable a high power input density across a bulk dielectric to be reduced below a breakdown power density at the antenna interface with the transmitting medium. The plurality of cones maintain a spacing between conductors which minimizes the generation of high order modes between the conductors. Further, the power input feeds are isolated at the input while enabling the output electromagnetic waves to add at the transmission interface. Thus, very large power signals from a pulse rf, or microwave source can be radiated.

  7. DNest3: Diffusive Nested Sampling

    NASA Astrophysics Data System (ADS)

    Brewer, Brendon

    2016-04-01

    DNest3 is a C++ implementation of Diffusive Nested Sampling (ascl:1010.029), a Markov Chain Monte Carlo (MCMC) algorithm for Bayesian Inference and Statistical Mechanics. Relative to older DNest versions, DNest3 has improved performance (in terms of the sampling overhead, likelihood evaluations still dominate in general) and is cleaner code: implementing new models should be easier than it was before. In addition, DNest3 is multi-threaded, so one can run multiple MCMC walkers at the same time, and the results will be combined together.

  8. Concentric Nested Toroidal Inflatable Structures

    NASA Technical Reports Server (NTRS)

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

    2010-01-01

    Assemblies comprising multiple limited- height toroidal inflatable structures nested in a concentric arrangement have been invented to obtain more design flexibility than can be obtained in single taller, wider toroidal inflatable structures (see figure). Originally intended for use as containers for habitats for humans in outer space or on remote planets, these and related prior inflatable structures could also be useful on Earth as lightweight, compactly stowable, portable special-purpose buildings that could be transported to remote locations and there inflated to full size and shape. In the case of a single inflatable toroidal structure, one important source of lack of design flexibility is the fact that an increase in outer diameter (which is sometimes desired) is necessarily accompanied by an increase in height (which is sometimes undesired). Increases in diameter and height can also cause difficulty in utilization of the resulting larger volume, in that it can become necessary to partition the volume by means of walls and floors, and features (e.g., stairs or ladders) must be added to enable vertical movement between floors. Moreover, ascending and descending between floors in a gravitational environment could pose unacceptable difficulty for the inhabitants under some circumstances. Another source of lack of design flexibility in a single toroidal inflatable structure is that for a given inflation pressure, an increase in the outer diameter of the structure necessarily entails an increase in the maximum stress in the structure. Because it is necessary to keep the maximum stress within the load-bearing capability of the structural materials, consistent with other aspects of the design, this may translate to a limit on the outer diameter. In an assembly comprising concentric nested toroidal structures, an increase in outer diameter does not necessarily entail an increase in height or a maximum stress in excess of the load-bearing capability of the structural

  9. Nested-cone transformer antenna

    DOEpatents

    Ekdahl, C.A.

    1991-05-28

    A plurality of conical transmission lines are concentrically nested to form an output antenna for pulsed-power, radio-frequency, and microwave sources. The diverging conical conductors enable a high power input density across a bulk dielectric to be reduced below a breakdown power density at the antenna interface with the transmitting medium. The plurality of cones maintain a spacing between conductors which minimizes the generation of high order modes between the conductors. Further, the power input feeds are isolated at the input while enabling the output electromagnetic waves to add at the transmission interface. Thus, very large power signals from a pulse rf, or microwave source can be radiated. 6 figures.

  10. Nested and Dynamic Contract Boundaries

    NASA Astrophysics Data System (ADS)

    Strickland, T. Stephen; Felleisen, Matthias

    Previous work on software contracts assumes fixed and statically known boundaries between the parties to a contract. Implementations of contract monitoring systems rely on this assumption to explain the nature of contract violations and to assign blame to violators. In this paper, we explain how to implement arbitrary, nested, and dynamic contract boundaries with two examples. First, we add nestable contract regions to a static, first-order module system. Second, we show that even a dynamic, higher-order, and hierarchical module system can be equipped with software contracts that support precise blame assignment.

  11. Genetic Architecture of Aluminum Tolerance in Rice (Oryza sativa) Determined through Genome-Wide Association Analysis and QTL Mapping

    PubMed Central

    Famoso, Adam N.; Zhao, Keyan; Clark, Randy T.; Tung, Chih-Wei; Wright, Mark H.; Bustamante, Carlos; Kochian, Leon V.; McCouch, Susan R.

    2011-01-01

    Aluminum (Al) toxicity is a primary limitation to crop productivity on acid soils, and rice has been demonstrated to be significantly more Al tolerant than other cereal crops. However, the mechanisms of rice Al tolerance are largely unknown, and no genes underlying natural variation have been reported. We screened 383 diverse rice accessions, conducted a genome-wide association (GWA) study, and conducted QTL mapping in two bi-parental populations using three estimates of Al tolerance based on root growth. Subpopulation structure explained 57% of the phenotypic variation, and the mean Al tolerance in Japonica was twice that of Indica. Forty-eight regions associated with Al tolerance were identified by GWA analysis, most of which were subpopulation-specific. Four of these regions co-localized with a priori candidate genes, and two highly significant regions co-localized with previously identified QTLs. Three regions corresponding to induced Al-sensitive rice mutants (ART1, STAR2, Nrat1) were identified through bi-parental QTL mapping or GWA to be involved in natural variation for Al tolerance. Haplotype analysis around the Nrat1 gene identified susceptible and tolerant haplotypes explaining 40% of the Al tolerance variation within the aus subpopulation, and sequence analysis of Nrat1 identified a trio of non-synonymous mutations predictive of Al sensitivity in our diversity panel. GWA analysis discovered more phenotype–genotype associations and provided higher resolution, but QTL mapping identified critical rare and/or subpopulation-specific alleles not detected by GWA analysis. Mapping using Indica/Japonica populations identified QTLs associated with transgressive variation where alleles from a susceptible aus or indica parent enhanced Al tolerance in a tolerant Japonica background. This work supports the hypothesis that selectively introgressing alleles across subpopulations is an efficient approach for trait enhancement in plant breeding programs and

  12. Genome-wide survey of Arabidopsis natural variation in downy mildew resistance using combined association and linkage mapping

    PubMed Central

    Nemri, Adnane; Atwell, Susanna; Tarone, Aaron M.; Huang, Yu S.; Zhao, Keyan; Studholme, David J.; Nordborg, Magnus; Jones, Jonathan D. G.

    2010-01-01

    The model plant Arabidopsis thaliana exhibits extensive natural variation in resistance to parasites. Immunity is often conferred by resistance (R) genes that permit recognition of specific races of a disease. The number of such R genes and their distribution are poorly understood. In this study, we investigated the basis for resistance to the downy mildew agent Hyaloperonospora arabidopsidis ex parasitica (Hpa) in a global sample of A. thaliana. We implemented a combined genome-wide mapping of resistance using populations of recombinant inbred lines and a collection of wild A. thaliana accessions. We tested the interaction between 96 host genotypes collected worldwide and five strains of Hpa. Then, a fraction of the species-wide resistance was genetically dissected using six recently constructed populations of recombinant inbred lines. We found that resistance is usually governed by single dominant R genes that are concentrated in four genomic regions only. We show that association genetics of resistance to diseases such as downy mildew enables increased mapping resolution from quantitative trait loci interval to candidate gene level. Association patterns in quantitative trait loci intervals indicate that the pool of A. thaliana resistance sources against the tested Hpa isolates may be predominantly confined to six RPP (Resistance to Hpa) loci isolated in previous studies. Our results suggest that combining association and linkage mapping could accelerate resistance gene discovery in plants. PMID:20479233

  13. Phase transitions in coupled map lattices and in associated probabilistic cellular automata.

    PubMed

    Just, Wolfram

    2006-10-01

    Analytical tools are applied to investigate piecewise linear coupled map lattices in terms of probabilistic cellular automata. The so-called disorder condition of probabilistic cellular automata is closely related with attracting sets in coupled map lattices. The importance of this condition for the suppression of phase transitions is illustrated by spatially one-dimensional systems. Invariant densities and temporal correlations are calculated explicitly. Ising type phase transitions are found for one-dimensional coupled map lattices acting on repelling sets and for a spatially two-dimensional Miller-Huse-like system with stable long time dynamics. Critical exponents are calculated within a finite size scaling approach. The relevance of detailed balance of the resulting probabilistic cellular automaton for the critical behavior is pointed out. PMID:17155155

  14. Interference Lattice-based Loop Nest Tilings for Stencil Computations

    NASA Technical Reports Server (NTRS)

    VanderWijngaart, Rob F.; Frumkin, Michael

    2000-01-01

    A common method for improving performance of stencil operations on structured multi-dimensional discretization grids is loop tiling. Tile shapes and sizes are usually determined heuristically, based on the size of the primary data cache. We provide a lower bound on the numbers of cache misses that must be incurred by any tiling, and a close achievable bound using a particular tiling based on the grid interference lattice. The latter tiling is used to derive highly efficient loop orderings. The total number of cache misses of a code is the sum of (necessary) cold misses and misses caused by elements being dropped from the cache between successive loads (replacement misses). Maximizing temporal locality is equivalent to minimizing replacement misses. Temporal locality of loop nests implementing stencil operations is optimized by tilings that avoid data conflicts. We divide the loop nest iteration space into conflict-free tiles, derived from the cache miss equation. The tiling involves the definition of the grid interference lattice an equivalence class of grid points whose images in main memory map to the same location in the cache-and the construction of a special basis for the lattice. Conflicts only occur on the boundaries of the tiles, unless the tiles are too thin. We show that the surface area of the tiles is bounded for grids of any dimensionality, and for caches of any associativity, provided the eccentricity of the fundamental parallelepiped (the tile spanned by the basis) of the lattice is bounded. Eccentricity is determined by two factors, aspect ratio and skewness. The aspect ratio of the parallelepiped can be bounded by appropriate array padding. The skewness can be bounded by the choice of a proper basis. Combining these two strategies ensures that pathologically thin tiles are avoided. They do not, however, minimize replacement misses per se. The reason is that tile visitation order influences the number of data conflicts on the tile boundaries. If two

  15. Construction of Genetic Linkage Maps and Comparative Genome Analysis of Catfish Using Gene-Associated Markers

    PubMed Central

    Kucuktas, Huseyin; Wang, Shaolin; Li, Ping; He, Chongbo; Xu, Peng; Sha, Zhenxia; Liu, Hong; Jiang, Yanliang; Baoprasertkul, Puttharat; Somridhivej, Benjaporn; Wang, Yaping; Abernathy, Jason; Guo, Ximing; Liu, Lei; Muir, William; Liu, Zhanjiang

    2009-01-01

    A genetic linkage map of the channel catfish genome (N = 29) was constructed using EST-based microsatellite and single nucleotide polymorphism (SNP) markers in an interspecific reference family. A total of 413 microsatellites and 125 SNP markers were polymorphic in the reference family. Linkage analysis using JoinMap 4.0 allowed mapping of 331 markers (259 microsatellites and 72 SNPs) to 29 linkage groups. Each linkage group contained 3–18 markers. The largest linkage group contained 18 markers and spanned 131.2 cM, while the smallest linkage group contained 14 markers and spanned only 7.9 cM. The linkage map covered a genetic distance of 1811 cM with an average marker interval of 6.0 cM. Sex-specific maps were also constructed; the recombination rate for females was 1.6 times higher than that for males. Putative conserved syntenies between catfish and zebrafish, medaka, and Tetraodon were established, but the overall levels of genome rearrangements were high among the teleost genomes. This study represents a first-generation linkage map constructed by using EST-derived microsatellites and SNPs, laying a framework for large-scale comparative genome analysis in catfish. The conserved syntenies identified here between the catfish and the three model fish species should facilitate structural genome analysis and evolutionary studies, but more importantly should facilitate functional inference of catfish genes. Given that determination of gene functions is difficult in nonmodel species such as catfish, functional genome analysis will have to rely heavily on the establishment of orthologies from model species. PMID:19171943

  16. Quantification of voxel-wise total fibre density: Investigating the problems associated with track-count mapping.

    PubMed

    Calamante, Fernando; Smith, Robert E; Tournier, Jacques-Donald; Raffelt, David; Connelly, Alan

    2015-08-15

    A biological parameter that would be valuable to be able to extract from diffusion MRI data is the local white matter axonal density. Track-density imaging (TDI) has been used as if it could provide such a measure; however, this has been the subject of controversy, primarily due to the fact that track-count quantitation is highly sensitive to tracking biases and errors. The spherical-deconvolution informed filtering of tractograms (SIFT) post-processing method was recently introduced to minimise tractography biases, and thus provides a more biologically meaningful measure that could be used in track-count mapping (i.e. TDI following SIFT). The TDI intensity following SIFT ideally corresponds to the orientational average of the fibre orientation distribution (FOD), which corresponds to the total Apparent Fibre Density (AFDtotal) within the AFD framework; in fact, AFDtotal provides a direct measure of local fibre density at native resolution that does not rely on fibre-tracking. In this study, we demonstrate problems associated with quantitative TDI investigations, which can be avoided by using SIFT processing or directly by using AFDtotal maps. We also characterise the intra- and inter-subject reproducibility of TDI maps (with and without SIFT pre-processing) and AFDtotal maps. It is shown that SIFT improves the quantitative characteristics of TDI, but is still vastly inferior to the properties of the AFDtotal parameter itself, because the latter does not require tracking. While standard TDI might be preferable in applications when high anatomical contrast is required, particularly when combined with super-resolution, for voxel-wise quantitation of total tract density (i.e. without tract orientation information) at native resolution, the total AFD maps are preferable to TDI or other related track-count maps. Regardless of the track-count measure, it should be noted that all of these voxel-averaged approaches discard important information that is retained in fibre

  17. Nest Mosquito Trap quantifies contact rates between nesting birds and mosquitoes

    PubMed Central

    Caillouët, Kevin A.; Riggan, Anna E.; Rider, Mark; Bulluck, Lesley P.

    2012-01-01

    Accurate estimates of host-vector contact rates are required for precise determination of arbovirus transmission intensity. We designed and tested a novel mosquito collection device, the Nest Mosquito Trap (NMT), to collect mosquitoes as they attempt to feed on unrestrained nesting birds in artificial nest boxes. In the laboratory, the NMT collected nearly one-third of the mosquitoes introduced to the nest boxes. We then used these laboratory data to estimate our capture efficiency of field-collected bird-seeking mosquitoes collected over 66 trap nights. We estimated that 7.5 mosquitoes per trap night attempted to feed on nesting birds in artificial nest boxes. Presence of the NMT did not have a negative effect on avian nest success when compared to occupied nest boxes that were not sampled with the trap. Future studies using the NMT may elucidate the role of nestlings in arbovirus transmission and further refine estimates of nesting bird and vector contact rates. PMID:22548555

  18. Nest guarding from observation blinds: strategy for improving Puerto Rican parrot nest success

    USGS Publications Warehouse

    Lindsey, G.D.

    1992-01-01

    The effectiveness of 17 yr of nestguarding from observation blinds for increasing reproductive success of the endangered Puerto Rican Parrot (Amazona vittata) is described. As personnel and time allowed, active nests were guarded part-time during the nest site exploration and selection s stage of the breeding cycle, and part-time to full-time when a nest contained eggs or chicks. Biologists identified nine categories of threat to the success of parrot nests. Since 1973, a minimum of 20 nests, which otherwise would have failed, successfully produced fledglings as a direct result of nest guarding and intervention. Nest success averaged 66% with nest guarding compared to an estimated 38% without guarding. Nest guarding from blinds can help maintain a wild population of a critically endangered species while other management techniques are being developed to stimulate population growth.

  19. Studies on nest construction and nest microclimate of the Baya weaver, Ploceus philippinus (Linn.).

    PubMed

    Asokan, S; Ali, A Mohamed Samsoor; Nagarajan, R

    2008-05-01

    The nest construction pattern at different stages of nest and variations in the nest microclimate, i.e., temperature and light intensity were assessed in different nests of Baya weaver (Ploceus philippinus) between November 2002 and March 2003 in Nagapattinam and Tiruvarur District of Tamil Nadu, India. The Baya weaver constructed nests in palm (Borassus flabellifer), coconut (Cocos nucifera) and date palm trees (Phoneix psuilla) and majority of the nests were found in the solitary palm. The male bird only involved in the construction and took 18 days to construct a single nest. The birds spent different amount of working hours (in terms of days) for completing various stages of nests viz., wad, ring and helmet stage and in which the 'helmet stage took a maximum of eight days. Furthermore, totally eight active nests were selected and once in a week the variations in the nest microclimate was investigated with reference to atmospheric temperature and light intensity (two active nests) across day throughout the study period. The mean temperature of the nests ranged from 25 degrees C to 29 degrees C and light intensity varied between 25 Lux and 625 Lux. The analysis of variance (ANOVA and ANCOVA) indicated that the nest microclimate varied among the nests in different hr of a day PMID:18972698

  20. Formalizing narratives using nested circumscription

    SciTech Connect

    Baral, C.; Gabaldon, A.; Provetti, A.

    1996-12-31

    The representation of narratives of actions and observations is a current issue in Knowledge Representation, where traditional plan-oriented treatments of action seem to fall short. To address narratives, Pinto and Reiter have extended Situation Calculus axioms, Kowalski and Sergot have introduced the Event Calculus in Logic Programming, and Baral et al. have defined the specification language L which allows to express actual and hypothetical situations in a uniform setting. The L entailment relation can formalize several forms of reasoning about actions and change. In this paper we illustrate a translation of L theories into Nested Abnormality Theories, a novel form of circumscription. The proof of soundness and completeness of the translation is the main technical result of the paper, but attention is also devoted to the features of Nested Abnormality Theories to capture commonsense reasoning in general and to clarify which assumptions a logical formalization forces upon a domain. These results also help clarifying the relationship between L and other recent circumscriptive formalization for narratives, such as Miller and Shanahan`s.

  1. Efficient Mapping of Plant Height Quantitative Trait Loci in a Sorghum Association Population With Introgressed Dwarfing Genes

    PubMed Central

    Brown, Patrick J.; Rooney, William L.; Franks, Cleve; Kresovich, Stephen

    2008-01-01

    Of the four major dwarfing genes described in sorghum, only Dw3 has been cloned. We used association mapping to characterize the phenotypic effects of the dw3 mutation and to fine map a second, epistatic dwarfing QTL on sorghum chromosome 9 (Sb-HT9.1). Our panel of 378 sorghum inbreds includes 230 sorghum conversion (SC) lines, which are exotic lines that have been introgressed with dwarfing quantitative trait loci (QTL) from a common parent. The causal mutation in dw3 associates with reduced lower internode length and an elongation of the apex, consistent with its role as an auxin efflux carrier. Lines carrying the dw3 mutation display high haplotype homozygosity over several megabases in the Dw3 region, but most markers linked to Dw3 do not associate significantly with plant height due to allele sharing between Dw3 and dw3 individuals. Using markers with a high mutation rate and the dw3 mutation as an interaction term, significant trait associations were detected across a 7-Mb region around Sb-HT9.1, largely due to higher detection power in the SC lines. Conversely, the likely QTL interval for Sb-HT9.1 was reduced to ∼100 kb, demonstrating that the unique structure of this association panel provides both power and resolution for a genomewide scan. PMID:18757942

  2. Quantitative trait loci for rice blast resistance detected in a local rice breeding population by genome-wide association mapping

    PubMed Central

    Shinada, Hiroshi; Yamamoto, Toshio; Sato, Hirokazu; Yamamoto, Eiji; Hori, Kiyosumi; Yonemaru, Junichi; Sato, Takashi; Fujino, Kenji

    2015-01-01

    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. PMID:26719741

  3. A somatic MAP3K3 mutation is associated with verrucous venous malformation.

    PubMed

    Couto, Javier A; Vivero, Matthew P; Kozakewich, Harry P W; Taghinia, Amir H; Mulliken, John B; Warman, Matthew L; Greene, Arin K

    2015-03-01

    Verrucous venous malformation (VVM), also called "verrucous hemangioma," is a non-hereditary, congenital, vascular anomaly comprised of aberrant clusters of malformed dermal venule-like channels underlying hyperkeratotic skin. We tested the hypothesis that VVM lesions arise as a consequence of a somatic mutation. We performed whole-exome sequencing (WES) on VVM tissue from six unrelated individuals and looked for somatic mutations affecting the same gene in specimens from multiple persons. We observed mosaicism for a missense mutation (NM_002401.3, c.1323C>G; NP_002392, p.Iso441Met) in mitogen-activated protein kinase kinase kinase 3 (MAP3K3) in three of six individuals. We confirmed the presence of this mutation via droplet digital PCR (ddPCR) in the three subjects and found the mutation in three additional specimens from another four participants. Mutant allele frequencies ranged from 6% to 19% in affected tissue. We did not observe this mutant allele in unaffected tissue or in affected tissue from individuals with other types of vascular anomalies. Studies using global and conditional Map3k3 knockout mice have previously implicated MAP3K3 in vascular development. MAP3K3 dysfunction probably causes VVM in humans. PMID:25728774

  4. In-silico mapping of quantitative trait loci for lactation-associated traits in inbred mice

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Significant variation exists for fecundity and maternal nurturing ability in inbred mice. Classical gene mapping approaches in mice have identified several quantitative trait loci (QTL) that account for some this variation. Current studies in our laboratory are aimed at identifying QTL genes that un...

  5. Single molecule quantitation and sequencing of rare translocations using microfluidic nested digital PCR.

    PubMed

    Shuga, Joe; Zeng, Yong; Novak, Richard; Lan, Qing; Tang, Xiaojiang; Rothman, Nathaniel; Vermeulen, Roel; Li, Laiyu; Hubbard, Alan; Zhang, Luoping; Mathies, Richard A; Smith, Martyn T

    2013-09-01

    Cancers are heterogeneous and genetically unstable. New methods are needed that provide the sensitivity and specificity to query single cells at the genetic loci that drive cancer progression, thereby enabling researchers to study the progression of individual tumors. Here, we report the development and application of a bead-based hemi-nested microfluidic droplet digital PCR (dPCR) technology to achieve 'quantitative' measurement and single-molecule sequencing of somatically acquired carcinogenic translocations at extremely low levels (<10(-6)) in healthy subjects. We use this technique in our healthy study population to determine the overall concentration of the t(14;18) translocation, which is strongly associated with follicular lymphoma. The nested dPCR approach improves the detection limit to 1×10(-7) or lower while maintaining the analysis efficiency and specificity. Further, the bead-based dPCR enabled us to isolate and quantify the relative amounts of the various clonal forms of t(14;18) translocation in these subjects, and the single-molecule sensitivity and resolution of dPCR led to the discovery of new clonal forms of t(14;18) that were otherwise masked by the conventional quantitative PCR measurements. In this manner, we created a quantitative map for this carcinogenic mutation in this healthy population and identified the positions on chromosomes 14 and 18 where the vast majority of these t(14;18) events occur. PMID:23873959

  6. Single molecule quantitation and sequencing of rare translocations using microfluidic nested digital PCR

    PubMed Central

    Shuga, Joe; Zeng, Yong; Novak, Richard; Lan, Qing; Tang, Xiaojiang; Rothman, Nathaniel; Vermeulen, Roel; Li, Laiyu; Hubbard, Alan; Zhang, Luoping; Mathies, Richard A.; Smith, Martyn T.

    2013-01-01

    Cancers are heterogeneous and genetically unstable. New methods are needed that provide the sensitivity and specificity to query single cells at the genetic loci that drive cancer progression, thereby enabling researchers to study the progression of individual tumors. Here, we report the development and application of a bead-based hemi-nested microfluidic droplet digital PCR (dPCR) technology to achieve ‘quantitative’ measurement and single-molecule sequencing of somatically acquired carcinogenic translocations at extremely low levels (<10−6) in healthy subjects. We use this technique in our healthy study population to determine the overall concentration of the t(14;18) translocation, which is strongly associated with follicular lymphoma. The nested dPCR approach improves the detection limit to 1 × 10−7 or lower while maintaining the analysis efficiency and specificity. Further, the bead-based dPCR enabled us to isolate and quantify the relative amounts of the various clonal forms of t(14;18) translocation in these subjects, and the single-molecule sensitivity and resolution of dPCR led to the discovery of new clonal forms of t(14;18) that were otherwise masked by the conventional quantitative PCR measurements. In this manner, we created a quantitative map for this carcinogenic mutation in this healthy population and identified the positions on chromosomes 14 and 18 where the vast majority of these t(14;18) events occur. PMID:23873959

  7. Fine mapping of the EDA gene: a translocation breakpoint is associated with a CpG island that is transcribed.

    PubMed Central

    Srivastava, A. K.; Montonen, O.; Saarialho-Kere, U.; Chen, E.; Baybayan, P.; Pispa, J.; Limon, J.; Schlessinger, D.; Kere, J.

    1996-01-01

    In order to identify the gene for human X-linked anhidrotic ectodermal dysplasia (EDA), a translocation breakpoint in a female with t(X;1)(q13.1;p36.3) and EDA (patient AK) was finely mapped. The EDA region contains five groups of rare-cutter restriction sites that define CpG islands. The two more centromeric of these islands are associated with transcripts of 3.5 kb and 1.8 kb. The third CpG island maps within <1 kb of the translocation breakpoint in patient AK, as indicated by a genomic rearrangement, and approximately 100 kb centromeric from another previously mapped translocation breakpoint (patient AnLy). Northern analysis with a probe from this CpG island detected an approximately 6-kb mRNA in several fetal tissues tested. An extended YAC contig of 1,200 kb with an average of fivefold coverage was constructed. The two most telomeric CpG islands map 350 kb telomeric of the two translocations. Taken together, the results suggest that the CpG island just proximal of the AK translocation breakpoint lies at the 5' end of a candidate gene for EDA. Images Figure 2 Figure 3 Figure 4 PMID:8554048

  8. 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

  9. 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

  10. Dense mapping of MYH9 localizes the strongest kidney disease associations to the region of introns 13 to 15

    PubMed Central

    Nelson, George W.; Freedman, Barry I.; Bowden, Donald W.; Langefeld, Carl D.; An, Ping; Hicks, Pamela J.; Bostrom, Meredith A.; Johnson, Randall C.; Kopp, Jeffrey B.; Winkler, Cheryl A.

    2010-01-01

    Admixture mapping recently identified MYH9 as a susceptibility gene for idiopathic focal segmental glomerulosclerosis (FSGS), HIV-associated nephropathy (HIVAN) and end-stage kidney disease attributed to hypertension (H-ESKD) in African Americans (AA). MYH9 encodes the heavy chain of non-muscle myosin IIA, a cellular motor involved in motility. A haplotype and its tagging SNPs spanning introns 12–23 were most strongly associated with kidney disease (OR 2–7; P < 10−8, recessive). To narrow the region of association and identify potential causal variation, we performed a dense-mapping study using 79 MYH9 SNPs in AA populations with FSGS, HIVAN and H-ESKD (typed for a subset of 46 SNPs), for a total of 2496 cases and controls. The strongest associations were for correlated SNPs rs5750250, rs2413396 and rs5750248 in introns 13, 14 and 15, a region of 5.6 kb. Rs5750250 showed OR 5.0, 8.0 and 2.8; P = 2 × 10−17, 2 × 10−10 and 3 × 10−22, respectively, for FSGS, HIVAN and H-ESKD; OR 5.7; P = 9 × 10−27 for combined FSGS and HIVAN, recessive. An independent association was observed for rs11912763 in intron 33. Neither the highly associated SNPs nor the results of resequencing MYH9 in 40 HIVAN or FSGS cases and controls revealed non-synonymous changes that could account for the disease associations. Rs2413396 and one of the highly associated SNPs in intron 23, rs4821480, are predicted splicing motif modifiers. Rs5750250 combined with rs11912763 had receiver operator characteristic (ROC) C statistics of 0.80, 0.73 and 0.65 for HIVAN, FSGS and H-ESKD, respectively, allowing prediction of genetic risk by typing two SNPs. PMID:20124285

  11. Sunflower (Helianthus annuus) pollination in California's Central Valley is limited by native bee nest site location.

    PubMed

    Sardiñas, Hillary S; Tom, Kathleen; Ponisio, Lauren Catherine; Rominger, Andrew; Kremen, Claire

    2016-03-01

    The delivery of ecosystem services by mobile organisms depends on the distribution of those organisms, which is, in turn, affected by resources at local and landscape scales. Pollinator-dependent crops rely on mobile animals like bees for crop production, and the spatial relationship between floral resources and nest location for these central-place foragers influences the delivery of pollination services. Current models that map pollination coverage in agricultural regions utilize landscape-level estimates of floral availability and nesting incidence inferred from expert opinion, rather than direct assessments. Foraging distance is often derived from proxies of bee body size, rather than direct measurements of foraging that account for behavioral responses to floral resource type and distribution. The lack of direct measurements of nesting incidence and foraging distances may lead to inaccurate mapping of pollination services. We examined the role of local-scale floral resource presence from hedgerow plantings on nest incidence of ground-nesting bees in field margins and within monoculture, conventionally managed sunflower fields in California's Central Valley. We tracked bee movement into fields using fluorescent powder. We then used these data to simulate the distribution of pollination services within a crop field. Contrary to expert opinion, we found that ground-nesting native bees nested both in fields and edges, though nesting rates declined with distance into field. Further, we detected no effect of field-margin floral enhancements on nesting. We found evidence of an exponential decay rate of bee movement into fields, indicating that foraging predominantly occurred in less than 1% of medium-sized bees' predicted typical foraging range. Although we found native bees nesting within agricultural fields, their restricted foraging movements likely centralize pollination near nest sites. Our data thus predict a heterogeneous distribution of pollination services

  12. Selection of anthropogenic features and vegetation characteristics by nesting Common Ravens in the sagebrush ecosystem

    USGS Publications Warehouse

    Howe, Kristy B.; Coates, Peter S.; Delehanty, David J.

    2014-01-01

    Common Raven (Corvus corax) numbers and distribution are increasing throughout the sagebrush steppe, influencing avian communities in complex ways. Anthropogenic structures are thought to increase raven populations by providing food and nesting subsidies, which is cause for concern because ravens are important nest predators of sensitive species, including Greater Sage-Grouse (Centrocercus urophasianus). During 2007–2009, we located raven nests in southeastern Idaho and conducted a resource selection analysis. We measured variables at multiple spatial scales for 72 unique nest locations, including landscape-level vegetation characteristics and anthropogenic structures. Using generalized linear mixed models and an information-theoretic approach, we found a 31% decrease in the odds of nesting by ravens for every 1 km increase in distance away from a transmission line. Furthermore, a 100-m increase in distance away from the edge of two different land cover types decreased the odds of nesting by 20%, and an increase in the amount of edge by 1 km within an area of 102.1 ha centered on the nest increased the odds of nesting by 49%. A post hoc analysis revealed that ravens were most likely to nest near edges of adjoining big sagebrush (Artemisia tridentata) and land cover types that were associated with direct human disturbance or fire. These findings contribute to our understanding of raven expansion into rural environments and could be used to make better-informed conservation decisions, especially in the face of increasing renewable energy development.

  13. Leatherback nests increasing significantly in Florida, USA; trends assessed over 30 years using multilevel modeling.

    PubMed

    Stewart, Kelly; Sims, Michelle; Meylan, Anne; Witherington, Blair; Brost, Beth; Crowder, Larry B

    2011-01-01

    Understanding population status for endangered species is critical to developing and evaluating recovery plans mandated by the Endangered Species Act. For sea turtles, changes in abundance are difficult to detect because most life stages occur in the water. Currently, nest counts are the most reliable way of assessing trends. We determined the rate of growth for leatherback turtle (Dermochelys coriacea) nest numbers in Florida (USA) using a multilevel Poisson regression. We modeled nest counts from 68 beaches over 30 years and, using beach-level covariates (including latitude), we allowed for partial pooling of information between neighboring beaches. This modeling approach is ideal for nest count data because it recognizes the hierarchical structure of the data while incorporating variables related to survey effort. Nesting has increased at all 68 beaches in Florida, with trends ranging from 3.1% to 16.3% per year. Overall, across the state, the number of nests has been increasing by 10.2% per year since 1979. Despite being a small population (probably < 1000 individuals), this nesting population may help achieve objectives in the federal recovery plan. This exponential growth rate mirrors trends observed for other Atlantic populations and may be driven partially by improved protection of nesting beaches. However, nesting is increasing even where beach protection has not been enhanced. Climate variability and associated marine food web dynamics, which could enhance productivity and reduce predators, may be driving this trend. PMID:21516903

  14. Dependency of microtubule-associated proteins (MAPs) for tubulin stability and assembly; use of estramustine phosphate in the study of microtubules.

    PubMed

    Fridén, B; Wallin, M

    1991-07-10

    Microtubule-associated proteins (MAPs) were separated from tubulin with several different methods. The ability of the isolated MAPs to reinduce assembly of phosphocellulose purified tubulin differed markedly between the different methods. MAPs isolated by addition of 0.35 M NaCl to taxol-stabilized microtubules stimulated tubulin assembly most effectively, while addition of 0.6 M NaCl produced MAPs with a substantially lower ability to stimulate tubulin assembly. The second best preparation was achieved with phosphocellulose chromatographic separation of MAPs with 0.6 M NaCl elution. The addition of estramustine phosphate to microtubules reconstituted of MAPs prepared by 0.35 M NaCl or phosphocellulose chromatography, induced less disassembly than for microtubules assembled from unseparated proteins, and was almost without effect on microtubules reconstituted from MAPs prepared by taxol and 0.6 M NaCl. Estramustine phosphate binds to the tubulin binding part of the MAPs, and the results do therefore indicate that the MAPs are altered by the separation methods. Since the MAPs are regarded as highly stable molecules, one probable alteration could be aggregation of the MAPs, as also indicated by the results. The purified tubulin itself seemed not to be affected by the phosphocellulose purification, since the microtubule proteins were unchanged by the low buffer strenght used during the cromatography. However, the assembly competence after a prolonged incubation of the microtubule proteins at 4 degrees C was dependent on intact bindings between the tubulin and MAPs. PMID:1681420

  15. Copper accumulation by stickleback nests containing spiggin.

    PubMed

    Pinho, G L L; Martins, C M G; Barber, I

    2016-07-01

    The three-spined stickleback is a ubiquitous fish of marine, brackish and freshwater ecosystems across the Northern hemisphere that presents intermediate sensitivity to copper. Male sticklebacks display a range of elaborate reproductive behaviours that include nest construction. To build the nests, each male binds nesting material together using an endogenous glycoprotein nesting glue, known as 'spiggin'. Spiggin is a cysteine-rich protein and, therefore, potentially binds heavy metals present in the environment. The aim of this study was to investigate the capacity of stickleback nests to accumulate copper from environmental sources. Newly built nests, constructed by male fish from polyester threads in laboratory aquaria, were immersed in copper solutions ranging in concentration from 21.1-626.6 μg Cu L(-1). Bundles of polyester threads from aquaria without male fish were also immersed in the same copper solutions. After immersion, nests presented higher amounts of copper than the thread bundles, indicating a higher capacity of nests to bind this metal. A significant, positive correlation between the concentration of copper in the exposure solution and in the exposed nests was identified, but there was no such relationship for thread bundles. Since both spiggin synthesis and male courtship behaviour are under the control of circulating androgens, we predicted that males with high courtship scores would produce and secrete high levels of the spiggin protein. In the present study, nests built by high courtship score males accumulated more copper than those built by low courtship score males. Considering the potential of spiggin to bind metals, the positive relationship between fish courtship and spiggin secretion seems to explain the higher amount of copper on the nests from the fish showing high behaviour scores. Further work is now needed to determine the consequences of the copper binding potential of spiggin in stickleback nests for the health and survival of

  16. Nests and nest sites of the San Miguel Island Song Sparrow

    USGS Publications Warehouse

    Kern, Michael D.; Sogge, Mark K.; Kern, Robert B.; Van Riper, Charles, III

    1993-01-01

    Nests and nest sites of the San Miguel Island (SMI) Song Sparrow (Melospiza melodia micronyx) are described; nests are compared with those of 16 other races of Song Sparrows. Bush lupins (Lupinus albifrons), coyote brush (Baccharis pilularis) and golden bush (Haplopappus venetus) were the shrubs used most commonly as nest sites by Song Sparrows on SMI. As a result of its location, the nest was effectively concealed from gray foxes (Urocyon littoralis), the major predator of this sparrow. Nest and nest site also moderated the combined chilling effects of cool air temperatures and strong northwesterly winds on the eggs and nestlings. Even in the absence of these moderating effects of the nest site, the energetic cost of incubation, estimated at 41-53% of the sparrow's resting metabolic rate, was modest. Twenty-nine percent of the canopy above the nest was open and as much as 73% of the nest cup was in the sun at midday, a time when surface temperatures of foliage, nest and nestlings sometimes exceeded 40 C. Whereas this exposure did not apparently reduce fledging success, it may explain why the incidence of addled eggs was so high in this population of Song Sparrows compared to others. Significant differences existed among races of Song Sparrows in the size, porosity and insulation of the nest. In most cases, these differences were not related to the latitude of the races' nesting areas.

  17. Genetic diversity and association mapping of bacterial blight and other horticulturally important traits with microsatellite markers in pomegranate from India.

    PubMed

    Singh, Nripendra Vikram; Abburi, Venkata Lakshmi; Ramajayam, D; Kumar, Ravinder; Chandra, Ram; Sharma, Kuldeep Kumar; Sharma, Jyotsana; Babu, K Dhinesh; Pal, Ram Krishna; Mundewadikar, Dhananjay M; Saminathan, Thangasamy; Cantrell, Robert; Nimmakayala, Padma; Reddy, Umesh K

    2015-08-01

    This genetic diversity study aimed to estimate the population structure and explore the use of association mapping strategies to identify linked markers for bacterial resistance, growth and fruit quality in pomegranate collections from India. In total, 88 accessions including 37 cultivated types were investigated. A total of 112 alleles were amplified by use of 44 publicly available microsatellites for estimating molecular genetic diversity and population structure. Neighbor-joining analysis, model-based population structure and principal component analysis corroborated the genetic relationships among wild-type and cultivated pomegranate collections from India. Our study placed all 88 germplasm into four clusters. We identified a cultivated clade of pomegranates in close proximity to Daru types of wild-type pomegranates that grow naturally near the foothills of the Himalayas. Admixture analysis sorted various lineages of cultivated pomegranates to their respective ancestral forms. We identified four linked markers for fruit weight, titratable acidity and bacterial blight severity. PGCT001 was found associated with both fruit weight and bacterial blight, and the association with fruit weight during both seasons analyzed was significant after Bonferroni correction. This research demonstrates effectiveness of microsatellites to resolve population structure among the wild and cultivar collection of pomegranates and future use for association mapping studies. PMID:25675870

  18. Blue jays nest in an unusual structure

    USGS Publications Warehouse

    Muths, Erin L.; Lyons, Curtis P.; Sedgwick, James A.

    2007-01-01

    We describe a successful Blue Jay (Cyanocitta cristata) nest in an unusual structure on the side of a building.  The nest was located near the edge of the species' range along the Front Range of the Rocky Mountains in Colorado.  The nest was completely obvious, suggesting that the structure itself provided adequate cover and sercurity for the jays.  Blue Jays appear to be declining in some areas of the United States such as the Southeast.  Structures such as the one we describe may be more useful in attracting Blue Jays than the nesting platforms available commercially.

  19. The design and function of birds' nests.

    PubMed

    Mainwaring, Mark C; Hartley, Ian R; Lambrechts, Marcel M; Deeming, D Charles

    2014-10-01

    All birds construct nests in which to lay eggs and/or raise offspring. Traditionally, it was thought that natural selection and the requirement to minimize the risk of predation determined the design of completed nests. However, it is becoming increasingly apparent that sexual selection also influences nest design. This is an important development as while species such as bowerbirds build structures that are extended phenotypic signals whose sole purpose is to attract a mate, nests contain eggs and/or offspring, thereby suggesting a direct trade-off between the conflicting requirements of natural and sexual selection. Nest design also varies adaptively in order to both minimize the detrimental effects of parasites and to create a suitable microclimate for parents and developing offspring in relation to predictable variation in environmental conditions. Our understanding of the design and function of birds' nests has increased considerably in recent years, and the evidence suggests that nests have four nonmutually exclusive functions. Consequently, we conclude that the design of birds' nests is far more sophisticated than previously realized and that nests are multifunctional structures that have important fitness consequences for the builder/s. PMID:25505520

  20. The design and function of birds' nests

    PubMed Central

    Mainwaring, Mark C; Hartley, Ian R; Lambrechts, Marcel M; Deeming, D Charles

    2014-01-01

    All birds construct nests in which to lay eggs and/or raise offspring. Traditionally, it was thought that natural selection and the requirement to minimize the risk of predation determined the design of completed nests. However, it is becoming increasingly apparent that sexual selection also influences nest design. This is an important development as while species such as bowerbirds build structures that are extended phenotypic signals whose sole purpose is to attract a mate, nests contain eggs and/or offspring, thereby suggesting a direct trade-off between the conflicting requirements of natural and sexual selection. Nest design also varies adaptively in order to both minimize the detrimental effects of parasites and to create a suitable microclimate for parents and developing offspring in relation to predictable variation in environmental conditions. Our understanding of the design and function of birds' nests has increased considerably in recent years, and the evidence suggests that nests have four nonmutually exclusive functions. Consequently, we conclude that the design of birds' nests is far more sophisticated than previously realized and that nests are multifunctional structures that have important fitness consequences for the builder/s. PMID:25505520

  1. Microtubule-associated protein 1S (MAP1S) bridges autophagic components with microtubules and mitochondria to affect autophagosomal biogenesis and degradation.

    PubMed

    Xie, Rui; Nguyen, Susan; McKeehan, Kerstin; Wang, Fen; McKeehan, Wallace L; Liu, Leyuan

    2011-03-25

    The ubiquitously distributed MAP1S is a homologue of the exclusively neuronal distributed microtubule-associated protein 1A and 1B (MAP1A/B). They give rise to multiple isoforms through similar post-translational modification. Isoforms of MAP1S have been implicated in microtubule dynamics and mitotic abnormalities and mitotic cell death. Here we show that ablation of the Map1s gene in mice caused reduction in the B-cell CLL/lymphoma 2 or xL (Bcl-2/xL) and cyclin-dependent kinase inhibitor 1B (P27) protein levels, accumulation of defective mitochondria, and severe defects in response to nutritive stress, suggesting defects in autophagosomal biogenesis and clearance. Furthermore, MAP1S isoforms interacted with the autophagosome-associated light chain 3 of MAP1A/B (LC3), a homologue of yeast autophagy-related gene 8 (ATG8), and recruited it to stable microtubules in a MAP1S and LC3 isoform-dependent mode. In addition, MAP1S interacted with mitochondrion-associated leucine-rich PPR-motif containing protein (LRPPRC) that interacts with the mitophagy initiator and Parkinson disease-related protein Parkin. The three-way interactions of MAP1S isoforms with LC3 and microtubules as well as the interaction of MAP1S with LRPPRC suggest that MAP1S isoforms may play positive roles in integration of autophagic components with microtubules and mitochondria in both autophagosomal biogenesis and degradation. For the first time, our results clarify roles of MAP1S in bridging microtubules and mitochondria with autophagic and mitophagic initiation, maturation, trafficking, and lysosomal clearance. Defects in the MAP1S-regulated autophagy may impact heart disease, cancers, neurodegenerative diseases, and a wide range of other diseases. PMID:21262964

  2. Mapping of stochastic dynamics onto associated quantum models and (d+1)-dimensional classical and static systems

    SciTech Connect

    Schneider, T.

    1986-06-01

    Much effort has been devoted to the subjects of dynamic, quantum, and classical critical phenomena, although these research fields developed rather independently. Recently, however, remarkable connections have been established, achieved by using the connection between the time-dependent Ginzburg-Landau equation (TDGL) in d dimensions, describing critical dynamics, and the Fokker-Planck equation. The latter is then reduced to an imaginary-time Schrodinger equation, defining the Hamiltonian of the quantum system, which in turn can be mapped onto a static and classical (d + 1)-dimensional counterpart. Another interesting aspect of these mappings is the simulation of quantum systems in terms of Langevin equations and the construction of quantum systems with soluble ground-state expectative values.

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

    NASA Astrophysics Data System (ADS)

    Byrne, Jenny; Grace, Marcus

    2010-03-01

    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 particular concepts related to microbial activity is presented and discussed in relation to the effectiveness of CoMPAT as a tool to draw out their ideas. It is proposed that this tool could be used to explore ideas about this and other science concepts from children in other age groups, and where language may be a barrier to participation.

  4. Functional Error Models to Accelerate Nested Sampling

    NASA Astrophysics Data System (ADS)

    Josset, L.; Elsheikh, A. H.; Demyanov, V.; Lunati, I.

    2014-12-01

    The main challenge in groundwater problems is the reliance on large numbers of unknown parameters with wide rage of associated uncertainties. To translate this uncertainty to quantities of interest (for instance the concentration of pollutant in a drinking well), a large number of forward flow simulations is required. To make the problem computationally tractable, Josset et al. (2013, 2014) introduced the concept of functional error models. It consists in two elements: a proxy model that is cheaper to evaluate than the full physics flow solver and an error model to account for the missing physics. The coupling of the proxy model and the error models provides reliable predictions that approximate the full physics model's responses. The error model is tailored to the problem at hand by building it for the question of interest. It follows a typical approach in machine learning where both the full physics and proxy models are evaluated for a training set (subset of realizations) and the set of responses is used to construct the error model using functional data analysis. Once the error model is devised, a prediction of the full physics response for a new geostatistical realization can be obtained by computing the proxy response and applying the error model. We propose the use of functional error models in a Bayesian inference context by combining it to the Nested Sampling (Skilling 2006; El Sheikh et al. 2013, 2014). Nested Sampling offers a mean to compute the Bayesian Evidence by transforming the multidimensional integral into a 1D integral. The algorithm is simple: starting with an active set of samples, at each iteration, the sample with the lowest likelihood is kept aside and replaced by a sample of higher likelihood. The main challenge is to find this sample of higher likelihood. We suggest a new approach: first the active set is sampled, both proxy and full physics models are run and the functional error model is build. Then, at each iteration of the Nested

  5. Tests of landscape influence: Nest predation and brood parasitism in fragmented ecosystems

    USGS Publications Warehouse

    Tewksbury, J.J.; Garner, L.; Garner, S.; Lloyd, J.D.; Saab, V.; Martin, T.E.

    2006-01-01

    The effects of landscape fragmentation on nest predation and brood parasitism, the two primary causes of avian reproductive failure, have been difficult to generalize across landscapes, yet few studies have clearly considered the context and spatial scale of fragmentation. Working in two river systems fragmented by agricultural and rural-housing development, we tracked nesting success and brood parasitism in >2500 bird nests in 38 patches of deciduous riparian woodland. Patches on both river systems were embedded in one of two local contexts (buffered from agriculture by coniferous forest, or adjacent to agriculture), but the abundance of agriculture and human habitation within 1 km of each patch was highly variable. We examined evidence for three models of landscape effects on nest predation based on (1) the relative importance of generalist agricultural nest predators, (2) predators associated with the natural habitats typically removed by agricultural development, or (3) an additive combination of these two predator communities. We found strong support for an additive predation model in which landscape features affect nest predation differently at different spatial scales. Riparian habitat with forest buffers had higher nest predation rates than sites adjacent to agriculture, but nest predation also increased with increasing agriculture in the larger landscape surrounding each site. These results suggest that predators living in remnant woodland buffers, as well as generalist nest predators associated with agriculture, affect nest predation rates, but they appear to respond at different spatial scales. Brood parasitism, in contrast, was unrelated to agricultural abundance on the landscape, but showed a strong nonlinear relationship with farm and house density, indicating a critical point at which increased human habitat causes increased brood parasitism. Accurate predictions regarding landscape effects on nest predation and brood parasitism will require an

  6. Arctic nesting geese: alaskan populations

    USGS Publications Warehouse

    Hupp, Jerry W.; Stehn, Robert A.; Ely, Craig R.; Derksen, Dirk V.

    1995-01-01

    While data for some areas are lacking, populations of greater white-fronted geese (Anser albifrons frontalis) and medium-sized Canada geese (Branta canadensis) in interior and northern Alaska appear stable or have increased (King and Derksen 1986). Although only a small number of lesser snow geese (Chen caerulescens caerulescens) nest in Alaska, substantial populations occur in Canada and Russia. Populations of Pacific black brant (B. bernicla nigricans), emperor geese (C. canagica), greater white-fronted geese, and cackling Canada geese (B.c. minima) on the Yukon-Kuskokwim Delta (YKD) of western Alaska have declined from their historical numbers and are the focus of special management efforts (USFWS 1989). In addition, populations of tule white-fronted geese (A.a. gambeli), Aleutian Canada geese (B.c. leucopareia), Vancouver Canada Geese (B.c. fulva), and dusky Canada geese (B.c. occidentalis) are of special concern because of their limited geographic distributions and small numbers.

  7. Automatic blocking of nested loops

    NASA Technical Reports Server (NTRS)

    Schreiber, Robert; Dongarra, Jack J.

    1990-01-01

    Blocked algorithms have much better properties of data locality and therefore can be much more efficient than ordinary algorithms when a memory hierarchy is involved. On the other hand, they are very difficult to write and to tune for particular machines. The reorganization is considered of nested loops through the use of known program transformations in order to create blocked algorithms automatically. The program transformations used are strip mining, loop interchange, and a variant of loop skewing in which invertible linear transformations (with integer coordinates) of the loop indices are allowed. Some problems are solved concerning the optimal application of these transformations. It is shown, in a very general setting, how to choose a nearly optimal set of transformed indices. It is then shown, in one particular but rather frequently occurring situation, how to choose an optimal set of block sizes.

  8. Nested trampoline resonators for optomechanics

    NASA Astrophysics Data System (ADS)

    Weaver, M. J.; Pepper, B.; Luna, F.; Buters, F. M.; Eerkens, H. J.; Welker, G.; Perock, B.; Heeck, K.; de Man, S.; Bouwmeester, D.

    2016-01-01

    Two major challenges in the development of optomechanical devices are achieving a low mechanical and optical loss rate and vibration isolation from the environment. We address both issues by fabricating trampoline resonators made from low pressure chemical vapor deposition Si3N4 with a distributed Bragg reflector mirror. We design a nested double resonator structure with 80 dB of mechanical isolation from the mounting surface at the inner resonator frequency, and we demonstrate up to 45 dB of isolation at lower frequencies in agreement with the design. We reliably fabricate devices with mechanical quality factors of around 400 000 at room temperature. In addition, these devices were used to form optical cavities with finesse up to 181 000 ± 1000. These promising parameters will enable experiments in the quantum regime with macroscopic mechanical resonators.

  9. Genetic Mapping and Exome Sequencing Identify Variants Associated with Five Novel Diseases

    PubMed Central

    Puffenberger, Erik G.; Jinks, Robert N.; Sougnez, Carrie; Cibulskis, Kristian; Willert, Rebecca A.; Achilly, Nathan P.; Cassidy, Ryan P.; Fiorentini, Christopher J.; Heiken, Kory F.; Lawrence, Johnny J.; Mahoney, Molly H.; Miller, Christopher J.; Nair, Devika T.; Politi, Kristin A.; Worcester, Kimberly N.; Setton, Roni A.; DiPiazza, Rosa; Sherman, Eric A.; Eastman, James T.; Francklyn, Christopher; Robey-Bond, Susan; Rider, Nicholas L.; Gabriel, Stacey; Morton, D. Holmes; Strauss, Kevin A.

    2012-01-01

    The Clinic for Special Children (CSC) has integrated biochemical and molecular methods into a rural pediatric practice serving Old Order Amish and Mennonite (Plain) children. Among the Plain people, we have used single nucleotide polymorphism (SNP) microarrays to genetically map recessive disorders to large autozygous haplotype blocks (mean = 4.4 Mb) that contain many genes (mean = 79). For some, uninformative mapping or large gene lists preclude disease-gene identification by Sanger sequencing. Seven such conditions were selected for exome sequencing at the Broad Institute; all had been previously mapped at the CSC using low density SNP microarrays coupled with autozygosity and linkage analyses. Using between 1 and 5 patient samples per disorder, we identified sequence variants in the known disease-causing genes SLC6A3 and FLVCR1, and present evidence to strongly support the pathogenicity of variants identified in TUBGCP6, BRAT1, SNIP1, CRADD, and HARS. Our results reveal the power of coupling new genotyping technologies to population-specific genetic knowledge and robust clinical data. PMID:22279524

  10. Fine Mapping of a QTL Associated with Kernel Row Number on Chromosome 1 of Maize

    PubMed Central

    Calderón, Claudia I.; Yandell, Brian S.; Doebley, John F.

    2016-01-01

    The genetic factors underlying changes in ear morphology, and particularly the inheritance of kernel row number (KRN), have been broadly investigated in diverse mapping populations in maize (Zea mays L.). In this study, we mapped a region on the long arm of chromosome 1 containing a QTL for KRN. This work was performed using a set of recombinant chromosome nearly isogenic lines (RCNILs) derived from a BC2S3 population produced using the inbred maize line W22 and teosinte (Zea mays ssp. parviglumis) as the parents. A set of 48 RCNILs was evaluated in the field during the summer of 2013 in order to perform the mapping. A QTL for KRN was found that explained approximately 51% of the phenotypic variance and had a 1.5-LOD confidence interval of 203 kb. Seven genes are described in this interval. One of these candidate genes may have been the target of domestication processes in maize and contributed to the shift from two kernel row ears in teosinte to a highly polystichous ear in maize. PMID:26930509

  11. Catastrophic health expenditure: a comparative analysis of empty-nest and non-empty-nest households with seniors in Shandong, China

    PubMed Central

    Yang, Tingting; Chu, Jie; Zhou, Chengchao; Medina, Alexis; Li, Cuicui; Jiang, Shan; Zheng, Wengui; Sun, Liyuan; Liu, Jing

    2016-01-01

    Objective The aim of this study was to compare the catastrophic health expenditure (CHE) prevalence and its determinants between empty-nest and non-empty-nest elderly households. Setting Shandong province of China. Participants A total of 2761 elderly households are included in the analysis. Results CHE incidence among elderly households was 44.9%. The CHE incidence of empty-nest singles (59.3%, p=0.000, OR=3.19) and empty-nest couples (52.9%, p=0.000, OR=2.45) are both statistically higher than that of non-empty-nest elderly households (31.4%). An inverse association was observed between CHE incidence and income level in all elderly household types. Factors including 1 or more household elderly members with non-communicable chronic diseases in the past 6 months, 1 or more elderly household members being hospitalised in the past year and lower household income, are significant risk factors for CHE in all 3 household types (p<0.05). Health insurance status was found to be a significant determinant of CHE among empty-nest singles and non-empty-nest households (p<0.05). Conclusions CHE incidence among elderly households is high in China. Empty-nest households are at higher risk for CHE than non-empty-nest households. Based on these findings, we suggest that special insurance be developed to broaden the coverage of health services and heighten the reimbursement rate for empty-nest elderly in the existing health insurance schemes. Financial and social protection interventions are also essential for identified at-risk subgroups among different types of elderly households. PMID:27381206

  12. Nest Suitability, Fine-Scale Population Structure and Male-Mediated Dispersal of a Solitary Ground Nesting Bee in an Urban Landscape

    PubMed Central

    López-Uribe, Margarita M.; Morreale, Stephen J.; Santiago, Christine K.; Danforth, Bryan N.

    2015-01-01

    Bees are the primary pollinators of flowering plants in almost all ecosystems. Worldwide declines in bee populations have raised awareness about the importance of their ecological role in maintaining ecosystem functioning. The naturally strong philopatric behavior that some bee species show can be detrimental to population viability through increased probability of inbreeding. Furthermore, bee populations found in human-altered landscapes, such as urban areas, can experience lower levels of gene flow and effective population sizes, increasing potential for inbreeding depression in wild bee populations. In this study, we investigated the fine-scale population structure of the solitary bee Colletes inaequalis in an urbanized landscape. First, we developed a predictive spatial model to detect suitable nesting habitat for this ground nesting bee and to inform our field search for nests. We genotyped 18 microsatellites in 548 female individuals collected from nest aggregations throughout the study area. Genetic relatedness estimates revealed that genetic similarity among individuals was slightly greater within nest aggregations than among randomly chosen individuals. However, genetic structure among nest aggregations was low (Nei’s GST = 0.011). Reconstruction of parental genotypes revealed greater genetic relatedness among females than among males within nest aggregations, suggesting male-mediated dispersal as a potentially important mechanism of population connectivity and inbreeding avoidance. Size of nesting patch was positively correlated with effective population size, but not with other estimators of genetic diversity. We detected a positive trend between geographic distance and genetic differentiation between nest aggregations. Our landscape genetic models suggest that increased urbanization is likely associated with higher levels of inbreeding. Overall, these findings emphasize the importance of density and distribution of suitable nesting patches for

  13. Nest suitability, fine-scale population structure and male-mediated dispersal of a solitary ground nesting bee in an urban landscape.

    PubMed

    López-Uribe, Margarita M; Morreale, Stephen J; Santiago, Christine K; Danforth, Bryan N

    2015-01-01

    Bees are the primary pollinators of flowering plants in almost all ecosystems. Worldwide declines in bee populations have raised awareness about the importance of their ecological role in maintaining ecosystem functioning. The naturally strong philopatric behavior that some bee species show can be detrimental to population viability through increased probability of inbreeding. Furthermore, bee populations found in human-altered landscapes, such as urban areas, can experience lower levels of gene flow and effective population sizes, increasing potential for inbreeding depression in wild bee populations. In this study, we investigated the fine-scale population structure of the solitary bee Colletes inaequalis in an urbanized landscape. First, we developed a predictive spatial model to detect suitable nesting habitat for this ground nesting bee and to inform our field search for nests. We genotyped 18 microsatellites in 548 female individuals collected from nest aggregations throughout the study area. Genetic relatedness estimates revealed that genetic similarity among individuals was slightly greater within nest aggregations than among randomly chosen individuals. However, genetic structure among nest aggregations was low (Nei's GST = 0.011). Reconstruction of parental genotypes revealed greater genetic relatedness among females than among males within nest aggregations, suggesting male-mediated dispersal as a potentially important mechanism of population connectivity and inbreeding avoidance. Size of nesting patch was positively correlated with effective population size, but not with other estimators of genetic diversity. We detected a positive trend between geographic distance and genetic differentiation between nest aggregations. Our landscape genetic models suggest that increased urbanization is likely associated with higher levels of inbreeding. Overall, these findings emphasize the importance of density and distribution of suitable nesting patches for enhancing

  14. Do seasonal patterns of rat snake (Pantherophis obsoletus) and black racer (Coluber constrictor) activity predict avian nest predation?

    PubMed

    DeGregorio, Brett A; Weatherhead, Patrick J; Ward, Michael P; Sperry, Jinelle H

    2016-04-01

    Avian nest success often varies seasonally and because predation is the primary cause of nest failure, seasonal variation in predator activity has been hypothesized to explain seasonal variation in nest success. Despite the fact that nest predator communities are often diverse, recent evidence from studies of snakes that are nest predators has lent some support to the link between snake activity and nest predation. However, the strength of the relationship has varied among studies. Explaining this variation is difficult, because none of these studies directly identified nest predators, the link between predator activity and nest survival was inferred. To address this knowledge gap, we examined seasonal variation in daily survival rates of 463 bird nests (of 17 bird species) and used cameras to document predator identity at 137 nests. We simultaneously quantified seasonal activity patterns of two local snake species (N = 30 individuals) using manual (2136 snake locations) and automated (89,165 movements detected) radiotelemetry. Rat snakes (Pantherophis obsoletus), the dominant snake predator at the site (~28% of observed nest predations), were most active in late May and early June, a pattern reported elsewhere for this species. When analyzing all monitored nests, we found no link between nest predation and seasonal activity of rat snakes. When analyzing only nests with known predator identities (filmed nests), however, we found that rat snakes were more likely to prey on nests during periods when they were moving the greatest distances. Similarly, analyses of all monitored nests indicated that nest survival was not linked to racer activity patterns, but racer-specific predation (N = 17 nests) of filmed nests was higher when racers were moving the greatest distances. Our results suggest that the activity of predators may be associated with higher predation rates by those predators, but that those effects can be difficult to detect when nest predator communities

  15. A network-driven approach for genome-wide association mapping

    PubMed Central

    Lee, Seunghak; Kong, Soonho; Xing, Eric P.

    2016-01-01

    Motivation: It remains a challenge to detect associations between genotypes and phenotypes because of insufficient sample sizes and complex underlying mechanisms involved in associations. Fortunately, it is becoming more feasible to obtain gene expression data in addition to genotypes and phenotypes, giving us new opportunities to detect true genotype–phenotype associations while unveiling their association mechanisms. Results: In this article, we propose a novel method, NETAM, that accurately detects associations between SNPs and phenotypes, as well as gene traits involved in such associations. We take a network-driven approach: NETAM first constructs an association network, where nodes represent SNPs, gene traits or phenotypes, and edges represent the strength of association between two nodes. NETAM assigns a score to each path from an SNP to a phenotype, and then identifies significant paths based on the scores. In our simulation study, we show that NETAM finds significantly more phenotype-associated SNPs than traditional genotype–phenotype association analysis under false positive control, taking advantage of gene expression data. Furthermore, we applied NETAM on late-onset Alzheimer’s disease data and identified 477 significant path associations, among which we analyzed paths related to beta-amyloid, estrogen, and nicotine pathways. We also provide hypothetical biological pathways to explain our findings. Availability and implementation: Software is available at http://www.sailing.cs.cmu.edu/. Contact: epxing@cs.cmu.edu PMID:27307613

  16. Greater sage-grouse nest predators in the Virginia Mountains of northwestern Nevada

    USGS Publications Warehouse

    Lockyer, Zachary B.; Coates, Peter S.; Casazza, Michael L.; Espinosa, Shawn; Delehanty, David J.

    2013-01-01

    Greater sage-grouse Centrocercus urophasianus, hereafter sage-grouse, populations have declined across their range due to the loss, degradation, and fragmentation of habitat. Habitat alterations can lead not only to vegetative changes but also to shifts in animal behavior and predator composition that may influence population vital rates, such as nest success. For example, common ravens Corvus corax are sage-grouse nest predators, and common raven abundance is positively associated with human-caused habitat alterations. Because nest success is a central component to sage-grouse population persistence, research that identifies factors influencing nest success will better inform conservation efforts. We used videography to unequivocally identify sage-grouse nest predators within the Virginia Mountains of northwestern Nevada, USA, from 2009 to 2011 and used maximum likelihood to calculate daily probability of nest survival. In the Virginia Mountains, fires, energy exploration, and other anthropogenic activities have altered historic sage-grouse habitat. We monitored 71 sage-grouse nests during the study, placing video cameras at 39 nests. Cumulative nest survival for all nests was 22.4% (95% CI, 13.0–33.4%), a survival rate that was significantly lower than other published results for sage-grouse in the Great Basin. Depredation was the primary cause for nest failure in our study (82.5%), and common ravens were the most frequent sage-grouse nest predator, accounting for 46.7% of nest depredations. We also successfully documented a suite of mammalian and reptilian species depredating sage-grouse nests, including some predators never previously confirmed in the literature to be sage-grouse nest predators (i.e., bobcats Lynx rufus and long-tailed weasels Mephitis frenata). Within the high elevation, disturbed habitat of the Virginia Mountains, low sage-grouse nest success may be limiting sage-grouse population growth. These results suggest that management actions that

  17. Presence of Breeding Birds Improves Body Condition for a Crocodilian Nest Protector

    PubMed Central

    Nell, Lucas A.; Frederick, Peter C.; Mazzotti, Frank J.; Vliet, Kent A.; Brandt, Laura A.

    2016-01-01

    Ecological associations where one species enhances habitat for another nearby species (facilitations) shape fundamental community dynamics and can promote niche expansion, thereby influencing how and where species persist and coexist. For the many breeding birds facing high nest-predation pressure, enemy-free space can be gained by nesting near more formidable animals for physical protection. While the benefits to protected species seem well documented, very few studies have explored whether and how protector species are affected by nest protection associations. Long-legged wading birds (Pelecaniformes and Ciconiiformes) actively choose nesting sites above resident American alligators (Alligator mississippiensis), apparently to take advantage of the protection from mammalian nest predators that alligator presence offers. Previous research has shown that wading bird nesting colonies could provide substantial food for alligators in the form of dropped chicks. We compared alligator body condition in similar habitat with and without wading bird nesting colonies present. Alligator morphometric body condition indices were significantly higher in colony than in non-colony locations, an effect that was statistically independent of a range of environmental variables. Since colonially nesting birds and crocodilians co-occur in many tropical and subtropical wetlands, our results highlight a potentially widespread keystone process between two ecologically important species-groups. These findings suggest the interaction is highly beneficial for both groups of actors, and illustrate how selective pressures may have acted to form and reinforce a strongly positive ecological interaction. PMID:26934602

  18. Presence of Breeding Birds Improves Body Condition for a Crocodilian Nest Protector.

    PubMed

    Nell, Lucas A; Frederick, Peter C; Mazzotti, Frank J; Vliet, Kent A; Brandt, Laura A

    2016-01-01

    Ecological associations where one species enhances habitat for another nearby species (facilitations) shape fundamental community dynamics and can promote niche expansion, thereby influencing how and where species persist and coexist. For the many breeding birds facing high nest-predation pressure, enemy-free space can be gained by nesting near more formidable animals for physical protection. While the benefits to protected species seem well documented, very few studies have explored whether and how protector species are affected by nest protection associations. Long-legged wading birds (Pelecaniformes and Ciconiiformes) actively choose nesting sites above resident American alligators (Alligator mississippiensis), apparently to take advantage of the protection from mammalian nest predators that alligator presence offers. Previous research has shown that wading bird nesting colonies could provide substantial food for alligators in the form of dropped chicks. We compared alligator body condition in similar habitat with and without wading bird nesting colonies present. Alligator morphometric body condition indices were significantly higher in colony than in non-colony locations, an effect that was statistically independent of a range of environmental variables. Since colonially nesting birds and crocodilians co-occur in many tropical and subtropical wetlands, our results highlight a potentially widespread keystone process between two ecologically important species-groups. These findings suggest the interaction is highly beneficial for both groups of actors, and illustrate how selective pressures may have acted to form and reinforce a strongly positive ecological interaction. PMID:26934602

  19. HapMap tag-SNP analysis confirms a role for COMT in schizophrenia risk and reveals a novel association.

    PubMed

    Voisey, J; Swagell, C D; Hughes, I P; Lawford, B R; Young, R M; Morris, C P

    2012-07-01

    Catechol-O-methyl transferase (COMT) encodes an enzyme involved in the metabolism of dopamine and maps to a commonly deleted region that increases schizophrenia risk. A non-synonymous polymorphism (rs4680) in COMT has been previously found to be associated with schizophrenia and results in altered activity levels of COMT. Using a haplotype block-based gene-tagging approach we conducted an association study of seven COMT single nucleotide polymorphisms (SNPs) in 160 patients with a DSM-IV diagnosis of schizophrenia and 250 controls in an Australian population. Two polymorphisms including rs4680 and rs165774 were found to be significantly associated with schizophrenia. The rs4680 results in a Val/Met substitution but the strongest association was shown by the novel SNP, rs165774, which may still be functional even though it is located in intron five. Individuals with schizophrenia were more than twice as likely to carry the GG genotype compared to the AA genotype for both the rs165774 and rs4680 SNPs. This association was slightly improved when males were analysed separately possibly indicating a degree of sexual dimorphism. Our results confirm that COMT is a good candidate for schizophrenia risk, by replicating the association with rs4680 and identifying a novel SNP association. PMID:20934310

  20. Genetic diversity, population structure, and association mapping of agronomic traits in waxy and normal maize inbred lines.

    PubMed

    Sa, K J; Park, J Y; Choi, S H; Kim, B W; Park, K J; Lee, J K

    2015-01-01

    Understanding genetic diversity, population structure, and linkage disequilibrium is a prerequisite for the association mapping of complex traits in a target population. In this study, the genetic diversity and population structure of 40 waxy and 40 normal inbred maize lines were investigated using 10 morphological traits and 200 simple sequence repeat (SSR) markers. Based on a population structure analysis, the 80 maize inbred lines were divided into three groups: I, II, and admixed. Significant marker-trait associations were identified between the markers and the 10 morphological traits, which were studied according to the model used to confirm the association. Using a general linear model, the lowest R(2) value (9.03) was detected in umc1139, which was associated with ear number, and the highest (43.97) was in umc1858, which was associated with plant height. Using a mixed linear model, the lowest R(2) value (18.74) was in umc1279, which was associated with ear weight; the highest (27.66) was in umc1858, which was associated with 100-kernel weight. The SSR markers identified in the present study may serve as useful molecular markers for selecting important yield and agronomic traits. These results will be useful for marker-assisted selection in maize breeding programs, to help breeders choose parental lines and markers for crosses. PMID:26214429

  1. Bayesian multilocus association mapping on ordinal and censored traits and its application to the analysis of genetic variation among Oryza sativa L. germplasms

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Association mapping can be a powerful tool for detecting quantitative trait loci (QTLs) without requiring line-crossing experiments. We previously proposed a Bayesian approach for simultaneously mapping multiple QTLs by a regression method that directly incorporates estimates of the population struc...

  2. Adaptive nest clustering and density-dependent nest survival in dabbling ducks

    USGS Publications Warehouse

    Ringelman, Kevin M.; Eadie, John M.; Ackerman, Joshua T.

    2014-01-01

    Density-dependent population regulation is observed in many taxa, and understanding the mechanisms that generate density dependence is especially important for the conservation of heavily-managed species. In one such system, North American waterfowl, density dependence is often observed at continental scales, and nest predation has long been implicated as a key factor driving this pattern. However, despite extensive research on this topic, it remains unclear if and how nest density influences predation rates. Part of this confusion may have arisen because previous studies have studied density-dependent predation at relatively large spatial and temporal scales. Because the spatial distribution of nests changes throughout the season, which potentially influences predator behavior, nest survival may vary through time at relatively small spatial scales. As such, density-dependent nest predation might be more detectable at a spatially- and temporally-refined scale and this may provide new insights into nest site selection and predator foraging behavior. Here, we used three years of data on nest survival of two species of waterfowl, mallards and gadwall, to more fully explore the relationship between local nest clustering and nest survival. Throughout the season, we found that the distribution of nests was consistently clustered at small spatial scales (˜50–400 m), especially for mallard nests, and that this pattern was robust to yearly variation in nest density and the intensity of predation. We demonstrated further that local nest clustering had positive fitness consequences – nests with closer nearest neighbors were more likely to be successful, a result that is counter to the general assumption that nest predation rates increase with nest density.

  3. Spawning chronology, nest site selection and nest success of smallmouth bass during benign streamflow conditions

    USGS Publications Warehouse

    Dauwalter, D.C.; Fisher, W.L.

    2007-01-01

    We documented the nesting chronology, nest site selection and nest success of smallmouth bass Micropterus dolomieu in an upstream (4th order) and downstream (5th order) reach of Baron Fork Creek, Oklahoma. Males started nesting in mid-Apr. when water temperatures increased to 16.9 C upstream, and in late-Apr. when temperatures increased to 16.2 C downstream. Streamflows were low (77% upstream to 82% downstream of mean Apr. streamflow, and 12 and 18% of meanjun. streamflow; 47 and 55 y of record), and decreased throughout the spawning period. Larger males nested first upstream, as has been observed in other populations, but not downstream. Upstream, progeny in 62 of 153 nests developed to swim-up stage. Downstream, progeny in 31 of 73 nests developed to swim-up. Nesting densities upstream (147/km) and downstream (100/km) were both higher than any densities previously reported. Males selected nest sites with intermediate water depths, low water velocity and near cover, behavior that is typical of smallmouth bass. Documented nest failures resulted from human disturbance, angling, and longear sunfish predation. Logistic exposure models showed that water velocity at the nest was negatively related and length of the guarding male was positively related to nest success upstream. Male length and number of degree days were both positively related to nest success downstream. Our results, and those of other studies, suggest that biological factors account for most nest failures during benign (stable, low flow) streamflow conditions, whereas nest failures attributed to substrate mobility or nest abandonment dominate when harsh streamflow conditions (spring floods) coincide with the spawning season.

  4. Structural analysis of raw and commercial farm edible bird nests.

    PubMed

    Kew, P E; Wong, S F; Lim, P K; Mak, J W

    2014-03-01

    Edible bird nests (EBNs) are consumed worldwide for various health benefits. EBNs are nests built from the saliva of swiftlets of Aerodramus species. The global market for EBNs is on the rise, especially from Hong Kong and mainland China. In the past, EBNs were harvested mainly from natural caves; however in the recent years, there has been a rapid growth of swiftlet farming. Little is known about the actual composition of EBNs except for protein, carbohydrate, ash and lipid contents, amino acids, vitamins and macro/ micronutrients. Besides the biochemical components of EBNs, are there any other structures that are associated with EBNs? This paper reports on the structural analysis of raw unprocessed farm and processed commercial EBNs. The raw EBNs were purchased from swiftlet farms in five locations in Peninsula Malaysia: Kuala Sanglang (Perlis; 6° 16' 0"N, 100° 12' 0"E), Pantai Remis (Perak; 4º 27' 0" N, 100º 38' 0" E), Kluang (Johor; 02º 012 303N 103º 192 583E), Kajang (Selangor; 2º 59' 0"N, 101º 47' 0"E) and Kota Bharu (Kelantan; 6º 8' 0"N, 102º 15' 0"E). The commercial nests were purchased from five different Chinese traditional medicinal shops (Companies A-E). A portion of each EBN was randomly broken into small fragments, attached to carbon tape and coated with gold and palladium particles for examination and photography under a scanning electron microscope. Structural analysis revealed the presence of mites, fungi, bacteria and feather strands on both the raw and commercial nests. Mite eggshells and faecal pellets, and body parts of other arthropods were seen only in the raw nests. The commercial nests had a variety of unidentified structures and substances coated on the nests' surfaces that were not found on the raw nests. The presence of these contaminants may jeopardise the quality of EBNs and pose health risks to consumers. Further identification of the mites and their allergens, fungi and bacteria are on-going and will be reported separately

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

    PubMed Central

    2011-01-01

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

  6. Nest marking behavior and chemical composition of olfactory cues involved in nest recognition in Megachile rotundata

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The present study examines the use of olfactory cues for nest recognition by Megachile rotundata (Fabricius) (Hymenoptera: Megachilidae), an economically important pollinator of seed alfalfa throughout western North America. In-nest observations revealed that nesting females drag their abdomen alon...

  7. Linkage disequilibrium, SNP frequency change due to selection, and association mapping in popcorn chromosome regions containing QTLs for quality traits

    PubMed Central

    Paes, Geísa Pinheiro; Viana, José Marcelo Soriano; Silva, Fabyano Fonseca e; Mundim, Gabriel Borges

    2016-01-01

    Abstract The objectives of this study were to assess linkage disequilibrium (LD) and selection-induced changes in single nucleotide polymorphism (SNP) frequency, and to perform association mapping in popcorn chromosome regions containing quantitative trait loci (QTLs) for quality traits. Seven tropical and two temperate popcorn populations were genotyped for 96 SNPs chosen in chromosome regions containing QTLs for quality traits. The populations were phenotyped for expansion volume, 100-kernel weight, kernel sphericity, and kernel density. The LD statistics were the difference between the observed and expected haplotype frequencies (D), the proportion of D relative to the expected maximum value in the population, and the square of the correlation between the values of alleles at two loci. Association mapping was based on least squares and Bayesian approaches. In the tropical populations, D-values greater than 0.10 were observed for SNPs separated by 100-150 Mb, while most of the D-values in the temperate populations were less than 0.05. Selection for expansion volume indirectly led to increase in LD values, population differentiation, and significant changes in SNP frequency. Some associations were observed for expansion volume and the other quality traits. The candidate genes are involved with starch, storage protein, lipid, and cell wall polysaccharides synthesis. PMID:27007903

  8. Genetic Diversity and Elite Allele Mining for Grain Traits in Rice (Oryza sativa L.) by Association Mapping

    PubMed Central

    Edzesi, Wisdom M.; Dang, Xiaojing; Liang, Lijun; Liu, Erbao; Zaid, Imdad U.; Hong, Delin

    2016-01-01

    Mining elite alleles for grain size and weight is of importance for the improvement of cultivated rice and selection for market demand. In this study, association mapping for grain traits was performed on a selected sample of 628 rice cultivars using 262 SSRs. Grain traits were evaluated by grain length (GL), grain width (GW), grain thickness (GT), grain length to width ratio (GL/GW), and 1000-grain weight (TGW) in 2013 and 2014. Our result showed abundant phenotypic and genetic diversities found in the studied population. In total, 2953 alleles were detected with an average of 11.3 alleles per locus. The population was divided into seven subpopulations and the levels of linkage disequilibrium (LD) ranged from 34 to 84 cM. Genome-wide association mapping detected 10 marker trait association (MTAs) loci for GL, 1MTAs locus for GW, 7 MTAs loci for GT, 3 MTAs loci for GL/GW, and 1 MTAs locus for TGW. Twenty-nine, 2, 10, 5, and 3 elite alleles were found for the GL, GW, GT, GL/GW, and TGW, respectively. Optimal cross designs were predicted for improving the target traits. The accessions containing elite alleles for grain traits mined in this study could be used for breeding rice cultivars and cloning the candidate genes. PMID:27375646

  9. Linkage disequilibrium, SNP frequency change due to selection, and association mapping in popcorn chromosome regions containing QTLs for quality traits.

    PubMed

    Paes, Geísa Pinheiro; Viana, José Marcelo Soriano; Silva, Fabyano Fonseca E; Mundim, Gabriel Borges

    2016-03-01

    The objectives of this study were to assess linkage disequilibrium (LD) and selection-induced changes in single nucleotide polymorphism (SNP) frequency, and to perform association mapping in popcorn chromosome regions containing quantitative trait loci (QTLs) for quality traits. Seven tropical and two temperate popcorn populations were genotyped for 96 SNPs chosen in chromosome regions containing QTLs for quality traits. The populations were phenotyped for expansion volume, 100-kernel weight, kernel sphericity, and kernel density. The LD statistics were the difference between the observed and expected haplotype frequencies (D), the proportion of D relative to the expected maximum value in the population, and the square of the correlation between the values of alleles at two loci. Association mapping was based on least squares and Bayesian approaches. In the tropical populations, D-values greater than 0.10 were observed for SNPs separated by 100-150 Mb, while most of the D-values in the temperate populations were less than 0.05. Selection for expansion volume indirectly led to increase in LD values, population differentiation, and significant changes in SNP frequency. Some associations were observed for expansion volume and the other quality traits. The candidate genes are involved with starch, storage protein, lipid, and cell wall polysaccharides synthesis. PMID:27007903

  10. Isotopic mapping of transition-state structural features associated with enzymic catalysis of methyl transfer

    SciTech Connect

    Rodgers, J.; Femec, D.A.; Schowen, R.L.

    1982-06-16

    For comparison of the molecular structures of nonenzymic and enzymic sulfur-to-oxygen transmethylation transition states by the use of kinetic isotope effects, a series of isotopic maps is produced. In these, contours of constant isotope effect are displayed vs. the Pauling bond orders B/sub CS/ and B/sub CO/, for the carbon-sulfur and carbon-oxygen bonds, respectively, taken as independent variables to describe the transition states. Maps are calculated by the BEBOVIB approach for k(CH/sub 3/)/k(CD/sub 3/), k(/sup 12/CH/sub 3/)/k(/sup 13/CH/sub 3/), k(/sup 16/O)/k(/sup 18/O), and k(/sup 32/S)/k(/sup 34/S), with two models for the reaction coordinate, two force-field assumptions, and four temperatures. Nonenzymic isotope effects and isotope effects for catechol-O-methyltransferase action are then used to construct figures on the CH/sub 3//CD/sub 3/ and /sup 12/CH/sub 3///sup 13/CH/sub 3/ maps which correspond to allowed spaces of transition-states structures. Superposition of the figures yields the spaces of transition-state structures simultaneously consistent with both hydrogen and carbon isotope effects. It is concluded that the enzyme compresses the S/sub N/2 transition state and that the compression of the C-O and C-S bonds may well be of the order of 0.15 A per bond and could conceivably be more than twice as large.

  11. [Nesting habitat characterization for Amazona oratrix (Psittaciformes: Psittacidae) in the Central Pacific, Mexico].

    PubMed

    Monterrubio-Rico, Tiberio C; Álvarez-Jara, Margarito; Tellez-Garcia, Loreno; Tena-Morelos, Carlos

    2014-09-01

    The nesting requirements of the Yellow-headed Parrot (Amazona oratrix) are poorly understood, despite their broad historical distribution, high demand for pet trade and current endangered status. Information concerning their nesting requirements is required in order to design specific restoration and conser- vation actions. To assess this, we studied their nesting ecology in the Central Pacific, Michoacan, Mexico during a ten year period. The analyzed variables ranged from local scale nest site characteristics such as nesting tree species, dimensions, geographic positions, diet and nesting forest patches structure, to large scale features such as vegetation use and climatic variables associated to the nesting tree distributions by an ecological niche model using Maxent. We also evaluated the parrot tolerance to land management regimes, and compared the Pacific nest trees with 18 nest trees recorded in an intensively managed private ranch in Tamaulipas, Gulf of Mexico. Parrots nested in tall trees with canopy level cavities in 92 nest-trees recorded from 11 tree species. The 72.8% of nesting occurred in trees of Astronium graveolens, and Enterolobium cyclocarpum which qualified as key- stone trees. The forests where the parrots nested, presented a maximum of 54 tree species, 50% of which were identified as food source; besides, these areas also had a high abundance of trees used as food supply. The lowest number of tree species and trees to forage occurred in an active cattle ranch, whereas the highest species rich- ness was observed in areas with natural recovery. The nesting cavity entrance height from above ground of the Pacific nesting trees resulted higher than those found in the Gulf of Mexico. We hypothesize that the differences may be attributed to Parrot behavioral differences adapting to differential poaching pressure and cavity avail- ability. Nesting trees were found in six vegetation types; however the parrots preferred conserved and riparian semi

  12. QTL Mapping in Three Rice Populations Uncovers Major Genomic Regions Associated with African Rice Gall Midge Resistance

    PubMed Central

    Semagn, Kassa; Sow, Mounirou; Nwilene, Francis; Kolade, Olufisayo; Bocco, Roland; Oyetunji, Olumoye; Mitchell-Olds, Thomas; Ndjiondjop, Marie-Noëlle

    2016-01-01

    African rice gall midge (AfRGM) is one of the most destructive pests of irrigated and lowland African ecologies. This study aimed to identify the quantitative trait loci (QTL) associated with AfRGM pest incidence and resistance in three independent bi-parental rice populations (ITA306xBW348-1, ITA306xTOG7106 and ITA306xTOS14519), and to conduct meta QTL (mQTL) analysis to explore whether any genomic regions are conserved across different genetic backgrounds. Composite interval mapping (CIM) conducted on the three populations independently uncovered a total of 28 QTLs associated with pest incidence (12) and pest severity (16). The number of QTLs per population associated with AfRGM resistance varied from three in the ITA306xBW348-1 population to eight in the ITA306xTOG7106 population. Each QTL individually explained 1.3 to 34.1% of the phenotypic variance. The major genomic region for AfRGM resistance had a LOD score and R2 of 60.0 and 34.1% respectively, and mapped at 111 cM on chromosome 4 (qAfrGM4) in the ITA306xTOS14519 population. The meta-analysis reduced the number of QTLs from 28 to 17 mQTLs, each explaining 1.3 to 24.5% of phenotypic variance, and narrowed the confidence intervals by 2.2 cM. There was only one minor effect mQTL on chromosome 1 that was common in the TOS14519 and TOG7106 genetic backgrounds; all other mQTLs were background specific. We are currently fine-mapping and validating the major effect genomic region on chromosome 4 (qAfRGM4). This is the first report in mapping the genomic regions associated with the AfRGM resistance, and will be highly useful for rice breeders. PMID:27508500

  13. QTL Mapping in Three Rice Populations Uncovers Major Genomic Regions Associated with African Rice Gall Midge Resistance.

    PubMed

    Yao, Nasser; Lee, Cheng-Ruei; Semagn, Kassa; Sow, Mounirou; Nwilene, Francis; Kolade, Olufisayo; Bocco, Roland; Oyetunji, Olumoye; Mitchell-Olds, Thomas; Ndjiondjop, Marie-Noëlle

    2016-01-01

    African rice gall midge (AfRGM) is one of the most destructive pests of irrigated and lowland African ecologies. This study aimed to identify the quantitative trait loci (QTL) associated with AfRGM pest incidence and resistance in three independent bi-parental rice populations (ITA306xBW348-1, ITA306xTOG7106 and ITA306xTOS14519), and to conduct meta QTL (mQTL) analysis to explore whether any genomic regions are conserved across different genetic backgrounds. Composite interval mapping (CIM) conducted on the three populations independently uncovered a total of 28 QTLs associated with pest incidence (12) and pest severity (16). The number of QTLs per population associated with AfRGM resistance varied from three in the ITA306xBW348-1 population to eight in the ITA306xTOG7106 population. Each QTL individually explained 1.3 to 34.1% of the phenotypic variance. The major genomic region for AfRGM resistance had a LOD score and R2 of 60.0 and 34.1% respectively, and mapped at 111 cM on chromosome 4 (qAfrGM4) in the ITA306xTOS14519 population. The meta-analysis reduced the number of QTLs from 28 to 17 mQTLs, each explaining 1.3 to 24.5% of phenotypic variance, and narrowed the confidence intervals by 2.2 cM. There was only one minor effect mQTL on chromosome 1 that was common in the TOS14519 and TOG7106 genetic backgrounds; all other mQTLs were background specific. We are currently fine-mapping and validating the major effect genomic region on chromosome 4 (qAfRGM4). This is the first report in mapping the genomic regions associated with the AfRGM resistance, and will be highly useful for rice breeders. PMID:27508500

  14. Teaching Ecological Interactions with Mud Dauber Nests.

    ERIC Educational Resources Information Center

    Matthews, Robert W.

    1997-01-01

    Describes the use of mud dauber wasp nests in laboratory activities in ecology and behavior and life science classes. Provides students with an opportunity to develop and practice basic skills including dissection, identification, observation, measurement, and communication. Discusses the life of mud daubers, obtaining and storing nests,…

  15. Olive Ridley Sea Turtle Hatching Success as a Function of the Microbial Abundance in Nest Sand at Ostional, Costa Rica

    PubMed Central

    Bézy, Vanessa S.; Valverde, Roldán A.; Plante, Craig J.

    2015-01-01

    Several studies have suggested that significant embryo mortality is caused by microbes, while high microbial loads are generated by the decomposition of eggs broken by later nesting turtles. This occurs commonly when nesting density is high, especially during mass nesting events (arribadas). However, no previous research has directly quantified microbial abundance and the associated effects on sea turtle hatching success at a nesting beach. The aim of this study was to test the hypothesis that the microbial abundance in olive ridley sea turtle nest sand affects the hatching success at Ostional, Costa Rica. We applied experimental treatments to alter the microbial abundance within the sand into which nests were relocated. We monitored temperature, oxygen, and organic matter content throughout the incubation period and quantified the microbial abundance within the nest sand using a quantitative polymerase chain reaction (qPCR) molecular analysis. The most successful treatment in increasing hatching success was the removal and replacement of nest sand. We found a negative correlation between hatching success and fungal abundance (fungal 18S rRNA gene copies g-1 nest sand). Of secondary importance in determining hatching success was the abundance of bacteria (bacterial 16S rRNA gene copies g-1 g-1 nest sand). Our data are consistent with the hypothesis that high microbial activity is responsible for the lower hatching success observed at Ostional beach. Furthermore, the underlying mechanism appears to be the deprivation of oxygen and exposure to higher temperatures resulting from microbial decomposition in the nest. PMID:25714355

  16. Agronomic and Seed Quality Traits Dissected by Genome-Wide Association Mapping in Brassica napus.

    PubMed

    Körber, Niklas; Bus, Anja; Li, Jinquan; Parkin, Isobel A P; Wittkop, Benjamin; Snowdon, Rod J; Stich, Benjamin

    2016-01-01

    In Brassica napus breeding, traits related to commercial success are of highest importance for plant breeders. However, such traits can only be assessed in an advanced developmental stage. Molecular markers genetically linked to such traits have the potential to accelerate the breeding process of B. napus by marker-assisted selection. Therefore, the objectives of this study were to identify (i) genome regions associated with the examined agronomic and seed quality traits, (ii) the interrelationship of population structure and the detected associations, and (iii) candidate genes for the revealed associations. The diversity set used in this study consisted of 405 B. napus inbred lines which were genotyped using a 6K single nucleotide polymorphism (SNP) array and phenotyped for agronomic and seed quality traits in field trials. In a genome-wide association study, we detected a total of 112 associations between SNPs and the seed quality traits as well as 46 SNP-trait associations for the agronomic traits with a P < 1.28e-05 (Bonferroni correction of α = 0.05) for the inbreds of the spring and winter trial. For the seed quality traits, a single SNP-sulfur concentration in seeds (SUL) association explained up to 67.3% of the phenotypic variance, whereas for the agronomic traits, a single SNP-blossom color (BLC) association explained up to 30.2% of the phenotypic variance. In a basic local alignment search tool (BLAST) search within a distance of 2.5 Mbp around these SNP-trait associations, 62 hits of potential candidate genes with a BLAST-score of ≥100 and a sequence identity of ≥70% to A. thaliana or B. rapa could be found for the agronomic SNP-trait associations and 187 hits of potential candidate genes for the seed quality SNP-trait associations. PMID:27066036

  17. Agronomic and Seed Quality Traits Dissected by Genome-Wide Association Mapping in Brassica napus

    PubMed Central

    Körber, Niklas; Bus, Anja; Li, Jinquan; Parkin, Isobel A. P.; Wittkop, Benjamin; Snowdon, Rod J.; Stich, Benjamin

    2016-01-01

    In Brassica napus breeding, traits related to commercial success are of highest importance for plant breeders. However, such traits can only be assessed in an advanced developmental stage. Molecular markers genetically linked to such traits have the potential to accelerate the breeding process of B. napus by marker-assisted selection. Therefore, the objectives of this study were to identify (i) genome regions associated with the examined agronomic and seed quality traits, (ii) the interrelationship of population structure and the detected associations, and (iii) candidate genes for the revealed associations. The diversity set used in this study consisted of 405 B. napus inbred lines which were genotyped using a 6K single nucleotide polymorphism (SNP) array and phenotyped for agronomic and seed quality traits in field trials. In a genome-wide association study, we detected a total of 112 associations between SNPs and the seed quality traits as well as 46 SNP-trait associations for the agronomic traits with a P < 1.28e-05 (Bonferroni correction of α = 0.05) for the inbreds of the spring and winter trial. For the seed quality traits, a single SNP-sulfur concentration in seeds (SUL) association explained up to 67.3% of the phenotypic variance, whereas for the agronomic traits, a single SNP-blossom color (BLC) association explained up to 30.2% of the phenotypic variance. In a basic local alignment search tool (BLAST) search within a distance of 2.5 Mbp around these SNP-trait associations, 62 hits of potential candidate genes with a BLAST-score of ≥100 and a sequence identity of ≥70% to A. thaliana or B. rapa could be found for the agronomic SNP-trait associations and 187 hits of potential candidate genes for the seed quality SNP-trait associations. PMID:27066036

  18. Genomic-associated Markers and comparative Genome Maps of Xanthomonas oryzae pv. oryzae and X. oryzae pv. oryzicola.

    PubMed

    Feng, Wenjie; Wang, Yi; Huang, Lisha; Feng, Chuanshun; Chu, Zhaohui; Ding, Xinhua; Yang, Long

    2015-09-01

    Xanthomonas oryzae pv. oryzae (Xoo) and X. oryzae pv. oryzicola (Xoc) cause two major seed quarantine diseases in rice, bacterial blight and bacterial leaf streak, respectively. Xoo and Xoc share high similarity in genomic sequence, which results in hard differentiation of the two pathogens. Genomic-associated Markers and comparative Genome Maps database (GMGM) is an integrated database providing comprehensive information including compared genome maps and full genomic-coverage molecular makers of Xoo and Xoc. This database was established based on bioinformatic analysis of complete sequenced genomes of several X. oryzae pathovars of which the similarity of the genomes was up to 91.39 %. The program was designed with a series of specific PCR primers, including 286 pairs of Xoo dominant markers, 288 pairs of Xoc dominant markers, and 288 pairs of Xoo and Xoc co-dominant markers, which were predicted to distinguish two pathovars. Test on a total of 40 donor pathogen strains using randomly selected 120 pairs of primers demonstrated that over 52.5 % of the primers were efficacious. The GMGM web portal ( http://biodb.sdau.edu.cn/gmgm/ ) will be a powerful tool that can present highly specific diagnostic markers, and it also provides information about comparative genome maps of the two pathogens for future evolution study. PMID:26093644

  19. On Initial Brain Activity Mapping of Associative Memory Code in the Hippocampus

    PubMed Central

    Tsien, Joe Z.; Li, Meng; Osan, Remus; Chen, Guifen; Lin, Longian; Lei Wang, Phillip; Frey, Sabine; Frey, Julietta; Zhu, Dajiang; Liu, Tianming; Zhao, Fang; Kuang, Hui

    2013-01-01

    It has been widely recognized that the understanding of the brain code would require large-scale recording and decoding of brain activity patterns. In 2007 with support from Georgia Research Alliance, we have launched the Brain Decoding Project Initiative with the basic idea which is now similarly advocated by BRAIN project or Brain Activity Map proposal. As the planning of the BRAIN project is currently underway, we share our insights and lessons from our efforts in mapping real-time episodic memory traces in the hippocampus of freely behaving mice. We show that appropriate large-scale statistical methods are essential to decipher and measure real-time memory traces and neural dynamics. We also provide an example of how the carefully designed, sometime thinking-outside-the-box, behavioral paradigms can be highly instrumental to the unraveling of memory-coding cell assembly organizing principle in the hippocampus. Our observations to date have led us to conclude that the specific-to-general categorical and combinatorial feature-coding cell assembly mechanism represents an emergent property for enabling the neural networks to generate and organize not only episodic memory, but also semantic knowledge and imagination. PMID:23838072

  20. A unified approach to analyzing nest success

    USGS Publications Warehouse

    Shaffer, T.L.

    2004-01-01

    Logistic regression has become increasingly popular for modeling nest success in terms of nest-specific explanatory variables. However, logistic regression models for nest fate are inappropriate when applied to data from nests found at various ages, for the same reason that the apparent estimator of nest success is biased (i.e. older clutches are more likely to be successful than younger clutches). A generalized linear model is presented and illustrated that gives ornithologists access to a flexible, suitable alternative to logistic regression that is appropriate when exposure periods vary, as they usually do. Unlike the Mayfield method and the logistic regression method of Aebischer (1999), the logistic-exposure model requires no assumptions about when nest losses occur. Nest survival models involving continuous and categorical explanatory variables, multi-way classifications, and time-specific (e.g. nest age) and random effects are easily implemented with the logistic-exposure model. Application of the model to a sample of Yellow-breasted Chat (Icteria virens) nests shows that logistic-exposure estimates for individual levels of categorical explanatory variables agree closely with estimates obtained with Johnson's (1979) constant-survival estimator. Use of the logistic-exposure method to model time-specific effects of nest age and date on survival of Blue-winged Teal (Anas discors) and Mallard (A. platyrhynchos) nests gives results comparable to those reported by Klett and Johnson (1982). However, the logistic-exposure approach is less subjective and much easier to implement than Klett and Johnson's method. In addition, logistic-exposure survival rate estimates are constrained to the (0,1) interval, whereas Klett and Johnson estimates are not. When applied to a sample of Mountain Plover (Charadrius montanus) nests, the logistic-exposure method gives results either identical to, or similar to, those obtained with the nest survival model in program MARK. I

  1. Mapping Associations between Interests and Personality: Toward a Conceptual Understanding of Individual Differences in Vocational Behavior

    ERIC Educational Resources Information Center

    Sullivan, Brandon A.; Hansen, Jo-Ida C.

    2004-01-01

    This study tested the hypothesis that previously reported associations between personality traits and vocational interests can be accounted for by associations between lower order personality traits and interests. Personality traits were explored using the Revised NEO Personality Inventory (P. T. Costa & R. R. McCrae, I992b), which measures the…

  2. Association mapping for yield and grain quality traits in rice (Oryza sativa L.)

    PubMed Central

    2010-01-01

    Association analysis was applied to a panel of accessions of Embrapa Rice Core Collection (ERiCC) with 86 SSR and field data from two experiments. A clear subdivision between lowland and upland accessions was apparent, thereby indicating the presence of population structure. Thirty-two accessions with admixed ancestry were identified through structure analysis, these being discarded from association analysis, thus leaving 210 accessions subdivided into two panels. The association of yield and grain-quality traits with SSR was undertaken with a mixed linear model, with markers and subpopulation as fixed factors, and kinship matrix as a random factor. Eight markers from the two appraised panels showed significant association with four different traits, although only one (RM190) maintained the marker-trait association across years and cultivation. The significant association detected between amylose content and RM190 was in agreement with previous QTL analyses in the literature. Herein, the feasibility of undertaking association analysis in conjunction with germplasm characterization was demonstrated, even when considering low marker density. The high linkage disequilibrium expected in rice lines and cultivars facilitates the detection of marker-trait associations for implementing marker assisted selection, and the mining of alleles related to important traits in germplasm. PMID:21637426

  3. Association mapping for yield and grain quality traits in rice (Oryza sativa L.).

    PubMed

    de Oliveira Borba, Tereza Cristina; Brondani, Rosana Pereira Vianello; Breseghello, Flávio; Coelho, Alexandre Siqueira Guedes; Mendonça, João Antônio; Rangel, Paulo Hideo Nakano; Brondani, Claudio

    2010-07-01

    Association analysis was applied to a panel of accessions of Embrapa Rice Core Collection (ERiCC) with 86 SSR and field data from two experiments. A clear subdivision between lowland and upland accessions was apparent, thereby indicating the presence of population structure. Thirty-two accessions with admixed ancestry were identified through structure analysis, these being discarded from association analysis, thus leaving 210 accessions subdivided into two panels. The association of yield and grain-quality traits with SSR was undertaken with a mixed linear model, with markers and subpopulation as fixed factors, and kinship matrix as a random factor. Eight markers from the two appraised panels showed significant association with four different traits, although only one (RM190) maintained the marker-trait