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Sample records for nested association mapping

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

    USDA-ARS?s Scientific Manuscript database

    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. Genetic characterization of the soybean Nested Association Mapping (NAM) population

    USDA-ARS?s Scientific Manuscript database

    A population of nested association mapping (NAM) families can be a valuable resource to a research community. A set of NAM families were developed by crossing 40 diverse soybean genotypes to the common hub cultivar IA 3023. The 41 parents were sequenced with next generation sequencing for single nuc...

  3. In silico genotyping of the maize nested association mapping population

    PubMed Central

    Guo, Baohong

    2010-01-01

    Nested Association Mapping (NAM) has been proposed as a means to combine the power of linkage mapping with the resolution of association mapping. It is enabled through sequencing or array genotyping of parental inbred lines while using low-cost, low-density genotyping technologies for their segregating progenies. For purposes of data analyses of NAM populations, parental genotypes at a large number of Single Nucleotide Polymorphic (SNP) loci need to be projected to their segregating progeny. Herein we demonstrate how approximately 0.5 million SNPs that have been genotyped in 26 parental lines of the publicly available maize NAM population can be projected onto their segregating progeny using only 1,106 SNP loci that have been genotyped in both the parents and their 5,000 progeny. The challenge is to estimate both the genotype and genetic location of the parental SNP genotypes in segregating progeny. Both challenges were met by estimating their expected genotypic values conditional on observed flanking markers through the use of both physical and linkage maps. About 90%, of 500,000 genotyped SNPs from the maize HapMap project, were assigned linkage map positions using linear interpolation between the maize Accessioned Gold Path (AGP) and NAM linkage maps. Of these, almost 70% provided high probability estimates of genotypes in almost 5,000 recombinant inbred lines. PMID:21289856

  4. Nested Association Mapping for Identification of Functional Markers

    PubMed Central

    Guo, Baohong; Sleper, David A.; Beavis, William D.

    2010-01-01

    Identification of functional markers (FMs) provides information about the genetic architecture underlying complex traits. An approach that combines the strengths of linkage and association mapping, referred to as nested association mapping (NAM), has been proposed to identify FMs in many plant species. The ability to identify and resolve FMs for complex traits depends upon a number of factors including frequency of FM alleles, magnitudes of their genetic effects, disequilibrium among functional and nonfunctional markers, statistical analysis methods, and mating design. The statistical characteristics of power, accuracy, and precision to identify FMs with a NAM population were investigated using three simulation studies. The simulated data sets utilized publicly available genetic sequences and simulated FMs were identified using least-squares variable selection methods. Results indicate that FMs with simple additive genetic effects that contribute at least 5% to the phenotypic variability in at least five segregating families of a NAM population consisting of recombinant inbred progeny derived from 28 matings with a single reference inbred will have adequate power to accurately and precisely identify FMs. This resolution and power are possible even for genetic architectures consisting of disequilibrium among multiple functional and nonfunctional markers in the same genomic region, although the resolution of FMs will deteriorate rapidly if more than two FMs are tightly linked within the same amplicon. Finally, nested mating designs involving several reference parents will have a greater likelihood of resolving FMs than single reference designs. PMID:20551444

  5. Genetic Architecture of a Rice Nested Association Mapping Population.

    PubMed

    Fragoso, Christopher A; Moreno, Maria; Wang, Zuoheng; Heffelfinger, Christopher; Arbelaez, Lady J; Aguirre, John A; Franco, Natalia; Romero, Luz E; Labadie, Karine; Zhao, Hongyu; Dellaporta, Stephen L; Lorieux, Mathias

    2017-06-07

    Describing the genetic diversity in the gene pool of crops will provide breeders with novel resources for varietal improvement. Nested Association Mapping (NAM) populations are uniquely suited for characterizing parental diversity through the shuffling and fixation of parental haplotypes. Here, we describe a set of 1879 rice NAM lines created through the selfing and single-seed descent of F1 hybrids derived from elite IR64 indica crossed with 10 diverse tropical japonica lines. Genotyping data indicated tropical japonica alleles were captured at every queried locus despite the presence of segregation distortion factors. Several distortion loci were mapped, both shared and unique, among the 10 populations. Using two-point and multi-point genetic map calculations, our datasets achieved the ∼1500 cM expected map size in rice. Finally, we highlighted the utility of the NAM lines for QTL mapping, including joint analysis across the 10 populations, by confirming known QTL locations for the trait days to heading. Copyright © 2017 Fragoso et al.

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

    USDA-ARS?s Scientific Manuscript database

    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...

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

    USDA-ARS?s Scientific Manuscript database

    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...

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

    USDA-ARS?s Scientific Manuscript database

    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...

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

    USDA-ARS?s Scientific Manuscript database

    Carbon (C) and nitrogen (N) metabolism are critical to plant growth and development and at the basis of yield and adaptation. We have applied high throughput metabolite analyses to over 12,000 diverse field grown samples from the maize nested association mapping population. This allowed us to identi...

  10. Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population

    USDA-ARS?s Scientific Manuscript database

    Nested association mapping (NAM) offers unprecedented power to resolve complex, quantitative traits to their causal loci. The maize NAM population, consisting of 5000 lines from 25 families representing the global diversity of maize, was evaluated for resistance to Southern leaf blight (SLB) diseas...

  11. 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

  12. Increased Power To Dissect Adaptive Traits in Global Sorghum Diversity Using a Nested Association Mapping Population

    PubMed Central

    Bouchet, Sophie; Olatoye, Marcus O.; Marla, Sandeep R.; Perumal, Ramasamy; Tesso, Tesfaye; Yu, Jianming; Tuinstra, Mitch; Morris, Geoffrey P.

    2017-01-01

    Adaptation of domesticated species to diverse agroclimatic regions has led to abundant trait diversity. However, the resulting population structure and genetic heterogeneity confounds association mapping of adaptive traits. To address this challenge in sorghum [Sorghum bicolor (L.) Moench]—a widely adapted cereal crop—we developed a nested association mapping (NAM) population using 10 diverse global lines crossed with an elite reference line RTx430. We characterized the population of 2214 recombinant inbred lines at 90,000 SNPs using genotyping-by-sequencing. The population captures ∼70% of known global SNP variation in sorghum, and 57,411 recombination events. Notably, recombination events were four- to fivefold enriched in coding sequences and 5′ untranslated regions of genes. To test the power of the NAM population for trait dissection, we conducted joint linkage mapping for two major adaptive traits, flowering time and plant height. We precisely mapped several known genes for these two traits, and identified several additional QTL. Considering all SNPs simultaneously, genetic variation accounted for 65% of flowering time variance and 75% of plant height variance. Further, we directly compared NAM to genome-wide association mapping (using panels of the same size) and found that flowering time and plant height QTL were more consistently identified with the NAM population. Finally, for simulated QTL under strong selection in diversity panels, the power of QTL detection was up to three times greater for NAM vs. association mapping with a diverse panel. These findings validate the NAM resource for trait mapping in sorghum, and demonstrate the value of NAM for dissection of adaptive traits. PMID:28592497

  13. Increased Power To Dissect Adaptive Traits in Global Sorghum Diversity Using a Nested Association Mapping Population.

    PubMed

    Bouchet, Sophie; Olatoye, Marcus O; Marla, Sandeep R; Perumal, Ramasamy; Tesso, Tesfaye; Yu, Jianming; Tuinstra, Mitch; Morris, Geoffrey P

    2017-06-01

    Adaptation of domesticated species to diverse agroclimatic regions has led to abundant trait diversity. However, the resulting population structure and genetic heterogeneity confounds association mapping of adaptive traits. To address this challenge in sorghum [Sorghum bicolor (L.) Moench]-a widely adapted cereal crop-we developed a nested association mapping (NAM) population using 10 diverse global lines crossed with an elite reference line RTx430. We characterized the population of 2214 recombinant inbred lines at 90,000 SNPs using genotyping-by-sequencing. The population captures ∼70% of known global SNP variation in sorghum, and 57,411 recombination events. Notably, recombination events were four- to fivefold enriched in coding sequences and 5' untranslated regions of genes. To test the power of the NAM population for trait dissection, we conducted joint linkage mapping for two major adaptive traits, flowering time and plant height. We precisely mapped several known genes for these two traits, and identified several additional QTL. Considering all SNPs simultaneously, genetic variation accounted for 65% of flowering time variance and 75% of plant height variance. Further, we directly compared NAM to genome-wide association mapping (using panels of the same size) and found that flowering time and plant height QTL were more consistently identified with the NAM population. Finally, for simulated QTL under strong selection in diversity panels, the power of QTL detection was up to three times greater for NAM vs. association mapping with a diverse panel. These findings validate the NAM resource for trait mapping in sorghum, and demonstrate the value of NAM for dissection of adaptive traits. Copyright © 2017 by the Genetics Society of America.

  14. Genetic Architecture of Maize Kernel Composition in the Nested Association Mapping and Inbred Association Panels1[W

    PubMed Central

    Cook, Jason P.; McMullen, Michael D.; Holland, James B.; Tian, Feng; Bradbury, Peter; Ross-Ibarra, Jeffrey; Buckler, Edward S.; Flint-Garcia, Sherry A.

    2012-01-01

    The maize (Zea mays) 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 joint-linkage quantitative trait locus mapping and genome-wide association studies (GWAS) for kernel starch, protein, and oil in the maize nested association mapping population, composed of 25 recombinant inbred line families derived from diverse inbred lines. Joint-linkage mapping revealed that the genetic architecture of kernel composition traits is controlled by 21–26 quantitative trait loci. Numerous GWAS associations were detected, including several oil and starch associations in acyl-CoA:diacylglycerol acyltransferase1-2, a gene that regulates oil composition and quantity. Results from nested association mapping were verified in a 282 inbred association panel using both GWAS and candidate gene association approaches. We identified many beneficial alleles that will be useful for improving kernel starch, protein, and oil content. PMID:22135431

  15. Numerous genetic loci identified for drought tolerance in the maize nested association mapping populations.

    PubMed

    Li, Chunhui; Sun, Baocheng; Li, Yongxiang; Liu, Cheng; Wu, Xun; Zhang, Dengfeng; Shi, Yunsu; Song, Yanchun; Buckler, Edward S; Zhang, Zhiwu; Wang, Tianyu; Li, Yu

    2016-11-08

    Maize requires more water than most other crops; therefore, the water use efficiency of this crop must be improved for maize production under undesirable land and changing environmental conditions. To elucidate the genetic control of drought in maize, we evaluated approximately 5000 inbred lines from 30 linkage-association joint mapping populations under two contrasting water regimes for seven drought-related traits, including yield and anthesis-silking interval (ASI). The joint linkage analysis was conducted to identify 220 quantitative trait loci (QTLs) under well-watered conditions and 169 QTLs under water-stressed conditions. The genome-wide association analysis identified 365 single nucleotide polymorphisms (SNPs) associated with drought-related traits, and these SNPs were located in 354 candidate genes. Fifty-two of these genes showed significant differential expression in the inbred line B73 under the well-watered and water-stressed conditions. In addition, genomic predictions suggested that the moderate-density SNPs obtained through genotyping-by-sequencing were able to make accurate predictions in the nested association mapping population for drought-related traits with moderate-to-high heritability under the water-stressed conditions. The results of the present study provide important information that can be used to understand the genetic basis of drought stress responses and facilitate the use of beneficial alleles for the improvement of drought tolerance in maize.

  16. Elementary maps on nest algebras

    NASA Astrophysics Data System (ADS)

    Li, Pengtong

    2006-08-01

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

  17. Nested association mapping for dissecting complex traits using Peanut 58K SNP array

    USDA-ARS?s Scientific Manuscript database

    Genome-wide association studies (GWAS) and linkage mapping have been the two most predominant strategies to dissect complex traits, but are limited by the occurrence of false positives reported for GWAS, and low resolution in the case of linkage analysis. This has led to the development of a joint a...

  18. 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

  19. Development and genetic characterization of an Advanced Backcross-Nested Association Mapping (AB-NAM) population of wild × cultivated barley

    USDA-ARS?s Scientific Manuscript database

    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 ...

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

    USDA-ARS?s Scientific Manuscript database

    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...

  1. 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

  2. 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

    2016-09-02

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

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

    SciTech Connect

    Saha, Malay C.; Brummer, E. Charles; Kaeppler, Shawn; Bhandari, Hem S.

    2016-10-28

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

    Andrade, Luciano Rogério Braatz de; Fritsche Neto, Roberto; Granato, Ítalo Stefanine Correia; Sant'Ana, Gustavo César; Morais, Pedro Patric Pinho; Borém, Aluízio

    2016-01-01

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

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

    PubMed

    Ogut, F; Bian, Y; Bradbury, P J; Holland, J B

    2015-06-01

    Quantitative trait locus (QTL) mapping has been used to dissect the genetic architecture of complex traits 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 alternative approach to QTL mapping with a wider scope of inference. Joint-multiple population analysis should have higher power to detect QTL shared among multiple families, but may have lower power to detect rare QTL. We compared prediction ability of single-family and joint-family QTL analysis methods with fivefold cross-validation for 6 diverse traits using the maize nested association mapping population, which comprises 25 biparental recombinant inbred families. Joint-family QTL analysis had higher mean prediction abilities than single-family QTL analysis for all traits at most significance thresholds, and was always better at more stringent significance thresholds. Most robust QTL (detected in >50% of data samples) were restricted to one family and were often not detected at high frequency by joint-family analysis, implying substantial genetic heterogeneity among families for complex traits in maize. The superior predictive ability of joint-family QTL models despite important genetic differences among families suggests that joint-family models capture sufficient smaller effect QTL that are shared across families to compensate for missing some rare large-effect QTL.

  7. Detecting the QTL-allele system conferring flowering date in a nested association mapping population of soybean using a novel procedure.

    PubMed

    Li, Shuguang; Cao, Yongce; He, Jianbo; Zhao, Tuanjie; Gai, Junyi

    2017-08-10

    The RTM-GWAS was chosen among five procedures to identify DTF QTL-allele constitution in a soybean NAM population; 139 QTLs with 496 alleles accounting for 81.7% of phenotypic variance were detected. Flowering date (days to flowering, DTF) is an ecological trait in soybean, closely related to its ability to adapt to areas. A nested association mapping (NAM) population consisting of four RIL populations (LM, ZM, MT and MW with M8206 as their common parent) was established and tested for their DTF under five environments. Using restriction-site-associated DNA sequencing the population was genotyped with SNP markers. The restricted two-stage multi-locus (RTM) genome-wide association study (GWAS) (RTM-GWAS) with SNP linkage disequilibrium block (SNPLDB) as multi-allele genomic markers performed the best among the five mapping procedures with software publicly available. It identified the greatest number of quantitative trait loci (QTLs) (139) and alleles (496) on 20 chromosomes covering almost all of the QTLs detected by four other mapping procedures. The RTM-GWAS provided the detected QTLs with highest genetic contribution but without overflowing and missing heritability problems (81.7% genetic contribution vs. heritability of 97.6%), while SNPLDB markers matched the NAM population property of multiple alleles per locus. The 139 QTLs with 496 alleles were organized into a QTL-allele matrix, showing the corresponding DTF genetic architecture of the five parents and the NAM population. All lines and parents comprised both positive and negative alleles, implying a great potential of recombination for early and late DTF improvement. From the detected QTL-allele system, 126 candidate genes were annotated and χ (2) tested as a DTF candidate gene system involving nine biological processes, indicating the trait a complex, involving several biological processes rather than only a handful of major genes.

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

    PubMed Central

    Ren, Yan; Hou, Weixiu; Lan, Caixia; Basnet, Bhoja R.; Singh, Ravi P.; Zhu, Wei; Cheng, Xiyong; Cui, Dangqun; Chen, Feng

    2017-01-01

    CIMMYT wheat (Triticum aestivum L.) lines Francolin#1 and Quaiu#3 displayed effective and stable adult plant resistance (APR) to Chinese Blumeria graminis f. sp. tritici isolates in the field. To elucidate their genetic basis of resistance, two recombinant inbred line (RIL) populations of their crosses with Avocet, the susceptible parent, were phenotyped in Zhengzhou and Shangqiu in the 2014–2015 and 2015–2016 cropping seasons. These populations were also genotyped with SSR (simple sequence repeat markers) and DArT (diversity arrays technology) markers. Two common significant quantitative trait loci (QTL) on wheat chromosomes 1BL and 4BL were detected in both populations by joint and individual inclusive composite interval mapping, explaining 20.3–28.7% and 9.6–15.9% of the phenotypic variance in Avocet × Francolin#1 and 4.8–11.5% and 10.8–18.9% in Avocet × Quaiu#3, respectively. Additional QTL were mapped on chromosomes 1DL and 5BL in Avocet × Francolin#1 and on 2DL and 6BS in Avocet × Quaiu#3. Among these, QPm.heau-1DL is probably a novel APR gene contributing 6.1–8.5% of total phenotypic variance. The QTL on 1BL corresponds to the pleiotropic multi-pathogen resistance gene Yr29/Lr46/Pm39, whereas the QTL on 2DL maps to a similar region where stripe rust resistance gene Yr54 is located. The QTL identified can potentially be used for the improvement of powdery mildew and rust resistance in wheat breeding. PMID:28798752

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

    PubMed Central

    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.

    2016-01-01

    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 (r2 = 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

  10. 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.

  11. 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

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

    PubMed

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

    2015-03-01

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

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

    PubMed

    Hung, H-Y; Browne, C; Guill, K; Coles, N; Eller, M; Garcia, A; Lepak, N; Melia-Hancock, S; Oropeza-Rosas, M; Salvo, S; Upadyayula, N; Buckler, E S; Flint-Garcia, S; McMullen, M D; Rocheford, T R; Holland, J B

    2012-05-01

    Appropriate selection of parents for the development of mapping populations is pivotal to maximizing the power of quantitative trait loci detection. Trait genotypic variation within a family is indicative of the family's informativeness for genetic studies. Accurate prediction of the most useful parental combinations within a species would help guide quantitative genetics studies. We tested the reliability of genotypic and phenotypic distance estimators between pairs of maize inbred lines to predict genotypic variation for quantitative traits within families derived from biparental crosses. We developed 25 families composed of ~200 random recombinant inbred lines each from crosses between a common reference parent inbred, B73, and 25 diverse maize inbreds. Parents and families were evaluated for 19 quantitative traits across up to 11 environments. Genetic distances (GDs) among parents were estimated with 44 simple sequence repeat and 2303 single-nucleotide polymorphism markers. GDs among parents had no predictive value for progeny variation, which is most likely due to the choice of neutral markers. In contrast, we observed for about half of the traits measured a positive correlation between phenotypic parental distances and within-family genetic variance estimates. Consequently, the choice of promising segregating populations can be based on selecting phenotypically diverse parents. These results are congruent with models of genetic architecture that posit numerous genes affecting quantitative traits, each segregating for allelic series, with dispersal of allelic effects across diverse genetic material. This architecture, common to many quantitative traits in maize, limits the predictive value of parental genotypic or phenotypic values on progeny variance.

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

    PubMed Central

    Hung, H-Y; Browne, C; Guill, K; Coles, N; Eller, M; Garcia, A; Lepak, N; Melia-Hancock, S; Oropeza-Rosas, M; Salvo, S; Upadyayula, N; Buckler, E S; Flint-Garcia, S; McMullen, M D; Rocheford, T R; Holland, J B

    2012-01-01

    Appropriate selection of parents for the development of mapping populations is pivotal to maximizing the power of quantitative trait loci detection. Trait genotypic variation within a family is indicative of the family's informativeness for genetic studies. Accurate prediction of the most useful parental combinations within a species would help guide quantitative genetics studies. We tested the reliability of genotypic and phenotypic distance estimators between pairs of maize inbred lines to predict genotypic variation for quantitative traits within families derived from biparental crosses. We developed 25 families composed of ∼200 random recombinant inbred lines each from crosses between a common reference parent inbred, B73, and 25 diverse maize inbreds. Parents and families were evaluated for 19 quantitative traits across up to 11 environments. Genetic distances (GDs) among parents were estimated with 44 simple sequence repeat and 2303 single-nucleotide polymorphism markers. GDs among parents had no predictive value for progeny variation, which is most likely due to the choice of neutral markers. In contrast, we observed for about half of the traits measured a positive correlation between phenotypic parental distances and within-family genetic variance estimates. Consequently, the choice of promising segregating populations can be based on selecting phenotypically diverse parents. These results are congruent with models of genetic architecture that posit numerous genes affecting quantitative traits, each segregating for allelic series, with dispersal of allelic effects across diverse genetic material. This architecture, common to many quantitative traits in maize, limits the predictive value of parental genotypic or phenotypic values on progeny variance. PMID:22027895

  15. Compositional assessments of key maize populations: B73 hybrids of the Nested Association Mapping founder lines and diverse landrace inbred lines.

    PubMed

    Venkatesh, Tyamagondlu V; Harrigan, George G; Perez, Tim; Flint-Garcia, Sherry

    2015-06-03

    The present study provides an assessment of the compositional diversity in maize B73 hybrids derived both from the Nested Association Mapping (NAM) founder lines and from a diverse collection of landrace accessions from North and South America. The NAM founders represent a key population of publicly available lines that are used extensively in the maize community to investigate the genetic basis of complex traits. Landraces are also of interest to the maize community as they offer the potential to discover new alleles that could be incorporated into modern maize lines. The compositional analysis of B73 hybrids from the 25 NAM founders and 24 inbred lines derived from landraces included measurements of proximates (protein, fat, ash, and starch), fibers, minerals, amino acids, fatty acids, tocopherols (α-, γ-, and δ-), β-carotene, phytic acid, and raffinose. Grain was harvested from a replicated trial in New York, USA. For each data set (NAM and landrace) canonical discriminant analysis allowed separation of distinct breeding groups (tropical, temperate, flint, mixed/intermediate) within each data set. Overall, results highlighted extensive variation in all composition components assessed for both sets of hybrids. The variation observed for some components within the landraces may therefore be of value for increasing their levels in modern maize lines. The study described here provided significant information on contributions of conventional breeding to crop compositional variation, as well as valuable information on key genetic resources for the maize community in the development of new improved lines.

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

    PubMed Central

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

    1993-01-01

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

  17. 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.

  18. Spatial association of nest construction by brown trout Salmo trutta.

    PubMed

    Youngson, A F; Piertney, S B; Thorley, J L; Malcolm, I A; Soulsby, C

    2011-03-01

    Spawning patterns in female brown trout Salmo trutta were examined by documenting the construction of nests in a small stream and later excavating them to recover progeny. The maternal provenance of nests was determined by genetic typing of embryos using microsatellite markers. Seventy-two nests, for which position and date of construction were known, were made by 59 individuals. Position and date of construction were known for a further 35 nests, comprising 11 Atlantic salmon Salmo salar nests and 24 nests which contained few or no progeny. Salmo trutta showed a behavioural preference for spawning near (≤ 1 m) prior nests; nests made by different individuals tended to accumulate in a spatial sequence that progressed upstream. The directionality of the association between prior and new nests suggests that later spawners use the residual depressions created by previous spawners as the first element of their own nests.

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

    USDA-ARS?s Scientific Manuscript database

    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 ...

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

    PubMed

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

    2016-03-16

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

  1. Complete excavation and mapping of a Texas leafcutting ant nest

    Treesearch

    John C. Moser

    2006-01-01

    A medium-sized nest of the Texas leafcutting ant, Atta texana (Buckley), in northern Louisiana was excavated completely, and a three-dimensional model of its external and subterranean features was constructed. In total, 97 fungus gardens, 27 dormancy cavities, and 45 detritus cavities were located. At the lower center of the funnel-shaped nest was a...

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

    PubMed

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

    2014-01-01

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

  3. 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

  4. Variables associated with nest survival of Golden-winged Warblers (Vermivora chrysoptera) among vegetation communities commonly used for nesting

    USGS Publications Warehouse

    Aldinger, Kyle R.; Terhune, Theron M.; Wood, Petra Bohall; Buehler, David A.; Bakermans, Marja H.; Confer,  John L.; Flaspohler, David J.; Larkin, Jeffrey L.; Loegering, John P.; Percy, Katie L.; Roth, Amber M.; Smalling, Curtis G.

    2015-01-01

    Among shrubland- and young forest-nesting bird species in North America, Golden-winged Warblers (Vermivora chrysoptera) are one of the most rapidly declining partly because of limited nesting habitat. Creation and management of high quality vegetation communities used for nesting are needed to reduce declines. Thus, we examined whether common characteristics could be managed across much of the Golden-winged Warbler’s breeding range to increase daily survival rate (DSR) of nests. We monitored 388 nests on 62 sites throughout Minnesota, Wisconsin, New York, North Carolina, Pennsylvania, Tennessee, and West Virginia. We evaluated competing DSR models in spatial-temporal (dominant vegetation type, population segment, state, and year), intraseasonal (nest stage and time-within-season), and vegetation model suites. The best-supported DSR models among the three model suites suggested potential associations between daily survival rate of nests and state, time-within-season, percent grass and Rubus cover within 1 m of the nest, and distance to later successional forest edge. Overall, grass cover (negative association with DSR above 50%) and Rubus cover (DSR lowest at about 30%) within 1 m of the nest and distance to later successional forest edge (negative association with DSR) may represent common management targets across our states for increasing Golden-winged Warbler DSR, particularly in the Appalachian Mountains population segment. Context-specific adjustments to management strategies, such as in wetlands or areas of overlap with Blue-winged Warblers (Vermivora cyanoptera), may be necessary to increase DSR for Golden-winged Warblers.

  5. Factors influencing predation associated with visits to artificial goose nests

    USGS Publications Warehouse

    Vacca, M. Michele; Handel, Colleen M.

    1988-01-01

    Artificial goose nests were used to determine what factors might increase predation after visits to nests of Cackling Canada Geese (Branta canadensis minima). We tested whether leaving the nest uncovered, marking the nest location with a flag, or placing the nest on an island or peninsula would increase the rate of predation. Predators destroyed significantly more of the nests with eggs exposed to view (61%) than of the nests with eggs covered with goose down (35%) (P < 0.05). However, the rate of predation was only slightly higher among nests located on peninsulas than on islands and equal proportions of flagged and unflagged nests were destroyed. We also determined that investigators attracted predators to the study area and caused an increase in predation at uncovered nests immediately after the visit. Covering the eggs with down essentially negated the effect of attracting predators when visiting the nest. Among the 46 nests destroyed, 78% were destroyed by birds and 22% by mammals. Results of our study suggested that visibility of exposed eggs rather than nest markers provided important cues to avian predators and that islands probably provided some refuge from mammalian predators. Investigators can take steps to minimize their impact on nesting success and should incorporate a measure of that impact in their studies.

  6. Nest site preferences of the Woodlark (Lullula arborea) and its association with artificial nest predation

    NASA Astrophysics Data System (ADS)

    Buehler, Roman; Bosco, Laura; Arlettaz, Raphaël; Jacot, Alain

    2017-01-01

    The Woodlark is an insectivorous bird, which is listed as a priority species in Switzerland. In Valais, a stronghold of this species in the country, the birds breed in intensively managed vineyards and show a preference for parcels with ground vegetation during territory establishment. As a ground-breeder, the species is highly vulnerable to nest predation by avian and mammal predators. The aims of our study were firstly to investigate nest site preferences of the woodlark within vineyards and secondly to compare the predation risk of artificial nests dependent of ground vegetation structure. Our results point out that the Woodlark prefers patches of tall and dense ground cover within vegetated vineyard parcels and avoids parcels that have been treated with herbicides. In a follow-up experiment we conducted a study comparing the predation rate of artificial nests between bare parcels (<20% vegetated area) and vegetated parcels (>40% vegetated area). Artificial nests equipped with one quail egg were distributed pairwise between two adjacent parcels that fulfilled the upper criteria and were monitored by trail cameras during 10-12 days. Predation rate was generally low (4 predation events) and only occurred in bare parcels. These data indicate that conspicuousness of avian nests may be decreased in vegetated parcels and that the amount of vegetation can lower the predation risk on ground breeding birds - another indication for the importance of ground vegetation for a successful conservation of the endangered Woodlark in Swiss vineyards.

  7. 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.

  8. Human chromosomal bands: nested structure, high-definition map and molecular basis.

    PubMed

    Costantini, Maria; Clay, Oliver; Federico, Concetta; Saccone, Salvatore; Auletta, Fabio; Bernardi, Giorgio

    2007-02-01

    In this paper, we report investigations on the nested structure, the high-definition mapping, and the molecular basis of the classical Giemsa and Reverse bands in human chromosomes. We found the rules according to which the approximately 3,200 isochores of the human genome are assembled in high (850-band) resolution bands, and the latter in low (400-band) resolution bands, so forming the nested mosaic structure of chromosomes. Moreover, we identified the borders of both sets of chromosomal bands at the DNA sequence level on the basis of our recent map of isochores, which represent the highest-resolution, ultimate bands. Indeed, beyond the 100-kb resolution of the isochore map, the guanine and cytosine (GC) profile of DNA becomes turbulent owing to the contribution of specific sequences such as exons, introns, interspersed repeats, CpG islands, etc. The isochore-based level of definition (100 kb) of chromosomal bands is much higher than the cytogenetic definition level (2-3 Mb). The major conclusions of this work concern the high degree of order found in the structure of chromosomal bands, their mapping at a high definition, and the solution of the long-standing problem of the molecular basis of chromosomal bands, as these could be defined on the basis of compositional DNA properties alone.

  9. 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

  10. 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.

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

    PubMed Central

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

    2016-01-01

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

  12. Radiofrequency catheter ablation of atrial fibrillation guided by spectral mapping of atrial fibrillation nests in sinus rhythm.

    PubMed

    Mateos, José Carlos Pachón; Mateos, Enrique I Pachón; Lobo, Tasso J; Pachón, Maria Zélia C; Mateos, Juán Carlos Pachón; Pachón, Denilda Queiroz V; Vargas, Remy Nelson A; Piegas, Leopoldo S; Jatene, Adib D

    2007-09-01

    Two types of myocardia can be observed through the endocardial spectral mapping (SM) in sinus rhythm: the compact type with a smooth spectrum and the fibrillar type with a segmented spectrum (atrial fibrillation nests). During the atrial fibrillation (AF), the compact type has an organized activation and low frequency (passive), whereas the fibrillar type has a rather disorganized activation and high frequency (active/resonant), with both being activated by high-frequency sustained tachycardia--the background tachycardia (BT). To describe the treatment of AF by the ablation of the AF nests and BT. 1) Catheter ablation of the AF nests with RF [4/8 mm-60 masculine/30-40 J/30s] guided by SM in sinus rhythm, outside the pulmonary vein; 2) atrial stimulation -300 ppm; 3) Additional ablation of the AF nests if AF is induced; 4) Focal ablation if BT and/or Flutter is induced; 5) Clinical follow-up+ ECG+ Holter. A total of 50+/-18 AF nests/patient were treated. After 11.3+/-8 m, 81 patients (88%) did not present AF (28.3% with antiarrhythmic drugs). After the ablation of the AF nests, AF was not reinduced in 61 patients (71%) and BT was induced and treated in 24 patients (26%). There were two episodes of pericardial bleeding (1 treated clinically and 1 surgically), caused by sheaths that are no longer used The SM in sinus rhythm can be used in the ablation of AF nests. During the AF, the AF nests present a reactive-resonant pattern and the compact myocardium is passive, stimulated by the high frequency of the BT. After the ablation of the AF nests and the BT, it was not possible to reinduce the sustained AF. The Ablation of AF nests outside the pulmonary veins showed to be safe and highly effective in the cure and/or clinical control of the AF.

  13. Genetic Properties of the Maize Nested Association Mapping Population

    USDA-ARS?s Scientific Manuscript database

    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...

  14. Ionomics of the Maize Nested Association Mapping Panel

    USDA-ARS?s Scientific Manuscript database

    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...

  15. Genetic properties of the maize nested association mapping population.

    PubMed

    McMullen, Michael D; Kresovich, Stephen; Villeda, Hector Sanchez; Bradbury, Peter; Li, Huihui; Sun, Qi; Flint-Garcia, Sherry; Thornsberry, Jeffry; Acharya, Charlotte; Bottoms, Christopher; Brown, Patrick; Browne, Chris; Eller, Magen; Guill, Kate; Harjes, Carlos; Kroon, Dallas; Lepak, Nick; Mitchell, Sharon E; Peterson, Brooke; Pressoir, Gael; Romero, Susan; Oropeza Rosas, Marco; Salvo, Stella; Yates, Heather; Hanson, Mark; Jones, Elizabeth; Smith, Stephen; Glaubitz, Jeffrey C; Goodman, Major; Ware, Doreen; Holland, James B; Buckler, Edward S

    2009-08-07

    Maize genetic diversity has been used to understand the molecular basis of phenotypic variation and to improve agricultural efficiency and sustainability. We crossed 25 diverse inbred maize lines to the B73 reference line, capturing a total of 136,000 recombination events. Variation for recombination frequencies was observed among families, influenced by local (cis) genetic variation. We identified evidence for numerous minor single-locus effects but little two-locus linkage disequilibrium or segregation distortion, which indicated a limited role for genes with large effects and epistatic interactions on fitness. We observed excess residual heterozygosity in pericentromeric regions, which suggested that selection in inbred lines has been less efficient in these regions because of reduced recombination frequency. This implies that pericentromeric regions may contribute disproportionally to heterosis.

  16. Variability of non-mutualistic filamentous fungi associated with Atta sexdens rubropilosa nests.

    PubMed

    Rodrigues, A; Pagnocca, F C; Bacci, M Júnior; Hebling, M J A; Bueno, O C; Pfenning, L H

    2005-01-01

    A survey of the filamentous fungi other than the symbiotic one found in association with Atta sexdens rubropilosa colonies was carried out. Different fungal species (27 taxa) were isolated a few days after treating the workers with toxic baits (sulfluramid; Mirex-S), from 40 laboratory and 20 field nests. Syncephalastrum racemosum (54%) and Escovopsis weberi (21%), Trichoderma harzianum (38%) and Fusarium oxysporum (23%) were the prevalent species in laboratory and field nests, respectively. Acremonium kiliense, Acremonium strictum, E. weberi, F. oxysporum, Fusarium solani, Moniliella suaveolens and T. harzianum were found in both nests' groups. We revealed that many filamentous fungi can co-exist in a dormant state inside the nests of these insects and some of them appear to be tightly associated with this environment.

  17. Fuzzy associative conjuncted maps network.

    PubMed

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

    2009-08-01

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

  18. 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.

  19. 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

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

    PubMed

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

    2014-03-01

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

  1. Invertebrate enemies and nest associates of the leaf-cutting ant Atta texana (Buckley) (Formicudae, Attini)

    Treesearch

    D.A. Waller; John C. Moser

    1990-01-01

    The complex nests of leaf-cutting ants (Formicidae; Attini) provide rich habitats for ant associates. These mounds consist of interconnected subterranean cavities that average 0.002 m3 in volume (Waler et al. 1938) and extend to depths of 7 m (Moser 1963). Many cavities contain fungus gardens, cultivated on live plant material, frass and debris....

  2. Transferability of habitat suitability models for nesting woodpeckers associated with wildfire

    Treesearch

    Quresh S. Latif; Vicki Saab; Jeff P. Hollenbeck; Jonathan G. Dudley

    2016-01-01

    Following wildfire, forest managers are challenged with meeting both socioeconomic demands (e.g., salvage logging) and mandates requiring habitat conservation for disturbance-associated wildlife (e.g., woodpeckers). Habitat suitability models for nesting woodpeckers can be informative, but tests of model transferability are needed to understand how broadly...

  3. An example of association mapping in Cacao.

    USDA-ARS?s Scientific Manuscript database

    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 ...

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

    PubMed

    Bednar, James A

    2009-01-01

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

  5. Higher nest predation risk in association with a top predator: mesopredator attraction?

    PubMed

    Morosinotto, Chiara; Thomson, Robert L; Hänninen, Mikko; Korpimäki, Erkki

    2012-10-01

    Breeding close to top predators is a widespread reproductive strategy. Breeding animals may gain indirect benefits if proximity to top predators results in a reduction of predation due to suppression of mesopredators. We tested if passerine birds gain protection from mesopredators by nesting within territories of a top predator, the Ural owl (Strix uralensis). We placed nest boxes for pied flycatchers (Ficedula hypoleuca) in Ural owl nest sites and in control sites (currently unoccupied by owls). The nest boxes were designed so that nest predation risk could be altered (experimentally increased) after flycatcher settlement; we considered predation rate as a proxy of mesopredator abundance. Overall, we found higher nest predation rates in treatment than in control sites. Flycatcher laying date did not differ between sites, but smaller clutches were laid in treatment sites compared to controls, suggesting a response to perceived predation risk. Relative nest predation rate varied between years, being higher in owl nest sites in 2 years but similar in another; this variation might be indirectly influenced by vole abundance. Proximity to Ural owl nests might represent a risky habitat for passerines. High predation rates within owl territories could be because small mesopredators that do not directly threaten owl nests are attracted to owl nest sites. This could be explained if some mesopredators use owl territories to gain protection from their own predators, or if top predators and mesopredators independently seek similar habitats.

  6. Earlier nesting by generalist predatory bird is associated with human responses to climate change.

    PubMed

    Smith, Shawn H; Steenhof, Karen; McClure, Christopher J W; Heath, Julie A

    2017-01-01

    Warming temperatures cause temporal changes in growing seasons and prey abundance that drive earlier breeding by birds, especially dietary specialists within homogeneous habitat. Less is known about how generalists respond to climate-associated shifts in growing seasons or prey phenology, which may occur at different rates across land cover types. We studied whether breeding phenology of a generalist predator, the American kestrel (Falco sparverius), was associated with shifts in growing seasons and, presumably, prey abundance, in a mosaic of non-irrigated shrub/grasslands and irrigated crops/pastures. We examined the relationship between remotely-sensed normalized difference vegetation index (NDVI) and abundance of small mammals that, with insects, constitute approximately 93% of kestrel diet biomass. We used NDVI to estimate the start of the growing season (SoGS) in irrigated and non-irrigated lands from 1992 to 2015 and tested whether either estimate of annual SoGS predicted the timing of kestrel nesting. Finally, we examined relationships among irrigated SoGS, weather and crop planting. NDVI was a useful proxy for kestrel prey because it predicted small mammal abundance and past studies showed that NDVI predicts insect abundance. NDVI-estimated SoGS advanced significantly in irrigated lands (β = -1·09 ± 0·30 SE) but not in non-irrigated lands (β = -0·57 ± 0·53). Average date of kestrel nesting advanced 15 days in the past 24 years and was positively associated with the SoGS in irrigated lands, but not the SoGS in non-irrigated lands. Advanced SoGS in irrigated lands was related to earlier planting of crops after relatively warm winters, which were more common in recent years. Despite different patterns of SoGS change between land cover types, kestrel nesting phenology shifted with earlier prey availability in irrigated lands. Kestrels may preferentially track prey in irrigated lands over non-irrigated lands because of higher quality prey on

  7. Genome-wide association mapping in plants.

    PubMed

    George, Andrew W; Cavanagh, Colin

    2015-06-01

    We present new association mapping methods which address the unique challenges of analyzing genome-wide data from multi-environment plant studies. Association studies on a genome-wide scale are being performed in plants. Unlike human studies, plant studies contain replicates whose data may be recorded across different environments. Plant studies also often employ elaborate experimental designs for controlling extraneous phenotypic variation. As a result, the genome-wide analysis of data from plant studies can be challenging. In this paper, we present QK-based association mapping for the analysis of data from plant association studies. In doing so, we have developed: (a) a general multivariate QK framework for association mapping in plant studies of arbitrary complexity; (b) a new weighted two-stage analysis approach for QK-based association mapping; (c) a heuristic procedure for determining when two-stage analysis is appropriate; and (d) a Monte Carlo sampling procedure for controlling the genome-wide type I error rate. We conduct a simulation study to evaluate the performance of our genome-wide mapping technique. We also analyze data from a multi-environment association study in wheat.

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

    USGS Publications Warehouse

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

    2008-01-01

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

  9. 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.

  10. Using survival analysis of artificial and Real Brewer's sparrow (Spizella breweri breweri) nests to model site level and nest site factors associated with nest success in the South Okanagan region of Canada

    Treesearch

    Pam Krannitz Kym Welstead

    2005-01-01

    Predation is the predominant cause of nest failure for the Brewer's Sparrow (Spizella breweri breweri), a provincially red-listed shrub-steppe species that has experienced significant declines throughout most of its range. We monitored Brewer’s Sparrow nests and conducted an artificial nest experiment, in the South Okanagan Valley,...

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

    PubMed Central

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

    2007-01-01

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

  12. A Minimally Invasive Method for Sampling Nest and Roost Cavities for Fungi: a Novel Approach to Identify the Fungi Associated with Cavity-Nesting Birds

    Treesearch

    Michelle A. Jusino; Daniel Lindner; John K. Cianchetti; Adam T. Grisé; Nicholas J. Brazee; Jeffrey R. Walters

    2014-01-01

    Relationships among cavity-nesting birds, trees, and wood decay fungi pose interesting management challenges and research questions in many systems. Ornithologists need to understand the relationships between cavity-nesting birds and fungi in order to understand the habitat requirements of these birds. Typically, researchers rely on fruiting body surveys to identify...

  13. 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

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

    USDA-ARS?s Scientific Manuscript database

    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...

  15. "Fibrous nests" in human hepatocellular carcinoma express a Wnt-induced gene signature associated with poor clinical outcome.

    PubMed

    Désert, Romain; Mebarki, Sihem; Desille, Mireille; Sicard, Marie; Lavergne, Elise; Renaud, Stéphanie; Bergeat, Damien; Sulpice, Laurent; Perret, Christine; Turlin, Bruno; Clément, Bruno; Musso, Orlando

    2016-12-01

    Hepatocellular carcinoma (HCC) is the 3rd cause of cancer-related death worldwide. Most cases arise in a background of chronic inflammation, extracellular matrix (ECM) remodeling, severe fibrosis and stem/progenitor cell amplification. Although HCCs are soft cellular tumors, they may contain fibrous nests within the tumor mass. Thus, the aim of this study was to explore cancer cell phenotypes in fibrous nests. Combined anatomic pathology, tissue microarray and real-time PCR analyses revealed that HCCs (n=82) containing fibrous nests were poorly differentiated, expressed Wnt pathway components and target genes, as well as markers of stem/progenitor cells, such as CD44, LGR5 and SOX9. Consistently, in severe liver fibroses (n=66) and in HCCs containing fibrous nests, weighted correlation analysis revealed a gene network including the myofibroblast marker ACTA2, the basement membrane components COL4A1 and LAMC1, the Wnt pathway members FZD1; FZD7; WNT2; LEF1; DKK1 and the Secreted Frizzled Related Proteins (SFRPs) 1; 2 and 5. Moreover, unbiased random survival forest analysis of a transcriptomic dataset of 247 HCC patients revealed high DKK1, COL4A1, SFRP1 and LAMC1 to be associated with advanced tumor staging as well as with bad overall and disease-free survival. In vitro, these genes were upregulated in liver cancer stem/progenitor cells upon Wnt-induced mesenchymal commitment and myofibroblast differentiation. In conclusion, fibrous nests express Wnt target genes, as well as markers of cancer stem cells and mesenchymal commitment. Fibrous nests embody the specific microenvironment of the cancer stem cell niche and can be detected by routine anatomic pathology analyses. Copyright © 2016 Elsevier Ltd. All rights reserved.

  16. 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

  17. 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

  18. {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.

  19. 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.

  20. 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)

  1. 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)

  2. Association mapping in an elite maize breeding population.

    PubMed

    Liu, Wenxin; Gowda, Manje; Steinhoff, Jana; Maurer, Hans Peter; Würschum, Tobias; Longin, Carl Friedrich Horst; Cossic, Frédéric; Reif, Jochen Christoph

    2011-09-01

    Association mapping (AM) is a powerful approach to dissect the genetic architecture of quantitative traits. The main goal of our study was to empirically compare several statistical methods of AM using data of an elite maize breeding program with respect to QTL detection power and possibility to correct for population stratification. These models were based on the inclusion of cofactors (Model A), cofactors and population effect (Model B), and SNP effects nested within populations (Model C). A total of 930 testcross progenies of an elite maize breeding population were field-evaluated for grain yield and grain moisture in multi-location trials and fingerprinted with 425 SNP markers. For grain yield, population stratification was effectively controlled by Model A. For grain moisture with a high ratio of variance among versus within populations, Model B should be applied in order to avoid potential false positives. Model C revealed large differences among allele substitution effects for trait-associated SNPs across multiple plant breeding populations. This heterogeneous SNP allele substitution effects have a severe impact for genomic selection studies, where SNP effects are often assumed to be independent of the genetic background.

  3. Host biomarkers are associated with progression to dengue haemorrhagic fever: a nested case-control study.

    PubMed

    Conroy, Andrea L; Gélvez, Margarita; Hawkes, Michael; Rajwans, Nimerta; Tran, Vanessa; Liles, W Conrad; Villar-Centeno, Luis Angel; Kain, Kevin C

    2015-11-01

    Dengue represents the most important arboviral infection worldwide. Onset of circulatory collapse can be unpredictable. Biomarkers that can identify individuals at risk of plasma leakage may facilitate better triage and clinical management. Using a nested case-control design, we randomly selected subjects from a prospective cohort study of dengue in Colombia (n=1582). Using serum collected within 96 hours of fever onset, we tested 19 biomarkers by ELISA in cases (developed dengue hemorrhagic fever or dengue shock syndrome (DHF/DSS); n=46), and controls (uncomplicated dengue fever (DF); n=65) and healthy controls (HC); n=15. Ang-1 levels were lower and angptl3, sKDR, sEng, sICAM-1, CRP, CXCL10/IP-10, IL-18 binding protein, CHI3L1, C5a and Factor D levels were increased in dengue compared to HC. sICAM-1, sEng and CXCL10/IP-10 were further elevated in subjects who subsequently developed DHF/DSS (p=0.008, p=0.028 and p=0.025, respectively). In a logistic regression model, age (odds ratio (OR) (95% CI): 0.95 (0.92-0.98), p=0.001), hyperesthesia/hyperalgesia (OR; 3.8 (1.4-10.4), p=0.008) and elevated sICAM-1 (>298ng/mL: OR; 6.3 (1.5-25.7), p=0.011) at presentation were independently associated with progression to DHF/DSS. These results suggest that inflammation and endothelial activation are important pathways in the pathogenesis of dengue and sICAM-1 levels may identify individuals at risk of plasma leakage. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

  4. 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

  5. Identification of Seven Treponema Species in Health- and Disease-Associated Dental Plaque by Nested PCR

    PubMed Central

    Willis, S. G.; Smith, K. S.; Dunn, V. L.; Gapter, L. A.; Riviere, K. H.; Riviere, G. R.

    1999-01-01

    Species-specific nested PCR was used to detect Treponema amylovorum, Treponema denticola, Treponema maltophilum, Treponema medium, Treponema pectinovorum, Treponema socranskii, and Treponema vincentii in dental plaque. Subjects with periodontitis harbored all species, but T. pectinovorum and T. vincentii were not found in plaque from disease-free subjects. PMID:9986879

  6. Identification of seven Treponema species in health- and disease-associated dental plaque by nested PCR.

    PubMed

    Willis, S G; Smith, K S; Dunn, V L; Gapter, L A; Riviere, K H; Riviere, G R

    1999-03-01

    Species-specific nested PCR was used to detect Treponema amylovorum, Treponema denticola, Treponema maltophilum, Treponema medium, Treponema pectinovorum, Treponema socranskii, and Treponema vincentii in dental plaque. Subjects with periodontitis harbored all species, but T. pectinovorum and T. vincentii were not found in plaque from disease-free subjects.

  7. Association of weather and nest-site structure with reproductive success in California spotted owls

    Treesearch

    Malcolm North; George Steger; Renee Denton; Gary Eberlein; Tom Munton; Ken Johnson

    2000-01-01

    Although the spotted owl (Strix occidentalis) has been intensively studied, factors influencing its reproduction are not well understood. We examined a 9-year demographic study of 51-86 pairs of the California spotted owl (S. o. occidentalis), weather conditions, and forest structure at nest sites in oak (Quercus sp.) woodland and...

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

    PubMed

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

    2013-02-01

    Breeding decisions in birds involve both mate and nest choice, and there is increasing evidence that social influences may modulate individual choices. Female preferences may be affected by other females' preferences and mutual choice cannot always be excluded, which makes the whole pattern more complex than assumed by most sexual selection models. Social transmission may be facilitated by particular social bonds, therefore prebreeding social networks may influence later mate choices. The other case where females share mate or resources is polygyny, generally viewed to only benefit males. If mutual benefits may arise then mechanisms should evolve to reduce the reproductive cost for females such as to reduce the cost of aggression by sharing their mate with a preferred same-sex social partner. We tested the hypothesis that females' mating decisions may be influenced by the prebreeding social network and that social partner relations established prior to breeding may share decisions (mate/sites) in a facultatively polygynous species, the European starling. Two experiments were designed to test the relative importance of male or nest by following the whole dynamics of the breeding cycle from the prebreeding period until mate and nest selection. In both cases socially isolated females tended to be excluded from breeding, while prebreeding social partners tended to share mates and to nest in close proximity, mate copying leading in some case to polygyny. The final pattern resulted both from female "likes and dislikes" and male preferences for some females. Aggressive interactions between females were rare. Vocal sharing between females may have been a clue for males as to the degree of social integration of these females. PsycINFO Database Record (c) 2013 APA, all rights reserved

  9. Comparison of Mixed-Model Approaches for Association Mapping

    USDA-ARS?s Scientific Manuscript database

    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. 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)

  11. 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)

  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

    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

  14. 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.

  15. 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.

  16. 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.    

  17. 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.

    PubMed

    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 MS(3) (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.

  18. 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.

  19. 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

    PubMed Central

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

    2012-01-01

    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 posttranslational 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. PMID:23208745

  20. 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.

  1. 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.

  2. Empty-nest-related psychological distress is associated with progression of brain white matter lesions and cognitive impairment in the elderly

    PubMed Central

    Duan, Dandan; Dong, Yuanli; Zhang, Hua; Zhao, Yingxin; Diao, Yutao; Cui, Yi; Wang, Juan; Chai, Qiang; Liu, Zhendong

    2017-01-01

    This study evaluated the association between empty-nest-related psychological distress and the progression of white matter lesions (WMLs) and cognitive impairment in 219 elderly subjects aged 60 years or over. Psychological distress was assessed using the University of California at Los Angeles Loneliness Scale (UCLA-LS) and Geriatric Depression Scale (GDS) Short-Form. Cognitive function was evaluated using the MMSE and MoCA. White matter hyperintensities (WMH) were assessed using magnetic resonance imaging. After 5.2-year follow-up, the reductions in MMSE and MoCA scores and the increases in periventricular (P)WMH, deep (D)WMH, and total WMH volumes in the empty-nest elderly were greater than those in the non-empty-nest elderly (P < 0.05). The reduced MMSE and MoCA scores and increased volumes of PWMH and total WMH in the empty-nest elderly living alone were greater than those in the empty-nest elderly living with a spouse (P < 0.05). UCLA-LS and GDS scores were significantly and independently associated with reduced MMSE and MoCA scores and the increased volumes of PWMH, DWMH, and total WMH. The results indicate that empty-nest-related psychological distress is associated with progression of WMLs and cognitive impairment in the elderly. PMID:28256594

  3. 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

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

    USDA-ARS?s Scientific Manuscript database

    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...

  5. Numerous genetic loci identified for drought tolerance in the maize nested association mapping populations

    USDA-ARS?s Scientific Manuscript database

    Maize requires more water than most other crops; therefore, the water use efficiency of this crop must be improved for maize production under undesirable land and changing environmental conditions. To elucidate the genetic control of drought in maize, we evaluated approximately 5000 inbred lines fr...

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

    USDA-ARS?s Scientific Manuscript database

    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...

  7. No Association of ApoE Genotype with Risk of Prostate Cancer: A Nested Case-Control Study.

    PubMed

    Liu, Hui; Shui, Irene M; Platz, Elizabeth A; Mucci, Lorelei A; Giovannucci, Edward L

    2015-10-01

    Previous studies found that low total cholesterol level was associated with a lower risk of high-grade prostate cancer. Apolipoprotein E (ApoE) isoform is associated with total cholesterol level. The aim of this study was to explore associations of ApoE isoforms with prostate cancer risk. We assessed ApoE genotypes and risk of prostate cancer in a prospective case-control study nested among men who provided a blood sample in 1993-95 within the Health Professionals Follow-up Study. We identified 1,169 incident cases of prostate cancer and 1,233 controls in follow-up through 2004. Associations of ApoE isoform and prostate cancer incidence were evaluated by logistic regression models. We found no statistically significant associations of ApoE variants with overall prostate cancer or Gleason sum ≤ 7 (3+4), Gleason sum ≥ 7 (4+3), clinically localized stage, or progression to metastasis or death. There was no evidence of effect modification by circulating total cholesterol or use of cholesterol-lowering drugs prior to diagnosis. ApoE variants were not associated with the risk of prostate cancer or aggressive disease. Our findings suggest that the mechanism of circulating cholesterol level affecting prostate cancer incidence may not rely on ApoE isoforms. ©2015 American Association for Cancer Research.

  8. Jet streak circulations associated with a moderate snowfall event as diagnosed from NGM model output. [Nested Grid Model

    NASA Technical Reports Server (NTRS)

    Kocin, Paul J.; Uccellini, Louis W.; Skillman, William C.; Grumm, Richard H.

    1989-01-01

    The existence, evolution, and interaction of vertical circulations associated with upper-level jet streaks during a moderate snowfall event are diagnosed using a nested grid model (NGM). The event itself is overviewed, and the diagnosis of transverse circulations utilizing NGM output is discussed. Focus is placed on the identification of the horizontal and vertical components of the circulation, the temporal evolution of the circulation, and the comparison of the circulation from successive model forecasts. A preliminary analysis of the model data indicates that the horizontal and vertical branches of the circulations can be diagnosed from the model output, and the horizontal and vertical components of the circulations may be identified and followed during an individual forecast cycle.

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

    PubMed

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

    2015-10-01

    Ecological constraints on independent breeding are recognised as major drivers of cooperative breeding across diverse lineages. How the prevalence and degree of cooperative breeding relates to ecological variation remains unresolved. Using a large data set of cooperative nesting in Polistes wasps we demonstrate that different aspects of cooperative breeding are likely to be driven by different aspects of climate. Whether or not a species forms cooperative groups is associated with greater short-term temperature fluctuations. In contrast, the number of cooperative foundresses increases in more benign environments with warmer, wetter conditions. The same data set reveals that intraspecific responses to climate variation do not mirror genus-wide trends and instead are highly heterogeneous among species. Collectively these data suggest that the ecological drivers that lead to the origin or loss of cooperation are different from those that influence the extent of its expression within populations. © 2015 John Wiley & Sons Ltd/CNRS.

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

    PubMed Central

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

    2015-01-01

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

  11. A carcinoma showing thymus-like elements of the thyroid arising in close association with solid cell nests: evidence for a precursor lesion?

    PubMed

    Yerly, Stéphane; Lobrinus, Johannes-Alexander; Bongiovanni, Massimo; Becker, Minerva; Zare, Maryam; Granger, Perrine; Pusztaszeri, Marc

    2013-04-01

    Carcinoma showing thymus-like elements (CASTLE) is a rare malignant neoplasm of the thyroid gland, morphologically and immunohistologically similar to a thymic carcinoma, whose histogenesis is still debated. Hypotheses include an origin from ectopic thymic tissue, vestige of the thymopharyngeal duct, or branchial pouch remnants from which solid cell nests (SC-nests) originate. The diagnosis of CASTLE may be treacherous due to its rarity and its propensity to mimic other poorly differentiated tumors such as squamous cell carcinoma. We present a case of CASTLE in a 58-year-old man initially diagnosed as a poorly differentiated squamous cell carcinoma both on fine-needle aspiration cytology (FNAC) and on biopsy, arising in close association with SC-nests. A thorough literature review, with special emphasis on its diagnosis and histogenesis of CASTLE, was also conducted. Magnetic resonance images revealed a 4.0-cm cervical mass on the left side of the trachea, involving the lateral middle/inferior portion of the left lobe of the thyroid gland. FNAC was performed with a diagnosis of "malignant cells, consistent with squamous cell carcinoma." A histological evaluation of the resected specimen revealed a malignant proliferation of cells, focally exhibiting a squamoid appearance, which were immunopositive for CD5 and p63. A diagnosis of CASTLE was made. The tumor was located in direct continuity with SC-Nests, and the cell morphology of both the SC-nests and CASTLE was very similar with merging. Moreover, the immunohistochemical expression profiles of most markers useful in the diagnosis of CASTLE were identical in the SC-nests. The inclusion of CASTLE in the differential diagnosis of poorly differentiated tumors of the thyroid region and the use of ancillary studies are essential to diagnose this rare entity associated with a relatively favorable prognosis. The close association of CASTLE with SC-nests opens the way to a new scenario for studies of its histogenesis.

  12. Comparison of Mixed-Model Approaches for Association Mapping

    PubMed Central

    Stich, Benjamin; Möhring, Jens; Piepho, Hans-Peter; Heckenberger, Martin; Buckler, Edward S.; Melchinger, Albrecht E.

    2008-01-01

    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 restricted maximum-likelihood (REML) estimate of the probability of two alleles at the same locus being identical in state but not identical by descent, and (iii) compare the results of association-mapping approaches based on adjusted entry means (two-step approaches) with the results of approaches in which the phenotypic data analysis and the association analysis were performed in one step (one-step approaches). On the basis of the phenotypic and genotypic data of 303 soft winter wheat (Triticum aestivum L.) inbreds, various association-mapping methods were evaluated. Spearman's rank correlation between P-values calculated on the basis of one- and two-stage association-mapping methods ranged from 0.63 to 0.93. The mixed-model association-mapping approaches using a kinship matrix estimated by REML are more appropriate for association mapping than the recently proposed QK method with respect to (i) the adherence to the nominal α-level and (ii) the adjusted power for detection of quantitative trait loci. Furthermore, we showed that our data set could be analyzed by using two-step approaches of the proposed association-mapping method without substantially increasing the empirical type I error rate in comparison to the corresponding one-step approaches. PMID:18245847

  13. 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.

  14. Resource quantity and quality determine the inter-specific associations between ecosystem engineers and resource users in a cavity-nest web.

    PubMed

    Robles, Hugo; Martin, Kathy

    2013-01-01

    While ecosystem engineering is a widespread structural force of ecological communities, the mechanisms underlying the inter-specific associations between ecosystem engineers and resource users are poorly understood. A proper knowledge of these mechanisms is, however, essential to understand how communities are structured. Previous studies suggest that increasing the quantity of resources provided by ecosystem engineers enhances populations of resource users. In a long-term study (1995-2011), we show that the quality of the resources (i.e. tree cavities) provided by ecosystem engineers is also a key feature that explains the inter-specific associations in a tree cavity-nest web. Red-naped sapsuckers (Sphyrapicusnuchalis) provided the most abundant cavities (52% of cavities, 0.49 cavities/ha). These cavities were less likely to be used than other cavity types by mountain bluebirds (Sialiacurrucoides), but provided numerous nest-sites (41% of nesting cavities) to tree swallows (Tachycinetabicolour). Swallows experienced low reproductive outputs in northern flicker (Colaptesauratus) cavities compared to those in sapsucker cavities (1.1 vs. 2.1 fledglings/nest), but the highly abundant flickers (33% of cavities, 0.25 cavities/ha) provided numerous suitable nest-sites for bluebirds (58%). The relative shortage of cavities supplied by hairy woodpeckers (Picoidesvillosus) and fungal/insect decay (<10% of cavities each, <0.09 cavities/ha) provided fewer breeding opportunities (<15% of nests), but represented high quality nest-sites for both bluebirds and swallows. Because both the quantity and quality of resources supplied by different ecosystem engineers may explain the amount of resources used by each resource user, conservation strategies may require different management actions to be implemented for the key ecosystem engineer of each resource user. We, therefore, urge the incorporation of both resource quantity and quality into models that assess community dynamics to

  15. Resource Quantity and Quality Determine the Inter-Specific Associations between Ecosystem Engineers and Resource Users in a Cavity-Nest Web

    PubMed Central

    Robles, Hugo; Martin, Kathy

    2013-01-01

    While ecosystem engineering is a widespread structural force of ecological communities, the mechanisms underlying the inter-specific associations between ecosystem engineers and resource users are poorly understood. A proper knowledge of these mechanisms is, however, essential to understand how communities are structured. Previous studies suggest that increasing the quantity of resources provided by ecosystem engineers enhances populations of resource users. In a long-term study (1995-2011), we show that the quality of the resources (i.e. tree cavities) provided by ecosystem engineers is also a key feature that explains the inter-specific associations in a tree cavity-nest web. Red-naped sapsuckers (Sphyrapicusnuchalis) provided the most abundant cavities (52% of cavities, 0.49 cavities/ha). These cavities were less likely to be used than other cavity types by mountain bluebirds (Sialiacurrucoides), but provided numerous nest-sites (41% of nesting cavities) to tree swallows (Tachycinetabicolour). Swallows experienced low reproductive outputs in northern flicker (Colaptesauratus) cavities compared to those in sapsucker cavities (1.1 vs. 2.1 fledglings/nest), but the highly abundant flickers (33% of cavities, 0.25 cavities/ha) provided numerous suitable nest-sites for bluebirds (58%). The relative shortage of cavities supplied by hairy woodpeckers (Picoidesvillosus) and fungal/insect decay (<10% of cavities each, <0.09 cavities/ha) provided fewer breeding opportunities (<15% of nests), but represented high quality nest-sites for both bluebirds and swallows. Because both the quantity and quality of resources supplied by different ecosystem engineers may explain the amount of resources used by each resource user, conservation strategies may require different management actions to be implemented for the key ecosystem engineer of each resource user. We, therefore, urge the incorporation of both resource quantity and quality into models that assess community dynamics to

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

    PubMed Central

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

    2016-01-01

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

  17. Bald Eagle nestling mortality associated with Argas radiatus and Argas ricei tick infestation and successful management with nest removal in Arizona, USA

    USGS Publications Warehouse

    Justice-Allen, Anne; Orr, Kathy; Schuler, Krysten L.; McCarty, Kyle; Jacobson, Kenneth; Meteyer, Carol

    2016-01-01

    Eight Bald Eagle (Haliaeetus leucocephalus) nestlings heavily infested with larval ticks were found in or under a nest near the confluence of the Verde and Salt rivers in Arizona in 2009-11. The 8-12-wk-old nestlings were slow to respond to stimuli and exhibited generalized muscle weakness or paresis of the pelvic limbs. Numerous cutaneous and subcutaneous hemorrhages were associated with sites of tick attachment. Ticks were identified as Argas radiatus and Argas ricei. Treatment with acaricides and infection with West Nile virus (WNV) may have confounded the clinical presentation in 2009 and 2010. However, WNV-negative birds exhibited similar signs in 2011. One nestling recovered from paresis within 36 h after the removal of all adult and larval ticks (>350) and was released within 3 wk. The signs present in the heavily infested Bald Eagle nestlings resembled signs associated with tick paralysis, a neurotoxin-mediated paralytic syndrome described in mammals, reptiles, and wild birds (though not eagles). Removal of the infested nest and construction of a nest platform in a different tree was necessary to break the cycle of infection. The original nesting pair constructed a new nest on the man-made platform and successfully fledged two Bald Eagles in 2012.

  18. Bald Eagle Nestling Mortality Associated with Argas radiatus and Argas ricei Tick Infestation and Successful Management with Nest Removal in Arizona, USA.

    PubMed

    Justice-Allen, Anne; Orr, Kathy; Schuler, Krysten; McCarty, Kyle; Jacobson, Kenneth; Meteyer, Carol

    2016-10-01

    Eight Bald Eagle ( Haliaeetus leucocephalus ) nestlings heavily infested with larval ticks were found in or under a nest near the confluence of the Verde and Salt rivers in Arizona in 2009-11. The 8-12-wk-old nestlings were slow to respond to stimuli and exhibited generalized muscle weakness or paresis of the pelvic limbs. Numerous cutaneous and subcutaneous hemorrhages were associated with sites of tick attachment. Ticks were identified as Argas radiatus and Argas ricei. Treatment with acaricides and infection with West Nile virus (WNV) may have confounded the clinical presentation in 2009 and 2010. However, WNV-negative birds exhibited similar signs in 2011. One nestling recovered from paresis within 36 h after the removal of all adult and larval ticks (>350) and was released within 3 wk. The signs present in the heavily infested Bald Eagle nestlings resembled signs associated with tick paralysis, a neurotoxin-mediated paralytic syndrome described in mammals, reptiles, and wild birds (though not eagles). Removal of the infested nest and construction of a nest platform in a different tree was necessary to break the cycle of infection. The original nesting pair constructed a new nest on the man-made platform and successfully fledged two Bald Eagles in 2012.

  19. 1. PHOTOCOPY OF ASSOCIATED MUTUAL FIRE INSURANCE MAP 1906: ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    1. PHOTOCOPY OF ASSOCIATED MUTUAL FIRE INSURANCE MAP - 1906: ROGERS LOCOMOTIVE WORKS, PATERSON, N.J. (4x5 NEGATIVE) - Rogers Locomotive & Machine Works, Spruce & Market Streets, Paterson, Passaic County, NJ

  20. Changes of loggerhead turtle (Caretta caretta) dive behavior associated with tropical storm passage during the inter-nesting period.

    PubMed

    Wilson, Maria; Tucker, Anton D; Beedholm, Kristian; Mann, David A

    2017-07-28

    To improve conservation strategies for threatened sea turtles more knowledge on their ecology, behavior, and how they cope with severe and changing weather conditions is needed. Satellite and animal motion datalogging tags were used to study the inter-nesting behavior of two female loggerhead turtles in the Gulf of Mexico, which regularly has hurricanes and tropical storms during nesting season. We contrast the behavioral patterns and swimming energetics of two turtles, the first tracked in calm weather and a second tracked before, during, and after a tropical storm. Turtle #1 was highly active and swam at the surface or submerged 95% of the time during the entire inter-nesting period with high estimated specific oxygen consumption rate (0.95 ml min(-1) kg(-0.83)). Turtle #2 was inactive for most of the first nine days of the inter-nesting period where she rested at the bottom (80% of the time) with low estimated oxygen consumption (0.62 ml min(-1) kg(-0.83)). Midway through the inter-nesting period turtle #2 encountered a tropical storm and became highly active (swimming 88% of the time during and 95% after the storm). Her oxygen consumption increased significantly to 0.97 ml min(-1) kg(-0.83) during and 0.98 ml min(-1) kg(-0.83) after the storm. However, despite of the tropical storm turtle #2 returned to the nesting beach, where she successfully re-nested 75 meters from her previous nest. Thus, the tropical storm had a minor effect on this female's individual nesting success, even though the storm caused 90% loss of Casey Key nests. © 2017. Published by The Company of Biologists Ltd.

  1. The Association between Asthma and Allergic Symptoms in Children and Phthalates in House Dust: A Nested Case–Control Study

    PubMed Central

    Bornehag, Carl-Gustaf; Sundell, Jan; Weschler, Charles J.; Sigsgaard, Torben; Lundgren, Björn; Hasselgren, Mikael; Hägerhed-Engman, Linda

    2004-01-01

    Global phthalate ester production has increased from very low levels at the end of World War II to approximately 3.5 million metric tons/year. The aim of the present study was to investigate potential associations between persistent allergic symptoms in children, which have increased markedly in developed countries over the past three decades, and the concentration of phthalates in dust collected from their homes. This investigation is a case–control study nested within a cohort of 10,852 children. From the cohort, we selected 198 cases with persistent allergic symptoms and 202 controls without allergic symptoms. A clinical and a technical team investigated each child and her or his environment. We found higher median concentrations of butyl benzyl phthalate (BBzP) in dust among cases than among controls (0.15 vs. 0.12 mg/g dust). Analyzing the case group by symptoms showed that BBzP was associated with rhinitis (p = 0.001) and eczema (p = 0.001), whereas di(2-ethylhexyl) phthalate (DEHP) was associated with asthma (p = 0.022). Furthermore, dose–response relationships for these associations are supported by trend analyses. This study shows that phthalates, within the range of what is normally found in indoor environments, are associated with allergic symptoms in children. We believe that the different associations of symptoms for the three major phthalates—BBzP, DEHP, and di-n-butyl phthalate—can be explained by a combination of chemical physical properties and toxicologic potential. Given the phthalate exposures of children worldwide, the results from this study of Swedish children have global implications. PMID:15471731

  2. Association of serum 25-hydroxyvitamin D with influenza in case-control study nested in a cohort of Japanese employees.

    PubMed

    Nanri, Akiko; Nakamoto, Kengo; Sakamoto, Nobuaki; Imai, Teppei; Akter, Shamima; Nonaka, Daisuke; Mizoue, Tetsuya

    2017-10-01

    Several intervention studies have examined the effect of vitamin D supplementation on influenza or influenza-like illness, but their results have been inconsistent. We prospectively examined the association of serum 25-hydroxyvitamin D with influenza among Japanese workers. We conducted a nested case-control study in a cohort of workers in 4 companies in the Kanto and Tokai areas of Japan. Physician-diagnosed influenza that occurred during the winter season was ascertained using a self-administered questionnaire. Two controls matched by company, sex, and age (and checkup date in 1 company) were selected for each case. Serum 25-hydroxyvitamin D concentrations at baseline were measured using a competitive protein binding assay. Odds ratio of influenza were estimated by conditional logistic regression with adjustment for covariates. Of 182 cases and 364 controls, 179 cases and 353 controls with complete data were included in the analysis. Serum 25-hydroxyvitamin D concentrations were not associated with a significantly lower risk of influenza; the multivariable-adjusted odds ratio for the highest (≥30 ng/mL) versus lowest category (<20 ng/mL) was 0.77 (95% confidence interval 0.37-1.59) (P for trend = 0.80). In a subgroup of participants without vaccination, vitamin D sufficiency (≥30 ng/mL) was associated with a significantly lower risk of influenza (odds ratio 0.14; 95% confidence interval 0.03-0.74). Overall, circulating 25-hydroxyvitamin D concentrations were not appreciably associated with influenza episodes. However, the lower influenza risk associated with vitamin D sufficiency among unvaccinated participants warrants further investigation. Copyright © 2016 Elsevier Ltd and European Society for Clinical Nutrition and Metabolism. All rights reserved.

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

    USDA-ARS?s Scientific Manuscript database

    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 ...

  4. Nesting of colon and ovarian cancer cells in the endothelial niche is associated with alterations in glycan and lipid metabolism

    PubMed Central

    Halama, Anna; Guerrouahen, Bella S.; Pasquier, Jennifer; Satheesh, Noothan J.; Suhre, Karsten; Rafii, Arash

    2017-01-01

    The metabolic phenotype of a cancer cell is determined by its genetic makeup and microenvironment, which dynamically modulates the tumor landscape. The endothelial cells provide both a promoting and protective microenvironment – a niche for cancer cells. Although metabolic alterations associated with cancer and its progression have been fairly defined, there is a significant gap in our understanding of cancer metabolism in context of its microenvironment. We deployed an in vitro co-culture system based on direct contact of cancer cells with endothelial cells (E4+EC), mimicking the tumor microenvironment. Metabolism of colon (HTC15 and HTC116) and ovarian (OVCAR3 and SKOV3) cancer cell lines was profiled with non-targeted metabolic approaches at different time points in the first 48 hours after co-culture was established. We found significant, coherent and non-cell line specific changes in fatty acids, glycerophospholipids and carbohydrates over time, induced by endothelial cell contact. The metabolic patterns pinpoint alterations in hexosamine biosynthetic pathway, glycosylation and lipid metabolism as crucial for cancer – endothelial cells interaction. We demonstrated that “Warburg effect” is not modulated in the initial stage of nesting of cancer cell in the endothelial niche. Our study provides novel insight into cancer cell metabolism in the context of the endothelial microenvironment. PMID:28051182

  5. Uncertain Associations of Major Bleeding and Concurrent Use of Antiplatelet Agents and Chinese Medications: A Nested Case-Crossover Study

    PubMed Central

    Yam, Felix K.

    2017-01-01

    Despite the evidence that some commonly used Chinese medications (CMs) have antiplatelet/anticoagulant effects, many patients still used antiplatelets combined with CMs. We conducted a nested case-crossover study to examine the associations between the concomitant use of antiplatelets and CMs and major bleeding using population-based health database in Taiwan. Among the cohort of 79,463 outpatients prescribed antiplatelets (e.g., aspirin and clopidogrel) continuously, 1,209 patients hospitalized with new occurring bleeding in 2012 and 2013 were included. Those recruited patients served as their own controls to compare different times of exposure to prespecified CMs (e.g., Asian ginseng and dong quai) and antiplatelet agents. The periods of case, control 1, and control 2 were defined as 1–4 weeks, 6–9 weeks, and 13–16 weeks before hospitalization, respectively. Conditional logistic regression analyses found that concurrent use of antiplatelet drugs with any of the prespecified CMs in the case period might not significantly increase the risks of bleeding over that in the control periods (OR = 1.00, 95% CI 0.51 to 1.95 and OR = 1.13, 95% CI 0.65 to 1.97). The study showed no strong relationships between hospitalization for major bleeding events and concurrent use of antiplatelet drugs with the prespecified CMs. PMID:28831288

  6. Association between use of oral-antidiabetic drugs and the risk of aortic aneurysm: a nested case-control analysis.

    PubMed

    Hsu, Chien-Yi; Su, Yu-Wen; Chen, Yung-Tai; Tsai, Shih-Hung; Chang, Chun-Chin; Li, Szu-Yuan; Huang, Po-Hsun; Chen, Jaw-Wen; Lin, Shing-Jong

    2016-09-01

    Pleiotropic effects on cardiovascular protection have been suggested in several oral antidiabetic drugs (OAD). The impacts of OADs on aortic aneurysm (AA) growth have been found in animal studies, but the evidence of their beneficial effects for AA protection in human are lacking. We investigated the relationship between OAD therapy and the risk of developing AA. We conducted a nested case-control analysis using the database extracted from Taiwan's National Health Insurance Research Database. The database consists of 1.2 million diabetic patients representing the majority of the type 2 diabetes population in Taiwan from 2000 to 2013. Cases were identified as those with either inpatient or outpatient diagnosis code of AA. One control was selected for each case matching on duration of follow-up, age, sex, urbanization, monthly income, severity of diabetes, and risk factor for AA. We identified variable classes of OADs, including metformin, sulfonylureas, thiazolidinedione (TZD), alpha-glucosidase inhibitors, meglitinide, dipeptidyl peptidase-4 (DPP-4) inhibitors prior to the development of AA. A total of 4468 cases diagnosed with AA and 4468 matched controls were identified. Metformin use, sulfonylurea use, and TZD were associated with lower risk of developing AA, odds ratio [OR] 0.72 (95 % confidence interval [CI] 0.64-0.80), 0.82 (95 % CI 0.74-0.92), and 0.82 (95 % CI 0.69-0.98), respectively. The effects of metformin and sulfonylurea on AA were dose responsive. Neither alpha-glucosidase inhibitors (OR 0.95; 95 % CI 0.81-1.11) nor DPP-4 inhibitors (OR 0.85; 95 % CI 0.68-1.07) was significantly associated with AA events. Metformin, sulfonylurea, and TZD treated patients were associated with lower risks of AA development, but not DPP-4 inhibitors or alpha-glucosidase inhibitor. The protective effects of hypoglycemic agents are further confirmed by the dose responsive relations in metformin and sulfonylurea groups.

  7. Factors associated with Clostridium difficile infection: A nested case-control study in a three year prospective cohort.

    PubMed

    Khanafer, Nagham; Vanhems, Philippe; Barbut, Frédéric; Luxemburger, Christine

    2017-04-01

    Clostridium difficile infection (CDI) is a serious medical condition that is associated with substantial morbidity and mortality. Identification of risk factors associated with CDI and prompt recognition of patients at risk is key to successfully preventing CDI. A 3-year prospective, observational, cohort study was conducted in a French university hospital and a nested case-control study was performed to identify risk factors for CDI. Inpatients aged 18 years or older, suffering from diarrhea suspected to be related to CDI, were asked to participate. A total of 945 patients were included, of which 233 cases had a confirmed CDI. CDI infection was more common in men (58.4%) (P = 0.04) compared with patients with diarrhea not related to C. difficile. Previous hospitalization (P < 0.001), prior treatment with antibiotics (P = 0.001) or antiperistaltics (P = 0.002), liver disease (P = 0.003), malnutrition (P < 0.001), and previous CDI (P < 0.001) were significantly more common in patients with CDI. Multivariate logistic regression analysis showed that exposure to antibiotics in the last 60 days (especially third generation cephalosporins and penicillins with β-lactamase inhibitor), chronic renal or liver disease, malnutrition or previous CDI, were associated with an independent high risk of CDI. Age was not related with CDI. This study showed that antibiotics and some comorbid conditions were predictors of CDI. Patients at high risk of acquiring CDI at the time of admission may benefit from careful monitoring of antibiotic prescriptions and early attention to infection control issues. In future, these "high-risk" patients may benefit from novel agents being developed to prevent CDI. Copyright © 2017 Elsevier Ltd. All rights reserved.

  8. Risk of arteriovenous fistula failure associated with hypnotic use in hemodialysis patients: a nested case-control study.

    PubMed

    Lin, Chao-Feng; Chiou, Hung-Yi; Chang, Ya-Hui; Liu, Ju-Chi; Hung, Yen-Ni; Chuang, Ming-Tsang; Chien, Li-Nien

    2016-08-01

    Hypnotic use might cause altered inflammatory processes, which have been suggested as being related to the mechanisms of arteriovenous fistula (AVF) failure. Therefore, we examined the association between the risk of AVF failure and hypnotic use in patients receiving hemodialysis (HD). A nested case-control study was conducted using data from the National Health Insurance Research Database of Taiwan. From 34 165 HD patients, 3676 patients receiving percutaneous transluminal angioplasty or surgical thrombectomy for AVF failure were matched to 14 704 control patients according to sex, age (±1 year), and the year of initial HD therapy. The risk of AVF failure was estimated based on conditional logistic regression after adjustment for the timing of AVF creation, HD frequency, comorbidities, and prescribed medications. Hypnotic use was measured prior to the date of AVF failure of case patients and the date of pseudo-AVF failure of controls. Compared with matched controls, case patients were more likely to be exposed to hypnotics 30 days or an average daily defined dose > 0.5 within 90 days before the date of AVF failure, with an adjusted odds ratio of 1.21 (95% confidence interval [CI]: 1.09-1.35, p < 0.001) and 1.36 (95%CI: 1.13-1.63, p = 0.001), respectively. Risk of AVF failure associated with hypnotic use was also observed among HD patients who were male, were younger than 65 years, had hypertension, and did not use statins. Hypnotic use among HD patients was associated with an increased risk of AVF failure. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  9. Seasonal changes in serum gonadal steroids associated with migration, mating, and nesting in the loggerhead sea turtle (Caretta caretta).

    PubMed

    Wibbels, T; Owens, D W; Limpus, C J; Reed, P C; Amoss, M S

    1990-07-01

    Adult male loggerhead sea turtles, Caretta caretta, exhibited a "prenuptial" spermatogenic cycle that was coincident with increased concentrations of serum testosterone (T). Serum T was high during the months when migration and mating have been recorded for males. In contrast to females, males appear to be annual breeders. Nine reproductively active female C. caretta (as verified through laparoscopy) were tagged with sonic transmitters and were repeatedly bled prior to migration. Four months prior to the nesting season, the ovaries of reproductively active females had hundreds of vitellogenic follicles of approximately 1.5 cm in diameter (i.e., half the size of ovulatory follicles). Approximately 4-6 weeks prior to migration from feeding grounds to mating and nesting areas, serum estradiol-17 beta (E2) concentrations increased significantly and remained high for approximately 4 weeks, suggesting a period of increased vitellogenesis. During a 1- to 2-week period prior to migration, serum E2 decreased significantly, while serum T concentrations increased (at least) until the time of migration. Serum T, E2, and progesterone (PRO) were elevated during nesting if a turtle was going to nest again during that nesting season. During the last nesting of a season, turtles had low serum concentrations of T, E2, and Pro. The prenuptial pattern of gonadal recrudescence and gonadal steroid production in both male and female C. caretta contrasts with those of many temperate freshwater turtles, and this type of reproductive pattern may have been facilitated by adaptation to a tropical marine environment.

  10. 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. Michael

    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.

  11. Mapping of disease-associated variants in admixed populations

    PubMed Central

    2011-01-01

    Recent developments in high-throughput genotyping and whole-genome sequencing will enhance the identification of disease loci in admixed populations. We discuss how a more refined estimation of ancestry benefits both admixture mapping and association mapping, making disease loci identification in admixed populations more powerful. High-throughput genotyping and sequencing will enable refined estimation of ancestry, thus enhancing disease loci identification in admixed populations PMID:21635713

  12. Factors Associated With Pediatric Ventilator-Associated Conditions in Six U.S. Hospitals: A Nested Case-Control Study.

    PubMed

    Cocoros, Noelle M; Priebe, Gregory; Gray, James E; Toltzis, Philip; Larsen, Gitte Y; Logan, Latania K; Coffin, Susan; Sammons, Julia S; Deakins, Kathleen; Horan, Kelly; Lakoma, Matthew; Young, Jessica; Burton, Michael; Klompas, Michael; Lee, Grace M

    2017-09-13

    A newly proposed surveillance definition for ventilator-associated conditions among neonatal and pediatric patients has been associated with increased morbidity and mortality among ventilated patients in cardiac ICU, neonatal ICU, and PICU. This study aimed to identify potential risk factors associated with pediatric ventilator-associated conditions. Retrospective cohort. Six U.S. hospitals PATIENTS:: Children less than or equal to 18 years old ventilated for greater than or equal to 1 day. None. We identified children with pediatric ventilator-associated conditions and matched them to children without ventilator-associated conditions. Medical records were reviewed for comorbidities and acute care factors. We used bivariate and multivariate conditional logistic regression models to identify factors associated with ventilator-associated conditions. We studied 192 pairs of ventilator-associated conditions cases and matched controls (113 in the PICU and cardiac ICU combined; 79 in the neonatal ICU). In the PICU/cardiac ICU, potential risk factors for ventilator-associated conditions included neuromuscular blockade (odds ratio, 2.29; 95% CI, 1.08-4.87), positive fluid balance (highest quartile compared with the lowest, odds ratio, 7.76; 95% CI, 2.10-28.6), and blood product use (odds ratio, 1.52; 95% CI, 0.70-3.28). Weaning from sedation (i.e., decreasing sedation) or interruption of sedation may be protective (odds ratio, 0.44; 95% CI, 0.18-1.11). In the neonatal ICU, potential risk factors included blood product use (odds ratio, 2.99; 95% CI, 1.02-8.78), neuromuscular blockade use (odds ratio, 3.96; 95% CI, 0.93-16.9), and recent surgical procedures (odds ratio, 2.19; 95% CI, 0.77-6.28). Weaning or interrupting sedation was protective (odds ratio, 0.07; 95% CI, 0.01-0.79). In mechanically ventilated neonates and children, we identified several possible risk factors associated with ventilator-associated conditions. Next steps include studying propensity

  13. Modeling nest survival of cavity-nesting birds in relation to postfire salvage logging

    Treesearch

    Vicki Saab; Robin E. Russell; Jay Rotella; Jonathan G. Dudley

    2011-01-01

    Salvage logging practices in recently burned forests often have direct effects on species associated with dead trees, particularly cavity-nesting birds. As such, evaluation of postfire management practices on nest survival rates of cavity nesters is necessary for determining conservation strategies. We monitored 1,797 nests of 6 cavity-nesting bird species: Lewis'...

  14. An association between newly diagnosed cutaneous T cell lymphoma and prior impetigo: a nested case-control study.

    PubMed

    Boursi, Ben; Haynes, Kevin; Mamtani, Ronac; Yang, Yu-Xiao

    2016-11-01

    Colonization with staphylococcus aureus (SA) is associated with disease activity and progression in patients with cutaneous T-cell lymphoma (CTCL) secondary to T-cell activation by bacterial superantigens. The aim of the current study was to evaluate the possible role of SA as an etiologic factor affecting CTCL initiation. We conducted a nested case-control study in a large population-representative database from the UK. Cases were defined as all patients with an incident diagnosis of mycosis fungoides (MF) or Sezary syndrome (SS) between 1995 and 2013. For every case, four eligible controls matched on age, sex, practice-site, and duration of follow-up were selected. Exposure of interest was clinical diagnosis of impetigo prior to CTCL diagnosis. Conditional logistic regression was used to calculate odds-ratio (ORs) and 95 % confidence-interval (CI) for CTCL risk. The results were further stratified according to age, sex and time interval between impetigo and CTCL diagnosis. The study population included 310 cases with MF or SS and 1223 matched controls. Among cases with CTCL 4.8 % (n = 15) had impetigo prior to cancer diagnosis compared to 2 % (n = 24) of controls. The adjusted OR for CTCL diagnosis among patients with prior impetigo was 2.33 (95 % CI 1.12-4.83). The risk was elevated among individuals with impetigo 1-5 years before cancer diagnosis (OR 3.33, 95 % CI 1.00-11.10). There was no change in risk among patients with impetigo more than 5 years before cancer diagnosis (OR 1.09, 95 % CI 0.35-3.37). Our results suggest a possible association between SA colonization and CTCL initiation that might serve as an important etiological factor for the disease.

  15. Paternal obesity is associated with IGF2 hypomethylation in newborns: results from a Newborn Epigenetics Study (NEST) cohort.

    PubMed

    Soubry, Adelheid; Schildkraut, Joellen M; Murtha, Amy; Wang, Frances; Huang, Zhiqing; Bernal, Autumn; Kurtzberg, Joanne; Jirtle, Randy L; Murphy, Susan K; Hoyo, Cathrine

    2013-02-06

    Data from epidemiological and animal model studies suggest that nutrition during pregnancy may affect the health status of subsequent generations. These transgenerational effects are now being explained by disruptions at the level of the epigenetic machinery. Besides in vitro environmental exposures, the possible impact on the reprogramming of methylation profiles at imprinted genes at a much earlier time point, such as during spermatogenesis or oogenesis, has not previously been considered. In this study, our aim was to determine associations between preconceptional obesity and DNA methylation profiles in the offspring, particularly at the differentially methylated regions (DMRs) of the imprinted Insulin-like Growth Factor 2 (IGF2) gene. We examined DNA from umbilical cord blood leukocytes from 79 newborns, born between July 2005 and November 2006 at Duke University Hospital, Durham, NC. Their mothers participated in the Newborn Epigenetics Study (NEST) during pregnancy. Parental characteristics were obtained via standardized questionnaires and medical records. DNA methylation patterns at two DMRs were analyzed by bisulfite pyrosequencing; one DMR upstream of IGF2 (IGF2 DMR), and one DMR upstream of the neighboring H19 gene (H19 DMR). Multiple regression models were used to determine potential associations between the offspring's DNA methylation patterns and parental obesity before conception. Obesity was defined as body mass index (BMI) ≥30 kg/m². Hypomethylation at the IGF2 DMR was associated with paternal obesity. Even after adjusting for several maternal and newborn characteristics, we observed a persistent inverse association between DNA methylation in the offspring and paternal obesity (β-coefficient was -5.28, P = 0.003). At the H19 DMR, no significant associations were detected between methylation patterns and paternal obesity. Our data suggest an increase in DNA methylation at the IGF2 and H19 DMRs among newborns from obese mothers, but a larger study

  16. Paternal obesity is associated with IGF2 hypomethylation in newborns: results from a Newborn Epigenetics Study (NEST) cohort

    PubMed Central

    2013-01-01

    Background Data from epidemiological and animal model studies suggest that nutrition during pregnancy may affect the health status of subsequent generations. These transgenerational effects are now being explained by disruptions at the level of the epigenetic machinery. Besides in vitro environmental exposures, the possible impact on the reprogramming of methylation profiles at imprinted genes at a much earlier time point, such as during spermatogenesis or oogenesis, has not previously been considered. In this study, our aim was to determine associations between preconceptional obesity and DNA methylation profiles in the offspring, particularly at the differentially methylated regions (DMRs) of the imprinted Insulin-like Growth Factor 2 (IGF2) gene. Methods We examined DNA from umbilical cord blood leukocytes from 79 newborns, born between July 2005 and November 2006 at Duke University Hospital, Durham, NC. Their mothers participated in the Newborn Epigenetics Study (NEST) during pregnancy. Parental characteristics were obtained via standardized questionnaires and medical records. DNA methylation patterns at two DMRs were analyzed by bisulfite pyrosequencing; one DMR upstream of IGF2 (IGF2 DMR), and one DMR upstream of the neighboring H19 gene (H19 DMR). Multiple regression models were used to determine potential associations between the offspring's DNA methylation patterns and parental obesity before conception. Obesity was defined as body mass index (BMI) ≥30 kg/m2. Results Hypomethylation at the IGF2 DMR was associated with paternal obesity. Even after adjusting for several maternal and newborn characteristics, we observed a persistent inverse association between DNA methylation in the offspring and paternal obesity (β-coefficient was -5.28, P = 0.003). At the H19 DMR, no significant associations were detected between methylation patterns and paternal obesity. Our data suggest an increase in DNA methylation at the IGF2 and H19 DMRs among newborns from obese

  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.

  18. 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.

  19. A nested case-control study indicating heavy metal residues in meconium associate with maternal gestational diabetes mellitus risk.

    PubMed

    Peng, Siyuan; Liu, Liangpo; Zhang, Xueqin; Heinrich, Joachim; Zhang, Jie; Schramm, Karl-Werner; Huang, Qingyu; Tian, Meiping; Eqani, Syed Ali Musstjab Akber Shah; Shen, Heqing

    2015-02-28

    Environmental pollutant exposure may play certain roles in the pathogenesis and progression of diabetes mellitus including gestational diabetes mellitus (GDM). We hypothesize that heavy metal exposure may trigger GDM during pregnancy. The objective of this study was to investigate the possible associations between selected heavy metal exposure and GDM risk. This investigation is a retrospective case-control study nested within a cohort of 1359 pregnant women. These participants were recruited in Xiamen Maternity and Child Care Hospital, China, during June to July, 2012. All their newborns' meconium samples were collected. By reviewing the antenatal care records, 166 GDM mothers were screened out from the 1359 participants; 137 of 166 GDM mothers offered their newborns' meconium samples for the metal analysis. Those 137 mothers were set as the case group. Similarly, 294 healthy mothers without any gestational complication were initially screened out from the rest 1193 non-GDM mothers. 190 of the 294 healthy mothers offered their newborns' meconium samples for the metal analysis. Those 190 mothers were set as the control group. Arsenic (As), mercury (Hg), lead (Pb), cadmium (Cd), and chromium (Cr) levels in these case-control meconium samples were measured by inductively coupled plasma mass spectrometry. The possible association between the metal levels and maternal GDM risk of studied subjects was assessed by binary logistic regression. GDM prevalence of 12.21% was observed in the investigated 1359 participants. The concentrations of As, Hg, Cr and Cd in studied cases were significantly higher (p < 0.05) than those of controls. After adjustments for maternal age, pre-pregnant body mass index, gravidity, parity, hepatitis B virus infection, and newborn sex, As, Cd and Cr were found to be positively associated with GDM prevalence in dose-dependent manners. Among them, As was detected in all samples and its levels associated the maternal GDM with the adjusted odds

  20. 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

  1. Association Mapping of Leaf Rust Response in Durum Wheat

    USDA-ARS?s Scientific Manuscript database

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

    USDA-ARS?s Scientific Manuscript database

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

  3. 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...

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

    Treesearch

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

    2015-01-01

    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...

  5. 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...

  6. Trends in Kaposi's sarcoma-associated Herpesvirus antibodies prior to the development of HIV-associated Kaposi's sarcoma: A nested case-control study

    PubMed Central

    Wakeham, Katie; Johnston, W Thomas; Nalwoga, Angela; Webb, Emily L; Mayanja, Billy N; Miley, Wendell; Elliott, Alison M; Whitby, Denise; Newton, Robert

    2015-01-01

    HIV-associated Kaposi's sarcoma (KS) is a public health challenge in sub-Saharan Africa since both the causative agent, Kaposi's sarcoma associated-herpesvirus (KSHV), and the major risk factor, HIV, are prevalent. In a nested case-control study within a long-standing clinical cohort in rural Uganda, we used stored sera to examine the evolution of antibody titres against the KSHV antigens K8.1 and latency-associated nuclear antigen (LANA) among 30 HIV-infected subjects who subsequently developed HIV-related KS (cases) and among 108 matched HIV/KSHV coinfected controls who did not develop KS. Throughout the 6 years prior to diagnosis, antibody titres to K8.1 and LANA were significantly higher among cases than controls (p < 0.0001), and titres increased prior to diagnosis in the cases. K8.1 titres differed more between KS cases and controls, compared to LANA titres. These differences in titre between cases and controls suggest a role for lytic viral replication in the pathogenesis of HIV-related KS in this setting. PMID:25395177

  7. 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.

  8. Land Use and land cover and associated maps

    USGS Publications Warehouse

    ,

    1982-01-01

    The Geological Survey is compiling land use and land cover and associated maps for the entire United States. Land use refers to man's activities which are directly related to the land. Land cover describes the vegetation, water, natural surface, and artificial constructions at the land surface. These maps will help satisfy a longstanding need for a consistent level of detail, standardization of categories, and appropriate use of scales of compilation for a type of data frequently used by land use planners, land managers, resource management planners, and others.

  9. 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.

  10. 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.

  11. Association between cardiovascular events and sodium-containing effervescent, dispersible, and soluble drugs: nested case-control study

    PubMed Central

    George, Jacob; Majeed, Waseem; Mackenzie, Isla S; Wei, Li

    2013-01-01

    Objective To determine whether patients taking formulations of drugs that contain sodium have a higher incidence of cardiovascular events compared with patients on non-sodium formulations of the same drugs. Design Nested case-control study. Setting UK Primary Care Patients registered on the Clinical Practice Research Datalink (CPRD). Participants All patients aged 18 or over who were prescribed at least two prescriptions of sodium-containing formulations or matched standard formulations of the same drug between January 1987 and December 2010. Main outcome measures Composite primary outcome of incident non-fatal myocardial infarction, incident non-fatal stroke, or vascular death. We performed 1:1 incidence density sampling matched controls using the UK Clinical Practice Research Datalink (CPRD). For the secondary analyses, cases were patients with the individual components of the primary study composite endpoint of hypertension, incident heart failure, and all cause mortality. Results 1 292 337 patients were included in the study cohort. Mean follow-up time was 7.23 years. A total of 61 072 patients with an incident cardiovascular event were matched with controls. For the primary endpoint of incident non-fatal myocardial infarction, incident non-fatal stroke, or vascular death the adjusted odds ratio for exposure to sodium-containing drugs was 1.16 (95% confidence interval 1.12 to 1.21). The adjusted odds ratios for the secondary endpoints were 1.22 (1.16 to 1.29) for incident non-fatal stroke, 1.28 (1.23 to 1.33) for all cause mortality, 7.18 (6.74 to 7.65) for hypertension, 0.98 (0.93 to 1.04) for heart failure, 0.94 (0.88 to 1.00) for incident non-fatal myocardial infarction, and 0.70 (0.31 to 1.59) for vascular death. The median time from date of first prescription (that is, date of entry into cohort) to first event was 3.92 years. Conclusions Exposure to sodium-containing formulations of effervescent, dispersible, and soluble medicines was associated with

  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. 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

  14. 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

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

    USGS Publications Warehouse

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

    2016-01-01

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

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

    PubMed Central

    Ion, D; Stoian, RV; Serban, MB

    2011-01-01

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

  17. 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.

  18. 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

  19. Estimating nest detection probabilities for white-winged dove nest transects in Tamaulipas, Mexico

    USGS Publications Warehouse

    Nichols, J.D.; Tomlinson, R.E.; Waggerman, G.

    1986-01-01

    Nest transects in nesting colonies provide one source of information on White-winged Dove (Zenaida asiatica asiatica) population status and reproduction. Nests are counted along transects using standardized field methods each year in Texas and northeastern Mexico by personnel associated with Mexico's Office of Flora and Fauna, the Texas Parks and Wildlife Department, and the U.S. Fish and Wildlife Service. Nest counts on transects are combined with information on the size of nesting colonies to estimate total numbers of nests in sampled colonies. Historically, these estimates have been based on the actual nest counts on transects and thus have required the assumption that all nests lying within transect boundaries are detected (seen) with a probability of one. Our objectives were to test the hypothesis that nest detection probability is one and, if rejected, to estimate this probability.

  20. 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

  1. 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.

  2. 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

  3. 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.

  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. Spatial dynamics of nesting behavior: lizards shift microhabitats to construct nests with beneficial thermal properties.

    PubMed

    Angilletta, Michael J; Sears, Michael W; Pringle, Robert M

    2009-10-01

    Because temperature affects the growth, development, and survival of embryos, oviparous mothers should discriminate carefully among available nesting sites. We combined a radiotelemetric study of animal movements with a spatial mapping of environmental temperatures to test predictions about the nesting behavior of the eastern fence lizard (Sceloporus undulatus). Females made large excursions from their typical home ranges to construct nests in exposed substrates. These excursions appeared to be related solely to nesting because all females returned to forested habitat immediately afterward. On average, <1% (range = 0-8%, n = 19) of the area used by a female during nesting was contained within the area used before and after nesting. The selection of nesting sites matched predictions based on laboratory studies of embryonic performance; specifically, females nested in extremely open habitat at a mean of 6 cm depth. Spatial mapping of soil temperatures revealed that temperatures of nesting areas exceeded those of areas typically used by females, indicating that females preferred to construct warm nests that speed embryonic growth and development. However, this behavior could reduce the survivorship of females because of the need to rapidly navigate unfamiliar and exposed terrain.

  6. Association mapping and the genomic consequences of selection in sunflower.

    PubMed

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

    2013-03-01

    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.

  7. 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

  8. RedeR: R/Bioconductor package for representing modular structures, nested networks and multiple levels of hierarchical associations

    PubMed Central

    2012-01-01

    Visualization and analysis of molecular networks are both central to systems biology. However, there still exists a large technological gap between them, especially when assessing multiple network levels or hierarchies. Here we present RedeR, an R/Bioconductor package combined with a Java core engine for representing modular networks. The functionality of RedeR is demonstrated in two different scenarios: hierarchical and modular organization in gene co-expression networks and nested structures in time-course gene expression subnetworks. Our results demonstrate RedeR as a new framework to deal with the multiple network levels that are inherent to complex biological systems. RedeR is available from http://bioconductor.org/packages/release/bioc/html/RedeR.html. PMID:22531049

  9. Mapping of genes associated with leptine content of tetraploid potato.

    PubMed

    Sagredo, B; Lafta, A; Casper, H; Lorenzen, J

    2006-12-01

    High content of leptine glycoalkaloids present in Solanum chacoense has been associated with genetic resistance to Colorado potato beetle (Leptinotarsa decemlineata [Say]). From an unrecorded accession of S. chacoense, the North Dakota State University breeding program has developed a tetraploid genotype, ND4382-19, that contains foliar leptines. In this study, using a segregating population, ND5873 (ND4382-19 x Chipeta), and GC-MS to analyze foliar content of alkaloids, two loci, involved in the synthesis of leptines were identified. They segregated as two complementary epistatic genes that allowed the synthesis of leptinidine (Lep) and acetyl-leptinidine (AL), respectively. Partial AFLP maps for both parents were developed using 97 individuals from population ND5873. The total lengths mapped for ND4382-19 and Chipeta were 1,883 and 1,021 cM, respectively. The marker for Lep was located at the distal end of simplex-coupling linkage group R37. Expansion of the initial mapping population and analysis of Lep-containing individuals allowed us to identify the linkage group (R35) that enabled synthesis of AL. By the use of simple sequence repeat markers, linkage group R37 (Lep) and linkage group R35 (AL) have been identified as homologs of chromosomes II and VIII, respectively.

  10. Association mapping in forest trees and fruit crops.

    PubMed

    Khan, M Awais; Korban, Schuyler S

    2012-06-01

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

  11. Management of western coniferous forest habitat for nesting accipiter hawks

    Treesearch

    Richard T. Reynolds

    1983-01-01

    Availability of nesting sites can limit accipiter populations. Because accipiters nest in dense forest stands, any alteration that opens these stands is likely to lessen their desirability as nest sites. Tree growth and the associated changes in the vegetative structure of aging nest sites limit the number of years sites will be suitable. Therefore, prospective...

  12. Whole-genome association mapping in elite inbred crop varieties.

    PubMed

    Waugh, Robbie; Marshall, David; Thomas, Bill; Comadran, Jordi; Russell, Joanne; Close, Tim; Stein, Nils; Hayes, Pat; Muehlbauer, Gary; Cockram, James; O'Sullivan, Donal; Mackay, Ian; Flavell, Andrew; Ramsay, Luke

    2010-11-01

    We have previously shown that linkage disequilibrium (LD) in the elite cultivated barley (Hordeum vulgare) gene pool extends, on average, for <1-5 cM. Based on this information, we have developed a platform for whole genome association studies that comprises a collection of elite lines that we have characterized at 3060 genome-wide single nucleotide polymorphism (SNP) marker loci. Interrogating this data set shows that significant population substructure is present within the elite gene pool and that diversity and LD vary considerably across each of the seven barley chromosomes. However, we also show that a subpopulation comprised of only the two-rowed spring germplasm is less structured and well suited to whole genome association studies without the need for extensive statistical intervention to account for structure. At the current marker density, the two-rowed spring population is suited for fine mapping simple traits that are located outside of the genetic centromeres with a resolution that is sufficient for candidate gene identification by exploiting conservation of synteny with fully sequenced model genomes and the emerging barley physical map.

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

    PubMed

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

    2006-12-05

    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.

  14. veqtl-mapper: variance association mapping for molecular phenotypes.

    PubMed

    Brown, Andrew Anand

    2017-09-01

    Genetic loci associated with the variance of phenotypic traits have been of recent interest as they can be signatures of genetic interactions, gene by environment interactions, parent of origin effects and canalization. We present a fast efficient tool to map loci affecting variance of gene expression and other molecular phenotypes in cis. Results: Applied to the publicly available Geuvadis gene expression dataset, we identify 816 loci associated with variance of gene expression using an additive model, and 32 showing differences in variance between homozygous and heterozygous alleles, signatures of parent of origin effects. Documentation and links to source code and binaries for linux can be found at https://funpopgen.github.io/veqm/ . andrew.brown@unige.ch. Supplementary data are available at Bioinformatics online.

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

    PubMed

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

    2010-07-01

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

  16. 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,…

  17. 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,…

  18. 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.

  19. Cavity Nesting Birds

    Treesearch

    Virgil E. Scott; Keith E. Evans; David R. Patton; Charles P. Stone

    1977-01-01

    Many species of cavity-nesting birds have declined because of habitat reduction. In the eastern United States, where primeval forests are gone, purple martins depend almost entirely on man-made nesting structures (Allen and Nice 1952). The hole-nesting population of peregrine falcons disappeared with the felling of the giant trees upon which they depended (Hickey and...

  20. 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.

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

    PubMed

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

    2015-12-01

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

  2. Effect of antenatal betamethasone treatment on microtubule-associated proteins MAP1B and MAP2 in fetal sheep

    PubMed Central

    Schwab, Matthias; Antonow-Schlorke, Iwa; Kühn, Birgit; Müller, Thomas; Schubert, Harald; Walter, Bernd; Sliwka, Ulrich; Nathanielsz, Peter W

    2001-01-01

    Betamethasone has been used extensively to accelerate fetal lung maturation, yet little is known of its effects on neuronal morphogenesis in the developing fetus. Microtubule-associated proteins (MAPs) are a diverse family of cytoskeletal proteins that are important for brain development and the maintenance of neuroarchitecture. Vehicle (n = 7) or betamethasone (10 μg h−1, n = 7) was infused I.V. to fetal sheep over 48 h beginning at 0.87 of gestation (128 days of gestation), producing fetal plasma betamethasone concentrations resembling those to which the human fetus is exposed during antenatal glucocorticoid therapy. Paraffin sections of the left hemisphere were stained with monoclonal antibodies against MAP1B and the MAP2 isoforms MAP2a,b,c and MAP2a,b. The level of the juvenile isoform MAP2c was determined by comparison of the two MAP2 immunostainings. We were able to detect MAP1B and MAP2 immunoreactivity (IR) in the fetal sheep brain. MAP2c was the major MAP2, constituting 90.2 % of the total MAP2. Betamethasone exposure diminished MAP1B IR in the frontal cortex and caudate putamen (P < 0.05) but not in the hippocampus. A decrease of MAP2 IR was found in the frontal cortex, hippocampus and caudate putamen (P < 0.05). Loss of MAP2 IR was mainly due to the loss of MAP2c IR. Haematoxylin–eosin staining did not demonstrate irreversible neuronal damage. Regional cerebral blood flow determined using coloured microspheres was significantly decreased by 28 % in the frontal cortex and by 36 % in the caudate putamen but not in the hippocampus 24 h after the onset of betamethasone exposure (P < 0.05). The loss of MAP1B and MAP2a,b,c IR showed a significant correlation to the cerebral blood flow decrease only in the frontal cortex (P < 0.05). These data suggest that mechanisms other than metabolic insufficiency caused by the decreased cerebral blood flow may contribute to the loss of MAPs. The results suggest that clinical doses of betamethasone may have acute

  3. 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.

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

    PubMed

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

    2016-01-01

    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. 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). 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). 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.

  5. 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

  6. Symptoms of anxiety and depression during pregnancy and their association with low birth weight in Chinese women: a nested case control study.

    PubMed

    Yang, Shaoping; Yang, Rong; Liang, Shengwen; Wang, Jing; Weaver, Nancy L; Hu, Ke; Hu, Ronghua; Trevathan, Edwin; Huang, Zhen; Zhang, Yiming; Yin, Ting; Chang, Jen Jen; Zhao, Jinzhu; Shen, Longjiao; Dong, Guanghui; Zheng, Tongzhang; Xu, Shunqing; Qian, Zhengmin; Zhang, Bin

    2017-04-01

    This study is a nested case control study from a population-based cohort study conducted in Wuhan, China. The aim is to estimate the association between symptoms of depression during pregnancy (DDP), anxiety during pregnancy(ADP), and depression with anxiety during pregnancy (DADP) and low birth weight (LBW) and to examine the extent to which preterm birth (PTB) moderates these associations. Logistic regression analyses were used to model associations between DDP, ADP, and DADP and LBW. Models were stratified by the presence or absence of PTB to examine moderating effects. From the cohort study, 2853 had a LBW baby (cases); 5457 pregnant women served as controls. Women with DDP or ADP only were not at higher risk of having a LBW baby, but DADP was associated with increased risk of LBW (crude OR 1.41, 95% CI 1.17-1.70; adjusted OR 1.29, 95% CI 1.07-1.57), and the significant association was particularly evident between DADP and LBW in PTB, but not in full-term births. Our data suggests that DADP is related to an increased risk of LBW and that this association is most present in PTBs.

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

    USDA-ARS?s Scientific Manuscript database

    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...

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

    PubMed Central

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

    2015-01-01

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

  9. Power comparison of admixture mapping and direct association analysis in genome-wide association studies.

    PubMed

    Qin, Huaizhen; Zhu, Xiaofeng

    2012-04-01

    When dense markers are available, one can interrogate almost every common variant across the genome via imputation and single nucleotide polymorphism (SNP) test, which has become a routine in current genome-wide association studies (GWASs). As a complement, admixture mapping exploits the long-range linkage disequilibrium (LD) generated by admixture between genetically distinct ancestral populations. It is then questionable whether admixture mapping analysis is still necessary in detecting the disease associated variants in admixed populations. We argue that admixture mapping is able to reduce the burden of massive comparisons in GWASs; it therefore can be a powerful tool to locate the disease variants with substantial allele frequency differences between ancestral populations. In this report we studied a two-stage approach, where candidate regions are defined by conducting admixture mapping at stage 1, and single SNP association tests are followed at stage 2 within the candidate regions defined at stage 1. We first established the genome-wide significance levels corresponding to the criteria to define the candidate regions at stage 1 by simulations. We next compared the power of the two-stage approach with direct association analysis. Our simulations suggest that the two-stage approach can be more powerful than the standard genome-wide association analysis when the allele frequency difference of a causal variant in ancestral populations, is larger than 0.4. Our conclusion is consistent with a theoretical prediction by Risch and Tang ([2006] Am J Hum Genet 79:S254). Surprisingly, our study also suggests that power can be improved when we use less strict criteria to define the candidate regions at stage 1.

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

    PubMed

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

    2012-01-01

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

  11. 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

  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

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

    2016-01-06

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

  13. Association mapping of seed oil content in Brassica napus and comparison with quantitative trait loci identified from linkage mapping.

    PubMed

    Zou, Jun; Jiang, Congcong; Cao, Zhengying; Li, Ruiyuan; Long, Yan; Chen, Sheng; Meng, Jinling

    2010-11-01

    Association mapping has been used increasingly in natural populations with rich genetic diversity to detect DNA-based markers that are associated with important agronomic traits. Brassica napus is an important oil crop with limited genetic diversity. "New-type" B. napus that is introgressed with subgenomic components from related species has been developed to broaden the genetic basis of "traditional" B. napus. In this study, new-type B. napus lines and a collection of traditional B. napus varieties from different countries were used as two different populations to evaluate seed oil content and to determine the efficacy of association mapping by comparison with previous study of linkage mapping. Relatively rich genetic diversity, but a higher level of linkage disequilibrium was observed in the new-type B. napus as compared with the traditional B. napus. Similarly, a larger variation in oil content and a greater number of associated markers were detected in the population of new-type B. napus. Meanwhile, more than half of the genetic loci, to which the associated markers corresponded, were located within the quantitative trait loci intervals identified previously in linkage mapping experiments, which demonstrated the power of association mapping in B. napus.

  14. Morphology of nested fullerenes

    SciTech Connect

    Srolovitz, D.J.; Safran, S.A.; Homyonfer, M.; Tenne, R. )

    1995-03-06

    We introduce a continuum model which shows that dislocations and/or grain boundaries are intrinsic features of nested fullerenes whose thickness exceeds a critical value to relieve the large inherent strains in these structures. The ratio of the thickness to the radius of the nested fullerenes is determined by the ratio of the surface to curvature and dislocation (or grain boundary) energies. Confirming experimental evidence is presented for nested fullerenes with small thicknesses and with spherosymmetric shapes.

  15. Ability to assess nest predation risk in secondary hole-nesting birds: an experimental study.

    PubMed

    Pöysä, Hannu; Ruusila, Vesa; Milonoff, Markku; Virtanen, Juha

    2001-01-01

    Because nest predation is the major source of nesting mortality in birds, site-specific predation risk may play an important role in determining birds' ability to select nest sites that reduce predation risk. This possibility has not been adequately tested. Here we report on 5-year experiments by which we studied, independently from birds' earlier experience with specific nest boxes, both the selection and predation risk of nest sites in the common goldeneye (Bucephala clangula). New, previously unoccupied nest boxes were erected in two habitat types on three study areas. Experimentally measured predation risk in the nest boxes varied between 0 and 1.0, i.e. goldeneye females could select a nest site along a wide gradient of possible predation-risk values. We did not find a difference in predation risk between occupied and unoccupied nest boxes, nor was the order of nest box occupation associated with predation risk. A power analysis revealed that our test had reasonably high power to reject a false null hypothesis. Our results suggest that common goldeneye females likely have not evolved an ability to assess predation risk of new, previously unoccupied nest sites.

  16. Lessons from dwarf8 on the strengths and weaknesses of structured association mapping

    USDA-ARS?s Scientific Manuscript database

    The strengths of association mapping lie in its resolution and allelic richness, but spurious associations arising from historical relationships and selection patterns need to be accounted for in statistical analyses. Here we reanalyze one of the first generation structured association mapping studi...

  17. Fine mapping by composite genome-wide association analysis.

    PubMed

    Casellas, Joaquim; Cañas-Álvarez, Jhon Jacobo; Fina, Marta; Piedrafita, Jesús; Cecchinato, Alessio

    2017-06-06

    Genome-wide association (GWA) studies play a key role in current genetics research, unravelling genomic regions linked to phenotypic traits of interest in multiple species. Nevertheless, the extent of linkage disequilibrium (LD) may provide confounding results when significant genetic markers span along several contiguous cM. In this study, we have adapted the composite interval mapping approach to the GWA framework (composite GWA), in order to evaluate the impact of including competing (possibly linked) genetic markers when testing for the additive allelic effect inherent to a given genetic marker. We tested model performance on simulated data sets under different scenarios (i.e., qualitative trait loci effects, LD between genetic markers and width of the genomic region involved in the analysis). Our results showed that the genomic region had a small impact on the number of competing single nucleotide polymorphisms (SNPs) as well as on the precision of the composite GWA analysis. A similar conclusion was derived from the preferable range of LD between the tested SNP and competing SNPs, although moderate-to-high LD seemed to attenuate the loss of statistical power. The composite GWA improved specificity and reduced the number of significant genetic markers. The composite GWA model contributes a novel point of view for GWA analyses where testing circumscribed to the genomic region flanking each SNP (delimited by the nearest competing SNPs) and conditioning on linked markers increases the precision to locate causal mutations, but possibly at the expense of power.

  18. 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

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

    PubMed

    Cerecero, Patricia; Hernández-Prado, Bernardo; Denova, Edgar; Valdés, Roxana; Vázquez, Gilberto; Camarillo, Eneida; Huitrón, Gerardo

    2013-05-01

    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. 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. 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). Serum concentration of uric acid is associated with 10-year global CR among individuals with high levels of physical inactivity.

  20. Non-microtubular localizations of microtubule-associated protein 6 (MAP6).

    PubMed

    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.

  1. Nests, tree holes, and the evolution of primate life histories.

    PubMed

    Kappeler, P M

    1998-01-01

    In contrast to the majority of primates, many prosimians, some New World monkeys, and the great apes rest in tree holes or self-constructed nests during their inactive periods. The goal of this comparative study was to examine possible functions of this interspecific variation. Information on resting behavior, maternal behavior, and basic life-history traits was gleaned from the literature and mapped onto a phylogenetic tree of primates for various comparative tests. Parsimony-based reconstructions revealed that only the use of nests or tree holes as shelters for young infants can be unequivocally reconstructed for various higher taxa, suggesting that it is functionally different from the use of shelters by adults (who may be accompanied by infants). Further reconstructions revealed that the ancestral primate was most likely nocturnal and solitary and produced a single infant that was initially left in a shelter and later carried orally to a parking place in the vegetation--a combination of traits exhibited by many living galagos. Evolutionary losses of the use of nests were concentrated among diurnal and nonsolitary taxa and weakly associated with evolutionary increases in body size. Thus, protective functions of nests or tree holes used by prosimians are either secondary or there are alternative ways of obtaining protection. Because the evolution of larger litters was significantly associated with the presence of shelters, the presence of relatively altricial young among prosimians best explains the use of nests and tree holes, which are in most but not all cases also used by adults. These shelters therefore play an integral part in the life-history strategies of primitive primates and their ancestors and evolved secondarily among anthropoids for other purposes.

  2. Cross-sectional association between smoking depictions in films and adolescent tobacco use nested in a British cohort study

    PubMed Central

    Waylen, Andrea E; Leary, Sam D; Ness, Andrew R; Tanski, Susanne E; Sargent, James D

    2012-01-01

    Objective To assess associations between exposure to smoking depictions in films and adolescent tobacco use in a British population cohort. Methods Data on exposure to smoking in films and smoking behaviour were collected from 5166 15-year-old adolescents in the UK. Main outcome measures were smoking initiation (ever tried a cigarette) and current smoking status. Social, family and behavioural factors were adjusted for, together with alcohol use and peer smoking as potential mediators. Data from all existing cross-sectional studies examining the effects of exposure to smoking in films were summarised in a meta-analysis. Results Higher exposure to smoking in films was associated with a dose-response increase in the risk of smoking initiation even after adjusting for confounders. Adolescents in the highest exposure quartile were 1.73 (95% CI 1.55 to 1.93) times (RR) more likely to initiate smoking than those in the lowest quartile. They were more likely to report current smoking after adjusting for social and familial factors (RR 1.47 (95% CI 1.07 to 2.02)), but the association attenuated after including behavioural factors (RR 1.34 (95% CI 0.95 to 1.87)). The meta-analysis shows that, after aggregation of all relevant data, viewing smoking in films increases the risk of smoking onset by over 100% (combined RR 2.13 (95% CI 1.76 to 2.57)) and the risk of current or established smoking behaviour by 68% (combined RR 1.68 (95% CI 0.40 to 2.01)). Conclusions This study provides evidence that adolescents in the UK and elsewhere who are exposed to smoking depictions in films are more likely to initiate smoking. Given the association between smoking and poor health outcomes, these data justify a review of film ratings. PMID:21933947

  3. Cross-sectional association between smoking depictions in films and adolescent tobacco use nested in a British cohort study.

    PubMed

    Waylen, Andrea E; Leary, Sam D; Ness, Andrew R; Tanski, Susanne E; Sargent, James D

    2011-10-01

    To assess associations between exposure to smoking depictions in films and adolescent tobacco use in a British population cohort. Data on exposure to smoking in films and smoking behaviour were collected from 5166 15-year-old adolescents in the UK. Main outcome measures were smoking initiation (ever tried a cigarette) and current smoking status. Social, family and behavioural factors were adjusted for, together with alcohol use and peer smoking as potential mediators. Data from all existing cross-sectional studies examining the effects of exposure to smoking in films were summarised in a meta-analysis. Higher exposure to smoking in films was associated with a dose-response increase in the risk of smoking initiation even after adjusting for confounders. Adolescents in the highest exposure quartile were 1.73 (95% CI 1.55 to 1.93) times (RR) more likely to initiate smoking than those in the lowest quartile. They were more likely to report current smoking after adjusting for social and familial factors (RR 1.47 (95% CI 1.07 to 2.02)), but the association attenuated after including behavioural factors (RR 1.34 (95% CI 0.95 to 1.87)). The meta-analysis shows that, after aggregation of all relevant data, viewing smoking in films increases the risk of smoking onset by over 100% (combined RR 2.13 (95% CI 1.76 to 2.57)) and the risk of current or established smoking behaviour by 68% (combined RR 1.68 (95% CI 0.40 to 2.01)). This study provides evidence that adolescents in the UK and elsewhere who are exposed to smoking depictions in films are more likely to initiate smoking. Given the association between smoking and poor health outcomes, these data justify a review of film ratings.

  4. A nested case–control study to determine the incidence and factors associated with unanticipated admissions following day care surgery

    PubMed Central

    Singh, Madhurita; Ponniah, Manickam; Jacob, KS

    2016-01-01

    Background and Aims: Day care surgery offers respite from hospitalisation for specific surgical procedures and has many advantages. However, occasionally patients who undergo such surgery require hospitalisation for unanticipated complications. We aimed to determine their incidence and to identify factors associated with unanticipated admissions in a tertiary care hospital in South India. Methods: During the 3-month study, 63 cases requiring admission and 126 randomly selected controls were taken from the 776 procedures that were performed were compared. The variables studied were patients’ demographic characteristics, pre-operative medical illness, personal habits, American Society of Anesthesiologists status, the diagnosis and surgical procedures, time since last meal, duration of anaesthesia and surgery, experience of the surgeon and anaesthetist, and intraoperative management (techniques, drugs, monitoring, etc.). Univariate and bivariate statistics were used to determine factors associated with unanticipated admissions. Results: The incidence of unanticipated admissions following day care surgery was 8.11%. The reasons for admission were anaesthetic (33.33%), surgical (15.87%), medical (6.34%) and social (44.44%). The factors significantly associated with unanticipated admissions included duration of anaesthesia more than 50 min (odds ratio [OR]: 3.179; 95% confidence interval [CI]: 1.503–6.722), and starting the last case after 3 pm (OR: 10.095; 95% CI: 2.418–42.148). Conclusion: Unanticipated admissions following day care surgery occur mainly due to anaesthetic, surgical, medical and social reasons. PMID:27942057

  5. Structure and phosphorylation of microtubule-associated protein 2 (MAP 2).

    PubMed Central

    Vallee, R

    1980-01-01

    Chymotryptic fragments of microtubule-associated protein 2 (MAP 2) containing the portion of the molecule responsible for promoting microtubule assembly were identified. These assembly-promoting fragments displaced intact MAP 2, but not MAP 1, from assembled microtubules. This indicates that the association of MAP 2 with the microtubule surface is reversible. Both the assembly-promoting fragments and fragments representing the portion of the MAP 2 molecule observed as a projection on the microtubule surface were found to contain sites for endogenous cyclic AMP-dependent phosphorylation. The projection fragments were capable of endogenous phosphorylation even after their physical separation from microtubules. This suggests an intimate association of a kinase activity with the projections. Detailed analysis of the properties of the chymotryptic fragments of MAP 2 has led to a map of the molecule showing the major sites of proteolytic attack and the sites of phosphorylation. Images PMID:6251448

  6. 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.

  7. 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)

  8. 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

  9. 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

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

    PubMed

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

    2016-02-25

    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. 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. 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  ears) 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. 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. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

  11. Nest-site selection by cavity-nesting birds in relation to postfire salvage logging

    Treesearch

    Victoria A. Saab; Robin E. Russell; Jonathan G. Dudley

    2009-01-01

    Large wildfire events in coniferous forests of the western United States are often followed by postfire timber harvest. The long-term impacts of postfire timber harvest on fire-associated cavity-nesting bird species are not well documented. We studied nest-site selection by cavity-nesting birds over a 10-year period (1994-2003), representing 1-11 years after fire, on...

  12. Helicobacter pylori specific nested PCR assay for the detection of 23S rRNA mutation associated with clarithromycin resistance

    PubMed Central

    Maeda, S; Yoshida, H; Ogura, K; Kanai, F; Shiratori, Y; Omata, M

    1998-01-01

    Background—Clarithromycin is one of the most important antibiotics for Helicobacter pylori eradication. However, 5-10% of strains are reported to be resistant. It has been shown that one point mutation in the 23S rRNA gene is associated with resistance to clarithromycin. 
Aims—To establish a polymerase chain reaction (PCR) system which amplifies a segment of the 23S rRNA gene containing the mutation points with primers specific for H pylori, so that H pylori infection and the mutation associated with clarithromycin resistance can be examined simultaneously. 
Methods—To detect H pylori infection and the mutation simultaneously, primers specific for the H pylori 23S rRNA gene were designed based on sequence conservation among H pylori strains and sequence specificity as compared with other bacteria. DNA from 57 cultured strains and from 39 gastric juice samples was amplified in the seminested 23S rRNA PCR. Clinical applicability was evaluated in 85patients. 
Results—DNA samples from 57 cultured strains were all amplified. The novel assay and the urease A PCR agreed in 37/39 gastric juice samples with no false positives. The assay did not amplify the DNA of bacteria other than H pylori. Eight of 85 samples had the mutation before treatment. In clarithromycin based treatment, eradication was achieved in 2/5 (40%) with the mutation and 29/34 (85%) without the mutation. 
Conclusion—The assay using gastric juice is quick (within 12 hours) and non-invasive (endoscopy not required), enabling rapid initiation of appropriate antibiotic treatment. 

 Keywords: Helicobacter pylori; eradication; clarithromycin; resistance; point mutation PMID:9863474

  13. 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

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

    PubMed

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

    2015-01-01

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

  15. Differential distribution of microtubule-associated proteins MAP-1 and MAP-2 in neurons of rat brain and association of MAP-1 with microtubules of neuroblastoma cells (clone N2A).

    PubMed Central

    Wiche, G; Briones, E; Hirt, H; Krepler, R; Artlieb, U; Denk, H

    1983-01-01

    To study the individual location of the microtubule proteins MAP-1 and MAP-2 in neuronal tissues and cells, antisera to electrophoretically purified MAP-1 and MAP-2 components were raised in rabbits. When frozen sections through rat brain were examined by immunofluorescence microscopy the antibodies to MAP-1 strongly stained a variety of nerve cells including dendrites and myelinated axons in the cerebrum and cerebellum. Antibodies to MAP-2 showed similar staining patterns, except that myelinated axons were unstained. These results were confirmed by immunoelectron microscopy of frozen sections through cerebellum using the peroxidase technique. Thereby, the association of MAP-1 with microtubules was also clearly demonstrated. When cultured mouse neuroblastoma N2A cells were examined by immunofluorescence microscopy the antiserum to MAP-1 brightly stained filamentous structures resembling microtubules, whereas relatively weak and diffuse staining of the cytoplasm was observed with the antiserum to MAP-2. In agreement with the immunolocalization, MAP-1, but not MAP-2, was found as a prominent component of microtubules proteins polymerized in vitro by taxol from soluble N2A cell extracts. Together these results indicate that neuronal microtubules are preferentially associated with distinct high mol. wt. polypeptides. Therefore, they support the concept that different complements of associated proteins determine distinct functions of microtubules. Images Fig. 1. Fig. 2. Fig. 3. Fig. 4. Fig. 5. PMID:6641705

  16. Associations of vitamin D pathway genes with circulating 25-hydroxyvitamin-D, 1,25-dihydroxyvitamin-D, and prostate cancer: a nested case-control study.

    PubMed

    Gilbert, Rebecca; Bonilla, Carolina; Metcalfe, Chris; Lewis, Sarah; Evans, David M; Fraser, William D; Kemp, John P; Donovan, Jenny L; Hamdy, Freddie C; Neal, David E; Lane, J Athene; Smith, George Davey; Lathrop, Mark; Martin, Richard M

    2015-02-01

    Vitamin D pathway single nucleotide polymorphisms (SNPs) are potentially useful proxies for investigating whether circulating vitamin D metabolites [total 25-hydroxyvitamin-D, 25(OH)D; 1,25-dihydroxyvitamin, 1,25(OH)2D] are causally related to prostate cancer. We investigated associations of sixteen SNPs across seven genes with prostate-specific antigen-detected prostate cancer. In a nested case-control study (within the ProtecT trial), we estimated odds ratios and 95 % confidence intervals (CIs) quantifying associations between SNPs and prostate cancer. Subgroup analyses investigated whether associations were stronger in men who had high/low sun exposure [a proxy for 25(OH)D]. We quantified associations of SNPs with stage (T1-T2/T3-T4) and grade (<7/≥7). Multiple variant scores included SNPs encoding proteins involved in 25(OH)D synthesis and metabolism. We included 1,275 prostate cancer cases (141 locally advanced, 385 high grades) and 2,062 healthy controls. Vitamin D-binding protein SNPs were associated with prostate cancer (rs4588-A: OR 1.20, CI 1.01, 1.41, p = 0.04; rs7041-T: OR 1.19, CI 1.02, 1.38, p = 0.03). Low 25(OH)D metabolism score was associated with high (vs low) grade (OR 0.76, CI 0.63, 0.93, p = 0.01); there was a similar association of its component variants: rs6013897-A in CYP24A1 (OR 0.78, CI 0.60, 1.01, p = 0.06) and rs10877012-T in CYP27B1 (OR 0.80, CI 0.63, 1.02, p = 0.07). There was no evidence that associations differed by level of sun exposure. We found some evidence that vitamin D pathway SNPs were associated with prostate cancer risk and grade, but not stage. There was no evidence of an association in men with deficient vitamin D (measured by having low sun exposure).

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

    PubMed

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

    2015-01-01

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

  18. MAP5: a novel brain microtubule-associated protein under strong developmental regulation.

    PubMed

    Riederer, B; Cohen, R; Matus, A

    1986-12-01

    A novel microtubule-associated protein, MAP5, is described, whose chemical properties and cytological distribution distinguish it from other known microtubule-associated proteins (MAPs). Its status as a MAP is indicated by the observations that (i) it co-assembles efficiently with microtubules in vitro, (ii) it is localized on microtubules in brain sections by immunogold staining with monoclonal antibody against MAP5 and (iii) immunoaffinity purified MAP5 stimulates tubulin polymerization. Immunoperoxidase staining of brain sections showed that MAP5 is present in neurons throughout the brain and that in them it is evenly distributed throughout axons, dendrites and cell bodies. In this respect it differs from previously described MAPs (1, 2, 3 and tau) which are differentially compartmentalized in brain neurons. MAP5 is not present in axon terminals, dendritic spines or other synaptic elements. It is present at substantially higher levels in neonatal brain than adult and it is more abundant than either MAP1 or MAP2a up to postnatal day 10. The fall in amount of MAP5, from juvenile to adult levels, is completed between postnatal days 10 and 20. This suggests that MAP5 is particularly important in modulating microtubule function during the formation of neuronal processes.

  19. Association Between Vascular Access Dysfunction and Subsequent Major Adverse Cardiovascular Events in Patients on Hemodialysis: A Population-Based Nested Case-Control Study.

    PubMed

    Kuo, Te-Hui; Tseng, Chien-Tzu; Lin, Wei-Hung; Chao, Jo-Yen; Wang, Wei-Ming; Li, Chung-Yi; Wang, Ming-Cheng

    2015-07-01

    The association between dialysis vascular access dysfunction and the risk of developing major adverse cardiovascular events (MACE) in hemodialysis patients is unclear and has not yet been investigated. We analyzed data from the National Health Insurance Research Database of Taiwan to quantify this association. Adopting a case-control design nested within a cohort of patients who received hemodialysis from 2001 to 2010, we identified 9711 incident cases of MACE during the stage of stable maintenance dialysis and 19,422 randomly selected controls matched to cases on age, gender, and duration of dialysis. Events of vascular access dysfunction in the 6-month period before the date of MACE onset (ie, index date) for cases and before index dates for controls were evaluated retrospectively. The presence of vascular access dysfunction was associated with a 1.385-fold higher odds of developing MACE as estimated from the logistic regression analysis. This represents a significantly increased adjusted odds ratio (OR) at 1.268 (95% confidence interval [CI] = 1.186-1.355) after adjustment for comorbidities and calendar years of initiating dialysis. We also noted a significant exposure-response trend (P < 0.001) between the frequency of vascular access dysfunction and MACE, with the greatest risk (adjusted OR = 1.840, 95% CI = 1.549-2.186) noted in patients with ≥3 vascular access events. We concluded that dialysis vascular access dysfunction was significantly associated with an increased risk of MACE. Hence, vascular access failure can be an early sign for MACE in patients receiving maintenance hemodialysis. Active monitoring and treatment of cardiovascular risk factors and related diseases, not merely managing vascular access dysfunction, would be required to reduce the risk of MACE.

  20. Genome-wide association mapping of crown rust resistance in oat elite germplasm

    USDA-ARS?s Scientific Manuscript database

    Oat crown rust, caused by Puccinia coronata f. sp. avenae, is a major constraint to oat production in many parts of the world. In this first comprehensive multi-environment genome-wide association map of oat crown rust, we used 2,972 SNPs genotyped on 631 oat lines for association mapping of quantit...

  1. Association between pre-diagnostic circulating vitamin D concentration and risk of colorectal cancer in European populations:a nested case-control study

    PubMed Central

    Bueno-de-Mesquita, H Bas; Ferrari, Pietro; van Duijnhoven, Franzel J B; Norat, Teresa; Pischon, Tobias; Jansen, Eugène H J M; Slimani, Nadia; Byrnes, Graham; Rinaldi, Sabina; Tjønneland, Anne; Olsen, Anja; Overvad, Kim; Boutron-Ruault, Marie-Christine; Clavel-Chapelon, Françoise; Morois, Sophie; Kaaks, Rudolf; Linseisen, Jakob; Boeing, Heiner; Bergmann, Manuela M; Trichopoulou, Antonia; Misirli, Gesthimani; Trichopoulos, Dimitrios; Berrino, Franco; Vineis, Paolo; Panico, Salvatore; Palli, Domenico; Tumino, Rosario; Ros, Martine M; van Gils, Carla H; Peeters, Petra H; Brustad, Magritt; Lund, Eiliv; Tormo, María-José; Ardanaz, Eva; Rodríguez, Laudina; Sánchez, Maria-José; Dorronsoro, Miren; Gonzalez, Carlos A; Hallmans, Göran; Palmqvist, Richard; Roddam, Andrew; Key, Timothy J; Khaw, Kay-Tee; Autier, Philippe; Hainaut, Pierre; Riboli, Elio

    2010-01-01

    Objective To examine the association between pre-diagnostic circulating vitamin D concentration, dietary intake of vitamin D and calcium, and the risk of colorectal cancer in European populations. Design Nested case-control study. Setting The study was conducted within the EPIC study, a cohort of more than 520 000 participants from 10 western European countries. Participants 1248 cases of incident colorectal cancer, which developed after enrolment into the cohort, were matched to 1248 controls Main outcome measures Circulating vitamin D concentration (25-hydroxy-vitamin-D, 25-(OH)D) was measured by enzyme immunoassay. Dietary and lifestyle data were obtained from questionnaires. Incidence rate ratios and 95% confidence intervals for the risk of colorectal cancer by 25-(OH)D concentration and levels of dietary calcium and vitamin D intake were estimated from multivariate conditional logistic regression models, with adjustment for potential dietary and other confounders. Results 25-(OH)D concentration showed a strong inverse linear dose-response association with risk of colorectal cancer (P for trend <0.001). Compared with a pre-defined mid-level concentration of 25-(OH)D (50.0-75.0 nmol/l), lower levels were associated with higher colorectal cancer risk (<25.0 nmol/l: incidence rate ratio 1.32 (95% confidence interval 0.87 to 2.01); 25.0-49.9 nmol/l: 1.28 (1.05 to 1.56), and higher concentrations associated with lower risk (75.0-99.9 nmol/l: 0.88 (0.68 to 1.13); ≥100.0 nmol/l: 0.77 (0.56 to 1.06)). In analyses by quintile of 25-(OH)D concentration, patients in the highest quintile had a 40% lower risk of colorectal cancer than did those in the lowest quintile (P<0.001). Subgroup analyses showed a strong association for colon but not rectal cancer (P for heterogeneity=0.048). Greater dietary intake of calcium was associated with a lower colorectal cancer risk. Dietary vitamin D was not associated with disease risk. Findings did not vary by sex and were not

  2. Protein content of the Hylesia metabus egg nest setae (Cramer [1775]) (Lepidoptera: Saturniidae) and its association with the parental investment for the reproductive success and lepidopterism.

    PubMed

    Cabrera, Gleysin; Lundberg, Ulf; Rodríguez-Ulloa, Arielis; Herrera, Melfran; Machado, Wendy; Portela, Madelón; Palomares, Sucel; Espinosa, Luis Ariel; Ramos, Yassel; Durán, Rosario; Besada, Vladimir; Vonasek, Eva; González, Luis Javier

    2017-01-06

    Hylesia metabus is a neotropical moth possessing toxic setae, which once in contact with the skin cause a severe dermatitis to humans known as lepidopterism. The only known function of the setae in the life cycle is to provide protection during the mating and egg-hatching stages. Approximately 65% of the protein content of the setae is a cluster of five proteases (28-45kDa) showing sequence homology to other S1A serine proteases. The N-glycans of a 40kDa protease are a mixture of neutral and sulfated G0F structures. The sulfated N-glycans have an important role in triggering the inflammatory response typical of lepidopterism while the proteolytic activity may promote the erosion of blood vessels and tissues causing focal hemorrhages. The presence of Chitinase and a 30kDa lipoprotein is probably related to the antifungal defense. In addition, chitin digestion of the setae may potentiate the inflammatory reaction caused by the toxins due to the formation of chitin adjuvants fragments. The combined effect of proteases and a chitinase may dissuade predating arthropods, by damaging their exoskeletons. Vitellogenin, a bacteriostatic protein, is able to recognize pathogen-associated patterns, which suggests its possible role in protecting the embryonated eggs from pathogenic microorganisms. The present study is the first report describing the different protein species present in the urticating egg nest setae of the neotropical moth Hylesia metabus - the most harmful of the Hylesia moths - causing a severe urticating dermatitis in humans known as lepidopterism. A distinctive feature of the venom is the presence of five different S1A serine proteases probably used to guarantee a more efficient degradation of a wider number of protein substrates. This work confirms that the presence of sulfated N-glycans is not an isolated finding since its presence has been demonstrated in two different proteases affirming that this PTM is of importance for the activation of the

  3. Culture-independent nested PCR method reveals high diversity of actinobacteria associated with the marine sponges Hymeniacidon perleve and Sponge sp.

    PubMed

    Xin, Yanjuan; Huang, Jianyu; Deng, Maicun; Zhang, Wei

    2008-11-01

    A culture-independent nested polymerase chain reaction (PCR) technique was used to investigate the diversity of actinobacteria communities associated with the sponges Hymeniacidon perleve and Sponge sp. The phylogenetic affiliation of sponge-derived actinobacteria was then assessed by 16S rRNA sequencing of cloned DNA fragments. A total of 196 positive clones were screened by restriction fragment length polymorphism (RFLP) analysis; 48 unique operational taxonomic units (OTUs) were selected for sequencing. Rarefaction analysis indicated that the clone libraries represented 93% and 94% of the total estimated diversity for the two species, respectively. Phylogenetic analysis of sequence data revealed representatives of various phylogenetic divisions, which were related to the following ten actinobacterial genera: Acidimicrobium, Corynebacterium, Propionibacterium, Actinomyces, Micrococcus, Microbacterium, Streptomyces, Mycobacterium, Cellulosimicrobium, Sporichthya, and unidentified actinobacterial clones. A sponge-specific, previously uncultured actinobacteria community grouped within the subclass Acidimicrobidae was discovered from both H. perleve and Sponge sp. Sequences belonging to Acidimicrobium in the H. perleve and the Sponge sp. clone libraries represented 33% and 24% of the clones, respectively. In the Sponge sp. clone library Mycobacterium dominated, accounting for 70% of all clones. The presence of Acidimicrobium and mycobacteria within two sponges can lay the groundwork for attempts to culture these interesting bacteria for industrial applications.

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

    PubMed

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

    2016-01-01

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

  5. Association of maternal serum homocysteine concentration levels in late stage of pregnancy with preterm births: a nested case-control study.

    PubMed

    Qiu, Xiantao; Gao, Fei; Qiu, Yuanyuan; Bao, Junjie; Gu, Xiaoqiong; Long, Yan; Liu, Fei; Cai, Minmin; Liu, Haiying

    2017-08-11

    To investigate the relationship between maternal serum homocysteine (Hcy) levels in the late stage of pregnancy and preterm birth. Other relevant biochemical parameters were measured to establish the normal reference interval of serum Hcy in both women in the late stage of pregnancy and neonates. The nested case-control study included 300 singleton pregnant women with preterm births between June 2013 and May 2015 and their premature delivered babies as a preterm group. Blood sample within three days before delivery was collected. Simultaneously, 300 healthy pregnant women admitted during the same time, and singleton mature neonates who had gestational week-matched blood sample were age-matched as a control group. Maternal serum levels of Hcy, total triglycerides, total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C), uric acid (UA), free fatty acids (FAA) and superoxide dismutase (SOD) were all higher in the preterm group than in the control group except high-density lipoprotein cholesterol (HDL-C). Serum levels of Hcy, TC, LDL-C, UA, FAA and SOD were higher in prematurely delivered neonates than in the control group except for HDL-C. The body weight of prematurely delivered neonates was negatively correlated with the maternal serum levels of Hcy and UA before delivery. Higher maternal serum Hcy levels were associated with preterm birth and neonatal body weight. Elevated maternal serum levels of Hcy might serve as a biomarker for preterm birth prediction.

  6. Disease severity associated with presence in subgingival plaque of Porphyromonas gingivalis, Aggregatibacter actinomycetemcomitans, and Tannerella forsythia, singly or in combination, as detected by nested multiplex PCR.

    PubMed

    Ready, D; D'Aiuto, F; Spratt, D A; Suvan, J; Tonetti, M S; Wilson, M

    2008-10-01

    This study used a nested multiplex PCR method to detect three periodontal pathogens in subgingival plaque collected before treatment and at 2 and 6 months posttreatment from 107 patients with severe, generalized periodontitis. The proportions of the patients who harbored these bacteria before periodontal treatment were as follows: Tannerella forsythia, 81%; Porphyromonas gingivalis, 78%; and Aggregatibacter (formerly Actinobacillus) actinomycetemcomitans, 47%. At 2 months posttreatment there was a significant reduction in the numbers of patients harboring P. gingivalis (46%; P < 0.001) or T. forsythia (63%; P = 0.043) but not A. actinomycetemcomitans (50%) compared to pretreatment data. At 6 months posttreatment, significantly fewer patients harbored P. gingivalis (43%; P < 0.001); A. actinomycetemcomitans, (31%; P = 0.025), or T. forsythia (63%; P = 0.030). Interestingly, at baseline and at 2 months posttherapy, subjects who harbored only a single pathogen had a greater level of periodontal disease than subjects who harbored two, or all three, of these periodontal pathogens. These data suggest that a reduction in the number of species present may be associated with an increase in the severity of periodontal diseases.

  7. 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

  8. Association between acetylsalicylic acid and the risk of dialysis-related infections or septicemia among incident hemodialysis patients: a nested case-control study.

    PubMed

    Harrak, Hind; Normand, Isabelle; Grinker, Rachel; Elftouh, Naoual; Laurin, Louis-Philippe; Lafrance, Jean-Philippe

    2015-07-28

    Vascular access-related infections and septicemia are the main causes of infections among hemodialysis patients, the majority of them caused by Staphylococcus species. Acetylsalicylic acid (ASA) has recently been reported with a probable antistaphylococcal activity. This study aimed to evaluate the effect of ASA on the risk of dialysis-related infection and septicemia among incident chronic hemodialysis patients. In a nested case-control study, we identified 449 cases of vascular access-related infections and septicemia, and 4156 controls between 2001 and 2007 from our incident chronic hemodialysis patients' cohort. Cases were defined as patients hospitalized with a main diagnosis of vascular access-related infection or septicemia on the discharge sheet (ICD-9 codes). Up to ten controls per case were selected by incidence density sampling and matched to cases on age, sex and follow-up time. ASA exposure was measured at the admission and categorized as: no use, low dose (80-324 mg/d), high dose (≥325 mg/d). Odds ratios (OR) for infections were estimated using multivariable conditional logistic regression analysis, adjusting for potential confounders. Compared to no use, neither dose of ASA was associated with a decreased risk of infection: low dose (OR 1.03, 95 % CI 0.82-1.28) and high dose (OR 1.30, 95 % CI 0.96-1.75). However, diabetes (OR = 1.32, 95 % CI = 1.07-1.62) and anticoagulant use (OR = 1.62, 95 % CI = 1.30-2.02) were associated with a higher risk. Among hemodialysis patients, ASA use was not associated with a reduced risk of hospitalizations for dialysis-related infections or septicemia. However, ASA may remain beneficial for its cardiovascular indications.

  9. Risk of acute liver injury associated with use of antibiotics. Comparative cohort and nested case-control studies using two primary care databases in Europe.

    PubMed

    Brauer, Ruth; Douglas, Ian; Garcia Rodriguez, Luis Alberto; Downey, Gerald; Huerta, Consuelo; de Abajo, Francisco; Bate, Andrew; Feudjo Tepie, Maurille; de Groot, Mark C H; Schlienger, Raymond; Reynolds, Robert; Smeeth, Liam; Klungel, Olaf; Ruigómez, Ana

    2016-03-01

    To assess the impact of varying study designs, exposure and outcome definitions on the risk of acute liver injury (ALI) associated with antibiotic use. The source population comprised of patients registered in two primary care databases, in the UK and in Spain. We identified a cohort consisting of new users of antibiotics during the study period (2004-2009) and non-users during the study period or in the previous year. Cases with ALI were identified within this cohort and classified as definite or probable, based on recorded medical information. The relative risk (RR) of ALI associated with antibiotic use was computed using Poisson regression. For the nested case-control analyses, up to five controls were matched to each case by age, sex, date and practice (in CPRD) and odds ratios (OR) were computed with conditional logistic regression. The age, sex and year adjusted RRs of definite ALI in the current antibiotic use periods was 10.04 (95% CI: 6.97-14.47) in CPRD and 5.76 (95% CI: 3.46-9.59) in BIFAP. In the case-control analyses adjusting for life-style, comorbidities and use of medications, the OR of ALI for current users of antibiotics was and 5.7 (95% CI: 3.46-9.36) in CPRD and 2.6 (95% CI: 1.26-5.37) in BIFAP. Guided by a common protocol, both cohort and case-control study designs found an increased risk of ALI associated with the use of antibiotics in both databases, independent of the exposure and case definitions used. However, the magnitude of the risk was higher in CPRD compared to BIFAP. Copyright © 2016 John Wiley & Sons, Ltd.

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

    PubMed Central

    2013-01-01

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

  11. 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.

  12. Clinical and epidemiological use of nested PCR targeting the repetitive element IS1111 associated with the transposase gene from Coxiella burnetii.

    PubMed

    Mares-Guia, Maria Angélica M M; Guterres, Alexandro; Rozental, Tatiana; Ferreira, Michelle Dos Santos; Lemos, Elba R S

    2017-08-24

    Q fever is a worldwide zoonosis caused by Coxiella burnetii-a small obligate intracellular Gram-negative bacterium found in a variety of animals. It is transmitted to humans by inhalation of contaminated aerosols from urine, feces, milk, amniotic fluid, placenta, abortion products, wool, and rarely by ingestion of raw milk from infected animals. Nested PCR can improve the sensitivity and specificity of testing while offering a suitable amplicon size for sequencing. Serial dilutions were performed tenfold to test the limit of detection, and the result was 10× detection of C. burnetti DNA with internal nested PCR primers relative to trans-PCR. Different biological samples were tested and identified only in nested PCR. This demonstrates the efficiency and effectiveness of the primers. Of the 19 samples, which amplify the partial sequence of C. burnetii, 12 were positive by conventional PCR and nested PCR. Seven samples-five spleen tissue samples from rodents and two tick samples-were only positive in nested PCR. With these new internal primers for trans-PCR, we demonstrate that our nested PCR assay for C. burnetii can achieve better results than conventional PCR. Published by Elsevier Editora Ltda.

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

    PubMed

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

    2008-10-01

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

  14. 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

  15. 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

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

    2012-03-01

    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 cases and 234 controls in the Alpha-Tocopherol, Beta-Carotene Cancer Prevention Study of Finnish men. ORs and 95% CIs 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 seemed to have a threshold between quartiles 2 to 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.

  16. Timing of nest vegetation measurement may obscure adaptive significance of nest-site characteristics: A simulation study.

    PubMed

    McConnell, Mark D; Monroe, Adrian P; Burger, Loren Wes; Martin, James A

    2017-02-01

    Advances in understanding avian nesting ecology are hindered by a prevalent lack of agreement between nest-site characteristics and fitness metrics such as nest success. We posit this is a result of inconsistent and improper timing of nest-site vegetation measurements. Therefore, we evaluated how the timing of nest vegetation measurement influences the estimated effects of vegetation structure on nest survival. We simulated phenological changes in nest-site vegetation growth over a typical nesting season and modeled how the timing of measuring that vegetation, relative to nest fate, creates bias in conclusions regarding its influence on nest survival. We modeled the bias associated with four methods of measuring nest-site vegetation: Method 1-measuring at nest initiation, Method 2-measuring at nest termination regardless of fate, Method 3-measuring at nest termination for successful nests and at estimated completion for unsuccessful nests, and Method 4-measuring at nest termination regardless of fate while also accounting for initiation date. We quantified and compared bias for each method for varying simulated effects, ranked models for each method using AIC, and calculated the proportion of simulations in which each model (measurement method) was selected as the best model. Our results indicate that the risk of drawing an erroneous or spurious conclusion was present in all methods but greater with Method 2 which is the most common method reported in the literature. Methods 1 and 3 were similarly less biased. Method 4 provided no additional value as bias was similar to Method 2 for all scenarios. While Method 1 is seldom practical to collect in the field, Method 3 is logistically practical and minimizes inherent bias. Implementation of Method 3 will facilitate estimating the effect of nest-site vegetation on survival, in the least biased way, and allow reliable conclusions to be drawn.

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

    NASA Astrophysics Data System (ADS)

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

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

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

    USDA-ARS?s Scientific Manuscript database

    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 ...

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

    USDA-ARS?s Scientific Manuscript database

    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...

  20. Association of CXCR4 expression with coronary collateralization in patients with chronic total coronary occlusion: A nested case-control study.

    PubMed

    Yang, Chun; Zhu, Wenjin; Han, Xiu; Ma, Aiqun; Bai, Ling; Xu, Feng

    2017-02-01

    CXCR4 signaling contributes to the development and progression of neovascularization. The objective of this study was to investigate whether CXCR4 expression in peripheral CD34+ cells associated with the coronary collateralization (CC) in patients with chronic total coronary occlusion (CTO). We measured CXCR4 expression in peripheral CD34+ cells and assessed its relation with CC in a nested case-control study including 78 cases and 78 matched controls aged 38-69years, assessed in January 2011 to December 2012 and with at least 1year of follow-up before the index date. Cases were defined as good coronary collateralization (GCC) according to the Rentrop scoring system (Rentrop score of 2 or 3); for each case, one age-matched control with poor coronary collateralization (PCC) (Rentrop score 0 or 1) was randomly selected from the study participants. Demographic, biochemical, and angiographic variables were collected. In multivariate analysis, the OR (95% CI) of CXCR4 expression was 0.018 (0.017 to 0.020) in patients with GCC versus PCC. Independent effect of CXCR4 expression on CC was (OR 0.012, 95% CI 0.010-0.014) when adjusted for other variables. A nonlinear relationship between CXCR4 expression and CC was observed. The CC degree increased when CXCR4 expression exceeded the turning point (30%) (OR 0.025, 95% CI 0.022-0.028; p<0.001). When the CXCR4 expression exceeded 75%, increased CXCR4 level could not promoted CC (OR 0.000, 95% CI 0.008-0.007; p=0.974). Increased CXCR4 level in peripheral CD34+ cells was associated with GCC in patients with CTO. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  1. 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.

  2. Increased urine semaphorin-3A is associated with renal damage in hypertensive patients with chronic kidney disease: a nested case–control study

    PubMed Central

    Ramesh, Ganesan; Jayakumar, Calpurnia; Leoncini, Giovanna; Garneri, Debora; Pontremoli, Roberto

    2014-01-01

    Background Semaphorins are guidance proteins implicated in several processes such as angiogenesis, organogenesis, cell migration, and cytokine release. Experimental studies showed that semaphorin-3a (SEMA3A) administration induces transient massive proteinuria, podocyte foot process effacement and endothelial cell damage in healthy animals. While SEMA3A signaling has been demonstrated to be mechanistically involved in experimental diabetic glomerulopathy and in acute kidney injury, to date its role in human chronic kidney disease (CKD) has not been investigated. Methods To test the hypothesis that SEMA3A may play a role in human CKD, we performed a cross-sectional, nested, case–control study on 151 matched hypertensive patients with and without CKD. SEMA3A was quantified in the urine (USEMA) by ELISA. Glomerular filtration rate was estimated (eGFR) by the CKD-EPI formula and albuminuria was measured as albumin-to-creatinine ratio (ACR). Results USEMA levels were positively correlated with urine ACR (p = 0.001) and serum creatinine (p < 0.001). USEMA was higher in patients with both components of renal damage as compared to those with only one and those with normal renal function (p < 0.007 and <0.001, respectively). The presence of increased USEMA levels (i.e. top quartile) entailed a fourfold higher risk of combined renal damage (p < 0.001) and an almost twofold higher risk of macroalbuminuria (p = 0.005) or of reduced eGFR, even adjusting for confounding factors (p = 0.002). Conclusions USEMA is independently associated with CKD in both diabetic and non diabetic hypertensive patients. Further studies may help clarify the mechanisms underlying this association and possibly the pathogenic changes leading to the development of CKD. PMID:24756974

  3. 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

  4. Induction of the autophagy-associated gene MAP1S via PU.1 supports APL differentiation.

    PubMed

    Haimovici, Aladin; Brigger, Daniel; Torbett, Bruce E; Fey, Martin F; Tschan, Mario P

    2014-09-01

    The PU.1 transcription factor is essential for myeloid development. We investigated if the microtubule-associated protein 1S (MAP1S) is a novel PU.1 target with a link to autophagy, a cellular recycling pathway. Comparable to PU.1, MAP1S expression was significantly repressed in primary AML blasts as compared to mature neutrophils. Accordingly, MAP1S expression was induced during neutrophil differentiation of CD34(+) progenitor and APL cells. Moreover, PU.1 bound to the MAP1S promoter and induced MAP1S expression during APL differentiation. Inhibiting MAP1S resulted in aberrant neutrophil differentiation and autophagy. Taken together, our findings implicate the PU.1-regulated MAP1S gene in neutrophil differentiation and autophagy control.

  5. Association mapping in Salix viminalis L. (Salicaceae) - identification of candidate genes associated with growth and phenology.

    PubMed

    Hallingbäck, Henrik R; Fogelqvist, Johan; Powers, Stephen J; Turrion-Gomez, Juan; Rossiter, Rachel; Amey, Joanna; Martin, Tom; Weih, Martin; Gyllenstrand, Niclas; Karp, Angela; Lagercrantz, Ulf; Hanley, Steven J; Berlin, Sofia; Rönnberg-Wästljung, Ann-Christin

    2016-05-01

    Willow species (Salix) are important as short-rotation biomass crops for bioenergy, which creates a demand for faster genetic improvement and breeding through deployment of molecular marker-assisted selection (MAS). To find markers associated with important adaptive traits, such as growth and phenology, for use in MAS, we genetically dissected the trait variation of a Salix viminalis (L.) population of 323 accessions. The accessions were sampled throughout northern Europe and were established at two field sites in Pustnäs, Sweden, and at Woburn, UK, offering the opportunity to assess the impact of genotype-by-environment interactions (G × E) on trait-marker associations. Field measurements were recorded for growth and phenology traits. The accessions were genotyped using 1536 SNP markers developed from phenology candidate genes and from genes previously observed to be differentially expressed in contrasting environments. Association mapping between 1233 of these SNPs and the measured traits was performed taking into account population structure and threshold selection bias. At a false discovery rate (FDR) of 0.2, 29 SNPs were associated with bud burst, leaf senescence, number of shoots or shoot diameter. The percentage of accession variation (Radj2) explained by these associations ranged from 0.3% to 4.4%, suggesting that the studied traits are controlled by many loci of limited individual impact. Despite this, a SNP in the EARLY FLOWERING 3 gene was repeatedly associated (FDR < 0.2) with bud burst. The rare homozygous genotype exhibited 0.4-1.0 lower bud burst scores than the other genotype classes on a five-grade scale. Consequently, this marker could be promising for use in MAS and the gene deserves further study. Otherwise, associations were less consistent across sites, likely due to their small Radj2 estimates and to considerable G × E interactions indicated by multivariate association analyses and modest trait accession correlations across sites (0.32-0.61).

  6. 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

  7. Nest Site Characteristics of Cavity Nesting Birds in Central Missouri

    Treesearch

    Jeffery D. Brawn; Bernice Tannenbaum; Keith E. Evans

    1984-01-01

    Two study sites in central Missouri oak-hickory forests were searched for nest sites of cavity nesting birds. Researchers located and measured 133 nests of 11 species. Cavity nesting bird habitat selection is affected by both snag characteristics and vegetation structure.

  8. Toxic elements and associations with hematology, plasma biochemistry, and protein electrophoresis in nesting loggerhead sea turtles (Caretta caretta) from Casey Key, Florida.

    PubMed

    Perrault, Justin R; Stacy, Nicole I; Lehner, Andreas F; Poor, Savannah K; Buchweitz, John P; Walsh, Catherine J

    2017-09-19

    Toxic elements (arsenic, cadmium, lead, mercury, selenium, thallium) are a group of contaminants that are known to elicit developmental, reproductive, general health, and immune system effects in reptiles, even at low concentrations. Reptiles, including marine turtles, are susceptible to accumulation of toxic elements due to their long life span, low metabolic rate, and highly efficient conversion of prey into biomass. The objectives of this study were to (1) document concentrations of arsenic, cadmium, lead, mercury, selenium, and thallium in whole blood and keratin from nesting loggerhead sea turtles (Caretta caretta) from Casey Key, Florida and document correlations thereof and (2) correlate whole blood toxic element concentrations to various hematological and plasma biochemistry analytes. Baselines for various hematological and plasma analytes and toxic elements in whole blood and keratin (i.e., scute) in nesting loggerheads are documented. Various correlations between the toxic elements and hematological and plasma biochemistry analytes were identified; however, the most intriguing were negative correlations between arsenic, cadmium, lead, and selenium with and α- and γ-globulins. Although various extrinsic and intrinsic variables such as dietary and feeding changes in nesting loggerheads need to be considered, this finding may suggest a link to altered humoral immunity. This study documents a suite of health variables of nesting loggerheads in correlation to contaminants and identifies the potential of toxic elements to impact the overall health of nesting turtles, thus presenting important implications for the conservation and management of this species. Copyright © 2017 Elsevier Ltd. All rights reserved.

  9. Association Mapping Reveals Genetic Loci Associated with Important Agronomic Traits in Lentinula edodes, Shiitake Mushroom

    PubMed Central

    Li, Chuang; Gong, Wenbing; Zhang, Lin; Yang, Zhiquan; Nong, Wenyan; Bian, Yinbing; Kwan, Hoi-Shan; Cheung, Man-Kit; Xiao, Yang

    2017-01-01

    Association mapping is a robust approach for the detection of quantitative trait loci (QTLs). Here, by genotyping 297 genome-wide molecular markers of 89 Lentinula edodes cultivars in China, the genetic diversity, population structure and genetic loci associated with 11 agronomic traits were examined. A total of 873 alleles were detected in the tested strains with a mean of 2.939 alleles per locus, and the Shannon's information index was 0.734. Population structure analysis revealed two robustly differentiated groups among the Chinese L. edodes cultivars (FST = 0.247). Using the mixed linear model, a total of 43 markers were detected to be significantly associated with four traits. The number of markers associated with traits ranged from 9 to 26, and the phenotypic variations explained by each marker varied from 12.07% to 31.32%. Apart from five previously reported markers, the remaining 38 markers were newly reported here. Twenty-one markers were identified as simultaneously linked to two to four traits, and five markers were associated with the same traits in cultivation tests performed in two consecutive years. The 43 traits-associated markers were related to 97 genes, and 24 of them were related to 10 traits-associated markers detected in both years or identified previously, 13 of which had a >2-fold expression change between the mycelium and primordium stages. Our study has provided candidate markers for marker-assisted selection (MAS) and useful clues for understanding the genetic architecture of agronomic traits in the shiitake mushroom. PMID:28261189

  10. 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

  11. MAPS

    Atmospheric Science Data Center

    2014-07-03

    ... Measurement of Air Pollution from Satellites (MAPS) data were collected during Space Shuttle flights in 1981, ... Facts Correlative Data  - CDIAC - Spring & Fall 1994 - Field and Aircraft Campaigns SCAR-B Block:  ...

  12. Diagnostic value of conjunctival swab sampling associated with nested PCR for different categories of dogs naturally exposed to Leishmania infantum infection.

    PubMed

    Di Muccio, Trentina; Veronesi, Fabrizia; Antognoni, Maria Teresa; Onofri, Andrea; Piergili Fioretti, Daniela; Gramiccia, Marina

    2012-08-01

    The objective of the present study was to evaluate the diagnostic performance of a noninvasive assay, conjunctival swab (CS) nested-PCR (n-PCR), for diagnosing canine leishmaniasis (CanL) in different stages of infection in comparison to the performance of the indirect immunofluorescence antibody test (IFAT), lymph node microscopy, and buffy coat n-PCR. To this end, we performed a cross-sectional survey among 253 nonselected dogs in areas of endemicity in central Italy. We also performed a longitudinal study of CS n-PCR among 20 sick dogs undergoing antileishmanial treatment. In the first study, among the 72 animals that were positive by at least one test (28.45%), CS n-PCR showed the best relative performance (76.38%), with a high concordance in comparison to standard IFAT serology (κ = 0.75). The highest positivity rates using CS n-PCR were found in asymptomatic infected dogs (84.2%) and sick dogs (77.8%); however, the sensitivity of the assay was not associated with the presence of clinical signs. In the follow-up study on treated sick dogs, CS n-PCR was the most sensitive assay, with promising prognostic value for relapses. The univariate analysis of risk factors for CanL based on CS n-PCR findings showed a significant correlation with age (P = 0.012), breed size (P = 0.026), habitat (P = 4.9 × 10(-4)), and previous therapy (P = 0.014). Overall, the results indicated that CS n-PCR was the most sensitive assay of the less invasive diagnostic methods and could represent a good option for the early and simple diagnosis of CanL infection in asymptomatic animals and for monitoring relapses in drug-treated dogs.

  13. 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

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

    USDA-ARS?s Scientific Manuscript database

    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...

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

    SciTech Connect

    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 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. 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

  16. The Association between Polypharmacy and Dementia: A Nested Case-Control Study Based on a 12-Year Longitudinal Cohort Database in South Korea

    PubMed Central

    Park, Hae-Young; Park, Ji-Won; Song, Hong Ji; Sohn, Hyun Soon; Kwon, Jin-Won

    2017-01-01

    Dementia is a major concern among growing chronic diseases in the aging society and its association with polypharmacy has not been adequately assessed. The objective of this study was to determine the association between polypharmacy and dementia through multiple statistical approaches. We conducted a nested case-control study for newly diagnosed dementia cases using the South Korean National Health Insurance Service sample cohort database (2002–2013, n = 1,025,340). Interactions between polypharmacy (an average use of ≥5 prescription drugs daily) and comorbidities or potentially inappropriate medications (PIMs) were tested. The odds ratios (ORs) for dementia were analyzed according to the presence of comorbidities, PIM uses, the average number of prescribed daily drugs, and significant interactions with polypharmacy using univariate and multiple logistic regression analyses. A higher prevalence of comorbidities, history of PIM use, higher PIM exposure, and higher proportion of polypharmacy were noted among cases than in controls. In the univariate analysis, the OR for dementia increased significantly with the increase in the number of prescribed drugs [1–<5 drugs: 1.72, 95% confidence interval (CI): 1.56–1.88; 5–<10 drugs: 2.64, 95% CI: 2.32–3.05; ≥10 drugs: 3.35, 95% CI: 2.38–4.71; <1 drug used as reference]. Polypharmacy was correlated with comorbidities and PIM use, and significant interactions were observed between polypharmacy and anticholinergics; H2-receptor antagonists; and comorbidities such as hypertension, peripheral or cerebrovascular disease, congestive heart failure, hemiplegia, diabetes, depression, all other mental disorders, chronic obstructive pulmonary disease, peptic ulcer disease, and chronic liver disease (p<0.001). In the multiple regression analysis, most cases exhibited increasing ORs for dementia with increasing polypharmacy levels. Moreover, the increase in OR was more evident in the absence of drugs or comorbidities that

  17. The Association between Polypharmacy and Dementia: A Nested Case-Control Study Based on a 12-Year Longitudinal Cohort Database in South Korea.

    PubMed

    Park, Hae-Young; Park, Ji-Won; Song, Hong Ji; Sohn, Hyun Soon; Kwon, Jin-Won

    2017-01-01

    Dementia is a major concern among growing chronic diseases in the aging society and its association with polypharmacy has not been adequately assessed. The objective of this study was to determine the association between polypharmacy and dementia through multiple statistical approaches. We conducted a nested case-control study for newly diagnosed dementia cases using the South Korean National Health Insurance Service sample cohort database (2002-2013, n = 1,025,340). Interactions between polypharmacy (an average use of ≥5 prescription drugs daily) and comorbidities or potentially inappropriate medications (PIMs) were tested. The odds ratios (ORs) for dementia were analyzed according to the presence of comorbidities, PIM uses, the average number of prescribed daily drugs, and significant interactions with polypharmacy using univariate and multiple logistic regression analyses. A higher prevalence of comorbidities, history of PIM use, higher PIM exposure, and higher proportion of polypharmacy were noted among cases than in controls. In the univariate analysis, the OR for dementia increased significantly with the increase in the number of prescribed drugs [1-<5 drugs: 1.72, 95% confidence interval (CI): 1.56-1.88; 5-<10 drugs: 2.64, 95% CI: 2.32-3.05; ≥10 drugs: 3.35, 95% CI: 2.38-4.71; <1 drug used as reference]. Polypharmacy was correlated with comorbidities and PIM use, and significant interactions were observed between polypharmacy and anticholinergics; H2-receptor antagonists; and comorbidities such as hypertension, peripheral or cerebrovascular disease, congestive heart failure, hemiplegia, diabetes, depression, all other mental disorders, chronic obstructive pulmonary disease, peptic ulcer disease, and chronic liver disease (p<0.001). In the multiple regression analysis, most cases exhibited increasing ORs for dementia with increasing polypharmacy levels. Moreover, the increase in OR was more evident in the absence of drugs or comorbidities that showed

  18. 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

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

    DOE PAGES

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

    2016-04-18

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

  20. Nest and home.

    PubMed

    Hediger, H

    1977-01-01

    A nest as a rather loose construction of plant material, as it is used by most birds and some of the lowest primates, never serves as a goal of flight, very rarely as a sleeping place but mainly as a support for the offspring. A home, however, as used by many nonprimate mammals and other vertebrates, is a solid construction or an excavation in a solid material (tree hole, burrow, etc.) which serves principally as a goal of flight in case of danger, also as a sleeping place and temporarily as a nest, that is a fix-point for raising the young. In the phylogeny of primates the nest has been given up very early. The sleeping nest of pongids has nothing to do with it. Whereas the most primitive primates using nests transport their young with the mouth, in all other primates the young has to grasp actively the mother's (parent's) hair to be tranported. When the hair disappeared phylogenetically, technical devices came into use.

  1. Cross-linking of microtubules by microtubule-associated proteins (MAPs) from the brine shrimp, Artemia.

    PubMed

    Campbell, E J; MacKinlay, S A; MacRae, T H

    1989-05-01

    Microtubules induced with taxol to assemble in cell-free extracts of the brine shrimp, Artemia, are cross-linked by microtubule-associated proteins (MAPs). When the MAPs, extracted from taxol-stabilized microtubules with 1 M-NaCl are co-assembled with purified Artemia or mammalian neural tubulin, reconstitution of cross-linking between microtubules occurs. The most prominent non-tubulin protein associated with reconstituted cross-linked microtubules has a molecular weight of 49,000 but we cannot yet exclude the possibility that other proteins may be responsible for the cross-linking. Cross-linkers are separated by varying distances while cross-linked microtubules, prepared under different conditions, are 6.9-7.7 nm apart. Cross-linking of microtubules by MAPs occurs whether MAPs are added to assembling tubulin or to microtubules, and it is not disrupted by ATP. The MAPs are heat-sensitive and do not stabilize microtubules to cold. Immunological characterization of Artemia MAPs on Western blots indicates that Artemia lack MAP 1, MAP 2 and tau. Our results clearly demonstrate that Artemia contain novel MAPs with the ability to cross-link microtubules from phylogenetically disparate organisms in an ATP-independent manner.

  2. Spatiotemporal patterns of duck nest density and predation risk: a multi-scale analysis of 18 years and more than 10,000 nests

    USGS Publications Warehouse

    Ringelman, Kevin M.; Eadie, John M.; Ackerman, Joshua T.; Sih, Andrew; Loughman, Daniel L.; Yarris, Gregory S.; Oldenburger, Shaun L.; McLandress, M. Robert

    2017-01-01

    Many avian species are behaviorally-plastic in selecting nest sites, and may shift to new locations or habitats following an unsuccessful breeding attempt. If there is predictable spatial variation in predation risk, the process of many individuals using prior experience to adaptively change nest sites may scale up to create shifting patterns of nest density at a population level. We used 18 years of waterfowl nesting data to assess whether there were areas of consistently high or low predation risk, and whether low-risk areas increased, and high-risk areas decreased in nest density the following year. We created kernel density maps of successful and unsuccessful nests in consecutive years and found no correlation in predation risk and no evidence for adaptive shifts, although nest density was correlated between years. We also examined between-year correlations in nest density and nest success at three smaller spatial scales: individual nesting fields (10–28 ha), 16-ha grid cells and 4-ha grid cells. Here, results were similar across all scales: we found no evidence for year-to-year correlation in nest success but found strong evidence that nest density was correlated between years, and areas of high nest success increased in nest density the following year. Prior research in this system has demonstrated that areas of high nest density have higher nest success, and taken together, our results suggest that ducks may adaptively select nest sites based on the local density of conspecifics, rather than the physical location of last year's nest. In unpredictable environments, current cues, such as the presence of active conspecific nests, may be especially useful in selecting nest sites. The cues birds use to select breeding locations and successfully avoid predators deserve continued attention, especially in systems of conservation concern.

  3. Quantifying the mapping precision of genome-wide association studies using whole-genome sequencing data.

    PubMed

    Wu, Yang; Zheng, Zhili; Visscher, Peter M; Yang, Jian

    2017-05-16

    Understanding the mapping precision of genome-wide association studies (GWAS), that is the physical distances between the top associated single-nucleotide polymorphisms (SNPs) and the causal variants, is essential to design fine-mapping experiments for complex traits and diseases. Using simulations based on whole-genome sequencing (WGS) data from 3642 unrelated individuals of European descent, we show that the association signals at rare causal variants (minor allele frequency ≤ 0.01) are very unlikely to be mapped to common variants in GWAS using either WGS data or imputed data and vice versa. We predict that at least 80% of the common variants identified from published GWAS using imputed data are within 33.5 Kbp of the causal variants, a resolution that is comparable with that using WGS data. Mapping precision at these loci will improve with increasing sample sizes of GWAS in the future. For rare variants, the mapping precision of GWAS using WGS data is extremely high, suggesting WGS is an efficient strategy to detect and fine-map rare variants simultaneously. We further assess the mapping precision by linkage disequilibrium between GWAS hits and causal variants and develop an online tool (gwasMP) to query our results with different thresholds of physical distance and/or linkage disequilibrium ( http://cnsgenomics.com/shiny/gwasMP ). Our findings provide a benchmark to inform future design and development of fine-mapping experiments and technologies to pinpoint the causal variants at GWAS loci.

  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. 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.

  6. Genome-Wide Association Mapping of Root Traits in the Context of Plant Hormone Research.

    PubMed

    Ristova, Daniela; Busch, Wolfgang

    2017-01-01

    Genome-wide association (GWA) mapping is a powerful method for the identification of alleles that underlie quantitative traits. It enables one to understand how genetic variation translates into phenotypic variation. In particular, plant hormone signaling pathways play a key role in shaping phenotypes. This chapter presents a protocol for genome-wide association mapping of root traits of Arabidopsis thaliana in the context of hormone research. We describe a specific protocol for acquiring primary and lateral root trait data that is appropriate for GWA studies using FIJI (ImageJ), and subsequent GWA mapping using a user-friendly Internet application.

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

    USDA-ARS?s Scientific Manuscript database

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

  8. 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.

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

    PubMed Central

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

    2013-01-01

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

  10. 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.

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

    PubMed

    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

    2015-10-01

    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.

  12. 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.

  13. The microtubule-associated protein MAP18 affects ROP2 GTPase activity during root hair growth.

    PubMed

    Kang, Erfang; Zheng, Mingzhi; Zhang, Yan; Yuan, Ming; Yalovsky, Shaul; Zhu, Lei; Fu, Ying

    2017-03-17

    Establishment and maintenance of the polar site are important for root hair tip growth. We previously reported that Arabidopsis (Arabidopsis thaliana) MICROTUBULE-ASSOCIATED PROTEIN18 (MAP18) functions in controlling the direction of pollen tube growth and root hair elongation. Additionally, the Rop GTPase ROP2 was reported as a positive regulator of both root hair initiation and tip growth in Arabidopsis. Both loss-of-function of ROP2 or knock-down of MAP18 leads to a decrease in root hair length, whereas overexpression of either MAP18 or ROP2 causes multiple tips or a branching hair phenotype. However, it is unclear whether MAP18 and ROP2 coordinately regulate root hair growth. In the present study, we demonstrate that MAP18 and ROP2 interact genetically and functionally. MAP18 physically interacts with ROP2 in vitro and in vivo and preferentially binds to the inactive form of the ROP2 protein. MAP18 promotes ROP2 activity during root hair tip growth. Further investigation revealed that MAP18 competes with RhoGTPase GDP dissociation inhibitor 1 (AtRhoGDI1)/SUPERCENTIPEDE1 (SCN1) for binding to ROP2, in turn affecting localization of active ROP2 in the plasma membrane of the root hair tip. These results reveal a novel function of MAP18 in the regulation of ROP2 activation during root hair growth.

  14. 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…

  15. 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…

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

    USGS Publications Warehouse

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

    1982-01-01

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

  17. The cavity-nest ant Temnothorax crassispinus prefers larger nests.

    PubMed

    Mitrus, S

    Colonies of the ant Temnothorax crassispinus inhabit mostly cavities in wood and hollow acorns. Typically in the field, nest sites that can be used by the ant are a limited resource. In a field experiment, it was investigated whether the ants prefer a specific size of nest, when different ones are available. In July 2011, a total of 160 artificial nests were placed in a beech-pine forest. Four artificial nests (pieces of wood with volume cavities, ca 415, 605, 730, and 980 mm(3), respectively) were located on each square meter of the experimental plot. One year later, shortly before the emergence of new sexuals, the nests were collected. In July 2012, colonies inhabited more frequently bigger nests. Among queenright colonies, the ones which inhabited bigger nests had more workers. However, there was no relationship between volume of nest and number of workers for queenless colonies. Queenright colonies from bigger nests produced more sexual individuals, but there was no correlation between number of workers and sex allocation ratio, or between volume of nest and sex allocation ratio. In a laboratory experiment where ant colonies were kept in 470 and 860 mm(3) nests, larger colonies allocated more energy to produce sexual individuals. The results of this study show the selectivity of T. crassispinus ants regarding the size of nest cavity, and that the nest volume has an impact on life history parameters.

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

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

  19. 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.

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

    USGS Publications Warehouse

    Antolos, Michelle; Roby, D.D.; Lyons, Donald E.; Anderson, Scott 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.

  1. 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

  2. Application of association mapping to understanding the genetic diversity of plant germplasm resources.

    PubMed

    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.

  3. Nest-site selection in the acorn woodpecker

    USGS Publications Warehouse

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

    1999-01-01

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

  4. 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.

  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.

  6. 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

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

    PubMed

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

    2014-10-01

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

  8. 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

  9. Admixture Mapping Identifies a Quantitative Trait Locus Associated with FEV1/FVC in the COPDGene Study

    PubMed Central

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

    2014-01-01

    African Americans are admixed with genetic contributions from European and African ancestral populations. Admixture mapping leverages this information to map genes influencing differential disease risk across populations. We performed admixture and association mapping in 3300 African American current or former smokers from the COPDGene Study. We analyzed estimated local ancestry and SNP genotype information to identify regions associated with FEV1/FVC, the ratio of forced expiratory volume in one second to forced vital capacity, measured by spirometry performed after bronchodilator administration. Global African ancestry inversely associated with FEV1/FVC (p = 0.035). Genome-wide admixture analysis, controlling for age, gender, body mass index, current smoking status, pack-years smoked, and four principal components summarizing the genetic background of African Americans in the COPDGene Study, identified a region on chromosome 12q14.1 associated with FEV1/FVC (p = 2.1 × 10-6) when regressed on local ancestry. Allelic association in this region of chromosome 12 identified an intronic variant in FAM19A2 (rs348644) as associated with FEV1/FVC (p=1.76 × 10-6). By combining admixture and association mapping, a marker on chromosome 12q14.1 was identified as being associated with reduced FEV1/FVC ratio among African-Americans in the COPDGene Study. PMID:25112515

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

    PubMed Central

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

    2016-01-01

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

  11. Nested Tracking Graphs

    DOE PAGES

    Lukasczyk, Jonas; Weber, Gunther; Maciejewski, Ross; ...

    2017-06-01

    Tracking graphs are a well established tool in topological analysis to visualize the evolution of components and their properties over time, i.e., when components appear, disappear, merge, and split. However, tracking graphs are limited to a single level threshold and the graphs may vary substantially even under small changes to the threshold. To examine the evolution of features for varying levels, users have to compare multiple tracking graphs without a direct visual link between them. We propose a novel, interactive, nested graph visualization based on the fact that the tracked superlevel set components for different levels are related to eachmore » other through their nesting hierarchy. This approach allows us to set multiple tracking graphs in context to each other and enables users to effectively follow the evolution of components for different levels simultaneously. We show the effectiveness of our approach on datasets from finite pointset methods, computational fluid dynamics, and cosmology simulations.« less

  12. Genome-Wide Association Mapping for Phenotypic Plasticity in Rice.

    PubMed

    Kikuchi, Shinji; Bheemanahalli, Raju; Jagadish, Krishna S V; Kumagai, Etsushi; Masuya, Yusuke; Kuroda, Eiki; Raghavan, Chitra; Dingkuhn, Michael; Abe, Akira; Shimono, Hiroyuki

    2017-03-31

    Phenotypic plasticity of plants in response to environmental changes is important for adapting to changing climate. Less attention has been paid to exploring the advantages of phenotypic plasticity in resource-rich environments to enhance the productivity of agricultural crops. Here, we examined genetic variation in phenotypic plasticity in indica rice (Oryza sativa L.) across two diverse panels: (i) a Phenomics of Rice Adaptation and Yield (PRAY) population comprising 301 accessions and (ii) a Multi-parent-Advanced-Generation-Inter-Cross (MAGIC) indica population comprising 151 accessions. Altered planting density was used as a proxy for elevated atmospheric CO2 response. Low planting density significantly increased panicle weight per plant compared with normal density, and the magnitude of the increase ranged from 1.10 to 2.78 times among accessions for the PRAY population and from 1.05 to 2.45 times for the MAGIC population. Genome-wide-association studies revealed three Environmental Responsiveness (ER) candidate alleles (qER1-3) that were associated with relative response of panicle weight to low density. Two of these alleles were tested in 13 genotypes to clarify their biomass responses during vegetative growth under elevated CO2 in Japan. Our study provides evidence for polymorphisms that control rice phenotypic plasticity in environments that are rich in resources such as light and CO2 .

  13. 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.

  14. 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

  15. Evaluation of bias associated with capture maps derived from nonlinear groundwater flow models

    USGS Publications Warehouse

    Nadler, Cara; Allander, Kip K.; Pohll, Greg; Morway, Eric; Naranjo, Ramon C.; Huntington, Justin

    2017-01-01

    The impact of groundwater withdrawal on surface water is a concern of water users and water managers, particularly in the arid western United States. Capture maps are useful tools to spatially assess the impact of groundwater pumping on water sources (e.g., streamflow depletion) and are being used more frequently for conjunctive management of surface water and groundwater. Capture maps have been derived using linear groundwater flow models and rely on the principle of superposition to demonstrate the effects of pumping in various locations on resources of interest. However, nonlinear models are often necessary to simulate head-dependent boundary conditions and unconfined aquifers. Capture maps developed using nonlinear models with the principle of superposition may over- or underestimate capture magnitude and spatial extent. This paper presents new methods for generating capture difference maps, which assess spatial effects of model nonlinearity on capture fraction sensitivity to pumping rate, and for calculating the bias associated with capture maps. The sensitivity of capture map bias to selected parameters related to model design and conceptualization for the arid western United States is explored. This study finds that the simulation of stream continuity, pumping rates, stream incision, well proximity to capture sources, aquifer hydraulic conductivity, and groundwater evapotranspiration extinction depth substantially affect capture map bias. Capture difference maps demonstrate that regions with large capture fraction differences are indicative of greater potential capture map bias. Understanding both spatial and temporal bias in capture maps derived from nonlinear groundwater flow models improves their utility and defensibility as conjunctive-use management tools.

  16. Nest-site selection and nest success of an Arctic-breeding passerine, Smith's Longspur, in a changing climate

    USGS Publications Warehouse

    McFarland, Heather R.; Kendall, Steve J.; Powell, Abby

    2017-01-01

    Despite changes in shrub cover and weather patterns associated with climate change in the Arctic, little is known about the breeding requirements of most passerines tied to northern regions. We investigated the nesting biology and nest habitat characteristics of Smith's Longspurs (Calcarius pictus) in 2 study areas in the Brooks Range of Alaska, USA. First, we examined variation in nesting phenology in relation to local temperatures. We then characterized nesting habitat and analyzed nest-site selection for a subset of nests (n = 86) in comparison with paired random points. Finally, we estimated the daily survival rate of 257 nests found in 2007–2013 with respect to both habitat characteristics and weather variables. Nest initiation was delayed in years with snow events, heavy rain, and freezing temperatures early in the breeding season. Nests were typically found in open, low-shrub tundra, and never among tall shrubs (mean shrub height at nests = 26.8 ± 6.7 cm). We observed weak nest-site selection patterns. Considering the similarity between nest sites and paired random points, coupled with the unique social mating system of Smith's Longspurs, we suggest that habitat selection may occur at the neighborhood scale and not at the nest-site scale. The best approximating model explaining nest survival suggested a positive relationship with the numbers of days above 21°C that an individual nest experienced; there was little support for models containing habitat variables. The daily nest survival rate was high (0.972–0.982) compared with that of most passerines in forested or grassland habitats, but similar to that of passerines nesting on tundra. Considering their high nesting success and ability to delay nest initiation during inclement weather, Smith's Longspurs may be resilient to predicted changes in weather regimes on the breeding grounds. Thus, the greatest threat to breeding Smith's Longspurs associated with climate change may be the loss of low

  17. 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.

  18. 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

  19. 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

  20. 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

  1. 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.

  2. Why Wasp Foundresses Change Nests: Relatedness, Dominance, and Nest Quality

    PubMed Central

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

    2012-01-01

    The costs and benefits of different social options are best understood when individuals can be followed as they make different choices, something that can be difficult in social insects. In this detailed study, we follow overwintered females of the social wasp Polistes carolina through different nesting strategies in a stratified habitat where nest site quality varies with proximity to a foraging area, and genetic relatedness among females is known. Females may initiate nests, join nests temporarily or permanently, or abandon nests. Females can become helpers or egglayers, effectively workers or queens. What they actually do can be predicted by a combination of ecological and relatedness factors. Advantages through increased lifetime success of individuals and nests drives foundresses of the social wasp Polistes from solitary to social nest founding. We studied reproductive options of spring foundresses of P. carolina by monitoring individually-marked wasps and assessing reproductive success of each foundress by using DNA microsatellites. We examined what behavioral decisions foundresses make after relaxing a strong ecological constraint, shortage of nesting sites. We also look at the reproductive consequences of different behaviors. As in other Polistes, the most successful strategy for a foundress was to initiate a nest as early as possible and then accept others as subordinates. A common feature for many P. carolina foundresses was, however, that they reassessed their reproductive options by actively monitoring other nests at the field site and sometimes moving permanently to new nests should that offer better (inclusive) fitness prospects compared to their original nests. A clear motivation for moving to new nests was high genetic relatedness; by the end of the foundress period all females were on nests with full sisters. PMID:23049791

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

    PubMed

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

    2012-01-01

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

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

    PubMed Central

    Liu, Qing-Hua; Arias, Sixto

    2016-01-01

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

  5. 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.

  6. Two Microtubule-associated Proteins of Arabidopsis MAP65s Promote Antiparallel Microtubule Bundling

    PubMed Central

    Gaillard, Jérémie; Neumann, Emmanuelle; Van Damme, Daniel; Stoppin-Mellet, Virginie; Ebel, Christine; Barbier, Elodie; Geelen, Danny

    2008-01-01

    The Arabidopsis MAP65s are a protein family with similarity to the microtubule-associated proteins PRC1/Ase1p that accumulate in the spindle midzone during late anaphase in mammals and yeast, respectively. Here we investigate the molecular and functional properties of AtMAP65-5 and improve our understanding of AtMAP65-1 properties. We demonstrate that, in vitro, both proteins promote the formation of a planar network of antiparallel microtubules. In vivo, we show that AtMAP65-5 selectively binds the preprophase band and the prophase spindle microtubule during prophase, whereas AtMAP65-1-GFP selectively binds the preprophase band but does not accumulate at the prophase spindle microtubules that coexists within the same cell. At later stages of mitosis, AtMAP65-1 and AtMAP65-5 differentially label the late spindle and phragmoplast. We present evidence for a mode of action for both proteins that involves the binding of monomeric units to microtubules that “zipper up” antiparallel arranged microtubules through the homodimerization of the N-terminal halves when adjacent microtubules encounter. PMID:18667529

  7. The Decay of Disease Association with Declining Linkage Disequilibrium: A Fine Mapping Theorem.

    PubMed

    Maadooliat, Mehdi; Bansal, Naveen K; Upadhya, Jiblal; Farazi, Manzur R; Li, Xiang; He, Max M; Hebbring, Scott J; Ye, Zhan; Schrodi, Steven J

    2016-01-01

    Several important and fundamental aspects of disease genetics models have yet to be described. One such property is the relationship of disease association statistics at a marker site closely linked to a disease causing site. A complete description of this two-locus system is of particular importance to experimental efforts to fine map association signals for complex diseases. Here, we present a simple relationship between disease association statistics and the decline of linkage disequilibrium from a causal site. Specifically, the ratio of Chi-square disease association statistics at a marker site and causal site is equivalent to the standard measure of pairwise linkage disequilibrium, r(2). A complete derivation of this relationship from a general disease model is shown. Quite interestingly, this relationship holds across all modes of inheritance. Extensive Monte Carlo simulations using a disease genetics model applied to chromosomes subjected to a standard model of recombination are employed to better understand the variation around this fine mapping theorem due to sampling effects. We also use this relationship to provide a framework for estimating properties of a non-interrogated causal site using data at closely linked markers. Lastly, we apply this way of examining association data from high-density genotyping in a large, publicly-available data set investigating extreme BMI. We anticipate that understanding the patterns of disease association decay with declining linkage disequilibrium from a causal site will enable more powerful fine mapping methods and provide new avenues for identifying causal sites/genes from fine-mapping studies.

  8. 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.

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

    PubMed

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

    2014-12-05

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

  10. 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.

  11. Combined linkage and association mapping of flowering time in Sunflower (Helianthus annuus L.).

    PubMed

    Cadic, Elena; Coque, Marie; Vear, Felicity; Grezes-Besset, Bruno; Pauquet, Jerôme; Piquemal, Joël; Lippi, Yannick; Blanchard, Philippe; Romestant, Michel; Pouilly, Nicolas; Rengel, David; Gouzy, Jerôme; Langlade, Nicolas; Mangin, Brigitte; Vincourt, Patrick

    2013-05-01

    Association mapping and linkage mapping were used to identify quantitative trait loci (QTL) and/or causative mutations involved in the control of flowering time in cultivated sunflower Helianthus annuus. A panel of 384 inbred lines was phenotyped through testcrosses with two tester inbred lines across 15 location × year combinations. A recombinant inbred line (RIL) population comprising 273 lines was phenotyped both per se and through testcrosses with one or two testers in 16 location × year combinations. In the association mapping approach, kinship estimation using 5,923 single nucleotide polymorphisms was found to be the best covariate to correct for effects of panel structure. Linkage disequilibrium decay ranged from 0.08 to 0.26 cM for a threshold of 0.20, after correcting for structure effects, depending on the linkage group (LG) and the ancestry of inbred lines. A possible hitchhiking effect is hypothesized for LG10 and LG08. A total of 11 regions across 10 LGs were found to be associated with flowering time, and QTLs were mapped on 11 LGs in the RIL population. Whereas eight regions were demonstrated to be common between the two approaches, the linkage disequilibrium approach did not detect a documented QTL that was confirmed using the linkage mapping approach.

  12. 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.

  13. 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

  14. Linkage disequilibrium and genome-wide association mapping in tetraploid wheat (Triticum turgidum L.).

    PubMed

    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.

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

    PubMed

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

    2008-11-01

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

  16. Case-control admixture mapping in Latino populations enriches for known asthma-associated genes

    PubMed Central

    Torgerson, Dara G.; Gignoux, Christopher R.; Galanter, Joshua M.; Drake, Katherine A.; Roth, Lindsey A.; Eng, Celeste; Huntsman, Scott; Torres, Raul; Avila, Pedro C.; Chapela, Rocio; Ford, Jean G.; Rodríguez-Santana, José R.; Rodríguez-Cintrón, William; Hernandez, Ryan D.; Burchard, Esteban G.

    2012-01-01

    Background Polymorphisms in more than 100 genes have been associated with asthma susceptibility, yet much of the heritability remains to be explained. Asthma disproportionately affects different racial and ethnic groups in the United States, suggesting that admixture mapping is a useful strategy to identify novel asthma-associated loci. Objective We sought to identify novel asthma-associated loci in Latino populations using case-control admixture mapping. Methods We performed genome-wide admixture mapping by comparing levels of local Native American, European, and African ancestry between children with asthma and nonasthmatic control subjects in Puerto Rican and Mexican populations. Within candidate peaks, we performed allelic tests of association, controlling for differences in local ancestry. Results Between the 2 populations, we identified a total of 62 admixture mapping peaks at a P value of less than 10−3 that were significantly enriched for previously identified asthma-associated genes (P = .0051). One of the peaks was statistically significant based on 100 permutations in the Mexican sample (6q15); however, it was not significant in Puerto Rican subjects. Another peak was identified at nominal significance in both populations (8q12); however, the association was observed with different ancestries. Conclusion Case-control admixture mapping is a promising strategy for identifying novel asthma-associated loci in Latino populations and implicates genetic variation at 6q15 and 8q12 regions with asthma susceptibility. This approach might be useful for identifying regions that contribute to both shared and population-specific differences in asthma susceptibility. PMID:22502797

  17. Case-control admixture mapping in Latino populations enriches for known asthma-associated genes.

    PubMed

    Torgerson, Dara G; Gignoux, Christopher R; Galanter, Joshua M; Drake, Katherine A; Roth, Lindsey A; Eng, Celeste; Huntsman, Scott; Torres, Raul; Avila, Pedro C; Chapela, Rocio; Ford, Jean G; Rodríguez-Santana, José R; Rodríguez-Cintrón, William; Hernandez, Ryan D; Burchard, Esteban G

    2012-07-01

    Polymorphisms in more than 100 genes have been associated with asthma susceptibility, yet much of the heritability remains to be explained. Asthma disproportionately affects different racial and ethnic groups in the United States, suggesting that admixture mapping is a useful strategy to identify novel asthma-associated loci. We sought to identify novel asthma-associated loci in Latino populations using case-control admixture mapping. We performed genome-wide admixture mapping by comparing levels of local Native American, European, and African ancestry between children with asthma and nonasthmatic control subjects in Puerto Rican and Mexican populations. Within candidate peaks, we performed allelic tests of association, controlling for differences in local ancestry. Between the 2 populations, we identified a total of 62 admixture mapping peaks at a P value of less than 10(-3) that were significantly enriched for previously identified asthma-associated genes (P= .0051). One of the peaks was statistically significant based on 100 permutations in the Mexican sample (6q15); however, it was not significant in Puerto Rican subjects. Another peak was identified at nominal significance in both populations (8q12); however, the association was observed with different ancestries. Case-control admixture mapping is a promising strategy for identifying novel asthma-associated loci in Latino populations and implicates genetic variation at 6q15 and 8q12 regions with asthma susceptibility. This approach might be useful for identifying regions that contribute to both shared and population-specific differences in asthma susceptibility. Copyright © 2012 American Academy of Allergy, Asthma & Immunology. Published by Mosby, Inc. All rights reserved.

  18. 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.

  19. Nesting of Morelet's crocodile, Crocodylus moreletii (Dumeril and Bibron), in Los Tuxtlas, Mexico.

    PubMed

    Villegas, A; Mendoza, G D; Arcos-García, J L; Reynoso, V H

    2017-03-16

    We evaluated the nesting by Crocodylus moreletii in Lago de Catemaco, Veracruz, southeastern, Mexico. During the nesting and hatching seasons, we searched for nests along the northern margins of the lake and small associated streams. We investigated egg mortality by weekly monitoring each of the nests found, recording sign of predation (tracks and holes dug into the nest) and the effect of water level fluctuations. We not found differences to nest between inland or flooded zones. However, we found that egg size varied among nests. In nests built inland, predation was the major cause of egg mortality whereas flooding resulted in more deaths of eggs in the flooding zone. Flooding killed 25% of eggs monitored in this study. We suggest that to increase nest success in the Morelet's crocodile it is necessary to promote conservation of nesting areas around the lake, recently occupied by urban or tourist developments.

  20. EAGLES NEST WILDERNESS, COLORADO.

    USGS Publications Warehouse

    Tweto, Ogden; Williams, Frank E.

    1984-01-01

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

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

    PubMed

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

    2011-10-01

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

  2. Magnetic Nested-Wind Scenarios for Bipolar Outflows: Preplanetary and YSO Nebular Shaping

    NASA Astrophysics Data System (ADS)

    Dennis, Timothy J.; Frank, Adam; Blackman, Eric G.; De Marco, Orsola; Balick, Bruce; Mitran, Sorin

    2009-12-01

    We present results of a series of magnetohydrodynamic (MHD) and hydrodynamic (HD) 2.5 dimensional simulations of the morphology of outflows driven by nested wide-angle winds, i.e., winds that emanate from a central star as well as from an orbiting accretion disk. While our results are broadly relevant to nested-wind systems, we have tuned the parameters of the simulations to touch on issues in both young stellar objects and planetary nebula (PN) studies. In particular, our studies connect to open issues in the early evolution of PNs. We find that nested MHD winds exhibit marked morphological differences from the single MHD wind case along both dimensions of the flow. Nested HD winds, on the other hand, give rise mainly to geometric distortions of an outflow that is topologically similar to the flow arising from a single stellar HD wind. Our MHD results are insensitive to changes in ambient temperature between ionized and un-ionized circumstellar environments. The results are sensitive to the relative mass-loss rates and the relative speeds of the stellar and disk winds. We also present synthetic emission maps of both nested MHD and HD simulations. We find that nested MHD winds show knots of emission appearing on-axis that do not appear in the HD case. The data presented in this paper were obtained from the Multimission Archive at the Space Telescope Science Institute (MAST). STScI is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS5-26555. Support for MAST for non-HST data is provided by the NASA Office of Space Science via grant NAG5-7584 and by other grants and contracts.

  3. Field guide to red tree vole nests

    Treesearch

    Damon B. Lesmeister; James K. Swingle

    2017-01-01

    Surveys for red tree vole (Arborimus longicaudus) nests require tree climbing because the species is a highly specialized arboreal rodent that live in the tree canopy of coniferous forests in western Oregon and northwestern California. Tree voles are associated with old coniferous forest (≥80 years old) that are structurally complex, but are often...

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

    PubMed

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

    2014-01-20

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

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

    PubMed Central

    2014-01-01

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

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

    SciTech Connect

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

    2015-04-24

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

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

    PubMed

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

    2015-06-01

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

  8. 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.

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

    USGS Publications Warehouse

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

    2003-01-01

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

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

    USDA-ARS?s Scientific Manuscript database

    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...

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

    USDA-ARS?s Scientific Manuscript database

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

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

    USDA-ARS?s Scientific Manuscript database

    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...

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

    USDA-ARS?s Scientific Manuscript database

    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...

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

    USDA-ARS?s Scientific Manuscript database

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

  15. 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.

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

    PubMed

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

    2016-10-01

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

  17. Factors associated with successful bilateral sentinel lymph node mapping in endometrial cancer.

    PubMed

    Tanner, Edward J; Sinno, Abdulrahman K; Stone, Rebecca L; Levinson, Kimberly L; Long, Kara C; Fader, Amanda N

    2015-09-01

    As our understanding of sentinel lymph node (SLN) mapping for endometrial cancer (EC) evolves, tailoring the technique to individual patients at high risk for failed mapping may result in a higher rate of successful bilateral mapping (SBM). The study objective is to identify patient, tumor, and surgeon factors associated with successful SBM in patients with EC and complex atypical hyperplasia (CAH). From September 2012 to November 2014, women with EC or CAH underwent SLN mapping via cervical injection followed by robot-assisted total laparoscopic hysterectomy (RA-TLH) at a tertiary care academic center. Completion lymphadenectomy and ultrastaging were performed according to an institutional protocol. Patient demographics, tumor and surgeon/intraoperative variables were prospectively collected and analyzed. Univariate and multivariate analyses were performed evaluating factors known or hypothesized to impact the rate of successful lymphatic mapping. RA-TLH and SLN mapping was performed in 111 women; 93 had EC and 18 had CAH. Eighty women had low grade and 31 had high grade disease. Overall, at least one SLN was identified in 85.6% of patients with SBM in 62.2% of patients. Dye choice (indocyanine green versus isosulfan blue), odds ratio (OR: 4.5), body mass index (OR: 0.95), and clinically enlarged lymph nodes (OR: 0.24) were associated with SBM rate on multivariate analyses. The use of indocyanine green dye was particularly beneficial in patients with a body mass index greater than 30. Injection dye, BMI, and clinically enlarged lymph nodes are important considerations when performing sentinel lymph node mapping for EC. Copyright © 2015 Elsevier Inc. All rights reserved.

  18. Genetic diversity and population structure of a diverse set of rice germplasm for association mapping.

    PubMed

    Jin, Liang; Lu, Yan; Xiao, Peng; Sun, Mei; Corke, Harold; Bao, Jinsong

    2010-08-01

    Germplasm diversity is the mainstay for crop improvement and genetic dissection of complex traits. Understanding genetic diversity, population structure, and the level and distribution of linkage disequilibrium (LD) in target populations is of great importance and a prerequisite for association mapping. In this study, 100 genome-wide simple sequence repeat (SSR) markers were used to assess genetic diversity, population structure, and LD of 416 rice accessions including landraces, cultivars and breeding lines collected mostly in China. A model-based population structure analysis divided the rice materials into seven subpopulations. 63% of the SSR pairs in these accessions were in LD, which was mostly due to an overall population structure, since the number of locus pairs in LD was reduced sharply within each subpopulation, with the SSR pairs in LD ranging from 5.9 to 22.9%. Among those SSR pairs showing significant LD, the intrachromosomal LD had an average of 25-50 cM in different subpopulations. Analysis of the phenotypic diversity of 25 traits showed that the population structure accounted for an average of 22.4% of phenotypic variation. An example association mapping for starch quality traits using both the candidate gene mapping and genome-wide mapping strategies based on the estimated population structure was conducted. Candidate gene mapping confirmed that the Wx and starch synthase IIa (SSIIa) genes could be identified as strongly associated with apparent amylose content (AAC) and pasting temperature (PT), respectively. More importantly, we revealed that the Wx gene was also strongly associated with PT. In addition to the major genes, we found five and seven SSRs were associated with AAC and PT, respectively, some of which have not been detected in previous linkage mapping studies. The results suggested that the population may be useful for the genome-wide marker-trait association mapping. This new association population has the potential to identify

  19. 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. © 2014 Wiley Periodicals, Inc.

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

    PubMed

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

    2014-11-01

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

  1. A new method for wireless video monitoring of bird nests

    Treesearch

    David I. King; Richard M. DeGraaf; Paul J. Champlin; Tracey B. Champlin

    2001-01-01

    Video monitoring of active bird nests is gaining popularity among researchers because it eliminates many of the biases associated with reliance on incidental observations of predation events or use of artificial nests, but the expense of video systems may be prohibitive. Also, the range and efficiency of current video monitoring systems may be limited by the need to...

  2. An 'ecological trap' for yellow warbler nest microhabitat selection

    Treesearch

    Quresh S. Latif; Sacha K. Heath; John T. Rotenberry

    2011-01-01

    Contrary to assumptions of habitat selection theory, fi eld studies frequently detect ‘ ecological traps ’ , where animals prefer habitats conferring lower fi tness than available alternatives. Evidence for traps includes cases where birds prefer breeding habitats associated with relatively high nest predation rates despite the importance of nest survival to avian fi...

  3. 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.

  4. Nest relocation using PVC "spotters"

    USGS Publications Warehouse

    Simon, John C.

    1998-01-01

    A simple device to aid in the rapid relocation of nests, composed on PVC pipe and tie wire, is described. A 16-18 cm length of pipe can be attached to a supporting structure with a section of wire and adjusted to point at the target nest by its discoverer. Used like an lensless spotting scope, the “spotter” allows other observers to quickly and reliably relocate the nest with minimal written or verbal description.

  5. Microtubule-associated proteins (MAPs): a monoclonal antibody to MAP 1 decorates microtubules in vitro but stains stress fibers and not microtubules in vivo.

    PubMed Central

    Asai, D J; Thompson, W C; Wilson, L; Dresden, C F; Schulman, H; Purich, D L

    1985-01-01

    A monoclonal antibody (mAb 7-1.1) was produced against a bovine brain microtubule-associated protein (MAP) preparation that had been separated from tubulin after initial purification by cycles of microtubule assembly and disassembly in vitro. The antibody reacted specifically with two high molecular weight polypeptides of the MAP 1 class, designated MAP 1.1 and MAP 1.2, and also with the surfaces of MAP 1-containing microtubules that had been assembled in vitro. Double immunofluorescence microscopy using mAb 7-1.1 and a well-characterized rabbit anti-tubulin antibody revealed that mAb 7-1.1 stained stress fibers in fixed and permeabilized cultured mammalian cells rather than microtubules. The antibody also stained cell nuclei in a punctate fashion. mAb 7-1.1 is one of a number of monoclonal antibodies that react with presumptive MAP 1 polypeptides. Some of the MAP 1 antibodies have been found to bind specifically to microtubules in fixed and permeabilized cells, while others have been reported to react with nonmicrotubule structures. Our results, together with the results of other investigations, indicate that "MAP 1" may be a family of several high molecular weight polypeptides that adventitiously behave as MAPs by the criterion of in vitro coassembly with tubulin through cycles of polymerization and depolymerization but whose cellular distributions, and perhaps functions, are varied. Images PMID:3883359

  6. Using Association Mapping in Teosinte to Investigate the Function of Maize Selection-Candidate Genes

    PubMed Central

    Weber, Allison L.; Zhao, Qiong; McMullen, Michael D.; Doebley, John F.

    2009-01-01

    Background Large-scale screens of the maize genome identified 48 genes that show the putative signature of artificial selection during maize domestication or improvement. These selection-candidate genes may act as quantitative trait loci (QTL) that control the phenotypic differences between maize and its progenitor, teosinte. The selection-candidate genes appear to be located closer in the genome to domestication QTL than expected by chance. Methods and Findings As a step toward defining the traits controlled by these genes, we performed phenotype-genotype association mapping in teosinte for 32 of the 48 plus three other selection-candidate genes. Our analyses assayed 32 phenotypic traits, many of which were altered during maize domestication or improvement. We observed several significant associations between SNPs in the selection-candidate genes and trait variation in teosinte. These included two associations that surpassed the Bonferroni correction and five instances where a gene significantly associated with the same trait in both of our association mapping panels. Despite these significant associations, when compared as a group the selection-candidate genes performed no better than randomly chosen genes. Conclusions Our results suggest association analyses can be helpful for identifying traits under the control of selection-candidate genes. Indeed, we present evidence for new functions for several selection-candidate genes. However, with the current set of selection-candidate genes and our association mapping strategy, we found very few significant associations overall and no more than we would have found with randomly chosen genes. We discuss possible reasons that a large number of significant genotype-phenotype associations were not discovered. PMID:20011044

  7. Allelic Analysis of Sheath Blight Resistance with Association Mapping in Rice

    PubMed Central

    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

  8. 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.

  9. Reimagining the Cuckoo's Nest.

    PubMed

    Rochefort, David A

    2017-09-27

    One Flew Over the Cuckoo's Nest (1962) by Ken Kesey and The Devil in Silver (2012) by Victor LaValle are two novels that focus on mental hospitalization as a medical and social practice. Published fifty years apart, however, the books possess important differences in setting, method, and message reflecting the times that spawned them. The purpose of this paper is to examine the changing documentary and metaphorical uses of the asylum novel by comparing an iconic work in the genre with a respectful, but divergent, successor. What emerges from this comparison is an appreciation of the literary conventions shared by Kesey and LaValle but also the ingredients that separate their work. Whereas Kesey produced an enduring tribute to the virtue of nonconformity, LaValle's social criticism expresses itself as a disturbing portrayal of class-based disparities and administrative dysfunction inside the contemporary American mental health system.

  10. KSC Eagle's Nest

    NASA Image and Video Library

    2014-03-07

    CAPE CANAVERAL, Fla. - A bald eagle perches in its nest in a tree along State Road 3 at NASA’s Kennedy Space Center in Florida. The center shares a boundary with the Merritt Island National Wildlife Refuge. The refuge encompasses 140,000 acres that are a habitat for more than 330 species of birds, 31 mammals, 117 fishes, and 65 amphibians and reptiles. It contains more than 1,000 known plant species. The marshes and open water of the refuge provide wintering areas for 23 species of migratory waterfowl, as well as a year-round home for great blue herons, great egrets, wood storks, cormorants, brown pelicans and other species of marsh and shore birds, and a variety of insects.

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

    USGS Publications Warehouse

    Shaffer, Terry L.; Grant, Todd A.

    2012-01-01

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

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

    PubMed

    Newmark, William D; Stanley, Thomas R

    2011-07-12

    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.

  13. 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.

  14. QTL mapping of physiological traits associated with salt tolerance in Medicago truncatula Recombinant Inbred Lines.

    PubMed

    Arraouadi, Soumaya; Badri, Mounawer; Abdelly, Chedly; Huguet, Thierry; Aouani, Mohamed Elarbi

    2012-02-01

    In this study, QTL mapping of physiological traits in the model Legume (Medicago truncatula) was performed using a set of RILs derived from LR5. Twelve parameters associated with Na+ and K+ content in leaves, stems and roots were measured. Broad-sense heritability of these traits was ranged from 0.15 to 0.83 in control and from 0.14 to 0.61 in salt stress. Variation among RILs was dependent on line, treatment and line by treatment effect. We mapped 6 QTLs in control, 2 in salt stress and 5 for sensitivity index. No major QTL was identified indicating that tolerance to salt stress is governed by several genes with low effects. Detected QTL for leaf, stem and root traits did not share the same map locations, suggesting that genes controlling transport of Na+ and K+ may be different. The maximum of QTL was observed on chromosome 1, no QTL was detected on chromosomes 5 and 6.

  15. 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

  16. 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.

  17. The Decay of Disease Association with Declining Linkage Disequilibrium: A Fine Mapping Theorem

    PubMed Central

    Maadooliat, Mehdi; Bansal, Naveen K.; Upadhya, Jiblal; Farazi, Manzur R.; Li, Xiang; He, Max M.; Hebbring, Scott J.; Ye, Zhan; Schrodi, Steven J.

    2016-01-01

    Several important and fundamental aspects of disease genetics models have yet to be described. One such property is the relationship of disease association statistics at a marker site closely linked to a disease causing site. A complete description of this two-locus system is of particular importance to experimental efforts to fine map association signals for complex diseases. Here, we present a simple relationship between disease association statistics and the decline of linkage disequilibrium from a causal site. Specifically, the ratio of Chi-square disease association statistics at a marker site and causal site is equivalent to the standard measure of pairwise linkage disequilibrium, r2. A complete derivation of this relationship from a general disease model is shown. Quite interestingly, this relationship holds across all modes of inheritance. Extensive Monte Carlo simulations using a disease genetics model applied to chromosomes subjected to a standard model of recombination are employed to better understand the variation around this fine mapping theorem due to sampling effects. We also use this relationship to provide a framework for estimating properties of a non-interrogated causal site using data at closely linked markers. Lastly, we apply this way of examining association data from high-density genotyping in a large, publicly-available data set investigating extreme BMI. We anticipate that understanding the patterns of disease association decay with declining linkage disequilibrium from a causal site will enable more powerful fine mapping methods and provide new avenues for identifying causal sites/genes from fine-mapping studies. PMID:28018425

  18. 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.

  19. Using Artificial Nests to Study Nest Predation in Birds

    ERIC Educational Resources Information Center

    Belthoff, James R.

    2005-01-01

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

  20. Map showing surface ruptures associated with the Mammoth Lakes, California, earthquakes of May 1980

    USGS Publications Warehouse

    Clark, M.M.; Yount, J.C.; Vaughn, P.R.; Zepeda, R.L.

    1982-01-01

    This map shows surface ruptures associated with the M 6 Mammoth Lakes earthquakes of May 25-27, 1980 (Sherburne, 1980). The ruptures were mapped during USGS field investigations May 28 to June 4 and July 14-19, 1980. The map also includes some of the ruptures recorded by California Division of Mines and Geology investigators May 26-31, June 26-27, and July 7-11, 1980 (Taylor and Bryant, 1980). Because most of the surface ruptures developed in either unconsolidated pumice, alluvium, or till (and many were on slopes of scarps created by earlier faulting), wind, rain and animals quickly erased many of the ruptures. In places, the minimum detectable slip was 3-10 mm. Thus the lines on the map do not record all of the ruptures that formed at the time of the earthquake. Many of the areas were we show gaps between lines on the map probably had cracks originally. 

  1. A consensus framework map of durum wheat (Triticum durum Desf.) suitable for linkage disequilibrium analysis and genome-wide association mapping.

    PubMed

    Maccaferri, Marco; Cane', Maria Angela; Sanguineti, Maria C; Salvi, Silvio; Colalongo, Maria C; Massi, Andrea; Clarke, Fran; Knox, Ron; Pozniak, Curtis J; Clarke, John M; Fahima, Tzion; Dubcovsky, Jorge; Xu, Steven; Ammar, Karim; Karsai, Ildikó; Vida, Gyula; Tuberosa, Roberto

    2014-10-07

    Durum wheat (Triticum durum Desf.) is a tetraploid cereal grown in the medium to low-precipitation areas of the Mediterranean Basin, North America and South-West Asia. Genomics applications in durum wheat have the potential to boost exploitation of genetic resources and to advance understanding of the genetics of important complex traits (e.g. resilience to environmental and biotic stresses). A dense and accurate consensus map specific for T. durum will greatly facilitate genetic mapping, functional genomics and marker-assisted improvement. High quality genotypic data from six core recombinant inbred line populations were used to obtain a consensus framework map of 598 simple sequence repeats (SSR) and Diversity Array Technology® (DArT) anchor markers (common across populations). Interpolation of unique markers from 14 maps allowed us to position a total of 2,575 markers in a consensus map of 2,463 cM. The T. durum A and B genomes were covered in their near totality based on the reference SSR hexaploid wheat map. The consensus locus order compared to those of the single component maps showed good correspondence, (average Spearman's rank correlation rho ρ value of 0.96). Differences in marker order and local recombination rate were observed between the durum and hexaploid wheat consensus maps. The consensus map was used to carry out a whole-genome search for genetic differentiation signatures and association to heading date in a panel of 183 accessions adapted to the Mediterranean areas. Linkage disequilibrium was found to decay below the r2 threshold=0.3 within 2.20 cM, on average. Strong molecular differentiations among sub-populations were mapped to 87 chromosome regions. A genome-wide association scan for heading date from 27 field trials in the Mediterranean Basin and in Mexico yielded 50 chromosome regions with evidences of association in multiple environments. The consensus map presented here was used as a reference for genetic diversity and mapping

  2. A powerful microbiome-based association test and a microbial taxa discovery framework for comprehensive association mapping.

    PubMed

    Koh, Hyunwook; Blaser, Martin J; Li, Huilin

    2017-04-24

    The role of the microbiota in human health and disease has been increasingly studied, gathering momentum through the use of high-throughput technologies. Further identification of the roles of specific microbes is necessary to better understand the mechanisms involved in diseases related to microbiome perturbations. Here, we introduce a new microbiome-based group association testing method, optimal microbiome-based association test (OMiAT). OMiAT is a data-driven testing method which takes an optimal test throughout different tests from the sum of powered score tests (SPU) and microbiome regression-based kernel association test (MiRKAT). We illustrate that OMiAT efficiently discovers significant association signals arising from varying microbial abundances and different relative contributions from microbial abundance and phylogenetic information. We also propose a way to apply it to fine-mapping of diverse upper-level taxa at different taxonomic ranks (e.g., phylum, class, order, family, and genus), as well as the entire microbial community, within a newly introduced microbial taxa discovery framework, microbiome comprehensive association mapping (MiCAM). Our extensive simulations demonstrate that OMiAT is highly robust and powerful compared with other existing methods, while correctly controlling type I error rates. Our real data analyses also confirm that MiCAM is especially efficient for the assessment of upper-level taxa by integrating OMiAT as a group analytic method. OMiAT is attractive in practice due to the high complexity of microbiome data and the unknown true nature of the state. MiCAM also provides a hierarchical association map for numerous microbial taxa and can also be used as a guideline for further investigation on the roles of discovered taxa in human health and disease.

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

    USGS Publications Warehouse

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

    1999-01-01

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

  4. 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.

  5. Association mapping of height and maturity across five environments using the sorghum mini core collection.

    PubMed

    Upadhyaya, Hari D; Wang, Yi-Hong; Sharma, Shivali; Singh, Sube

    2012-06-01

    Sorghum is a potential energy crop thanks to its high biomass productivity and low input. Biomass yield in sorghum is defined by height and maturity. To develop molecular breeding tools for genetic improvement of these two traits, we have identified simple sequence repeat markers linked to height and maturity using a pool-based association mapping technique. The sorghum mini core collection was evaluated across five environments for height and maturity. Seven tall and seven short accessions were selected based on their height in all environments. Likewise, six early- and 10 late-maturing accessions were selected mostly based on their maturity in two post-rainy seasons. Two additional height pools were constructed based on phenotypes in one environment. The three pairs of pools were screened with 703 SSR markers and 39 polymorphic markers were confirmed by individual genotyping. Association mapping of the 39 markers with 242 accessions from the mini core collection identified five markers associated with maturity or height. All were clustered on chromosomes 6, 9, and 10 with previously mapped height and maturity markers or QTLs. One marker associated with both height and maturity was 84 kb from recently cloned Ma1. These markers will lay a foundation for identifying additional height and maturity genes in sorghum.

  6. Association Mapping of Kernel Size and Milling Quality in Wheat (Triticum aestivum L.) Cultivars

    PubMed Central

    Breseghello, Flavio; Sorrells, Mark E.

    2006-01-01

    Association mapping is a method for detection of gene effects based on linkage disequilibrium (LD) that complements QTL analysis in the development of tools for molecular plant breeding. In this study, association mapping was performed on a selected sample of 95 cultivars of soft winter wheat. Population structure was estimated on the basis of 36 unlinked simple-sequence repeat (SSR) markers. The extent of LD was estimated on chromosomes 2D and part of 5A, relative to the LD observed among unlinked markers. Consistent LD on chromosome 2D was <1 cM, whereas in the centromeric region of 5A, LD extended for ∼5 cM. Association of 62 SSR loci on chromosomes 2D, 5A, and 5B with kernel morphology and milling quality was analyzed through a mixed-effects model, where subpopulation was considered as a random factor and the marker tested was considered as a fixed factor. Permutations were used to adjust the threshold of significance for multiple testing within chromosomes. In agreement with previous QTL analysis, significant markers for kernel size were detected on the three chromosomes tested, and alleles potentially useful for selection were identified. Our results demonstrated that association mapping could complement and enhance previous QTL information for marker-assisted selection. PMID:16079235

  7. Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars.

    PubMed

    Breseghello, Flavio; Sorrells, Mark E

    2006-02-01

    Association mapping is a method for detection of gene effects based on linkage disequilibrium (LD) that complements QTL analysis in the development of tools for molecular plant breeding. In this study, association mapping was performed on a selected sample of 95 cultivars of soft winter wheat. Population structure was estimated on the basis of 36 unlinked simple-sequence repeat (SSR) markers. The extent of LD was estimated on chromosomes 2D and part of 5A, relative to the LD observed among unlinked markers. Consistent LD on chromosome 2D was <1 cM, whereas in the centromeric region of 5A, LD extended for approximately 5 cM. Association of 62 SSR loci on chromosomes 2D, 5A, and 5B with kernel morphology and milling quality was analyzed through a mixed-effects model, where subpopulation was considered as a random factor and the marker tested was considered as a fixed factor. Permutations were used to adjust the threshold of significance for multiple testing within chromosomes. In agreement with previous QTL analysis, significant markers for kernel size were detected on the three chromosomes tested, and alleles potentially useful for selection were identified. Our results demonstrated that association mapping could complement and enhance previous QTL information for marker-assisted selection.

  8. 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.

  9. 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. © 2013 Scandinavian Plant Physiology Society.

  10. The metabolic cost of nesting: body condition and blood parameters of Caiman crocodilus and Melanosuchus niger in Central Amazonia.

    PubMed

    Barão-Nóbrega, José António Lemos; Marioni, Boris; Botero-Arias, Robinson; Nogueira, António José Arsénia; Lima, Emerson Silva; Magnusson, William Ernest; Da Silveira, Ronis; Marcon, Jaydione Luiz

    2017-06-19

    Although nesting ecology is well studied in several crocodilian species, it is not known how nest attendance influences physiology and body condition of nesting females. In this study, we describe body condition and serum biochemical values of nesting female, non-nesting female and male spectacled caiman (Caiman crocodilus) and black caiman (Melanosuchus niger) in two areas of Central Amazonia. We also evaluated the effect of nest age and nest distance to water on body condition and blood parameters of nesting females. Body condition and plasmatic concentrations of glucose, triglycerides, lactate and uric acid of nesting females were significantly different from those of non-nesting females and males in C. crocodilus, but not in M. niger. Our study also demonstrated that nest age and distance to water had a negative effect on female body condition in C. crocodilus, but not in M. niger. Female C. crocodilus attending older nests or nests built further away from permanent water bodies tended to have lower body condition. Our results demonstrate that the nesting strategy of C. crocodilus has a metabolic cost associated with nest attendance for nesting females, which appear to depend on accumulated energetic reserves during nest attendance. In contrast, nest attendance had little effect on the physiology of female M. niger.

  11. Haplotype Association Mapping Identifies a Candidate Gene Region in Mice Infected With Staphylococcus aureus.

    PubMed

    Johnson, Nicole V; Ahn, Sun Hee; Deshmukh, Hitesh; Levin, Mikhail K; Nelson, Charlotte L; Scott, William K; Allen, Andrew; Fowler, Vance G; Cowell, Lindsay G

    2012-06-01

    Exposure to Staphylococcus aureus has a variety of outcomes, from asymptomatic colonization to fatal infection. Strong evidence suggests that host genetics play an important role in susceptibility, but the specific host genetic factors involved are not known. The availability of genome-wide single nucleotide polymorphism (SNP) data for inbred Mus musculus strains means that haplotype association mapping can be used to identify candidate susceptibility genes. We applied haplotype association mapping to Perlegen SNP data and kidney bacterial counts from Staphylococcus aureus-infected mice from 13 inbred strains and detected an associated block on chromosome 7. Strong experimental evidence supports the result: a separate study demonstrated the presence of a susceptibility locus on chromosome 7 using consomic mice. The associated block contains no genes, but lies within the gene cluster of the 26-member extended kallikrein gene family, whose members have well-recognized roles in the generation of antimicrobial peptides and the regulation of inflammation. Efficient mixed-model association (EMMA) testing of all SNPs with two alleles and located within the gene cluster boundaries finds two significant associations: one of the three polymorphisms defining the associated block and one in the gene closest to the block, Klk1b11. In addition, we find that 7 of the 26 kallikrein genes are differentially expressed between susceptible and resistant mice, including the Klk1b11 gene. These genes represent a promising set of candidate genes influencing susceptibility to Staphylococcus aureus.

  12. Genome-wide association study and admixture mapping reveal new loci associated with total IgE levels in Latinos.

    PubMed

    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

    2015-06-01

    IgE is a key mediator of allergic inflammation, and its levels are frequently increased in patients with allergic disorders. We sought to identify genetic variants associated with IgE levels in Latinos. We performed a genome-wide association study and admixture mapping of total IgE levels in 3334 Latinos from the Genes-environments & Admixture in Latino Americans (GALA II) study. Replication was evaluated in 454 Latinos, 1564 European Americans, and 3187 African Americans from independent studies. We confirmed associations of 6 genes identified by means of previous genome-wide association studies and identified a novel genome-wide significant association of a polymorphism in the zinc finger protein 365 gene (ZNF365) with total IgE levels (rs200076616, P = 2.3 × 10(-8)). We next identified 4 admixture mapping peaks (6p21.32-p22.1, 13p22-31, 14q23.2, and 22q13.1) at which 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 IgE levels (P = 4.95 × 10(-8)). All but 22q13.1 were replicated in an independent sample of Latinos, and 2 of the peaks were replicated in African Americans (6p21.32-p22.1 and 14q23.2). Fine mapping of 6p21.32-p22.1 identified 6 genome-wide significant single nucleotide polymorphisms in Latinos, 2 of which replicated in European Americans. Another single nucleotide polymorphism was peak-wide significant within 14q23.2 in African Americans (rs1741099, P = 3.7 × 10(-6)) and replicated in non-African American samples (P = .011). We confirmed genetic associations at 6 genes and identified novel associations within ZNF365, HLA-DQA1, and 14q23.2. Our results highlight the importance of studying diverse multiethnic populations to uncover novel loci associated with total IgE levels. Copyright © 2014 American Academy of Allergy, Asthma & Immunology. All rights reserved.

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

    DOE PAGES

    Kaplow, Irene M.; MacIsaac, Julia L.; Mah, Sarah M.; ...

    2015-04-24

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

  14. A low-cost open-source SNP genotyping platform for association mapping applications.

    PubMed

    Macdonald, Stuart J; Pastinen, Tomi; Genissel, Anne; Cornforth, Theodore W; Long, Anthony D

    2005-01-01

    Association mapping aimed at identifying DNA polymorphisms that contribute to variation in complex traits entails genotyping a large number of single-nucleotide polymorphisms (SNPs) in a very large panel of individuals. Few technologies, however, provide inexpensive high-throughput genotyping. Here, we present an efficient approach developed specifically for genotyping large fixed panels of diploid individuals. The cost-effective, open-source nature of our methodology may make it particularly attractive to those working in nonmodel systems.

  15. A low-cost open-source SNP genotyping platform for association mapping applications

    PubMed Central

    Macdonald, Stuart J; Pastinen, Tomi; Genissel, Anne; Cornforth, Theodore W; Long, Anthony D

    2005-01-01

    Association mapping aimed at identifying DNA polymorphisms that contribute to variation in complex traits entails genotyping a large number of single-nucleotide polymorphisms (SNPs) in a very large panel of individuals. Few technologies, however, provide inexpensive high-throughput genotyping. Here, we present an efficient approach developed specifically for genotyping large fixed panels of diploid individuals. The cost-effective, open-source nature of our methodology may make it particularly attractive to those working in nonmodel systems. PMID:16356268

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

    PubMed Central

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

    2016-01-01

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

  17. Transferability and fine mapping of genome-wide associated loci for lipids in African Americans.

    PubMed

    Adeyemo, Adebowale; Bentley, Amy R; Meilleur, Katherine G; Doumatey, Ayo P; Chen, Guanjie; Zhou, Jie; Shriner, Daniel; Huang, Hanxia; Herbert, Alan; Gerry, Norman P; Christman, Michael F; Rotimi, Charles N

    2012-09-21

    A recent, large genome-wide association study (GWAS) of European ancestry individuals has identified multiple genetic variants influencing serum lipids. Studies of the transferability of these associations to African Americans remain few, an important limitation given interethnic differences in serum lipids and the disproportionate burden of lipid-associated metabolic diseases among African Americans. We attempted to evaluate the transferability of 95 lipid-associated loci recently identified in European ancestry individuals to 887 non-diabetic, unrelated African Americans from a population-based sample in the Washington, DC area. Additionally, we took advantage of the generally reduced linkage disequilibrium among African ancestry populations in comparison to European ancestry populations to fine-map replicated GWAS signals. We successfully replicated reported associations for 10 loci (CILP2/SF4, STARD3, LPL, CYP7A1, DOCK7/ANGPTL3, APOE, SORT1, IRS1, CETP, and UBASH3B). Through trans-ethnic fine-mapping, we were able to reduce associated regions around 75% of the loci that replicated. Between this study and previous work in African Americans, 40 of the 95 loci reported in a large GWAS of European ancestry individuals also influence lipid levels in African Americans. While there is now evidence that the lipid-influencing role of a number of genetic variants is observed in both European and African ancestry populations, the still considerable lack of concordance highlights the importance of continued ancestry-specific studies to elucidate the genetic underpinnings of these traits.

  18. 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

  19. The Nest Home

    SciTech Connect

    Pickerill, Heath

    2016-07-11

    The purpose of the project was to build a competitive solar-powered house for the U.S. Department of Energy Solar Decathlon 2015 held in Irvine, California. The house, named the Nest Home, was an innovative design that works with the environment to meet the needs of the occupants, identified as a growing family. Reused materials were instrumental in the design. Three refurbished shipping containers composed the primary structure of the house, creating an open floor plan that defies common architecture for container homes. The exterior siding was made of deconstructed shipping pallets collected locally. Other recycled products included carpet composed of discarded fishing nets, denim batting made of recycled blue jeans that outperform traditional fiberglass insulation in sound proofing and thermal resistance, and kitchen cabinets that were purchased used and refinished. Collectively these elements formed a well-balanced blend of modern design, comfort, and sustainability. The house was Missouri University of Science and Technology’s sixth entry in the DOE Solar Decathlon. Missouri S&T has been invited to compete in six of the seven decathlons held, more than any other university worldwide. The house was brought back to Rolla after the Decathlon in California where it has been placed in its permanent location on the S&T campus.

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

    PubMed Central

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

    2016-01-01

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

  1. 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

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

    PubMed Central

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

    2016-01-01

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

  3. Differential expression of microtubule associated protein MAP-2 in developing cochleovestibular neurons and its modulation by neurotrophin-3.

    PubMed

    San José, I; Vázquez, E; García-Atares, N; Huerta, J J; Vega, J A; Represa, J

    1997-06-01

    Microtubule associated proteins (MAPs) are essential cytoskeletal proteins in developing neurons. The present study was undertaken to analyze the expression of MAP2 and its isoforms (a,b,c) during the embryonal and early post-hatching development of chicken cochleovestibular ganglion (CVG) neurons. Moreover, we have investigated MAP2 expression in primary cultures of CVG neurons, and whether it is regulated by neurotrophin-3 (NT3). The expression of MAP2 immunoreactivity (IR) was studied using both Western blot and immunohistochemistry on tissue sections and primary cultures. In vivo MAP2c was expressed from incubation day 4 (E4) to E10, and MAP2b was found in all embryonal stages studied and at post-hatching day 10 (P10), whereas MAP2a was restricted to the post-hatching periods. The cellular localization of IR was in the neuronal perikarya and their peripheral processes (dendrites) but not in axons. Primary cultures matched the in vivo pattern of MAP2 expression, and IR was localized in neuronal cell bodies and the initial segment of the neuronal processes. Exogenous NT3 regulated the expression of MAP2 isoforms in a dose dependent manner. At the survival dose of 0.5 ng/ml NT3, the main MAP2 expression was MAP2c. Conversely, at the neuritogenic dose of 5 ng/ml NT3 increased MAP2b and MAP2a expression, but not MAP2c. The present results demonstrate that MAP2 isoforms are developmentally regulated, thus suggesting that each isoform is specifically involved in CVG neuron maturation. Furthermore, we provide evidence of MAP2 regulation in culture by the neurotrophic factor NT3.

  4. Design of laying nests in furnished cages: influence of nesting material, nest box position and seclusion.

    PubMed

    Struelens, E; Tuyttens, F A M; Janssen, A; Leroy, T; Audoorn, L; Vranken, E; de Baere, K; Odberg, F; Berckmans, D; Zoons, J; Sonck, B

    2005-02-01

    (1) Preferences for three nesting materials and nest box positions were investigated simultaneously in two trials using a furnished cage: one with 18 individual laying hens and one with 18 groups of 5 hens. Following a habituation period in pre-test cages, every hen or group of hens was tested for 2 d: once without and once with plastic flaps at the entrance of the nest boxes. (2) Hens preferred peat and artificial turf to coated wire mesh for egg laying. (3) One nest box position was clearly preferred to both other nest boxes. The hens' choice of nest box position was influenced by the pre-test cage in which they had been habituated. (4) The presence of plastic flaps at the entrance of the nest boxes had no influence on the proportion of eggs laid on the different nesting materials or on the proportion of floor eggs. (5) Individual and group testing resulted in the same overall results despite the presence of a distinct group effect.

  5. Quantitative trait Loci association mapping by imputation of strain origins in multifounder crosses.

    PubMed

    Zhou, Jin J; Ghazalpour, Anatole; Sobel, Eric M; Sinsheimer, Janet S; Lange, Kenneth

    2012-02-01

    Although mapping quantitative traits in inbred strains is simpler than mapping the analogous traits in humans, classical inbred crosses suffer from reduced genetic diversity compared to experimental designs involving outbred animal populations. Multiple crosses, for example the Complex Trait Consortium's eight-way cross, circumvent these difficulties. However, complex mating schemes and systematic inbreeding raise substantial computational difficulties. Here we present a method for locally imputing the strain origins of each genotyped animal along its genome. Imputed origins then serve as mean effects in a multivariate Gaussian model for testing association between trait levels and local genomic variation. Imputation is a combinatorial process that assigns the maternal and paternal strain origin of each animal on the basis of observed genotypes and prior pedigree information. Without smoothing, imputation is likely to be ill-defined or jump erratically from one strain to another as an animal's genome is traversed. In practice, one expects to see long stretches where strain origins are invariant. Smoothing can be achieved by penalizing strain changes from one marker to the next. A dynamic programming algorithm then solves the strain imputation process in one quick pass through the genome of an animal. Imputation accuracy exceeds 99% in practical examples and leads to high-resolution mapping in simulated and real data. The previous fastest quantitative trait loci (QTL) mapping software for dense genome scans reduced compute times to hours. Our implementation further reduces compute times from hours to minutes with no loss in statistical power. Indeed, power is enhanced for full pedigree data.

  6. 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

  7. Autophagic Marker MAP1LC3B Expression Levels Are Associated with Carotid Atherosclerosis Symptomatology

    PubMed Central

    Swaminathan, Bhairavi; Goikuria, Haize; Vega, Reyes; Rodríguez-Antigüedad, Alfredo; López Medina, Antonio; Freijo, María del Mar; Vandenbroeck, Koen; Alloza, Iraide

    2014-01-01

    Objectives The mechanism by which atheroma plaque becomes unstable is not completely understood to date but analysis of differentially expressed genes in stable versus unstable plaques may provide clues. This will be crucial toward disclosing the mechanistic basis of plaque instability, and may help to identify prognostic biomarkers for ischaemic events. The objective of our study was to identify differences in expression levels of 59 selected genes between symptomatic patients (unstable plaques) and asymptomatic patients (stable plaques). Methods 80 carotid plaques obtained by carotid endarterectomy and classified as symptomatic (>70% stenosis) or asymptomatic (>80% stenosis) were used in this study. The expression levels of 59 genes were quantified by qPCR on RNA extracted from the carotid plaques obtained by endarterectomy and analyzed by means of various bioinformatic tools. Results Several genes associated with autophagy pathways displayed differential expression levels between asymptomatic and symptomatic (i.e. MAP1LC3B, RAB24, EVA1A). In particular, mRNA levels of MAP1LC3B, an autophagic marker, showed a 5−fold decrease in symptomatic samples, which was confirmed in protein blots. Immune system−related factors and endoplasmic reticulum-associated markers (i.e. ERP27, ITPR1, ERO1LB, TIMP1, IL12B) emerged as differently expressed genes between asymptomatic and symptomatic patients. Conclusions Carotid atherosclerotic plaques in which MAP1LC3B is underexpressed would not be able to benefit from MAP1LC3B−associated autophagy. This may lead to accumulation of dead cells at lesion site with subsequent plaque destabilization leading to cerebrovascular events. Identified biomarkers and network interactions may represent novel targets for development of treatments against plaque destabilization and thus for the prevention of cerebrovascular events. PMID:25503069

  8. 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

  9. Mapping the sensory perception of apple using descriptive sensory evaluation in a genome wide association study

    PubMed Central

    Amyotte, Beatrice; Bowen, Amy J.; Banks, Travis; Rajcan, Istvan; Somers, Daryl J.

    2017-01-01

    Breeding apples is a long-term endeavour and it is imperative that new cultivars are selected to have outstanding consumer appeal. This study has taken the approach of merging sensory science with genome wide association analyses in order to map the human perception of apple flavour and texture onto the apple genome. The goal was to identify genomic associations that could be used in breeding apples for improved fruit quality. A collection of 85 apple cultivars was examined over two years through descriptive sensory evaluation by a trained sensory panel. The trained sensory panel scored randomized sliced samples of each apple cultivar for seventeen taste, flavour and texture attributes using controlled sensory evaluation practices. In addition, the apple collection was subjected to genotyping by sequencing for marker discovery. A genome wide association analysis suggested significant genomic associations for several sensory traits including juiciness, crispness, mealiness and fresh green apple flavour. The findings include previously unreported genomic regions that could be used in apple breeding and suggest that similar sensory association mapping methods could be applied in other plants. PMID:28231290

  10. Mapping the sensory perception of apple using descriptive sensory evaluation in a genome wide association study.

    PubMed

    Amyotte, Beatrice; Bowen, Amy J; Banks, Travis; Rajcan, Istvan; Somers, Daryl J

    2017-01-01

    Breeding apples is a long-term endeavour and it is imperative that new cultivars are selected to have outstanding consumer appeal. This study has taken the approach of merging sensory science with genome wide association analyses in order to map the human perception of apple flavour and texture onto the apple genome. The goal was to identify genomic associations that could be used in breeding apples for improved fruit quality. A collection of 85 apple cultivars was examined over two years through descriptive sensory evaluation by a trained sensory panel. The trained sensory panel scored randomized sliced samples of each apple cultivar for seventeen taste, flavour and texture attributes using controlled sensory evaluation practices. In addition, the apple collection was subjected to genotyping by sequencing for marker discovery. A genome wide association analysis suggested significant genomic associations for several sensory traits including juiciness, crispness, mealiness and fresh green apple flavour. The findings include previously unreported genomic regions that could be used in apple breeding and suggest that similar sensory association mapping methods could be applied in other plants.

  11. 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

  12. Flexibility in nest density and social structure in invasive populations of the Argentine ant, Linepithema humile.

    PubMed

    Ingram, Krista K

    2002-12-01

    The extraordinary success of unicolonial insect invaders has renewed interest in the origins and maintenance of unicoloniality, a social system characterized by the absence of aggressive behavior between individuals of neighboring conspecific nests. In this study, I explore how traits associated with unicoloniality, particularly nest budding and the local exchange of workers between nests, vary across environments. Comparisons of nest characteristics in three introduced populations of Argentine ants, Linepithema humile, reveal considerable variation in nest density and social structure across populations. The population with the highest nest density has smaller, less productive nests and fewer queens per nest than the two populations with low nest densities. Nestmate relatedness is low in all populations, but multi-locus genotype analyses reveal that levels of connectivity vary among populations. In particular, high nest density is associated with higher levels of genotypic similarity between nests. Assignment distances in the two populations with low nest density are similar to a native population, suggesting that the amount of mixing between neighboring nests is shared among some native and introduced populations. Because the study populations are similar in age and genetic diversity, these results suggest that the social structure of L. humile populations depend on the ecological context. Understanding the patterns of expression of unicolonial traits in different environments helps to shed light on the origins of unicoloniality and to explain the success of Argentine ants as invaders.

  13. Response of predators to Western Sandpiper nest exclosures

    USGS Publications Warehouse

    Niehaus, Amanda C.; Ruthrauff, Daniel R.; McCaffery, Brian J.

    2004-01-01

    In 2001, predator exclosures were used to protect nests of the Western Sandpiper (Calidris mauri) in western Alaska. During the exclosure experiment, nest contents in exclosures had significantly higher daily survival rates than control nests, however, late in the study predators began to cue in on exclosures and predate the nest contents. An Arctic Fox (Alopex lagopus) dug under one exclosure and took the newly hatched chicks, and Long-tailed Jaegers (Stercorarius longicaudus) learned to associate exclosures with active nests and repeatedly visited them. The jaegers attempted to gain access to exclosed nests and pursued adult sandpipers as they emerged from the exclosures. The exclosures were removed to reduce potential mortality to adult and young sandpipers, but subsequently, post-exclosure nests had lower daily survival rates than controls during the same time period. Predation of post-exclosure eggs and chicks highlighted the lasting influence of the exclosure treatment on offspring survival because predators probably remembered nest locations. Researchers are urged to use caution when considering use of predator exclosures in areas where jaegers occur.

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

    PubMed

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

    2009-08-01

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

  15. Nest site selection in native and exotic trees by Black-chinned Hummingbirds

    Treesearch

    Deborah M. Finch; Jeffrey Kelly

    2002-01-01

    We studied nest site selection and nesting success in Black-chinned Hummingbirds (Archilochus alexandri) along the middle Rio Grande, New Mexico. The study was conducted in association with an exotic woody plant removal program to determine whether the removal of exotic plants would affect wildlife populations and nesting success, either positively or negatively. Point...

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

    USDA-ARS?s Scientific Manuscript database

    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...

  17. 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

    2014-10-28

    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.

  18. 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.

  19. Fine mapping of E(kp)-1, a locus associated with silkworm (Bombyx mori) proleg development.

    PubMed

    Xiang, H; Li, M; Yang, F; Guo, Q; Zhan, S; Lin, H; Miao, X; Huang, Y

    2008-05-01

    The silkworm homeotic mutant E(kp) has a pair of rudimentary abdominal legs, called prolegs, in its A2 segment. This phenotype is caused by a single dominant mutation at the E(kp)-1 locus, which was previously mapped to chromosome 6. To explore the possible association of Hox genes with proleg development in the silkworm, a map-based cloning strategy was used to isolate the E(kp)-1 locus. Five E(kp)-1-linked simple sequence repeat markers on chromosome 6 were used to generate a low-resolution map with a total genetic distance of 39.5 cM. Four additional cleaved amplified polymorphic sequence markers were developed based on the initial map. The closest marker to E(kp)-1 was at a genetic distance of 2.7 cM. A high-resolution genetic map was constructed using nine BC1 segregating populations consisting of 2396 individuals. Recombination suppression was observed in the vicinity of E(kp)-1. Four molecular markers were tightly linked to E(kp)-1, and three were clustered with it. These markers were used to screen a BAC library. A single bacterial artificial chromosome (BAC) clone spanning the E(kp)-1 locus was identified, and E(kp)-1 was delimited to a region less than 220 kb long that included the Hox gene abdominal-A and a non-coding locus, iab-4. These results provide essential information for the isolation of this locus, which may shed light on the mechanism of proleg development in the silkworm and possibly in Lepidoptera.

  20. Cytotoxin-Associated Gene A-Negative Strains of Helicobacter pylori as a Potential Risk Factor of Pancreatic Cancer: A Meta-Analysis Based on Nested Case-Control Studies.

    PubMed

    Chen, Xin-Zu; Wang, Rui; Chen, Hai-Ning; Hu, Jian-Kun

    2015-11-01

    Risk of pancreatic cancer between Helicobacter pylori infected and noninfected persons is controversial, and therefore a meta-analysis was performed. PubMed was searched up to September 2014. Only population-based nested case-control studies comparing the serological prevalence of Helicobacter pylori between pancreatic cancer cases and cancer-free controls were eligible. Pooled odds ratios (ORs) and 95% confidence intervals (CIs) for pancreatic cancer risk between Helicobacter pylori infected and noninfected persons were estimated. Five eligible nested case-control studies were included, with 1446 pancreatic cancer cases and 2235 cancer-free controls. On the whole, the proportion of pancreatic cancer cases among those infected with Helicobacter pylori was not significant different from those noninfected (OR, 0.99; 95% CI, 0.65-1.50; P = 0.96). Likewise, seropositivity of cytotoxin-associated gene A (CagA) showed nonsignificant association with pancreatic cancer (OR, 0.92; 95% CI, 0.65-1.30; P = 0.63). The CagA-positive virulent strains of Helicobacter pylori did not increase the risk of pancreatic cancer (OR, 0.97; 95% CI, 0.50-1.89; P = 0.93). However, CagA-negative nonvirulent strains of Helicobacter pylori had a significant increased risk for pancreatic cancer (OR, 1.47; 95% CI, 1.11-1.96; P = 0.008). The CagA-negative non-virulent strains of Helicobacter pylori may be a potential risk factor of pancreatic cancer. High-quality prospective large-scaled studies are required for more conclusive results.

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

    PubMed

    Misra, Sunayana; Bihari, Chhagan

    2016-04-01

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

  2. Plasmacytoma-associated neuronal glycoprotein, Pang, maps to mouse chromosome 6 and human chromosome 3

    SciTech Connect

    Mock, B.A.; McBride, O.W.; Kozak, C.A.

    1996-06-01

    A new member of the immunoglobulin/fibronectin superfamily of adhesion molecules, Pang (plasmacytoma-associated neuronal glycoprotein), was recently isolated from a plasmacytoma. In previous studies, Pang was found to be normally expressed in the brain and ectopically activated by intracisternal A-type particle long terminal repeats in plasmacytomas. In this study, Pang was initially mapped to mouse Chr 6 by somatic cell hybrid analysis and further positioned on the chromosome between Wnt7a and Pcp1. Southern blot analysis of human-rodent somatic cell hybrids together with predictions from the mouse map location indicate that human PANG is located at 3p26. 13 refs., 1 fig., 1 tab.

  3. Effect of "missing" information on fast mapping by individuals with vocabulary limitations associated with intellectual disability.

    PubMed

    Wilkinson, Krista

    2007-01-01

    One phenomenon of language development is a dramatic increase in vocabulary size, driven by rapid word learning. For individuals with intellectual disabilities, the size of the lexicon often lags behind what would be expected both for CA and MA. I examined how well individuals with severely limited receptive vocabulary associated with intellectual disability retained a new word-picture map after a single exposure under conditions of varying difficulty. This study was a direct replication of a previous investigation with typically developing preschool children, enabling a direct comparison. Individuals with intellectual disabilities performed equally as well as control children in the initial exposure phase but poorer when asked to remember the initial map in the presence of other novel distracters or labels.

  4. Do Predation Rates on Artificial Nests Accurately Reflect Predation Rates on Natural Bird Nests?

    Treesearch

    David I. King; Richard M. DeGraaf; Curtice R. Griffin; Thomas J. Maier

    1999-01-01

    Artificial nests are widely used in avian field studies. However, it is unclear how well predation rates on artificial nests reflect predation rates on natural nests. Therefore, we compared survival rates of artificial nests (unused natural nests baited with House Sparrow eggs) with survival rates of active bird nests in the same habitat at the same sites. Survival...

  5. 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

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

    PubMed

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

    2015-04-01

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

  7. Association mapping of seed quality traits using the Canadian flax (Linum usitatissimum L.) core collection.

    PubMed

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

    2014-04-01

    The identification of stable QTL for seed quality traits by association mapping of a diverse panel of linseed accessions establishes the foundation for assisted breeding and future fine mapping in linseed. Linseed oil is valued for its food and non-food applications. Modifying its oil content and fatty acid (FA) profiles to meet market needs in a timely manner requires clear understanding of their quantitative trait loci (QTL) architectures, which have received little attention to date. Association mapping is an efficient approach to identify QTL in germplasm collections. In this study, we explored the quantitative nature of seed quality traits including oil content (OIL), palmitic acid, stearic acid, oleic acid, linoleic acid (LIO) linolenic acid (LIN) and iodine value in a flax core collection of 390 accessions assayed with 460 microsatellite markers. The core collection was grown in a modified augmented design at two locations over 3 years and phenotypic data for all seven traits were obtained from all six environments. Significant phenotypic diversity and moderate to high heritability for each trait (0.73-0.99) were observed. Most of the candidate QTL were stable as revealed by multivariate analyses. Nine candidate QTL were identified, varying from one for OIL to three for LIO and LIN. Candidate QTL for LIO and LIN co-localized with QTL previously identified in bi-parental populations and some mapped nearby genes known to be involved in the FA biosynthesis pathway. Fifty-eight percent of the QTL alleles were absent (private) in the Canadian cultivars suggesting that the core collection possesses QTL alleles potentially useful to improve seed quality traits. The candidate QTL identified herein will establish the foundation for future marker-assisted breeding in linseed.

  8. 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.

  9. Identification of exercise capacity QTL using association mapping in inbred mice.

    PubMed

    Courtney, Sean M; Massett, Michael P

    2012-10-02

    There are large interindividual differences in exercise capacity. It is well established that there is a genetic basis for these differences. However, the genetic factors underlying this variation are undefined. Therefore, the purpose of this study was to identify novel putative quantitative trait loci (QTL) for exercise capacity by measuring exercise capacity in inbred mice and performing genome-wide association mapping. Exercise capacity, defined as run time and work, was assessed in male mice (n = 6) from 34 strains of classical and wild-derived inbred mice performing a graded treadmill test. Genome-wide association mapping was performed with an efficient mixed-model association (EMMA) algorithm to identify QTL. Exercise capacity was significantly different across strains. Run time varied by 2.7-fold between the highest running strain (C58/J) and the lowest running strain (A/J). These same strains showed a 16.5-fold difference in work. Significant associations were identified for exercise time on chromosomes 1, 2, 7, 11, and 13. The QTL interval on chromosome 2 (~168 Mb) contains one gene, Nfatc2, and overlaps with a suggestive QTL for training responsiveness in humans. These results provide phenotype data on the widest range of inbred strains tested thus far and indicate that genetic background significantly influences exercise capacity. Furthermore, the novel QTLs identified in the current study provide new targets for investigating the underlying mechanisms for variation in exercise capacity.

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

    PubMed

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

    2014-01-10

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

  11. Association mapping of seed and disease resistance traits in Theobroma cacao L.

    PubMed

    Motilal, Lambert A; Zhang, Dapeng; Mischke, Sue; Meinhardt, Lyndel W; Boccara, Michel; Fouet, Olivier; Lanaud, Claire; Umaharan, Pathmanathan

    2016-12-01

    Microsatellite and single nucleotide polymorphism markers that could be used in marker assisted breeding of cacao were identified for number of filled seeds, black pod resistance and witches' broom disease resistance. An association mapping approach was employed to identify markers for seed number and resistance to black pod and witches' broom disease (WBD) in cacao (Theobroma cacao L.). Ninety-five microsatellites (SSRs) and 775 single nucleotide polymorphisms (SNPs) were assessed on 483 unique trees in the International Cocoa Genebank Trinidad (ICGT). Linkage disequilibrium (LD) and association mapping studies were conducted to identify markers to tag the phenotypic traits. Decay of LD occurred over an average 9.3 cM for chromosomes 1-9 and 2.5 cM for chromosome 10. Marker/trait associations were generally identified based on general linear models (GLMs) that incorporated principal components from molecular information on relatedness factor. Seven markers (mTcCIR 8, 66, 126, 212; TcSNP368, 697, 1370) on chromosomes 1 and 9 were identified for number of filled seeds (NSEED). A single marker was found for black pod resistance (mTcCIR280) on chromosome 3, whereas six markers on chromosomes 4, 5, 6, 8, and 10 were detected for WBD (mTcCIR91, 183; TcSNP375, 720, 1230 and 1374). It is expected that this association mapping study in cacao would contribute to the knowledge of the genetic determinism of cocoa traits and that the markers identified herein would prove useful in marker assisted breeding of cacao.

  12. Genome wide association mapping for grain shape traits in indica rice.

    PubMed

    Feng, Yue; Lu, Qing; Zhai, Rongrong; Zhang, Mengchen; Xu, Qun; Yang, Yaolong; Wang, Shan; Yuan, Xiaoping; Yu, Hanyong; Wang, Yiping; Wei, Xinghua

    2016-10-01

    Using genome-wide association mapping, 47 SNPs within 27 significant loci were identified for four grain shape traits, and 424 candidate genes were predicted from public database. Grain shape is a key determinant of grain yield and quality in rice (Oryza sativa L.). However, our knowledge of genes controlling rice grain shape remains limited. Genome-wide association mapping based on linkage disequilibrium (LD) has recently emerged as an effective approach for identifying genes or quantitative trait loci (QTL) underlying complex traits in plants. In this study, association mapping based on 5291 single nucleotide polymorphisms (SNPs) was conducted to identify significant loci associated with grain shape traits in a global collection of 469 diverse rice accessions. A total of 47 SNPs were located in 27 significant loci for four grain traits, and explained ~44.93-65.90 % of the phenotypic variation for each trait. In total, 424 candidate genes within a 200 kb extension region (±100 kb of each locus) of these loci were predicted. Of them, the cloned genes GS3 and qSW5 showed very strong effects on grain length and grain width in our study. Comparing with previously reported QTLs for grain shape traits, we found 11 novel loci, including 3, 3, 2 and 3 loci for grain length, grain width, grain length-width ratio and thousand grain weight, respectively. Validation of these new loci would be performed in the future studies. These results revealed that besides GS3 and qSW5, multiple novel loci and mechanisms were involved in determining rice grain shape. These findings provided valuable information for understanding of the genetic control of grain shape and molecular marker assistant selection (MAS) breeding in rice.

  13. 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

  14. 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…

  15. Presence of intestinal Mycobacterium avium subspecies paratuberculosis (MAP) DNA is not associated with altered MMP expression in ulcerative colitis

    PubMed Central

    2011-01-01

    Background Mycobacterium avium subspecies paratuberculosis (MAP) is suspected to be a causative agent in human Crohn's disease (CD). Recent evidence suggests that pathogenic mycobacteria and MAP can induce the expression of Matrix Metalloproteinases (MMP), which are the main proteases in the pathogenesis of mucosal ulcerations in inflammatory bowel disease (IBD). Within this study we assessed the prevalence of intestinal MAP specific DNA in patients with Crohn's disease, ulcerative colitis (UC), and healthy controls. We further analysed regulation patterns of MMPs in mucosal tissues of UC patients with and without intestinal MAP DNA detection. Methods Colonic biopsy samples were obtained from 63 Norwegian and German IBD patients and 21 healthy controls. RNA was quantified by quantitative real-time polymerase chain reaction (PCR) to study MMP gene expression in both pathological and healthy mucosal specimens. The presence of MAP DNA in colonic mucosa was examined using MAP specific PCR. Results MAP DNA was detected in 20% of UC patients and 33% of healthy controls but only in 7% of patients with CD. UC patients treated with corticosteroids exhibited a significantly increased frequency of intestinal MAP DNA compared to those not receiving corticosteroids. Expression of MMP-1, -2, -7, -9, -13, -19, -28 and TNF-α did not differ between UC patients with presence of intestinal MAP DNA compared to those without. MMP-2, MMP-9 and MMP-13 were significantly decreased in UC patients receiving corticosteroids. Conclusions The presence of intestinal MAP specific DNA is not associated with altered MMP expression in UC in vivo. Corticosteroids are associated with increased detection of intestinal MAP DNA and decreased expression of certain MMPs. Frequent detection of MAP DNA in healthy controls might be attributable to the wide environmental distribution of MAP and its presence in the food-chain. PMID:21477272

  16. NEST: Noble Element Simulation Technique

    NASA Astrophysics Data System (ADS)

    Szydagis, M.; Barry, N.; Kazkaz, K.; Mock, J.; Stolp, D.; Sweany, M.; Tripathi, M.; Uvarov, S.; Walsh, N.; Woods, M.

    2013-07-01

    NEST (Noble Element Simulation Technique) offers comprehensive, accurate, and precise simulation of the excitation, ionization, and corresponding scintillation and electroluminescence processes in liquid noble elements, useful for direct dark matter detectors, double beta decay searches, PET scans, and general radiation detection technology. Written in C++, NEST is an add-on module for the Geant4 simulation package that incorporates more detailed physics than is currently available into the simulation of scintillation. NEST is of particular use for low-energy nuclear recoils. All available liquid xenon data on nuclear recoils and electron recoils to date have been taken into consideration in arriving at the current models. NEST also handles the magnitude of the light and charge yields of nuclear recoils, including their electric field dependence, thereby shedding light on the possibility of detection or exclusion of a low-mass dark matter WIMP by liquid xenon detectors.

  17. Pre-nesting and nesting behavior of the Swainson's warbler

    USGS Publications Warehouse

    Meanley, B.

    1969-01-01

    The Swainson?s Warbler is one of the least known of southern birds. Although fairly common in some parts of its summer range, observations of its breeding biology have been made by very few persons. The present study was conducted mostly at Macon, Georgia; Pendleton Ferry, Arkansas; and Dismal Swamp, Virginia....In central Georgia and east-central Arkansas, Swainson?s Warblers usually arrive on their territories during the first two weeks in April. Territories in several localities ranged in size from 0.3 to 4.8 acres. A color-marked Arkansas male occupied the same territory for at least four months. Hostile encounters between territorial male Swainson?s Warblers usually take place along the boundary of adjacent territories. Paired males were more aggressive than unpaired males. Toward the end of an encounter one of the two males would usually perform a display in which the wing and tail feathers were spread and the tail vibrated. Following boundary encounters males drifted back onto their territories and usually sang unbroken courses of songs for several minutes.....During pre-nesting at Macon, a mated pair spent the day mostly on the ground within 20 feet of each other, often foragin g 3 to 4 feet apart. What may have been a form of courtship display, in which the male flew from a perch down to the female and either pecked her rump or pounced on her, occurred about three times each hour throughout the day. During this period the male sang less than at other times during the breeding season.....First nests are usually built by the first week in May. Although other investigators reported finding nests of this species outside of the defended territory, all nests that I have found were within the territory. The large, bulky nest of this species usually is placed 2-6 feet above the ground. It is built by the female from materials gathered close to the nest site; and takes two or three days to complete.....Three and occasionally four white eggs are laid. The female

  18. Association of Parkinsonism or Parkinson Disease with Polypharmacy in the Year Preceding Diagnosis: A Nested Case-Control Study in South Korea.

    PubMed

    Park, Hae-Young; Park, Ji-Won; Sohn, Hyun Soon; Kwon, Jin-Won

    2017-06-20

    Published studies on the association between polypharmacy and parkinsonism or Parkinson disease are very limited. The objective of this study was to investigate whether polypharmacy is associated with parkinsonism or Parkinson disease in elderly patients. From a South Korean national health insurance sample cohort database for 2002-2013, we matched parkinsonism cases (defined by diagnosis codes for parkinsonism/Parkinson disease) and Parkinson disease cases (patients who had records for both Parkinson disease diagnosis and anti-Parkinson disease drug prescriptions) with controls. Logistic regression analysis evaluated the associations of parkinsonism/Parkinson disease with polypharmacy (i.e., five or more prescribed daily drugs) during the year preceding parkinsonism/Parkinson disease diagnosis, medications potentially associated with parkinsonism, and comorbidity status (using the Charlson Comorbidity Index score and hospitalization records). The study population included 6209 cases and 24,836 controls for parkinsonism and 1331 cases and 5324 controls for Parkinson disease. In univariate logistic regression, odds ratios for parkinsonism/Parkinson disease increased significantly with increased polypharmacy, medications potentially associated with parkinsonism, Charlson Comorbidity Index score, or prior hospitalizations. In multiple logistic regression, odds ratios for parkinsonism/Parkinson disease (adjusted for medications potentially associated with parkinsonism and comorbidities) also increased with increased polypharmacy. Odds ratios (95% confidence interval) for Parkinson disease were higher than those for parkinsonism with stronger statistical significance: 1.41 (1.28-1.55) and 2.17 (1.84-2.57) for parkinsonism and 2.87 (2.30-3.58) and 4.75 (3.39-6.66) for Parkinson disease for between five and ten prescribed daily drugs and ten or more drugs, respectively. Polypharmacy in the year preceding diagnosis may be associated with an increased risk for parkinsonism

  19. 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.

  20. 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.

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

    PubMed Central

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

    2011-01-01

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

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

    PubMed

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

    2011-09-13

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

  3. 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.

  4. Identification of genetic loci associated with crude protein and mineral concentrations in alfalfa (Medicago sativa) using association mapping.

    PubMed

    Jia, Congjun; Wu, Xinming; Chen, Min; Wang, Yunqi; Liu, Xiqiang; Gong, Pan; Xu, Qingfang; Wang, Xuemin; Gao, Hongwen; Wang, Zan

    2017-06-06

    Alfalfa (Medicago sativa) is one of the most important legume forage species in China and many other countries of the world. It provides a quality source of proteins and minerals to animals. Genetic underpinnings for these important traits, however, are elusive. An alfalfa (M. sativa) association mapping study for six traits, namely crude protein (CP), rumen undegraded protein (RUP), and four mineral elements (Ca, K, Mg and P), was conducted in three consecutive years using a large collection encompassing 336 genotypes genotyped with 85 simple sequence repeat (SSR) markers. All the traits were significantly influenced by genotype, environment, and genotype × environment interaction. Eight-five significant associations (P < 0.005) were identified. Among these, five associations with Ca were repeatedly observed and six co-localized associations were identified. The identified marker alleles significantly associated with the traits provided important information for understanding genetic controls of alfalfa quality. The markers could be used in assisting selection for the individual traits in breeding populations for developing new alfalfa cultivars.

  5. Mapping genetic variants associated with beta-adrenergic responses in inbred mice.

    PubMed

    Hersch, Micha; Peter, Bastian; Kang, Hyun Min; Schüpfer, Fanny; Abriel, Hugues; Pedrazzini, Thierry; Eskin, Eleazar; Beckmann, Jacques S; Bergmann, Sven; Maurer, Fabienne

    2012-01-01

    β-blockers and β-agonists are primarily used to treat cardiovascular diseases. Inter-individual variability in response to both drug classes is well recognized, yet the identity and relative contribution of the genetic players involved are poorly understood. This work is the first genome-wide association study (GWAS) addressing the values and susceptibility of cardiovascular-related traits to a selective β(1)-blocker, Atenolol (ate), and a β-agonist, Isoproterenol (iso). The phenotypic dataset consisted of 27 highly heritable traits, each measured across 22 inbred mouse strains and four pharmacological conditions. The genotypic panel comprised 79922 informative SNPs of the mouse HapMap resource. Associations were mapped by Efficient Mixed Model Association (EMMA), a method that corrects for the population structure and genetic relatedness of the various strains. A total of 205 separate genome-wide scans were analyzed. The most significant hits include three candidate loci related to cardiac and body weight, three loci for electrocardiographic (ECG) values, two loci for the susceptibility of atrial weight index to iso, four loci for the susceptibility of systolic blood pressure (SBP) to perturbations of the β-adrenergic system, and one locus for the responsiveness of QTc (p<10(-8)). An additional 60 loci were suggestive for one or the other of the 27 traits, while 46 others were suggestive for one or the other drug effects (p<10(-6)). Most hits tagged unexpected regions, yet at least two loci for the susceptibility of SBP to β-adrenergic drugs pointed at members of the hypothalamic-pituitary-thyroid axis. Loci for cardiac-related traits were preferentially enriched in genes expressed in the heart, while 23% of the testable loci were replicated with datasets of the Mouse Phenome Database (MPD). Altogether these data and validation tests indicate that the mapped loci are relevant to the traits and responses studied.

  6. 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

  7. Developing a vulnerability mapping methodology: applying the water-associated disease index to dengue in Malaysia.

    PubMed

    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

  8. 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.

  9. Genetic diversity and association mapping of seed vigor in rice (Oryza sativa L.).

    PubMed

    Dang, Xiaojing; Thi, Thu Giang Tran; Dong, Guanshan; Wang, Hui; Edzesi, Wisdom Mawuli; Hong, Delin

    2014-06-01

    Seed vigor is closely related to direct seeding in rice (Oryza sativa L.). Previous quantitative trait locus (QTL) studies for seed vigor were mainly derived from bi-parental segregating populations and no report from natural populations. In this study, association mapping for seed vigor was performed on a selected sample of 540 rice cultivars (419 from China and 121 from Vietnam). Population structure was estimated on the basis of 262 simple sequence repeat (SSR) markers. Seed vigor was evaluated by root length (RL), shoot length (SL) and shoot dry weight in 2011 and 2012. Abundant phenotypic and genetic diversities were found in the studied population. The population was divided into seven subpopulations, and the levels of linkage disequilibrium (LD) ranged from 10 to 80 cM. We identified 27 marker-trait associations involving 18 SSR markers for three traits. According to phenotypic effects for alleles of the detected QTLs, elite alleles were mined. These elite alleles could be used to design parental combinations and the expected results would be obtained by pyramiding or substituting the elite alleles per QTL (apart from possible epistatic effects). Our results demonstrate that association mapping can complement and enhance previous QTL information for marker-assisted selection and breeding by design.

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

    PubMed

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

    2013-09-01

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

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

    PubMed Central

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

    2013-01-01

    Asthma originates from genetic and environmental factors with about half the risk of disease attributable to heritable causes. Genome-wide association studies, mostly in populations of European ancestry, have identified numerous asthma-associated single nucleotide polymorphisms (SNPs). Studies in populations with diverse ancestries allow both for identification of robust associations that replicate across ethnic groups and for improved resolution of associated loci due to different patterns of linkage disequilibrium between ethnic groups. Here we report on an analysis of 745 African-American subjects with asthma and 3,238 African-American control subjects from the Candidate Gene Association Resource (CARe) Consortium, including analysis of SNPs imputed using 1,000 Genomes reference panels and adjustment for local ancestry. We show strong evidence that variation near RAD50/IL13, implicated in studies of European ancestry individuals, replicates in individuals largely of African ancestry. Fine mapping in African ancestry populations also refined the variants of interest for this association. We also provide strong or nominal evidence of replication at loci near ORMDL3/GSDMB, IL1RLML18R1, and 10pl4, all previously associated with asthma in European or Japanese populations, but not at the PYHIN1 locus previously reported in studies of African-American samples. These results improve the understanding of asthma genetics and further demonstrate the utility of genetic studies in populations other than those of largely European ancestry. PMID:23666277

  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. Nest quality limits the number of hole-nesting passerines in their natural cavity-rich habitat

    NASA Astrophysics Data System (ADS)

    Lõhmus, Asko; Remm, Jaanus

    2005-03-01

    We experimentally tested whether the lack of high-quality nest holes may limit the number of secondary cavity-nesters in cavity-rich habitats. We mapped and measured natural tree-holes in 10 mature aspen forests in Estonia. In five experimental plots, we provided nest-boxes on trees having suitable cavities for hole-nesting passerines. This improved the quality of available cavities but retained their total number (due to territoriality, sites in the same tree could not be occupied simultaneously) and location on the landscape. In the next breeding season, the density of hole-nesting passerines increased in experimental plots but remained at the same level in control plots. The increase was due to the species that used boxes: Parus major that preferred these over natural cavities, and Ficedula hypoleuca that used both nest types more opportunistically. We concluded that the quality of cavities can influence the numbers of hole-nesting birds in old cavity-rich forests, also; probably, adaptive habitat selection is the proximate mechanism in this case.

  15. 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

  16. 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.

  17. Saturated fat intake and alcohol consumption modulate the association between the APOE polymorphism and risk of future coronary heart disease: a nested case-control study in the Spanish EPIC cohort.

    PubMed

    Corella, Dolores; Portolés, Olga; Arriola, Larraitz; Chirlaque, María Dolores; Barrricarte, Aurelio; Francés, Francesc; Huerta, José María; Larrañaga, Nerea; Martínez, Carmen; Martinez-Camblor, Pablo; Molina, Esther; Navarro, Carmen; Quirós, Jose R; Rodríguez, Laudina; Sánchez, María José; Ros, Emilio; Sala, Nuria; González, Carlos A; Moreno-Iribas, Concepción

    2011-05-01

    The association is still not clear between the common APOE polymorphism and coronary heart disease (CHD) risk, nor its modulation by diet. Thus, our aim was to study the association between the APOE genotypes and incident CHD and how dietary fat and alcohol consumption modify these effects. We performed a nested case-control study in the Spanish European Prospective Investigation into Cancer and Nutrition cohort. Healthy men and women (41,440, 30-69 years) were followed up over a 10-year period, with the incident CHD cases being identified. We analyzed 534 incident CHD cases and 1123 controls. APOE, dietary intake and plasma lipids were determined at baseline. The APOE polymorphism was significantly associated with low-density lipoprotein cholesterol (LDL-C), and gene-alcohol interactions in determining LDL-C were detected. In the whole population, the E2 allele was significantly associated with a lower CHD risk than E3/E3 subjects [odds ratio (OR), 0.58; 95% confidence interval (CI), 0.38-0.89]. The E4 allele did not reach statistical significance vs. E3/E3 (OR, 1.17; 95% CI, 0.88-1.58). However, saturated fat intake modified the effect of the APOE polymorphism in determining CHD risk. When saturated fat intake was low (<10% of energy), no statistically significant association between the APOE polymorphism and CHD risk was observed (P=.682). However, with higher intake (≥10%), the polymorphism was significant (P=.005), and the differences between E2 and E4 carriers were magnified (OR for E4 vs. E2, 3.33; 95% CI, 1.61-6.90). Alcohol consumption also modified the effect of the APOE on CHD risk. In conclusion, in this Mediterranean population, the E2 allele is associated with lower CHD risk, and this association is modulated by saturated fat and alcohol consumption. Copyright © 2011 Elsevier Inc. All rights reserved.

  18. 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.

  19. 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.

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

    PubMed

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

    2016-08-12

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

  1. Association mapping for drought tolerance in barley at the reproductive stage.

    PubMed

    Abou-Elwafa, Salah Fatouh

    2016-02-01

    Drought is an important abiotic stress causing the major crop losses worldwide. Identification of genomic regions associated with drought-related traits is essential for improving drought tolerance in barley. Association mapping was implemented to investigate the associations between 76 SSR markers and six drought-related traits on a set of 107 barley accessions evaluated under well-watered and drought-stressed conditions. Highly significant differences between well-watered and drought-stressed conditions were observed in all measured traits. A high level of polymorphism with SSR markers was observed. A total of 36 significant marker-trait associations for drought-related traits were detected. A high extent of significant LD (>61%) was observed between markers on different chromosomes, suggesting epistatic interaction. Several molecular markers are significantly associated with more than one phenotypic trait, suggesting the possible presence of pleiotropic or indirect effects. The phenotypic variation, explained by individual marker-trait associations, ranged from 6.33% to 35.78%.

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

    PubMed Central

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

    2013-01-01

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

  3. A hierarchy of associations in hippocampo-cortical systems: cognitive maps and navigation strategies.

    PubMed

    Banquet, J P; Gaussier, Ph; Quoy, M; Revel, A; Burnod, Y

    2005-06-01

    In this letter we describe a hippocampo-cortical model of spatial processing and navigation based on a cascade of increasingly complex associative processes that are also relevant for other hippocampal functions such as episodic memory. Associative learning of different types and the related pattern encoding-recognition take place at three successive levels: (1) an object location level, which computes the landmarks from merged multimodal sensory inputs in the parahippocampal cortices; (2) a subject location level, which computes place fields by combination of local views and movement-related information in the entorhinal cortex; and (3) a spatiotemporal level, which computes place transitions from contiguous place fields in the CA3-CA1 region, which form building blocks for learning temporospatial sequences. At the cell population level, superficial entorhinal place cells encode spatial, context-independent maps as landscapes of activity; populations of transition cells in the CA3-CA1 region encode context-dependent maps as sequences of transitions, which form graphs in prefrontal-parietal cortices. The model was tested on a robot moving in a real environment; these tests produced results that could help to interpret biological data. Two different goal-oriented navigation strategies were displayed depending on the type of map used by the system. Thanks to its multilevel, multimodal integration and behavioral implementation, the model suggests functional interpretations for largely unaccounted structural differences between hippocampo-cortical systems. Further, spatiotemporal information, a common denominator shared by several brain structures, could serve as a cognitive processing frame and a functional link, for example, during spatial navigation and episodic memory, as suggested by the applications of the model to other domains, temporal sequence learning and imitation in particular.

  4. 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.

  5. 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

  6. The mouse QTL map helps interpret human genome-wide association studies for HDL cholesterol.

    PubMed

    Leduc, Magalie S; Lyons, Malcolm; Darvishi, Katayoon; Walsh, Kenneth; Sheehan, Susan; Amend, Sarah; Cox, Allison; Orho-Melander, Marju; Kathiresan, Sekar; Paigen, Beverly; Korstanje, Ron

    2011-06-01

    Genome-wide association (GWA) studies represent a powerful strategy for identifying susceptibility genes for complex diseases in human populations but results must be confirmed and replicated. Because of the close homology between mouse and human genomes, the mouse can be used to add evidence to genes suggested by human studies. We used the mouse quantitative trait loci (QTL) map to interpret results from a GWA study for genes associated with plasma HDL cholesterol levels. We first positioned single nucleotide polymorphisms (SNPs) from a human GWA study on the genomic map for mouse HDL QTL. We then used mouse bioinformatics, sequencing, and expression studies to add evidence for one well-known HDL gene (Abca1) and three newly identified genes (Galnt2, Wwox, and Cdh13), thus supporting the results of the human study. For GWA peaks that occur in human haplotype blocks with multiple genes, we examined the homologous regions in the mouse to prioritize the genes using expression, sequencing, and bioinformatics from the mouse model, showing that some genes were unlikely candidates and adding evidence for candidate genes Mvk and Mmab in one haplotype block and Fads1 and Fads2 in the second haplotype block. Our study highlights the value of mouse genetics for evaluating genes found in human GWA studies.

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

    PubMed

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

    2013-10-23

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