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Sample records for high quality snp

  1. SNP Data Quality Control in a National Beef and Dairy Cattle System and Highly Accurate SNP Based Parentage Verification and Identification

    Directory of Open Access Journals (Sweden)

    Matthew C. McClure

    2018-03-01

    Full Text Available A major use of genetic data is parentage verification and identification as inaccurate pedigrees negatively affect genetic gain. Since 2012 the international standard for single nucleotide polymorphism (SNP verification in Bos taurus cattle has been the ISAG SNP panels. While these ISAG panels provide an increased level of parentage accuracy over microsatellite markers (MS, they can validate the wrong parent at ≤1% misconcordance rate levels, indicating that more SNP are needed if a more accurate pedigree is required. With rapidly increasing numbers of cattle being genotyped in Ireland that represent 61 B. taurus breeds from a wide range of farm types: beef/dairy, AI/pedigree/commercial, purebred/crossbred, and large to small herd size the Irish Cattle Breeding Federation (ICBF analyzed different SNP densities to determine that at a minimum ≥500 SNP are needed to consistently predict only one set of parents at a ≤1% misconcordance rate. For parentage validation and prediction ICBF uses 800 SNP (ICBF800 selected based on SNP clustering quality, ISAG200 inclusion, call rate (CR, and minor allele frequency (MAF in the Irish cattle population. Large datasets require sample and SNP quality control (QC. Most publications only deal with SNP QC via CR, MAF, parent-progeny conflicts, and Hardy-Weinberg deviation, but not sample QC. We report here parentage, SNP QC, and a genomic sample QC pipelines to deal with the unique challenges of >1 million genotypes from a national herd such as SNP genotype errors from mis-tagging of animals, lab errors, farm errors, and multiple other issues that can arise. We divide the pipeline into two parts: a Genotype QC and an Animal QC pipeline. The Genotype QC identifies samples with low call rate, missing or mixed genotype classes (no BB genotype or ABTG alleles present, and low genotype frequencies. The Animal QC handles situations where the genotype might not belong to the listed individual by identifying: >1 non

  2. SAQC: SNP Array Quality Control

    Directory of Open Access Journals (Sweden)

    Li Ling-Hui

    2011-04-01

    Full Text Available Abstract Background Genome-wide single-nucleotide polymorphism (SNP arrays containing hundreds of thousands of SNPs from the human genome have proven useful for studying important human genome questions. Data quality of SNP arrays plays a key role in the accuracy and precision of downstream data analyses. However, good indices for assessing data quality of SNP arrays have not yet been developed. Results We developed new quality indices to measure the quality of SNP arrays and/or DNA samples and investigated their statistical properties. The indices quantify a departure of estimated individual-level allele frequencies (AFs from expected frequencies via standardized distances. The proposed quality indices followed lognormal distributions in several large genomic studies that we empirically evaluated. AF reference data and quality index reference data for different SNP array platforms were established based on samples from various reference populations. Furthermore, a confidence interval method based on the underlying empirical distributions of quality indices was developed to identify poor-quality SNP arrays and/or DNA samples. Analyses of authentic biological data and simulated data show that this new method is sensitive and specific for the detection of poor-quality SNP arrays and/or DNA samples. Conclusions This study introduces new quality indices, establishes references for AFs and quality indices, and develops a detection method for poor-quality SNP arrays and/or DNA samples. We have developed a new computer program that utilizes these methods called SNP Array Quality Control (SAQC. SAQC software is written in R and R-GUI and was developed as a user-friendly tool for the visualization and evaluation of data quality of genome-wide SNP arrays. The program is available online (http://www.stat.sinica.edu.tw/hsinchou/genetics/quality/SAQC.htm.

  3. SNP-PHAGE – High throughput SNP discovery pipeline

    Directory of Open Access Journals (Sweden)

    Cregan Perry B

    2006-10-01

    Full Text Available Abstract Background Single nucleotide polymorphisms (SNPs as defined here are single base sequence changes or short insertion/deletions between or within individuals of a given species. As a result of their abundance and the availability of high throughput analysis technologies SNP markers have begun to replace other traditional markers such as restriction fragment length polymorphisms (RFLPs, amplified fragment length polymorphisms (AFLPs and simple sequence repeats (SSRs or microsatellite markers for fine mapping and association studies in several species. For SNP discovery from chromatogram data, several bioinformatics programs have to be combined to generate an analysis pipeline. Results have to be stored in a relational database to facilitate interrogation through queries or to generate data for further analyses such as determination of linkage disequilibrium and identification of common haplotypes. Although these tasks are routinely performed by several groups, an integrated open source SNP discovery pipeline that can be easily adapted by new groups interested in SNP marker development is currently unavailable. Results We developed SNP-PHAGE (SNP discovery Pipeline with additional features for identification of common haplotypes within a sequence tagged site (Haplotype Analysis and GenBank (-dbSNP submissions. This tool was applied for analyzing sequence traces from diverse soybean genotypes to discover over 10,000 SNPs. This package was developed on UNIX/Linux platform, written in Perl and uses a MySQL database. Scripts to generate a user-friendly web interface are also provided with common queries for preliminary data analysis. A machine learning tool developed by this group for increasing the efficiency of SNP discovery is integrated as a part of this package as an optional feature. The SNP-PHAGE package is being made available open source at http://bfgl.anri.barc.usda.gov/ML/snp-phage/. Conclusion SNP-PHAGE provides a bioinformatics

  4. Development and Applications of a High Throughput Genotyping Tool for Polyploid Crops: Single Nucleotide Polymorphism (SNP Array

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    Qian You

    2018-02-01

    Full Text Available Polypoid species play significant roles in agriculture and food production. Many crop species are polyploid, such as potato, wheat, strawberry, and sugarcane. Genotyping has been a daunting task for genetic studies of polyploid crops, which lags far behind the diploid crop species. Single nucleotide polymorphism (SNP array is considered to be one of, high-throughput, relatively cost-efficient and automated genotyping approaches. However, there are significant challenges for SNP identification in complex, polyploid genomes, which has seriously slowed SNP discovery and array development in polyploid species. Ploidy is a significant factor impacting SNP qualities and validation rates of SNP markers in SNP arrays, which has been proven to be a very important tool for genetic studies and molecular breeding. In this review, we (1 discussed the pros and cons of SNP array in general for high throughput genotyping, (2 presented the challenges of and solutions to SNP calling in polyploid species, (3 summarized the SNP selection criteria and considerations of SNP array design for polyploid species, (4 illustrated SNP array applications in several different polyploid crop species, then (5 discussed challenges, available software, and their accuracy comparisons for genotype calling based on SNP array data in polyploids, and finally (6 provided a series of SNP array design and genotype calling recommendations. This review presents a complete overview of SNP array development and applications in polypoid crops, which will benefit the research in molecular breeding and genetics of crops with complex genomes.

  5. A Whole Genome Association Study on Meat Quality Traits Using High Density SNP Chips in a Cross between Korean Native Pig and Landrace

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    K.-T Lee

    2012-11-01

    Full Text Available A whole genome association (WGA study was performed to detect significant polymorphisms for meat quality traits in an F2 cross population (N = 478 that were generated with Korean native pig sires and Landrace dams in National Livestock Research Institute, Songwhan, Korea. The animals were genotyped using Illumina porcine 60k SNP beadchips, in which a set of 46,865 SNPs were available for the WGA analyses on ten carcass quality traits; live weight, crude protein, crude lipids, crude ash, water holding capacity, drip loss, shear force, CIE L, CIE a and CIE b. Phenotypes were regressed on additive and dominance effects for each SNP using a simple linear regression model, after adjusting for sex, sire and slaughter stage as fixed effects. With the significant SNPs for each trait (p<0.001, a stepwise regression procedure was applied to determine the best set of SNPs with the additive and/or dominance effects. A total of 106 SNPs, or quantitative trait loci (QTL were detected, and about 32 to 66% of the total phenotypic variation was explained by the significant SNPs for each trait. The QTL were identified in most porcine chromosomes (SSCs, in which majority of the QTL were detected in SSCs 1, 2, 12, 13, 14 and 16. Several QTL clusters were identified on SSCs 12, 16 and 17, and a cluster of QTL influencing crude protein, crude lipid, drip loss, shear force, CIE a and CIE b were located between 20 and 29 Mb of SSC12. A pleiotropic QTL for drip loss, CIE L and CIE b was also detected on SSC16. These QTL need to be validated in commercial pig populations for genetic improvement in meat quality via marker-assisted selection.

  6. New generation pharmacogenomic tools: a SNP linkage disequilibrium Map, validated SNP assay resource, and high-throughput instrumentation system for large-scale genetic studies.

    Science.gov (United States)

    De La Vega, Francisco M; Dailey, David; Ziegle, Janet; Williams, Julie; Madden, Dawn; Gilbert, Dennis A

    2002-06-01

    Since public and private efforts announced the first draft of the human genome last year, researchers have reported great numbers of single nucleotide polymorphisms (SNPs). We believe that the availability of well-mapped, quality SNP markers constitutes the gateway to a revolution in genetics and personalized medicine that will lead to better diagnosis and treatment of common complex disorders. A new generation of tools and public SNP resources for pharmacogenomic and genetic studies--specifically for candidate-gene, candidate-region, and whole-genome association studies--will form part of the new scientific landscape. This will only be possible through the greater accessibility of SNP resources and superior high-throughput instrumentation-assay systems that enable affordable, highly productive large-scale genetic studies. We are contributing to this effort by developing a high-quality linkage disequilibrium SNP marker map and an accompanying set of ready-to-use, validated SNP assays across every gene in the human genome. This effort incorporates both the public sequence and SNP data sources, and Celera Genomics' human genome assembly and enormous resource ofphysically mapped SNPs (approximately 4,000,000 unique records). This article discusses our approach and methodology for designing the map, choosing quality SNPs, designing and validating these assays, and obtaining population frequency ofthe polymorphisms. We also discuss an advanced, high-performance SNP assay chemisty--a new generation of the TaqMan probe-based, 5' nuclease assay-and high-throughput instrumentation-software system for large-scale genotyping. We provide the new SNP map and validation information, validated SNP assays and reagents, and instrumentation systems as a novel resource for genetic discoveries.

  7. Development of maizeSNP3072, a high-throughput compatible SNP array, for DNA fingerprinting identification of Chinese maize varieties.

    Science.gov (United States)

    Tian, Hong-Li; Wang, Feng-Ge; Zhao, Jiu-Ran; Yi, Hong-Mei; Wang, Lu; Wang, Rui; Yang, Yang; Song, Wei

    2015-01-01

    Single nucleotide polymorphisms (SNPs) are abundant and evenly distributed throughout the maize ( Zea mays L.) genome. SNPs have several advantages over simple sequence repeats, such as ease of data comparison and integration, high-throughput processing of loci, and identification of associated phenotypes. SNPs are thus ideal for DNA fingerprinting, genetic diversity analysis, and marker-assisted breeding. Here, we developed a high-throughput and compatible SNP array, maizeSNP3072, containing 3072 SNPs developed from the maizeSNP50 array. To improve genotyping efficiency, a high-quality cluster file, maizeSNP3072_GT.egt, was constructed. All 3072 SNP loci were localized within different genes, where they were distributed in exons (43 %), promoters (21 %), 3' untranslated regions (UTRs; 22 %), 5' UTRs (9 %), and introns (5 %). The average genotyping failure rate using these SNPs was only 6 %, or 3 % using the cluster file to call genotypes. The genotype consistency of repeat sample analysis on Illumina GoldenGate versus Infinium platforms exceeded 96.4 %. The minor allele frequency (MAF) of the SNPs averaged 0.37 based on data from 309 inbred lines. The 3072 SNPs were highly effective for distinguishing among 276 examined hybrids. Comparative analysis using Chinese varieties revealed that the 3072SNP array showed a better marker success rate and higher average MAF values, evaluation scores, and variety-distinguishing efficiency than the maizeSNP50K array. The maizeSNP3072 array thus can be successfully used in DNA fingerprinting identification of Chinese maize varieties and shows potential as a useful tool for germplasm resource evaluation and molecular marker-assisted breeding.

  8. Application of high resolution SNP arrays in patients with congenital ...

    Indian Academy of Sciences (India)

    clinical experience in implementing whole-genome high-resolution SNP arrays to investigate 33 patients with syndromic and .... Online Mendelian Inheritance in Man database (OMIM, ..... of damaged mitochondria through either autophagy or mito- ..... malformations: associations with maternal and infant character- istics in a ...

  9. SNP calling using genotype model selection on high-throughput sequencing data

    KAUST Repository

    You, Na

    2012-01-16

    Motivation: A review of the available single nucleotide polymorphism (SNP) calling procedures for Illumina high-throughput sequencing (HTS) platform data reveals that most rely mainly on base-calling and mapping qualities as sources of error when calling SNPs. Thus, errors not involved in base-calling or alignment, such as those in genomic sample preparation, are not accounted for.Results: A novel method of consensus and SNP calling, Genotype Model Selection (GeMS), is given which accounts for the errors that occur during the preparation of the genomic sample. Simulations and real data analyses indicate that GeMS has the best performance balance of sensitivity and positive predictive value among the tested SNP callers. © The Author 2012. Published by Oxford University Press. All rights reserved.

  10. Heap: a highly sensitive and accurate SNP detection tool for low-coverage high-throughput sequencing data

    KAUST Repository

    Kobayashi, Masaaki; Ohyanagi, Hajime; Takanashi, Hideki; Asano, Satomi; Kudo, Toru; Kajiya-Kanegae, Hiromi; Nagano, Atsushi J.; Tainaka, Hitoshi; Tokunaga, Tsuyoshi; Sazuka, Takashi; Iwata, Hiroyoshi; Tsutsumi, Nobuhiro; Yano, Kentaro

    2017-01-01

    and GP depends on not only their mathematical models, but the quality and quantity of variants employed in the analysis. In NGS single nucleotide polymorphism (SNP) calling, conventional tools ideally require more reads for higher SNP sensitivity

  11. High-throughput SNP genotyping in the highly heterozygous genome of Eucalyptus: assay success, polymorphism and transferability across species

    Science.gov (United States)

    2011-01-01

    Background High-throughput SNP genotyping has become an essential requirement for molecular breeding and population genomics studies in plant species. Large scale SNP developments have been reported for several mainstream crops. A growing interest now exists to expand the speed and resolution of genetic analysis to outbred species with highly heterozygous genomes. When nucleotide diversity is high, a refined diagnosis of the target SNP sequence context is needed to convert queried SNPs into high-quality genotypes using the Golden Gate Genotyping Technology (GGGT). This issue becomes exacerbated when attempting to transfer SNPs across species, a scarcely explored topic in plants, and likely to become significant for population genomics and inter specific breeding applications in less domesticated and less funded plant genera. Results We have successfully developed the first set of 768 SNPs assayed by the GGGT for the highly heterozygous genome of Eucalyptus from a mixed Sanger/454 database with 1,164,695 ESTs and the preliminary 4.5X draft genome sequence for E. grandis. A systematic assessment of in silico SNP filtering requirements showed that stringent constraints on the SNP surrounding sequences have a significant impact on SNP genotyping performance and polymorphism. SNP assay success was high for the 288 SNPs selected with more rigorous in silico constraints; 93% of them provided high quality genotype calls and 71% of them were polymorphic in a diverse panel of 96 individuals of five different species. SNP reliability was high across nine Eucalyptus species belonging to three sections within subgenus Symphomyrtus and still satisfactory across species of two additional subgenera, although polymorphism declined as phylogenetic distance increased. Conclusions This study indicates that the GGGT performs well both within and across species of Eucalyptus notwithstanding its nucleotide diversity ≥2%. The development of a much larger array of informative SNPs across

  12. Development and characterization of a high density SNP genotyping assay for cattle.

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    Lakshmi K Matukumalli

    Full Text Available The success of genome-wide association (GWA studies for the detection of sequence variation affecting complex traits in human has spurred interest in the use of large-scale high-density single nucleotide polymorphism (SNP genotyping for the identification of quantitative trait loci (QTL and for marker-assisted selection in model and agricultural species. A cost-effective and efficient approach for the development of a custom genotyping assay interrogating 54,001 SNP loci to support GWA applications in cattle is described. A novel algorithm for achieving a compressed inter-marker interval distribution proved remarkably successful, with median interval of 37 kb and maximum predicted gap of <350 kb. The assay was tested on a panel of 576 animals from 21 cattle breeds and six outgroup species and revealed that from 39,765 to 46,492 SNP are polymorphic within individual breeds (average minor allele frequency (MAF ranging from 0.24 to 0.27. The assay also identified 79 putative copy number variants in cattle. Utility for GWA was demonstrated by localizing known variation for coat color and the presence/absence of horns to their correct genomic locations. The combination of SNP selection and the novel spacing algorithm allows an efficient approach for the development of high-density genotyping platforms in species having full or even moderate quality draft sequence. Aspects of the approach can be exploited in species which lack an available genome sequence. The BovineSNP50 assay described here is commercially available from Illumina and provides a robust platform for mapping disease genes and QTL in cattle.

  13. SNP Discovery and Development of a High-Density Genotyping Array for Sunflower

    Science.gov (United States)

    Bachlava, Eleni; Taylor, Christopher A.; Tang, Shunxue; Bowers, John E.; Mandel, Jennifer R.; Burke, John M.; Knapp, Steven J.

    2012-01-01

    Recent advances in next-generation DNA sequencing technologies have made possible the development of high-throughput SNP genotyping platforms that allow for the simultaneous interrogation of thousands of single-nucleotide polymorphisms (SNPs). Such resources have the potential to facilitate the rapid development of high-density genetic maps, and to enable genome-wide association studies as well as molecular breeding approaches in a variety of taxa. Herein, we describe the development of a SNP genotyping resource for use in sunflower (Helianthus annuus L.). This work involved the development of a reference transcriptome assembly for sunflower, the discovery of thousands of high quality SNPs based on the generation and analysis of ca. 6 Gb of transcriptome re-sequencing data derived from multiple genotypes, the selection of 10,640 SNPs for inclusion in the genotyping array, and the use of the resulting array to screen a diverse panel of sunflower accessions as well as related wild species. The results of this work revealed a high frequency of polymorphic SNPs and relatively high level of cross-species transferability. Indeed, greater than 95% of successful SNP assays revealed polymorphism, and more than 90% of these assays could be successfully transferred to related wild species. Analysis of the polymorphism data revealed patterns of genetic differentiation that were largely congruent with the evolutionary history of sunflower, though the large number of markers allowed for finer resolution than has previously been possible. PMID:22238659

  14. Application of high resolution SNP arrays in patients with congenital ...

    Indian Academy of Sciences (India)

    TING-YING LEI

    lent oligonucleotide-based array-CGH to determine the exact breakpoints in 14 patients with partial deletions of chromo- some 13q21.1-qter. They were able to refine the smallest deletion region linked to cleft lip/palate (13q31.3–13q33.1). Except for the arrays that measure DNA copy number differ- ences only, SNP arrays, ...

  15. Combining target enrichment with barcode multiplexing for high throughput SNP discovery

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    Lunke Sebastian

    2010-11-01

    Full Text Available Abstract Background The primary goal of genetic linkage analysis is to identify genes affecting a phenotypic trait. After localisation of the linkage region, efficient genetic dissection of the disease linked loci requires that functional variants are identified across the loci. These functional variations are difficult to detect due to extent of genetic diversity and, to date, incomplete cataloguing of the large number of variants present both within and between populations. Massively parallel sequencing platforms offer unprecedented capacity for variant discovery, however the number of samples analysed are still limited by cost per sample. Some progress has been made in reducing the cost of resequencing using either multiplexing methodologies or through the utilisation of targeted enrichment technologies which provide the ability to resequence genomic areas of interest rather that full genome sequencing. Results We developed a method that combines current multiplexing methodologies with a solution-based target enrichment method to further reduce the cost of resequencing where region-specific sequencing is required. Our multiplex/enrichment strategy produced high quality data with nominal reduction of sequencing depth. We undertook a genotyping study and were successful in the discovery of novel SNP alleles in all samples at uniplex, duplex and pentaplex levels. Conclusion Our work describes the successful combination of a targeted enrichment method and index barcode multiplexing to reduce costs, time and labour associated with processing large sample sets. Furthermore, we have shown that the sequencing depth obtained is adequate for credible SNP genotyping analysis at uniplex, duplex and pentaplex levels.

  16. Casein SNP in Norwegian goats: additive and dominance effects on milk composition and quality

    Science.gov (United States)

    2011-01-01

    Background The four casein proteins in goat milk are encoded by four closely linked casein loci (CSN1S1, CSN2, CSN1S2 and CSN3) within 250 kb on caprine chromosome 6. A deletion in exon 12 of CSN1S1, so far reported only in Norwegian goats, has been found at high frequency (0.73). Such a high frequency is difficult to explain because the national breeding goal selects against the variant's effect. Methods In this study, 575 goats were genotyped for 38 Single Nucleotide Polymorphisms (SNP) located within the four casein genes. Milk production records of these goats were obtained from the Norwegian Dairy Goat Control. Test-day mixed models with additive and dominance fixed effects of single SNP were fitted in a model including polygenic effects. Results Significant additive effects of single SNP within CSN1S1 and CSN3 were found for fat % and protein %, milk yield and milk taste. The allele with the deletion showed additive and dominance effects on protein % and fat %, and overdominance effects on milk quantity (kg) and lactose %. At its current frequency, the observed dominance (overdominance) effects of the deletion allele reduced its substitution effect (and additive genetic variance available for selection) in the population substantially. Conclusions The selection pressure of conventional breeding on the allele with the deletion is limited due to the observed dominance (overdominance) effects. Inclusion of molecular information in the national breeding scheme will reduce the frequency of this deletion in the population. PMID:21864407

  17. A high-density SNP map for accurate mapping of seed fibre QTL in Brassica napus L.

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    Liezhao Liu

    Full Text Available A high density genetic linkage map for the complex allotetraploid crop species Brassica napus (oilseed rape was constructed in a late-generation recombinant inbred line (RIL population, using genome-wide single nucleotide polymorphism (SNP markers assayed by the Brassica 60 K Infinium BeadChip Array. The linkage map contains 9164 SNP markers covering 1832.9 cM. 1232 bins account for 7648 of the markers. A subset of 2795 SNP markers, with an average distance of 0.66 cM between adjacent markers, was applied for QTL mapping of seed colour and the cell wall fiber components acid detergent lignin (ADL, cellulose and hemicellulose. After phenotypic analyses across four different environments a total of 11 QTL were detected for seed colour and fiber traits. The high-density map considerably improved QTL resolution compared to the previous low-density maps. A previously identified major QTL with very high effects on seed colour and ADL was pinpointed to a narrow genome interval on chromosome A09, while a minor QTL explaining 8.1% to 14.1% of variation for ADL was detected on chromosome C05. Five and three QTL accounting for 4.7% to 21.9% and 7.3% to 16.9% of the phenotypic variation for cellulose and hemicellulose, respectively, were also detected. To our knowledge this is the first description of QTL for seed cellulose and hemicellulose in B. napus, representing interesting new targets for improving oil content. The high density SNP genetic map enables navigation from interesting B. napus QTL to Brassica genome sequences, giving useful new information for understanding the genetics of key seed quality traits in rapeseed.

  18. Highly effective SNP-based association mapping and management of recessive defects in livestock

    DEFF Research Database (Denmark)

    Charlier, Carole; Coppieters, Wouter; Rollin, Frédéric

    2008-01-01

    The widespread use of elite sires by means of artificial insemination in livestock breeding leads to the frequent emergence of recessive genetic defects, which cause significant economic and animal welfare concerns. Here we show that the availability of genome-wide, high-density SNP panels, combi...

  19. SNP discovery and High Resolution Melting Analysis from massive transcriptome sequencing in the California red abalone Haliotis rufescens.

    Science.gov (United States)

    Valenzuela-Muñoz, Valentina; Araya-Garay, José Miguel; Gallardo-Escárate, Cristian

    2013-06-01

    The California red abalone, Haliotis rufescens that belongs to the Haliotidae family, is the largest species of abalone in the world that has sustained the major fishery and aquaculture production in the USA and Mexico. This native mollusk has not been evaluated or assigned a conservation category even though in the last few decades it was heavily exploited until it disappeared in some areas along the California coast. In Chile, the red abalone was introduced in the 1970s from California wild abalone stocks for the purposes of aquaculture. Considering the number of years that the red abalone has been cultivated in Chile crucial genetic information is scarce and critical issues remain unresolved. This study reports and validates novel single nucleotide polymorphisms (SNP) markers for the red abalone H. rufescens using cDNA pyrosequencing. A total of 622 high quality SNPs were identified in 146 sequences with an estimated frequency of 1 SNP each 1000bp. Forty-five SNPs markers with functional information for gene ontology were selected. Of these, 8 were polymorphic among the individuals screened: Heat shock protein 70 (HSP70), vitellogenin (VTG), lysin, alginate lyase enzyme (AL), Glucose-regulated protein 94 (GRP94), fructose-bisphosphate aldolase (FBA), sulfatase 1A precursor (S1AP) and ornithine decarboxylase antizyme (ODC). Two additional sequences were also identified with polymorphisms but no similarities with known proteins were achieved. To validate the putative SNP markers, High Resolution Melting Analysis (HRMA) was conducted in a wild and hatchery-bred population. Additionally, SNP cross-amplifications were tested in two further native abalone species, Haliotis fulgens and Haliotis corrugata. This study provides novel candidate genes that could be used to evaluate loss of genetic diversity due to hatchery selection or inbreeding effects. Copyright © 2013 Elsevier B.V. All rights reserved.

  20. A procedure for the detection of linkage with high density SNP arrays in a large pedigree with colorectal cancer

    International Nuclear Information System (INIS)

    Middeldorp, Anneke; Wijnen, Juul T; Wezel, Tom van; Jagmohan-Changur, Shantie; Helmer, Quinta; Klift, Heleen M van der; Tops, Carli MJ; Vasen, Hans FA; Devilee, Peter; Morreau, Hans; Houwing-Duistermaat, Jeanine J

    2007-01-01

    The apparent dominant model of colorectal cancer (CRC) inheritance in several large families, without mutations in known CRC susceptibility genes, suggests the presence of so far unidentified genes with strong or moderate effect on the development of CRC. Linkage analysis could lead to identification of susceptibility genes in such families. In comparison to classical linkage analysis with multi-allelic markers, single nucleotide polymorphism (SNP) arrays have increased information content and can be processed with higher throughput. Therefore, SNP arrays can be excellent tools for linkage analysis. However, the vast number of SNPs on the SNP arrays, combined with large informative pedigrees (e.g. >35–40 bits), presents us with a computational complexity that is challenging for existing statistical packages or even exceeds their capacity. We therefore setup a procedure for linkage analysis in large pedigrees and validated the method by genotyping using SNP arrays of a colorectal cancer family with a known MLH1 germ line mutation. Quality control of the genotype data was performed in Alohomora, Mega2 and SimWalk2, with removal of uninformative SNPs, Mendelian inconsistencies and Mendelian consistent errors, respectively. Linkage disequilibrium was measured by SNPLINK and Merlin. Parametric linkage analysis using two flanking markers was performed using MENDEL. For multipoint parametric linkage analysis and haplotype analysis, SimWalk2 was used. On chromosome 3, in the MLH1-region, a LOD score of 1.9 was found by parametric linkage analysis using two flanking markers. On chromosome 11 a small region with LOD 1.1 was also detected. Upon linkage disequilibrium removal, multipoint linkage analysis yielded a LOD score of 2.1 in the MLH1 region, whereas the LOD score dropped to negative values in the region on chromosome 11. Subsequent haplotype analysis in the MLH1 region perfectly matched the mutation status of the family members. We developed a workflow for linkage

  1. SNP high-throughput screening in grapevine using the SNPlex™ genotyping system

    Directory of Open Access Journals (Sweden)

    Velasco Riccardo

    2008-01-01

    Full Text Available Abstract Background Until recently, only a small number of low- and mid-throughput methods have been used for single nucleotide polymorphism (SNP discovery and genotyping in grapevine (Vitis vinifera L.. However, following completion of the sequence of the highly heterozygous genome of Pinot Noir, it has been possible to identify millions of electronic SNPs (eSNPs thus providing a valuable source for high-throughput genotyping methods. Results Herein we report the first application of the SNPlex™ genotyping system in grapevine aiming at the anchoring of an eukaryotic genome. This approach combines robust SNP detection with automated assay readout and data analysis. 813 candidate eSNPs were developed from non-repetitive contigs of the assembled genome of Pinot Noir and tested in 90 progeny of Syrah × Pinot Noir cross. 563 new SNP-based markers were obtained and mapped. The efficiency rate of 69% was enhanced to 80% when multiple displacement amplification (MDA methods were used for preparation of genomic DNA for the SNPlex assay. Conclusion Unlike other SNP genotyping methods used to investigate thousands of SNPs in a few genotypes, or a few SNPs in around a thousand genotypes, the SNPlex genotyping system represents a good compromise to investigate several hundred SNPs in a hundred or more samples simultaneously. Therefore, the use of the SNPlex assay, coupled with whole genome amplification (WGA, is a good solution for future applications in well-equipped laboratories.

  2. Detecting selection signatures between Duroc and Duroc synthetic pig populations using high-density SNP chip.

    Science.gov (United States)

    Edea, Z; Hong, J-K; Jung, J-H; Kim, D-W; Kim, Y-M; Kim, E-S; Shin, S S; Jung, Y C; Kim, K-S

    2017-08-01

    The development of high throughput genotyping techniques has facilitated the identification of selection signatures of pigs. The detection of genomic selection signals in a population subjected to differential selection pressures may provide insights into the genes associated with economically and biologically important traits. To identify genomic regions under selection, we genotyped 488 Duroc (D) pigs and 155 D × Korean native pigs (DKNPs) using the Porcine SNP70K BeadChip. By applying the F ST and extended haplotype homozygosity (EHH-Rsb) methods, we detected genes under directional selection associated with growth/stature (DOCK7, PLCB4, HS2ST1, FBP2 and TG), carcass and meat quality (TG, COL14A1, FBXO5, NR3C1, SNX7, ARHGAP26 and DPYD), number of teats (LOC100153159 and LRRC1), pigmentation (MME) and ear morphology (SOX5), which are all mostly near or at fixation. These results could be a basis for investigating the underlying mutations associated with observed phenotypic variation. Validation using genome-wide association analysis would also facilitate the inclusion of some of these markers in genetic evaluation programs. © 2017 Stichting International Foundation for Animal Genetics.

  3. Development and validation of a high density SNP genotyping array for Atlantic salmon (Salmo salar)

    Science.gov (United States)

    2014-01-01

    Background Dense single nucleotide polymorphism (SNP) genotyping arrays provide extensive information on polymorphic variation across the genome of species of interest. Such information can be used in studies of the genetic architecture of quantitative traits and to improve the accuracy of selection in breeding programs. In Atlantic salmon (Salmo salar), these goals are currently hampered by the lack of a high-density SNP genotyping platform. Therefore, the aim of the study was to develop and test a dense Atlantic salmon SNP array. Results SNP discovery was performed using extensive deep sequencing of Reduced Representation (RR-Seq), Restriction site-Associated DNA (RAD-Seq) and mRNA (RNA-Seq) libraries derived from farmed and wild Atlantic salmon samples (n = 283) resulting in the discovery of > 400 K putative SNPs. An Affymetrix Axiom® myDesign Custom Array was created and tested on samples of animals of wild and farmed origin (n = 96) revealing a total of 132,033 polymorphic SNPs with high call rate, good cluster separation on the array and stable Mendelian inheritance in our sample. At least 38% of these SNPs are from transcribed genomic regions and therefore more likely to include functional variants. Linkage analysis utilising the lack of male recombination in salmonids allowed the mapping of 40,214 SNPs distributed across all 29 pairs of chromosomes, highlighting the extensive genome-wide coverage of the SNPs. An identity-by-state clustering analysis revealed that the array can clearly distinguish between fish of different origins, within and between farmed and wild populations. Finally, Y-chromosome-specific probes included on the array provide an accurate molecular genetic test for sex. Conclusions This manuscript describes the first high-density SNP genotyping array for Atlantic salmon. This array will be publicly available and is likely to be used as a platform for high-resolution genetics research into traits of evolutionary and economic importance in

  4. High-resolution SNP array analysis of patients with developmental disorder and normal array CGH results

    Directory of Open Access Journals (Sweden)

    Siggberg Linda

    2012-09-01

    Full Text Available Abstract Background Diagnostic analysis of patients with developmental disorders has improved over recent years largely due to the use of microarray technology. Array methods that facilitate copy number analysis have enabled the diagnosis of up to 20% more patients with previously normal karyotyping results. A substantial number of patients remain undiagnosed, however. Methods and Results Using the Genome-Wide Human SNP array 6.0, we analyzed 35 patients with a developmental disorder of unknown cause and normal array comparative genomic hybridization (array CGH results, in order to characterize previously undefined genomic aberrations. We detected no seemingly pathogenic copy number aberrations. Most of the vast amount of data produced by the array was polymorphic and non-informative. Filtering of this data, based on copy number variant (CNV population frequencies as well as phenotypically relevant genes, enabled pinpointing regions of allelic homozygosity that included candidate genes correlating to the phenotypic features in four patients, but results could not be confirmed. Conclusions In this study, the use of an ultra high-resolution SNP array did not contribute to further diagnose patients with developmental disorders of unknown cause. The statistical power of these results is limited by the small size of the patient cohort, and interpretation of these negative results can only be applied to the patients studied here. We present the results of our study and the recurrence of clustered allelic homozygosity present in this material, as detected by the SNP 6.0 array.

  5. Model SNP development for complex genomes based on hexaploid oat using high-throughput 454 sequencing technology

    Directory of Open Access Journals (Sweden)

    Chao Shiaoman

    2011-01-01

    Full Text Available Abstract Background Genetic markers are pivotal to modern genomics research; however, discovery and genotyping of molecular markers in oat has been hindered by the size and complexity of the genome, and by a scarcity of sequence data. The purpose of this study was to generate oat expressed sequence tag (EST information, develop a bioinformatics pipeline for SNP discovery, and establish a method for rapid, cost-effective, and straightforward genotyping of SNP markers in complex polyploid genomes such as oat. Results Based on cDNA libraries of four cultivated oat genotypes, approximately 127,000 contigs were assembled from approximately one million Roche 454 sequence reads. Contigs were filtered through a novel bioinformatics pipeline to eliminate ambiguous polymorphism caused by subgenome homology, and 96 in silico SNPs were selected from 9,448 candidate loci for validation using high-resolution melting (HRM analysis. Of these, 52 (54% were polymorphic between parents of the Ogle1040 × TAM O-301 (OT mapping population, with 48 segregating as single Mendelian loci, and 44 being placed on the existing OT linkage map. Ogle and TAM amplicons from 12 primers were sequenced for SNP validation, revealing complex polymorphism in seven amplicons but general sequence conservation within SNP loci. Whole-amplicon interrogation with HRM revealed insertions, deletions, and heterozygotes in secondary oat germplasm pools, generating multiple alleles at some primer targets. To validate marker utility, 36 SNP assays were used to evaluate the genetic diversity of 34 diverse oat genotypes. Dendrogram clusters corresponded generally to known genome composition and genetic ancestry. Conclusions The high-throughput SNP discovery pipeline presented here is a rapid and effective method for identification of polymorphic SNP alleles in the oat genome. The current-generation HRM system is a simple and highly-informative platform for SNP genotyping. These techniques provide

  6. High-density SNP assay development for genetic analysis in maritime pine (Pinus pinaster).

    Science.gov (United States)

    Plomion, C; Bartholomé, J; Lesur, I; Boury, C; Rodríguez-Quilón, I; Lagraulet, H; Ehrenmann, F; Bouffier, L; Gion, J M; Grivet, D; de Miguel, M; de María, N; Cervera, M T; Bagnoli, F; Isik, F; Vendramin, G G; González-Martínez, S C

    2016-03-01

    Maritime pine provides essential ecosystem services in the south-western Mediterranean basin, where it covers around 4 million ha. Its scattered distribution over a range of environmental conditions makes it an ideal forest tree species for studies of local adaptation and evolutionary responses to climatic change. Highly multiplexed single nucleotide polymorphism (SNP) genotyping arrays are increasingly used to study genetic variation in living organisms and for practical applications in plant and animal breeding and genetic resource conservation. We developed a 9k Illumina Infinium SNP array and genotyped maritime pine trees from (i) a three-generation inbred (F2) pedigree, (ii) the French breeding population and (iii) natural populations from Portugal and the French Atlantic coast. A large proportion of the exploitable SNPs (2052/8410, i.e. 24.4%) segregated in the mapping population and could be mapped, providing the densest ever gene-based linkage map for this species. Based on 5016 SNPs, natural and breeding populations from the French gene pool exhibited similar level of genetic diversity. Population genetics and structure analyses based on 3981 SNP markers common to the Portuguese and French gene pools revealed high levels of differentiation, leading to the identification of a set of highly differentiated SNPs that could be used for seed provenance certification. Finally, we discuss how the validated SNPs could facilitate the identification of ecologically and economically relevant genes in this species, improving our understanding of the demography and selective forces shaping its natural genetic diversity, and providing support for new breeding strategies. © 2015 John Wiley & Sons Ltd.

  7. Construction and evaluation of a high-density SNP array for the Pacific oyster (Crassostrea gigas.

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    Haigang Qi

    Full Text Available Single nucleotide polymorphisms (SNPs are widely used in genetics and genomics research. The Pacific oyster (Crassostrea gigas is an economically and ecologically important marine bivalve, and it possesses one of the highest levels of genomic DNA variation among animal species. Pacific oyster SNPs have been extensively investigated; however, the mechanisms by which these SNPs may be used in a high-throughput, transferable, and economical manner remain to be elucidated. Here, we constructed an oyster 190K SNP array using Affymetrix Axiom genotyping technology. We designed 190,420 SNPs on the chip; these SNPs were selected from 54 million SNPs identified through re-sequencing of 472 Pacific oysters collected in China, Japan, Korea, and Canada. Our genotyping results indicated that 133,984 (70.4% SNPs were polymorphic and successfully converted on the chip. The SNPs were distributed evenly throughout the oyster genome, located in 3,595 scaffolds with a length of ~509.4 million; the average interval spacing was 4,210 bp. In addition, 111,158 SNPs were distributed in 21,050 coding genes, with an average of 5.3 SNPs per gene. In comparison with genotypes obtained through re-sequencing, ~69% of the converted SNPs had a concordance rate of >0.971; the mean concordance rate was 0.966. Evaluation based on genotypes of full-sib family individuals revealed that the average genotyping accuracy rate was 0.975. Carrying 133 K polymorphic SNPs, our oyster 190K SNP array is the first commercially available high-density SNP chip for mollusks, with the highest throughput. It represents a valuable tool for oyster genome-wide association studies, fine linkage mapping, and population genetics.

  8. Development and evaluation of the first high-throughput SNP array for common carp (Cyprinus carpio).

    Science.gov (United States)

    Xu, Jian; Zhao, Zixia; Zhang, Xiaofeng; Zheng, Xianhu; Li, Jiongtang; Jiang, Yanliang; Kuang, Youyi; Zhang, Yan; Feng, Jianxin; Li, Chuangju; Yu, Juhua; Li, Qiang; Zhu, Yuanyuan; Liu, Yuanyuan; Xu, Peng; Sun, Xiaowen

    2014-04-24

    A large number of single nucleotide polymorphisms (SNPs) have been identified in common carp (Cyprinus carpio) but, as yet, no high-throughput genotyping platform is available for this species. C. carpio is an important aquaculture species that accounts for nearly 14% of freshwater aquaculture production worldwide. We have developed an array for C. carpio with 250,000 SNPs and evaluated its performance using samples from various strains of C. carpio. The SNPs used on the array were selected from two resources: the transcribed sequences from RNA-seq data of four strains of C. carpio, and the genome re-sequencing data of five strains of C. carpio. The 250,000 SNPs on the resulting array are distributed evenly across the reference C.carpio genome with an average spacing of 6.6 kb. To evaluate the SNP array, 1,072 C. carpio samples were collected and tested. Of the 250,000 SNPs on the array, 185,150 (74.06%) were found to be polymorphic sites. Genotyping accuracy was checked using genotyping data from a group of full-siblings and their parents, and over 99.8% of the qualified SNPs were found to be reliable. Analysis of the linkage disequilibrium on all samples and on three domestic C.carpio strains revealed that the latter had the longer haplotype blocks. We also evaluated our SNP array on 80 samples from eight species related to C. carpio, with from 53,526 to 71,984 polymorphic SNPs. An identity by state analysis divided all the samples into three clusters; most of the C. carpio strains formed the largest cluster. The Carp SNP array described here is the first high-throughput genotyping platform for C. carpio. Our evaluation of this array indicates that it will be valuable for farmed carp and for genetic and population biology studies in C. carpio and related species.

  9. mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications.

    Science.gov (United States)

    Hach, Faraz; Sarrafi, Iman; Hormozdiari, Farhad; Alkan, Can; Eichler, Evan E; Sahinalp, S Cenk

    2014-07-01

    High throughput sequencing (HTS) platforms generate unprecedented amounts of data that introduce challenges for processing and downstream analysis. While tools that report the 'best' mapping location of each read provide a fast way to process HTS data, they are not suitable for many types of downstream analysis such as structural variation detection, where it is important to report multiple mapping loci for each read. For this purpose we introduce mrsFAST-Ultra, a fast, cache oblivious, SNP-aware aligner that can handle the multi-mapping of HTS reads very efficiently. mrsFAST-Ultra improves mrsFAST, our first cache oblivious read aligner capable of handling multi-mapping reads, through new and compact index structures that reduce not only the overall memory usage but also the number of CPU operations per alignment. In fact the size of the index generated by mrsFAST-Ultra is 10 times smaller than that of mrsFAST. As importantly, mrsFAST-Ultra introduces new features such as being able to (i) obtain the best mapping loci for each read, and (ii) return all reads that have at most n mapping loci (within an error threshold), together with these loci, for any user specified n. Furthermore, mrsFAST-Ultra is SNP-aware, i.e. it can map reads to reference genome while discounting the mismatches that occur at common SNP locations provided by db-SNP; this significantly increases the number of reads that can be mapped to the reference genome. Notice that all of the above features are implemented within the index structure and are not simple post-processing steps and thus are performed highly efficiently. Finally, mrsFAST-Ultra utilizes multiple available cores and processors and can be tuned for various memory settings. Our results show that mrsFAST-Ultra is roughly five times faster than its predecessor mrsFAST. In comparison to newly enhanced popular tools such as Bowtie2, it is more sensitive (it can report 10 times or more mappings per read) and much faster (six times or

  10. Multiplex target enrichment using DNA indexing for ultra-high throughput SNP detection.

    LENUS (Irish Health Repository)

    Kenny, Elaine M

    2011-02-01

    Screening large numbers of target regions in multiple DNA samples for sequence variation is an important application of next-generation sequencing but an efficient method to enrich the samples in parallel has yet to be reported. We describe an advanced method that combines DNA samples using indexes or barcodes prior to target enrichment to facilitate this type of experiment. Sequencing libraries for multiple individual DNA samples, each incorporating a unique 6-bp index, are combined in equal quantities, enriched using a single in-solution target enrichment assay and sequenced in a single reaction. Sequence reads are parsed based on the index, allowing sequence analysis of individual samples. We show that the use of indexed samples does not impact on the efficiency of the enrichment reaction. For three- and nine-indexed HapMap DNA samples, the method was found to be highly accurate for SNP identification. Even with sequence coverage as low as 8x, 99% of sequence SNP calls were concordant with known genotypes. Within a single experiment, this method can sequence the exonic regions of hundreds of genes in tens of samples for sequence and structural variation using as little as 1 μg of input DNA per sample.

  11. A SNP based high-density linkage map of Apis cerana reveals a high recombination rate similar to Apis mellifera.

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    Yuan Yuan Shi

    Full Text Available BACKGROUND: The Eastern honey bee, Apis cerana Fabricius, is distributed in southern and eastern Asia, from India and China to Korea and Japan and southeast to the Moluccas. This species is also widely kept for honey production besides Apis mellifera. Apis cerana is also a model organism for studying social behavior, caste determination, mating biology, sexual selection, and host-parasite interactions. Few resources are available for molecular research in this species, and a linkage map was never constructed. A linkage map is a prerequisite for quantitative trait loci mapping and for analyzing genome structure. We used the Chinese honey bee, Apis cerana cerana to construct the first linkage map in the Eastern honey bee. RESULTS: F2 workers (N = 103 were genotyped for 126,990 single nucleotide polymorphisms (SNPs. After filtering low quality and those not passing the Mendel test, we obtained 3,000 SNPs, 1,535 of these were informative and used to construct a linkage map. The preliminary map contains 19 linkage groups, we then mapped the 19 linkage groups to 16 chromosomes by comparing the markers to the genome of A. mellfiera. The final map contains 16 linkage groups with a total of 1,535 markers. The total genetic distance is 3,942.7 centimorgans (cM with the largest linkage group (180 loci measuring 574.5 cM. Average marker interval for all markers across the 16 linkage groups is 2.6 cM. CONCLUSION: We constructed a high density linkage map for A. c. cerana with 1,535 markers. Because the map is based on SNP markers, it will enable easier and faster genotyping assays than randomly amplified polymorphic DNA or microsatellite based maps used in A. mellifera.

  12. SNP Arrays

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    Jari Louhelainen

    2016-10-01

    Full Text Available The papers published in this Special Issue “SNP arrays” (Single Nucleotide Polymorphism Arrays focus on several perspectives associated with arrays of this type. The range of papers vary from a case report to reviews, thereby targeting wider audiences working in this field. The research focus of SNP arrays is often human cancers but this Issue expands that focus to include areas such as rare conditions, animal breeding and bioinformatics tools. Given the limited scope, the spectrum of papers is nothing short of remarkable and even from a technical point of view these papers will contribute to the field at a general level. Three of the papers published in this Special Issue focus on the use of various SNP array approaches in the analysis of three different cancer types. Two of the papers concentrate on two very different rare conditions, applying the SNP arrays slightly differently. Finally, two other papers evaluate the use of the SNP arrays in the context of genetic analysis of livestock. The findings reported in these papers help to close gaps in the current literature and also to give guidelines for future applications of SNP arrays.

  13. Development of admixture mapping panels for African Americans from commercial high-density SNP arrays

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    Dunston Georgia M

    2010-07-01

    Full Text Available Abstract Background Admixture mapping is a powerful approach for identifying genetic variants involved in human disease that exploits the unique genomic structure in recently admixed populations. To use existing published panels of ancestry-informative markers (AIMs for admixture mapping, markers have to be genotyped de novo for each admixed study sample and samples representing the ancestral parental populations. The increased availability of dense marker data on commercial chips has made it feasible to develop panels wherein the markers need not be predetermined. Results We developed two panels of AIMs (~2,000 markers each based on the Affymetrix Genome-Wide Human SNP Array 6.0 for admixture mapping with African American samples. These two AIM panels had good map power that was higher than that of a denser panel of ~20,000 random markers as well as other published panels of AIMs. As a test case, we applied the panels in an admixture mapping study of hypertension in African Americans in the Washington, D.C. metropolitan area. Conclusions Developing marker panels for admixture mapping from existing genome-wide genotype data offers two major advantages: (1 no de novo genotyping needs to be done, thereby saving costs, and (2 markers can be filtered for various quality measures and replacement markers (to minimize gaps can be selected at no additional cost. Panels of carefully selected AIMs have two major advantages over panels of random markers: (1 the map power from sparser panels of AIMs is higher than that of ~10-fold denser panels of random markers, and (2 clusters can be labeled based on information from the parental populations. With current technology, chip-based genome-wide genotyping is less expensive than genotyping ~20,000 random markers. The major advantage of using random markers is the absence of ascertainment effects resulting from the process of selecting markers. The ability to develop marker panels informative for ancestry from

  14. Heap: a highly sensitive and accurate SNP detection tool for low-coverage high-throughput sequencing data

    KAUST Repository

    Kobayashi, Masaaki

    2017-04-20

    Recent availability of large-scale genomic resources enables us to conduct so called genome-wide association studies (GWAS) and genomic prediction (GP) studies, particularly with next-generation sequencing (NGS) data. The effectiveness of GWAS and GP depends on not only their mathematical models, but the quality and quantity of variants employed in the analysis. In NGS single nucleotide polymorphism (SNP) calling, conventional tools ideally require more reads for higher SNP sensitivity and accuracy. In this study, we aimed to develop a tool, Heap, that enables robustly sensitive and accurate calling of SNPs, particularly with a low coverage NGS data, which must be aligned to the reference genome sequences in advance. To reduce false positive SNPs, Heap determines genotypes and calls SNPs at each site except for sites at the both ends of reads or containing a minor allele supported by only one read. Performance comparison with existing tools showed that Heap achieved the highest F-scores with low coverage (7X) restriction-site associated DNA sequencing reads of sorghum and rice individuals. This will facilitate cost-effective GWAS and GP studies in this NGS era. Code and documentation of Heap are freely available from https://github.com/meiji-bioinf/heap (29 March 2017, date last accessed) and our web site (http://bioinf.mind.meiji.ac.jp/lab/en/tools.html (29 March 2017, date last accessed)).

  15. High-throughput SNP genotyping in Cucurbita pepo for map construction and quantitative trait loci mapping.

    Science.gov (United States)

    Esteras, Cristina; Gómez, Pedro; Monforte, Antonio J; Blanca, José; Vicente-Dólera, Nelly; Roig, Cristina; Nuez, Fernando; Picó, Belén

    2012-02-22

    Cucurbita pepo is a member of the Cucurbitaceae family, the second- most important horticultural family in terms of economic importance after Solanaceae. The "summer squash" types, including Zucchini and Scallop, rank among the highest-valued vegetables worldwide. There are few genomic tools available for this species.The first Cucurbita transcriptome, along with a large collection of Single Nucleotide Polymorphisms (SNP), was recently generated using massive sequencing. A set of 384 SNP was selected to generate an Illumina GoldenGate assay in order to construct the first SNP-based genetic map of Cucurbita and map quantitative trait loci (QTL). We herein present the construction of the first SNP-based genetic map of Cucurbita pepo using a population derived from the cross of two varieties with contrasting phenotypes, representing the main cultivar groups of the species' two subspecies: Zucchini (subsp. pepo) × Scallop (subsp. ovifera). The mapping population was genotyped with 384 SNP, a set of selected EST-SNP identified in silico after massive sequencing of the transcriptomes of both parents, using the Illumina GoldenGate platform. The global success rate of the assay was higher than 85%. In total, 304 SNP were mapped, along with 11 SSR from a previous map, giving a map density of 5.56 cM/marker. This map was used to infer syntenic relationships between C. pepo and cucumber and to successfully map QTL that control plant, flowering and fruit traits that are of benefit to squash breeding. The QTL effects were validated in backcross populations. Our results show that massive sequencing in different genotypes is an excellent tool for SNP discovery, and that the Illumina GoldenGate platform can be successfully applied to constructing genetic maps and performing QTL analysis in Cucurbita. This is the first SNP-based genetic map in the Cucurbita genus and is an invaluable new tool for biological research, especially considering that most of these markers are located in

  16. QualitySNP: a pipeline for detecting single nucleotide polymorphisms and insertions/deletions in EST data from diploid and polyploid species

    Directory of Open Access Journals (Sweden)

    Voorrips Roeland E

    2006-10-01

    Full Text Available Abstract Background Single nucleotide polymorphisms (SNPs are important tools in studying complex genetic traits and genome evolution. Computational strategies for SNP discovery make use of the large number of sequences present in public databases (in most cases as expressed sequence tags (ESTs and are considered to be faster and more cost-effective than experimental procedures. A major challenge in computational SNP discovery is distinguishing allelic variation from sequence variation between paralogous sequences, in addition to recognizing sequencing errors. For the majority of the public EST sequences, trace or quality files are lacking which makes detection of reliable SNPs even more difficult because it has to rely on sequence comparisons only. Results We have developed a new algorithm to detect reliable SNPs and insertions/deletions (indels in EST data, both with and without quality files. Implemented in a pipeline called QualitySNP, it uses three filters for the identification of reliable SNPs. Filter 1 screens for all potential SNPs and identifies variation between or within genotypes. Filter 2 is the core filter that uses a haplotype-based strategy to detect reliable SNPs. Clusters with potential paralogs as well as false SNPs caused by sequencing errors are identified. Filter 3 screens SNPs by calculating a confidence score, based upon sequence redundancy and quality. Non-synonymous SNPs are subsequently identified by detecting open reading frames of consensus sequences (contigs with SNPs. The pipeline includes a data storage and retrieval system for haplotypes, SNPs and alignments. QualitySNP's versatility is demonstrated by the identification of SNPs in EST datasets from potato, chicken and humans. Conclusion QualitySNP is an efficient tool for SNP detection, storage and retrieval in diploid as well as polyploid species. It is available for running on Linux or UNIX systems. The program, test data, and user manual are available at

  17. Development of high-throughput SNP-based genotyping in Acacia auriculiformis x A. mangium hybrids using short-read transcriptome data

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    Wong Melissa ML

    2012-12-01

    Full Text Available Abstract Background Next Generation Sequencing has provided comprehensive, affordable and high-throughput DNA sequences for Single Nucleotide Polymorphism (SNP discovery in Acacia auriculiformis and Acacia mangium. Like other non-model species, SNP detection and genotyping in Acacia are challenging due to lack of genome sequences. The main objective of this study is to develop the first high-throughput SNP genotyping assay for linkage map construction of A. auriculiformis x A. mangium hybrids. Results We identified a total of 37,786 putative SNPs by aligning short read transcriptome data from four parents of two Acacia hybrid mapping populations using Bowtie against 7,839 de novo transcriptome contigs. Given a set of 10 validated SNPs from two lignin genes, our in silico SNP detection approach is highly accurate (100% compared to the traditional in vitro approach (44%. Further validation of 96 SNPs using Illumina GoldenGate Assay gave an overall assay success rate of 89.6% and conversion rate of 37.5%. We explored possible factors lowering assay success rate by predicting exon-intron boundaries and paralogous genes of Acacia contigs using Medicago truncatula genome as reference. This assessment revealed that presence of exon-intron boundary is the main cause (50% of assay failure. Subsequent SNPs filtering and improved assay design resulted in assay success and conversion rate of 92.4% and 57.4%, respectively based on 768 SNPs genotyping. Analysis of clustering patterns revealed that 27.6% of the assays were not reproducible and flanking sequence might play a role in determining cluster compression. In addition, we identified a total of 258 and 319 polymorphic SNPs in A. auriculiformis and A. mangium natural germplasms, respectively. Conclusion We have successfully discovered a large number of SNP markers in A. auriculiformis x A. mangium hybrids using next generation transcriptome sequencing. By using a reference genome from the most closely

  18. Genome-wide SNP discovery in tetraploid alfalfa using 454 sequencing and high resolution melting analysis

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    Zhao Patrick X

    2011-07-01

    Full Text Available Abstract Background Single nucleotide polymorphisms (SNPs are the most common type of sequence variation among plants and are often functionally important. We describe the use of 454 technology and high resolution melting analysis (HRM for high throughput SNP discovery in tetraploid alfalfa (Medicago sativa L., a species with high economic value but limited genomic resources. Results The alfalfa genotypes selected from M. sativa subsp. sativa var. 'Chilean' and M. sativa subsp. falcata var. 'Wisfal', which differ in water stress sensitivity, were used to prepare cDNA from tissue of clonally-propagated plants grown under either well-watered or water-stressed conditions, and then pooled for 454 sequencing. Based on 125.2 Mb of raw sequence, a total of 54,216 unique sequences were obtained including 24,144 tentative consensus (TCs sequences and 30,072 singletons, ranging from 100 bp to 6,662 bp in length, with an average length of 541 bp. We identified 40,661 candidate SNPs distributed throughout the genome. A sample of candidate SNPs were evaluated and validated using high resolution melting (HRM analysis. A total of 3,491 TCs harboring 20,270 candidate SNPs were located on the M. truncatula (MT 3.5.1 chromosomes. Gene Ontology assignments indicate that sequences obtained cover a broad range of GO categories. Conclusions We describe an efficient method to identify thousands of SNPs distributed throughout the alfalfa genome covering a broad range of GO categories. Validated SNPs represent valuable molecular marker resources that can be used to enhance marker density in linkage maps, identify potential factors involved in heterosis and genetic variation, and as tools for association mapping and genomic selection in alfalfa.

  19. SNP calling using genotype model selection on high-throughput sequencing data

    KAUST Repository

    You, Na; Murillo, Gabriel; Su, Xiaoquan; Zeng, Xiaowei; Xu, Jian; Ning, Kang; Zhang, ShouDong; Zhu, Jian-Kang; Cui, Xinping

    2012-01-01

    calling SNPs. Thus, errors not involved in base-calling or alignment, such as those in genomic sample preparation, are not accounted for.Results: A novel method of consensus and SNP calling, Genotype Model Selection (GeMS), is given which accounts

  20. SNP variation in the promoter of the PRKAG3 gene and association with meat quality traits in pig.

    Science.gov (United States)

    Ryan, Marion T; Hamill, Ruth M; O'Halloran, Aisling M; Davey, Grace C; McBryan, Jean; Mullen, Anne M; McGee, Chris; Gispert, Marina; Southwood, Olwen I; Sweeney, Torres

    2012-07-25

    The PRKAG3 gene encodes the γ3 subunit of adenosine monophosphate activated protein kinase (AMPK), a protein that plays a key role in energy metabolism in skeletal muscle. Non-synonymous single nucleotide polymorphisms (SNPs) in this gene such as I199V are associated with important pork quality traits. The objective of this study was to investigate the relationship between gene expression of the PRKAG3 gene, SNP variation in the PRKAG3 promoter and meat quality phenotypes in pork. PRKAG3 gene expression was found to correlate with a number of traits relating to glycolytic potential (GP) and intramuscular fat (IMF) in three phenotypically diverse F1 crosses comprising of 31 Large White, 23 Duroc and 32 Pietrain sire breeds. The majority of associations were observed in the Large White cross. There was a significant association between genotype at the g.-311A>G locus and PRKAG3 gene expression in the Large White cross. In the same population, ten novel SNPs were identified within a 1.3 kb region spanning the promoter and from this three major haplotypes were inferred. Two tagging SNPs (g.-995A>G and g.-311A>G) characterised the haplotypes within the promoter region being studied. These two SNPs were subsequently genotyped in larger populations consisting of Large White (n = 98), Duroc (n = 99) and Pietrain (n = 98) purebreds. Four major haplotypes including promoter SNP's g.-995A>G and g.-311A>G and I199V were inferred. In the Large White breed, HAP1 was associated with IMF% in the M. longissmus thoracis et lumborum (LTL) and driploss%. HAP2 was associated with IMFL% GP-influenced traits pH at 24 hr in LTL (pHULT), pH at 45 min in LTL (pH(45)LT) and pH at 45 min in the M. semimembranosus muscle (pH(45)SM). HAP3 was associated with driploss%, pHULT pH(45)LT and b* Minolta. In the Duroc breed, associations were observed between HAP1 and driploss% and pHUSM. No associations were observed with the remaining haplotypes (HAP2, HAP3 and HAP4) in the Duroc breed. The

  1. Evaluation of Bovine High-Density SNP Genotyping Array in Indigenous Dairy Cattle Breeds.

    Science.gov (United States)

    Dash, S; Singh, A; Bhatia, A K; Jayakumar, S; Sharma, A; Singh, S; Ganguly, I; Dixit, S P

    2018-04-03

    In total 52 samples of Sahiwal ( 19 ), Tharparkar ( 17 ), and Gir ( 16 ) were genotyped by using BovineHD SNP chip to analyze minor allele frequency (MAF), genetic diversity, and linkage disequilibrium among these cattle. The common SNPs of BovineHD and 54K SNP Chips were also extracted and evaluated for their performance. Only 40%-50% SNPs of these arrays was found informative for genetic analysis in these cattle breeds. The overall mean of MAF for SNPs of BovineHD SNPChip was 0.248 ± 0.006, 0.241 ± 0.007, and 0.242 ± 0.009 in Sahiwal, Tharparkar and Gir, respectively, while that for 54K SNPs was on lower side. The average Reynold's genetic distance between breeds ranged from 0.042 to 0.055 based on BovineHD Beadchip, and from 0.052 to 0.084 based on 54K SNP Chip. The estimates of genetic diversity based on HD and 54K chips were almost same and, hence, low density chip seems to be good enough to decipher genetic diversity of these cattle breeds. The linkage disequilibrium started decaying (r 2  < 0.2) at 140 kb inter-marker distance and, hence, a 20K low density customized SNP array from HD chip could be designed for genomic selection in these cattle else the 54K Bead Chip as such will be useful.

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

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    Huihui Yu

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

  3. SNP variation in the promoter of the PRKAG3 gene and association with meat quality traits in pig

    Directory of Open Access Journals (Sweden)

    Ryan Marion T

    2012-07-01

    Full Text Available Abstract Background The PRKAG3 gene encodes the γ3 subunit of adenosine monophosphate activated protein kinase (AMPK, a protein that plays a key role in energy metabolism in skeletal muscle. Non-synonymous single nucleotide polymorphisms (SNPs in this gene such as I199V are associated with important pork quality traits. The objective of this study was to investigate the relationship between gene expression of the PRKAG3 gene, SNP variation in the PRKAG3 promoter and meat quality phenotypes in pork. Results PRKAG3 gene expression was found to correlate with a number of traits relating to glycolytic potential (GP and intramuscular fat (IMF in three phenotypically diverse F1 crosses comprising of 31 Large White, 23 Duroc and 32 Pietrain sire breeds. The majority of associations were observed in the Large White cross. There was a significant association between genotype at the g.-311A>G locus and PRKAG3 gene expression in the Large White cross. In the same population, ten novel SNPs were identified within a 1.3 kb region spanning the promoter and from this three major haplotypes were inferred. Two tagging SNPs (g.-995A>G and g.-311A>G characterised the haplotypes within the promoter region being studied. These two SNPs were subsequently genotyped in larger populations consisting of Large White (n = 98, Duroc (n = 99 and Pietrain (n = 98 purebreds. Four major haplotypes including promoter SNP’s g.-995A>G and g.-311A>G and I199V were inferred. In the Large White breed, HAP1 was associated with IMF% in the M. longissmus thoracis et lumborum (LTL and driploss%. HAP2 was associated with IMFL% GP-influenced traits pH at 24 hr in LTL (pHULT, pH at 45 min in LTL (pH45LT and pH at 45 min in the M. semimembranosus muscle (pH45SM. HAP3 was associated with driploss%, pHULT pH45LT and b* Minolta. In the Duroc breed, associations were observed between HAP1 and driploss% and pHUSM. No associations were observed with the remaining haplotypes (HAP2

  4. High-density SNP genotyping of tomato (Solanum lycopersicum L. reveals patterns of genetic variation due to breeding.

    Directory of Open Access Journals (Sweden)

    Sung-Chur Sim

    Full Text Available The effects of selection on genome variation were investigated and visualized in tomato using a high-density single nucleotide polymorphism (SNP array. 7,720 SNPs were genotyped on a collection of 426 tomato accessions (410 inbreds and 16 hybrids and over 97% of the markers were polymorphic in the entire collection. Principal component analysis (PCA and pairwise estimates of F(st supported that the inbred accessions represented seven sub-populations including processing, large-fruited fresh market, large-fruited vintage, cultivated cherry, landrace, wild cherry, and S. pimpinellifolium. Further divisions were found within both the contemporary processing and fresh market sub-populations. These sub-populations showed higher levels of genetic diversity relative to the vintage sub-population. The array provided a large number of polymorphic SNP markers across each sub-population, ranging from 3,159 in the vintage accessions to 6,234 in the cultivated cherry accessions. Visualization of minor allele frequency revealed regions of the genome that distinguished three representative sub-populations of cultivated tomato (processing, fresh market, and vintage, particularly on chromosomes 2, 4, 5, 6, and 11. The PCA loadings and F(st outlier analysis between these three sub-populations identified a large number of candidate loci under positive selection on chromosomes 4, 5, and 11. The extent of linkage disequilibrium (LD was examined within each chromosome for these sub-populations. LD decay varied between chromosomes and sub-populations, with large differences reflective of breeding history. For example, on chromosome 11, decay occurred over 0.8 cM for processing accessions and over 19.7 cM for fresh market accessions. The observed SNP variation and LD decay suggest that different patterns of genetic variation in cultivated tomato are due to introgression from wild species and selection for market specialization.

  5. High-throughput bacterial SNP typing identifies distinct clusters of Salmonella Typhi causing typhoid in Nepalese children

    LENUS (Irish Health Repository)

    Holt, Kathryn E

    2010-05-31

    Abstract Background Salmonella Typhi (S. Typhi) causes typhoid fever, which remains an important public health issue in many developing countries. Kathmandu, the capital of Nepal, is an area of high incidence and the pediatric population appears to be at high risk of exposure and infection. Methods We recently defined the population structure of S. Typhi, using new sequencing technologies to identify nearly 2,000 single nucleotide polymorphisms (SNPs) that can be used as unequivocal phylogenetic markers. Here we have used the GoldenGate (Illumina) platform to simultaneously type 1,500 of these SNPs in 62 S. Typhi isolates causing severe typhoid in children admitted to Patan Hospital in Kathmandu. Results Eight distinct S. Typhi haplotypes were identified during the 20-month study period, with 68% of isolates belonging to a subclone of the previously defined H58 S. Typhi. This subclone was closely associated with resistance to nalidixic acid, with all isolates from this group demonstrating a resistant phenotype and harbouring the same resistance-associated SNP in GyrA (Phe83). A secondary clone, comprising 19% of isolates, was observed only during the second half of the study. Conclusions Our data demonstrate the utility of SNP typing for monitoring bacterial populations over a defined period in a single endemic setting. We provide evidence for genotype introduction and define a nalidixic acid resistant subclone of S. Typhi, which appears to be the dominant cause of severe pediatric typhoid in Kathmandu during the study period.

  6. A SNP Harvester Analysis to Better Detect SNPs of CCDC158 Gene That Are Associated with Carcass Quality Traits in Hanwoo

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    Jea-Young Lee

    2013-06-01

    Full Text Available The purpose of this study was to investigate interaction effects of genes using a Harvester method. A sample of Korean cattle, Hanwoo (n = 476 was chosen from the National Livestock Research Institute of Korea that were sired by 50 Korean proven bulls. The steers were born between the spring of 1998 and the autumn of 2002 and reared under a progeny-testing program at the Daekwanryeong and Namwon branches of NLRI. The steers were slaughtered at approximately 24 months of age and carcass quality traits were measured. A SNP Harvester method was applied with a support vector machine (SVM to detect significant SNPs in the CCDC158 gene and interaction effects between the SNPs that were associated with average daily gains, cold carcass weight, longissimus dorsi muscle area, and marbling scores. The statistical significance of the major SNP combinations was evaluated with x2-statistics. The genotype combinations of three SNPs, g.34425+102 A>T(AA, g.4102636T>G(GT, and g.11614+19G>T(GG had a greater effect than the rest of SNP combinations, e.g. 0.82 vs. 0.75 kg, 343 vs. 314 kg, 80.4 vs 74.7 cm2, and 7.35 vs. 5.01, for the four respective traits (p<0.001. Also, the estimates were greater compared with single SNPs analyzed (the greatest estimates were 0.76 kg, 320 kg, 75.5 cm2, and 5.31, respectively. This result suggests that the SNP Harvester method is a good option when multiple SNPs and interaction effects are tested. The significant SNPs could be applied to improve meat quality of Hanwoo via marker-assisted selection.

  7. Design of a High Density SNP Genotyping Assay in the Pig Using SNPs Identified and Characterized by Next Generation Sequencing Technology

    Science.gov (United States)

    Ramos, Antonio M.; Crooijmans, Richard P. M. A.; Affara, Nabeel A.; Amaral, Andreia J.; Archibald, Alan L.; Beever, Jonathan E.; Bendixen, Christian; Churcher, Carol; Clark, Richard; Dehais, Patrick; Hansen, Mark S.; Hedegaard, Jakob; Hu, Zhi-Liang; Kerstens, Hindrik H.; Law, Andy S.; Megens, Hendrik-Jan; Milan, Denis; Nonneman, Danny J.; Rohrer, Gary A.; Rothschild, Max F.; Smith, Tim P. L.; Schnabel, Robert D.; Van Tassell, Curt P.; Taylor, Jeremy F.; Wiedmann, Ralph T.; Schook, Lawrence B.; Groenen, Martien A. M.

    2009-01-01

    Background The dissection of complex traits of economic importance to the pig industry requires the availability of a significant number of genetic markers, such as single nucleotide polymorphisms (SNPs). This study was conducted to discover several hundreds of thousands of porcine SNPs using next generation sequencing technologies and use these SNPs, as well as others from different public sources, to design a high-density SNP genotyping assay. Methodology/Principal Findings A total of 19 reduced representation libraries derived from four swine breeds (Duroc, Landrace, Large White, Pietrain) and a Wild Boar population and three restriction enzymes (AluI, HaeIII and MspI) were sequenced using Illumina's Genome Analyzer (GA). The SNP discovery effort resulted in the de novo identification of over 372K SNPs. More than 549K SNPs were used to design the Illumina Porcine 60K+SNP iSelect Beadchip, now commercially available as the PorcineSNP60. A total of 64,232 SNPs were included on the Beadchip. Results from genotyping the 158 individuals used for sequencing showed a high overall SNP call rate (97.5%). Of the 62,621 loci that could be reliably scored, 58,994 were polymorphic yielding a SNP conversion success rate of 94%. The average minor allele frequency (MAF) for all scorable SNPs was 0.274. Conclusions/Significance Overall, the results of this study indicate the utility of using next generation sequencing technologies to identify large numbers of reliable SNPs. In addition, the validation of the PorcineSNP60 Beadchip demonstrated that the assay is an excellent tool that will likely be used in a variety of future studies in pigs. PMID:19654876

  8. Survey of SSC12 regions affecting fatty acid composition of intramuscular fat using high density SNP data

    Directory of Open Access Journals (Sweden)

    María eMuñoz

    2012-01-01

    Full Text Available Fatty acid composition is a critical aspect of pork because it affects sensorial and technological aspects of meat quality and it is relevant for human health. Previous studies identified significant QTLs in porcine chromosome 12 for fatty acid profile of backfat and intramuscular fat. In the present study, 374 SNPs mapped in SSC12 from the 60K Porcine SNP Beadchip were used. We have combined linkage and association analyses with expression data analysis in order to identify regions of SSC12 that could affect fatty acid composition of intramuscular fat in longissimus muscle. The QTL scan showed a region around the 60 cM position that significantly affects palmitic fatty acid and two related fatty acid indexes. The Iberian QTL allele increased the palmitic content (+2.6% of mean trait. This QTL does not match any of those reported in the previous study on fatty acid composition of backfat, suggesting different genetic control acting at both tissues. The SNP association analyses showed significant associations with linolenic and palmitic acids besides several indexes. Among the polymorphisms that affect palmitic fatty acid and match the QTL region at 60 cM, there were three that mapped in the Phosphatidylcholine Transfer Protein (PCTP gene and one in the Acetyl-CoA Carboxylase  gene (ACACA. Interestingly one of the PCTP SNPs also affected significantly unsaturated and double bound indexes and the ratio between polyunsaturated/monounsaturated fatty acids. Differential expression was assessed on longissimus muscle conditional on the genotype of the QTL and on the most significant SNPs, according to the results obtained in the former analyses. Results from the microarray expression analyses, validated by RT-qPCR, showed that PCTP expression levels significantly vary depending on the QTL as well as on the own PCTP genotype. The results obtained with the different approaches point out the PCTP gene as a powerful candidate underlying the QTL for

  9. Detection of genomic signatures for pig hairlessness using high-density SNP data

    Directory of Open Access Journals (Sweden)

    Ying SU,Yi LONG,Xinjun LIAO,Huashui AI,Zhiyan ZHANG,Bin YANG,Shijun XIAO,Jianhong TANG,Wenshui XIN,Lusheng HUANG,Jun REN,Nengshui DING

    2014-12-01

    Full Text Available Hair provides thermal regulation for mammals and protects the skin from wounds, bites and ultraviolet (UV radiation, and is important in adaptation to volatile environments. Pigs in nature are divided into hairy and hairless, which provide a good model for deciphering the molecular mechanisms of hairlessness. We conducted a genomic scan for genetically differentiated regions between hairy and hairless pigs using 60K SNP data, with the aim to better understand the genetic basis for the hairless phenotype in pigs. A total of 38405 SNPs in 498 animals from 36 diverse breeds were used to detect genomic signatures for pig hairlessness by estimating between-population (FST values. Seven diversifying signatures between Yucatan hairless pig and hairy pigs were identified on pig chromosomes (SSC 1, 3, 7, 8, 10, 11 and 16, and the biological functions of two notable genes, RGS17 and RB1, were revealed. When Mexican hairless pigs were contrasted with hairypigs, strong signatures were detected on SSC1 and SSC10, which harbor two functionally plausible genes, REV3L and BAMBI. KEGG pathway analysis showed a subset of overrepresented genes involved in the T cell receptor signaling pathway, MAPK signaling pathway and the tight junction pathways. All of these pathways may be important in local adaptability of hairless pigs. The potential mechanisms underlying the hairless phenotype in pigs are reported for the first time. RB1 and BAMBI are interesting candidate genes for the hairless phenotype in Yucatan hairless and Mexico hairless pigs, respectively. RGS17, REV3L, ICOS and RASGRP1 as well as other genes involved in the MAPK and T cell receptor signaling pathways may be important in environmental adaption by improved tolerance to UV damage in hairless pigs. These findings improve our understanding of the genetic basis for inherited hairlessness in pigs.

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

    Science.gov (United States)

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

    2013-11-20

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

  11. Genomewide high-density SNP linkage analysis of non-BRCA1/2 breast cancer families identifies various candidate regions and has greater power than microsatellite studies

    NARCIS (Netherlands)

    A. González-Neira (Anna); J.M. Rosa-Rosa; A. Osorio (Ana); E. Gonzalez (Emilio); M.C. Southey (Melissa); O. Sinilnikova (Olga); H. Lynch (Henry); R.A. Oldenburg (Rogier); C.J. van Asperen (Christi); N. Hoogerbrugge (Nicoline); G. Pita (Guillermo); P. Devilee (Peter); D. Goldgar (David); J. Benítez (Javier)

    2007-01-01

    textabstractBackground: The recent development of new high-throughput technologies for SNP genotyping has opened the possibility of taking a genome-wide linkage approach to the search for new candidate genes involved in heredity diseases. The two major breast cancer susceptibility genes BRCA1 and

  12. LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structures.

    Science.gov (United States)

    Ryan, Michael; Diekhans, Mark; Lien, Stephanie; Liu, Yun; Karchin, Rachel

    2009-06-01

    LS-SNP/PDB is a new WWW resource for genome-wide annotation of human non-synonymous (amino acid changing) SNPs. It serves high-quality protein graphics rendered with UCSF Chimera molecular visualization software. The system is kept up-to-date by an automated, high-throughput build pipeline that systematically maps human nsSNPs onto Protein Data Bank structures and annotates several biologically relevant features. LS-SNP/PDB is available at (http://ls-snp.icm.jhu.edu/ls-snp-pdb) and via links from protein data bank (PDB) biology and chemistry tabs, UCSC Genome Browser Gene Details and SNP Details pages and PharmGKB Gene Variants Downloads/Cross-References pages.

  13. Supplementing High-Density SNP Microarrays for Additional Coverage of Disease-Related Genes: Addiction as a Paradigm

    Energy Technology Data Exchange (ETDEWEB)

    SacconePhD, Scott F [Washington University, St. Louis; Chesler, Elissa J [ORNL; Bierut, Laura J [Washington University, St. Louis; Kalivas, Peter J [Medical College of South Carolina, Charleston; Lerman, Caryn [University of Pennsylvania; Saccone, Nancy L [Washington University, St. Louis; Uhl, George R [Johns Hopkins University; Li, Chuan-Yun [Peking University; Philip, Vivek M [ORNL; Edenberg, Howard [Indiana University; Sherry, Steven [National Center for Biotechnology Information; Feolo, Michael [National Center for Biotechnology Information; Moyzis, Robert K [Johns Hopkins University; Rutter, Joni L [National Institute of Drug Abuse

    2009-01-01

    Commercial SNP microarrays now provide comprehensive and affordable coverage of the human genome. However, some diseases have biologically relevant genomic regions that may require additional coverage. Addiction, for example, is thought to be influenced by complex interactions among many relevant genes and pathways. We have assembled a list of 486 biologically relevant genes nominated by a panel of experts on addiction. We then added 424 genes that showed evidence of association with addiction phenotypes through mouse QTL mappings and gene co-expression analysis. We demonstrate that there are a substantial number of SNPs in these genes that are not well represented by commercial SNP platforms. We address this problem by introducing a publicly available SNP database for addiction. The database is annotated using numeric prioritization scores indicating the extent of biological relevance. The scores incorporate a number of factors such as SNP/gene functional properties (including synonymy and promoter regions), data from mouse systems genetics and measures of human/mouse evolutionary conservation. We then used HapMap genotyping data to determine if a SNP is tagged by a commercial microarray through linkage disequilibrium. This combination of biological prioritization scores and LD tagging annotation will enable addiction researchers to supplement commercial SNP microarrays to ensure comprehensive coverage of biologically relevant regions.

  14. Construction of an SNP-based high-density linkage map for flax (Linum usitatissimum L.) using specific length amplified fragment sequencing (SLAF-seq) technology.

    Science.gov (United States)

    Yi, Liuxi; Gao, Fengyun; Siqin, Bateer; Zhou, Yu; Li, Qiang; Zhao, Xiaoqing; Jia, Xiaoyun; Zhang, Hui

    2017-01-01

    Flax is an important crop for oil and fiber, however, no high-density genetic maps have been reported for this species. Specific length amplified fragment sequencing (SLAF-seq) is a high-resolution strategy for large scale de novo discovery and genotyping of single nucleotide polymorphisms. In this study, SLAF-seq was employed to develop SNP markers in an F2 population to construct a high-density genetic map for flax. In total, 196.29 million paired-end reads were obtained. The average sequencing depth was 25.08 in male parent, 32.17 in the female parent, and 9.64 in each F2 progeny. In total, 389,288 polymorphic SLAFs were detected, from which 260,380 polymorphic SNPs were developed. After filtering, 4,638 SNPs were found suitable for genetic map construction. The final genetic map included 4,145 SNP markers on 15 linkage groups and was 2,632.94 cM in length, with an average distance of 0.64 cM between adjacent markers. To our knowledge, this map is the densest SNP-based genetic map for flax. The SNP markers and genetic map reported in here will serve as a foundation for the fine mapping of quantitative trait loci (QTLs), map-based gene cloning and marker assisted selection (MAS) for flax.

  15. Genomewide high-density SNP linkage analysis of non-BRCA1/2 breast cancer families identifies various candidate regions and has greater power than microsatellite studies

    Directory of Open Access Journals (Sweden)

    Gonzalez-Neira Anna

    2007-08-01

    Full Text Available Abstract Background The recent development of new high-throughput technologies for SNP genotyping has opened the possibility of taking a genome-wide linkage approach to the search for new candidate genes involved in heredity diseases. The two major breast cancer susceptibility genes BRCA1 and BRCA2 are involved in 30% of hereditary breast cancer cases, but the discovery of additional breast cancer predisposition genes for the non-BRCA1/2 breast cancer families has so far been unsuccessful. Results In order to evaluate the power improvement provided by using SNP markers in a real situation, we have performed a whole genome screen of 19 non-BRCA1/2 breast cancer families using 4720 genomewide SNPs with Illumina technology (Illumina's Linkage III Panel, with an average distance of 615 Kb/SNP. We identified six regions on chromosomes 2, 3, 4, 7, 11 and 14 as candidates to contain genes involved in breast cancer susceptibility, and additional fine mapping genotyping using microsatellite markers around linkage peaks confirmed five of them, excluding the region on chromosome 3. These results were consistent in analyses that excluded SNPs in high linkage disequilibrium. The results were compared with those obtained previously using a 10 cM microsatellite scan (STR-GWS and we found lower or not significant linkage signals with STR-GWS data compared to SNP data in all cases. Conclusion Our results show the power increase that SNPs can supply in linkage studies.

  16. Network-based regularization for high dimensional SNP data in the case-control study of Type 2 diabetes.

    Science.gov (United States)

    Ren, Jie; He, Tao; Li, Ye; Liu, Sai; Du, Yinhao; Jiang, Yu; Wu, Cen

    2017-05-16

    Over the past decades, the prevalence of type 2 diabetes mellitus (T2D) has been steadily increasing around the world. Despite large efforts devoted to better understand the genetic basis of the disease, the identified susceptibility loci can only account for a small portion of the T2D heritability. Some of the existing approaches proposed for the high dimensional genetic data from the T2D case-control study are limited by analyzing a few number of SNPs at a time from a large pool of SNPs, by ignoring the correlations among SNPs and by adopting inefficient selection techniques. We propose a network constrained regularization method to select important SNPs by taking the linkage disequilibrium into account. To accomodate the case control study, an iteratively reweighted least square algorithm has been developed within the coordinate descent framework where optimization of the regularized logistic loss function is performed with respect to one parameter at a time and iteratively cycle through all the parameters until convergence. In this article, a novel approach is developed to identify important SNPs more effectively through incorporating the interconnections among them in the regularized selection. A coordinate descent based iteratively reweighed least squares (IRLS) algorithm has been proposed. Both the simulation study and the analysis of the Nurses's Health Study, a case-control study of type 2 diabetes data with high dimensional SNP measurements, demonstrate the advantage of the network based approach over the competing alternatives.

  17. Extending the scope of diagnostic chromosome analysis: detection of single gene defects using high-resolution SNP microarrays.

    Science.gov (United States)

    Bruno, Damien L; Stark, Zornitza; Amor, David J; Burgess, Trent; Butler, Kathy; Corrie, Sylvea; Francis, David; Ganesamoorthy, Devika; Hills, Louise; James, Paul A; O'Rielly, Darren; Oertel, Ralph; Savarirayan, Ravi; Prabhakara, Krishnamurthy; Salce, Nicholas; Slater, Howard R

    2011-12-01

    Microarray analysis has provided significant advances in the diagnosis of conditions resulting from submicroscopic chromosome abnormalities. It has been recommended that array testing should be a "first tier" test in the evaluation of individuals with intellectual disability, developmental delay, congenital anomalies, and autism. The availability of arrays with increasingly high probe coverage and resolution has increased the detection of decreasingly small copy number changes (CNCs) down to the intragenic or even exon level. Importantly, arrays that genotype SNPs also detect extended regions of homozygosity. We describe 14 examples of single gene disorders caused by intragenic changes from a consecutive set of 6,500 tests using high-resolution SNP microarrays. These cases illustrate the increased scope of cytogenetic testing beyond dominant chromosome rearrangements that typically contain many genes. Nine of the cases confirmed the clinical diagnosis, that is, followed a "phenotype to genotype" approach. Five were diagnosed by the laboratory analysis in the absence of a specific clinical diagnosis, that is, followed a "genotype to phenotype" approach. Two were clinically significant, incidental findings. The importance of astute clinical assessment and laboratory-clinician consultation is emphasized to optimize the value of microarrays in the diagnosis of disorders caused by single gene copy number and sequence mutations. © 2011 Wiley-Liss, Inc.

  18. Coupling amplified DNA from flow-sorted chromosomes to high-density SNP mapping in barley

    Directory of Open Access Journals (Sweden)

    Bartoš Jan

    2008-06-01

    Full Text Available Abstract Background Flow cytometry facilitates sorting of single chromosomes and chromosome arms which can be used for targeted genome analysis. However, the recovery of microgram amounts of DNA needed for some assays requires sorting of millions of chromosomes which is laborious and time consuming. Yet, many genomic applications such as development of genetic maps or physical mapping do not require large DNA fragments. In such cases time-consuming de novo sorting can be minimized by utilizing whole-genome amplification. Results Here we report a protocol optimized in barley including amplification of DNA from only ten thousand chromosomes, which can be isolated in less than one hour. Flow-sorted chromosomes were treated with proteinase K and amplified using Phi29 multiple displacement amplification (MDA. Overnight amplification in a 20-microlitre reaction produced 3.7 – 5.7 micrograms DNA with a majority of products between 5 and 30 kb. To determine the purity of sorted fractions and potential amplification bias we used quantitative PCR for specific genes on each chromosome. To extend the analysis to a whole genome level we performed an oligonucleotide pool assay (OPA for interrogation of 1524 loci, of which 1153 loci had known genetic map positions. Analysis of unamplified genomic DNA of barley cv. Akcent using this OPA resulted in 1426 markers with present calls. Comparison with three replicates of amplified genomic DNA revealed >99% concordance. DNA samples from amplified chromosome 1H and a fraction containing chromosomes 2H – 7H were examined. In addition to loci with known map positions, 349 loci with unknown map positions were included. Based on this analysis 40 new loci were mapped to 1H. Conclusion The results indicate a significant potential of using this approach for physical mapping. Moreover, the study showed that multiple displacement amplification of flow-sorted chromosomes is highly efficient and representative which

  19. Design and characterization of a 52K SNP chip for goats.

    Directory of Open Access Journals (Sweden)

    Gwenola Tosser-Klopp

    Full Text Available The success of Genome Wide Association Studies in the discovery of sequence variation linked to complex traits in humans has increased interest in high throughput SNP genotyping assays in livestock species. Primary goals are QTL detection and genomic selection. The purpose here was design of a 50-60,000 SNP chip for goats. The success of a moderate density SNP assay depends on reliable bioinformatic SNP detection procedures, the technological success rate of the SNP design, even spacing of SNPs on the genome and selection of Minor Allele Frequencies (MAF suitable to use in diverse breeds. Through the federation of three SNP discovery projects consolidated as the International Goat Genome Consortium, we have identified approximately twelve million high quality SNP variants in the goat genome stored in a database together with their biological and technical characteristics. These SNPs were identified within and between six breeds (meat, milk and mixed: Alpine, Boer, Creole, Katjang, Saanen and Savanna, comprising a total of 97 animals. Whole genome and Reduced Representation Library sequences were aligned on >10 kb scaffolds of the de novo goat genome assembly. The 60,000 selected SNPs, evenly spaced on the goat genome, were submitted for oligo manufacturing (Illumina, Inc and published in dbSNP along with flanking sequences and map position on goat assemblies (i.e. scaffolds and pseudo-chromosomes, sheep genome V2 and cattle UMD3.1 assembly. Ten breeds were then used to validate the SNP content and 52,295 loci could be successfully genotyped and used to generate a final cluster file. The combined strategy of using mainly whole genome Next Generation Sequencing and mapping on a contig genome assembly, complemented with Illumina design tools proved to be efficient in producing this GoatSNP50 chip. Advances in use of molecular markers are expected to accelerate goat genomic studies in coming years.

  20. Dissection of Genetic Factors underlying Wheat Kernel Shape and Size in an Elite × Nonadapted Cross using a High Density SNP Linkage Map

    Directory of Open Access Journals (Sweden)

    Ajay Kumar

    2016-03-01

    Full Text Available Wheat kernel shape and size has been under selection since early domestication. Kernel morphology is a major consideration in wheat breeding, as it impacts grain yield and quality. A population of 160 recombinant inbred lines (RIL, developed using an elite (ND 705 and a nonadapted genotype (PI 414566, was extensively phenotyped in replicated field trials and genotyped using Infinium iSelect 90K assay to gain insight into the genetic architecture of kernel shape and size. A high density genetic map consisting of 10,172 single nucleotide polymorphism (SNP markers, with an average marker density of 0.39 cM/marker, identified a total of 29 genomic regions associated with six grain shape and size traits; ∼80% of these regions were associated with multiple traits. The analyses showed that kernel length (KL and width (KW are genetically independent, while a large number (∼59% of the quantitative trait loci (QTL for kernel shape traits were in common with genomic regions associated with kernel size traits. The most significant QTL was identified on chromosome 4B, and could be an ortholog of major rice grain size and shape gene or . Major and stable loci also were identified on the homeologous regions of Group 5 chromosomes, and in the regions of (6A and (7A genes. Both parental genotypes contributed equivalent positive QTL alleles, suggesting that the nonadapted germplasm has a great potential for enhancing the gene pool for grain shape and size. This study provides new knowledge on the genetic dissection of kernel morphology, with a much higher resolution, which may aid further improvement in wheat yield and quality using genomic tools.

  1. Dissection of Genetic Factors underlying Wheat Kernel Shape and Size in an Elite × Nonadapted Cross using a High Density SNP Linkage Map.

    Science.gov (United States)

    Kumar, Ajay; Mantovani, E E; Seetan, R; Soltani, A; Echeverry-Solarte, M; Jain, S; Simsek, S; Doehlert, D; Alamri, M S; Elias, E M; Kianian, S F; Mergoum, M

    2016-03-01

    Wheat kernel shape and size has been under selection since early domestication. Kernel morphology is a major consideration in wheat breeding, as it impacts grain yield and quality. A population of 160 recombinant inbred lines (RIL), developed using an elite (ND 705) and a nonadapted genotype (PI 414566), was extensively phenotyped in replicated field trials and genotyped using Infinium iSelect 90K assay to gain insight into the genetic architecture of kernel shape and size. A high density genetic map consisting of 10,172 single nucleotide polymorphism (SNP) markers, with an average marker density of 0.39 cM/marker, identified a total of 29 genomic regions associated with six grain shape and size traits; ∼80% of these regions were associated with multiple traits. The analyses showed that kernel length (KL) and width (KW) are genetically independent, while a large number (∼59%) of the quantitative trait loci (QTL) for kernel shape traits were in common with genomic regions associated with kernel size traits. The most significant QTL was identified on chromosome 4B, and could be an ortholog of major rice grain size and shape gene or . Major and stable loci also were identified on the homeologous regions of Group 5 chromosomes, and in the regions of (6A) and (7A) genes. Both parental genotypes contributed equivalent positive QTL alleles, suggesting that the nonadapted germplasm has a great potential for enhancing the gene pool for grain shape and size. This study provides new knowledge on the genetic dissection of kernel morphology, with a much higher resolution, which may aid further improvement in wheat yield and quality using genomic tools. Copyright © 2016 Crop Science Society of America.

  2. High-density single nucleotide polymorphism (SNP) array mapping in Brassica oleracea: identification of QTL associated with carotenoid variation in broccoli florets.

    Science.gov (United States)

    Brown, Allan F; Yousef, Gad G; Chebrolu, Kranthi K; Byrd, Robert W; Everhart, Koyt W; Thomas, Aswathy; Reid, Robert W; Parkin, Isobel A P; Sharpe, Andrew G; Oliver, Rebekah; Guzman, Ivette; Jackson, Eric W

    2014-09-01

    A high-resolution genetic linkage map of B. oleracea was developed from a B. napus SNP array. The work will facilitate genetic and evolutionary studies in Brassicaceae. A broccoli population, VI-158 × BNC, consisting of 150 F2:3 families was used to create a saturated Brassica oleracea (diploid: CC) linkage map using a recently developed rapeseed (Brassica napus) (tetraploid: AACC) Illumina Infinium single nucleotide polymorphism (SNP) array. The map consisted of 547 non-redundant SNP markers spanning 948.1 cM across nine chromosomes with an average interval size of 1.7 cM. As the SNPs are anchored to the genomic reference sequence of the rapid cycling B. oleracea TO1000, we were able to estimate that the map provides 96 % coverage of the diploid genome. Carotenoid analysis of 2 years data identified 3 QTLs on two chromosomes that are associated with up to half of the phenotypic variation associated with the accumulation of total or individual compounds. By searching the genome sequences of the two related diploid species (B. oleracea and B. rapa), we further identified putative carotenoid candidate genes in the region of these QTLs. This is the first description of the use of a B. napus SNP array to rapidly construct high-density genetic linkage maps of one of the constituent diploid species. The unambiguous nature of these markers with regard to genomic sequences provides evidence to the nature of genes underlying the QTL, and demonstrates the value and impact this resource will have on Brassica research.

  3. SNP interaction pattern identifier (SIPI)

    DEFF Research Database (Denmark)

    Lin, Hui Yi; Chen, Dung Tsa; Huang, Po Yu

    2017-01-01

    Motivation: Testing SNP-SNP interactions is considered as a key for overcoming bottlenecks of genetic association studies. However, related statistical methods for testing SNP-SNP interactions are underdeveloped. Results: We propose the SNP Interaction Pattern Identifier (SIPI), which tests 45...

  4. SNP genotyping technologies

    DEFF Research Database (Denmark)

    Studer, Bruno; Kölliker, Roland

    2013-01-01

    In the recent years, single nucleotide polymorphism (SNP) markers have emerged as the marker technology of choice for plant genetics and breeding applications. Besides the efficient technologies available for SNP discovery even in complex genomes, one of the main reasons for this is the availabil...

  5. Association between genetic subgroups of pancreatic ductal adenocarcinoma defined by high density 500 K SNP-arrays and tumor histopathology.

    Directory of Open Access Journals (Sweden)

    María Laura Gutiérrez

    Full Text Available The specific genes and genetic pathways associated with pancreatic ductal adenocarcinoma are still largely unknown partially due to the low resolution of the techniques applied so far to their study. Here we used high-density 500 K single nucleotide polymorphism (SNP-arrays to define those chromosomal regions which most commonly harbour copy number (CN alterations and loss of heterozygozity (LOH in a series of 20 PDAC tumors and we correlated the corresponding genetic profiles with the most relevant clinical and histopathological features of the disease. Overall our results showed that primary PDAC frequently display (>70% extensive gains of chromosomes 1q, 7q, 8q and 20q, together with losses of chromosomes 1p, 9p, 12q, 17p and 18q, such chromosomal regions harboring multiple cancer- and PDAC-associated genes. Interestingly, these alterations clustered into two distinct genetic profiles characterized by gains of the 2q14.2, 3q22.1, 5q32, 10q26.13, 10q26.3, 11q13.1, 11q13.3, 11q13.4, 16q24.1, 16q24.3, 22q13.1, 22q13.31 and 22q13.32 chromosomal regions (group 1; n = 9 versus gains at 1q21.1 and losses of the 1p36.11, 6q25.2, 9p22.1, 9p24.3, 17p13.3 and Xp22.33 chromosomal regions (group 2; n = 11. From the clinical and histopathological point of view, group 1 cases were associated with smaller and well/moderately-differentiated grade I/II PDAC tumors, whereas and group 2 PDAC displayed a larger size and they mainly consisted of poorly-differentiated grade III carcinomas. These findings confirm the cytogenetic complexity and heterozygozity of PDAC and provide evidence for the association between tumor cytogenetics and its histopathological features. In addition, we also show that the altered regions identified harbor multiple cancer associate genes that deserve further investigation to determine their relevance in the pathogenesis of PDAC.

  6. SNP genotyping by DNA photoligation: application to SNP detection of genes from food crops

    Energy Technology Data Exchange (ETDEWEB)

    Yoshimura, Yoshinaga; Ohtake, Tomoko; Okada, Hajime; Fujimoto, Kenzo [School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292 (Japan); Ami, Takehiro [Innovation Plaza Ishikawa, Japan Science and Technology Agency, 2-13 Asahidai, Nomi, Ishikawa 923-1211 (Japan); Tsukaguchi, Tadashi, E-mail: kenzo@jaist.ac.j [Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi, Ishikawa 921-8836 (Japan)

    2009-06-15

    We describe a simple and inexpensive single-nucleotide polymorphism (SNP) typing method, using DNA photoligation with 5-carboxyvinyl-2'-deoxyuridine and two fluorophores. This SNP-typing method facilitates qualitative determination of genes from indica and japonica rice, and showed a high degree of single nucleotide specificity up to 10 000. This method can be used in the SNP typing of actual genomic DNA samples from food crops.

  7. SNP genotyping by DNA photoligation: application to SNP detection of genes from food crops

    Directory of Open Access Journals (Sweden)

    Yoshinaga Yoshimura, Tomoko Ohtake, Hajime Okada, Takehiro Ami, Tadashi Tsukaguchi and Kenzo Fujimoto

    2009-01-01

    Full Text Available We describe a simple and inexpensive single-nucleotide polymorphism (SNP typing method, using DNA photoligation with 5-carboxyvinyl-2'-deoxyuridine and two fluorophores. This SNP-typing method facilitates qualitative determination of genes from indica and japonica rice, and showed a high degree of single nucleotide specificity up to 10 000. This method can be used in the SNP typing of actual genomic DNA samples from food crops.

  8. An Improved Opposition-Based Learning Particle Swarm Optimization for the Detection of SNP-SNP Interactions

    Science.gov (United States)

    Shang, Junliang; Sun, Yan; Li, Shengjun; Liu, Jin-Xing; Zheng, Chun-Hou; Zhang, Junying

    2015-01-01

    SNP-SNP interactions have been receiving increasing attention in understanding the mechanism underlying susceptibility to complex diseases. Though many works have been done for the detection of SNP-SNP interactions, the algorithmic development is still ongoing. In this study, an improved opposition-based learning particle swarm optimization (IOBLPSO) is proposed for the detection of SNP-SNP interactions. Highlights of IOBLPSO are the introduction of three strategies, namely, opposition-based learning, dynamic inertia weight, and a postprocedure. Opposition-based learning not only enhances the global explorative ability, but also avoids premature convergence. Dynamic inertia weight allows particles to cover a wider search space when the considered SNP is likely to be a random one and converges on promising regions of the search space while capturing a highly suspected SNP. The postprocedure is used to carry out a deep search in highly suspected SNP sets. Experiments of IOBLPSO are performed on both simulation data sets and a real data set of age-related macular degeneration, results of which demonstrate that IOBLPSO is promising in detecting SNP-SNP interactions. IOBLPSO might be an alternative to existing methods for detecting SNP-SNP interactions. PMID:26236727

  9. Genome-Wide SNP Detection, Validation, and Development of an 8K SNP Array for Apple

    NARCIS (Netherlands)

    Chagné, D.; Crowhurst, R.N.; Troggio, M.; Davey, M.W.; Gilmore, B.; Lawley, C.; Vanderzande, S.; Hellens, R.P.; Kumar, S.; Cestaro, A.; Velasco, R.; Main, D.; Rees, J.D.; Iezzoni, A.F.; Mockler, T.; Wilhelm, L.; Weg, van de W.E.; Gardiner, S.E.; Bassil, N.; Peace, C.

    2012-01-01

    As high-throughput genetic marker screening systems are essential for a range of genetics studies and plant breeding applications, the International RosBREED SNP Consortium (IRSC) has utilized the Illumina Infinium® II system to develop a medium- to high-throughput SNP screening tool for genome-wide

  10. dbSNP

    Data.gov (United States)

    U.S. Department of Health & Human Services — dbSNP is a database of single nucleotide polymorphisms (SNPs) and multiple small-scale variations that include insertions/deletions, microsatellites, and...

  11. Use of genotyping by sequencing data to develop a high-throughput and multifunctional SNP panel for conservation applications in Pacific lamprey.

    Science.gov (United States)

    Hess, Jon E; Campbell, Nathan R; Docker, Margaret F; Baker, Cyndi; Jackson, Aaron; Lampman, Ralph; McIlraith, Brian; Moser, Mary L; Statler, David P; Young, William P; Wildbill, Andrew J; Narum, Shawn R

    2015-01-01

    Next-generation sequencing data can be mined for highly informative single nucleotide polymorphisms (SNPs) to develop high-throughput genomic assays for nonmodel organisms. However, choosing a set of SNPs to address a variety of objectives can be difficult because SNPs are often not equally informative. We developed an optimal combination of 96 high-throughput SNP assays from a total of 4439 SNPs identified in a previous study of Pacific lamprey (Entosphenus tridentatus) and used them to address four disparate objectives: parentage analysis, species identification and characterization of neutral and adaptive variation. Nine of these SNPs are FST outliers, and five of these outliers are localized within genes and significantly associated with geography, run-timing and dwarf life history. Two of the 96 SNPs were diagnostic for two other lamprey species that were morphologically indistinguishable at early larval stages and were sympatric in the Pacific Northwest. The majority (85) of SNPs in the panel were highly informative for parentage analysis, that is, putatively neutral with high minor allele frequency across the species' range. Results from three case studies are presented to demonstrate the broad utility of this panel of SNP markers in this species. As Pacific lamprey populations are undergoing rapid decline, these SNPs provide an important resource to address critical uncertainties associated with the conservation and recovery of this imperiled species. © 2014 John Wiley & Sons Ltd.

  12. Genome-wide detection of CNVs in Chinese indigenous sheep with different types of tails using ovine high-density 600K SNP arrays

    OpenAIRE

    Zhu, Caiye; Fan, Hongying; Yuan, Zehu; Hu, Shijin; Ma, Xiaomeng; Xuan, Junli; Wang, Hongwei; Zhang, Li; Wei, Caihong; Zhang, Qin; Zhao, Fuping; Du, Lixin

    2016-01-01

    Chinese indigenous sheep can be classified into three types based on tail morphology: fat-tailed, fat-rumped, and thin-tailed sheep, of which the typical breeds are large-tailed Han sheep, Altay sheep, and Tibetan sheep, respectively. To unravel the genetic mechanisms underlying the phenotypic differences among Chinese indigenous sheep with tails of three different types, we used ovine high-density 600K SNP arrays to detect genome-wide copy number variation (CNV). In large-tailed Han sheep, A...

  13. fcGENE: a versatile tool for processing and transforming SNP datasets.

    Directory of Open Access Journals (Sweden)

    Nab Raj Roshyara

    Full Text Available Modern analysis of high-dimensional SNP data requires a number of biometrical and statistical methods such as pre-processing, analysis of population structure, association analysis and genotype imputation. Software used for these purposes often rely on specific and incompatible input and output data formats. Therefore extensive data management including multiple format conversions is necessary during analyses.In order to support fast and efficient management and bio-statistical quality control of high-dimensional SNP data, we developed the publically available software fcGENE using C++ object-oriented programming language. This software simplifies and automates the use of different existing analysis packages, especially during the workflow of genotype imputations and corresponding analyses.fcGENE transforms SNP data and imputation results into different formats required for a large variety of analysis packages such as PLINK, SNPTEST, HAPLOVIEW, EIGENSOFT, GenABEL and tools used for genotype imputation such as MaCH, IMPUTE, BEAGLE and others. Data Management tasks like merging, splitting, extracting SNP and pedigree information can be performed. fcGENE also supports a number of bio-statistical quality control processes and quality based filtering processes at SNP- and sample-wise level. The tool also generates templates of commands required to run specific software packages, especially those required for genotype imputation. We demonstrate the functionality of fcGENE by example workflows of SNP data analyses and provide a comprehensive manual of commands, options and applications.We have developed a user-friendly open-source software fcGENE, which comprehensively supports SNP data management, quality control and analysis workflows. Download statistics and corresponding feedbacks indicate that software is highly recognised and extensively applied by the scientific community.

  14. Comprehensive high-resolution genomic profiling and cytogenetics of human chondrocyte cultures by GTG-banding, locus-specific FISH, SKY and SNP array.

    Science.gov (United States)

    Wallenborn, M; Petters, O; Rudolf, D; Hantmann, H; Richter, M; Ahnert, P; Rohani, L; Smink, J J; Bulwin, G C; Krupp, W; Schulz, R M; Holland, H

    2018-04-23

    In the development of cell-based medicinal products, it is crucial to guarantee that the application of such an advanced therapy medicinal product (ATMP) is safe for the patients. The consensus of the European regulatory authorities is: "In conclusion, on the basis of the state of art, conventional karyotyping can be considered a valuable and useful technique to analyse chromosomal stability during preclinical studies". 408 chondrocyte samples (84 monolayers and 324 spheroids) from six patients were analysed using trypsin-Giemsa staining, spectral karyotyping and fluorescence in situ hybridisation, to evaluate the genetic stability of an ATMP named Spherox®. Single nucleotide polymorphism (SNP) array analysis was performed on chondrocyte spheroids from five of the six donors. Applying this combination of techniques, the genetic analyses performed revealed no significant genetic instability until passage 3 in monolayer cells and interphase cells from spheroid cultures at different time points. Clonal occurrence of polyploid metaphases and endoreduplications were identified associated with prolonged cultivation time. Also, gonosomal losses were observed in chondrocyte spheroids, with increasing passage and duration of the differentiation phase. Interestingly, in one of the donors, chromosomal aberrations that are also described in extraskeletal myxoid chondrosarcoma were identified. The SNP array analysis exhibited chromosomal aberrations in two donors and copy neutral losses of heterozygosity regions in four donors. This study showed the necessity of combined genetic analyses at defined cultivation time points in quality studies within the field of cell therapy.

  15. Forensic genetic SNP typing of low-template DNA and highly degraded DNA from crime case samples.

    Science.gov (United States)

    Børsting, Claus; Mogensen, Helle Smidt; Morling, Niels

    2013-05-01

    Heterozygote imbalances leading to allele drop-outs and disproportionally large stutters leading to allele drop-ins are known stochastic phenomena related to STR typing of low-template DNA (LtDNA). The large stutters and the many drop-ins in typical STR stutter positions are artifacts from the PCR amplification of tandem repeats. These artifacts may be avoided by typing bi-allelic markers instead of STRs. In this work, the SNPforID multiplex assay was used to type LtDNA. A sensitized SNP typing protocol was introduced, that increased signal strengths without increasing noise and without affecting the heterozygote balance. Allele drop-ins were only observed in experiments with 25 pg of DNA and not in experiments with 50 and 100 pg of DNA. The allele drop-in rate in the 25 pg experiments was 0.06% or 100 times lower than what was previously reported for STR typing of LtDNA. A composite model and two different consensus models were used to interpret the SNP data. Correct profiles with 42-49 SNPs were generated from the 50 and 100 pg experiments, whereas a few incorrect genotypes were included in the generated profiles from the 25 pg experiments. With the strict consensus model, between 35 and 48 SNPs were correctly typed in the 25 pg experiments and only one allele drop-out (error rate: 0.07%) was observed in the consensus profiles. A total of 28 crime case samples were selected for typing with the sensitized SNPforID protocol. The samples were previously typed with old STR kits during the crime case investigation and only partial profiles (0-6 STRs) were obtained. Eleven of the samples could not be quantified with the Quantifiler™ Human DNA Quantification kit because of partial or complete inhibition of the PCR. For eight of these samples, SNP typing was only possible when the buffer and DNA polymerase used in the original protocol was replaced with the AmpFℓSTR(®) SEfiler Plus™ Master Mix, which was developed specifically for challenging forensic samples. All

  16. Three gangliogliomas: results of GTG-banding, SKY, genome-wide high resolution SNP-array, gene expression and review of the literature.

    Science.gov (United States)

    Xu, Li-Xin; Holland, Heidrun; Kirsten, Holger; Ahnert, Peter; Krupp, Wolfgang; Bauer, Manfred; Schober, Ralf; Mueller, Wolf; Fritzsch, Dominik; Meixensberger, Jürgen; Koschny, Ronald

    2015-04-01

    According to the World Health Organization gangliogliomas are classified as well-differentiated and slowly growing neuroepithelial tumors, composed of neoplastic mature ganglion and glial cells. It is the most frequent tumor entity observed in patients with long-term epilepsy. Comprehensive cytogenetic and molecular cytogenetic data including high-resolution genomic profiling (single nucleotide polymorphism (SNP)-array) of gangliogliomas are scarce but necessary for a better oncological understanding of this tumor entity. For a detailed characterization at the single cell and cell population levels, we analyzed genomic alterations of three gangliogliomas using trypsin-Giemsa banding (GTG-banding) and by spectral karyotyping (SKY) in combination with SNP-array and gene expression array experiments. By GTG and SKY, we could confirm frequently detected chromosomal aberrations (losses within chromosomes 10, 13 and 22; gains within chromosomes 5, 7, 8 and 12), and identify so far unknown genetic aberrations like the unbalanced non-reciprocal translocation t(1;18)(q21;q21). Interestingly, we report on the second so far detected ganglioglioma with ring chromosome 1. Analyses of SNP-array data from two of the tumors and respective germline DNA (peripheral blood) identified few small gains and losses and a number of copy-neutral regions with loss of heterozygosity (LOH) in germline and in tumor tissue. In comparison to germline DNA, tumor tissues did not show substantial regions with significant loss or gain or with newly developed LOH. Gene expression analyses of tumor-specific genes revealed similarities in the profile of the analyzed samples regarding different relevant pathways. Taken together, we describe overlapping but also distinct and novel genetic aberrations of three gangliogliomas. © 2014 Japanese Society of Neuropathology.

  17. Association study of phenology, yield and quality related traits in table grapes using SSR and SNP markers

    OpenAIRE

    Zarouri, Belkacem

    2016-01-01

    The advent of cheaper high throughput genotyping technologies and the availability of large germplasm collections encouraged the extension of Genome-Wide Association Studies (GWAS) to crop plants. However, to date these strategies have not yet been tested in grapevine (Vitis vinífera L.). Taking advantage of the availability of a large grapevine germplasm collection maintained at the germplasm bank of El Encín (Alcalá de Henares, Madrid, Spain) and the relatively affordable genotyping tools, ...

  18. Forensic genetic SNP typing of low-template DNA and highly degraded DNA from crime case samples

    DEFF Research Database (Denmark)

    Børsting, Claus; Mogensen, Helle Smidt; Morling, Niels

    2013-01-01

    the heterozygote balance. Allele drop-ins were only observed in experiments with 25 pg of DNA and not in experiments with 50 and 100 pg of DNA. The allele drop-in rate in the 25 pg experiments was 0.06% or 100 times lower than what was previously reported for STR typing of LtDNA. A composite model and two......Heterozygote imbalances leading to allele drop-outs and disproportionally large stutters leading to allele drop-ins are known stochastic phenomena related to STR typing of low-template DNA (LtDNA). The large stutters and the many drop-ins in typical STR stutter positions are artifacts from the PCR...... amplification of tandem repeats. These artifacts may be avoided by typing bi-allelic markers instead of STRs. In this work, the SNPforID multiplex assay was used to type LtDNA. A sensitized SNP typing protocol was introduced, that increased signal strengths without increasing noise and without affecting...

  19. Development and implementation of a highly-multiplexed SNP array for genetic mapping in maritime pine and comparative mapping with loblolly pine

    Directory of Open Access Journals (Sweden)

    Garnier-Géré Pauline

    2011-07-01

    Full Text Available Abstract Background Single nucleotide polymorphisms (SNPs are the most abundant source of genetic variation among individuals of a species. New genotyping technologies allow examining hundreds to thousands of SNPs in a single reaction for a wide range of applications such as genetic diversity analysis, linkage mapping, fine QTL mapping, association studies, marker-assisted or genome-wide selection. In this paper, we evaluated the potential of highly-multiplexed SNP genotyping for genetic mapping in maritime pine (Pinus pinaster Ait., the main conifer used for commercial plantation in southwestern Europe. Results We designed a custom GoldenGate assay for 1,536 SNPs detected through the resequencing of gene fragments (707 in vitro SNPs/Indels and from Sanger-derived Expressed Sequenced Tags assembled into a unigene set (829 in silico SNPs/Indels. Offspring from three-generation outbred (G2 and inbred (F2 pedigrees were genotyped. The success rate of the assay was 63.6% and 74.8% for in silico and in vitro SNPs, respectively. A genotyping error rate of 0.4% was further estimated from segregating data of SNPs belonging to the same gene. Overall, 394 SNPs were available for mapping. A total of 287 SNPs were integrated with previously mapped markers in the G2 parental maps, while 179 SNPs were localized on the map generated from the analysis of the F2 progeny. Based on 98 markers segregating in both pedigrees, we were able to generate a consensus map comprising 357 SNPs from 292 different loci. Finally, the analysis of sequence homology between mapped markers and their orthologs in a Pinus taeda linkage map, made it possible to align the 12 linkage groups of both species. Conclusions Our results show that the GoldenGate assay can be used successfully for high-throughput SNP genotyping in maritime pine, a conifer species that has a genome seven times the size of the human genome. This SNP-array will be extended thanks to recent sequencing effort using

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

    Science.gov (United States)

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

    2018-06-01

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

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

    Directory of Open Access Journals (Sweden)

    Peipei Zhang

    2017-05-01

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

  2. Multiplex PCR with minisequencing as an effective high-throughput SNP typing method for formalin-fixed tissue

    DEFF Research Database (Denmark)

    Gilbert, Marcus T P; Sanchez, Juan J; Haselkorn, Tamara

    2007-01-01

    , multiplex PCR with minisequencing (MPMS), on 92 DNA extractions performed on six archival FFPE samples of variable DNA quality, which date between 9 and 25 years old. On the three extracts with highest quality, we found the assay efficiency to be near 100%. However, the efficiency of the lowest quality...... extracts varied significantly. In this study, we demonstrate that although direct measures of DNA concentration in the extracts provide no useful information with regard to subsequent MPMS success, the success of the assay can be determined to some degree a priori, through initial screening of the DNA...... quality using a simple quantitative real-time PCR (qPCR) assay for nuclear DNA, and/or an assay of the maximum PCR amplifiable size of nuclear DNA. MPMS promises to be of significant use in future genetic studies on FFPE material. It provides a streamlined approach for retrieving a large amount of genetic...

  3. Development of highly reliable in silico SNP resource and genotyping assay from exome capture and sequencing: an example from black spruce (Picea mariana).

    Science.gov (United States)

    Pavy, Nathalie; Gagnon, France; Deschênes, Astrid; Boyle, Brian; Beaulieu, Jean; Bousquet, Jean

    2016-03-01

    Picea mariana is a widely distributed boreal conifer across Canada and the subject of advanced breeding programmes for which population genomics and genomic selection approaches are being developed. Targeted sequencing was achieved after capturing P. mariana exome with probes designed from the sequenced transcriptome of Picea glauca, a distant relative. A high capture efficiency of 75.9% was reached although spruce has a complex and large genome including gene sequences interspersed by some long introns. The results confirmed the relevance of using probes from congeneric species to perform successfully interspecific exome capture in the genus Picea. A bioinformatics pipeline was developed including stringent criteria that helped detect a set of 97,075 highly reliable in silico SNPs. These SNPs were distributed across 14,909 genes. Part of an Infinium iSelect array was used to estimate the rate of true positives by validating 4267 of the predicted in silico SNPs by genotyping trees from P. mariana populations. The true positive rate was 96.2% for in silico SNPs, compared to a genotyping success rate of 96.7% for a set 1115 P. mariana control SNPs recycled from previous genotyping arrays. These results indicate the high success rate of the genotyping array and the relevance of the selection criteria used to delineate the new P. mariana in silico SNP resource. Furthermore, in silico SNPs were generally of medium to high frequency in natural populations, thus providing high informative value for future population genomics applications. © 2015 John Wiley & Sons Ltd.

  4. Development of COS-SNP and HRM markers for high-throughput and reliable haplotype-based detection of Lr14a in durum wheat (Triticum durum Desf.).

    Science.gov (United States)

    Terracciano, Irma; Maccaferri, Marco; Bassi, Filippo; Mantovani, Paola; Sanguineti, Maria C; Salvi, Silvio; Simková, Hana; Doležel, Jaroslav; Massi, Andrea; Ammar, Karim; Kolmer, James; Tuberosa, Roberto

    2013-04-01

    Leaf rust (Puccinia triticina Eriks. & Henn.) is a major disease affecting durum wheat production. The Lr14a-resistant gene present in the durum wheat cv. Creso and its derivative cv. Colosseo is one of the best characterized leaf-rust resistance sources deployed in durum wheat breeding. Lr14a has been mapped close to the simple sequence repeat markers gwm146, gwm344 and wmc10 in the distal portion of the chromosome arm 7BL, a gene-dense region. The objectives of this study were: (1) to enrich the Lr14a region with single nucleotide polymorphisms (SNPs) and high-resolution melting (HRM)-based markers developed from conserved ortholog set (COS) genes and from sequenced Diversity Array Technology (DArT(®)) markers; (2) to further investigate the gene content and colinearity of this region with the Brachypodium and rice genomes. Ten new COS-SNP and five HRM markers were mapped within an 8.0 cM interval spanning Lr14a. Two HRM markers pinpointed the locus in an interval of HRM designed for agarose gel electrophoresis/KASPar(®) assays and high-resolution melting analysis, respectively, as well as the double-marker combinations ubw14/ubw18, ubw14/ubw35 and wPt-4038-HRM-ubw35 will be useful for germplasm haplotyping and for molecular-assisted breeding.

  5. Exhaustive Genome-Wide Search for SNP-SNP Interactions Across 10 Human Diseases

    Directory of Open Access Journals (Sweden)

    William Murk

    2016-07-01

    Full Text Available The identification of statistical SNP-SNP interactions may help explain the genetic etiology of many human diseases, but exhaustive genome-wide searches for these interactions have been difficult, due to a lack of power in most datasets. We aimed to use data from the Resource for Genetic Epidemiology Research on Adult Health and Aging (GERA study to search for SNP-SNP interactions associated with 10 common diseases. FastEpistasis and BOOST were used to evaluate all pairwise interactions among approximately N = 300,000 single nucleotide polymorphisms (SNPs with minor allele frequency (MAF ≥ 0.15, for the dichotomous outcomes of allergic rhinitis, asthma, cardiac disease, depression, dermatophytosis, type 2 diabetes, dyslipidemia, hemorrhoids, hypertensive disease, and osteoarthritis. A total of N = 45,171 subjects were included after quality control steps were applied. These data were divided into discovery and replication subsets; the discovery subset had > 80% power, under selected models, to detect genome-wide significant interactions (P < 10−12. Interactions were also evaluated for enrichment in particular SNP features, including functionality, prior disease relevancy, and marginal effects. No interaction in any disease was significant in both the discovery and replication subsets. Enrichment analysis suggested that, for some outcomes, interactions involving SNPs with marginal effects were more likely to be nominally replicated, compared to interactions without marginal effects. If SNP-SNP interactions play a role in the etiology of the studied conditions, they likely have weak effect sizes, involve lower-frequency variants, and/or involve complex models of interaction that are not captured well by the methods that were utilized.

  6. Whole-genome single-nucleotide polymorphism (SNP marker discovery and association analysis with the eicosapentaenoic acid (EPA and docosahexaenoic acid (DHA content in Larimichthys crocea

    Directory of Open Access Journals (Sweden)

    Shijun Xiao

    2016-12-01

    Full Text Available Whole-genome single-nucleotide polymorphism (SNP markers are valuable genetic resources for the association and conservation studies. Genome-wide SNP development in many teleost species are still challenging because of the genome complexity and the cost of re-sequencing. Genotyping-By-Sequencing (GBS provided an efficient reduced representative method to squeeze cost for SNP detection; however, most of recent GBS applications were reported on plant organisms. In this work, we used an EcoRI-NlaIII based GBS protocol to teleost large yellow croaker, an important commercial fish in China and East-Asia, and reported the first whole-genome SNP development for the species. 69,845 high quality SNP markers that evenly distributed along genome were detected in at least 80% of 500 individuals. Nearly 95% randomly selected genotypes were successfully validated by Sequenom MassARRAY assay. The association studies with the muscle eicosapentaenoic acid (EPA and docosahexaenoic acid (DHA content discovered 39 significant SNP markers, contributing as high up to ∼63% genetic variance that explained by all markers. Functional genes that involved in fat digestion and absorption pathway were identified, such as APOB, CRAT and OSBPL10. Notably, PPT2 Gene, previously identified in the association study of the plasma n-3 and n-6 polyunsaturated fatty acid level in human, was re-discovered in large yellow croaker. Our study verified that EcoRI-NlaIII based GBS could produce quality SNP markers in a cost-efficient manner in teleost genome. The developed SNP markers and the EPA and DHA associated SNP loci provided invaluable resources for the population structure, conservation genetics and genomic selection of large yellow croaker and other fish organisms.

  7. Fast High-Quality Noise

    DEFF Research Database (Denmark)

    Frisvad, Jeppe Revall; Wyvill, Geoff

    2007-01-01

    At the moment the noise functions available in a graphics programmer's toolbox are either slow to compute or they involve grid-line artifacts making them of lower quality. In this paper we present a real-time noise computation with no grid-line artifacts or other regularity problems. In other words......, we put a new tool in the box that computes fast high-quality noise. In addition to being free of artifacts, the noise we present does not rely on tabulated data (everything is computed on the fly) and it is easy to adjust quality vs. quantity for the noise. The noise is based on point rendering (like...... spot noise), but it extends to more than two dimensions. The fact that it is based on point rendering makes art direction of the noise much easier....

  8. Genome-Wide SNP Detection, Validation, and Development of an 8K SNP Array for Apple

    Science.gov (United States)

    Chagné, David; Crowhurst, Ross N.; Troggio, Michela; Davey, Mark W.; Gilmore, Barbara; Lawley, Cindy; Vanderzande, Stijn; Hellens, Roger P.; Kumar, Satish; Cestaro, Alessandro; Velasco, Riccardo; Main, Dorrie; Rees, Jasper D.; Iezzoni, Amy; Mockler, Todd; Wilhelm, Larry; Van de Weg, Eric; Gardiner, Susan E.; Bassil, Nahla; Peace, Cameron

    2012-01-01

    As high-throughput genetic marker screening systems are essential for a range of genetics studies and plant breeding applications, the International RosBREED SNP Consortium (IRSC) has utilized the Illumina Infinium® II system to develop a medium- to high-throughput SNP screening tool for genome-wide evaluation of allelic variation in apple (Malus×domestica) breeding germplasm. For genome-wide SNP discovery, 27 apple cultivars were chosen to represent worldwide breeding germplasm and re-sequenced at low coverage with the Illumina Genome Analyzer II. Following alignment of these sequences to the whole genome sequence of ‘Golden Delicious’, SNPs were identified using SoapSNP. A total of 2,113,120 SNPs were detected, corresponding to one SNP to every 288 bp of the genome. The Illumina GoldenGate® assay was then used to validate a subset of 144 SNPs with a range of characteristics, using a set of 160 apple accessions. This validation assay enabled fine-tuning of the final subset of SNPs for the Illumina Infinium® II system. The set of stringent filtering criteria developed allowed choice of a set of SNPs that not only exhibited an even distribution across the apple genome and a range of minor allele frequencies to ensure utility across germplasm, but also were located in putative exonic regions to maximize genotyping success rate. A total of 7867 apple SNPs was established for the IRSC apple 8K SNP array v1, of which 5554 were polymorphic after evaluation in segregating families and a germplasm collection. This publicly available genomics resource will provide an unprecedented resolution of SNP haplotypes, which will enable marker-locus-trait association discovery, description of the genetic architecture of quantitative traits, investigation of genetic variation (neutral and functional), and genomic selection in apple. PMID:22363718

  9. Genome-wide SNP detection, validation, and development of an 8K SNP array for apple.

    Directory of Open Access Journals (Sweden)

    David Chagné

    Full Text Available As high-throughput genetic marker screening systems are essential for a range of genetics studies and plant breeding applications, the International RosBREED SNP Consortium (IRSC has utilized the Illumina Infinium® II system to develop a medium- to high-throughput SNP screening tool for genome-wide evaluation of allelic variation in apple (Malus×domestica breeding germplasm. For genome-wide SNP discovery, 27 apple cultivars were chosen to represent worldwide breeding germplasm and re-sequenced at low coverage with the Illumina Genome Analyzer II. Following alignment of these sequences to the whole genome sequence of 'Golden Delicious', SNPs were identified using SoapSNP. A total of 2,113,120 SNPs were detected, corresponding to one SNP to every 288 bp of the genome. The Illumina GoldenGate® assay was then used to validate a subset of 144 SNPs with a range of characteristics, using a set of 160 apple accessions. This validation assay enabled fine-tuning of the final subset of SNPs for the Illumina Infinium® II system. The set of stringent filtering criteria developed allowed choice of a set of SNPs that not only exhibited an even distribution across the apple genome and a range of minor allele frequencies to ensure utility across germplasm, but also were located in putative exonic regions to maximize genotyping success rate. A total of 7867 apple SNPs was established for the IRSC apple 8K SNP array v1, of which 5554 were polymorphic after evaluation in segregating families and a germplasm collection. This publicly available genomics resource will provide an unprecedented resolution of SNP haplotypes, which will enable marker-locus-trait association discovery, description of the genetic architecture of quantitative traits, investigation of genetic variation (neutral and functional, and genomic selection in apple.

  10. SNP detection for massively parallel whole-genome resequencing

    DEFF Research Database (Denmark)

    Li, Ruiqiang; Li, Yingrui; Fang, Xiaodong

    2009-01-01

    -genome or target region resequencing. Here, we have developed a consensus-calling and SNP-detection method for sequencing-by-synthesis Illumina Genome Analyzer technology. We designed this method by carefully considering the data quality, alignment, and experimental errors common to this technology. All...... of this information was integrated into a single quality score for each base under Bayesian theory to measure the accuracy of consensus calling. We tested this methodology using a large-scale human resequencing data set of 36x coverage and assembled a high-quality nonrepetitive consensus sequence for 92.......25% of the diploid autosomes and 88.07% of the haploid X chromosome. Comparison of the consensus sequence with Illumina human 1M BeadChip genotyped alleles from the same DNA sample showed that 98.6% of the 37,933 genotyped alleles on the X chromosome and 98% of 999,981 genotyped alleles on autosomes were covered...

  11. SNP discovery in the transcriptome of white Pacific shrimp Litopenaeus vannamei by next generation sequencing.

    Directory of Open Access Journals (Sweden)

    Yang Yu

    Full Text Available The application of next generation sequencing technology has greatly facilitated high throughput single nucleotide polymorphism (SNP discovery and genotyping in genetic research. In the present study, SNPs were discovered based on two transcriptomes of Litopenaeus vannamei (L. vannamei generated from Illumina sequencing platform HiSeq 2000. One transcriptome of L. vannamei was obtained through sequencing on the RNA from larvae at mysis stage and its reference sequence was de novo assembled. The data from another transcriptome were downloaded from NCBI and the reads of the two transcriptomes were mapped separately to the assembled reference by BWA. SNP calling was performed using SAMtools. A total of 58,717 and 36,277 SNPs with high quality were predicted from the two transcriptomes, respectively. SNP calling was also performed using the reads of two transcriptomes together, and a total of 96,040 SNPs with high quality were predicted. Among these 96,040 SNPs, 5,242 and 29,129 were predicted as non-synonymous and synonymous SNPs respectively. Characterization analysis of the predicted SNPs in L. vannamei showed that the estimated SNP frequency was 0.21% (one SNP per 476 bp and the estimated ratio for transition to transversion was 2.0. Fifty SNPs were randomly selected for validation by Sanger sequencing after PCR amplification and 76% of SNPs were confirmed, which indicated that the SNPs predicted in this study were reliable. These SNPs will be very useful for genetic study in L. vannamei, especially for the high density linkage map construction and genome-wide association studies.

  12. Influence of the interaction between environmental quality and T102C SNP in the HTR2A gene on fibromyalgia susceptibility.

    Science.gov (United States)

    Mergener, Michelle; Becker, Roze Mary Ribas; dos Santos, Adriana Freitag; dos Santos, Geraldine Alves; de Andrade, Fabiana Michelsen

    2011-12-01

    This study aimed to investigate the genetic influence of the T102C polymorphism of the 2A serotonin receptor gene (HTR2A) and its interaction with environmental aspects, such as exposure to noise, traffic, climate, and opportunities to acquire new information, physical protection, and security, among others, as possible risk factors for developing fibromyalgia syndrome (FMS). Forty-one FMS patients and 49 controls were evaluated. Environmental factors were evaluated by application of the V domain of the WHOQOL-100 questionnaire. Patients were asked that their answers represented only the periods preceding the onset of symptoms. The T102C variant of the HTR2A gene was determined through PCR/RFLP. Among patients, the frequency of carriers of the 102C allele was higher than in controls (76.5% vs. 50%; P = 0.028). The scores of the V domain were lower in patients than in controls, indicating a worst perception of the environmental quality by patients (P quality of social care and health" together with the presence of the 102C allele also increased this chance by more than 90-fold (P = 0.005). However, carriers of the same allele who have high quality social care and health are not at a higher risk to develop FMS. These data suggest that these factors may predispose to FMS, especially in carriers of the 102C allele. However, studies with larger samples are required to confirm this hypothesis.

  13. An integrated SNP mining and utilization (ISMU) pipeline for next generation sequencing data.

    Science.gov (United States)

    Azam, Sarwar; Rathore, Abhishek; Shah, Trushar M; Telluri, Mohan; Amindala, BhanuPrakash; Ruperao, Pradeep; Katta, Mohan A V S K; Varshney, Rajeev K

    2014-01-01

    Open source single nucleotide polymorphism (SNP) discovery pipelines for next generation sequencing data commonly requires working knowledge of command line interface, massive computational resources and expertise which is a daunting task for biologists. Further, the SNP information generated may not be readily used for downstream processes such as genotyping. Hence, a comprehensive pipeline has been developed by integrating several open source next generation sequencing (NGS) tools along with a graphical user interface called Integrated SNP Mining and Utilization (ISMU) for SNP discovery and their utilization by developing genotyping assays. The pipeline features functionalities such as pre-processing of raw data, integration of open source alignment tools (Bowtie2, BWA, Maq, NovoAlign and SOAP2), SNP prediction (SAMtools/SOAPsnp/CNS2snp and CbCC) methods and interfaces for developing genotyping assays. The pipeline outputs a list of high quality SNPs between all pairwise combinations of genotypes analyzed, in addition to the reference genome/sequence. Visualization tools (Tablet and Flapjack) integrated into the pipeline enable inspection of the alignment and errors, if any. The pipeline also provides a confidence score or polymorphism information content value with flanking sequences for identified SNPs in standard format required for developing marker genotyping (KASP and Golden Gate) assays. The pipeline enables users to process a range of NGS datasets such as whole genome re-sequencing, restriction site associated DNA sequencing and transcriptome sequencing data at a fast speed. The pipeline is very useful for plant genetics and breeding community with no computational expertise in order to discover SNPs and utilize in genomics, genetics and breeding studies. The pipeline has been parallelized to process huge datasets of next generation sequencing. It has been developed in Java language and is available at http://hpc.icrisat.cgiar.org/ISMU as a standalone

  14. A SNP-centric database for the investigation of the human genome

    Directory of Open Access Journals (Sweden)

    Kohane Isaac S

    2004-03-01

    Full Text Available Abstract Background Single Nucleotide Polymorphisms (SNPs are an increasingly important tool for genetic and biomedical research. Although current genomic databases contain information on several million SNPs and are growing at a very fast rate, the true value of a SNP in this context is a function of the quality of the annotations that characterize it. Retrieving and analyzing such data for a large number of SNPs often represents a major bottleneck in the design of large-scale association studies. Description SNPper is a web-based application designed to facilitate the retrieval and use of human SNPs for high-throughput research purposes. It provides a rich local database generated by combining SNP data with the Human Genome sequence and with several other data sources, and offers the user a variety of querying, visualization and data export tools. In this paper we describe the structure and organization of the SNPper database, we review the available data export and visualization options, and we describe how the architecture of SNPper and its specialized data structures support high-volume SNP analysis. Conclusions The rich annotation database and the powerful data manipulation and presentation facilities it offers make SNPper a very useful online resource for SNP research. Its success proves the great need for integrated and interoperable resources in the field of computational biology, and shows how such systems may play a critical role in supporting the large-scale computational analysis of our genome.

  15. SNP design from 454 sequencing of Podosphaera plantaginis transcriptome reveals a genetically diverse pathogen metapopulation with high levels of mixed-genotype infection.

    Directory of Open Access Journals (Sweden)

    Charlotte Tollenaere

    Full Text Available Molecular tools may greatly improve our understanding of pathogen evolution and epidemiology but technical constraints have hindered the development of genetic resources for parasites compared to free-living organisms. This study aims at developing molecular tools for Podosphaera plantaginis, an obligate fungal pathogen of Plantago lanceolata. This interaction has been intensively studied in the Åland archipelago of Finland with epidemiological data collected from over 4,000 host populations annually since year 2001.A cDNA library of a pooled sample of fungal conidia was sequenced on the 454 GS-FLX platform. Over 549,411 reads were obtained and annotated into 45,245 contigs. Annotation data was acquired for 65.2% of the assembled sequences. The transcriptome assembly was screened for SNP loci, as well as for functionally important genes (mating-type genes and potential effector proteins. A genotyping assay of 27 SNP loci was designed and tested on 380 infected leaf samples from 80 populations within the Åland archipelago. With this panel we identified 85 multilocus genotypes (MLG with uneven frequencies across the pathogen metapopulation. Approximately half of the sampled populations contain polymorphism. Our genotyping protocol revealed mixed-genotype infection within a single host leaf to be common. Mixed infection has been proposed as one of the main drivers of pathogen evolution, and hence may be an important process in this pathosystem.The developed SNP panel offers exciting research perspectives for future studies in this well-characterized pathosystem. Also, the transcriptome provides an invaluable novel genomic resource for powdery mildews, which cause significant yield losses on commercially important crops annually. Furthermore, the features that render genetic studies in this system a challenge are shared with the majority of obligate parasitic species, and hence our results provide methodological insights from SNP calling to field

  16. Forensic SNP genotyping with SNaPshot

    DEFF Research Database (Denmark)

    Fondevila, M; Børsting, C; Phillips, C

    2017-01-01

    to routine STR profiling, use of SNaPshot is an important part of the development of SNP sets for a wide range of forensic applications with these markers, from genotyping highly degraded DNA with very short amplicons to the introduction of SNPs to ascertain the ancestry and physical characteristics......This review explores the key factors that influence the optimization, routine use, and profile interpretation of the SNaPshot single-base extension (SBE) system applied to forensic single-nucleotide polymorphism (SNP) genotyping. Despite being a mainly complimentary DNA genotyping technique...... of an unidentified contact trace donor. However, this technology, as resourceful as it is, displays several features that depart from the usual STR genotyping far enough to demand a certain degree of expertise from the forensic analyst before tackling the complex casework on which SNaPshot application provides...

  17. The Use of High-Density SNP Array to Map Homozygosity in Consanguineous Families to Efficiently Identify Candidate Genes: Application to Woodhouse-Sakati Syndrome

    Directory of Open Access Journals (Sweden)

    Molly B. Sheridan

    2015-01-01

    Full Text Available Two consanguineous Qatari siblings presented for evaluation: a 17-4/12-year-old male with hypogonadotropic hypogonadism, alopecia, intellectual disability, and microcephaly and his 19-year-old sister with primary amenorrhea, alopecia, and normal cognition. Both required hormone treatment to produce secondary sex characteristics and pubertal development beyond Tanner 1. SNP array analysis of both probands was performed to detect shared regions of homozygosity which may harbor homozygous mutations in a gene causing their common features of abnormal pubertal development, alopecia, and variable cognitive delay. Our patients shared multiple homozygous genomic regions; ten shared regions were >1 Mb in length and constituted 0.99% of the genome. DCAF17, encoding a transmembrane nuclear protein of uncertain function, was the only gene identified in a homozygous region known to cause hypogonadotropic hypogonadism. DCAF17 mutations are associated with Woodhouse-Sakati syndrome, a rare disorder characterized by alopecia, hypogonadotropic hypogonadism, sensorineural hearing loss, diabetes mellitus, and extrapyramidal movements. Sequencing of the coding exons and flanking intronic regions of DCAF17 in the proband revealed homozygosity for a previously described founder mutation (c.436delC. Targeted DCAF17 sequencing of his affected sibling revealed the same homozygous mutation. This family illustrates the utility of SNP array testing in consanguineous families to efficiently and inexpensively identify regions of genomic homozygosity in which genetic candidates for recessive conditions can be identified.

  18. Exome sequencing generates high quality data in non-target regions

    Directory of Open Access Journals (Sweden)

    Guo Yan

    2012-05-01

    Full Text Available Abstract Background Exome sequencing using next-generation sequencing technologies is a cost efficient approach to selectively sequencing coding regions of human genome for detection of disease variants. A significant amount of DNA fragments from the capture process fall outside target regions, and sequence data for positions outside target regions have been mostly ignored after alignment. Result We performed whole exome sequencing on 22 subjects using Agilent SureSelect capture reagent and 6 subjects using Illumina TrueSeq capture reagent. We also downloaded sequencing data for 6 subjects from the 1000 Genomes Project Pilot 3 study. Using these data, we examined the quality of SNPs detected outside target regions by computing consistency rate with genotypes obtained from SNP chips or the Hapmap database, transition-transversion (Ti/Tv ratio, and percentage of SNPs inside dbSNP. For all three platforms, we obtained high-quality SNPs outside target regions, and some far from target regions. In our Agilent SureSelect data, we obtained 84,049 high-quality SNPs outside target regions compared to 65,231 SNPs inside target regions (a 129% increase. For our Illumina TrueSeq data, we obtained 222,171 high-quality SNPs outside target regions compared to 95,818 SNPs inside target regions (a 232% increase. For the data from the 1000 Genomes Project, we obtained 7,139 high-quality SNPs outside target regions compared to 1,548 SNPs inside target regions (a 461% increase. Conclusions These results demonstrate that a significant amount of high quality genotypes outside target regions can be obtained from exome sequencing data. These data should not be ignored in genetic epidemiology studies.

  19. Identification of SNP barcode biomarkers for genes associated with facial emotion perception using particle swarm optimization algorithm.

    Science.gov (United States)

    Chuang, Li-Yeh; Lane, Hsien-Yuan; Lin, Yu-Da; Lin, Ming-Teng; Yang, Cheng-Hong; Chang, Hsueh-Wei

    2014-01-01

    Facial emotion perception (FEP) can affect social function. We previously reported that parts of five tested single-nucleotide polymorphisms (SNPs) in the MET and AKT1 genes may individually affect FEP performance. However, the effects of SNP-SNP interactions on FEP performance remain unclear. This study compared patients with high and low FEP performances (n = 89 and 93, respectively). A particle swarm optimization (PSO) algorithm was used to identify the best SNP barcodes (i.e., the SNP combinations and genotypes that revealed the largest differences between the high and low FEP groups). The analyses of individual SNPs showed no significant differences between the high and low FEP groups. However, comparisons of multiple SNP-SNP interactions involving different combinations of two to five SNPs showed that the best PSO-generated SNP barcodes were significantly associated with high FEP score. The analyses of the joint effects of the best SNP barcodes for two to five interacting SNPs also showed that the best SNP barcodes had significantly higher odds ratios (2.119 to 3.138; P < 0.05) compared to other SNP barcodes. In conclusion, the proposed PSO algorithm effectively identifies the best SNP barcodes that have the strongest associations with FEP performance. This study also proposes a computational methodology for analyzing complex SNP-SNP interactions in social cognition domains such as recognition of facial emotion.

  20. Genotyping by sequencing for SNP-based linkage analysis and identification of QTLs linked to fruit quality traits in Japanese plum (Prunus salicina Lindl.)

    Science.gov (United States)

    Marker-assisted selection (MAS) in stone fruit (Prunus species) breeding is currently difficult to achieve due to the polygenic nature of themost relevant agronomic traits linked to fruit quality. Genotyping by sequencing (GBS), however, provides a large quantity of useful data suitable for finemapp...

  1. Availability of high quality weather data measurements

    DEFF Research Database (Denmark)

    Andersen, Elsa; Johansen, Jakob Berg; Furbo, Simon

    In the period 2016-2017 the project “Availability of high quality weather data measurements” is carried out at Department of Civil Engineering at the Technical University of Denmark. The aim of the project is to establish measured high quality weather data which will be easily available...... for the building energy branch and the solar energy branch in their efforts to achieve energy savings and for researchers and students carrying out projects where measured high quality weather data are needed....

  2. Report on ISFG SNP Panel Discussion

    DEFF Research Database (Denmark)

    Butler, John M.; Budowle, B.; Gill, P.

    2008-01-01

    Six scientists presented their views and experience with single nucleotide polymorphism (SNP) markers, multiplexes, and methods regarding their potential application in forensic identity and relationship testing. Benefits and limitations of SNPs were reviewed, as were different SNP marker...

  3. Alkali-developable silicone-based negative photoresist (SNP) for deep UV, electron beam, and X-ray lithographies

    International Nuclear Information System (INIS)

    Ban, Hiroshi; Tanaka, Akinobu; Kawai, Yoshio; Deguchi, Kimiyoshi

    1989-01-01

    A new silicone-based negative photoresist (SNP) developable with alkaline aqueous solutions is prepared. SNP composed of acetylated phenylsilsesquioxane oligomer and azidopyrene is applied to deep UV, electron beam (EB), and X-ray lithographies. SNP slightly swells in alkaline developers, thus exhibiting exceptionally high resolution characteristics for a negative resist. The resistance of SNP to oxygen reactive ion etching is approximately 30 times greater than that of conventional novolac resists. (author)

  4. Rapid identification of tomato Sw-5 resistance-breaking isolates of Tomato spotted wilt virus using high resolution melting and TaqMan SNP Genotyping assays as allelic discrimination techniques.

    Directory of Open Access Journals (Sweden)

    Valentina di Rienzo

    Full Text Available In tomato, resistance to Tomato spotted wilt virus (TSWV is conferred by the dominant gene, designated Sw-5. Virulent Sw-5 resistance breaking (SRB mutants of TSWV have been reported on Sw-5 tomato cultivars. Two different PCR-based allelic discrimination techniques, namely Custom TaqMan™ SNP Genotyping and high-resolution melting (HRM assays, were developed and compared for their ability to distinguish between avirulent (Sw-5 non-infecting, SNI and SRB biotypes. TaqMan assays proved to be more sensitive (threshold of detection in a range of 50-70 TSWV RNA copies and more reliable than HRM, assigning 25 TSWV isolates to their correct genotype with an accuracy of 100%. Moreover, the TaqMan SNP assays were further improved developing a rapid and simple protocol that included crude leaf extraction for RNA template preparations. On the other hand, HRM assays showed higher levels of sensitivity than TaqMan when used to co-detect both biotypes in different artificial mixtures. These diagnostic assays contributed to gain preliminary information on the epidemiology of TSWV isolates in open field conditions. In fact, the presented data suggest that SRB isolates are present as stable populations established year round, persisting on both winter (globe artichoke and summer (tomato crops, in the same cultivated areas of Southern Italy.

  5. Zerodur polishing process for high surface quality and high efficiency

    International Nuclear Information System (INIS)

    Tesar, A.; Fuchs, B.

    1992-08-01

    Zerodur is a glass-ceramic composite importance in applications where temperature instabilities influence optical and mechanical performance, such as in earthbound and spaceborne telescope mirror substrates. Polished Zerodur surfaces of high quality have been required for laser gyro mirrors. Polished surface quality of substrates affects performance of high reflection coatings. Thus, the interest in improving Zerodur polished surface quality has become more general. Beyond eliminating subsurface damage, high quality surfaces are produced by reducing the amount of hydrated material redeposited on the surface during polishing. With the proper control of polishing parameters, such surfaces exhibit roughnesses of < l Angstrom rms. Zerodur polishing was studied to recommend a high surface quality polishing process which could be easily adapted to standard planetary continuous polishing machines and spindles. This summary contains information on a polishing process developed at LLNL which reproducibly provides high quality polished Zerodur surfaces at very high polishing efficiencies

  6. Engineering high quality medical software

    CERN Document Server

    Coronato, Antonio

    2018-01-01

    This book focuses on high-confidence medical software in the growing field of e-health, telecare services and health technology. It covers the development of methodologies and engineering tasks together with standards and regulations for medical software.

  7. HIGH-THROUGHPUT IDENTIFICATION OF THE PREDOMINANT MALARIA PARASITE CLONE IN COMPLEX BLOOD STAGE INFECTIONS USING A MULTI-SNP MOLECULAR HAPLOTYPING ASSAY

    Science.gov (United States)

    COLE-TOBIAN, JENNIFER L.; ZIMMERMAN, PETER A.; KING, CHRISTOPHER L.

    2013-01-01

    Individuals living in malaria endemic areas are often infected with multiple parasite clones. Currently used single nucleotide polymorphism (SNP) genotyping methods for malaria parasites are cumbersome; furthermore, few methods currently exist that can rapidly determine the most abundant clone in these complex infections. Here we describe an oligonucleotide ligation assay (OLA) to distinguish SNPs in the Plasmodium vivax Duffy binding protein gene (Pvdbp) at 14 polymorphic residues simultaneously. Allele abundance is determined by the highest mean fluorescent intensity of each allele. Using mixtures of plasmids encoding known haplotypes of the Pvdbp, single clones of P. vivax parasites from infected Aotus monkeys, and well-defined mixed infections from field samples, we were able to identify the predominant Pvdbp genotype with > 93% accuracy when the dominant clone is twice as abundant as a lesser genotype and > 97% of the time if the ratio was 5:1 or greater. Thus, the OLA can accurately, reproducibly, and rapidly determine the predominant parasite haplotype in complex blood stage infections. PMID:17255222

  8. Genome-wide ENU mutagenesis in combination with high density SNP analysis and exome sequencing provides rapid identification of novel mouse models of developmental disease.

    Directory of Open Access Journals (Sweden)

    Georgina Caruana

    Full Text Available Mice harbouring gene mutations that cause phenotypic abnormalities during organogenesis are invaluable tools for linking gene function to normal development and human disorders. To generate mouse models harbouring novel alleles that are involved in organogenesis we conducted a phenotype-driven, genome-wide mutagenesis screen in mice using the mutagen N-ethyl-N-nitrosourea (ENU.ENU was injected into male C57BL/6 mice and the mutations transmitted through the germ-line. ENU-induced mutations were bred to homozygosity and G3 embryos screened at embryonic day (E 13.5 and E18.5 for abnormalities in limb and craniofacial structures, skin, blood, vasculature, lungs, gut, kidneys, ureters and gonads. From 52 pedigrees screened 15 were detected with anomalies in one or more of the structures/organs screened. Using single nucleotide polymorphism (SNP-based linkage analysis in conjunction with candidate gene or next-generation sequencing (NGS we identified novel recessive alleles for Fras1, Ift140 and Lig1.In this study we have generated mouse models in which the anomalies closely mimic those seen in human disorders. The association between novel mutant alleles and phenotypes will lead to a better understanding of gene function in normal development and establish how their dysfunction causes human anomalies and disease.

  9. Making a chocolate chip: development and evaluation of a 6K SNP array for Theobroma cacao.

    Science.gov (United States)

    Livingstone, Donald; Royaert, Stefan; Stack, Conrad; Mockaitis, Keithanne; May, Greg; Farmer, Andrew; Saski, Christopher; Schnell, Ray; Kuhn, David; Motamayor, Juan Carlos

    2015-08-01

    Theobroma cacao, the key ingredient in chocolate production, is one of the world's most important tree fruit crops, with ∼4,000,000 metric tons produced across 50 countries. To move towards gene discovery and marker-assisted breeding in cacao, a single-nucleotide polymorphism (SNP) identification project was undertaken using RNAseq data from 16 diverse cacao cultivars. RNA sequences were aligned to the assembled transcriptome of the cultivar Matina 1-6, and 330,000 SNPs within coding regions were identified. From these SNPs, a subset of 6,000 high-quality SNPs were selected for inclusion on an Illumina Infinium SNP array: the Cacao6kSNP array. Using Cacao6KSNP array data from over 1,000 cacao samples, we demonstrate that our custom array produces a saturated genetic map and can be used to distinguish among even closely related genotypes. Our study enhances and expands the genetic resources available to the cacao research community, and provides the genome-scale set of tools that are critical for advancing breeding with molecular markers in an agricultural species with high genetic diversity. © The Author 2015. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

  10. SNP markers retrieval for a non-model species: a practical approach

    Directory of Open Access Journals (Sweden)

    Shahin Arwa

    2012-01-01

    Full Text Available Abstract Background SNP (Single Nucleotide Polymorphism markers are rapidly becoming the markers of choice for applications in breeding because of next generation sequencing technology developments. For SNP development by NGS technologies, correct assembly of the huge amounts of sequence data generated is essential. Little is known about assembler's performance, especially when dealing with highly heterogeneous species that show a high genome complexity and what the possible consequences are of differences in assemblies on SNP retrieval. This study tested two assemblers (CAP3 and CLC on 454 data from four lily genotypes and compared results with respect to SNP retrieval. Results CAP3 assembly resulted in higher numbers of contigs, lower numbers of reads per contig, and shorter average read lengths compared to CLC. Blast comparisons showed that CAP3 contigs were highly redundant. Contrastingly, CLC in rare cases combined paralogs in one contig. Redundant and chimeric contigs may lead to erroneous SNPs. Filtering for redundancy can be done by blasting selected SNP markers to the contigs and discarding all the SNP markers that show more than one blast hit. Results on chimeric contigs showed that only four out of 2,421 SNP markers were selected from chimeric contigs. Conclusion In practice, CLC performs better in assembling highly heterogeneous genome sequences compared to CAP3, and consequently SNP retrieval is more efficient. Additionally a simple flow scheme is suggested for SNP marker retrieval that can be valid for all non-model species.

  11. Partitioned learning of deep Boltzmann machines for SNP data.

    Science.gov (United States)

    Hess, Moritz; Lenz, Stefan; Blätte, Tamara J; Bullinger, Lars; Binder, Harald

    2017-10-15

    Learning the joint distributions of measurements, and in particular identification of an appropriate low-dimensional manifold, has been found to be a powerful ingredient of deep leaning approaches. Yet, such approaches have hardly been applied to single nucleotide polymorphism (SNP) data, probably due to the high number of features typically exceeding the number of studied individuals. After a brief overview of how deep Boltzmann machines (DBMs), a deep learning approach, can be adapted to SNP data in principle, we specifically present a way to alleviate the dimensionality problem by partitioned learning. We propose a sparse regression approach to coarsely screen the joint distribution of SNPs, followed by training several DBMs on SNP partitions that were identified by the screening. Aggregate features representing SNP patterns and the corresponding SNPs are extracted from the DBMs by a combination of statistical tests and sparse regression. In simulated case-control data, we show how this can uncover complex SNP patterns and augment results from univariate approaches, while maintaining type 1 error control. Time-to-event endpoints are considered in an application with acute myeloid leukemia patients, where SNP patterns are modeled after a pre-screening based on gene expression data. The proposed approach identified three SNPs that seem to jointly influence survival in a validation dataset. This indicates the added value of jointly investigating SNPs compared to standard univariate analyses and makes partitioned learning of DBMs an interesting complementary approach when analyzing SNP data. A Julia package is provided at 'http://github.com/binderh/BoltzmannMachines.jl'. binderh@imbi.uni-freiburg.de. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  12. SNP-SNP interactions in breast cancer susceptibility

    International Nuclear Information System (INIS)

    Onay, Venüs Ümmiye; Ozcelik, Hilmi; Briollais, Laurent; Knight, Julia A; Shi, Ellen; Wang, Yuanyuan; Wells, Sean; Li, Hong; Rajendram, Isaac; Andrulis, Irene L

    2006-01-01

    Breast cancer predisposition genes identified to date (e.g., BRCA1 and BRCA2) are responsible for less than 5% of all breast cancer cases. Many studies have shown that the cancer risks associated with individual commonly occurring single nucleotide polymorphisms (SNPs) are incremental. However, polygenic models suggest that multiple commonly occurring low to modestly penetrant SNPs of cancer related genes might have a greater effect on a disease when considered in combination. In an attempt to identify the breast cancer risk conferred by SNP interactions, we have studied 19 SNPs from genes involved in major cancer related pathways. All SNPs were genotyped by TaqMan 5'nuclease assay. The association between the case-control status and each individual SNP, measured by the odds ratio and its corresponding 95% confidence interval, was estimated using unconditional logistic regression models. At the second stage, two-way interactions were investigated using multivariate logistic models. The robustness of the interactions, which were observed among SNPs with stronger functional evidence, was assessed using a bootstrap approach, and correction for multiple testing based on the false discovery rate (FDR) principle. None of these SNPs contributed to breast cancer risk individually. However, we have demonstrated evidence for gene-gene (SNP-SNP) interaction among these SNPs, which were associated with increased breast cancer risk. Our study suggests cross talk between the SNPs of the DNA repair and immune system (XPD-[Lys751Gln] and IL10-[G(-1082)A]), cell cycle and estrogen metabolism (CCND1-[Pro241Pro] and COMT-[Met108/158Val]), cell cycle and DNA repair (BARD1-[Pro24Ser] and XPD-[Lys751Gln]), and within carcinogen metabolism (GSTP1-[Ile105Val] and COMT-[Met108/158Val]) pathways. The importance of these pathways and their communication in breast cancer predisposition has been emphasized previously, but their biological interactions through SNPs have not been described

  13. SNP-SNP interactions in breast cancer susceptibility

    Directory of Open Access Journals (Sweden)

    Wang Yuanyuan

    2006-05-01

    Full Text Available Abstract Background Breast cancer predisposition genes identified to date (e.g., BRCA1 and BRCA2 are responsible for less than 5% of all breast cancer cases. Many studies have shown that the cancer risks associated with individual commonly occurring single nucleotide polymorphisms (SNPs are incremental. However, polygenic models suggest that multiple commonly occurring low to modestly penetrant SNPs of cancer related genes might have a greater effect on a disease when considered in combination. Methods In an attempt to identify the breast cancer risk conferred by SNP interactions, we have studied 19 SNPs from genes involved in major cancer related pathways. All SNPs were genotyped by TaqMan 5'nuclease assay. The association between the case-control status and each individual SNP, measured by the odds ratio and its corresponding 95% confidence interval, was estimated using unconditional logistic regression models. At the second stage, two-way interactions were investigated using multivariate logistic models. The robustness of the interactions, which were observed among SNPs with stronger functional evidence, was assessed using a bootstrap approach, and correction for multiple testing based on the false discovery rate (FDR principle. Results None of these SNPs contributed to breast cancer risk individually. However, we have demonstrated evidence for gene-gene (SNP-SNP interaction among these SNPs, which were associated with increased breast cancer risk. Our study suggests cross talk between the SNPs of the DNA repair and immune system (XPD-[Lys751Gln] and IL10-[G(-1082A], cell cycle and estrogen metabolism (CCND1-[Pro241Pro] and COMT-[Met108/158Val], cell cycle and DNA repair (BARD1-[Pro24Ser] and XPD-[Lys751Gln], and within carcinogen metabolism (GSTP1-[Ile105Val] and COMT-[Met108/158Val] pathways. Conclusion The importance of these pathways and their communication in breast cancer predisposition has been emphasized previously, but their

  14. Comprehensive evaluation of SNP identification with the Restriction Enzyme-based Reduced Representation Library (RRL method

    Directory of Open Access Journals (Sweden)

    Du Ye

    2012-02-01

    Full Text Available Abstract Background Restriction Enzyme-based Reduced Representation Library (RRL method represents a relatively feasible and flexible strategy used for Single Nucleotide Polymorphism (SNP identification in different species. It has remarkable advantage of reducing the complexity of the genome by orders of magnitude. However, comprehensive evaluation for actual efficacy of SNP identification by this method is still unavailable. Results In order to evaluate the efficacy of Restriction Enzyme-based RRL method, we selected Tsp 45I enzyme which covers 266 Mb flanking region of the enzyme recognition site according to in silico simulation on human reference genome, then we sequenced YH RRL after Tsp 45I treatment and obtained reads of which 80.8% were mapped to target region with an 20-fold average coverage, about 96.8% of target region was covered by at least one read and 257 K SNPs were identified in the region using SOAPsnp software. Compared with whole genome resequencing data, we observed false discovery rate (FDR of 13.95% and false negative rate (FNR of 25.90%. The concordance rate of homozygote loci was over 99.8%, but that of heterozygote were only 92.56%. Repeat sequences and bases quality were proved to have a great effect on the accuracy of SNP calling, SNPs in recognition sites contributed evidently to the high FNR and the low concordance rate of heterozygote. Our results indicated that repeat masking and high stringent filter criteria could significantly decrease both FDR and FNR. Conclusions This study demonstrates that Restriction Enzyme-based RRL method was effective for SNP identification. The results highlight the important role of bias and the method-derived defects represented in this method and emphasize the special attentions noteworthy.

  15. Light whole genome sequence for SNP discovery across domestic cat breeds

    Directory of Open Access Journals (Sweden)

    Driscoll Carlos

    2010-06-01

    Full Text Available Abstract Background The domestic cat has offered enormous genomic potential in the veterinary description of over 250 hereditary disease models as well as the occurrence of several deadly feline viruses (feline leukemia virus -- FeLV, feline coronavirus -- FECV, feline immunodeficiency virus - FIV that are homologues to human scourges (cancer, SARS, and AIDS respectively. However, to realize this bio-medical potential, a high density single nucleotide polymorphism (SNP map is required in order to accomplish disease and phenotype association discovery. Description To remedy this, we generated 3,178,297 paired fosmid-end Sanger sequence reads from seven cats, and combined these data with the publicly available 2X cat whole genome sequence. All sequence reads were assembled together to form a 3X whole genome assembly allowing the discovery of over three million SNPs. To reduce potential false positive SNPs due to the low coverage assembly, a low upper-limit was placed on sequence coverage and a high lower-limit on the quality of the discrepant bases at a potential variant site. In all domestic cats of different breeds: female Abyssinian, female American shorthair, male Cornish Rex, female European Burmese, female Persian, female Siamese, a male Ragdoll and a female African wildcat were sequenced lightly. We report a total of 964 k common SNPs suitable for a domestic cat SNP genotyping array and an additional 900 k SNPs detected between African wildcat and domestic cats breeds. An empirical sampling of 94 discovered SNPs were tested in the sequenced cats resulting in a SNP validation rate of 99%. Conclusions These data provide a large collection of mapped feline SNPs across the cat genome that will allow for the development of SNP genotyping platforms for mapping feline diseases.

  16. Quality management manual for production of high quality cassava flour

    DEFF Research Database (Denmark)

    Dziedzoave, Nanam Tay; Abass, Adebayo Busura; Amoa-Awua, Wisdom K.

    The high quality cassava flour (HQCF) industry has just started to evolve in Africa and elsewhere. The sustainability of the growing industry, the profitability of small- and medium-scale enterprises (SMEs) that are active in the industry and good-health of consumers can best be guaranteed through...... the adoption of proper quality and food safety procedures. Cassava processing enterprises involved in the productionof HQCF must therefore be commited to the quality and food safety of the HQCF. They must have the right technology, appropriate processing machhinery, standard testing instruments...... and the necessary technical expertise. This quality manual was therefore developed to guide small- to medium-scale cassava in the design and implematation of Hazard Analysis Critical Control Point (HACCP) system and Good manufacturing Practices (GMP) plans for HQCF production. It describes the HQCF production...

  17. High quality-factor optical resonators

    International Nuclear Information System (INIS)

    Henriet, Rémi; Salzenstein, Patrice; Coillet, Aurélien; Saleh, Khaldoun; Chembo, Yanne K; Ristic, Davor; Ferrari, Maurizio; Mortier, Michel; Rasoloniaina, Alphonse; Dumeige, Yannick; Féron, Patrice; Cibiel, Gilles; Llopis, Olivier

    2014-01-01

    Various resonators are investigated for microwave photonic applications. Micro-sphere, disk and fiber ring resonators were designed, realized and characterized. Obtained quality factors are as high as Q = 10 10 . (paper)

  18. Novel approach for deriving genome wide SNP analysis data from archived blood spots

    Science.gov (United States)

    2012-01-01

    Background The ability to transport and store DNA at room temperature in low volumes has the advantage of optimising cost, time and storage space. Blood spots on adapted filter papers are popular for this, with FTA (Flinders Technology Associates) Whatman™TM technology being one of the most recent. Plant material, plasmids, viral particles, bacteria and animal blood have been stored and transported successfully using this technology, however the method of porcine DNA extraction from FTA Whatman™TM cards is a relatively new approach, allowing nucleic acids to be ready for downstream applications such as PCR, whole genome amplification, sequencing and subsequent application to single nucleotide polymorphism microarrays has hitherto been under-explored. Findings DNA was extracted from FTA Whatman™TM cards (following adaptations of the manufacturer’s instructions), whole genome amplified and subsequently analysed to validate the integrity of the DNA for downstream SNP analysis. DNA was successfully extracted from 288/288 samples and amplified by WGA. Allele dropout post WGA, was observed in less than 2% of samples and there was no clear evidence of amplification bias nor contamination. Acceptable call rates on porcine SNP chips were also achieved using DNA extracted and amplified in this way. Conclusions DNA extracted from FTA Whatman cards is of a high enough quality and quantity following whole genomic amplification to perform meaningful SNP chip studies. PMID:22974252

  19. High-quality compressive ghost imaging

    Science.gov (United States)

    Huang, Heyan; Zhou, Cheng; Tian, Tian; Liu, Dongqi; Song, Lijun

    2018-04-01

    We propose a high-quality compressive ghost imaging method based on projected Landweber regularization and guided filter, which effectively reduce the undersampling noise and improve the resolution. In our scheme, the original object is reconstructed by decomposing of regularization and denoising steps instead of solving a minimization problem in compressive reconstruction process. The simulation and experimental results show that our method can obtain high ghost imaging quality in terms of PSNR and visual observation.

  20. Construction of a high-density DArTseq SNP-based genetic map and identification of genomic regions with segregation distortion in a genetic population derived from a cross between feral and cultivated-type watermelon.

    Science.gov (United States)

    Ren, Runsheng; Ray, Rumiana; Li, Pingfang; Xu, Jinhua; Zhang, Man; Liu, Guang; Yao, Xiefeng; Kilian, Andrzej; Yang, Xingping

    2015-08-01

    Watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai] is an economically important vegetable crop grown extensively worldwide. To facilitate the identification of agronomically important traits and provide new information for genetic and genomic research on this species, a high-density genetic linkage map of watermelon was constructed using an F2 population derived from a cross between elite watermelon cultivar K3 and wild watermelon germplasm PI 189225. Based on a sliding window approach, a total of 1,161 bin markers representing 3,465 SNP markers were mapped onto 11 linkage groups corresponding to the chromosome pair number of watermelon. The total length of the genetic map is 1,099.2 cM, with an average distance between bins of 1.0 cM. The number of markers in each chromosome varies from 62 in chromosome 07 to 160 in chromosome 05. The length of individual chromosomes ranged between 61.8 cM for chromosome 07 and 140.2 cM for chromosome 05. A total of 616 SNP bin markers showed significant (P watermelon cultivar K3 allele and 103 were skewed toward PI 189225. The number of SNPs and InDels per Mb varied considerably across the segregation distorted regions (SDRs) on each chromosome, and a mixture of dense and sparse SNPs and InDel SDRs coexisted on some chromosomes suggesting that SDRs were randomly distributed throughout the genome. Recombination rates varied greatly among each chromosome, from 2.0 to 4.2 centimorgans per megabase (cM/Mb). An inconsistency was found between the genetic and physical positions on the map for a segment on chromosome 11. The high-density genetic map described in the present study will facilitate fine mapping of quantitative trait loci, the identification of candidate genes, map-based cloning, as well as marker-assisted selection (MAS) in watermelon breeding programs.

  1. SNP2Structure: A Public and Versatile Resource for Mapping and Three-Dimensional Modeling of Missense SNPs on Human Protein Structures

    Directory of Open Access Journals (Sweden)

    Difei Wang

    2015-01-01

    Full Text Available One of the long-standing challenges in biology is to understand how non-synonymous single nucleotide polymorphisms (nsSNPs change protein structure and further affect their function. While it is impractical to solve all the mutated protein structures experimentally, it is quite feasible to model the mutated structures in silico. Toward this goal, we built a publicly available structure database resource (SNP2Structure, https://apps.icbi.georgetown.edu/snp2structure focusing on missense mutations, msSNP. Compared with web portals with similar aims, SNP2Structure has the following major advantages. First, our portal offers direct comparison of two related 3D structures. Second, the protein models include all interacting molecules in the original PDB structures, so users are able to determine regions of potential interaction changes when a protein mutation occurs. Third, the mutated structures are available to download locally for further structural and functional analysis. Fourth, we used Jsmol package to display the protein structure that has no system compatibility issue. SNP2Structure provides reliable, high quality mapping of nsSNPs to 3D protein structures enabling researchers to explore the likely functional impact of human disease-causing mutations.

  2. Population genetic analysis of ascertained SNP data

    Directory of Open Access Journals (Sweden)

    Nielsen Rasmus

    2004-03-01

    Full Text Available Abstract The large single nucleotide polymorphism (SNP typing projects have provided an invaluable data resource for human population geneticists. Almost all of the available SNP loci, however, have been identified through a SNP discovery protocol that will influence the allelic distributions in the sampled loci. Standard methods for population genetic analysis based on the available SNP data will, therefore, be biased. This paper discusses the effect of this ascertainment bias on allelic distributions and on methods for quantifying linkage disequilibrium and estimating demographic parameters. Several recently developed methods for correcting for the ascertainment bias will also be discussed.

  3. A High-Density Integrated DArTseq SNP-Based Genetic Map of Pisum fulvum and Identification of QTLs Controlling Rust Resistance

    Directory of Open Access Journals (Sweden)

    Eleonora Barilli

    2018-02-01

    Full Text Available Pisum fulvum, a wild relative of pea is an important source of allelic diversity to improve the genetic resistance of cultivated species against fungal diseases of economic importance like the pea rust caused by Uromyces pisi. To unravel the genetic control underlying resistance to this fungal disease, a recombinant inbred line (RIL population was generated from a cross between two P. fulvum accessions, IFPI3260 and IFPI3251, and genotyped using Diversity Arrays Technology. A total of 9,569 high-quality DArT-Seq and 8,514 SNPs markers were generated. Finally, a total of 12,058 markers were assembled into seven linkage groups, equivalent to the number of haploid chromosomes of P. fulvum and P. sativum. The newly constructed integrated genetic linkage map of P. fulvum covered an accumulated distance of 1,877.45 cM, an average density of 1.19 markers cM−1 and an average distance between adjacent markers of 1.85 cM. The composite interval mapping revealed three QTLs distributed over two linkage groups that were associated with the percentage of rust disease severity (DS%. QTLs UpDSII and UpDSIV were located in the LGs II and IV respectively and were consistently identified both in adult plants over 3 years at the field (Córdoba, Spain and in seedling plants under controlled conditions. Whenever they were detected, their contribution to the total phenotypic variance varied between 19.8 and 29.2. A third QTL (UpDSIV.2 was also located in the LGIVand was environmentally specific as was only detected for DS % in seedlings under controlled conditions. It accounted more than 14% of the phenotypic variation studied. Taking together the data obtained in the study, it could be concluded that the expression of resistance to fungal diseases in P. fulvum originates from the resistant parent IFPI3260.

  4. Fabrication of high-quality brazed joints

    International Nuclear Information System (INIS)

    Orlov, A.V.

    1980-01-01

    Problem of ensuring of joint high-quality when brazing different parts in power engineering is considered. To obtain high-quality joints it is necessary to correctly design brazed joint and to choose a gap width, overlap length and fillet radius; to clean up carefully the surfaces to be brazed and fix them properly one relative to another; to apply a solder so as to provide its flowing into the gap and sticking in it; to exactly regulate thermal conditions of brazing. High quality and reliability of brazed joints are ensured by the application of solders based on noble metals, and cheap solders based on nickel, manganese and copper. Joints brazed with nickel base solders may operate at temperatures as high as 888 deg C

  5. TOTAL QUALITY MANAGEMENT IN HIGH EDUCATION

    Directory of Open Access Journals (Sweden)

    Hasan SERİN, Alper AYTEKİN

    2009-01-01

    Full Text Available The approach of Total Quality Management (TQM has been even more common and most recently its use in high education has been discussed. Likewise the enterprises producing various products, universities have also inputs, processes, and outputs. Due to conditions of competition, universities have to improve the qualities of these inputs, processes, and outputs, according to satisfaction, demands, and expectations of internal and external customers. If the TQM has been implemented in the universities with a manner that aims for customer satisfaction (students, lecturers, public and private establishments, and families, supports constant development, ensures participatory approach, and encourages working in groups, it will provide universities with effectiveness, efficiency, dynamics, and economics. In this study, common problems of universities, definitions of quality and TQM in high education, customer concept at universities, and factors affecting the quality of education have been explained. Besides, in order TQM approach to be successfully implemented in the universities, various suggestions have been presented.

  6. Development of a single nucleotide polymorphism (SNP) marker for ...

    African Journals Online (AJOL)

    The nature of the single nucleotide polymorphism (SNP) marker was validated by DNA sequencing of the parental PCR products. Using high resolution melt (HRM) profiles and normalised difference plots, we successfully differentiated the homozygous dominant (wild type), homozygous recessive (LPA) and heterozygous ...

  7. Large SNP arrays for genotyping in crop plants

    Indian Academy of Sciences (India)

    Genotyping with large numbers of molecular markers is now an indispensable tool within plant genetics and breeding. Especially through the identification of large numbers of single nucleotide polymorphism (SNP) markers using the novel high-throughput sequencing technologies, it is now possible to reliably identify many ...

  8. SNP Discovery In Marine Fish Species By 454 Sequencing

    DEFF Research Database (Denmark)

    Panitz, Frank; Nielsen, Rasmus Ory; van Houdt, Jeroen K J

    2011-01-01

    Based on the 454 Next-Generation-Sequencing technology (Roche) a high throughput screening method was devised in order to generate novel genetic markers (SNPs). SNP discovery was performed for three target species of marine fish: hake (Merluccius merluccius), herring (Clupea harengus) and sole...

  9. An improved PSO algorithm for generating protective SNP barcodes in breast cancer.

    Directory of Open Access Journals (Sweden)

    Li-Yeh Chuang

    Full Text Available BACKGROUND: Possible single nucleotide polymorphism (SNP interactions in breast cancer are usually not investigated in genome-wide association studies. Previously, we proposed a particle swarm optimization (PSO method to compute these kinds of SNP interactions. However, this PSO does not guarantee to find the best result in every implement, especially when high-dimensional data is investigated for SNP-SNP interactions. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we propose IPSO algorithm to improve the reliability of PSO for the identification of the best protective SNP barcodes (SNP combinations and genotypes with maximum difference between cases and controls associated with breast cancer. SNP barcodes containing different numbers of SNPs were computed. The top five SNP barcode results are retained for computing the next SNP barcode with a one-SNP-increase for each processing step. Based on the simulated data for 23 SNPs of six steroid hormone metabolisms and signalling-related genes, the performance of our proposed IPSO algorithm is evaluated. Among 23 SNPs, 13 SNPs displayed significant odds ratio (OR values (1.268 to 0.848; p<0.05 for breast cancer. Based on IPSO algorithm, the jointed effect in terms of SNP barcodes with two to seven SNPs show significantly decreasing OR values (0.84 to 0.57; p<0.05 to 0.001. Using PSO algorithm, two to four SNPs show significantly decreasing OR values (0.84 to 0.77; p<0.05 to 0.001. Based on the results of 20 simulations, medians of the maximum differences for each SNP barcode generated by IPSO are higher than by PSO. The interquartile ranges of the boxplot, as well as the upper and lower hinges for each n-SNP barcode (n = 3∼10 are more narrow in IPSO than in PSO, suggesting that IPSO is highly reliable for SNP barcode identification. CONCLUSIONS/SIGNIFICANCE: Overall, the proposed IPSO algorithm is robust to provide exact identification of the best protective SNP barcodes for breast cancer.

  10. Effect of forage quality in faeces from different ruminant species fed high and low quality forage

    DEFF Research Database (Denmark)

    Jalali, A R; Nørgaard, P; Nielsen, M O

    2010-01-01

    Effect of forage quality in faeces from different ruminant species fed high and low quality forage......Effect of forage quality in faeces from different ruminant species fed high and low quality forage...

  11. Assuring quality in high-consequence engineering

    Energy Technology Data Exchange (ETDEWEB)

    Hoover, Marcey L.; Kolb, Rachel R.

    2014-03-01

    In high-consequence engineering organizations, such as Sandia, quality assurance may be heavily dependent on staff competency. Competency-dependent quality assurance models are at risk when the environment changes, as it has with increasing attrition rates, budget and schedule cuts, and competing program priorities. Risks in Sandia's competency-dependent culture can be mitigated through changes to hiring, training, and customer engagement approaches to manage people, partners, and products. Sandia's technical quality engineering organization has been able to mitigate corporate-level risks by driving changes that benefit all departments, and in doing so has assured Sandia's commitment to excellence in high-consequence engineering and national service.

  12. SNP-RFLPing 2: an updated and integrated PCR-RFLP tool for SNP genotyping

    Directory of Open Access Journals (Sweden)

    Chang Hsueh-Wei

    2010-04-01

    Full Text Available Abstract Background PCR-restriction fragment length polymorphism (RFLP assay is a cost-effective method for SNP genotyping and mutation detection, but the manual mining for restriction enzyme sites is challenging and cumbersome. Three years after we constructed SNP-RFLPing, a freely accessible database and analysis tool for restriction enzyme mining of SNPs, significant improvements over the 2006 version have been made and incorporated into the latest version, SNP-RFLPing 2. Results The primary aim of SNP-RFLPing 2 is to provide comprehensive PCR-RFLP information with multiple functionality about SNPs, such as SNP retrieval to multiple species, different polymorphism types (bi-allelic, tri-allelic, tetra-allelic or indels, gene-centric searching, HapMap tagSNPs, gene ontology-based searching, miRNAs, and SNP500Cancer. The RFLP restriction enzymes and the corresponding PCR primers for the natural and mutagenic types of each SNP are simultaneously analyzed. All the RFLP restriction enzyme prices are also provided to aid selection. Furthermore, the previously encountered updating problems for most SNP related databases are resolved by an on-line retrieval system. Conclusions The user interfaces for functional SNP analyses have been substantially improved and integrated. SNP-RFLPing 2 offers a new and user-friendly interface for RFLP genotyping that can be used in association studies and is freely available at http://bio.kuas.edu.tw/snp-rflping2.

  13. SNP-RFLPing 2: an updated and integrated PCR-RFLP tool for SNP genotyping.

    Science.gov (United States)

    Chang, Hsueh-Wei; Cheng, Yu-Huei; Chuang, Li-Yeh; Yang, Cheng-Hong

    2010-04-08

    PCR-restriction fragment length polymorphism (RFLP) assay is a cost-effective method for SNP genotyping and mutation detection, but the manual mining for restriction enzyme sites is challenging and cumbersome. Three years after we constructed SNP-RFLPing, a freely accessible database and analysis tool for restriction enzyme mining of SNPs, significant improvements over the 2006 version have been made and incorporated into the latest version, SNP-RFLPing 2. The primary aim of SNP-RFLPing 2 is to provide comprehensive PCR-RFLP information with multiple functionality about SNPs, such as SNP retrieval to multiple species, different polymorphism types (bi-allelic, tri-allelic, tetra-allelic or indels), gene-centric searching, HapMap tagSNPs, gene ontology-based searching, miRNAs, and SNP500Cancer. The RFLP restriction enzymes and the corresponding PCR primers for the natural and mutagenic types of each SNP are simultaneously analyzed. All the RFLP restriction enzyme prices are also provided to aid selection. Furthermore, the previously encountered updating problems for most SNP related databases are resolved by an on-line retrieval system. The user interfaces for functional SNP analyses have been substantially improved and integrated. SNP-RFLPing 2 offers a new and user-friendly interface for RFLP genotyping that can be used in association studies and is freely available at http://bio.kuas.edu.tw/snp-rflping2.

  14. Producing high-quality slash pine seeds

    Science.gov (United States)

    James Barnett; Sue Varela

    2003-01-01

    Slash pine is a desirable species. It serves many purposes and is well adapted to poorly drained flatwoods and seasonally flooded areas along the lower Coastal Plain of the Southeastern US. The use of high-quality seeds has been shown to produce uniform seedlings for outplanting, which is key to silvicultural success along the Coastal Plain and elsewhere. We present...

  15. Endorectal high dose rate brachytherapy quality assurance

    International Nuclear Information System (INIS)

    Devic, S.; Vuong, T.; Evans, M.; Podgorsak, E.

    2008-01-01

    We describe our quality assurance method for preoperative high dose rate (HDR) brachytherapy of endorectal tumours. Reproduction of the treatment planning dose distribution on a daily basis is crucial for treatment success. Due to the cylindrical symmetry, two types of adjustments are necessary: applicator rotation and dose distribution shift along the applicator axis. (author)

  16. High Quality Virtual Reality for Architectural Exhibitions

    DEFF Research Database (Denmark)

    Kreutzberg, Anette

    2016-01-01

    This paper will summarise the findings from creating and implementing a visually high quality Virtual Reality (VR) experiment as part of an international architecture exhibition. It was the aim to represent the architectural spatial qualities as well as the atmosphere created from combining natural...... and artificial lighting in a prominent not yet built project. The outcome is twofold: Findings concerning the integration of VR in an exhibition space and findings concerning the experience of the virtual space itself. In the exhibition, an important aspect was the unmanned exhibition space, requiring the VR...... experience to be self-explanatory. Observations of different visitor reactions to the unmanned VR experience compared with visitor reactions at guided tours with personal instructions are evaluated. Data on perception of realism, spatial quality and light in the VR model were collected with qualitative...

  17. Quantitative analysis of low-density SNP data for parentage assignment and estimation of family contributions to pooled samples.

    Science.gov (United States)

    Henshall, John M; Dierens, Leanne; Sellars, Melony J

    2014-09-02

    While much attention has focused on the development of high-density single nucleotide polymorphism (SNP) assays, the costs of developing and running low-density assays have fallen dramatically. This makes it feasible to develop and apply SNP assays for agricultural species beyond the major livestock species. Although low-cost low-density assays may not have the accuracy of the high-density assays widely used in human and livestock species, we show that when combined with statistical analysis approaches that use quantitative instead of discrete genotypes, their utility may be improved. The data used in this study are from a 63-SNP marker Sequenom® iPLEX Platinum panel for the Black Tiger shrimp, for which high-density SNP assays are not currently available. For quantitative genotypes that could be estimated, in 5% of cases the most likely genotype for an individual at a SNP had a probability of less than 0.99. Matrix formulations of maximum likelihood equations for parentage assignment were developed for the quantitative genotypes and also for discrete genotypes perturbed by an assumed error term. Assignment rates that were based on maximum likelihood with quantitative genotypes were similar to those based on maximum likelihood with perturbed genotypes but, for more than 50% of cases, the two methods resulted in individuals being assigned to different families. Treating genotypes as quantitative values allows the same analysis framework to be used for pooled samples of DNA from multiple individuals. Resulting correlations between allele frequency estimates from pooled DNA and individual samples were consistently greater than 0.90, and as high as 0.97 for some pools. Estimates of family contributions to the pools based on quantitative genotypes in pooled DNA had a correlation of 0.85 with estimates of contributions from DNA-derived pedigree. Even with low numbers of SNPs of variable quality, parentage testing and family assignment from pooled samples are

  18. Characterization of a Wheat Breeders' Array suitable for high-throughput SNP genotyping of global accessions of hexaploid bread wheat (Triticum aestivum).

    Science.gov (United States)

    Allen, Alexandra M; Winfield, Mark O; Burridge, Amanda J; Downie, Rowena C; Benbow, Harriet R; Barker, Gary L A; Wilkinson, Paul A; Coghill, Jane; Waterfall, Christy; Davassi, Alessandro; Scopes, Geoff; Pirani, Ali; Webster, Teresa; Brew, Fiona; Bloor, Claire; Griffiths, Simon; Bentley, Alison R; Alda, Mark; Jack, Peter; Phillips, Andrew L; Edwards, Keith J

    2017-03-01

    Targeted selection and inbreeding have resulted in a lack of genetic diversity in elite hexaploid bread wheat accessions. Reduced diversity can be a limiting factor in the breeding of high yielding varieties and crucially can mean reduced resilience in the face of changing climate and resource pressures. Recent technological advances have enabled the development of molecular markers for use in the assessment and utilization of genetic diversity in hexaploid wheat. Starting with a large collection of 819 571 previously characterized wheat markers, here we describe the identification of 35 143 single nucleotide polymorphism-based markers, which are highly suited to the genotyping of elite hexaploid wheat accessions. To assess their suitability, the markers have been validated using a commercial high-density Affymetrix Axiom ® genotyping array (the Wheat Breeders' Array), in a high-throughput 384 microplate configuration, to characterize a diverse global collection of wheat accessions including landraces and elite lines derived from commercial breeding communities. We demonstrate that the Wheat Breeders' Array is also suitable for generating high-density genetic maps of previously uncharacterized populations and for characterizing novel genetic diversity produced by mutagenesis. To facilitate the use of the array by the wheat community, the markers, the associated sequence and the genotype information have been made available through the interactive web site 'CerealsDB'. © 2016 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

  19. X-chromosome SNP analyses in 11 human Mediterranean populations show a high overall genetic homogeneity except in North-west Africans (Moroccans)

    DEFF Research Database (Denmark)

    Tomas Mas, Carmen; Sanchez Sanchez, Juan Jose; Barbaro, Anna

    2008-01-01

    BACKGROUND: Due to its history, with a high number of migration events, the Mediterranean basin represents a challenging area for population genetic studies. A large number of genetic studies have been carried out in the Mediterranean area using different markers but no consensus has been reached...

  20. Frequent LOH at hMLH1, a highly variable SNP in hMSH3, and negligible coding instability in ovarian cancer

    DEFF Research Database (Denmark)

    Arzimanoglou, I.I.; Hansen, L.L.; Chong, D.

    2002-01-01

    the mismatch DNA repair genes in ovarian cancer (OC), using a sensitive, accurate and reliable protocol we have developed. MATERIALS AND METHODS: A combination of high-resolution GeneScan software analysis and automated DNA cycle sequencing was used. RESULTS: Negligible coding MSI was observed in selected...

  1. High quality transportation fuels from renewable feedstock

    Energy Technology Data Exchange (ETDEWEB)

    Lindfors, Lars Peter

    2010-09-15

    Hydrotreating of vegetable oils is novel process for producing high quality renewable diesel. Hydrotreated vegetable oils (HVO) are paraffinic hydrocarbons. They are free of aromatics, have high cetane numbers and reduce emissions. HVO can be used as component or as such. HVO processes can also be modified to produce jet fuel. GHG savings by HVO use are significant compared to fossil fuels. HVO is already in commercial production. Neste Oil is producing its NExBTL diesel in two plants. Production of renewable fuels will be limited by availability of sustainable feedstock. Therefore R and D efforts are made to expand feedstock base further.

  2. Boiling curve in high quality flow boiling

    International Nuclear Information System (INIS)

    Shiralkar, B.S.; Hein, R.A.; Yadigaroglu, G.

    1980-01-01

    The post dry-out heat transfer regime of the flow boiling curve was investigated experimentally for high pressure water at high qualities. The test section was a short round tube located downstream of a hot patch created by a temperature controlled segment of tubing. Results from the experiment showed that the distance from the dryout point has a significant effect on the downstream temperatures and there was no unique boiling curve. The heat transfer coefficients measured sufficiently downstream of the dryout point could be correlated using the Heineman correlation for superheated steam, indicating that the droplet deposition effects could be neglected in this region

  3. Breeding and maintaining high-quality insects

    DEFF Research Database (Denmark)

    Jensen, Kim; Kristensen, Torsten Nygård; Heckmann, Lars-Henrik

    2017-01-01

    Insects have a large potential for sustainably enhancing global food and feed production, and commercial insect production is a rising industry of high economic value. Insects suitable for production typically have fast growth, short generation time, efficient nutrient utilization, high...... reproductive potential, and thrive at high density. Insects may cost-efficiently convert agricultural and industrial food by-products into valuable protein once the technology is finetuned. However, since insect mass production is a new industry, the technology needed to efficiently farm these animals is still...... in a starting phase. Here, we discuss the challenges and precautions that need to be considered when breeding and maintaining high-quality insect populations for food and feed. This involves techniques typically used in domestic animal breeding programs including maintaining genetically healthy populations...

  4. A Larger Chocolate Chip—Development of a 15K Theobroma cacao L. SNP Array to Create High-Density Linkage Maps

    Directory of Open Access Journals (Sweden)

    Donald Livingstone

    2017-12-01

    Full Text Available Cacao (Theobroma cacao L. is an important cash crop in tropical regions around the world and has a rich agronomic history in South America. As a key component in the cosmetic and confectionary industries, millions of people worldwide use products made from cacao, ranging from shampoo to chocolate. An Illumina Infinity II array was created using 13,530 SNPs identified within a small diversity panel of cacao. Of these SNPs, 12,643 derive from variation within annotated cacao genes. The genotypes of 3,072 trees were obtained, including two mapping populations from Ecuador. High-density linkage maps for these two populations were generated and compared to the cacao genome assembly. Phenotypic data from these populations were combined with the linkage maps to identify the QTLs for yield and disease resistance.

  5. A Larger Chocolate Chip-Development of a 15K Theobroma cacao L. SNP Array to Create High-Density Linkage Maps.

    Science.gov (United States)

    Livingstone, Donald; Stack, Conrad; Mustiga, Guiliana M; Rodezno, Dayana C; Suarez, Carmen; Amores, Freddy; Feltus, Frank A; Mockaitis, Keithanne; Cornejo, Omar E; Motamayor, Juan C

    2017-01-01

    Cacao ( Theobroma cacao L.) is an important cash crop in tropical regions around the world and has a rich agronomic history in South America. As a key component in the cosmetic and confectionary industries, millions of people worldwide use products made from cacao, ranging from shampoo to chocolate. An Illumina Infinity II array was created using 13,530 SNPs identified within a small diversity panel of cacao. Of these SNPs, 12,643 derive from variation within annotated cacao genes. The genotypes of 3,072 trees were obtained, including two mapping populations from Ecuador. High-density linkage maps for these two populations were generated and compared to the cacao genome assembly. Phenotypic data from these populations were combined with the linkage maps to identify the QTLs for yield and disease resistance.

  6. A SNP resource for Douglas-fir: de novo transcriptome assembly and SNP detection and validation.

    Science.gov (United States)

    Howe, Glenn T; Yu, Jianbin; Knaus, Brian; Cronn, Richard; Kolpak, Scott; Dolan, Peter; Lorenz, W Walter; Dean, Jeffrey F D

    2013-02-28

    Douglas-fir (Pseudotsuga menziesii), one of the most economically and ecologically important tree species in the world, also has one of the largest tree breeding programs. Although the coastal and interior varieties of Douglas-fir (vars. menziesii and glauca) are native to North America, the coastal variety is also widely planted for timber production in Europe, New Zealand, Australia, and Chile. Our main goal was to develop a SNP resource large enough to facilitate genomic selection in Douglas-fir breeding programs. To accomplish this, we developed a 454-based reference transcriptome for coastal Douglas-fir, annotated and evaluated the quality of the reference, identified putative SNPs, and then validated a sample of those SNPs using the Illumina Infinium genotyping platform. We assembled a reference transcriptome consisting of 25,002 isogroups (unique gene models) and 102,623 singletons from 2.76 million 454 and Sanger cDNA sequences from coastal Douglas-fir. We identified 278,979 unique SNPs by mapping the 454 and Sanger sequences to the reference, and by mapping four datasets of Illumina cDNA sequences from multiple seed sources, genotypes, and tissues. The Illumina datasets represented coastal Douglas-fir (64.00 and 13.41 million reads), interior Douglas-fir (80.45 million reads), and a Yakima population similar to interior Douglas-fir (8.99 million reads). We assayed 8067 SNPs on 260 trees using an Illumina Infinium SNP genotyping array. Of these SNPs, 5847 (72.5%) were called successfully and were polymorphic. Based on our validation efficiency, our SNP database may contain as many as ~200,000 true SNPs, and as many as ~69,000 SNPs that could be genotyped at ~20,000 gene loci using an Infinium II array-more SNPs than are needed to use genomic selection in tree breeding programs. Ultimately, these genomic resources will enhance Douglas-fir breeding and allow us to better understand landscape-scale patterns of genetic variation and potential responses to

  7. FunctSNP: an R package to link SNPs to functional knowledge and dbAutoMaker: a suite of Perl scripts to build SNP databases

    Directory of Open Access Journals (Sweden)

    Watson-Haigh Nathan S

    2010-06-01

    Full Text Available Abstract Background Whole genome association studies using highly dense single nucleotide polymorphisms (SNPs are a set of methods to identify DNA markers associated with variation in a particular complex trait of interest. One of the main outcomes from these studies is a subset of statistically significant SNPs. Finding the potential biological functions of such SNPs can be an important step towards further use in human and agricultural populations (e.g., for identifying genes related to susceptibility to complex diseases or genes playing key roles in development or performance. The current challenge is that the information holding the clues to SNP functions is distributed across many different databases. Efficient bioinformatics tools are therefore needed to seamlessly integrate up-to-date functional information on SNPs. Many web services have arisen to meet the challenge but most work only within the framework of human medical research. Although we acknowledge the importance of human research, we identify there is a need for SNP annotation tools for other organisms. Description We introduce an R package called FunctSNP, which is the user interface to custom built species-specific databases. The local relational databases contain SNP data together with functional annotations extracted from online resources. FunctSNP provides a unified bioinformatics resource to link SNPs with functional knowledge (e.g., genes, pathways, ontologies. We also introduce dbAutoMaker, a suite of Perl scripts, which can be scheduled to run periodically to automatically create/update the customised SNP databases. We illustrate the use of FunctSNP with a livestock example, but the approach and software tools presented here can be applied also to human and other organisms. Conclusions Finding the potential functional significance of SNPs is important when further using the outcomes from whole genome association studies. FunctSNP is unique in that it is the only R

  8. A set of 14 DIP-SNP markers to detect unbalanced DNA mixtures.

    Science.gov (United States)

    Liu, Zhizhen; Liu, Jinding; Wang, Jiaqi; Chen, Deqing; Liu, Zidong; Shi, Jie; Li, Zeqin; Li, Wenyan; Zhang, Gengqian; Du, Bing

    2018-03-04

    Unbalanced DNA mixture is still a difficult problem for forensic practice. DIP-STRs are useful markers for detection of minor DNA but they are not widespread in the human genome and having long amplicons. In this study, we proposed a novel type of genetic marker, termed DIP-SNP. DIP-SNP refers to the combination of INDEL and SNP in less than 300bp length of human genome. The multiplex PCR and SNaPshot assay were established for 14 DIP-SNP markers in a Chinese Han population from Shanxi, China. This novel compound marker allows detection of the minor DNA contributor with sensitivity from 1:50 to 1:1000 in a DNA mixture of any gender with 1 ng-10 ng DNA template. Most of the DIP-SNP markers had a relatively high probability of informative alleles with an average I value of 0.33. In all, we proposed DIP-SNP as a novel kind of genetic marker for detection of minor contributor from unbalanced DNA mixture and established the detection method by associating the multiplex PCR and SNaPshot assay. DIP-SNP polymorphisms are promising markers for forensic or clinical mixture examination because they are shorter, widespread and higher sensitive. Copyright © 2018 Elsevier Inc. All rights reserved.

  9. Ascertainment biases in SNP chips affect measures of population divergence

    DEFF Research Database (Denmark)

    Albrechtsen, Anders; Nielsen, Finn Cilius; Nielsen, Rasmus

    2010-01-01

    Chip-based high-throughput genotyping has facilitated genome-wide studies of genetic diversity. Many studies have utilized these large data sets to make inferences about the demographic history of human populations using measures of genetic differentiation such as F(ST) or principal component...... on direct sequencing. In addition, we also analyze publicly available genome-wide data. We demonstrate that the ascertainment biases will distort measures of human diversity and possibly change conclusions drawn from these measures in some times unexpected ways. We also show that details of the genotyping...... analyses. However, the single nucleotide polymorphism (SNP) chip data suffer from ascertainment biases caused by the SNP discovery process in which a small number of individuals from selected populations are used as discovery panels. In this study, we investigate the effect of the ascertainment bias...

  10. Electrochemical Li Topotactic Reaction in Layered SnP3 for Superior Li-Ion Batteries

    Science.gov (United States)

    Park, Jae-Wan; Park, Cheol-Min

    2016-10-01

    The development of new anode materials having high electrochemical performances and interesting reaction mechanisms is highly required to satisfy the need for long-lasting mobile electronic devices and electric vehicles. Here, we report a layer crystalline structured SnP3 and its unique electrochemical behaviors with Li. The SnP3 was simply synthesized through modification of Sn crystallography by combination with P and its potential as an anode material for LIBs was investigated. During Li insertion reaction, the SnP3 anode showed an interesting two-step electrochemical reaction mechanism comprised of a topotactic transition (0.7-2.0 V) and a conversion (0.0-2.0 V) reaction. When the SnP3-based composite electrode was tested within the topotactic reaction region (0.7-2.0 V) between SnP3 and LixSnP3 (x ≤ 4), it showed excellent electrochemical properties, such as a high volumetric capacity (1st discharge/charge capacity was 840/663 mA h cm-3) with a high initial coulombic efficiency, stable cycle behavior (636 mA h cm-3 over 100 cycles), and fast rate capability (550 mA h cm-3 at 3C). This layered SnP3 anode will be applicable to a new anode material for rechargeable LIBs.

  11. Method for synthesis of high quality graphene

    Science.gov (United States)

    Lanzara, Alessandra [Piedmont, CA; Schmid, Andreas K [Berkeley, CA; Yu, Xiaozhu [Berkeley, CA; Hwang, Choonkyu [Albany, CA; Kohl, Annemarie [Beneditkbeuern, DE; Jozwiak, Chris M [Oakland, CA

    2012-03-27

    A method is described herein for the providing of high quality graphene layers on silicon carbide wafers in a thermal process. With two wafers facing each other in close proximity, in a first vacuum heating stage, while maintained at a vacuum of around 10.sup.-6 Torr, the wafer temperature is raised to about 1500.degree. C., whereby silicon evaporates from the wafer leaving a carbon rich surface, the evaporated silicon trapped in the gap between the wafers, such that the higher vapor pressure of silicon above each of the wafers suppresses further silicon evaporation. As the temperature of the wafers is raised to about 1530.degree. C. or more, the carbon atoms self assemble themselves into graphene.

  12. High quality data: An evaluation of AIM data quality and data quality procedures

    Science.gov (United States)

    The goal of every monitoring program is to collect high-quality data which can then be used to provide information to decision makers. The Bureau of Land Management (BLM) Assessment, Inventory, and Monitoring (AIM) program is one such data set which provides rangeland status, condition, and trend in...

  13. High-picture quality industrial CT scanner

    International Nuclear Information System (INIS)

    Shoji, Takao; Nishide, Akihiko; Fujii, Masashi.

    1989-01-01

    Industrial X-ray-CT-scanners, which provide cross-sectional images of a tested sample without destroying it, are attracting attention as a new nondestructive inspection device. In 1982, Toshiba commenced the development of industrial CT scanners, and introduced the 'TOSCANER' -3000 and-4000 series. Now, the state of the art 'TOSCANER'-20000 series of CT systems has been developed incorporating the latest computer tomography and image processing technology, such as the T9506 image processor. One of the advantages of this system is its applicability to a wide range of X-ray energy . The 'TOSCANER'-20000 series can be utilized for inspecting castings and other materials with relatively low-transparency to X-rays, as well as ceramics, composite materials and other materials with high X-ray transparency. A further feature of the new system is its high-picture quality, with a high-spatial resolution resulting from a pixel size of 0.2x0.2(mm). (author)

  14. [Quality management is associated with high quality services in health care].

    Science.gov (United States)

    Nielsen, Tenna Hassert; Riis, Allan; Mainz, Jan; Jensen, Anne-Louise Degn

    2013-12-09

    In these years, quality management has been the focus in order to meet high quality services for the patients in Danish health care. This article provides information on quality management and quality improvement and it evaluates its effectiveness in achieving better organizational structures, processes and results in Danish health-care organizations. Our findings generally support that quality management is associated with high quality services in health care.

  15. Optical studies of high quality synthetic diamond

    International Nuclear Information System (INIS)

    Sharp, S.J.

    1999-01-01

    This thesis is concerned with the study of fundamental and defect induced optical properties of synthetic diamond grown using high pressure, high temperature (HPHT) synthesis or chemical vapour deposition (CVD). The primary technique used for investigation is cathodoluminescence (including imaging and decay-time measurements) in addition to other forms of optical spectroscopy. This thesis is timely in that the crystallinity and purity of synthetic diamond has increased ten fold over the last few years. The diamond exciton emission, which is easily quenched by the presence of defects, is studied in high quality samples in detail. In addition the ability now exists to engineer the isotopic content of synthetic diamond to a high degree of accuracy. The experimental chapters are divided as follows: Chapter 2: High resolution, low temperature spectra reveal a splitting of the free-exciton phonon recombination emission peaks and the bound-exciton zero phonon line. Included are measurements of the variation in intensity and decay-time as a function of temperature. Chapter 3: The shift in energy of the phonon-assisted free-exciton phonon replicas with isotopic content has been measured. The shift is in agreement with the results of interatomic force model for phonon scattering due to isotope disorder. Chapter 4: A study of the shift in energy with isotopic content of the diamond of the GR1 band due to the neutral vacancy has allowed a verification of the theoretical predictions due to the Jahn Teller effect. Chapter 5: The spatial distribution of the free-exciton luminescence is studied in HPHT synthetic and CVD diamond. A variation in intensity with distance from the surface is interpreted as a significant non-radiative loss of excitons to the surface. Chapter 6: The decay-times of all known self-interstitial related centres have been measured in order to calculate the concentration of these centres present in electron irradiated diamond. (author)

  16. High Quality Data for Grid Integration Studies

    Energy Technology Data Exchange (ETDEWEB)

    Clifton, Andrew; Draxl, Caroline; Sengupta, Manajit; Hodge, Bri-Mathias

    2017-01-22

    As variable renewable power penetration levels increase in power systems worldwide, renewable integration studies are crucial to ensure continued economic and reliable operation of the power grid. The existing electric grid infrastructure in the US in particular poses significant limitations on wind power expansion. In this presentation we will shed light on requirements for grid integration studies as far as wind and solar energy are concerned. Because wind and solar plants are strongly impacted by weather, high-resolution and high-quality weather data are required to drive power system simulations. Future data sets will have to push limits of numerical weather prediction to yield these high-resolution data sets, and wind data will have to be time-synchronized with solar data. Current wind and solar integration data sets are presented. The Wind Integration National Dataset (WIND) Toolkit is the largest and most complete grid integration data set publicly available to date. A meteorological data set, wind power production time series, and simulated forecasts created using the Weather Research and Forecasting Model run on a 2-km grid over the continental United States at a 5-min resolution is now publicly available for more than 126,000 land-based and offshore wind power production sites. The National Solar Radiation Database (NSRDB) is a similar high temporal- and spatial resolution database of 18 years of solar resource data for North America and India. The need for high-resolution weather data pushes modeling towards finer scales and closer synchronization. We also present how we anticipate such datasets developing in the future, their benefits, and the challenges with using and disseminating such large amounts of data.

  17. SNPdetector: a software tool for sensitive and accurate SNP detection.

    Directory of Open Access Journals (Sweden)

    Jinghui Zhang

    2005-10-01

    Full Text Available Identification of single nucleotide polymorphisms (SNPs and mutations is important for the discovery of genetic predisposition to complex diseases. PCR resequencing is the method of choice for de novo SNP discovery. However, manual curation of putative SNPs has been a major bottleneck in the application of this method to high-throughput screening. Therefore it is critical to develop a more sensitive and accurate computational method for automated SNP detection. We developed a software tool, SNPdetector, for automated identification of SNPs and mutations in fluorescence-based resequencing reads. SNPdetector was designed to model the process of human visual inspection and has a very low false positive and false negative rate. We demonstrate the superior performance of SNPdetector in SNP and mutation analysis by comparing its results with those derived by human inspection, PolyPhred (a popular SNP detection tool, and independent genotype assays in three large-scale investigations. The first study identified and validated inter- and intra-subspecies variations in 4,650 traces of 25 inbred mouse strains that belong to either the Mus musculus species or the M. spretus species. Unexpected heterozygosity in CAST/Ei strain was observed in two out of 1,167 mouse SNPs. The second study identified 11,241 candidate SNPs in five ENCODE regions of the human genome covering 2.5 Mb of genomic sequence. Approximately 50% of the candidate SNPs were selected for experimental genotyping; the validation rate exceeded 95%. The third study detected ENU-induced mutations (at 0.04% allele frequency in 64,896 traces of 1,236 zebra fish. Our analysis of three large and diverse test datasets demonstrated that SNPdetector is an effective tool for genome-scale research and for large-sample clinical studies. SNPdetector runs on Unix/Linux platform and is available publicly (http://lpg.nci.nih.gov.

  18. Polygenic analysis of genome-wide SNP data identifies common variants on allergic rhinitis

    DEFF Research Database (Denmark)

    Mohammadnejad, Afsaneh; Brasch-Andersen, Charlotte; Haagerup, Annette

    Background: Allergic Rhinitis (AR) is a complex disorder that affects many people around the world. There is a high genetic contribution to the development of the AR, as twins and family studies have estimated heritability of more than 33%. Due to the complex nature of the disease, single SNP...... analysis has limited power in identifying the genetic variations for AR. We combined genome-wide association analysis (GWAS) with polygenic risk score (PRS) in exploring the genetic basis underlying the disease. Methods: We collected clinical data on 631 Danish subjects with AR cases consisting of 434...... sibling pairs and unrelated individuals and control subjects of 197 unrelated individuals. SNP genotyping was done by Affymetrix Genome-Wide Human SNP Array 5.0. SNP imputation was performed using "IMPUTE2". Using additive effect model, GWAS was conducted in discovery sample, the genotypes...

  19. Interest in genomic SNP testing for prostate cancer risk: a pilot survey.

    Science.gov (United States)

    Hall, Michael J; Ruth, Karen J; Chen, David Yt; Gross, Laura M; Giri, Veda N

    2015-01-01

    Advancements in genomic testing have led to the identification of single nucleotide polymorphisms (SNPs) associated with prostate cancer. The clinical utility of SNP tests to evaluate prostate cancer risk is unclear. Studies have not examined predictors of interest in novel genomic SNP tests for prostate cancer risk in a diverse population. Consecutive participants in the Fox Chase Prostate Cancer Risk Assessment Program (PRAP) (n = 40) and unselected men from surgical urology clinics (n = 40) completed a one-time survey. Items examined interest in genomic SNP testing for prostate cancer risk, knowledge, impact of unsolicited findings, and psychosocial factors including health literacy. Knowledge of genomic SNP tests was low in both groups, but interest was higher among PRAP men (p testing in both groups. Multivariable modeling identified several predictors of higher interest in a genomic SNP test including higher perceived risk (p = 0.025), indicating zero reasons for not wanting testing (vs ≥1 reason) (p = 0.013), and higher health literacy (p = 0.016). Knowledge of genomic SNP testing was low in this sample, but higher among high-risk men. High-risk status may increase interest in novel genomic tests, while low literacy may lessen interest.

  20. Detecting imbalanced expression of SNP alleles by minisequencing on microarrays

    Directory of Open Access Journals (Sweden)

    Dahlgren Andreas

    2004-10-01

    Full Text Available Abstract Background Each of the human genes or transcriptional units is likely to contain single nucleotide polymorphisms that may give rise to sequence variation between individuals and tissues on the level of RNA. Based on recent studies, differential expression of the two alleles of heterozygous coding single nucleotide polymorphisms (SNPs may be frequent for human genes. Methods with high accuracy to be used in a high throughput setting are needed for systematic surveys of expressed sequence variation. In this study we evaluated two formats of multiplexed, microarray based minisequencing for quantitative detection of imbalanced expression of SNP alleles. We used a panel of ten SNPs located in five genes known to be expressed in two endothelial cell lines as our model system. Results The accuracy and sensitivity of quantitative detection of allelic imbalance was assessed for each SNP by constructing regression lines using a dilution series of mixed samples from individuals of different genotype. Accurate quantification of SNP alleles by both assay formats was evidenced for by R2 values > 0.95 for the majority of the regression lines. According to a two sample t-test, we were able to distinguish 1–9% of a minority SNP allele from a homozygous genotype, with larger variation between SNPs than between assay formats. Six of the SNPs, heterozygous in either of the two cell lines, were genotyped in RNA extracted from the endothelial cells. The coefficient of variation between the fluorescent signals from five parallel reactions was similar for cDNA and genomic DNA. The fluorescence signal intensity ratios measured in the cDNA samples were compared to those in genomic DNA to determine the relative expression levels of the two alleles of each SNP. Four of the six SNPs tested displayed a higher than 1.4-fold difference in allelic ratios between cDNA and genomic DNA. The results were verified by allele-specific oligonucleotide hybridisation and

  1. Compression and fast retrieval of SNP data.

    Science.gov (United States)

    Sambo, Francesco; Di Camillo, Barbara; Toffolo, Gianna; Cobelli, Claudio

    2014-11-01

    The increasing interest in rare genetic variants and epistatic genetic effects on complex phenotypic traits is currently pushing genome-wide association study design towards datasets of increasing size, both in the number of studied subjects and in the number of genotyped single nucleotide polymorphisms (SNPs). This, in turn, is leading to a compelling need for new methods for compression and fast retrieval of SNP data. We present a novel algorithm and file format for compressing and retrieving SNP data, specifically designed for large-scale association studies. Our algorithm is based on two main ideas: (i) compress linkage disequilibrium blocks in terms of differences with a reference SNP and (ii) compress reference SNPs exploiting information on their call rate and minor allele frequency. Tested on two SNP datasets and compared with several state-of-the-art software tools, our compression algorithm is shown to be competitive in terms of compression rate and to outperform all tools in terms of time to load compressed data. Our compression and decompression algorithms are implemented in a C++ library, are released under the GNU General Public License and are freely downloadable from http://www.dei.unipd.it/~sambofra/snpack.html. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  2. SNP marker detection and genotyping in tilapia

    NARCIS (Netherlands)

    Bers, van N.E.M.; Crooijmans, R.P.M.A.; Groenen, M.A.M.; Dibbits, B.W.; Komen, J.

    2012-01-01

    We have generated a unique resource consisting of nearly 175 000 short contig sequences and 3569 SNP markers from the widely cultured GIFT (Genetically Improved Farmed Tilapia) strain of Nile tilapia (Oreochromis niloticus). In total, 384 SNPs were selected to monitor the wider applicability of the

  3. Snap: an integrated SNP annotation platform

    DEFF Research Database (Denmark)

    Li, Shengting; Ma, Lijia; Li, Heng

    2007-01-01

    Snap (Single Nucleotide Polymorphism Annotation Platform) is a server designed to comprehensively analyze single genes and relationships between genes basing on SNPs in the human genome. The aim of the platform is to facilitate the study of SNP finding and analysis within the framework of medical...

  4. Ensuring High-Quality Learning for All

    Science.gov (United States)

    Núñez, Elsa M.

    2018-01-01

    The Association of American Colleges and Universities (AAC&U) has embarked on a sustained program to enhance the quality of student learning on campuses, while also supporting AAC&U members' efforts to bring liberal education to all sectors of society. This commitment to quality and equity in service to democracy forms the basis for…

  5. Direct inference of SNP heterozygosity rates and resolution of LOH detection.

    Directory of Open Access Journals (Sweden)

    Xiaohong Li

    2007-11-01

    Full Text Available Single nucleotide polymorphisms (SNPs have been increasingly utilized to investigate somatic genetic abnormalities in premalignancy and cancer. LOH is a common alteration observed during cancer development, and SNP assays have been used to identify LOH at specific chromosomal regions. The design of such studies requires consideration of the resolution for detecting LOH throughout the genome and identification of the number and location of SNPs required to detect genetic alterations in specific genomic regions. Our study evaluated SNP distribution patterns and used probability models, Monte Carlo simulation, and real human subject genotype data to investigate the relationships between the number of SNPs, SNP HET rates, and the sensitivity (resolution for detecting LOH. We report that variances of SNP heterozygosity rate in dbSNP are high for a large proportion of SNPs. Two statistical methods proposed for directly inferring SNP heterozygosity rates require much smaller sample sizes (intermediate sizes and are feasible for practical use in SNP selection or verification. Using HapMap data, we showed that a region of LOH greater than 200 kb can be reliably detected, with losses smaller than 50 kb having a substantially lower detection probability when using all SNPs currently in the HapMap database. Higher densities of SNPs may exist in certain local chromosomal regions that provide some opportunities for reliably detecting LOH of segment sizes smaller than 50 kb. These results suggest that the interpretation of the results from genome-wide scans for LOH using commercial arrays need to consider the relationships among inter-SNP distance, detection probability, and sample size for a specific study. New experimental designs for LOH studies would also benefit from considering the power of detection and sample sizes required to accomplish the proposed aims.

  6. The impact of SNP fingerprinting and parentage analysis on the effectiveness of variety recommendations in cacao

    Science.gov (United States)

    Evidence for the impact of mislabeling and/or pollen contamination on consistency of field performance has been lacking to reinforce the need for strict adherence to quality control protocols in cacao seed garden and germplasm plot management. The present study used SNP fingerprinting at 64 loci to ...

  7. Identification of Mendelian inconsistencies between SNP and pedigree Information of Sibs

    NARCIS (Netherlands)

    Calus, M.P.L.; Mulder, H.A.; Bastiaansen, J.W.M.

    2011-01-01

    Background Using SNP genotypes to apply genomic selection in breeding programs is becoming common practice. Tools to edit and check the quality of genotype data are required. Checking for Mendelian inconsistencies makes it possible to identify animals for which pedigree information and genotype

  8. High Efficiency, Illumination Quality OLEDs for Lighting

    Energy Technology Data Exchange (ETDEWEB)

    Joseph Shiang; James Cella; Kelly Chichak; Anil Duggal; Kevin Janora; Chris Heller; Gautam Parthasarathy; Jeffery Youmans; Joseph Shiang

    2008-03-31

    The goal of the program was to demonstrate a 45 lumen per watt white light device based upon the use of multiple emission colors through the use of solution processing. This performance level is a dramatic extension of the team's previous 15 LPW large area illumination device. The fundamental material system was based upon commercial polymer materials. The team was largely able to achieve these goals, and was able to deliver to DOE a 90 lumen illumination source that had an average performance of 34 LPW a 1000 cd/m{sup 2} with peak performances near 40LPW. The average color temperature is 3200K and the calculated CRI 85. The device operated at a brightness of approximately 1000cd/m{sup 2}. The use of multiple emission colors particularly red and blue, provided additional degrees of design flexibility in achieving white light, but also required the use of a multilayered structure to separate the different recombination zones and prevent interconversion of blue emission to red emission. The use of commercial materials had the advantage that improvements by the chemical manufacturers in charge transport efficiency, operating life and material purity could be rapidly incorporated without the expenditure of additional effort. The program was designed to take maximum advantage of the known characteristics of these material and proceeded in seven steps. (1) Identify the most promising materials, (2) assemble them into multi-layer structures to control excitation and transport within the OLED, (3) identify materials development needs that would optimize performance within multilayer structures, (4) build a prototype that demonstrates the potential entitlement of the novel multilayer OLED architecture (5) integrate all of the developments to find the single best materials set to implement the novel multilayer architecture, (6) further optimize the best materials set, (7) make a large area high illumination quality white OLED. A photo of the final deliverable is shown

  9. Optimal Design of Low-Density SNP Arrays for Genomic Prediction: Algorithm and Applications.

    Directory of Open Access Journals (Sweden)

    Xiao-Lin Wu

    Full Text Available Low-density (LD single nucleotide polymorphism (SNP arrays provide a cost-effective solution for genomic prediction and selection, but algorithms and computational tools are needed for the optimal design of LD SNP chips. A multiple-objective, local optimization (MOLO algorithm was developed for design of optimal LD SNP chips that can be imputed accurately to medium-density (MD or high-density (HD SNP genotypes for genomic prediction. The objective function facilitates maximization of non-gap map length and system information for the SNP chip, and the latter is computed either as locus-averaged (LASE or haplotype-averaged Shannon entropy (HASE and adjusted for uniformity of the SNP distribution. HASE performed better than LASE with ≤1,000 SNPs, but required considerably more computing time. Nevertheless, the differences diminished when >5,000 SNPs were selected. Optimization was accomplished conditionally on the presence of SNPs that were obligated to each chromosome. The frame location of SNPs on a chip can be either uniform (evenly spaced or non-uniform. For the latter design, a tunable empirical Beta distribution was used to guide location distribution of frame SNPs such that both ends of each chromosome were enriched with SNPs. The SNP distribution on each chromosome was finalized through the objective function that was locally and empirically maximized. This MOLO algorithm was capable of selecting a set of approximately evenly-spaced and highly-informative SNPs, which in turn led to increased imputation accuracy compared with selection solely of evenly-spaced SNPs. Imputation accuracy increased with LD chip size, and imputation error rate was extremely low for chips with ≥3,000 SNPs. Assuming that genotyping or imputation error occurs at random, imputation error rate can be viewed as the upper limit for genomic prediction error. Our results show that about 25% of imputation error rate was propagated to genomic prediction in an Angus

  10. Tag SNP selection via a genetic algorithm.

    Science.gov (United States)

    Mahdevar, Ghasem; Zahiri, Javad; Sadeghi, Mehdi; Nowzari-Dalini, Abbas; Ahrabian, Hayedeh

    2010-10-01

    Single Nucleotide Polymorphisms (SNPs) provide valuable information on human evolutionary history and may lead us to identify genetic variants responsible for human complex diseases. Unfortunately, molecular haplotyping methods are costly, laborious, and time consuming; therefore, algorithms for constructing full haplotype patterns from small available data through computational methods, Tag SNP selection problem, are convenient and attractive. This problem is proved to be an NP-hard problem, so heuristic methods may be useful. In this paper we present a heuristic method based on genetic algorithm to find reasonable solution within acceptable time. The algorithm was tested on a variety of simulated and experimental data. In comparison with the exact algorithm, based on brute force approach, results show that our method can obtain optimal solutions in almost all cases and runs much faster than exact algorithm when the number of SNP sites is large. Our software is available upon request to the corresponding author.

  11. CFSAN SNP Pipeline: an automated method for constructing SNP matrices from next-generation sequence data

    Directory of Open Access Journals (Sweden)

    Steve Davis

    2015-08-01

    Full Text Available The analysis of next-generation sequence (NGS data is often a fragmented step-wise process. For example, multiple pieces of software are typically needed to map NGS reads, extract variant sites, and construct a DNA sequence matrix containing only single nucleotide polymorphisms (i.e., a SNP matrix for a set of individuals. The management and chaining of these software pieces and their outputs can often be a cumbersome and difficult task. Here, we present CFSAN SNP Pipeline, which combines into a single package the mapping of NGS reads to a reference genome with Bowtie2, processing of those mapping (BAM files using SAMtools, identification of variant sites using VarScan, and production of a SNP matrix using custom Python scripts. We also introduce a Python package (CFSAN SNP Mutator that when given a reference genome will generate variants of known position against which we validate our pipeline. We created 1,000 simulated Salmonella enterica sp. enterica Serovar Agona genomes at 100× and 20× coverage, each containing 500 SNPs, 20 single-base insertions and 20 single-base deletions. For the 100× dataset, the CFSAN SNP Pipeline recovered 98.9% of the introduced SNPs and had a false positive rate of 1.04 × 10−6; for the 20× dataset 98.8% of SNPs were recovered and the false positive rate was 8.34 × 10−7. Based on these results, CFSAN SNP Pipeline is a robust and accurate tool that it is among the first to combine into a single executable the myriad steps required to produce a SNP matrix from NGS data. Such a tool is useful to those working in an applied setting (e.g., food safety traceback investigations as well as for those interested in evolutionary questions.

  12. Analysis of high-quality modes in open chaotic microcavities

    International Nuclear Information System (INIS)

    Fang, W.; Yamilov, A.; Cao, H.

    2005-01-01

    We present a numerical study of the high-quality modes in two-dimensional dielectric stadium microcavities. Although the classical ray mechanics is fully chaotic in a stadium billiard, all of the high-quality modes show a 'strong scar' around unstable periodic orbits. When the deformation (ratio of the length of the straight segments over the diameter of the half circles) is small, the high-quality modes correspond to whispering-gallery-type trajectories and their quality factors decrease monotonically with increasing deformation. At large deformation, each high-quality mode is associated with multiple unstable periodic orbits. Its quality factor changes nonmonotonically with the deformation, and there exists an optimal deformation for each mode at which its quality factor reaches a local maximum. This unusual behavior is attributed to the interference of waves propagating along different constituent orbits that could minimize light leakage out of the cavity

  13. High quality steel casting for energy technics

    International Nuclear Information System (INIS)

    Schuster, F.; Koefler, G.

    1982-01-01

    The casting of several chromium-molybdenum steels for steam and hydraulic turbines is discussed. Non-destructive testing of the castings is performed demonstrating the safety for use in nuclear technology. The effect of metallurgical parameters on steel casting quality, the heat treatment, and the effect of construction design on costs for fettling and repair weldings are considered. (Auth.)

  14. Identification of Laying-Related SNP Markers in Geese Using RAD Sequencing.

    Directory of Open Access Journals (Sweden)

    ShiGang Yu

    Full Text Available Laying performance is an important economical trait of goose production. As laying performance is of low heritability, it is of significance to develop a marker-assisted selection (MAS strategy for this trait. Definition of sequence variation related to the target trait is a prerequisite of quantitating MAS, but little is presently known about the goose genome, which greatly hinders the identification of genetic markers for the laying traits of geese. Recently developed restriction site-associated DNA (RAD sequencing is a possible approach for discerning large-scale single nucleotide polymorphism (SNP and reducing the complexity of a genome without having reference genomic information available. In the present study, we developed a pooled RAD sequencing strategy for detecting geese laying-related SNP. Two DNA pools were constructed, each consisting of equal amounts of genomic DNA from 10 individuals with either high estimated breeding value (HEBV or low estimated breeding value (LEBV. A total of 139,013 SNP were obtained from 42,291,356 sequences, of which 18,771,943 were for LEBV and 23,519,413 were for HEBV cohorts. Fifty-five SNP which had different allelic frequencies in the two DNA pools were further validated by individual-based AS-PCR genotyping in the LEBV and HEBV cohorts. Ten out of 55 SNP exhibited distinct allele distributions in these two cohorts. These 10 SNP were further genotyped in a goose population of 492 geese to verify the association with egg numbers. The result showed that 8 of 10 SNP were associated with egg numbers. Additionally, liner regression analysis revealed that SNP Record-111407, 106975 and 112359 were involved in a multiplegene network affecting laying performance. We used IPCR to extend the unknown regions flanking the candidate RAD tags. The obtained sequences were subjected to BLAST to retrieve the orthologous genes in either ducks or chickens. Five novel genes were cloned for geese which harbored the

  15. SNPServer: a real-time SNP discovery tool.

    Science.gov (United States)

    Savage, David; Batley, Jacqueline; Erwin, Tim; Logan, Erica; Love, Christopher G; Lim, Geraldine A C; Mongin, Emmanuel; Barker, Gary; Spangenberg, German C; Edwards, David

    2005-07-01

    SNPServer is a real-time flexible tool for the discovery of SNPs (single nucleotide polymorphisms) within DNA sequence data. The program uses BLAST, to identify related sequences, and CAP3, to cluster and align these sequences. The alignments are parsed to the SNP discovery software autoSNP, a program that detects SNPs and insertion/deletion polymorphisms (indels). Alternatively, lists of related sequences or pre-assembled sequences may be entered for SNP discovery. SNPServer and autoSNP use redundancy to differentiate between candidate SNPs and sequence errors. For each candidate SNP, two measures of confidence are calculated, the redundancy of the polymorphism at a SNP locus and the co-segregation of the candidate SNP with other SNPs in the alignment. SNPServer is available at http://hornbill.cspp.latrobe.edu.au/snpdiscovery.html.

  16. Indoor Air Quality in High Performance Schools

    Science.gov (United States)

    High performance schools are facilities that improve the learning environment while saving energy, resources, and money. The key is understanding the lifetime value of high performance schools and effectively managing priorities, time, and budget.

  17. saSNP Approach for Scalable SNP Analyses of Multiple Bacterial or Viral Genomes

    Energy Technology Data Exchange (ETDEWEB)

    Gardner, Shea [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Slezak, Tom [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2010-07-27

    With the flood of whole genome finished and draft microbial sequences, we need faster, more scalable bioinformatics tools for sequence comparison. An algorithm is described to find single nucleotide polymorphisms (SNPs) in whole genome data. It scales to hundreds of bacterial or viral genomes, and can be used for finished and/or draft genomes available as unassembled contigs. The method is fast to compute, finding SNPs and building a SNP phylogeny in seconds to hours. We use it to identify thousands of putative SNPs from all publicly available Filoviridae, Poxviridae, foot-and-mouth disease virus, Bacillus, and Escherichia coli genomes and plasmids. The SNP-based trees that result are consistent with known taxonomy and trees determined in other studies. The approach we describe can handle as input hundreds of gigabases of sequence in a single run. The algorithm is based on k-mer analysis using a suffix array, so we call it saSNP.

  18. Forensic typing of autosomal SNPs with a 29 SNP-multiplex--results of a collaborative EDNAP exercise.

    Science.gov (United States)

    Sanchez, J J; Børsting, C; Balogh, K; Berger, B; Bogus, M; Butler, J M; Carracedo, A; Court, D Syndercombe; Dixon, L A; Filipović, B; Fondevila, M; Gill, P; Harrison, C D; Hohoff, C; Huel, R; Ludes, B; Parson, W; Parsons, T J; Petkovski, E; Phillips, C; Schmitter, H; Schneider, P M; Vallone, P M; Morling, N

    2008-06-01

    We report the results of an inter-laboratory exercise on typing of autosomal single nucleotide polymorphisms (SNP) for forensic genetic investigations in crime cases. The European DNA Profiling Group (EDNAP), a working group under the International Society for Forensic Genetics (ISFG), organised the exercise. A total of 11 European and one US forensic genetic laboratories tested a subset of a 52 SNP-multiplex PCR kit developed by the SNPforID consortium. The 52 SNP-multiplex kit amplifies 52 DNA fragments with 52 autosomal SNP loci in one multiplex PCR. The 52 SNPs are detected in two separate single base extension (SBE) multiplex reactions with 29 and 23 SNPs, respectively, using SNaPshot kit, capillary electrophoresis and multicolour fluorescence detection. For practical reasons, only the 29 SBE multiplex reaction was carried out by the participating laboratories. A total of 11 bloodstains on FTA cards including a sample of poor quality and a negative control were sent to the laboratories together with the essential reagents for the initial multiplex PCR and the multiplex SBE reaction. The total SNP locus dropout rate was 2.8% and more than 50% of the dropouts were observed with the poor quality sample. The overall rate of discrepant SNP allele assignments was 2.0%. Two laboratories reported 60% of all the discrepancies. Two laboratories reported all 29 SNP alleles in all 10 positive samples correctly. The results of the collaborative exercise were surprisingly good and demonstrate that SNP typing with SBE, capillary electrophoresis and multicolour detection methods can be developed for forensic genetics.

  19. Genome-Wide Association Study for Identification and Validation of Novel SNP Markers for Sr6 Stem Rust Resistance Gene in Bread Wheat.

    Science.gov (United States)

    Mourad, Amira M I; Sallam, Ahmed; Belamkar, Vikas; Wegulo, Stephen; Bowden, Robert; Jin, Yue; Mahdy, Ezzat; Bakheit, Bahy; El-Wafaa, Atif A; Poland, Jesse; Baenziger, Peter S

    2018-01-01

    Stem rust (caused by Puccinia graminis f. sp. tritici Erikss. & E. Henn.), is a major disease in wheat ( Triticum aestivium L.). However, in recent years it occurs rarely in Nebraska due to weather and the effective selection and gene pyramiding of resistance genes. To understand the genetic basis of stem rust resistance in Nebraska winter wheat, we applied genome-wide association study (GWAS) on a set of 270 winter wheat genotypes (A-set). Genotyping was carried out using genotyping-by-sequencing and ∼35,000 high-quality SNPs were identified. The tested genotypes were evaluated for their resistance to the common stem rust race in Nebraska (QFCSC) in two replications. Marker-trait association identified 32 SNP markers, which were significantly (Bonferroni corrected P < 0.05) associated with the resistance on chromosome 2D. The chromosomal location of the significant SNPs (chromosome 2D) matched the location of Sr6 gene which was expected in these genotypes based on pedigree information. A highly significant linkage disequilibrium (LD, r 2 ) was found between the significant SNPs and the specific SSR marker for the Sr6 gene ( Xcfd43 ). This suggests the significant SNP markers are tagging Sr6 gene. Out of the 32 significant SNPs, eight SNPs were in six genes that are annotated as being linked to disease resistance in the IWGSC RefSeq v1.0. The 32 significant SNP markers were located in nine haplotype blocks. All the 32 significant SNPs were validated in a set of 60 different genotypes (V-set) using single marker analysis. SNP markers identified in this study can be used in marker-assisted selection, genomic selection, and to develop KASP (Kompetitive Allele Specific PCR) marker for the Sr6 gene. Novel SNPs for Sr6 gene, an important stem rust resistant gene, were identified and validated in this study. These SNPs can be used to improve stem rust resistance in wheat.

  20. SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation

    DEFF Research Database (Denmark)

    Panitz, Frank; Stengaard, Henrik; Hornshoj, Henrik

    2007-01-01

    MOTIVATION: Single nucleotide polymorphisms (SNPs) analysis is an important means to study genetic variation. A fast and cost-efficient approach to identify large numbers of novel candidates is the SNP mining of large scale sequencing projects. The increasing availability of sequence trace data...... manual annotation, which is immediately accessible and can be easily shared with external collaborators. RESULTS: Large-scale SNP mining of polymorphisms bases on porcine EST sequences yielded more than 7900 candidate SNPs in coding regions (cSNPs), which were annotated relative to the human genome. Non...

  1. A SNP-Based Molecular Barcode for Characterization of Common Wheat.

    Directory of Open Access Journals (Sweden)

    LiFeng Gao

    Full Text Available Wheat is grown as a staple crop worldwide. It is important to develop an effective genotyping tool for this cereal grain both to identify germplasm diversity and to protect the rights of breeders. Single-nucleotide polymorphism (SNP genotyping provides a means for developing a practical, rapid, inexpensive and high-throughput assay. Here, we investigated SNPs as robust markers of genetic variation for typing wheat cultivars. We identified SNPs from an array of 9000 across a collection of 429 well-known wheat cultivars grown in China, of which 43 SNP markers with high minor allele frequency and variations discriminated the selected wheat varieties and their wild ancestors. This SNP-based barcode will allow for the rapid and precise identification of wheat germplasm resources and newly released varieties and will further assist in the wheat breeding program.

  2. A 34K SNP genotyping array for Populus trichocarpa: design, application to the study of natural populations and transferability to other Populus species.

    Science.gov (United States)

    Geraldes, A; Difazio, S P; Slavov, G T; Ranjan, P; Muchero, W; Hannemann, J; Gunter, L E; Wymore, A M; Grassa, C J; Farzaneh, N; Porth, I; McKown, A D; Skyba, O; Li, E; Fujita, M; Klápště, J; Martin, J; Schackwitz, W; Pennacchio, C; Rokhsar, D; Friedmann, M C; Wasteneys, G O; Guy, R D; El-Kassaby, Y A; Mansfield, S D; Cronk, Q C B; Ehlting, J; Douglas, C J; Tuskan, G A

    2013-03-01

    Genetic mapping of quantitative traits requires genotypic data for large numbers of markers in many individuals. For such studies, the use of large single nucleotide polymorphism (SNP) genotyping arrays still offers the most cost-effective solution. Herein we report on the design and performance of a SNP genotyping array for Populus trichocarpa (black cottonwood). This genotyping array was designed with SNPs pre-ascertained in 34 wild accessions covering most of the species latitudinal range. We adopted a candidate gene approach to the array design that resulted in the selection of 34 131 SNPs, the majority of which are located in, or within 2 kb of, 3543 candidate genes. A subset of the SNPs on the array (539) was selected based on patterns of variation among the SNP discovery accessions. We show that more than 95% of the loci produce high quality genotypes and that the genotyping error rate for these is likely below 2%. We demonstrate that even among small numbers of samples (n = 10) from local populations over 84% of loci are polymorphic. We also tested the applicability of the array to other species in the genus and found that the number of polymorphic loci decreases rapidly with genetic distance, with the largest numbers detected in other species in section Tacamahaca. Finally, we provide evidence for the utility of the array to address evolutionary questions such as intraspecific studies of genetic differentiation, species assignment and the detection of natural hybrids. © 2013 Blackwell Publishing Ltd.

  3. Analysis of SNP rs16754 of WT1 gene in a series of de novo acute myeloid leukemia patients.

    Science.gov (United States)

    Luna, Irene; Such, Esperanza; Cervera, Jose; Barragán, Eva; Jiménez-Velasco, Antonio; Dolz, Sandra; Ibáñez, Mariam; Gómez-Seguí, Inés; López-Pavía, María; Llop, Marta; Fuster, Óscar; Oltra, Silvestre; Moscardó, Federico; Martínez-Cuadrón, David; Senent, M Leonor; Gascón, Adriana; Montesinos, Pau; Martín, Guillermo; Bolufer, Pascual; Sanz, Miguel A

    2012-12-01

    The single nucleotide polymorphism (SNP) rs16754 of the WT1 gene has been previously described as a possible prognostic marker in normal karyotype acute myeloid leukemia (AML) patients. Nevertheless, the findings in this field are not always reproducible in different series. One hundred and seventy-five adult de novo AML patients were screened with two different methods for the detection of SNP rs16754: high-resolution melting (HRM) and FRET hybridization probes. Direct sequencing was used to validate both techniques. The SNP was detected in 52 out of 175 patients (30 %), both by HRM and hybridization probes. Direct sequencing confirmed that every positive sample in the screening methods had a variation in the DNA sequence. Patients with the wild-type genotype (WT1(AA)) for the SNP rs16754 were significantly younger than those with the heterozygous WT1(AG) genotype. No other difference was observed for baseline characteristic or outcome between patients with or without the SNP. Both techniques are equally reliable and reproducible as screening methods for the detection of the SNP rs16754, allowing for the selection of those samples that will need to be sequenced. We were unable to confirm the suggested favorable outcome of SNP rs16754 in de novo AML.

  4. Quality Assurance Strategy for Existing Homes: Final Quality Management Primer for High Performing Homes

    Energy Technology Data Exchange (ETDEWEB)

    Del Bianco, M.; Taggart, J.; Sikora, J.; Wood, A.

    2012-12-01

    This guide is designed to help Building America (BA) Teams understand quality management and its role in transitioning from conventional to high performance home building and remodeling. It explains what quality means, the value of quality management systems, the unique need for QMS when building high performing homes, and the first steps to a implementing a comprehensive QMS. This document provides a framework and context for BA teams when they encounter builders and remodelers.

  5. Quality Assurance Strategy for Existing Homes. Final Quality Management Primer for High Performing Homes

    Energy Technology Data Exchange (ETDEWEB)

    Del Bianco, M. [NAHB Research Center Industry Partnership, Upper Marlboro, MD (United States); Taggart, J. [NAHB Research Center Industry Partnership, Upper Marlboro, MD (United States); Sikora, J. [NAHB Research Center Industry Partnership, Upper Marlboro, MD (United States); Wood, A. [NAHB Research Center Industry Partnership, Upper Marlboro, MD (United States)

    2012-12-01

    This guide is designed to help Building America (BA) teams understand quality management and its role in transitioning from conventional to high performance home building and remodeling. It explains what quality means, the value of quality management systems, the unique need for QMS when building high performing homes, and the first steps to a implementing a comprehensive QMS. This document provides a framework and context for BA teams when they encounter builders and remodelers.

  6. The Generalized Higher Criticism for Testing SNP-Set Effects in Genetic Association Studies

    Science.gov (United States)

    Barnett, Ian; Mukherjee, Rajarshi; Lin, Xihong

    2017-01-01

    It is of substantial interest to study the effects of genes, genetic pathways, and networks on the risk of complex diseases. These genetic constructs each contain multiple SNPs, which are often correlated and function jointly, and might be large in number. However, only a sparse subset of SNPs in a genetic construct is generally associated with the disease of interest. In this article, we propose the generalized higher criticism (GHC) to test for the association between an SNP set and a disease outcome. The higher criticism is a test traditionally used in high-dimensional signal detection settings when marginal test statistics are independent and the number of parameters is very large. However, these assumptions do not always hold in genetic association studies, due to linkage disequilibrium among SNPs and the finite number of SNPs in an SNP set in each genetic construct. The proposed GHC overcomes the limitations of the higher criticism by allowing for arbitrary correlation structures among the SNPs in an SNP-set, while performing accurate analytic p-value calculations for any finite number of SNPs in the SNP-set. We obtain the detection boundary of the GHC test. We compared empirically using simulations the power of the GHC method with existing SNP-set tests over a range of genetic regions with varied correlation structures and signal sparsity. We apply the proposed methods to analyze the CGEM breast cancer genome-wide association study. Supplementary materials for this article are available online. PMID:28736464

  7. [Relationship between genetic polymorphisms of 3 SNP loci in 5-HTT gene and paranoid schizophrenia].

    Science.gov (United States)

    Xuan, Jin-Feng; Ding, Mei; Pang, Hao; Xing, Jia-Xin; Sun, Yi-Hua; Yao, Jun; Zhao, Yi; Li, Chun-Mei; Wang, Bao-Jie

    2012-12-01

    To investigate the population genetic data of 3 SNP loci (rs25533, rs34388196 and rs1042173) of 5-hydroxytryptamine transporter (5-HTT) gene and the association with paranoid schizophrenia. Three SNP loci of 5-HTT gene were examined in 132 paranoid schizophrenia patients and 150 unrelated healthy individuals of Northern Chinese Han population by PCR-RFLP technique. The Hardy-Weinberg equilibrium test was performed using the chi-square test and the data of haplotype frequency and population genetics parameters were statistically analyzed. Among these three SNP loci, four haplotypes were obtained. There were no statistically significant differences between the patient group and the control group (P > 0.05). The DP values of the 3 SNP loci were 0.276, 0.502 and 0.502. The PIC of them were 0.151, 0.281 and 0.281. The PE of them were 0.014, 0.072 and 0.072. The three SNP loci and four haplotypes of 5-HTT gene have no association with paranoid schizophrenia, while the polymorphism still have high potential application in forensic practice.

  8. Underestimated effect sizes in GWAS: fundamental limitations of single SNP analysis for dichotomous phenotypes.

    Directory of Open Access Journals (Sweden)

    Sven Stringer

    Full Text Available Complex diseases are often highly heritable. However, for many complex traits only a small proportion of the heritability can be explained by observed genetic variants in traditional genome-wide association (GWA studies. Moreover, for some of those traits few significant SNPs have been identified. Single SNP association methods test for association at a single SNP, ignoring the effect of other SNPs. We show using a simple multi-locus odds model of complex disease that moderate to large effect sizes of causal variants may be estimated as relatively small effect sizes in single SNP association testing. This underestimation effect is most severe for diseases influenced by numerous risk variants. We relate the underestimation effect to the concept of non-collapsibility found in the statistics literature. As described, continuous phenotypes generated with linear genetic models are not affected by this underestimation effect. Since many GWA studies apply single SNP analysis to dichotomous phenotypes, previously reported results potentially underestimate true effect sizes, thereby impeding identification of true effect SNPs. Therefore, when a multi-locus model of disease risk is assumed, a multi SNP analysis may be more appropriate.

  9. Inequality in Preschool Quality? Community-Level Disparities in Access to High-Quality Learning Environments

    Science.gov (United States)

    Bassok, Daphna; Galdo, Eva

    2016-01-01

    In recent years, unequal access to high-quality preschool has emerged as a growing public policy concern. Because of data limitations, it is notoriously difficult to measure disparities in access to early learning opportunities across communities and particularly challenging to quantify gaps in access to "high-quality" programs. Research…

  10. Fine-scaled human genetic structure revealed by SNP microarrays.

    Science.gov (United States)

    Xing, Jinchuan; Watkins, W Scott; Witherspoon, David J; Zhang, Yuhua; Guthery, Stephen L; Thara, Rangaswamy; Mowry, Bryan J; Bulayeva, Kazima; Weiss, Robert B; Jorde, Lynn B

    2009-05-01

    We report an analysis of more than 240,000 loci genotyped using the Affymetrix SNP microarray in 554 individuals from 27 worldwide populations in Africa, Asia, and Europe. To provide a more extensive and complete sampling of human genetic variation, we have included caste and tribal samples from two states in South India, Daghestanis from eastern Europe, and the Iban from Malaysia. Consistent with observations made by Charles Darwin, our results highlight shared variation among human populations and demonstrate that much genetic variation is geographically continuous. At the same time, principal components analyses reveal discernible genetic differentiation among almost all identified populations in our sample, and in most cases, individuals can be clearly assigned to defined populations on the basis of SNP genotypes. All individuals are accurately classified into continental groups using a model-based clustering algorithm, but between closely related populations, genetic and self-classifications conflict for some individuals. The 250K data permitted high-level resolution of genetic variation among Indian caste and tribal populations and between highland and lowland Daghestani populations. In particular, upper-caste individuals from Tamil Nadu and Andhra Pradesh form one defined group, lower-caste individuals from these two states form another, and the tribal Irula samples form a third. Our results emphasize the correlation of genetic and geographic distances and highlight other elements, including social factors that have contributed to population structure.

  11. Psoriasis prediction from genome-wide SNP profiles

    Directory of Open Access Journals (Sweden)

    Fang Xiangzhong

    2011-01-01

    Full Text Available Abstract Background With the availability of large-scale genome-wide association study (GWAS data, choosing an optimal set of SNPs for disease susceptibility prediction is a challenging task. This study aimed to use single nucleotide polymorphisms (SNPs to predict psoriasis from searching GWAS data. Methods Totally we had 2,798 samples and 451,724 SNPs. Process for searching a set of SNPs to predict susceptibility for psoriasis consisted of two steps. The first one was to search top 1,000 SNPs with high accuracy for prediction of psoriasis from GWAS dataset. The second one was to search for an optimal SNP subset for predicting psoriasis. The sequential information bottleneck (sIB method was compared with classical linear discriminant analysis(LDA for classification performance. Results The best test harmonic mean of sensitivity and specificity for predicting psoriasis by sIB was 0.674(95% CI: 0.650-0.698, while only 0.520(95% CI: 0.472-0.524 was reported for predicting disease by LDA. Our results indicate that the new classifier sIB performs better than LDA in the study. Conclusions The fact that a small set of SNPs can predict disease status with average accuracy of 68% makes it possible to use SNP data for psoriasis prediction.

  12. SNP-SNP interaction analysis of NF-κB signaling pathway on breast cancer survival

    DEFF Research Database (Denmark)

    Jamshidi, Maral; Fagerholm, Rainer; Khan, Sofia

    2015-01-01

    of SNP pairs without and with an interaction term. We found two interacting pairs associating with prognosis: patients simultaneously homozygous for the rare alleles of rs5996080 and rs7973914 had worse survival (HRinteraction 6.98, 95% CI=3.3-14.4, P=1.42E-07), and patients carrying at least one rare...

  13. A SNP Genotyping Array for Hexaploid Oat

    Directory of Open Access Journals (Sweden)

    Nicholas A. Tinker

    2014-11-01

    Full Text Available Recognizing a need in cultivated hexaploid oat ( L. for a reliable set of reference single nucleotide polymorphisms (SNPs, we have developed a 6000 (6K BeadChip design containing 257 Infinium I and 5486 Infinium II designs corresponding to 5743 SNPs. Of those, 4975 SNPs yielded successful assays after array manufacturing. These SNPs were discovered based on a variety of bioinformatics pipelines in complementary DNA (cDNA and genomic DNA originating from 20 or more diverse oat cultivars. The array was validated in 1100 samples from six recombinant inbred line (RIL mapping populations and sets of diverse oat cultivars and breeding lines, and provided approximately 3500 discernible Mendelian polymorphisms. Here, we present an annotation of these SNPs, including methods of discovery, gene identification and orthology, population-genetic characteristics, and tentative positions on an oat consensus map. We also evaluate a new cluster-based method of calling SNPs. The SNP design sequences are made publicly available, and the full SNP genotyping platform is available for commercial purchase from an independent third party.

  14. V-MitoSNP: visualization of human mitochondrial SNPs

    Directory of Open Access Journals (Sweden)

    Tsui Ke-Hung

    2006-08-01

    Full Text Available Abstract Background Mitochondrial single nucleotide polymorphisms (mtSNPs constitute important data when trying to shed some light on human diseases and cancers. Unfortunately, providing relevant mtSNP genotyping information in mtDNA databases in a neatly organized and transparent visual manner still remains a challenge. Amongst the many methods reported for SNP genotyping, determining the restriction fragment length polymorphisms (RFLPs is still one of the most convenient and cost-saving methods. In this study, we prepared the visualization of the mtDNA genome in a way, which integrates the RFLP genotyping information with mitochondria related cancers and diseases in a user-friendly, intuitive and interactive manner. The inherent problem associated with mtDNA sequences in BLAST of the NCBI database was also solved. Description V-MitoSNP provides complete mtSNP information for four different kinds of inputs: (1 color-coded visual input by selecting genes of interest on the genome graph, (2 keyword search by locus, disease and mtSNP rs# ID, (3 visualized input of nucleotide range by clicking the selected region of the mtDNA sequence, and (4 sequences mtBLAST. The V-MitoSNP output provides 500 bp (base pairs flanking sequences for each SNP coupled with the RFLP enzyme and the corresponding natural or mismatched primer sets. The output format enables users to see the SNP genotype pattern of the RFLP by virtual electrophoresis of each mtSNP. The rate of successful design of enzymes and primers for RFLPs in all mtSNPs was 99.1%. The RFLP information was validated by actual agarose electrophoresis and showed successful results for all mtSNPs tested. The mtBLAST function in V-MitoSNP provides the gene information within the input sequence rather than providing the complete mitochondrial chromosome as in the NCBI BLAST database. All mtSNPs with rs number entries in NCBI are integrated in the corresponding SNP in V-MitoSNP. Conclusion V-MitoSNP is a web

  15. Reference-free SNP discovery for the Eurasian beaver from restriction site-associated DNA paired-end data.

    Science.gov (United States)

    Senn, Helen; Ogden, Rob; Cezard, Timothee; Gharbi, Karim; Iqbal, Zamin; Johnson, Eric; Kamps-Hughes, Nick; Rosell, Frank; McEwing, Ross

    2013-06-01

    In this study, we used restriction site-associated DNA (RAD) sequencing to discover SNP markers suitable for population genetic and parentage analysis with the aim of using them for monitoring the reintroduction of the Eurasian beaver (Castor fibre) to Scotland. In the absence of a reference genome for beaver, we built contigs and discovered SNPs within them using paired-end RAD data, so as to have sufficient flanking region around the SNPs to conduct marker design. To do this, we used a simple pipeline which catalogued the Read 1 data in stacks and then used the assembler cortex_var to conduct de novo assembly and genotyping of multiple samples using the Read 2 data. The analysis of around 1.1 billion short reads of sequence data was reduced to a set of 2579 high-quality candidate SNP markers that were polymorphic in Norwegian and Bavarian beaver. Both laboratory validation of a subset of eight of the SNPs (1.3% error) and internal validation by confirming patterns of Mendelian inheritance in a family group (0.9% error) confirmed the success of this approach. © 2013 John Wiley & Sons Ltd.

  16. Leaf Transcriptome Sequencing for Identifying Genic-SSR Markers and SNP Heterozygosity in Crossbred Mango Variety 'Amrapali' (Mangifera indica L.).

    Science.gov (United States)

    Mahato, Ajay Kumar; Sharma, Nimisha; Singh, Akshay; Srivastav, Manish; Jaiprakash; Singh, Sanjay Kumar; Singh, Anand Kumar; Sharma, Tilak Raj; Singh, Nagendra Kumar

    2016-01-01

    Mango (Mangifera indica L.) is called "king of fruits" due to its sweetness, richness of taste, diversity, large production volume and a variety of end usage. Despite its huge economic importance genomic resources in mango are scarce and genetics of useful horticultural traits are poorly understood. Here we generated deep coverage leaf RNA sequence data for mango parental varieties 'Neelam', 'Dashehari' and their hybrid 'Amrapali' using next generation sequencing technologies. De-novo sequence assembly generated 27,528, 20,771 and 35,182 transcripts for the three genotypes, respectively. The transcripts were further assembled into a non-redundant set of 70,057 unigenes that were used for SSR and SNP identification and annotation. Total 5,465 SSR loci were identified in 4,912 unigenes with 288 type I SSR (n ≥ 20 bp). One hundred type I SSR markers were randomly selected of which 43 yielded PCR amplicons of expected size in the first round of validation and were designated as validated genic-SSR markers. Further, 22,306 SNPs were identified by aligning high quality sequence reads of the three mango varieties to the reference unigene set, revealing significantly enhanced SNP heterozygosity in the hybrid Amrapali. The present study on leaf RNA sequencing of mango varieties and their hybrid provides useful genomic resource for genetic improvement of mango.

  17. Prediction of bread-making quality using size exclusion high ...

    African Journals Online (AJOL)

    Variation in the distribution of protein molecular weight in wheat (Triticum aestivum), influences breadmaking quality of wheat cultivars, resulting in either poor or good bread. The objective of this study was to predict breadmaking quality of wheat cultivars using size exclusion high performance liquid chromatography.

  18. Adoption and impact of high quality bambara flour (HQBF ...

    African Journals Online (AJOL)

    Adoption and impact of high quality bambara flour (HQBF) technology in the ... consumer acceptability/quality of products, credit, availability of raw materials, and ... as a result of 12.5 per cent increase in demand for bambara-based products.

  19. Development and validation of a 20K single nucleotide polymorphism (SNP) whole genome genotyping array for apple (Malus × domestica Borkh).

    Science.gov (United States)

    Bianco, Luca; Cestaro, Alessandro; Sargent, Daniel James; Banchi, Elisa; Derdak, Sophia; Di Guardo, Mario; Salvi, Silvio; Jansen, Johannes; Viola, Roberto; Gut, Ivo; Laurens, Francois; Chagné, David; Velasco, Riccardo; van de Weg, Eric; Troggio, Michela

    2014-01-01

    High-density SNP arrays for genome-wide assessment of allelic variation have made high resolution genetic characterization of crop germplasm feasible. A medium density array for apple, the IRSC 8K SNP array, has been successfully developed and used for screens of bi-parental populations. However, the number of robust and well-distributed markers contained on this array was not sufficient to perform genome-wide association analyses in wider germplasm sets, or Pedigree-Based Analysis at high precision, because of rapid decay of linkage disequilibrium. We describe the development of an Illumina Infinium array targeting 20K SNPs. The SNPs were predicted from re-sequencing data derived from the genomes of 13 Malus × domestica apple cultivars and one accession belonging to a crab apple species (M. micromalus). A pipeline for SNP selection was devised that avoided the pitfalls associated with the inclusion of paralogous sequence variants, supported the construction of robust multi-allelic SNP haploblocks and selected up to 11 entries within narrow genomic regions of ±5 kb, termed focal points (FPs). Broad genome coverage was attained by placing FPs at 1 cM intervals on a consensus genetic map, complementing them with FPs to enrich the ends of each of the chromosomes, and by bridging physical intervals greater than 400 Kbps. The selection also included ∼3.7K validated SNPs from the IRSC 8K array. The array has already been used in other studies where ∼15.8K SNP markers were mapped with an average of ∼6.8K SNPs per full-sib family. The newly developed array with its high density of polymorphic validated SNPs is expected to be of great utility for Pedigree-Based Analysis and Genomic Selection. It will also be a valuable tool to help dissect the genetic mechanisms controlling important fruit quality traits, and to aid the identification of marker-trait associations suitable for the application of Marker Assisted Selection in apple breeding programs.

  20. Development and validation of a 20K single nucleotide polymorphism (SNP whole genome genotyping array for apple (Malus × domestica Borkh.

    Directory of Open Access Journals (Sweden)

    Luca Bianco

    Full Text Available High-density SNP arrays for genome-wide assessment of allelic variation have made high resolution genetic characterization of crop germplasm feasible. A medium density array for apple, the IRSC 8K SNP array, has been successfully developed and used for screens of bi-parental populations. However, the number of robust and well-distributed markers contained on this array was not sufficient to perform genome-wide association analyses in wider germplasm sets, or Pedigree-Based Analysis at high precision, because of rapid decay of linkage disequilibrium. We describe the development of an Illumina Infinium array targeting 20K SNPs. The SNPs were predicted from re-sequencing data derived from the genomes of 13 Malus × domestica apple cultivars and one accession belonging to a crab apple species (M. micromalus. A pipeline for SNP selection was devised that avoided the pitfalls associated with the inclusion of paralogous sequence variants, supported the construction of robust multi-allelic SNP haploblocks and selected up to 11 entries within narrow genomic regions of ±5 kb, termed focal points (FPs. Broad genome coverage was attained by placing FPs at 1 cM intervals on a consensus genetic map, complementing them with FPs to enrich the ends of each of the chromosomes, and by bridging physical intervals greater than 400 Kbps. The selection also included ∼3.7K validated SNPs from the IRSC 8K array. The array has already been used in other studies where ∼15.8K SNP markers were mapped with an average of ∼6.8K SNPs per full-sib family. The newly developed array with its high density of polymorphic validated SNPs is expected to be of great utility for Pedigree-Based Analysis and Genomic Selection. It will also be a valuable tool to help dissect the genetic mechanisms controlling important fruit quality traits, and to aid the identification of marker-trait associations suitable for the application of Marker Assisted Selection in apple breeding programs.

  1. Development and Validation of a 20K Single Nucleotide Polymorphism (SNP) Whole Genome Genotyping Array for Apple (Malus × domestica Borkh)

    Science.gov (United States)

    Bianco, Luca; Cestaro, Alessandro; Sargent, Daniel James; Banchi, Elisa; Derdak, Sophia; Di Guardo, Mario; Salvi, Silvio; Jansen, Johannes; Viola, Roberto; Gut, Ivo; Laurens, Francois; Chagné, David; Velasco, Riccardo; van de Weg, Eric; Troggio, Michela

    2014-01-01

    High-density SNP arrays for genome-wide assessment of allelic variation have made high resolution genetic characterization of crop germplasm feasible. A medium density array for apple, the IRSC 8K SNP array, has been successfully developed and used for screens of bi-parental populations. However, the number of robust and well-distributed markers contained on this array was not sufficient to perform genome-wide association analyses in wider germplasm sets, or Pedigree-Based Analysis at high precision, because of rapid decay of linkage disequilibrium. We describe the development of an Illumina Infinium array targeting 20K SNPs. The SNPs were predicted from re-sequencing data derived from the genomes of 13 Malus × domestica apple cultivars and one accession belonging to a crab apple species (M. micromalus). A pipeline for SNP selection was devised that avoided the pitfalls associated with the inclusion of paralogous sequence variants, supported the construction of robust multi-allelic SNP haploblocks and selected up to 11 entries within narrow genomic regions of ±5 kb, termed focal points (FPs). Broad genome coverage was attained by placing FPs at 1 cM intervals on a consensus genetic map, complementing them with FPs to enrich the ends of each of the chromosomes, and by bridging physical intervals greater than 400 Kbps. The selection also included ∼3.7K validated SNPs from the IRSC 8K array. The array has already been used in other studies where ∼15.8K SNP markers were mapped with an average of ∼6.8K SNPs per full-sib family. The newly developed array with its high density of polymorphic validated SNPs is expected to be of great utility for Pedigree-Based Analysis and Genomic Selection. It will also be a valuable tool to help dissect the genetic mechanisms controlling important fruit quality traits, and to aid the identification of marker-trait associations suitable for the application of Marker Assisted Selection in apple breeding programs. PMID:25303088

  2. Quack: A quality assurance tool for high throughput sequence data.

    Science.gov (United States)

    Thrash, Adam; Arick, Mark; Peterson, Daniel G

    2018-05-01

    The quality of data generated by high-throughput DNA sequencing tools must be rapidly assessed in order to determine how useful the data may be in making biological discoveries; higher quality data leads to more confident results and conclusions. Due to the ever-increasing size of data sets and the importance of rapid quality assessment, tools that analyze sequencing data should quickly produce easily interpretable graphics. Quack addresses these issues by generating information-dense visualizations from FASTQ files at a speed far surpassing other publicly available quality assurance tools in a manner independent of sequencing technology. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

  3. Innovative and high quality education through Open Education and OER

    OpenAIRE

    Stracke, Christian M.

    2017-01-01

    Online presentation and webinar by Stracke, C. M. (2017, 18 December) on "Innovative and high quality education through Open Education and OER" for the Belt and Road Open Education Learning Week by the Beijing Normal University, China.

  4. Improving high quality, equitable maternal health services in Malawi ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    Improving high quality, equitable maternal health services in Malawi (IMCHA) ... In response, the Ministry of Health implemented a Standards-Based Management and Recognition for Reproductive Health initiative to improve ... Total funding.

  5. High Quality Education and Learning for All through Open Education

    NARCIS (Netherlands)

    Stracke, Christian M.

    2016-01-01

    Keynote at the International Lensky Education Forum 2016, Yakutsk, Republic of Sakha, Russian Federation, by Stracke, C. M. (2016, 16 August): "High Quality Education and Learning for All through Open Education"

  6. SNPhylo: a pipeline to construct a phylogenetic tree from huge SNP data.

    Science.gov (United States)

    Lee, Tae-Ho; Guo, Hui; Wang, Xiyin; Kim, Changsoo; Paterson, Andrew H

    2014-02-26

    Phylogenetic trees are widely used for genetic and evolutionary studies in various organisms. Advanced sequencing technology has dramatically enriched data available for constructing phylogenetic trees based on single nucleotide polymorphisms (SNPs). However, massive SNP data makes it difficult to perform reliable analysis, and there has been no ready-to-use pipeline to generate phylogenetic trees from these data. We developed a new pipeline, SNPhylo, to construct phylogenetic trees based on large SNP datasets. The pipeline may enable users to construct a phylogenetic tree from three representative SNP data file formats. In addition, in order to increase reliability of a tree, the pipeline has steps such as removing low quality data and considering linkage disequilibrium. A maximum likelihood method for the inference of phylogeny is also adopted in generation of a tree in our pipeline. Using SNPhylo, users can easily produce a reliable phylogenetic tree from a large SNP data file. Thus, this pipeline can help a researcher focus more on interpretation of the results of analysis of voluminous data sets, rather than manipulations necessary to accomplish the analysis.

  7. Vitis phylogenomics: hybridization intensities from a SNP array outperform genotype calls.

    Directory of Open Access Journals (Sweden)

    Allison J Miller

    Full Text Available Understanding relationships among species is a fundamental goal of evolutionary biology. Single nucleotide polymorphisms (SNPs identified through next generation sequencing and related technologies enable phylogeny reconstruction by providing unprecedented numbers of characters for analysis. One approach to SNP-based phylogeny reconstruction is to identify SNPs in a subset of individuals, and then to compile SNPs on an array that can be used to genotype additional samples at hundreds or thousands of sites simultaneously. Although powerful and efficient, this method is subject to ascertainment bias because applying variation discovered in a representative subset to a larger sample favors identification of SNPs with high minor allele frequencies and introduces bias against rare alleles. Here, we demonstrate that the use of hybridization intensity data, rather than genotype calls, reduces the effects of ascertainment bias. Whereas traditional SNP calls assess known variants based on diversity housed in the discovery panel, hybridization intensity data survey variation in the broader sample pool, regardless of whether those variants are present in the initial SNP discovery process. We apply SNP genotype and hybridization intensity data derived from the Vitis9kSNP array developed for grape to show the effects of ascertainment bias and to reconstruct evolutionary relationships among Vitis species. We demonstrate that phylogenies constructed using hybridization intensities suffer less from the distorting effects of ascertainment bias, and are thus more accurate than phylogenies based on genotype calls. Moreover, we reconstruct the phylogeny of the genus Vitis using hybridization data, show that North American subgenus Vitis species are monophyletic, and resolve several previously poorly known relationships among North American species. This study builds on earlier work that applied the Vitis9kSNP array to evolutionary questions within Vitis vinifera

  8. Functional characterization of the Thr946Ala SNP at the type 1 diabetes IFIH1 locus.

    Science.gov (United States)

    Zouk, Hana; Marchand, Luc; Li, Quan; Polychronakos, Constantin

    2014-02-01

    The Thr allele at the Thr946Ala non-synonymous single-nucleotide polymorphism (nsSNP) in the IFIH1 gene confers risk for type 1 diabetes (T1D). IFIH1 binds viral double-stranded RNA (dsRNA), inducing a type I interferon (IFN) response. Reports of this nsSNP's role in IFIH1 expression regulation have produced conflicting results and a study evaluating transfected Thr946Ala protein alleles in an artificial system overexpressing IFIH1 shows that the SNP does not affect IFH1 function. In this study, we examine the effects of the Thr946Ala polymorphism on IFN-α response in a cell line that endogenously expresses physiological levels of IFIH1. Eleven lymphoblastoid cell lines (LCLs) homozygous for the major predisposing allele (Thr/Thr) and 6 LCLs homozygous for the minor protective allele (Ala/Ala) were electroporated with the viral dsRNA mimic, poly I:C, in three independent experiments. Media were collected 24 hours later and measured for IFN-α production by ELISA. Basal IFN response is minimal in mock-transfected cells from both genotypes and increases by about 8-fold in cells treated with poly I:C. LCLs with the Ala/Ala genotype have slightly higher IFN-α levels than their Thr/Thr counterparts but this did not reach statistical significance because of the large variability of the IFN response, due mostly to two high outliers (biological, not technical). A larger sample size would be needed to determine whether the Thr946Ala SNP affects the poly I:C-driven IFN-α response. Additionally, the possibility that this nsSNP recognizes viral dsRNA specificities cannot be ruled out. Thus, the mechanism of the observed association of this SNP with T1D remains to be determined.

  9. Emblems of Quality in Higher Education. Developing and Sustaining High-Quality Programs.

    Science.gov (United States)

    Haworth, Jennifer Grant; Conrad, Clifton F.

    This book proposes an "engagement" theory of program quality to evaluate and improve higher education programs at all degree levels. Based on interviews with 781 participants in a national study of Masters degree programs, it focuses on the interactive roles of students, faculty, and administrators in developing high-quality programs…

  10. Design and Characterization of a 52K SNP Chip for Goats

    NARCIS (Netherlands)

    Tosser-klopp, G.; Bardou, P.; Bouchez, O.; Cabau, C.; Crooijmans, R.P.M.A.; Dong, Y.; Donnadieu-Tonon, C.; Eggen, A.; Heuven, H.C.M.; Jamli, S.; Jiken, A.J.; Klopp, C.; Lawley, C.T.; McEwen, J.; Martin, P.; Moreno, C.R.; Mulsant, P.; Nabihoudine, I.; Pailhoux, E.; Palhiere, I.; Rupp, R.; Sarry, J.; Sayre, B.L.; Tircazes, A.; Wang, J.; Wang, W.; Zhang, W.G.

    2014-01-01

    The success of Genome Wide Association Studies in the discovery of sequence variation linked to complex traits in humans has increased interest in high throughput SNP genotyping assays in livestock species. Primary goals are QTL detection and genomic selection. The purpose here was design of a

  11. The Association of FTO SNP rs9939609 with Weight Gain at University

    NARCIS (Netherlands)

    Meisel, S.F.; Beeken, R.J.; Jaarsveld, C.H.M. van; Wardle, J.

    2015-01-01

    AIM: We tested the hypothesis that the obesity-associated FTO SNP rs9939609 would be associated with clinically significant weight gain (>/= 5% of initial body weight) in the first year of university; a time identified as high risk for weight gain. METHODS: We collected anthropometric data from

  12. Affymetrix SNP array data for wild Dutch great tits (Parus major)

    NARCIS (Netherlands)

    Silva, Da Vinicius; Laine, Veronika N.; Bosse, M.; Oers, C.H.J.; Dibbits, B.W.; Visser, M.E.; Crooijmans, R.P.M.A.; Groenen, M.

    2018-01-01

    The great tit is a widely studied passerine bird species in ecology that, in the past decades, has provided important insights into speciation, phenology, behavior and microevolution. After completion of the great tit genome sequence, a customized high density 650k SNP array was developed enabling

  13. SNIT: SNP identification for strain typing

    Directory of Open Access Journals (Sweden)

    Reifman Jaques

    2011-09-01

    Full Text Available Abstract With ever-increasing numbers of microbial genomes being sequenced, efficient tools are needed to perform strain-level identification of any newly sequenced genome. Here, we present the SNP identification for strain typing (SNIT pipeline, a fast and accurate software system that compares a newly sequenced bacterial genome with other genomes of the same species to identify single nucleotide polymorphisms (SNPs and small insertions/deletions (indels. Based on this information, the pipeline analyzes the polymorphic loci present in all input genomes to identify the genome that has the fewest differences with the newly sequenced genome. Similarly, for each of the other genomes, SNIT identifies the input genome with the fewest differences. Results from five bacterial species show that the SNIT pipeline identifies the correct closest neighbor with 75% to 100% accuracy. The SNIT pipeline is available for download at http://www.bhsai.org/snit.html

  14. High quality, high efficiency welding technology for nuclear power plants

    International Nuclear Information System (INIS)

    Aoki, Shigeyuki; Nagura, Yasumi

    1996-01-01

    For nuclear power plants, it is required to ensure the safety under the high reliability and to attain the high rate of operation. In the manufacture and installation of the machinery and equipment, the welding techniques which become the basis exert large influence to them. For the purpose of improving joint performance and excluding human errors, welding heat input and the number of passes have been reduced, the automation of welding has been advanced, and at present, narrow gap arc welding and high energy density welding such as electron beam welding and laser welding have been put to practical use. Also in the welding of pipings, automatic gas metal arc welding is employed. As for the welding of main machinery and equipment, there are the welding of the joints that constitute pressure boundaries, the build-up welding on the internal surfaces of pressure vessels for separating primary water from them, and the sealing welding of heating tubes and tube plates in steam generators. These weldings are explained. The welding of pipings and the state of development and application of new welding methods are reported. (K.I.)

  15. (SNP) markers for the Chinese black sleeper, Bostrychus sinensis

    African Journals Online (AJOL)

    We characterized 11 single nucleotide ploymorphism (SNP) markers for the Chinese black sleeper, Bostrychus sinensis. These markers were isolated from a genomic library and tested in ten geographically distant individuals of B. sinensis. Polymorphisms of these SNP loci were assessed using a wild population including ...

  16. Concrete Waste Recycling Process for High Quality Aggregate

    International Nuclear Information System (INIS)

    Ishikura, Takeshi; Fujii, Shin-ichi

    2008-01-01

    Large amount of concrete waste generates during nuclear power plant (NPP) dismantling. Non-contaminated concrete waste is assumed to be disposed in a landfill site, but that will not be the solution especially in the future, because of decreasing tendency of the site availability and natural resources. Concerning concrete recycling, demand for roadbeds and backfill tends to be less than the amount of dismantled concrete generated in a single rural site, and conventional recycled aggregate is limited of its use to non-structural concrete, because of its inferior quality to ordinary natural aggregate. Therefore, it is vital to develop high quality recycled aggregate for general uses of dismantled concrete. If recycled aggregate is available for high structural concrete, the dismantling concrete is recyclable as aggregate for industry including nuclear field. Authors developed techniques on high quality aggregate reclamation for large amount of concrete generated during NPP decommissioning. Concrete of NPP buildings has good features for recycling aggregate; large quantity of high quality aggregate from same origin, record keeping of the aggregate origin, and little impurities in dismantled concrete such as wood and plastics. The target of recycled aggregate in this development is to meet the quality criteria for NPP concrete as prescribed in JASS 5N 'Specification for Nuclear Power Facility Reinforced Concrete' and JASS 5 'Specification for Reinforced Concrete Work'. The target of recycled aggregate concrete is to be comparable performance with ordinary aggregate concrete. The high quality recycled aggregate production techniques are assumed to apply for recycling for large amount of non-contaminated concrete. These techniques can also be applied for slightly contaminated concrete dismantled from radiological control area (RCA), together with free release survey. In conclusion: a technology on dismantled concrete recycling for high quality aggregate was developed

  17. High-quality planar high-Tc Josephson junctions

    International Nuclear Information System (INIS)

    Bergeal, N.; Grison, X.; Lesueur, J.; Faini, G.; Aprili, M.; Contour, J.P.

    2005-01-01

    Reproducible high-T c Josephson junctions have been made in a rather simple two-step process using ion irradiation. A microbridge (1 to 5 μm wide) is firstly designed by ion irradiating a c-axis-oriented YBa 2 Cu 3 O 7-δ film through a gold mask such as the nonprotected part becomes insulating. A lower T c part is then defined within the bridge by irradiating with a much lower fluence through a narrow slit (20 nm) opened in a standard electronic photoresist. These planar junctions, whose settings can be finely tuned, exhibit reproducible and nearly ideal Josephson characteristics. This process can be used to produce complex Josephson circuits

  18. SNP discovery in candidate adaptive genes using exon capture in a free-ranging alpine ungulate

    Science.gov (United States)

    Roffler, Gretchen H.; Amish, Stephen J.; Smith, Seth; Cosart, Ted F.; Kardos, Marty; Schwartz, Michael K.; Luikart, Gordon

    2016-01-01

    Identification of genes underlying genomic signatures of natural selection is key to understanding adaptation to local conditions. We used targeted resequencing to identify SNP markers in 5321 candidate adaptive genes associated with known immunological, metabolic and growth functions in ovids and other ungulates. We selectively targeted 8161 exons in protein-coding and nearby 5′ and 3′ untranslated regions of chosen candidate genes. Targeted sequences were taken from bighorn sheep (Ovis canadensis) exon capture data and directly from the domestic sheep genome (Ovis aries v. 3; oviAri3). The bighorn sheep sequences used in the Dall's sheep (Ovis dalli dalli) exon capture aligned to 2350 genes on the oviAri3 genome with an average of 2 exons each. We developed a microfluidic qPCR-based SNP chip to genotype 476 Dall's sheep from locations across their range and test for patterns of selection. Using multiple corroborating approaches (lositan and bayescan), we detected 28 SNP loci potentially under selection. We additionally identified candidate loci significantly associated with latitude, longitude, precipitation and temperature, suggesting local environmental adaptation. The three methods demonstrated consistent support for natural selection on nine genes with immune and disease-regulating functions (e.g. Ovar-DRA, APC, BATF2, MAGEB18), cell regulation signalling pathways (e.g. KRIT1, PI3K, ORRC3), and respiratory health (CYSLTR1). Characterizing adaptive allele distributions from novel genetic techniques will facilitate investigation of the influence of environmental variation on local adaptation of a northern alpine ungulate throughout its range. This research demonstrated the utility of exon capture for gene-targeted SNP discovery and subsequent SNP chip genotyping using low-quality samples in a nonmodel species.

  19. Key factors for a high-quality VR experience

    Science.gov (United States)

    Champel, Mary-Luc; Doré, Renaud; Mollet, Nicolas

    2017-09-01

    For many years, Virtual Reality has been presented as a promising technology that could deliver a truly new experience to users. The media and entertainment industry is now investigating the possibility to offer a video-based VR 360 experience. Nevertheless, there is a substantial risk that VR 360 could have the same fate as 3DTV if it cannot offer more than just being the next fad. The present paper aims at presenting the various quality factors required for a high-quality VR experience. More specifically, this paper will focus on the main three VR quality pillars: visual, audio and immersion.

  20. Process to Continuously Melt, Refine and Cast High Quality Steel

    Energy Technology Data Exchange (ETDEWEB)

    None

    2005-09-01

    The purpose of this project is to conduct research and development targeted at designing a revolutionary steelmaking process. This process will deliver high quality steel from scrap to the casting mold in one continuous process and will be safer, more productive, and less capital intensive to build and operate than conventional steelmaking. The new process will produce higher quality steel faster than traditional batch processes while consuming less energy and other resources.

  1. High-quality cardiopulmonary resuscitation: current and future directions.

    Science.gov (United States)

    Abella, Benjamin S

    2016-06-01

    Cardiopulmonary resuscitation (CPR) represents the cornerstone of cardiac arrest resuscitation care. Prompt delivery of high-quality CPR can dramatically improve survival outcomes; however, the definitions of optimal CPR have evolved over several decades. The present review will discuss the metrics of CPR delivery, and the evidence supporting the importance of CPR quality to improve clinical outcomes. The introduction of new technologies to quantify metrics of CPR delivery has yielded important insights into CPR quality. Investigations using CPR recording devices have allowed the assessment of specific CPR performance parameters and their relative importance regarding return of spontaneous circulation and survival to hospital discharge. Additional work has suggested new opportunities to measure physiologic markers during CPR and potentially tailor CPR delivery to patient requirements. Through recent laboratory and clinical investigations, a more evidence-based definition of high-quality CPR continues to emerge. Exciting opportunities now exist to study quantitative metrics of CPR and potentially guide resuscitation care in a goal-directed fashion. Concepts of high-quality CPR have also informed new approaches to training and quality improvement efforts for cardiac arrest care.

  2. De novo SNP discovery in the Scandinavian brown bear (Ursus arctos.

    Directory of Open Access Journals (Sweden)

    Anita J Norman

    Full Text Available Information about relatedness between individuals in wild populations is advantageous when studying evolutionary, behavioural and ecological processes. Genomic data can be used to determine relatedness between individuals either when no prior knowledge exists or to confirm suspected relatedness. Here we present a set of 96 SNPs suitable for inferring relatedness for brown bears (Ursus arctos within Scandinavia. We sequenced reduced representation libraries from nine individuals throughout the geographic range. With consensus reads containing putative SNPs, we applied strict filtering criteria with the aim of finding only high-quality, highly-informative SNPs. We tested 150 putative SNPs of which 96% were validated on a panel of 68 individuals. Ninety-six of the validated SNPs with the highest minor allele frequency were selected. The final SNP panel includes four mitochondrial markers, two monomorphic Y-chromosome sex-determination markers, three X-chromosome SNPs and 87 autosomal SNPs. From our validation sample panel, we identified two previously known parent-offspring dyads with reasonable accuracy. This panel of SNPs is a promising tool for inferring relatedness in the brown bear population in Scandinavia.

  3. UPD detection using homozygosity profiling with a SNP genotyping microarray.

    Science.gov (United States)

    Papenhausen, Peter; Schwartz, Stuart; Risheg, Hiba; Keitges, Elisabeth; Gadi, Inder; Burnside, Rachel D; Jaswaney, Vikram; Pappas, John; Pasion, Romela; Friedman, Kenneth; Tepperberg, James

    2011-04-01

    Single nucleotide polymorphism (SNP) based chromosome microarrays provide both a high-density whole genome analysis of copy number and genotype. In the past 21 months we have analyzed over 13,000 samples primarily referred for developmental delay using the Affymetrix SNP/CN 6.0 version array platform. In addition to copy number, we have focused on the relative distribution of allele homozygosity (HZ) throughout the genome to confirm a strong association of uniparental disomy (UPD) with regions of isoallelism found in most confirmed cases of UPD. We sought to determine whether a long contiguous stretch of HZ (LCSH) greater than a threshold value found only in a single chromosome would correlate with UPD of that chromosome. Nine confirmed UPD cases were retrospectively analyzed with the array in the study, each showing the anticipated LCSH with the smallest 13.5 Mb in length. This length is well above the average longest run of HZ in a set of control patients and was then set as the prospective threshold for reporting possible UPD correlation. Ninety-two cases qualified at that threshold, 46 of those had molecular UPD testing and 29 were positive. Including retrospective cases, 16 showed complete HZ across the chromosome, consistent with total isoUPD. The average size LCSH in the 19 cases that were not completely HZ was 46.3 Mb with a range of 13.5-127.8 Mb. Three patients showed only segmental UPD. Both the size and location of the LCSH are relevant to correlation with UPD. Further studies will continue to delineate an optimal threshold for LCSH/UPD correlation. Copyright © 2011 Wiley-Liss, Inc.

  4. Differential growth of Mycobacterium leprae strains (SNP genotypes) in armadillos.

    Science.gov (United States)

    Sharma, Rahul; Singh, Pushpendra; Pena, Maria; Subramanian, Ramesh; Chouljenko, Vladmir; Kim, Joohyun; Kim, Nayong; Caskey, John; Baudena, Marie A; Adams, Linda B; Truman, Richard W

    2018-04-14

    Leprosy (Hansen's Disease) has occurred throughout human history, and persists today at a low prevalence in most populations. Caused by Mycobacterium leprae, the infection primarily involves the skin, mucosa and peripheral nerves. The susceptible host range for Mycobacterium leprae is quite narrow. Besides humans, nine banded armadillos (Dasypus novemcinctus) and red squirrels (Sciurus vulgaris) are the only other natural hosts for M. leprae, but only armadillos recapitulate the disease as seen in humans. Armadillos across the Southern United States harbor a single predominant genotypic strain (SNP Type-3I) of M. leprae, which is also implicated in the zoonotic transmission of leprosy. We investigated, whether the zoonotic strain (3I) has any notable growth advantages in armadillos over another genetically distant strain-type (SNP Type-4P) of M. leprae, and if M. leprae strains manifest any notably different pathology among armadillos. We co-infected armadillos (n = 6) with 2 × 10 9 highly viable M. leprae of both strains and assessed the relative growth and dissemination of each strain in the animals. We also analyzed 12 additional armadillos, 6 each individually infected with the same quantity of either strain. The infections were allowed to fulminate and the clinical manifestations of the disease were noted. Animals were humanely sacrificed at the terminal stage of infection and the number of bacilli per gram of liver, spleen and lymph node tissue were enumerated by Q-PCR assay. The growth of M. leprae strain 4P was significantly higher (P leprae strains within armadillos suggest there are notable pathological variations between M. leprae strain-types. Copyright © 2018. Published by Elsevier B.V.

  5. Next Generation High Quality Videoconferencing Service for the LHC

    CERN Multimedia

    CERN. Geneva

    2012-01-01

    In recent times, we have witnessed an explosion of video initiatives in the industry worldwide. Several advancements in video technology are currently improving the way we interact and collaborate. These advancements are forcing tendencies and overall experiences: any device in any network can be used to collaborate, in most cases with an overall high quality. To cope with this technology progresses, CERN IT Department has taken the leading role to establish strategies and directions to improve the user experience in remote dispersed meetings and remote collaboration at large in the worldwide LHC communities. Due to the high rate of dispersion in the LHC user communities, these are critically dependent of videoconferencing technology, with a need of robustness and high quality for the best possible user experience. We will present an analysis of the factors that influenced the technical and strategic choices to improve the reliability, efficiency and overall quality of the LHC remote sessions. In particular, ...

  6. IMPACT OF RESILIENCE, ICT SUPPORT AND QUALITY OF STUDENT'S LIFE ON QUALITY OF HIGH EDUCATION PROCESS

    Directory of Open Access Journals (Sweden)

    Zorica Lazic

    2016-12-01

    Full Text Available Answers to the questions of how and in what way the quality of life of students, resilience and ICT support affects the quality of high education we will get through this work where main objective is to define a network of processes and process management ensuring more quality and more innovative managing and service provision, therefore satisfying the needs of service users - in this case the students of the university. To collect the relevant data in the thematic analysis of this paper, the method of interviewing by questionnaires was applied. The sample survey was conducted among undergraduate students, teachers and staff of the Teacher Training Faculty in Uzice.

  7. Interactions Between SNP Alleles at Multiple Loci and Variation in Skin Pigmentation in 122 Caucasians

    Directory of Open Access Journals (Sweden)

    Sumiko Anno

    2007-01-01

    Full Text Available This study was undertaken to clarify the molecular basis for human skin color variation and the environmental adaptability to ultraviolet irradiation, with the ultimate goal of predicting the impact of changes in future environments on human health risk. One hundred twenty-two Caucasians living in Toledo, Ohio participated. Back and cheek skin were assayed for melanin as a quantitative trait marker. Buccal cell samples were collected and used for DNA extraction. DNA was used for SNP genotyping using the Masscode™ system, which entails two-step PCR amplification and a platform chemistry which allows cleavable mass spectrometry tags. The results show gene-gene interaction between SNP alleles at multiple loci (not necessarily on the same chromosome contributes to inter-individual skin color variation while suggesting a high probability of linkage disequilibrium. Confirmation of these findings requires further study with other ethic groups to analyze the associations between SNP alleles at multiple loci and human skin color variation. Our overarching goal is to use remote sensing data to clarify the interaction between atmospheric environments and SNP allelic frequency and investigate human adaptability to ultraviolet irradiation. Such information should greatly assist in the prediction of the health effects of future environmental changes such as ozone depletion and increased ultraviolet exposure. If such health effects are to some extent predictable, it might be possible to prepare for such changes in advance and thus reduce the extent of their impact.

  8. Genome-wide SNP identification in multiple morphotypes of allohexaploid tall fescue (Festuca arundinacea Schreb

    Directory of Open Access Journals (Sweden)

    Hand Melanie L

    2012-06-01

    Full Text Available Abstract Background Single nucleotide polymorphisms (SNPs provide essential tools for the advancement of research in plant genomics, and the development of SNP resources for many species has been accelerated by the capabilities of second-generation sequencing technologies. The current study aimed to develop and use a novel bioinformatic pipeline to generate a comprehensive collection of SNP markers within the agriculturally important pasture grass tall fescue; an outbreeding allopolyploid species displaying three distinct morphotypes: Continental, Mediterranean and rhizomatous. Results A bioinformatic pipeline was developed that successfully identified SNPs within genotypes from distinct tall fescue morphotypes, following the sequencing of 414 polymerase chain reaction (PCR – generated amplicons using 454 GS FLX technology. Equivalent amplicon sets were derived from representative genotypes of each morphotype, including six Continental, five Mediterranean and one rhizomatous. A total of 8,584 and 2,292 SNPs were identified with high confidence within the Continental and Mediterranean morphotypes respectively. The success of the bioinformatic approach was demonstrated through validation (at a rate of 70% of a subset of 141 SNPs using both SNaPshot™ and GoldenGate™ assay chemistries. Furthermore, the quantitative genotyping capability of the GoldenGate™ assay revealed that approximately 30% of the putative SNPs were accessible to co-dominant scoring, despite the hexaploid genome structure. The sub-genome-specific origin of each SNP validated from Continental tall fescue was predicted using a phylogenetic approach based on comparison with orthologous sequences from predicted progenitor species. Conclusions Using the appropriate bioinformatic approach, amplicon resequencing based on 454 GS FLX technology is an effective method for the identification of polymorphic SNPs within the genomes of Continental and Mediterranean tall fescue. The

  9. Evaluation of the Ion Torrent™ HID SNP 169-plex

    DEFF Research Database (Denmark)

    Børsting, Claus; Fordyce, Sarah L; Olofsson, Jill Katharina

    2014-01-01

    The Ion Torrent™ HID SNP assay amplified 136 autosomal SNPs and 33 Y-chromosome markers in one PCR and the markers were subsequently typed using the Ion PGM™ second generation sequencing platform. A total of 51 of the autosomal SNPs were selected from the SNPforID panel that is routinely used...... in our ISO 17025 accredited laboratory. Concordance between the Ion Torrent™ HID SNP assay and the SNPforID assay was tested by typing 44 Iraqis twice with the Ion Torrent™ HID SNP assay. The same samples were previously typed with the SNPforID assay and the Y-chromosome haplogroups of the individuals...

  10. Learning Disabilities and Achieving High-Quality Education Standards

    Science.gov (United States)

    Gartland, Debi; Strosnider, Roberta

    2017-01-01

    This is an official document of the National Joint Committee on Learning Disabilities (NJCLD), of which Council for Learning Disabilities is a long-standing, active member. With this position paper, NJCLD advocates for the implementation of high-quality education standards (HQES) for students with learning disabilities (LD) and outlines the…

  11. extraction of high quality dna from polysaccharides-secreting ...

    African Journals Online (AJOL)

    cistvr

    A DNA extraction method using CTAB was used for the isolation of genomic DNA from ten. Xanthomonas campestris pathovars, ten isolates of Xanthomonas albilineans and one isolate of. Pseudomonas rubrisubalbicans. High quality DNA was obtained that was ideal for molecular analy- ses. Extracellular polysaccharides ...

  12. Negative Binomial charts for monitoring high-quality processes

    NARCIS (Netherlands)

    Albers, Willem/Wim

    Good control charts for high quality processes are often based on the number of successes between failures. Geometric charts are simplest in this respect, but slow in recognizing moderately increased failure rates p. Improvement can be achieved by waiting until r > 1 failures have occurred, i.e. by

  13. Synthesis and spectroscopic study of high quality alloy Cdx S ...

    Indian Academy of Sciences (India)

    Wintec

    In the present study, we report the synthesis of high quality CdxZn1–xS nanocrystals alloy at. 150°C with .... (XRD) using a Siemens model D 500, powder X-ray ... decays were analysed using IBH DAS6 software. 3. ... This alloying process is.

  14. Methods and systems for fabricating high quality superconducting tapes

    Science.gov (United States)

    Majkic, Goran; Selvamanickam, Venkat

    2018-02-13

    An MOCVD system fabricates high quality superconductor tapes with variable thicknesses. The MOCVD system can include a gas flow chamber between two parallel channels in a housing. A substrate tape is heated and then passed through the MOCVD housing such that the gas flow is perpendicular to the tape's surface. Precursors are injected into the gas flow for deposition on the substrate tape. In this way, superconductor tapes can be fabricated with variable thicknesses, uniform precursor deposition, and high critical current densities.

  15. Managing quality inside a high-technology project organization

    OpenAIRE

    Jokinen, T. (Tauno)

    2004-01-01

    Abstract This action research addresses the deployment of Total Quality Management (TQM) principles in a high-technology new product development organisation. During the period of study, the organisation grew fast. High-technology product development and hypergrowth provided a unique combination of extreme conditions for the study. The existing concepts of TQM are presented as an organised map enabling strategic analysis for an implementation plan. The history of TQM dates back to the ...

  16. [Quality of sleep and academic performance in high school students].

    Science.gov (United States)

    Bugueño, Maithe; Curihual, Carolina; Olivares, Paulina; Wallace, Josefa; López-AlegrÍa, Fanny; Rivera-López, Gonzalo; Oyanedel, Juan Carlos

    2017-09-01

    Sleeping and studying are the day-to-day activities of a teenager attending school. To determine the quality of sleep and its relationship to the academic performance among students attending morning and afternoon shifts in a public high school. Students of the first and second year of high school answered an interview about socio-demographic background, academic performance, student activities and subjective sleep quality; they were evaluated using the Pittsburgh Sleep Quality Index (PSQI). The interview was answered by 322 first year students aged 15 ± 5 years attending the morning shift and 364 second year students, aged 16 ± 0.5 years, attending the afternoon shift. The components: sleep latency, habitual sleep efficiency, sleep disturbance, drug use and daytime dysfunction were similar and classified as good in both school shifts. The components subjective sleep quality and duration of sleep had higher scores among students of the morning shift. The mean grades during the first semester of the students attending morning and afternoon shifts were 5.9 and 5.8, respectively (of a scale from 1 to 7). Among students of both shifts, the PSQI scale was associated inversely and significantly with academic performance. A bad sleep quality influences academic performance in these students.

  17. Highly qualified does not equal high quality: A study of urban stakeholders' perceptions of quality in science teaching

    Science.gov (United States)

    Miranda, Rommel Joseph

    By employing qualitative methods, this study sought to determine the perceptions that urban stakeholders hold about what characteristics should distinguish a high school science teacher whom they would consider to demonstrate high quality in science teaching. A maximum variation sample of six science teachers, three school administrators, six parents and six students from a large urban public school district were interviewed using semi-structured, in-depth interview techniques. From these data, a list of observable characteristics which urban stakeholders hold as evidence of high quality in science teaching was generated. Observational techniques were utilized to determine the extent to which six urban high school science teachers, who meet the NCLB Act criteria for being "highly qualified", actually possessed the characteristics which these stakeholders hold as evidence of high quality in science teaching. Constant comparative analysis was used to analyze the data set. The findings suggest that urban stakeholders perceive that a high school science teacher who demonstrates high quality in science teaching should be knowledgeable about their subject matter, their student population, and should be resourceful; should possess an academic background in science and professional experience in science teaching; should exhibit professionalism, a passion for science and teaching, and a dedication to teaching and student learning; should be skillful in planning and preparing science lessons and in organizing the classroom, in presenting the subject matter to students, in conducting a variety of hands-on activities, and in managing a classroom; and should assess whether students complete class goals and objectives, and provide feedback about grades for students promptly. The findings further reveal that some of the urban high school science teachers who were deemed to be "highly qualified", as defined by the NCLB Act, engaged in practices that threatened quality in science

  18. High quality digital holographic reconstruction on analog film

    Science.gov (United States)

    Nelsen, B.; Hartmann, P.

    2017-05-01

    High quality real-time digital holographic reconstruction, i.e. at 30 Hz frame rates, has been at the forefront of research and has been hailed as the holy grail of display systems. While these efforts have produced a fascinating array of computer algorithms and technology, many applications of reconstructing high quality digital holograms do not require such high frame rates. In fact, applications such as 3D holographic lithography even require a stationary mask. Typical devices used for digital hologram reconstruction are based on spatial-light-modulator technology and this technology is great for reconstructing arbitrary holograms on the fly; however, it lacks the high spatial resolution achievable by its analog counterpart, holographic film. Analog holographic film is therefore the method of choice for reconstructing highquality static holograms. The challenge lies in taking a static, high-quality digitally calculated hologram and effectively writing it to holographic film. We have developed a theoretical system based on a tunable phase plate, an intensity adjustable high-coherence laser and a slip-stick based piezo rotation stage to effectively produce a digitally calculated hologram on analog film. The configuration reproduces the individual components, both the amplitude and phase, of the hologram in the Fourier domain. These Fourier components are then individually written on the holographic film after interfering with a reference beam. The system is analogous to writing angularly multiplexed plane waves with individual component phase control.

  19. SNP discovery in the bovine milk transcriptome using RNA-Seq technology.

    Science.gov (United States)

    Cánovas, Angela; Rincon, Gonzalo; Islas-Trejo, Alma; Wickramasinghe, Saumya; Medrano, Juan F

    2010-12-01

    High-throughput sequencing of RNA (RNA-Seq) was developed primarily to analyze global gene expression in different tissues. However, it also is an efficient way to discover coding SNPs. The objective of this study was to perform a SNP discovery analysis in the milk transcriptome using RNA-Seq. Seven milk samples from Holstein cows were analyzed by sequencing cDNAs using the Illumina Genome Analyzer system. We detected 19,175 genes expressed in milk samples corresponding to approximately 70% of the total number of genes analyzed. The SNP detection analysis revealed 100,734 SNPs in Holstein samples, and a large number of those corresponded to differences between the Holstein breed and the Hereford bovine genome assembly Btau4.0. The number of polymorphic SNPs within Holstein cows was 33,045. The accuracy of RNA-Seq SNP discovery was tested by comparing SNPs detected in a set of 42 candidate genes expressed in milk that had been resequenced earlier using Sanger sequencing technology. Seventy of 86 SNPs were detected using both RNA-Seq and Sanger sequencing technologies. The KASPar Genotyping System was used to validate unique SNPs found by RNA-Seq but not observed by Sanger technology. Our results confirm that analyzing the transcriptome using RNA-Seq technology is an efficient and cost-effective method to identify SNPs in transcribed regions. This study creates guidelines to maximize the accuracy of SNP discovery and prevention of false-positive SNP detection, and provides more than 33,000 SNPs located in coding regions of genes expressed during lactation that can be used to develop genotyping platforms to perform marker-trait association studies in Holstein cattle.

  20. (SNP) assay for population stratification test between eastern Asians

    African Journals Online (AJOL)

    Yomi

    2012-01-03

    Jan 3, 2012 ... program STRUCTURE 2.0, which uses a Markov chain Monte. Carlo (MCMC) algorithm to cluster individuals into different cryptic ... HapMap project. .... Evaluation of the 124-plex SNP typing microarray for forensic testing.

  1. A single nucleotide polymorphism (SNP) assay for population ...

    African Journals Online (AJOL)

    A single nucleotide polymorphism (SNP) assay for population stratification test ... phenotypes and unlinked candidate loci in case-control and cohort studies of ... Key words: Chinese, Japanese, population stratification, ancestry informative ...

  2. Long quantum channels for high-quality entanglement transfer

    International Nuclear Information System (INIS)

    Banchi, L; Apollaro, T J G; Cuccoli, A; Verrucchi, P; Vaia, R

    2011-01-01

    High-quality quantum-state and entanglement transfer can be achieved in an unmodulated spin bus operating in the ballistic regime, which occurs when the endpoint qubits A and B are nonperturbatively coupled to the chain by a suitable exchange interaction j 0 . Indeed, the transition amplitude characterizing the transfer quality exhibits a maximum for a finite optimal value j opt 0 (N), where N is the channel length. We show that j opt 0 (N) scales as N -1/6 for large N and that it ensures a high-quality entanglement transfer even in the limit of arbitrarily long channels, almost independently of the channel initialization. For instance, for any chain length the average quantum-state transmission fidelity exceeds 90% and decreases very little in a broad neighbourhood of j opt 0 (N). We emphasize that, taking the reverse point of view, should j 0 be experimentally constrained, high-quality transfer can still be obtained by adjusting the channel length to its optimal value. (paper)

  3. Integration study of high quality teaching resources in universities

    Directory of Open Access Journals (Sweden)

    Honglu Liu

    2012-12-01

    Full Text Available Purpose: The development level and quality of education depend on the merits and efficiency in the use of teaching resources, especially in the case of obvious contradiction between the demand and supply of teaching resources. So to integrate teaching resources, improve the efficiency in the use of high quality teaching resources, and take the road of content development to enhance the competitiveness of education has become very important and urgent.Design/methodology/approach: On the basis of analysis on the teaching resources of universities and the problems they faced, this paper introduced the basic concepts of cloud storage, and built the integration architecture of high quality teaching resources in universities based on the cloud storage.Findings and Originality/value: The HDFS-based cloud storage proposed in this paper is a dynamically adjustable and Internet-based storage solution, and the users can access storage targets using the network through a common and easy-to-use protocol and application programming interfaces. This new technology is useful for end users benefits. With the continuous development and improvement of cloud storage, it will necessarily result in more and more applications in the institutions of higher learning and education network.Originality/value: This paper introduced the cloud storage into the integration of high quality teaching resources in universities first and as a new form of service, it can be a good solution.

  4. Examination of Operation Quality for High-frequent Railway Operation

    DEFF Research Database (Denmark)

    Landex, Alex; Kaas, Anders H.

    2009-01-01

    take the first train in their direction. The article examines four different approaches to examine operation quality for high-frequent operation that are based on the experiences of the passengers. These approaches are the service frequency of the operation, travel time extension, a combination......The examination of operation quality for high-frequent operation requires other approaches than the typical evaluation of punctuality (trains on time) and reliability (operated trains). This is because passengers in high-frequent railway systems do not necessarily notice train delays as they just...... of the service frequency and travel time approaches, and passenger delays. The service frequency and travel time approaches are simple measurements with low complexity and complement each other. Therefore, the article recommends combining the service frequency and travel time approaches to get a more accurate...

  5. Identification of Mendelian inconsistencies between SNP and pedigree information of sibs

    Directory of Open Access Journals (Sweden)

    Calus Mario PL

    2011-10-01

    Full Text Available Abstract Background Using SNP genotypes to apply genomic selection in breeding programs is becoming common practice. Tools to edit and check the quality of genotype data are required. Checking for Mendelian inconsistencies makes it possible to identify animals for which pedigree information and genotype information are not in agreement. Methods Straightforward tests to detect Mendelian inconsistencies exist that count the number of opposing homozygous marker (e.g. SNP genotypes between parent and offspring (PAR-OFF. Here, we develop two tests to identify Mendelian inconsistencies between sibs. The first test counts SNP with opposing homozygous genotypes between sib pairs (SIBCOUNT. The second test compares pedigree and SNP-based relationships (SIBREL. All tests iteratively remove animals based on decreasing numbers of inconsistent parents and offspring or sibs. The PAR-OFF test, followed by either SIB test, was applied to a dataset comprising 2,078 genotyped cows and 211 genotyped sires. Theoretical expectations for distributions of test statistics of all three tests were calculated and compared to empirically derived values. Type I and II error rates were calculated after applying the tests to the edited data, while Mendelian inconsistencies were introduced by permuting pedigree against genotype data for various proportions of animals. Results Both SIB tests identified animal pairs for which pedigree and genomic relationships could be considered as inconsistent by visual inspection of a scatter plot of pairwise pedigree and SNP-based relationships. After removal of 235 animals with the PAR-OFF test, SIBCOUNT (SIBREL identified 18 (22 additional inconsistent animals. Seventeen animals were identified by both methods. The numbers of incorrectly deleted animals (Type I error, were equally low for both methods, while the numbers of incorrectly non-deleted animals (Type II error, were considerably higher for SIBREL compared to SIBCOUNT. Conclusions

  6. Quality and efficiency in high dimensional Nearest neighbor search

    KAUST Repository

    Tao, Yufei; Yi, Ke; Sheng, Cheng; Kalnis, Panos

    2009-01-01

    Nearest neighbor (NN) search in high dimensional space is an important problem in many applications. Ideally, a practical solution (i) should be implementable in a relational database, and (ii) its query cost should grow sub-linearly with the dataset size, regardless of the data and query distributions. Despite the bulk of NN literature, no solution fulfills both requirements, except locality sensitive hashing (LSH). The existing LSH implementations are either rigorous or adhoc. Rigorous-LSH ensures good quality of query results, but requires expensive space and query cost. Although adhoc-LSH is more efficient, it abandons quality control, i.e., the neighbor it outputs can be arbitrarily bad. As a result, currently no method is able to ensure both quality and efficiency simultaneously in practice. Motivated by this, we propose a new access method called the locality sensitive B-tree (LSB-tree) that enables fast highdimensional NN search with excellent quality. The combination of several LSB-trees leads to a structure called the LSB-forest that ensures the same result quality as rigorous-LSH, but reduces its space and query cost dramatically. The LSB-forest also outperforms adhoc-LSH, even though the latter has no quality guarantee. Besides its appealing theoretical properties, the LSB-tree itself also serves as an effective index that consumes linear space, and supports efficient updates. Our extensive experiments confirm that the LSB-tree is faster than (i) the state of the art of exact NN search by two orders of magnitude, and (ii) the best (linear-space) method of approximate retrieval by an order of magnitude, and at the same time, returns neighbors with much better quality. © 2009 ACM.

  7. High quality flux control system for electron gun evaporation

    International Nuclear Information System (INIS)

    Appelbloom, A.M.; Hadley, P.; van der Marel, D.; Mooij, J.E.

    1991-01-01

    This paper reports on a high quality flux control system for electron gun evaporation developed and tested for the MBE growth of high temperature superconductors. The system can be applied to any electron gun without altering the electron gun itself. Essential elements of the system are a high bandwidth mass spectrometer, control electronics and a high voltage modulator to sweep the electron beam over the melt at high frequencies. the sweep amplitude of the electron beam is used to control the evaporation flux at high frequencies. The feedback loop of the system has a bandwidth of over 100 Hz, which makes it possible to grow superlattices and layered structures in a fast and precisely controlled manner

  8. Safety and quality management at the high flux reactor Petten

    International Nuclear Information System (INIS)

    Zurita, A.; Ahlf, J.

    1995-01-01

    The High Flux Reactor (HFR) is one high power multi-purpose materials testing research reactor of the tank-in-pool type, cooled and moderated by light-water. It is operated at 45 MW at a prescribed schedule of 11 cycles per year, each comprising 25 operation days and three shut-down days. Since the licence for the operation of HFR was granted in 1962, a total of 14 amendments to the original licence have been made following different modifications in the installations. In the meantime, international nuclear standards were developed, especially in the framework of the NUSS programme of the IAEA, which were adopted by the Dutch Licensing Authorities. In order to implement the new standards, the situation at the HFR was comprehensively reviewed in the course of an audit performed by the Dutch Licensing Authorities in 1988. This also resulted in formulating the task of setting-up an 'HFR - Integral Quality Assurance Handbook' (HFR-IQAD) involving both organizations JRCIAM and ECN, which had the unique framework and basic guideline to assure the safe and efficient operation and exploitation of the HFR and to promote safety and quality in all aspects of HFR related activities. The assurance of safe and efficient operation and exploitation of the HFR is condensed together under the concepts of safety and quality of services and is achieved through the safety and quality management. (orig.)

  9. Wellbeing Understanding in High Quality Healthcare Informatics and Telepractice.

    Science.gov (United States)

    Fiorini, Rodolfo A; De Giacomo, Piero; L'Abate, Luciano

    2016-01-01

    The proper use of healthcare informatics technology and multidimensional conceptual clarity are fundamental to create and boost outstanding clinical and telepractice results. Avoiding even terminology ambiguities is mandatory for high quality of care service. For instance, well-being or wellbeing is a different way to write the same concept only, or there is a good deal of ambiguity around the meanings of these terms the way they are written. In personal health, healthcare and healthcare informatics, this kind of ambiguity and lack of conceptual clarity has been called out repeatedly over the past 50 years. It is time to get the right, terse scenario. We present a brief review to develop and achieve ultimate wellbeing understanding for practical high quality healthcare informatics and telepractice application. This article presents an innovative point of view on deeper wellbeing understanding towards its increased clinical effective application.

  10. Quality assurance system for sitting high risk facilities

    International Nuclear Information System (INIS)

    Rodriguez, Aymee; Peralta, Jose L.; Fernandez, Manuel

    1999-01-01

    The paper shows how we have conceived and designed the quality assurance system for the site selection process of an area for sitting the facility of high risk in correspondence with the approved methodology. The results obtained in the implementation of the system have permitted the satisfactory performance of each one the expected stage, defining the most favorable sectors in order to continue the studies of the repository site for the disposal of low and intermedium. (author)

  11. High-quality uniform dry transfer of graphene to polymers.

    Science.gov (United States)

    Lock, Evgeniya H; Baraket, Mira; Laskoski, Matthew; Mulvaney, Shawn P; Lee, Woo K; Sheehan, Paul E; Hines, Daniel R; Robinson, Jeremy T; Tosado, Jacob; Fuhrer, Michael S; Hernández, Sandra C; Walton, Scott G

    2012-01-11

    In this paper we demonstrate high-quality, uniform dry transfer of graphene grown by chemical vapor deposition on copper foil to polystyrene. The dry transfer exploits an azide linker molecule to establish a covalent bond to graphene and to generate greater graphene-polymer adhesion compared to that of the graphene-metal foil. Thus, this transfer approach provides a novel alternative route for graphene transfer, which allows for the metal foils to be reused. © 2011 American Chemical Society

  12. Coupling of high-quality-factor optical resonators

    International Nuclear Information System (INIS)

    Salzenstein, Patrice; Henriet, Rémi; Coillet, Aurélien; Chembo, Yanne K; Mortier, Michel; Sérier-Brault, Hélène; Rasoloniaina, Alphonse; Dumeige, Yannick; Féron, Patrice

    2013-01-01

    We improve theoretically and experimentally the problem of the coupling between a high Q-factor resonator and its external coupler. We have observed oscillations of ringing induced by the sweeping of the excitation frequency of an active microsphere. Thanks to this approach, the quality factor of an optical resonator was measured and we obtained Q = 5.8 × 10 8 . (paper)

  13. A high throughput DNA extraction method with high yield and quality

    Directory of Open Access Journals (Sweden)

    Xin Zhanguo

    2012-07-01

    Full Text Available Abstract Background Preparation of large quantity and high quality genomic DNA from a large number of plant samples is a major bottleneck for most genetic and genomic analyses, such as, genetic mapping, TILLING (Targeting Induced Local Lesion IN Genome, and next-generation sequencing directly from sheared genomic DNA. A variety of DNA preparation methods and commercial kits are available. However, they are either low throughput, low yield, or costly. Here, we describe a method for high throughput genomic DNA isolation from sorghum [Sorghum bicolor (L. Moench] leaves and dry seeds with high yield, high quality, and affordable cost. Results We developed a high throughput DNA isolation method by combining a high yield CTAB extraction method with an improved cleanup procedure based on MagAttract kit. The method yielded large quantity and high quality DNA from both lyophilized sorghum leaves and dry seeds. The DNA yield was improved by nearly 30 fold with 4 times less consumption of MagAttract beads. The method can also be used in other plant species, including cotton leaves and pine needles. Conclusion A high throughput system for DNA extraction from sorghum leaves and seeds was developed and validated. The main advantages of the method are low cost, high yield, high quality, and high throughput. One person can process two 96-well plates in a working day at a cost of $0.10 per sample of magnetic beads plus other consumables that other methods will also need.

  14. Dynamic variable selection in SNP genotype autocalling from APEX microarray data

    Directory of Open Access Journals (Sweden)

    Zamar Ruben H

    2006-11-01

    Full Text Available Abstract Background Single nucleotide polymorphisms (SNPs are DNA sequence variations, occurring when a single nucleotide – adenine (A, thymine (T, cytosine (C or guanine (G – is altered. Arguably, SNPs account for more than 90% of human genetic variation. Our laboratory has developed a highly redundant SNP genotyping assay consisting of multiple probes with signals from multiple channels for a single SNP, based on arrayed primer extension (APEX. This mini-sequencing method is a powerful combination of a highly parallel microarray with distinctive Sanger-based dideoxy terminator sequencing chemistry. Using this microarray platform, our current genotype calling system (known as SNP Chart is capable of calling single SNP genotypes by manual inspection of the APEX data, which is time-consuming and exposed to user subjectivity bias. Results Using a set of 32 Coriell DNA samples plus three negative PCR controls as a training data set, we have developed a fully-automated genotyping algorithm based on simple linear discriminant analysis (LDA using dynamic variable selection. The algorithm combines separate analyses based on the multiple probe sets to give a final posterior probability for each candidate genotype. We have tested our algorithm on a completely independent data set of 270 DNA samples, with validated genotypes, from patients admitted to the intensive care unit (ICU of St. Paul's Hospital (plus one negative PCR control sample. Our method achieves a concordance rate of 98.9% with a 99.6% call rate for a set of 96 SNPs. By adjusting the threshold value for the final posterior probability of the called genotype, the call rate reduces to 94.9% with a higher concordance rate of 99.6%. We also reversed the two independent data sets in their training and testing roles, achieving a concordance rate up to 99.8%. Conclusion The strength of this APEX chemistry-based platform is its unique redundancy having multiple probes for a single SNP. Our

  15. Methods and systems for fabricating high quality superconducting tapes

    Energy Technology Data Exchange (ETDEWEB)

    Majkic, Goran; Selvamanickam, Venkat

    2018-02-13

    An MOCVD system fabricates high quality superconductor tapes with variable thicknesses. The MOCVD system can include a gas flow chamber between two parallel channels in a housing. A substrate tape is heated and then passed through the MOCVD housing such that the gas flow is perpendicular to the tape's surface. Precursors are injected into the gas flow for deposition on the substrate tape. In this way, superconductor tapes can be fabricated with variable thicknesses, uniform precursor deposition, and high critical current densities.

  16. High quality mask storage in an advanced Logic-Fab

    Science.gov (United States)

    Jähnert, Carmen; Fritsche, Silvio

    2012-02-01

    High efficient mask logistics as well as safe and high quality mask storage are essential requirements within an advanced lithography area of a modern logic waferfab. Fast operational availability of the required masks at the exposure tool with excellent mask condition requires a safe mask handling, safeguarding of high mask quality over the whole mask usage time without any quality degradation and an intelligent mask logistics. One big challenge is the prevention of haze on high advanced phase shift masks used in a high volume production line for some thousands of 248nm or 193nm exposures. In 2008 Infineon Dresden qualified a customer specific developed semi-bare mask storage system from DMSDynamic Micro Systems in combination with a high advanced mask handling and an interconnected complex logistic system. This high-capacity mask storage system DMS M1900.22 for more than 3000 masks with fully automated mask and box handling as well as full-blown XCDA purge has been developed and adapted to the Infineon Lithotoollandscape using Nikon and SMIF reticle cases. Advanced features for ESD safety and mask security, mask tracking via RFID and interactions with the exposure tools were developed and implemented. The stocker is remote controlled by the iCADA-RSM system, ordering of the requested mask directly from the affected exposure tool allows fast access. This paper discusses the advantages and challenges for this approach as well as the practical experience gained during the implementation of the new system which improves the fab performance with respect to mask quality, security and throughput. Especially the realization of an extremely low and stable humidity level in addition with a well controlled air flow at each mask surface, preventing masks from haze degradation and particle contamination, turns out to be a notable technical achievement. The longterm stability of haze critical masks has been improved significantly. Relevant environmental parameters like

  17. Heterogeneous computing architecture for fast detection of SNP-SNP interactions.

    Science.gov (United States)

    Sluga, Davor; Curk, Tomaz; Zupan, Blaz; Lotric, Uros

    2014-06-25

    The extent of data in a typical genome-wide association study (GWAS) poses considerable computational challenges to software tools for gene-gene interaction discovery. Exhaustive evaluation of all interactions among hundreds of thousands to millions of single nucleotide polymorphisms (SNPs) may require weeks or even months of computation. Massively parallel hardware within a modern Graphic Processing Unit (GPU) and Many Integrated Core (MIC) coprocessors can shorten the run time considerably. While the utility of GPU-based implementations in bioinformatics has been well studied, MIC architecture has been introduced only recently and may provide a number of comparative advantages that have yet to be explored and tested. We have developed a heterogeneous, GPU and Intel MIC-accelerated software module for SNP-SNP interaction discovery to replace the previously single-threaded computational core in the interactive web-based data exploration program SNPsyn. We report on differences between these two modern massively parallel architectures and their software environments. Their utility resulted in an order of magnitude shorter execution times when compared to the single-threaded CPU implementation. GPU implementation on a single Nvidia Tesla K20 runs twice as fast as that for the MIC architecture-based Xeon Phi P5110 coprocessor, but also requires considerably more programming effort. General purpose GPUs are a mature platform with large amounts of computing power capable of tackling inherently parallel problems, but can prove demanding for the programmer. On the other hand the new MIC architecture, albeit lacking in performance reduces the programming effort and makes it up with a more general architecture suitable for a wider range of problems.

  18. Construction of High-Quality Camel Immune Antibody Libraries.

    Science.gov (United States)

    Romão, Ema; Poignavent, Vianney; Vincke, Cécile; Ritzenthaler, Christophe; Muyldermans, Serge; Monsion, Baptiste

    2018-01-01

    Single-domain antibodies libraries of heavy-chain only immunoglobulins from camelids or shark are enriched for high-affinity antigen-specific binders by a short in vivo immunization. Thus, potent binders are readily retrieved from relatively small-sized libraries of 10 7 -10 8 individual transformants, mostly after phage display and panning on a purified target. However, the remaining drawback of this strategy arises from the need to generate a dedicated library, for nearly every envisaged target. Therefore, all the procedures that shorten and facilitate the construction of an immune library of best possible quality are definitely a step forward. In this chapter, we provide the protocol to generate a high-quality immune VHH library using the Golden Gate Cloning strategy employing an adapted phage display vector where a lethal ccdB gene has to be substituted by the VHH gene. With this procedure, the construction of the library can be shortened to less than a week starting from bleeding the animal. Our libraries exceed 10 8 individual transformants and close to 100% of the clones harbor a phage display vector having an insert with the length of a VHH gene. These libraries are also more economic to make than previous standard approaches using classical restriction enzymes and ligations. The quality of the Nanobodies that are retrieved from immune libraries obtained by Golden Gate Cloning is identical to those from immune libraries made according to the classical procedure.

  19. Development of a rapid SNP-typing assay to differentiate Bifidobacterium animalis ssp. lactis strains used in probiotic-supplemented dairy products.

    Science.gov (United States)

    Lomonaco, Sara; Furumoto, Emily J; Loquasto, Joseph R; Morra, Patrizia; Grassi, Ausilia; Roberts, Robert F

    2015-02-01

    Identification at the genus, species, and strain levels is desirable when a probiotic microorganism is added to foods. Strains of Bifidobacterium animalis ssp. lactis (BAL) are commonly used worldwide in dairy products supplemented with probiotic strains. However, strain discrimination is difficult because of the high degree of genome identity (99.975%) between different genomes of this subspecies. Typing of monomorphic species can be carried out efficiently by targeting informative single nucleotide polymorphisms (SNP). Findings from a previous study analyzing both reference and commercial strains of BAL identified SNP that could be used to discriminate common strains into 8 groups. This paper describes development of a minisequencing assay based on the primer extension reaction (PER) targeting multiple SNP that can allow strain differentiation of BAL. Based on previous data, 6 informative SNP were selected for further testing, and a multiplex preliminary PCR was optimized to amplify the DNA regions containing the selected SNP. Extension primers (EP) annealing immediately adjacent to the selected SNP were developed and tested in simplex and multiplex PER to evaluate their performance. Twenty-five strains belonging to 9 distinct genomic clusters of B. animalis ssp. lactis were selected and analyzed using the developed minisequencing assay, simultaneously targeting the 6 selected SNP. Fragment analysis was subsequently carried out in duplicate and demonstrated that the assay yielded 8 specific profiles separating the most commonly used commercial strains. This novel multiplex PER approach provides a simple, rapid, flexible SNP-based subtyping method for proper characterization and identification of commercial probiotic strains of BAL from fermented dairy products. To assess the usefulness of this method, DNA was extracted from yogurt manufactured with and without the addition of B. animalis ssp. lactis BB-12. Extracted DNA was then subjected to the minisequencing

  20. Using SNP array to identify aneuploidy and segmental imbalance in translocation carriers

    Directory of Open Access Journals (Sweden)

    B. Xiong

    2014-12-01

    In addition to genetic testing techniques, the embryo biopsy stage (polar body, cleavage embryo or blastocyst and the mode of embryo transfer (fresh or frozen embryos can affect the outcome of PGD. It is now generally recommended that blastomere biopsy should be replaced by blastocyst biopsy to avoid a high mosaic rate and biopsy-related damage to cleavage-stage embryos, which might affect embryo development. However, more clinical data are required to confirm that the technique of SNP array-based PGD (SNP-PGD combined with trophectoderm (TE biopsy and frozen embryo transfer (FET is superior to traditional FISH-PGD combined with Day 3 (D3 blastomere biopsy and fresh embryo transfer.

  1. RASSF1A and the rs2073498 Cancer Associated SNP

    International Nuclear Information System (INIS)

    Donninger, Howard; Barnoud, Thibaut; Nelson, Nick; Kassler, Suzanna; Clark, Jennifer; Cummins, Timothy D.; Powell, David W.; Nyante, Sarah; Millikan, Robert C.; Clark, Geoffrey J.

    2011-01-01

    RASSF1A is one of the most frequently inactivated tumor suppressors yet identified in human cancer. It is pro-apoptotic and appears to function as a scaffolding protein that interacts with a variety of other tumor suppressors to modulate their function. It can also complex with the Ras oncoprotein and may serve to integrate pro-growth and pro-death signaling pathways. A SNP has been identified that is present in approximately 29% of European populations [rs2073498, A(133)S]. Several studies have now presented evidence that this SNP is associated with an enhanced risk of developing breast cancer. We have used a proteomics based approach to identify multiple differences in the pattern of protein/protein interactions mediated by the wild type compared to the SNP variant protein. We have also identified a significant difference in biological activity between wild type and SNP variant protein. However, we have found only a very modest association of the SNP with breast cancer predisposition.

  2. High beam quality and high energy short-pulse laser with MOPA

    Science.gov (United States)

    Jin, Quanwei; Pang, Yu; Jiang, JianFeng; Tan, Liang; Cui, Lingling; Wei, Bin; Sun, Yinhong; Tang, Chun

    2018-03-01

    A high energy, high beam quality short-pulse diode-pumped Nd:YAG master oscillator power-amplifier (MOPA) laser with two amplifier stages is demonstrated. The two-rod birefringence compensation was used as beam quality controlling methods, which presents a short-pulse energy of 40 mJ with a beam quality value of M2 = 1.2 at a repetition rate of 400Hz. The MOPA system delivers a short-pulse energy of 712.5 mJ with a pulse width of 12.4 ns.The method of spherical aberration compensation is improved the beam quality, a M2 factor of 2.3 and an optical-to-optical efficiency of 27.7% is obtained at the maximum laser out power.The laser obtained 1.4J out energy with polarization integration.

  3. HRM and SNaPshot as alternative forensic SNP genotyping methods.

    Science.gov (United States)

    Mehta, Bhavik; Daniel, Runa; McNevin, Dennis

    2017-09-01

    Single nucleotide polymorphisms (SNPs) have been widely used in forensics for prediction of identity, biogeographical ancestry (BGA) and externally visible characteristics (EVCs). Single base extension (SBE) assays, most notably SNaPshot® (Thermo Fisher Scientific), are commonly used for forensic SNP genotyping as they can be employed on standard instrumentation in forensic laboratories (e.g. capillary electrophoresis). High resolution melt (HRM) analysis is an alternative method and is a simple, fast, single tube assay for low throughput SNP typing. This study compares HRM and SNaPshot®. HRM produced reproducible and concordant genotypes at 500 pg, however, difficulties were encountered when genotyping SNPs with high GC content in flanking regions and differentiating variants of symmetrical SNPs. SNaPshot® was reproducible at 100 pg and is less dependent on SNP choice. HRM has a shorter processing time in comparison to SNaPshot®, avoids post PCR contamination risk and has potential as a screening tool for many forensic applications.

  4. Development of nuclear quality high pressure valve bellows in Canada

    International Nuclear Information System (INIS)

    Janzen, P.; Astill, C.J.

    1978-06-01

    Concurrent with the decision to use bellows stem sealed nuclear valves where feasible in commercial-scale CANDU plants, AECL undertook to develop an indigenous high pressure valve bellows technology. This program included developing the capability to fabricate improved high pressure valve bellows in conjunction with a Canadian manufacturer. This paper describes the evolution of a two-stage bellows fabrication process involving: (1) manufacture of discrete lengths of precision thin wall telescoping tubes - from preparation of strip blanks through edge grinding and edge forming to longitudinal welding; (2) forming of bellows from tube assemblies using a novel combination of mechanical inward forming followed by hydraulic outward forming. Bellows of Inconel 600 and Inconel 625 have been manufactured and evaluated. Test results indicate comparable to improved performance over alternative high quality bellows. (author)

  5. Fat Quality Influences the Obesogenic Effect of High Fat Diets

    Directory of Open Access Journals (Sweden)

    Raffaella Crescenzo

    2015-11-01

    Full Text Available High fat and/or carbohydrate intake are associated with an elevated risk for obesity and chronic diseases such as diabetes and cardiovascular diseases. The harmful effects of a high fat diet could be different, depending on dietary fat quality. In fact, high fat diets rich in unsaturated fatty acids are considered less deleterious for human health than those rich in saturated fat. In our previous studies, we have shown that rats fed a high fat diet developed obesity and exhibited a decrease in oxidative capacity and an increase in oxidative stress in liver mitochondria. To investigate whether polyunsaturated fats could attenuate the above deleterious effects of high fat diets, energy balance and body composition were assessed after two weeks in rats fed isocaloric amounts of a high-fat diet (58.2% by energy rich either in lard or safflower/linseed oil. Hepatic functionality, plasma parameters, and oxidative status were also measured. The results show that feeding on safflower/linseed oil diet attenuates the obesogenic effect of high fat diets and ameliorates the blood lipid profile. Conversely, hepatic steatosis and mitochondrial oxidative stress appear to be negatively affected by a diet rich in unsaturated fatty acids.

  6. Leaf Transcriptome Sequencing for Identifying Genic-SSR Markers and SNP Heterozygosity in Crossbred Mango Variety ‘Amrapali’ (Mangifera indica L.)

    Science.gov (United States)

    Mahato, Ajay Kumar; Sharma, Nimisha; Singh, Akshay; Srivastav, Manish; Jaiprakash; Singh, Sanjay Kumar; Singh, Anand Kumar; Sharma, Tilak Raj; Singh, Nagendra Kumar

    2016-01-01

    Mango (Mangifera indica L.) is called “king of fruits” due to its sweetness, richness of taste, diversity, large production volume and a variety of end usage. Despite its huge economic importance genomic resources in mango are scarce and genetics of useful horticultural traits are poorly understood. Here we generated deep coverage leaf RNA sequence data for mango parental varieties ‘Neelam’, ‘Dashehari’ and their hybrid ‘Amrapali’ using next generation sequencing technologies. De-novo sequence assembly generated 27,528, 20,771 and 35,182 transcripts for the three genotypes, respectively. The transcripts were further assembled into a non-redundant set of 70,057 unigenes that were used for SSR and SNP identification and annotation. Total 5,465 SSR loci were identified in 4,912 unigenes with 288 type I SSR (n ≥ 20 bp). One hundred type I SSR markers were randomly selected of which 43 yielded PCR amplicons of expected size in the first round of validation and were designated as validated genic-SSR markers. Further, 22,306 SNPs were identified by aligning high quality sequence reads of the three mango varieties to the reference unigene set, revealing significantly enhanced SNP heterozygosity in the hybrid Amrapali. The present study on leaf RNA sequencing of mango varieties and their hybrid provides useful genomic resource for genetic improvement of mango. PMID:27736892

  7. High quality electron beams from a laser wakefield accelerator

    Energy Technology Data Exchange (ETDEWEB)

    Wiggins, S M; Issac, R C; Welsh, G H; Brunetti, E; Shanks, R P; Anania, M P; Cipiccia, S; Manahan, G G; Aniculaesei, C; Ersfeld, B; Islam, M R; Burgess, R T L; Vieux, G; Jaroszynski, D A [SUPA, Department of Physics, University of Strathclyde, Glasgow (United Kingdom); Gillespie, W A [SUPA, Division of Electronic Engineering and Physics, University of Dundee, Dundee (United Kingdom); MacLeod, A M [School of Computing and Creative Technologies, University of Abertay Dundee, Dundee (United Kingdom); Van der Geer, S B; De Loos, M J, E-mail: m.wiggins@phys.strath.ac.u [Pulsar Physics, Burghstraat 47, 5614 BC Eindhoven (Netherlands)

    2010-12-15

    High quality electron beams have been produced in a laser-plasma accelerator driven by femtosecond laser pulses with a peak power of 26 TW. Electrons are produced with an energy up to 150 MeV from the 2 mm gas jet accelerator and the measured rms relative energy spread is less than 1%. Shot-to-shot stability in the central energy is 3%. Pepper-pot measurements have shown that the normalized transverse emittance is {approx}1{pi} mm mrad while the beam charge is in the range 2-10 pC. The generation of high quality electron beams is understood from simulations accounting for beam loading of the wakefield accelerating structure. Experiments and self-consistent simulations indicate that the beam peak current is several kiloamperes. Efficient transportation of the beam through an undulator is simulated and progress is being made towards the realization of a compact, high peak brilliance free-electron laser operating in the vacuum ultraviolet and soft x-ray wavelength ranges.

  8. Sleep quality and its relationship with quality of life among high-risk pregnant women (gestational diabetes and hypertension).

    Science.gov (United States)

    Saadati, Fatemeh; Sehhatiei Shafaei, Fahimeh; Mirghafourvand, Mozhgan

    2018-01-01

    Sleep is one of the most basic human requirements. This research aims at determining the status of sleep quality and its relationship with quality of life among high-risk pregnant women in Tabriz, Iran, in 2015. This research was a sectional study done on 364 qualified women in 28-36 weeks of pregnancy suffering from mild preeclampsia and gestational diabetes. The sampling was done as convenience. Personal-social-midwifery questionnaire, Pittsburg sleep quality, and quality of life in pregnancy (QOL-ORAV) were used for gathering data. Multivariate linear regression model was used for determining the relationship between sleep quality and its subsets with quality of life and controlling confounders. In the current study, the prevalence of sleep disturbance was 96.4%. Mean (SD) of the total score of sleep quality was 10.1 (4.1) and the total score of quality of life was 61.7 (17.3). According to Pearson's correlation test, there was statistically significant relationship between quality of life and sleep quality and all its subsets except sleep duration and use of sleep medication (p quality of life. The findings of current research show that sleep quality is low among high-risk pregnant women and quality of life is medium. So, it is necessary that required training is given by health cares for improving sleep quality and quality of life to mothers.

  9. MDM2 SNP309 and SNP285 Act as Negative Prognostic Markers for Non-small Cell Lung Cancer Adenocarcinoma Patients

    Science.gov (United States)

    Deben, Christophe; Op de Beeck, Ken; Van den Bossche, Jolien; Jacobs, Julie; Lardon, Filip; Wouters, An; Peeters, Marc; Van Camp, Guy; Rolfo, Christian; Deschoolmeester, Vanessa; Pauwels, Patrick

    2017-01-01

    Objectives: Two functional polymorphisms in the MDM2 promoter region, SNP309T>G and SNP285G>C, have been shown to impact MDM2 expression and cancer risk. Currently available data on the prognostic value of MDM2 SNP309 in non-small cell lung cancer (NSCLC) is contradictory and unavailable for SNP285. The goal of this study was to clarify the role of these MDM2 SNPs in the outcome of NSCLC patients. Materials and Methods: In this study we genotyped SNP309 and SNP285 in 98 NSCLC adenocarcinoma patients and determined MDM2 mRNA and protein levels. In addition, we assessed the prognostic value of these common SNPs on overall and progression free survival, taking into account the TP53 status of the tumor. Results and Conclusion: We found that the SNP285C allele, but not the SNP309G allele, was significantly associated with increased MDM2 mRNA expression levels (p = 0.025). However, we did not observe an association with MDM2 protein levels for SNP285. The SNP309G allele was significantly associated with the presence of wild type TP53 (p = 0.047) and showed a strong trend towards increased MDM2 protein levels (p = 0.068). In addition, patients harboring the SNP309G allele showed a worse overall survival, but only in the presence of wild type TP53. The SNP285C allele was significantly associated with an early age of diagnosis and metastasis. Additionally, the SNP285C allele acted as an independent predictor for worse progression free survival (HR = 3.97; 95% CI = 1.51 - 10.42; p = 0.005). Our data showed that both SNP309 (in the presence of wild type TP53) and SNP285 act as negative prognostic markers for NSCLC patients, implicating a prominent role for these variants in the outcome of these patients. PMID:28819417

  10. Present status of high quality beam facility at Waseda University

    International Nuclear Information System (INIS)

    Washio, M.; Kawai, H.; Hama, Y.; Kudo, N.; Kobayashi, M.; Kuribayasi, T.; Kawaguchi, M.; Kuroda, R.; Maeda, K.; Nagasawa, F.; Ueyama, D.; Hizume, K.; Wang, X.J.; Hayano, H.; Urakawa, J.; Kashiwagi, S.

    2004-01-01

    A research project named High-Tech Research Center Project has been conducted at Waseda University. In this project, an RF gun system has been used for production of low emittance and short bunched electron beam. The experiments for the electron beam quality measurement have been carried out by slit scan techniques, etc. Short pulsed x-ray with the energy range of so-called water window has been generation by the inverse compton scattering. Further, the pulse radiolysis system has been constructed, and the stroboscopic pulse radiolysis has been applied for the detection of hydrated electron in picosecond time region. (author)

  11. Anti-Stokes Luminescence in High Quality Quantum Wells

    Science.gov (United States)

    Vinattieri, A.; Bogani, F.; Miotto, A.; Ceccherini, S.

    1997-11-01

    We present a detailed investigation of the anti-Stokes (AS) luminescence which originates from exciton recombination when below gap excitation is used, in a set of high quality quantum well structures. We observe strong excitonic resonances in the AS signal as measured from photoluminescence and photoluminescence excitation spectra. We demonstrate that neither the electromagnetic coupling between the wells nor the morphological disorder can explain this up-conversion effect. Time-resolved luminescence data after ps excitation and fs correlation spectroscopy results provide clear evidence of the occurrence of a two-step absorption which is assisted by the exciton population resonantly excited by the first photon.

  12. The quality of high-energy X-ray beams

    International Nuclear Information System (INIS)

    LaRiviere, P.D.

    1989-01-01

    Supplement 17 of the British Journal of Radiology is a survey of central-axis depth doses for radiotherapy machines, patterned largely on BJR Supplement 11 (1972). Inspection of high-energy X-ray depth doses for a 10 x 10 cm field at an SSD of 100 cm disclosed large differences between the two sets of data, especially for qualities above 8 MV, e.g. a depth dose of 80% at 10 cm is rated at about 19 MV according to BJR Supplement 11, and 23 MV according to BJR Supplement 17. It was found that Supplement 17 depth-dose data above 8 MV were erratic, but Supplement 11 data could be represented by an analytical expression, providing a unique means of assigning MV quality. It was also found that dose-weighted average energy of the filtered beam plotted smoothly against depth dose. For dosimetric purposes, it is suggested that this parameter be used as a true measure of beam quality, removing discrepancies introduced by the use of nominal MV for this purpose. (author)

  13. CCD Astrophotography High-Quality Imaging from the Suburbs

    CERN Document Server

    Stuart, Adam

    2006-01-01

    This is a reference book for amateur astronomers who have become interested in CCD imaging. Those glorious astronomical images found in astronomy magazines might seem out of reach to newcomers to CCD imaging, but this is not the case. Great pictures are attainable with modest equipment. Adam Stuart’s many beautiful images, reproduced in this book, attest to the quality of – initially – a beginner’s efforts. Chilled-chip astronomical CCD-cameras and software are also wonderful tools for cutting through seemingly impenetrable light-pollution. CCD Astrophotography from the Suburbs describes one man’s successful approach to the problem of getting high-quality astronomical images under some of the most light-polluted conditions. Here is a complete and thoroughly tested program that will help every CCD-beginner to work towards digital imaging of the highest quality. It is equally useful to astronomers who have perfect observing conditions, as to those who have to observe from light-polluted city skies.

  14. Identification of SNP and SSR Markers in Finger Millet Using Next Generation Sequencing Technologies.

    Science.gov (United States)

    Gimode, Davis; Odeny, Damaris A; de Villiers, Etienne P; Wanyonyi, Solomon; Dida, Mathews M; Mneney, Emmarold E; Muchugi, Alice; Machuka, Jesse; de Villiers, Santie M

    2016-01-01

    Finger millet is an important cereal crop in eastern Africa and southern India with excellent grain storage quality and unique ability to thrive in extreme environmental conditions. Since negligible attention has been paid to improving this crop to date, the current study used Next Generation Sequencing (NGS) technologies to develop both Simple Sequence Repeat (SSR) and Single Nucleotide Polymorphism (SNP) markers. Genomic DNA from cultivated finger millet genotypes KNE755 and KNE796 was sequenced using both Roche 454 and Illumina technologies. Non-organelle sequencing reads were assembled into 207 Mbp representing approximately 13% of the finger millet genome. We identified 10,327 SSRs and 23,285 non-homeologous SNPs and tested 101 of each for polymorphism across a diverse set of wild and cultivated finger millet germplasm. For the 49 polymorphic SSRs, the mean polymorphism information content (PIC) was 0.42, ranging from 0.16 to 0.77. We also validated 92 SNP markers, 80 of which were polymorphic with a mean PIC of 0.29 across 30 wild and 59 cultivated accessions. Seventy-six of the 80 SNPs were polymorphic across 30 wild germplasm with a mean PIC of 0.30 while only 22 of the SNP markers showed polymorphism among the 59 cultivated accessions with an average PIC value of 0.15. Genetic diversity analysis using the polymorphic SNP markers revealed two major clusters; one of wild and another of cultivated accessions. Detailed STRUCTURE analysis confirmed this grouping pattern and further revealed 2 sub-populations within wild E. coracana subsp. africana. Both STRUCTURE and genetic diversity analysis assisted with the correct identification of the new germplasm collections. These polymorphic SSR and SNP markers are a significant addition to the existing 82 published SSRs, especially with regard to the previously reported low polymorphism levels in finger millet. Our results also reveal an unexploited finger millet genetic resource that can be included in the regional

  15. Identification of SNP and SSR Markers in Finger Millet Using Next Generation Sequencing Technologies.

    Directory of Open Access Journals (Sweden)

    Davis Gimode

    Full Text Available Finger millet is an important cereal crop in eastern Africa and southern India with excellent grain storage quality and unique ability to thrive in extreme environmental conditions. Since negligible attention has been paid to improving this crop to date, the current study used Next Generation Sequencing (NGS technologies to develop both Simple Sequence Repeat (SSR and Single Nucleotide Polymorphism (SNP markers. Genomic DNA from cultivated finger millet genotypes KNE755 and KNE796 was sequenced using both Roche 454 and Illumina technologies. Non-organelle sequencing reads were assembled into 207 Mbp representing approximately 13% of the finger millet genome. We identified 10,327 SSRs and 23,285 non-homeologous SNPs and tested 101 of each for polymorphism across a diverse set of wild and cultivated finger millet germplasm. For the 49 polymorphic SSRs, the mean polymorphism information content (PIC was 0.42, ranging from 0.16 to 0.77. We also validated 92 SNP markers, 80 of which were polymorphic with a mean PIC of 0.29 across 30 wild and 59 cultivated accessions. Seventy-six of the 80 SNPs were polymorphic across 30 wild germplasm with a mean PIC of 0.30 while only 22 of the SNP markers showed polymorphism among the 59 cultivated accessions with an average PIC value of 0.15. Genetic diversity analysis using the polymorphic SNP markers revealed two major clusters; one of wild and another of cultivated accessions. Detailed STRUCTURE analysis confirmed this grouping pattern and further revealed 2 sub-populations within wild E. coracana subsp. africana. Both STRUCTURE and genetic diversity analysis assisted with the correct identification of the new germplasm collections. These polymorphic SSR and SNP markers are a significant addition to the existing 82 published SSRs, especially with regard to the previously reported low polymorphism levels in finger millet. Our results also reveal an unexploited finger millet genetic resource that can be included

  16. Genome rearrangements detected by SNP microarrays in individuals with intellectual disability referred with possible Williams syndrome.

    Directory of Open Access Journals (Sweden)

    Ariel M Pani

    2010-08-01

    Full Text Available Intellectual disability (ID affects 2-3% of the population and may occur with or without multiple congenital anomalies (MCA or other medical conditions. Established genetic syndromes and visible chromosome abnormalities account for a substantial percentage of ID diagnoses, although for approximately 50% the molecular etiology is unknown. Individuals with features suggestive of various syndromes but lacking their associated genetic anomalies pose a formidable clinical challenge. With the advent of microarray techniques, submicroscopic genome alterations not associated with known syndromes are emerging as a significant cause of ID and MCA.High-density SNP microarrays were used to determine genome wide copy number in 42 individuals: 7 with confirmed alterations in the WS region but atypical clinical phenotypes, 31 with ID and/or MCA, and 4 controls. One individual from the first group had the most telomeric gene in the WS critical region deleted along with 2 Mb of flanking sequence. A second person had the classic WS deletion and a rearrangement on chromosome 5p within the Cri du Chat syndrome (OMIM:123450 region. Six individuals from the ID/MCA group had large rearrangements (3 deletions, 3 duplications, one of whom had a large inversion associated with a deletion that was not detected by the SNP arrays.Combining SNP microarray analyses and qPCR allowed us to clone and sequence 21 deletion breakpoints in individuals with atypical deletions in the WS region and/or ID or MCA. Comparison of these breakpoints to databases of genomic variation revealed that 52% occurred in regions harboring structural variants in the general population. For two probands the genomic alterations were flanked by segmental duplications, which frequently mediate recurrent genome rearrangements; these may represent new genomic disorders. While SNP arrays and related technologies can identify potentially pathogenic deletions and duplications, obtaining sequence information

  17. Proper joint analysis of summary association statistics requires the adjustment of heterogeneity in SNP coverage pattern.

    Science.gov (United States)

    Zhang, Han; Wheeler, William; Song, Lei; Yu, Kai

    2017-07-07

    As meta-analysis results published by consortia of genome-wide association studies (GWASs) become increasingly available, many association summary statistics-based multi-locus tests have been developed to jointly evaluate multiple single-nucleotide polymorphisms (SNPs) to reveal novel genetic architectures of various complex traits. The validity of these approaches relies on the accurate estimate of z-score correlations at considered SNPs, which in turn requires knowledge on the set of SNPs assessed by each study participating in the meta-analysis. However, this exact SNP coverage information is usually unavailable from the meta-analysis results published by GWAS consortia. In the absence of the coverage information, researchers typically estimate the z-score correlations by making oversimplified coverage assumptions. We show through real studies that such a practice can generate highly inflated type I errors, and we demonstrate the proper way to incorporate correct coverage information into multi-locus analyses. We advocate that consortia should make SNP coverage information available when posting their meta-analysis results, and that investigators who develop analytic tools for joint analyses based on summary data should pay attention to the variation in SNP coverage and adjust for it appropriately. Published by Oxford University Press 2017. This work is written by US Government employees and is in the public domain in the US.

  18. Percutaneous vertebroplasty with a high-quality rotational angiographic unit

    Energy Technology Data Exchange (ETDEWEB)

    Pedicelli, Alessandro [Department of Bioimaging and Radiological Sciences, Catholic University of Sacred Heart, Policl. A.Gemelli, l.go Gemelli 1, 00168 Rome (Italy)], E-mail: apedicelli@rm.unicatt.it; Rollo, Massimo [Department of Bioimaging and Radiological Sciences, Catholic University of Sacred Heart, Policl. A.Gemelli, l.go Gemelli 1, 00168 Rome (Italy)], E-mail: mrollo@rm.unicatt.it; Piano, Mariangela [Department of Bioimaging and Radiological Sciences, Catholic University of Sacred Heart, Policl. A.Gemelli, l.go Gemelli 1, 00168 Rome (Italy)], E-mail: mariangela.piano@gmail.com; Re, Thomas J. [Department of Bioimaging and Radiological Sciences, Catholic University of Sacred Heart, Policl. A.Gemelli, l.go Gemelli 1, 00168 Rome (Italy)], E-mail: tomjre@gmail.com; Cipriani, Maria C. [Department of Gerontology, Catholic University of Sacred Heart, Policl. A.Gemelli, l.go Gemelli 1, 00168 Rome (Italy)], E-mail: alexped@yahoo.com; Colosimo, Cesare [Department of Bioimaging and Radiological Sciences, Catholic University of Sacred Heart, Policl. A.Gemelli, l.go Gemelli 1, 00168 Rome (Italy)], E-mail: colosimo@rm.unicatt.it; Bonomo, Lorenzo [Department of Bioimaging and Radiological Sciences, Catholic University of Sacred Heart, Policl. A.Gemelli, l.go Gemelli 1, 00168 Rome (Italy)], E-mail: lbonomo@rm.unicatt.it

    2009-02-15

    We evaluated the reliability of a rotational angiographic unit (RA) with flat-panel detector as a single technique to guide percutaneous vertebroplasty (PVP) and for post-procedure assessment by 2D and 3D reformatted images. Fifty-five consecutive patients (104 vertebral bodies) were treated under RA fluoroscopy. Rotational acquisitions with 2D and 3D reconstruction were obtained in all patients for immediate post-procedure assessment. In complex cases, this technique was also used to evaluate the needle position during the procedure. All patients underwent CT scan after the procedure. RA and CT findings were compared. In all cases, a safe trans-pedicular access and an accurate control of the bone-cement injection were successfully performed with high-quality fluoroscopy, even at the thoracic levels and in case of vertebra plana. 2D and 3D rotational reconstructions permitted CT-like images that clearly showed needle position and were similar to CT findings in depicting intrasomatic implant-distribution. RA detected 40 cement leakages compared to 42 demonstrated by CT and showed overall 95% sensitivity and 100% specificity compared to CT for final post-procedure assessment. Our preliminary results suggest that high-quality RA is reliable and safe as a single technique for PVP guidance, control and post-procedure assessment. It permits fast and cost-effective procedures avoiding multi-modality imaging.

  19. Computer-aided control of high-quality cast iron

    Directory of Open Access Journals (Sweden)

    S. Pietrowski

    2008-04-01

    Full Text Available The study discusses the possibility of control of the high-quality grey cast iron and ductile iron using the author’s genuine computer programs. The programs have been developed with the help of algorithms based on statistical relationships that are said to exist between the characteristic parameters of DTA curves and properties, like Rp0,2, Rm, A5 and HB. It has been proved that the spheroidisation and inoculation treatment of cast iron changes in an important way the characteristic parameters of DTA curves, thus enabling a control of these operations as regards their correctness and effectiveness, along with the related changes in microstructure and mechanical properties of cast iron. Moreover, some examples of statistical relationships existing between the typical properties of ductile iron and its control process were given for cases of the melts consistent and inconsistent with the adopted technology.A test stand for control of the high-quality cast iron and respective melts has been schematically depicted.

  20. Automated high speed volume computed tomography for inline quality control

    International Nuclear Information System (INIS)

    Hanke, R.; Kugel, A.; Troup, P.

    2004-01-01

    Increasing complexity of innovative products as well as growing requirements on quality and reliability call for more detailed knowledge about internal structures of manufactured components rather by 100 % inspection than just by sampling test. A first-step solution, like radioscopic inline inspection machines, equipped with automated data evaluation software, have become state of the art in the production floor during the last years. However, these machines provide just ordinary two-dimensional information and deliver no volume data e.g. to evaluate exact position or shape of detected defects. One way to solve this problem is the application of X-ray computed tomography (CT). Compared to the performance of the first generation medical scanners (scanning times of many hours), today, modern Volume CT machines for industrial applications need about 5 minutes for a full object scan depending on the object size. Of course, this is still too long to introduce this powerful method into the inline production quality control. In order to gain acceptance, the scanning time including subsequent data evaluation must be decreased significantly and adapted to the manufacturing cycle times. This presentation demonstrates the new technical set up, reconstruction results and the methods for high-speed volume data evaluation of a new fully automated high-speed CT scanner with cycle times below one minute for an object size of less than 15 cm. This will directly create new opportunities in design and construction of more complex objects. (author)

  1. Production of high quality water for oil sands application

    Energy Technology Data Exchange (ETDEWEB)

    Beaudette-Hodsman, C.; Macleod, B. [Pall Corp., Mississauga, ON (Canada); Venkatadri, R. [Pall Corp., East Hills, NY (United States)

    2008-10-15

    This paper described a pressurized microfiltration membrane system installed at an oil sands extraction site in Alberta. The system was designed to complement a reverse osmosis (RO) system installed at the site to produce the high quality feed water required by the system's boilers. Groundwater in the region exhibited moderate total suspended solids and high alkalinity and hardness levels, and the RO system required feed water with a silt density index of 3 or less. The conventional pretreatment system used at the site was slowing down production due to the severe fouling of the RO membranes. The new microfiltration system contained an automated PVDF hollow fiber microfiltration membrane system contained in a trailer. Suspended particles and bacteria were captured within the filter, and permeate was sent to the RO unit. Within 6 hours of being installed, the unit was producing water with SDI values in the range of 1.0 to 2.5. It was concluded that the microfiltration system performed reliably regardless of wide variations in feed water quality and flow rates. 3 refs., 1 tab., 8 figs.

  2. High Framingham risk score decreases quality of life in adults

    Directory of Open Access Journals (Sweden)

    Christian Yosaputra

    2010-04-01

    Full Text Available Cardiovascular disease (CVD risk factors, such as diabetes, hypertension, hypercholesterolemia, smoking, and obesity tend to occur together in the general population. Increasing prevalence of multiple CVD risk factors has been related to increased risk of death from coronary heart disease and stroke. Studies have suggested that people with several risk factors of CVD may have impaired health-related quality of life. The objective of this study was to assess the association of CVD risk factors with quality of life (QOL among adults aged 40 to 65 years. A cross-sectional study was conducted involving 220 subjects 40 - 65 years of age at a health center. The CVD risk factors were assessed using the Framingham risk score that is the standard instrument for assessment of the risk of a first cardiac event. The risk factors assessed were age, smoking, blood pressure, total cholesterol and high density lipoprotein cholesterol concentrations. QOL was assessed by means of the WHOQOL-BREF instrument that had been prevalidated. The results of the study showed that 28.2% of subjects were smokers, 56.4% had stage 1 hypertension, 42.8% high total cholesterol and 13.6% low HDL cholesterol. The high risk group amounted to 45.5% and 42.3% constitued an intermediate risk group. High CVD risk scores were significantly associated with a low QOL for all domains (physical, psychological, social and environment (p=0.000. Preventing or reducing the multiple CVD risk factors to improve QOL is necessary among adults.

  3. A response to Yu et al. "A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array", BMC Bioinformatics 2007, 8: 145.

    Science.gov (United States)

    Rueda, Oscar M; Diaz-Uriarte, Ramon

    2007-10-16

    Yu et al. (BMC Bioinformatics 2007,8: 145+) have recently compared the performance of several methods for the detection of genomic amplification and deletion breakpoints using data from high-density single nucleotide polymorphism arrays. One of the methods compared is our non-homogenous Hidden Markov Model approach. Our approach uses Markov Chain Monte Carlo for inference, but Yu et al. ran the sampler for a severely insufficient number of iterations for a Markov Chain Monte Carlo-based method. Moreover, they did not use the appropriate reference level for the non-altered state. We rerun the analysis in Yu et al. using appropriate settings for both the Markov Chain Monte Carlo iterations and the reference level. Additionally, to show how easy it is to obtain answers to additional specific questions, we have added a new analysis targeted specifically to the detection of breakpoints. The reanalysis shows that the performance of our method is comparable to that of the other methods analyzed. In addition, we can provide probabilities of a given spot being a breakpoint, something unique among the methods examined. Markov Chain Monte Carlo methods require using a sufficient number of iterations before they can be assumed to yield samples from the distribution of interest. Running our method with too small a number of iterations cannot be representative of its performance. Moreover, our analysis shows how our original approach can be easily adapted to answer specific additional questions (e.g., identify edges).

  4. Automated Theorem Proving in High-Quality Software Design

    Science.gov (United States)

    Schumann, Johann; Swanson, Keith (Technical Monitor)

    2001-01-01

    The amount and complexity of software developed during the last few years has increased tremendously. In particular, programs are being used more and more in embedded systems (from car-brakes to plant-control). Many of these applications are safety-relevant, i.e. a malfunction of hardware or software can cause severe damage or loss. Tremendous risks are typically present in the area of aviation, (nuclear) power plants or (chemical) plant control. Here, even small problems can lead to thousands of casualties and huge financial losses. Large financial risks also exist when computer systems are used in the area of telecommunication (telephone, electronic commerce) or space exploration. Computer applications in this area are not only subject to safety considerations, but also security issues are important. All these systems must be designed and developed to guarantee high quality with respect to safety and security. Even in an industrial setting which is (or at least should be) aware of the high requirements in Software Engineering, many incidents occur. For example, the Warshaw Airbus crash, was caused by an incomplete requirements specification. Uncontrolled reuse of an Ariane 4 software module was the reason for the Ariane 5 disaster. Some recent incidents in the telecommunication area, like illegal "cloning" of smart-cards of D2GSM handies, or the extraction of (secret) passwords from German T-online users show that also in this area serious flaws can happen. Due to the inherent complexity of computer systems, most authors claim that only a rigorous application of formal methods in all stages of the software life cycle can ensure high quality of the software and lead to real safe and secure systems. In this paper, we will have a look, in how far automated theorem proving can contribute to a more widespread application of formal methods and their tools, and what automated theorem provers (ATPs) must provide in order to be useful.

  5. A High-Density SNP Genetic Linkage Map and QTL Analysis of Growth-Related Traits in a Hybrid Family of Oysters (Crassostrea gigas × Crassostrea angulata Using Genotyping-by-Sequencing

    Directory of Open Access Journals (Sweden)

    Jinpeng Wang

    2016-05-01

    Full Text Available Oysters are among the most important species in global aquaculture. Crassostrea gigas, and its subspecies C. angulata, are the major cultured species. To determine the genetic basis of growth-related traits in oysters, we constructed a second-generation linkage map from 3367 single-nucleotide polymorphisms (SNPs based on genotyping-by-sequencing, genotyped from a C. gigas × C. angulata hybrid family. These 3367 SNPs were distributed on 1695 markers, which were assigned to 10 linkage groups. The genetic linkage map had a total length of 1084.3 cM, with an average of 0.8 cM between markers; it thus represents the densest genetic map constructed for oysters to date. Twenty-seven quantitative trait loci (QTL for five growth-related traits were detected. These QTL could explain 4.2–7.7% (mean = 5.4% of the phenotypic variation. In total, 50.8% of phenotypic variance for shell width, 7.7% for mass weight, and 34.1% for soft tissue weight were explained. The detected QTL were distributed among eight linkage groups, and more than half (16 were concentrated within narrow regions in their respective linkage groups. Thirty-eight annotated genes were identified within the QTL regions, two of which are key genes for carbohydrate metabolism. Other genes were found to participate in assembly and regulation of the actin cytoskeleton, signal transduction, and regulation of cell differentiation and development. The newly developed high-density genetic map, and the QTL and candidate genes identified provide a valuable genetic resource and a basis for marker-assisted selection for C. gigas and C. angulata.

  6. SUPLEMENTASI Lactobacillus acidophilus SNP-2 PADA TAPE DAN PENGARUHNYA PADA RELAWAN [Supplementation of Lactocbacillus acidophilus SNP-2 Into Tape and its Effect to the Volunteer

    Directory of Open Access Journals (Sweden)

    Endang S Rahayu1

    2004-08-01

    Full Text Available Functional food is defined as any potentially healthful food or food ingredient that may provide a health benefit beyond the traditional nutrients it contains. Many researches have been conducted on the health benefit of probiotic (life bacterial cells, one of the ingredient of functional foods. One of the potential bacteria used for probiotic agent and also involved in traditional fermented foods are lactic acid bacteria (LAB. Previous research showed that Lactobacillus acidophilus SNP-2 isolated from faecal material of healthy infant is resistant to acid and bile salt, and has an antagonistic effect against several enteric bacterial pathogens. The objective of this research was to study the effect of L. acidophilus SNP-2 as probiotic agent to the health benefits. These bacteria were supplemented into tape ketan (fermented sticky rice, the indigenous Indonesian fermented food. Tape ketan was chosen as the carrier of probiotic biomass based on the high population of LAB in this product, i.e., 1.3 x 108 CFU/g. Addition of L. acidophilus SNP-2 biomass prior to fermentation of tape ketan resulted in a higher total of LAB cells, i.e. 2.1 x 109 CFU/g compared to the amount of 1.5 x 108 CFU/g when the addition was done after fermentation. Consumption of tape ketan containing probiotic agent by the volunteers increased the population of lactobacilli (from 1.7x107 CFU/g to 9.9x107 CFU/g and decreased the population of enterobacteriacea (from 5.4x109 CFU/g to 4.4x108 in their faecal material. This phenomenon revealed that probiotic agent was able to colonize and inhibit the growth of enterobacteriaceae in the gastrointestinal tract. The result implied that tape ketan can be used as a carrier for probiotic agent and it can be categorized as functional food

  7. Recruiting and retaining high-quality teachers in rural areas.

    Science.gov (United States)

    Monk, David H

    2007-01-01

    In examining recruitment and retention of teachers in rural areas, David Monk begins by noting the numerous possible characteristics of rural communities--small size, sparse settlement, distance from population concentrations, and an economic reliance on agricultural industries that are increasingly using seasonal and immigrant workers to minimize labor costs. Many, though not all, rural areas, he says, are seriously impoverished. Classes in rural schools are relatively small, and teachers tend to report satisfaction with their work environments and relatively few problems with discipline. But teacher turnover is often high, and hiring can be difficult. Monk observes that rural schools have a below-average share of highly trained teachers. Compensation in rural schools tends to be low, perhaps because of a lower fiscal capacity in rural areas, thus complicating efforts to attract and retain teachers. Several student characteristics, including relatively large shares of students with special needs and with limited English skills and lower shares of students attending college, can also make it difficult to recruit and retain high-quality teachers. Other challenges include meeting the needs of highly mobile children of low-income migrant farm workers. With respect to public policy, Monk asserts a need to focus on a subcategory of what might be called hard-to-staff rural schools rather than to develop a blanket set of policies for all rural schools. In particular, he recommends a focus on such indicators as low teacher qualifications, teaching in fields far removed from the area of training, difficulty in hiring, high turnover, a lack of diversity among teachers in the school, and the presence of migrant farm workers' children. Successful efforts to stimulate economic growth in these areas would be highly beneficial. He also calls attention to the potential for modern telecommunication and computing technologies to offset some of the drawbacks associated with teaching

  8. Sodium nitroprusside (SNP) alleviates the oxidative stress induced ...

    African Journals Online (AJOL)

    Oxidative damage is often induced by abiotic stress, nitric oxide (NO) is considered as a functional molecule in modulating antioxidant metabolism of plants. In the present study, effects of sodium nitroprusside (SNP), a NO donor, on the phenotype, antioxidant capacity and chloroplast ultrastructure of cucumber leaves were ...

  9. Genomic scans for selective sweeps using SNP data

    DEFF Research Database (Denmark)

    Nielsen, Rasmus; Williamson, Scott; Kim, Yuseob

    2005-01-01

    of the selection coefficient. To illustrate the method, we apply our approach to data from the Seattle SNP project and to Chromosome 2 data from the HapMap project. In Chromosome 2, the most extreme signal is found in the lactase gene, which previously has been shown to be undergoing positive selection. Evidence...

  10. Phenylethynylpyrene excimer forming hybridization probes for fluorescence SNP detection

    DEFF Research Database (Denmark)

    Prokhorenko, Igor A.; Astakhova, Irina V.; Momynaliev, Kuvat T.

    2009-01-01

    Excimer formation is a unique feature of some fluorescent dyes (e.g., pyrene) which can be used for probing the proximity of biomolecules. Pyrene excimer fluorescence has previously been used for homogeneous detection of single nucleotide polymorphism (SNP) on DNA. 1-Phenylethynylpyrene (1-1-PEPy...

  11. (SNP) markers for the Chinese black sleeper, Bostrychus sinensis

    African Journals Online (AJOL)

    ajl yemi

    2011-04-25

    Apr 25, 2011 ... Polynesia, north to Japan and south to Australia (Kottelat et al., 1993; Masuda ... developed the first set of SNP markers for Chinese black sleeper which can ... Then, the. 44 primer pairs were designed based on all the cloning.

  12. Do you really know where this SNP goes?

    Science.gov (United States)

    The release of build 10.2 of the swine genome was a marked improvement over previous builds and has proven extremely useful. However, as most know, there are regions of the genome that this particular build does not accurately represent. For instance, nearly 25% of the 62,162 SNP on the Illumina Por...

  13. SNP based heritability estimation using a Bayesian approach

    DEFF Research Database (Denmark)

    Krag, Kristian; Janss, Luc; Mahdi Shariati, Mohammad

    2013-01-01

    . Differences in family structure were in general not found to influence the estimation of the heritability. For the sample sizes used in this study, a 10-fold increase of SNP density did not improve precision estimates compared with set-ups with a less dense distribution of SNPs. The methods used in this study...

  14. Genome wide in silico SNP-tumor association analysis

    International Nuclear Information System (INIS)

    Qiu, Ping; Wang, Luquan; Kostich, Mitch; Ding, Wei; Simon, Jason S; Greene, Jonathan R

    2004-01-01

    Carcinogenesis occurs, at least in part, due to the accumulation of mutations in critical genes that control the mechanisms of cell proliferation, differentiation and death. Publicly accessible databases contain millions of expressed sequence tag (EST) and single nucleotide polymorphism (SNP) records, which have the potential to assist in the identification of SNPs overrepresented in tumor tissue. An in silico SNP-tumor association study was performed utilizing tissue library and SNP information available in NCBI's dbEST (release 092002) and dbSNP (build 106). A total of 4865 SNPs were identified which were present at higher allele frequencies in tumor compared to normal tissues. A subset of 327 (6.7%) SNPs induce amino acid changes to the protein coding sequences. This approach identified several SNPs which have been previously associated with carcinogenesis, as well as a number of SNPs that now warrant further investigation This novel in silico approach can assist in prioritization of genes and SNPs in the effort to elucidate the genetic mechanisms underlying the development of cancer

  15. SNP typing on the NanoChip electronic microarray

    DEFF Research Database (Denmark)

    Børsting, Claus; Sanchez Sanchez, Juan Jose; Morling, Niels

    2005-01-01

    We describe a single nucleotide polymorphism (SNP) typing protocol developed for the NanoChip electronic microarray. The NanoChip array consists of 100 electrodes covered by a thin hydrogel layer containing streptavidin. An electric currency can be applied to one, several, or all electrodes...

  16. In silico characterization of functional SNP within the oestrogen ...

    Indian Academy of Sciences (India)

    MAHA REBAÕ

    (polyphen-2, SNAP), as well as by the ESEfinder program, and one nonsense nsSNP was found. For noncoding ... mon type of genetic variation in the human genome that are ...... polymorphisms in type 2 diabetes mellitus and in android type.

  17. In silico characterization of functional SNP within the oestrogen ...

    Indian Academy of Sciences (India)

    MAHA REBAÕ

    found that one SNP in 5 UTR may potentially change protein expression level, nine SNPs were found to affect miRNA binding site and 28 SNPs might affect ..... Riancho et al. 2010), breast cancer (Tapper et al. 2008; Ding et al. .... in postmenopausal women: associations with common estrogen receptor alpha polymorphic ...

  18. Agronomic and seed quality traits dissected by genome-wide association mapping in Brassica napus

    Directory of Open Access Journals (Sweden)

    Niklas eKörber

    2016-03-01

    Full Text Available In Brassica napus breeding, traits related to commercial success are of highest importance for plant breeders. However, such traits can only be assessed in an advanced developmental stage. % as well as require high experimental effort due to their quantitative inheritance and the importance of genotype*environment interaction. Molecular markers genetically linked to such traits have the potential to accelerate the breeding process of B. napus by marker-assisted selection. Therefore, the objectives of this study were to identify (i genome regions associated with the examined agronomic and seed quality traits, (ii the interrelationship of population structure and the detected associations, and (iii candidate genes for the revealed associations. The diversity set used in this study consisted of 405 Brassica napus inbred lines which were genotyped using a 6K single nucleotide polymorphism (SNP array and phenotyped for agronomic and seed quality traits in field trials. In a genome-wide association study, we detected a total of 112 associations between SNPs and the seed quality traits as well as 46 SNP-trait associations for the agronomic traits with a P-value 100 and a sequence identity of > 70 % to A. thaliana or B. rapa could be found for the agronomic SNP-trait associations and 187 hits of potential candidate genes for the seed quality SNP-trait associations.

  19. Routine quality control of high dose rate brachytherapy equipment

    International Nuclear Information System (INIS)

    Guzman Calcina, Carmen S.; Almeida, Adelaide de; Rocha, Jose R. Oliveira

    2001-01-01

    A Quality Assurance program should be installed also for High Dose Rate brachytherapy, in the order to achieve a correct dose administration to the patient and for the safety to those involved directly with the treatment. The work presented here has the following purposes: Analyze the types of equipment tests presented by the official protocols (TG40, TG56 e ARCAL XXX), evaluate the brachytherapy routine tests of protocols from various national and international radiotherapy services and compare the latter with those presented in the official protocols. As a result, we conclude the following: TG56 presents a higher number of tests when compared to the other official protocols and most of the tests presented by the analyzed services are present in TG56. A suggestion for a basic protocol is presented, emphasizing the periodicity and tolerance level of each of the tests. (author)

  20. High quality diesel fuels by VO-LSGO hydrotreatment

    Energy Technology Data Exchange (ETDEWEB)

    Stanica-Ezeanu, Dorin; Juganaru, Traian [Petroleum and Gas Univ. of Ploiesti (Romania)

    2013-06-01

    The aim of the paper is to obtain a high quality Diesel fuel by hydro-deoxigenation of vegetable oils (VO) mixed with a low sulfur gasoil (LSGO). The process is possible by using a bi-functional catalyst Ni-Mo supported by an activated Al{sub 2}O{sub 3} containing 2% Ultrastable Y-zeolite. The experimental conditions were: T =340 - 380 C, Pressure = 50 bar, LHSV = 1,5 h{sup -1}, H{sub 2}/Feed ratio = 15 mole H{sub 2} /mole liquid feed. The liquid product was separated in two fractions: a light distillate (similar to gasoline) and a heavy distillate (boiling point > 200 C) with very good characteristics for Diesel engines. The reaction chemistry is very complex, but the de-oxygenation process is decisive for the chemical structure of hydrocarbons from final product. Finally, a schema for the reaction mechanism is proposed. (orig.)

  1. Supercapacitors based on high-quality graphene scrolls

    Science.gov (United States)

    Zeng, Fanyan; Kuang, Yafei; Liu, Gaoqin; Liu, Rui; Huang, Zhongyuan; Fu, Chaopeng; Zhou, Haihui

    2012-06-01

    High-quality graphene scrolls (GSS) with a unique scrolled topography are designed using a microexplosion method. Their capacitance properties are investigated by cyclic voltammetry, galvanostatic charge-discharge and electrical impedance spectroscopy. Compared with the specific capacity of 110 F g-1 for graphene sheets, a remarkable capacity of 162.2 F g-1 is obtained at the current density of 1.0 A g-1 in 6 M KOH aqueous solution owing to the unique scrolled structure of GSS. The capacity value is increased by about 50% only because of the topological change of graphene sheets. Meanwhile, GSS exhibit excellent long-term cycling stability along with 96.8% retained after 1000 cycles at 1.0 A g-1. These encouraging results indicate that GSS based on the topological structure of graphene sheets are a kind of promising material for supercapacitors.

  2. A roadmap to high quality chemically prepared graphene

    Energy Technology Data Exchange (ETDEWEB)

    Gengler, Regis Y N; Spyrou, Konstantinos; Rudolf, Petra, E-mail: r.gengler@rug.n, E-mail: p.rudolf@rug.n [Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747AG Groningen (Netherlands)

    2010-09-22

    Graphene was discovered half a decade ago and proved the existence of a two-dimensional system which becomes stable as a result of 3D corrugation. It appeared very quickly that this exceptional material had truly outstanding electronic, mechanical, thermal and optical properties. Consequently a broad range of applications appeared, as the graphene science speedily moved forward. Since then, a lot of effort has been devoted not only to the study of graphene but also to its fabrication. Here we review the chemical approaches to graphene production, their advantages as well as their downsides. Our aim is to draw a roadmap of today's most reliable path to high quality graphene via chemical preparation.

  3. High quality factor HTS Josephson junctions on low loss substrates

    Energy Technology Data Exchange (ETDEWEB)

    Stornaiuolo, D; Longobardi, L; Massarotti, D; Barone, A; Tafuri, F [CNR-SPIN Napoli, Complesso Universitario di Monte Sant' Angelo, via Cinthia, 80126 Napoli (Italy); Papari, G; Carillo, F [NEST, CNR-NANO and Scuola Normale Superiore, Piazza San Silvestro 12, 56127 Pisa (Italy); Cennamo, N [Dipartimento Ingegneria dell' Informazione, Seconda Universita degli Studi di Napoli, via Roma 29, 81031 Aversa (Italy)

    2011-04-15

    We have extended the off-axis biepitaxial technique to produce YBCO grain boundary junctions on low loss substrates. Excellent transport properties have been reproducibly found, with remarkable values of the quality factor I{sub c}R{sub n} (with I{sub c} the critical current and R{sub n} the normal state resistance) above 10 mV, far higher than the values commonly reported in the literature for high temperature superconductor (HTS) based Josephson junctions. The outcomes are consistent with a picture of a more uniform grain boundary region along the current path. This work supports a possible implementation of grain boundary junctions for various applications including terahertz sensors and HTS quantum circuits in the presence of microwaves.

  4. A roadmap to high quality chemically prepared graphene

    International Nuclear Information System (INIS)

    Gengler, Regis Y N; Spyrou, Konstantinos; Rudolf, Petra

    2010-01-01

    Graphene was discovered half a decade ago and proved the existence of a two-dimensional system which becomes stable as a result of 3D corrugation. It appeared very quickly that this exceptional material had truly outstanding electronic, mechanical, thermal and optical properties. Consequently a broad range of applications appeared, as the graphene science speedily moved forward. Since then, a lot of effort has been devoted not only to the study of graphene but also to its fabrication. Here we review the chemical approaches to graphene production, their advantages as well as their downsides. Our aim is to draw a roadmap of today's most reliable path to high quality graphene via chemical preparation.

  5. CHOREOGRAPHIC METHODS FOR CREATING NOVEL, HIGH QUALITY DANCE

    Directory of Open Access Journals (Sweden)

    David Kirsh

    2016-02-01

    Full Text Available We undertook a detailed ethnographic study of the dance creation process of a noted choreographer and his distinguished troupe. All choreographer dancer interactions were videoed, the choreographer and dancers were interviewed extensively each day, as well as other observations and tests performed. The choreographer used three main methods to produce high quality and novel content: showing, making-on, and tasking. We present, analyze and evaluate these methods, and show how these approaches allow the choreographer to increase the creative output of the dancers and him. His methods, although designed for dance, apply more generally to other creative endeavors, especially where brainstorming is involved, and where the creative process is distributed over many individuals. His approach is also a case study in multi-modal direction, owing to the range of mechanisms he uses to communicate and direct.

  6. Biotransformation of Organic Waste into High Quality Fertilizer

    DEFF Research Database (Denmark)

    Bryndum, Sofie

    Agriculture faces several challenges of future provision of nutrients such as limited P reserves and increasing prices of synthetic fertilizers and recycling of nutrients from organic waste can be an important strategy for the long-term sustainability of the agricultural systems. Organically...... and S, is often low; and (3) the unbalanced composition of nutrients rarely matches crop demands. Therefore the objective of this project was to investigate the potential for (1) recycling nutrients from agro-industrial wastes and (2) compost biotransformation into high-quality organic fertilizers...... other uses into fertilizer use would be unlikely. An estimated ~50 % of the total organic waste pool, primarily consisting of animal manure and waste from the processing of sugar cane, coffee, oil palm and oranges, is currently being re-used as “fertilizers”, meaning it is eventually returned...

  7. Calmodulin-like protein 3 is an estrogen receptor alpha coregulator for gene expression and drug response in a SNP, estrogen, and SERM-dependent fashion.

    Science.gov (United States)

    Qin, Sisi; Ingle, James N; Liu, Mohan; Yu, Jia; Wickerham, D Lawrence; Kubo, Michiaki; Weinshilboum, Richard M; Wang, Liewei

    2017-08-18

    We previously performed a case-control genome-wide association study in women treated with selective estrogen receptor modulators (SERMs) for breast cancer prevention and identified single nucleotide polymorphisms (SNPs) in ZNF423 as potential biomarkers for response to SERM therapy. The ZNF423rs9940645 SNP, which is approximately 200 bp away from the estrogen response elements, resulted in the SNP, estrogen, and SERM-dependent regulation of ZNF423 expression and, "downstream", that of BRCA1. Electrophoretic mobility shift assay-mass spectrometry was performed to identify proteins binding to the ZNF423 SNP and coordinating with estrogen receptor alpha (ERα). Clustered, regularly interspaced short palindromic repeats (CRISPR)/Cas9 genome editing was applied to generate ZR75-1 breast cancer cells with different ZNF423 SNP genotypes. Both cultured cells and mouse xenograft models with different ZNF423 SNP genotypes were used to study the cellular responses to SERMs and poly(ADP-ribose) polymerase (PARP) inhibitors. We identified calmodulin-like protein 3 (CALML3) as a key sensor of this SNP and a coregulator of ERα, which contributes to differential gene transcription regulation in an estrogen and SERM-dependent fashion. Furthermore, using CRISPR/Cas9-engineered ZR75-1 breast cancer cells with different ZNF423 SNP genotypes, striking differences in cellular responses to SERMs and PARP inhibitors, alone or in combination, were observed not only in cells but also in a mouse xenograft model. Our results have demonstrated the mechanism by which the ZNF423 rs9940645 SNP might regulate gene expression and drug response as well as its potential role in achieving more highly individualized breast cancer therapy.

  8. Application of high resolution SNP arrays in patients with congenital ...

    Indian Academy of Sciences (India)

    TING-YING LEI

    a serine/threonine phosphatase involved in the modulation of glycogen synthesis in the ... diabetes and maturity-onset diabetes of the young (MODY). (Dunn et al. 2006) .... Acknowledgement. We thank the families for participating in this study.

  9. RESEARCH ARTICLE Application of high resolution SNP arrays in ...

    Indian Academy of Sciences (India)

    User

    found that 4 of them were inherited from a healthy parent and were considered to be .... retardation, skeletal problems and craniofacial dysmorphism; congenital cleft lip and palate and .... The authors declare no competing financial interests.

  10. Introgression Browser: High throughput whole-genome SNP visualization

    NARCIS (Netherlands)

    Aflitos, S.A.; Sanchez Perez, G.F.; Ridder, de D.; Fransz, P.; Schranz, M.E.; Jong, de J.H.S.G.M.; Peters, S.A.

    2015-01-01

    Breeding by introgressive hybridization is a pivotal strategy to broaden the genetic basis of crops. Usually, the desired traits are monitored in consecutive crossing generations by marker-assisted selection, but their analyses fail in chromosome regions where crossover recombinants are rare or not

  11. Introgression browser: high-throughput whole-genome SNP visualization

    NARCIS (Netherlands)

    Alves Aflitos, S.; Sanchez-Perez, G.; de Ridder, D.; Fransz, P.; Schranz, M.E.; de Jong, H.; Peters, S.A.

    2015-01-01

    Breeding by introgressive hybridization is a pivotal strategy to broaden the genetic basis of crops. Usually, the desired traits are monitored in consecutive crossing generations by marker-assisted selection, but their analyses fail in chromosome regions where crossover recombinants are rare or not

  12. High quality protein microarray using in situ protein purification

    Directory of Open Access Journals (Sweden)

    Fleischmann Robert D

    2009-08-01

    Full Text Available Abstract Background In the postgenomic era, high throughput protein expression and protein microarray technologies have progressed markedly permitting screening of therapeutic reagents and discovery of novel protein functions. Hexa-histidine is one of the most commonly used fusion tags for protein expression due to its small size and convenient purification via immobilized metal ion affinity chromatography (IMAC. This purification process has been adapted to the protein microarray format, but the quality of in situ His-tagged protein purification on slides has not been systematically evaluated. We established methods to determine the level of purification of such proteins on metal chelate-modified slide surfaces. Optimized in situ purification of His-tagged recombinant proteins has the potential to become the new gold standard for cost-effective generation of high-quality and high-density protein microarrays. Results Two slide surfaces were examined, chelated Cu2+ slides suspended on a polyethylene glycol (PEG coating and chelated Ni2+ slides immobilized on a support without PEG coating. Using PEG-coated chelated Cu2+ slides, consistently higher purities of recombinant proteins were measured. An optimized wash buffer (PBST composed of 10 mM phosphate buffer, 2.7 mM KCl, 140 mM NaCl and 0.05% Tween 20, pH 7.4, further improved protein purity levels. Using Escherichia coli cell lysates expressing 90 recombinant Streptococcus pneumoniae proteins, 73 proteins were successfully immobilized, and 66 proteins were in situ purified with greater than 90% purity. We identified several antigens among the in situ-purified proteins via assays with anti-S. pneumoniae rabbit antibodies and a human patient antiserum, as a demonstration project of large scale microarray-based immunoproteomics profiling. The methodology is compatible with higher throughput formats of in vivo protein expression, eliminates the need for resin-based purification and circumvents

  13. The structure of high-quality aluminium cast iron

    Directory of Open Access Journals (Sweden)

    D. Kopyciński

    2012-01-01

    Full Text Available In this study presents the analyse of aluminium iron cast structure (as-cast condition which are used in high temperature. While producing the casts of aluminium iron major influence has been preserve the structure of technological process parameters. The addition to Fe-C-Al alloy V, Ti, Cr leads to the improvement of functional and mechanical cast qualities. In this study, a method was investigated to eliminate the presence of undesirable Al4C3 phases in a aluminium cast iron structure and thus improve the production process. V and Ti additions in aluminium cast iron allows to development of FeAl - VC or TiC alloys. In particular, V or Ti contents above 5 wt.% were found to totally eliminate the presence of Al4C3. In addition, preliminary work indicates that the alloy with the FeAl - VC or TiC structure reveals high oxidation resistance. The introduction of 5 wt.% chromium to aluminium cast iron strengthened Al4C3 precipitate. Thus, the resultant alloy can be considered an intermetallic FeAl matrix strengthened by VC and TiC or modified Al4C3 reinforcements.

  14. High-Quality Seismic Observations of Sonic Booms

    Science.gov (United States)

    Wurman, Gilead; Haering, Edward A., Jr.; Price, Michael J.

    2011-01-01

    The SonicBREWS project (Sonic Boom Resistant Earthquake Warning Systems) is a collaborative effort between Seismic Warning Systems, Inc. and NASA Dryden Flight Research Center. This project aims to evaluate the effects of sonic booms on Earthquake Warning Systems in order to prevent such systems from experiencing false alarms due to sonic booms. The airspace above the Antelope Valley, California includes the High Altitude Supersonic Corridor and the Black Mountain Supersonic Corridor. These corridors are among the few places in the US where supersonic flight is permitted, and sonic booms are commonplace in the Antelope Valley. One result of this project is a rich dataset of high-quality accelerometer records of sonic booms which can shed light on the interaction between these atmospheric phenomena and the solid earth. Nearly 100 sonic booms were recorded with low-noise triaxial MEMS accelerometers recording 1000 samples per second. The sonic booms had peak overpressures ranging up to approximately 10 psf and were recorded in three flight series in 2010 and 2011. Each boom was recorded with up to four accelerometers in various array configurations up to 100 meter baseline lengths, both in the built environment and the free field. All sonic booms were also recorded by nearby microphones. We present the results of the project in terms of the potential for sonic-boom-induced false alarms in Earthquake Warning Systems, and highlight some of the interesting features of the dataset.

  15. High-quality remote interactive imaging in the operating theatre

    Science.gov (United States)

    Grimstead, Ian J.; Avis, Nick J.; Evans, Peter L.; Bocca, Alan

    2009-02-01

    We present a high-quality display system that enables the remote access within an operating theatre of high-end medical imaging and surgical planning software. Currently, surgeons often use printouts from such software for reference during surgery; our system enables surgeons to access and review patient data in a sterile environment, viewing real-time renderings of MRI & CT data as required. Once calibrated, our system displays shades of grey in Operating Room lighting conditions (removing any gamma correction artefacts). Our system does not require any expensive display hardware, is unobtrusive to the remote workstation and works with any application without requiring additional software licenses. To extend the native 256 levels of grey supported by a standard LCD monitor, we have used the concept of "PseudoGrey" where slightly off-white shades of grey are used to extend the intensity range from 256 to 1,785 shades of grey. Remote access is facilitated by a customized version of UltraVNC, which corrects remote shades of grey for display in the Operating Room. The system is successfully deployed at Morriston Hospital, Swansea, UK, and is in daily use during Maxillofacial surgery. More formal user trials and quantitative assessments are being planned for the future.

  16. Blueprint for action: steps toward a high-quality, high-value maternity care system.

    Science.gov (United States)

    Angood, Peter B; Armstrong, Elizabeth Mitchell; Ashton, Diane; Burstin, Helen; Corry, Maureen P; Delbanco, Suzanne F; Fildes, Barbara; Fox, Daniel M; Gluck, Paul A; Gullo, Sue Leavitt; Howes, Joanne; Jolivet, R Rima; Laube, Douglas W; Lynne, Donna; Main, Elliott; Markus, Anne Rossier; Mayberry, Linda; Mitchell, Lynn V; Ness, Debra L; Nuzum, Rachel; Quinlan, Jeffrey D; Sakala, Carol; Salganicoff, Alina

    2010-01-01

    Childbirth Connection hosted a 90th Anniversary national policy symposium, Transforming Maternity Care: A High Value Proposition, on April 3, 2009, in Washington, DC. Over 100 leaders from across the range of stakeholder perspectives were actively engaged in the symposium work to improve the quality and value of U.S. maternity care through broad system improvement. A multi-disciplinary symposium steering committee guided the strategy from its inception and contributed to every phase of the project. The "Blueprint for Action: Steps Toward a High Quality, High Value Maternity Care System", issued by the Transforming Maternity Care Symposium Steering Committee, answers the fundamental question, "Who needs to do what, to, for, and with whom to improve the quality of maternity care over the next five years?" Five stakeholder workgroups collaborated to propose actionable strategies in 11 critical focus areas for moving expeditiously toward the realization of the long term "2020 Vision for a High Quality, High Value Maternity Care System", also published in this issue. Following the symposium these workgroup reports and recommendations were synthesized into the current blueprint. For each critical focus area, the "Blueprint for Action" presents a brief problem statement, a set of system goals for improvement in that area, and major recommendations with proposed action steps to achieve them. This process created a clear sightline to action that if enacted could improve the structure, process, experiences of care, and outcomes of the maternity care system in ways that when anchored in the culture can indeed transform maternity care. Copyright 2010 Jacobs Institute of Women

  17. Stress and sleep quality in high school brazilian adolescents

    Directory of Open Access Journals (Sweden)

    Gema Mesquita

    2010-06-01

    Full Text Available OBJECTIVE: The objective of the present study is to analyze the effect of stress on sleep quality in a group of adolescents. METHOD: Two high schools in Alfenas, southern Minas Gerais State, Brazil, were chosen to participate in the study. The sample consisted of both genders (n=160 with 65.63% females. The age range of participants was 15 to18 years. The Pittsburgh Sleep Quality Index (PSQI was applied for collection of data to quantify sleep quality. The Lipp Inventory of Stress Symptoms that objectively identifies symptoms of stress was applied. RESULTS: It was observed that 23.53% of stressed students and 45.33% of unstressed ones sleep well; 76.47% of stressed pupils and 54.67% of those unstressed do not sleep well. With regard to school performance, a mean of 0.65 was found for stressed students and 0.60 for those without stress, Mann-Whitney (p=0.0596. CONCLUSION: Stress contributed to raising the percentage of poor sleepers, as ell as increasing ean school performance.OBJETIVO: O objetivo do presente estudo foi analisar a influência do stress sobre a qualidade do sono em um grupo de adolescentes. MÉTODO: Foram escolhidas duas instituições educacionais do ensino médio, na cidade de Alfenas, sul de Minas Gerais, Brasil. A amostra foi composta por ambos os sexos (n=160, com 65,63% do sexo feminino. A faixa etária dos participantes foi de 15 a 18 anos. Para a coleta de dados aplicou-se: Índice de Qualidade de Sono de Pittsburgh (IQSP utilizado para quantificar a qualidade do sono; o Inventário de Sintomas de Stress para Adultos de Lipp (ISSL que identifica de modo objetivo a sintomatologia de stress foi aplicado. RESULTADOS: Observou-se que 23,53% dos estressados dormem bem e 45,33% dos não estressados dormem bem; 76,47% dos estressados não dormem bem e 54,67% dos não estressados não dormem bem. Quanto ao rendimento escolar têm-se as médias 0,65 para os alunos estressados e 0,60 para aqueles que não sofrem de stress, Mann

  18. High-quality endoscope reprocessing decreases endoscope contamination.

    Science.gov (United States)

    Decristoforo, P; Kaltseis, J; Fritz, A; Edlinger, M; Posch, W; Wilflingseder, D; Lass-Flörl, C; Orth-Höller, D

    2018-02-24

    Several outbreaks of severe infections due to contamination of gastrointestinal (GI) endoscopes, mainly duodenoscopes, have been described. The rate of microbial endoscope contamination varies dramatically in literature. The aim of this multicentre prospective study was to evaluate the hygiene quality of endoscopes and automated endoscope reprocessors (AERs) in Tyrol/Austria. In 2015 and 2016, a total of 463 GI endoscopes and 105 AERs from 29 endoscopy centres were analysed by a routine (R) and a combined routine and advanced (CRA) sampling procedure and investigated for microbial contamination by culture-based and molecular-based analyses. The contamination rate of GI endoscopes was 1.3%-4.6% according to the national guideline, suggesting that 1.3-4.6 patients out of 100 could have had contacts with hygiene-relevant microorganisms through an endoscopic intervention. Comparison of R and CRA sampling showed 1.8% of R versus 4.6% of CRA failing the acceptance criteria in phase I and 1.3% of R versus 3.0% of CRA samples failing in phase II. The most commonly identified indicator organism was Pseudomonas spp., mainly Pseudomonas oleovorans. None of the tested viruses were detected in 40 samples. While AERs in phase I failed (n = 9, 17.6%) mainly due to technical faults, phase II revealed lapses (n = 6, 11.5%) only on account of microbial contamination of the last rinsing water, mainly with Pseudomonas spp. In the present study the contamination rate of endoscopes was low compared with results from other European countries, possibly due to the high quality of endoscope reprocessing, drying and storage. Copyright © 2018 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

  19. 76 FR 45397 - Export Inspection and Weighing Waiver for High Quality Specialty Grain Transported in Containers

    Science.gov (United States)

    2011-07-29

    ...-AB18 Export Inspection and Weighing Waiver for High Quality Specialty Grain Transported in Containers... permanent a waiver due to expire on July 31, 2012, for high quality specialty grain exported in containers... of high quality specialty grain exported in containers are small entities that up until recently...

  20. Genomic variation in myeloma: design, content, and initial application of the Bank On A Cure SNP Panel to detect associations with progression-free survival

    Directory of Open Access Journals (Sweden)

    Fang Gang

    2008-09-01

    Full Text Available Abstract Background We have engaged in an international program designated the Bank On A Cure, which has established DNA banks from multiple cooperative and institutional clinical trials, and a platform for examining the association of genetic variations with disease risk and outcomes in multiple myeloma. We describe the development and content of a novel custom SNP panel that contains 3404 SNPs in 983 genes, representing cellular functions and pathways that may influence disease severity at diagnosis, toxicity, progression or other treatment outcomes. A systematic search of national databases was used to identify non-synonymous coding SNPs and SNPs within transcriptional regulatory regions. To explore SNP associations with PFS we compared SNP profiles of short term (less than 1 year, n = 70 versus long term progression-free survivors (greater than 3 years, n = 73 in two phase III clinical trials. Results Quality controls were established, demonstrating an accurate and robust screening panel for genetic variations, and some initial racial comparisons of allelic variation were done. A variety of analytical approaches, including machine learning tools for data mining and recursive partitioning analyses, demonstrated predictive value of the SNP panel in survival. While the entire SNP panel showed genotype predictive association with PFS, some SNP subsets were identified within drug response, cellular signaling and cell cycle genes. Conclusion A targeted gene approach was undertaken to develop an SNP panel that can test for associations with clinical outcomes in myeloma. The initial analysis provided some predictive power, demonstrating that genetic variations in the myeloma patient population may influence PFS.

  1. SNP-finding in pig mitochondrial ESTs

    DEFF Research Database (Denmark)

    Scheibye-Alsing, Karsten; Cirera Salicio, Susanna; Gilchrist, M.J.

    2008-01-01

    The Sino-Danish pig genome project produced 685 851 ESTs (Gorodkin et al. 2007), of which 41 499 originated from the mitochondrial genome. In this study, the mitochondrial ESTs were assembled, and 374 putative SNPs were found. Chromatograms for the ESTs containing SNPs were manually inspected, an......, and 112 total (52 non-synonymous) SNPs were found to be of high confidence (five of them are close to disease-causing SNPs in humans). Nine of the high-confidence SNPs were tested experimentally, and eight were confirmed. The SNPs can be accessed online at http://pigest.ku.dk/more.mito...

  2. Genome-Wide SNP Discovery and Analysis of Genetic Diversity in Farmed Sika Deer (Cervus nippon in Northeast China Using Double-Digest Restriction Site-Associated DNA Sequencing

    Directory of Open Access Journals (Sweden)

    Hengxing Ba

    2017-09-01

    Full Text Available Sika deer are an economically valuable species owing to their use in traditional Chinese medicine, particularly their velvet antlers. Sika deer in northeast China are mostly farmed in enclosure. Therefore, genetic management of farmed sika deer would benefit from detailed knowledge of their genetic diversity. In this study, we generated over 1.45 billion high-quality paired-end reads (288 Gbp across 42 unrelated individuals using double-digest restriction site-associated DNA sequencing (ddRAD-seq. A total of 96,188 (29.63% putative biallelic SNP loci were identified with an average sequencing depth of 23×. Based on the analysis, we found that the majority of the loci had a deficit of heterozygotes (FIS >0 and low values of Hobs, which could be due to inbreeding and Wahlund effects. We also developed a collection of high-quality SNP probes that will likely be useful in a variety of applications in genotyping for cervid species in the future.

  3. Genome-Wide SNP Discovery and Analysis of Genetic Diversity in Farmed Sika Deer (Cervus nippon) in Northeast China Using Double-Digest Restriction Site-Associated DNA Sequencing.

    Science.gov (United States)

    Ba, Hengxing; Jia, Boyin; Wang, Guiwu; Yang, Yifeng; Kedem, Gilead; Li, Chunyi

    2017-09-07

    Sika deer are an economically valuable species owing to their use in traditional Chinese medicine, particularly their velvet antlers. Sika deer in northeast China are mostly farmed in enclosure. Therefore, genetic management of farmed sika deer would benefit from detailed knowledge of their genetic diversity. In this study, we generated over 1.45 billion high-quality paired-end reads (288 Gbp) across 42 unrelated individuals using double-digest restriction site-associated DNA sequencing (ddRAD-seq). A total of 96,188 (29.63%) putative biallelic SNP loci were identified with an average sequencing depth of 23×. Based on the analysis, we found that the majority of the loci had a deficit of heterozygotes (F IS >0) and low values of H obs , which could be due to inbreeding and Wahlund effects. We also developed a collection of high-quality SNP probes that will likely be useful in a variety of applications in genotyping for cervid species in the future. Copyright © 2017 Ba et al.

  4. Identification, Characterization, and Mapping of a Novel SNP Associated with Body Color Transparency in Juvenile Red Sea Bream (Pagrus major).

    Science.gov (United States)

    Sawayama, Eitaro; Noguchi, Daiki; Nakayama, Kei; Takagi, Motohiro

    2018-03-23

    We previously reported a body color deformity in juvenile red sea bream, which shows transparency in the juvenile stage because of delayed chromatophore development compared with normal individuals, and this finding suggested a genetic cause based on parentage assessments. To conduct marker-assisted selection to eliminate broodstock inheriting the causative gene, developing DNA markers associated with the phenotype was needed. We first conducted SNP mining based on AFLP analysis using bulked-DNA from normal and transparent individuals. One SNP was identified from a transparent-specific AFLP fragment, which significantly associated with transparent individuals. Two alleles (A/G) were observed in this locus, and the genotype G/G was dominantly observed in the transparent groups (97.1%) collected from several production lots produced from different broodstock populations. A few normal individuals inherited the G/G genotype (5.0%), but the A/A and A/G genotypes were dominantly observed in the normal groups. The homologs region of the SNP was searched using a medaka genome database, and intron 12 of the Nell2a gene (located on chromosome 6 of the medaka genome) was highly matched. We also mapped the red sea bream Nell2a gene on the previously developed linkage maps, and this gene was mapped on a male linkage group, LG4-M. The newly found SNP was useful in eliminating broodstock possessing the causative gene of the body color transparency observed in juvenile stage of red sea bream.

  5. Characterizing associations and SNP-environment interactions for GWAS-identified prostate cancer risk markers--results from BPC3.

    Directory of Open Access Journals (Sweden)

    Sara Lindstrom

    2011-02-01

    Full Text Available Genome-wide association studies (GWAS have identified multiple single nucleotide polymorphisms (SNPs associated with prostate cancer risk. However, whether these associations can be consistently replicated, vary with disease aggressiveness (tumor stage and grade and/or interact with non-genetic potential risk factors or other SNPs is unknown. We therefore genotyped 39 SNPs from regions identified by several prostate cancer GWAS in 10,501 prostate cancer cases and 10,831 controls from the NCI Breast and Prostate Cancer Cohort Consortium (BPC3. We replicated 36 out of 39 SNPs (P-values ranging from 0.01 to 10⁻²⁸. Two SNPs located near KLK3 associated with PSA levels showed differential association with Gleason grade (rs2735839, P = 0.0001 and rs266849, P = 0.0004; case-only test, where the alleles associated with decreasing PSA levels were inversely associated with low-grade (as defined by Gleason grade < 8 tumors but positively associated with high-grade tumors. No other SNP showed differential associations according to disease stage or grade. We observed no effect modification by SNP for association with age at diagnosis, family history of prostate cancer, diabetes, BMI, height, smoking or alcohol intake. Moreover, we found no evidence of pair-wise SNP-SNP interactions. While these SNPs represent new independent risk factors for prostate cancer, we saw little evidence for effect modification by other SNPs or by the environmental factors examined.

  6. [Genetic diversity analysis of Andrographis paniculata in China based on SRAP and SNP].

    Science.gov (United States)

    Chen, Rong; Wang, Xiao-Yun; Song, Yu-Ning; Zhu, Yun-feng; Wang, Peng-liang; Li, Min; Zhong, Guo-Yue

    2014-12-01

    In order to reveal genetic diversity of domestic Andrographis paniculata and its impact on quality, genetic backgrounds of 103 samples from 7 provinces in China were analyzed using SRAP marker and SNP marker. Genetic structures of the A. paniculata populations were estimated with Powermarker V 3.25 and Mega 6.0 software, and polymorphic SNPs were identified with CodonCode Aligner software. The results showed that the genetic distances of domestic A. paniculata germplasm ranged from 0. 01 to 0.09, and no polymorphic SNPs were discovered in coding sequence fragments of ent-copalyl diphosphate synthase. A. paniculata germplasm from various regions in China had poor genetic diversity. This phenomenon was closely related to strict self-fertilization and earlier introduction from the same origin. Therefore, genetic background had little impact on variable qualities of A. paniculata in domestic market. Mutation breeding, polyploid breeding and molecular breeding were proposed as promising strategies in germplasm innovation.

  7. SNP discovery and chromosome anchoring provide the first physically-anchored hexaploid oat map and reveal synteny with model species.

    Directory of Open Access Journals (Sweden)

    Rebekah E Oliver

    Full Text Available A physically anchored consensus map is foundational to modern genomics research; however, construction of such a map in oat (Avena sativa L., 2n = 6x = 42 has been hindered by the size and complexity of the genome, the scarcity of robust molecular markers, and the lack of aneuploid stocks. Resources developed in this study include a modified SNP discovery method for complex genomes, a diverse set of oat SNP markers, and a novel chromosome-deficient SNP anchoring strategy. These resources were applied to build the first complete, physically-anchored consensus map of hexaploid oat. Approximately 11,000 high-confidence in silico SNPs were discovered based on nine million inter-varietal sequence reads of genomic and cDNA origin. GoldenGate genotyping of 3,072 SNP assays yielded 1,311 robust markers, of which 985 were mapped in 390 recombinant-inbred lines from six bi-parental mapping populations ranging in size from 49 to 97 progeny. The consensus map included 985 SNPs and 68 previously-published markers, resolving 21 linkage groups with a total map distance of 1,838.8 cM. Consensus linkage groups were assigned to 21 chromosomes using SNP deletion analysis of chromosome-deficient monosomic hybrid stocks. Alignments with sequenced genomes of rice and Brachypodium provide evidence for extensive conservation of genomic regions, and renewed encouragement for orthology-based genomic discovery in this important hexaploid species. These results also provide a framework for high-resolution genetic analysis in oat, and a model for marker development and map construction in other species with complex genomes and limited resources.

  8. Long-Run Benefits from Universal High-Quality Preschooling

    DEFF Research Database (Denmark)

    Bauchmüller, Robert; Gørtz, Mette; Rasmussen, Astrid Würtz

    2014-01-01

    This paper investigates the role of preschool quality for children's school performance at the end of primary school. We construct five structural quality indicators based on unique Danish administrative register data. 30,444 children finishing primary school's 9th grade in 2008 and who attended ...... in children's test results in Danish. Boys benefit more from preschool quality than girls. Ethnic minority children benefit from higher staff stability....

  9. Low-quality birds do not display high-quality signals: The cysteine-pheomelanin mechanism of honesty

    Science.gov (United States)

    Galván, Ismael; Wakamatsu, Kazumasa; Camarero, Pablo R; Mateo, Rafael; Alonso-Alvarez, Carlos

    2015-01-01

    The mechanisms that make that the costs of producing high-quality signals are unaffordable to low-quality signalers are a current issue in animal communication. The size of the melanin-based bib of male house sparrows Passer domesticus honestly signals quality. We induced the development of new bibs while treating males with buthionine-sulfoximine (BSO), a substance that depletes the levels of the antioxidant glutathione (GSH) and the amino acid cysteine, two elements that switch melanogenesis from eumelanin to pheomelanin. Final bib size is negatively related to pheomelanin levels in the bib feathers. BSO reduced cysteine and GSH levels in all birds, but improved phenotypes (bibs larger than controls) were only expressed by high-quality birds (BSO birds with largest bibs initially). Negative associations between final bib size and cysteine levels in erythrocytes, and between pheomelanin and cysteine levels, were observed in high-quality birds only. These findings suggest that a mechanism uncoupling pheomelanin and cysteine levels may have evolved in low-quality birds to avoid producing bibs of size not corresponding to their quality and greater relative costs. Indeed, greater oxidative stress in cells was not observed in low-quality birds. This may represent the first mechanism maintaining signal honesty without producing greater relative costs on low-quality signalers. PMID:25330349

  10. Systems and processes that ensure high quality care.

    Science.gov (United States)

    Bassett, Sally; Westmore, Kathryn

    2012-10-01

    This is the second in a series of articles examining the components of good corporate governance. It considers how the structures and processes for quality governance can affect an organisation's ability to be assured about the quality of care. Complex information systems and procedures can lead to poor quality care, but sound structures and processes alone are insufficient to ensure good governance, and behavioural factors play a significant part in making sure that staff are enabled to provide good quality care. The next article in this series looks at how the information reporting of an organisation can affect its governance.

  11. Characterization of non equilibrium effects on high quality critical flows

    International Nuclear Information System (INIS)

    Camelo, E.; Lemonnier, H.; Ochterbeck, J.

    1995-01-01

    The appropriate design of various pieces of safety equipment such as relief systems, relies on the accurate description of critical flow phenomena. Most of the systems of industrial interest are willing to be described by one-dimensional area-averaged models and a large fraction of them involves multi-component high gas quality flows. Within these circumstances, the flow is very likely to be of an annular dispersed nature and its description by two-fluid models requires various closure relations. Among the most sensitive closures, there is the interfacial area and the liquid entrained fraction. The critical flowrate depends tremendously on the accurate description of the non equilibrium which results from the correctness of the closure equations. In this study, two-component flows are emphasized and non equilibrium results mainly form the differences in the phase velocities. It is therefore of the utmost importance to have reliable data to characterize non equilibrium phenomena and to assess the validity of the closure models. A comprehensive description of air-water nozzle flows, with emphasis on the effect of the nozzle geometry, has been undertaken and some of the results are presented here which helps understanding the overall flow dynamics. Besides the critical flowrate, the presented material includes pressure profiles, droplet size and velocity, liquid film flowrate and liquid film thickness

  12. Characterization of non equilibrium effects on high quality critical flows

    Energy Technology Data Exchange (ETDEWEB)

    Camelo, E.; Lemonnier, H.; Ochterbeck, J. [Commissariat a l Energie Atomique, Grenoble (France)] [and others

    1995-09-01

    The appropriate design of various pieces of safety equipment such as relief systems, relies on the accurate description of critical flow phenomena. Most of the systems of industrial interest are willing to be described by one-dimensional area-averaged models and a large fraction of them involves multi-component high gas quality flows. Within these circumstances, the flow is very likely to be of an annular dispersed nature and its description by two-fluid models requires various closure relations. Among the most sensitive closures, there is the interfacial area and the liquid entrained fraction. The critical flowrate depends tremendously on the accurate description of the non equilibrium which results from the correctness of the closure equations. In this study, two-component flows are emphasized and non equilibrium results mainly form the differences in the phase velocities. It is therefore of the utmost importance to have reliable data to characterize non equilibrium phenomena and to assess the validity of the closure models. A comprehensive description of air-water nozzle flows, with emphasis on the effect of the nozzle geometry, has been undertaken and some of the results are presented here which helps understanding the overall flow dynamics. Besides the critical flowrate, the presented material includes pressure profiles, droplet size and velocity, liquid film flowrate and liquid film thickness.

  13. Utility of the pooling approach as applied to whole genome association scans with high-density Affymetrix microarrays

    Directory of Open Access Journals (Sweden)

    Gray Joanna

    2010-11-01

    Full Text Available Abstract Background We report an attempt to extend the previously successful approach of combining SNP (single nucleotide polymorphism microarrays and DNA pooling (SNP-MaP employing high-density microarrays. Whereas earlier studies employed a range of Affymetrix SNP microarrays comprising from 10 K to 500 K SNPs, this most recent investigation used the 6.0 chip which displays 906,600 SNP probes and 946,000 probes for the interrogation of CNVs (copy number variations. The genotyping assay using the Affymetrix SNP 6.0 array is highly demanding on sample quality due to the small feature size, low redundancy, and lack of mismatch probes. Findings In the first study published so far using this microarray on pooled DNA, we found that pooled cheek swab DNA could not accurately predict real allele frequencies of the samples that comprised the pools. In contrast, the allele frequency estimates using blood DNA pools were reasonable, although inferior compared to those obtained with previously employed Affymetrix microarrays. However, it might be possible to improve performance by developing improved analysis methods. Conclusions Despite the decreasing costs of genome-wide individual genotyping, the pooling approach may have applications in very large-scale case-control association studies. In such cases, our study suggests that high-quality DNA preparations and lower density platforms should be preferred.

  14. A mitochondrial DNA SNP multiplex assigning Caucasians into 36 haplo- and subhaplogroups

    DEFF Research Database (Denmark)

    Mikkelsen, Martin; Rockenbauer, Eszter; Sørensen, Erik

    2008-01-01

    Mitochondrial DNA (mtDNA) is maternally inherited without recombination events and has a high copy number, which makes mtDNA analysis feasible even when genomic DNA is sparse or degraded. Here, we present a SNP typing assay with 33 previously described mtDNA coding region SNPs for haplogroup...... previously typed by sequencing of the mitochondrial HV1 and HV2 regions. Haplogroup assignments based on mtDNA coding region SNPs and sequencing of HV1 and HV2 regions gave identical results for 27% of the samples, and except for one sample, differences in haplogroup assignments were at the subhaplogroup...

  15. Image Quality in High-resolution and High-cadence Solar Imaging

    Science.gov (United States)

    Denker, C.; Dineva, E.; Balthasar, H.; Verma, M.; Kuckein, C.; Diercke, A.; González Manrique, S. J.

    2018-03-01

    Broad-band imaging and even imaging with a moderate bandpass (about 1 nm) provides a photon-rich environment, where frame selection (lucky imaging) becomes a helpful tool in image restoration, allowing us to perform a cost-benefit analysis on how to design observing sequences for imaging with high spatial resolution in combination with real-time correction provided by an adaptive optics (AO) system. This study presents high-cadence (160 Hz) G-band and blue continuum image sequences obtained with the High-resolution Fast Imager (HiFI) at the 1.5-meter GREGOR solar telescope, where the speckle-masking technique is used to restore images with nearly diffraction-limited resolution. The HiFI employs two synchronized large-format and high-cadence sCMOS detectors. The median filter gradient similarity (MFGS) image-quality metric is applied, among others, to AO-corrected image sequences of a pore and a small sunspot observed on 2017 June 4 and 5. A small region of interest, which was selected for fast-imaging performance, covered these contrast-rich features and their neighborhood, which were part of Active Region NOAA 12661. Modifications of the MFGS algorithm uncover the field- and structure-dependency of this image-quality metric. However, MFGS still remains a good choice for determining image quality without a priori knowledge, which is an important characteristic when classifying the huge number of high-resolution images contained in data archives. In addition, this investigation demonstrates that a fast cadence and millisecond exposure times are still insufficient to reach the coherence time of daytime seeing. Nonetheless, the analysis shows that data acquisition rates exceeding 50 Hz are required to capture a substantial fraction of the best seeing moments, significantly boosting the performance of post-facto image restoration.

  16. Assessing SNP-SNP interactions among DNA repair, modification and metabolism related pathway genes in breast cancer susceptibility.

    Directory of Open Access Journals (Sweden)

    Yadav Sapkota

    Full Text Available Genome-wide association studies (GWASs have identified low-penetrance common variants (i.e., single nucleotide polymorphisms, SNPs associated with breast cancer susceptibility. Although GWASs are primarily focused on single-locus effects, gene-gene interactions (i.e., epistasis are also assumed to contribute to the genetic risks for complex diseases including breast cancer. While it has been hypothesized that moderately ranked (P value based weak single-locus effects in GWASs could potentially harbor valuable information for evaluating epistasis, we lack systematic efforts to investigate SNPs showing consistent associations with weak statistical significance across independent discovery and replication stages. The objectives of this study were i to select SNPs showing single-locus effects with weak statistical significance for breast cancer in a GWAS and/or candidate-gene studies; ii to replicate these SNPs in an independent set of breast cancer cases and controls; and iii to explore their potential SNP-SNP interactions contributing to breast cancer susceptibility. A total of 17 SNPs related to DNA repair, modification and metabolism pathway genes were selected since these pathways offer a priori knowledge for potential epistatic interactions and an overall role in breast carcinogenesis. The study design included predominantly Caucasian women (2,795 cases and 4,505 controls from Alberta, Canada. We observed two two-way SNP-SNP interactions (APEX1-rs1130409 and RPAP1-rs2297381; MLH1-rs1799977 and MDM2-rs769412 in logistic regression that conferred elevated risks for breast cancer (P(interaction<7.3 × 10(-3. Logic regression identified an interaction involving four SNPs (MBD2-rs4041245, MLH1-rs1799977, MDM2-rs769412, BRCA2-rs1799943 (P(permutation = 2.4 × 10(-3. SNPs involved in SNP-SNP interactions also showed single-locus effects with weak statistical significance, while BRCA2-rs1799943 showed stronger statistical significance (P

  17. Quality Assurance Roadmap for High Performance Residential Buildings

    Energy Technology Data Exchange (ETDEWEB)

    None

    2008-10-05

    This report outlines the approach to quality assurance in the construction process for new residential construction, including seven process steps from the assessment of current construction practice, through design and documentation changes, to training and quality control for on-site personnel.

  18. Paying for High- and Low-Quality Teaching

    Science.gov (United States)

    Schacter, John; Thum, Yeow Meng

    2004-01-01

    The extensive research on teacher quality has led to two conclusions. First, there are large and significant differences among teachers in terms of their capacity to improve student achievement. Second, these differences are not captured by common measures of teacher qualifications (E.A. Hanushek, Teacher quality, in: L.T. Izumi, W.M. Evers…

  19. Robust Demographic Inference from Genomic and SNP Data

    Science.gov (United States)

    Excoffier, Laurent; Dupanloup, Isabelle; Huerta-Sánchez, Emilia; Sousa, Vitor C.; Foll, Matthieu

    2013-01-01

    We introduce a flexible and robust simulation-based framework to infer demographic parameters from the site frequency spectrum (SFS) computed on large genomic datasets. We show that our composite-likelihood approach allows one to study evolutionary models of arbitrary complexity, which cannot be tackled by other current likelihood-based methods. For simple scenarios, our approach compares favorably in terms of accuracy and speed with , the current reference in the field, while showing better convergence properties for complex models. We first apply our methodology to non-coding genomic SNP data from four human populations. To infer their demographic history, we compare neutral evolutionary models of increasing complexity, including unsampled populations. We further show the versatility of our framework by extending it to the inference of demographic parameters from SNP chips with known ascertainment, such as that recently released by Affymetrix to study human origins. Whereas previous ways of handling ascertained SNPs were either restricted to a single population or only allowed the inference of divergence time between a pair of populations, our framework can correctly infer parameters of more complex models including the divergence of several populations, bottlenecks and migration. We apply this approach to the reconstruction of African demography using two distinct ascertained human SNP panels studied under two evolutionary models. The two SNP panels lead to globally very similar estimates and confidence intervals, and suggest an ancient divergence (>110 Ky) between Yoruba and San populations. Our methodology appears well suited to the study of complex scenarios from large genomic data sets. PMID:24204310

  20. A re-evaluation of 32S(n,p) cross sections from threshold to 5 MeV

    International Nuclear Information System (INIS)

    Fu, C.Y.

    1989-01-01

    Two evaluations of the 32 S(n,p) reaction cross sections, currently being used for the Nagasaki and Hiroshima dosimetry studies, yielded results that differ significantly. These two evaluations were reviewed and both were found to be quite old and without benefit of modern theoretical guidance and recent experimental data, hence inadequate in view of its relative importance for the present application. The necessity for a re-evaluation is further enhanced by the fact that: the present data search has uncovered a relatively high-quality data set that was not known previously, a generalized Bayes-theorem code is now available for averaging the various data sets with uncertainties and generating uncertainties for the results, effects on data combination of differing energy resolution in the various measurements can now be accounted for, and the ENDF/B-VI standards for 238 U(n,f) cross sections have become available for renormalizing two of the available data sets. The re-evaluation is performed to 5 MeV, the upper energy limit for the present purpose. 8 refs., 2 figs

  1. OTG-snpcaller: an optimized pipeline based on TMAP and GATK for SNP calling from ion torrent data.

    Directory of Open Access Journals (Sweden)

    Pengyuan Zhu

    Full Text Available Because the new Proton platform from Life Technologies produced markedly different data from those of the Illumina platform, the conventional Illumina data analysis pipeline could not be used directly. We developed an optimized SNP calling method using TMAP and GATK (OTG-snpcaller. This method combined our own optimized processes, Remove Duplicates According to AS Tag (RDAST and Alignment Optimize Structure (AOS, together with TMAP and GATK, to call SNPs from Proton data. We sequenced four sets of exomes captured by Agilent SureSelect and NimbleGen SeqCap EZ Kit, using Life Technology's Ion Proton sequencer. Then we applied OTG-snpcaller and compared our results with the results from Torrent Variants Caller. The results indicated that OTG-snpcaller can reduce both false positive and false negative rates. Moreover, we compared our results with Illumina results generated by GATK best practices, and we found that the results of these two platforms were comparable. The good performance in variant calling using GATK best practices can be primarily attributed to the high quality of the Illumina sequences.

  2. OTG-snpcaller: an optimized pipeline based on TMAP and GATK for SNP calling from ion torrent data.

    Science.gov (United States)

    Zhu, Pengyuan; He, Lingyu; Li, Yaqiao; Huang, Wenpan; Xi, Feng; Lin, Lin; Zhi, Qihuan; Zhang, Wenwei; Tang, Y Tom; Geng, Chunyu; Lu, Zhiyuan; Xu, Xun

    2014-01-01

    Because the new Proton platform from Life Technologies produced markedly different data from those of the Illumina platform, the conventional Illumina data analysis pipeline could not be used directly. We developed an optimized SNP calling method using TMAP and GATK (OTG-snpcaller). This method combined our own optimized processes, Remove Duplicates According to AS Tag (RDAST) and Alignment Optimize Structure (AOS), together with TMAP and GATK, to call SNPs from Proton data. We sequenced four sets of exomes captured by Agilent SureSelect and NimbleGen SeqCap EZ Kit, using Life Technology's Ion Proton sequencer. Then we applied OTG-snpcaller and compared our results with the results from Torrent Variants Caller. The results indicated that OTG-snpcaller can reduce both false positive and false negative rates. Moreover, we compared our results with Illumina results generated by GATK best practices, and we found that the results of these two platforms were comparable. The good performance in variant calling using GATK best practices can be primarily attributed to the high quality of the Illumina sequences.

  3. Teaching quality: High school students' autonomy and competence.

    Science.gov (United States)

    León, Jaime; Medina-Garrido, Elena; Ortega, Miriam

    2018-05-01

    How teachers manage class learning and interact with students affects students’ motivation and engagement. However, it could be that the effect of students’ representation of teaching quality on the students’ motivation varies between classes. Students from 90 classes participated in the study. We used multilevel random structural equation modeling to analyze whether the relationship of the students’ perception of teaching quality (as an indicator of the students’ mental representation) and students’ motivation varies between classes, and if this variability depends on the class assessment of teaching quality (as an indicator of teaching quality). The effect of teachers’ structure on the regression slope of student perception of student competence was .127. The effect of teachers’ autonomy support on the regression slope of student perception of student autonomy was .066. With this study we contribute a more detailed description of the relationship between teaching quality, competence and autonomy.

  4. Use of Sequenom sample ID Plus® SNP genotyping in identification of FFPE tumor samples.

    Directory of Open Access Journals (Sweden)

    Jessica K Miller

    Full Text Available Short tandem repeat (STR analysis, such as the AmpFlSTR® Identifiler® Plus kit, is a standard, PCR-based human genotyping method used in the field of forensics. Misidentification of cell line and tissue DNA can be costly if not detected early; therefore it is necessary to have quality control measures such as STR profiling in place. A major issue in large-scale research studies involving archival formalin-fixed paraffin embedded (FFPE tissues is that varying levels of DNA degradation can result in failure to correctly identify samples using STR genotyping. PCR amplification of STRs of several hundred base pairs is not always possible when DNA is degraded. The Sample ID Plus® panel from Sequenom allows for human DNA identification and authentication using SNP genotyping. In comparison to lengthy STR amplicons, this multiplexing PCR assay requires amplification of only 76-139 base pairs, and utilizes 47 SNPs to discriminate between individual samples. In this study, we evaluated both STR and SNP genotyping methods of sample identification, with a focus on paired FFPE tumor/normal DNA samples intended for next-generation sequencing (NGS. The ability to successfully validate the identity of FFPE samples can enable cost savings by reducing rework.

  5. GACT: a Genome build and Allele definition Conversion Tool for SNP imputation and meta-analysis in genetic association studies.

    Science.gov (United States)

    Sulovari, Arvis; Li, Dawei

    2014-07-19

    Genome-wide association studies (GWAS) have successfully identified genes associated with complex human diseases. Although much of the heritability remains unexplained, combining single nucleotide polymorphism (SNP) genotypes from multiple studies for meta-analysis will increase the statistical power to identify new disease-associated variants. Meta-analysis requires same allele definition (nomenclature) and genome build among individual studies. Similarly, imputation, commonly-used prior to meta-analysis, requires the same consistency. However, the genotypes from various GWAS are generated using different genotyping platforms, arrays or SNP-calling approaches, resulting in use of different genome builds and allele definitions. Incorrect assumptions of identical allele definition among combined GWAS lead to a large portion of discarded genotypes or incorrect association findings. There is no published tool that predicts and converts among all major allele definitions. In this study, we have developed a tool, GACT, which stands for Genome build and Allele definition Conversion Tool, that predicts and inter-converts between any of the common SNP allele definitions and between the major genome builds. In addition, we assessed several factors that may affect imputation quality, and our results indicated that inclusion of singletons in the reference had detrimental effects while ambiguous SNPs had no measurable effect. Unexpectedly, exclusion of genotypes with missing rate > 0.001 (40% of study SNPs) showed no significant decrease of imputation quality (even significantly higher when compared to the imputation with singletons in the reference), especially for rare SNPs. GACT is a new, powerful, and user-friendly tool with both command-line and interactive online versions that can accurately predict, and convert between any of the common allele definitions and between genome builds for genome-wide meta-analysis and imputation of genotypes from SNP-arrays or deep

  6. A large-scale chromosome-specific SNP discovery guideline.

    Science.gov (United States)

    Akpinar, Bala Ani; Lucas, Stuart; Budak, Hikmet

    2017-01-01

    Single-nucleotide polymorphisms (SNPs) are the most prevalent type of variation in genomes that are increasingly being used as molecular markers in diversity analyses, mapping and cloning of genes, and germplasm characterization. However, only a few studies reported large-scale SNP discovery in Aegilops tauschii, restricting their potential use as markers for the low-polymorphic D genome. Here, we report 68,592 SNPs found on the gene-related sequences of the 5D chromosome of Ae. tauschii genotype MvGB589 using genomic and transcriptomic sequences from seven Ae. tauschii accessions, including AL8/78, the only genotype for which a draft genome sequence is available at present. We also suggest a workflow to compare SNP positions in homologous regions on the 5D chromosome of Triticum aestivum, bread wheat, to mark single nucleotide variations between these closely related species. Overall, the identified SNPs define a density of 4.49 SNPs per kilobyte, among the highest reported for the genic regions of Ae. tauschii so far. To our knowledge, this study also presents the first chromosome-specific SNP catalog in Ae. tauschii that should facilitate the association of these SNPs with morphological traits on chromosome 5D to be ultimately targeted for wheat improvement.

  7. A robust SNP barcode for typing Mycobacterium tuberculosis complex strains

    KAUST Repository

    Coll, Francesc

    2014-09-01

    Strain-specific genomic diversity in the Mycobacterium tuberculosis complex (MTBC) is an important factor in pathogenesis that may affect virulence, transmissibility, host response and emergence of drug resistance. Several systems have been proposed to classify MTBC strains into distinct lineages and families. Here, we investigate single-nucleotide polymorphisms (SNPs) as robust (stable) markers of genetic variation for phylogenetic analysis. We identify ∼92k SNP across a global collection of 1,601 genomes. The SNP-based phylogeny is consistent with the gold-standard regions of difference (RD) classification system. Of the ∼7k strain-specific SNPs identified, 62 markers are proposed to discriminate known circulating strains. This SNP-based barcode is the first to cover all main lineages, and classifies a greater number of sublineages than current alternatives. It may be used to classify clinical isolates to evaluate tools to control the disease, including therapeutics and vaccines whose effectiveness may vary by strain type. © 2014 Macmillan Publishers Limited.

  8. New developments in high quality grey cast irons

    Directory of Open Access Journals (Sweden)

    Iulian Riposan

    2014-07-01

    Full Text Available The paper reviews original data obtained by the present authors, revealed in recent separate publications, describing specific procedures for high quality grey irons, and reflecting the forecast needs of the worldwide iron foundry industry. High power, medium frequency coreless induction furnaces are commonly used in electric melting grey iron foundries. This has resulted in low sulphur (1,500 °C, contributing to unfavourable conditions for graphite nucleation. Thin wall castings are increasingly produced by these electric melt shops with a risk of greater eutectic undercooling during solidification. The paper focused on two groups of grey cast irons and their specific problems: carbides and graphite morphology control in lower carbon equivalent high strength irons (CE=3.4%-3.8%, and austenite dendrite promotion in eutectic and slightly hypereutectic irons (CE=4.1%-4.5%, in order to increase their strength characteristics. There are 3 stages and 3 steps involving graphite formation, iron chemistry and iron processing that appear to be important. The concept in the present paper sustains a threestage model for nucleating flake graphite [(Mn,XS type nuclei]. There are three important groups of elements (deoxidizer, Mn/S, and inoculant and three technological stages in electric melting of iron (superheat, pre-conditioning of base iron, final inoculation. Attention is drawn to a control factor (%Mn x (%S ensuring it equals to 0.03 – 0.06, accompanied by 0.005wt.%–0.010wt.% Al and/or Zr content in inoculated irons. It was found that iron powder addition promotes austenite dendrite formation in eutectic and slightly eutectic, acting as reinforcement for the eutectic cells. But, there is an accompanying possible negative influence on the characteristics of the (Mn,XS type graphite nuclei (change the morphology of nuclei from polygonal compact to irregular polygonal, and therefore promote chill tendency in treated irons. A double addition (iron

  9. A high yielding, better quality chickpea mutant variety 'NIFA-95'

    International Nuclear Information System (INIS)

    Hassan, S.; Javed, M.A.; Khattak, S.U.K.; Iqbal, M.M.

    2001-01-01

    Chickpea or gram (Cicer arietinum L.) is an important legume crop of Pakistan, grown on over one million hectares annually. The national average yield of the crop is very low (0.5 t/ha) and thus the country had to spent about 2 billion rupees ($ 50 million) on import of pulses. The main causes of low yield are non-availability of genetic sources for resistance to various diseases especially gram blight Ascochyta rabiei (Pass.) Lab., insect pest (Pod borer) and non-adoption of proper production technology by the farmers. This calls for earnest efforts of breeders to evolve high yielding and disease resistant varieties of chickpea for provision of quality seeds to the farming community to increase production of this important crop. Seeds of a highly blight susceptible variety '6153' were irradiated at 200 Gy dose of gamma radiation in 1985 and the promising mutant line CMN-446-4 was selected in M3 generation on the basis of disease resistance, greater number of pods and better plant type. After confirmation of its resistance to blight in M 4 and M 5 , the mutant line was evaluated in various trials at different locations. In the advanced and zonal yield trials during 1993-95, the line CMN-446-4 produced the highest grain yield of 2,600 kg/ha as compared to the rest of the mutants and varieties. The line was also evaluated in the chickpea national uniform yield trial, conducted on over 11 locations in the country during 1993-94. In this trial, the mutant line ranked 3rd by producing an average yield of 1,528 kg/ha as compared to the two check varieties 'Punjab-91' (1,316 kg/ha) and 'Paidar-91' (1,391 kg/ha). The mutant line CMN-446-4 is moderately resistant to gram blight, highly resistant to stored pest (pulse beetle), contains 25.3% more protein as compared to the parental variety 6153 and is also better in nitrogen fixing capacity.The proposal for release of the mutant line CMN-446-4 as a new variety under the name 'NIFA-95' for general cultivation in the rainfed

  10. Feasibility of RNA and DNA Extraction from Fresh Pipelle and Archival Endometrial Tissues for Use in Gene Expression and SNP Arrays

    Directory of Open Access Journals (Sweden)

    Heather D. Kissel

    2013-01-01

    Full Text Available Identifying molecular markers of endometrial hyperplasia (neoplasia progression is critical to cancer prevention. To assess RNA and DNA quantity and quality from routinely collected endometrial samples and evaluate the performance of RNA- and DNA-based arrays across endometrial tissue types, we collected fresh frozen (FF Pipelle, FF curettage, and formalin-fixed paraffin-embedded (FFPE hysterectomy specimens (benign indications from eight women. Additionally, neoplastic and uninvolved tissues from 24 FFPE archival hysterectomy specimens with endometrial hyperplasias and carcinomas were assessed. RNA was extracted from 15 of 16 FF and 51 of 51 FFPE samples, with yields >1.2 μg for 13/15 (87% FF and 50/51 (98% FFPE samples. Extracted RNA was of high quality; all samples performed successfully on the Illumina whole-genome cDNA-mediated annealing, selection, extension, and ligation (WG-DASL array and performance did not vary by tissue type. While DNA quantity from FFPE samples was excellent, quality was not sufficient for successful performance on the Affymetrix SNP Array 6.0. In conclusion, FF Pipelle samples, which are minimally invasive, yielded excellent quantity and quality of RNA for gene expression arrays (similar to FF curettage and should be considered for use in genomic studies. FFPE-derived DNA should be evaluated on new rapidly evolving sequencing platforms.

  11. Marcadores SNP: conceitos básicos, aplicações no manejo e no melhoramento animal e perspectivas para o futuro SNP markers: basic concepts, applications in animal breeding and management and perspectives for the future

    Directory of Open Access Journals (Sweden)

    Alexandre Rodrigues Caetano

    2009-07-01

    molecular markers to characterize genetic resources and generate tools for animal breeding and management date from the end of the 80s. In the last 20 years the technologies to generate molecular data went through several innovation cycles. The last wave of technological innovations represents a true revolution, bringing methods to identify and genotype SNP (Single Nucleotide Polymorphism markers in large scale. High density DNA chips were generated to genotype from tens of thousands to hundreds of thousands of SNPs in a single assay. Furthermore, other medium density technologies allow for the genotyping of tens to hundreds of makers, in high numbers of samples, with very high speed and automation. These new technologies allowed for the generation of new applications, such as the methods to genetically evaluate and select animals based on their Genomic Value (Genomic Estimated Breeding Value - GEBV. The statistical methods for genomic evaluation and selection are in full development, but the technology already became reality with the release of the first bull summary for the Holstein breed with GEBVs for milk production and quality traits in January 2009. In addition, these technologies brought new options for development of diagnostic tests for paternity testing, individual identification, traceability, etc. Also, these new technologies to genotype SNP markers facilitated the development of outsourcing companies to generate molecular data, allowing any group to conduct advanced experiments, always using the most advanced technologies, without the need of investments into equipment.

  12. Physics and quality assurance for high dose rate brachytherapy

    International Nuclear Information System (INIS)

    Anderson, Lowell L.

    1995-01-01

    Purpose: To review the physical aspects of high dose rate (HDR) brachytherapy, including commissioning and quality assurance, source calibration and dose distribution measurements, and treatment planning methods. Following the introduction of afterloading in brachytherapy, development efforts to make it 'remote' culminated in 1964 with the near-simultaneous appearance of remote afterloaders in five major medical centers. Four of these machines were 'high dose rate', three employing 60Co and one (the GammaMed) using a single, cable-mounted 192Ir source. Stepping-motor source control was added to the GammaMed in 1974, making it the precursor of modern remote afterloaders, which are now suitable for interstitial as well as intracavitary brachytherapy by virtue of small source-diameter and indexer-accessed multiple channels. Because the 192Ir sources currently used in HDR remote afterloaders are supplied at a nominal air-kerma strength of 11.4 cGy cm2 s-1 (10 Ci), are not collimated in clinical use, and emit a significant fraction (15%) of photons at energies greater than 600 keV, shielding and facility design must be undertaken as carefully and thoroughly as for external beam installations. Licensing requirements of regulatory agencies must be met with respect both to maximum permissible dose limits and to the existence and functionality of safety devices (door interlocks, radiation monitors, etc.). Commissioning and quality assurance procedures that must be documented for HDR remote afterloading relate to (1) machine, applicator, guide-tube, and facility functionality checks, (2) source calibration, (3) emergency response readiness, (4) planning software evaluation, and (5) independent checks of clinical dose calculations. Source calibration checks must be performed locally, either by in-air measurement of air kerma strength or with a well ionization chamber calibrated (by an accredited standards laboratory) against an in-air measurement of air kerma strength for the

  13. Twin pregnancy possibly associated with high semen quality

    DEFF Research Database (Denmark)

    Asklund, Camilla; Jensen, Tina Kold; Jørgensen, Niels

    2007-01-01

    BACKGROUND: Recent studies found an association between a long waiting time to pregnancy (TTP) and reduced probability of twinning and a reduced dizygotic (DZ) twinning rate in subfertile men. However, it remains unsolved whether semen quality is associated with twin offspring. We therefore studied...... the semen quality in a group of fathers of naturally conceived twins. METHODS: In this study, 37 fathers of DZ twins and 15 fathers of monozygotic (MZ) twins participated, and 349 normal fertile men served as a reference group. All men delivered a semen sample, underwent a physical examination and completed...... points higher than the reference group (P semen quality than the reference group, which supports...

  14. snpTree - a web-server to identify and construct SNP trees from whole genome sequence data

    DEFF Research Database (Denmark)

    Leekitcharoenphon, Pimlapas; Kaas, Rolf Sommer; Thomsen, Martin Christen Frølund

    2012-01-01

    identify SNPs and construct phylogenetic trees from WGS as well as from assembled genomes or contigs. WGS data in fastq format are aligned to reference genomes by BWA while contigs in fasta format are processed by Nucmer. SNPs are concatenated based on position on reference genome and a tree is constructed...... to differentiate and classify isolates. One of the successfully and broadly used methods is analysis of single nucletide polymorphisms (SNPs). Currently, there are different tools and methods to identify SNPs including various options and cut-off values. Furthermore, all current methods require bioinformatic...... skills. Thus, we lack a standard and simple automatic tool to determine SNPs and construct phylogenetic tree from WGS data. Results Here we introduce snpTree, a server for online-automatic SNPs analysis. This tool is composed of different SNPs analysis suites, perl and python scripts. snpTree can...

  15. High quality ceramic coatings sprayed by high efficiency hypersonic plasma spraying gun

    International Nuclear Information System (INIS)

    Zhu Sheng; Xu Binshi; Yao JiuKun

    2005-01-01

    This paper introduced the structure of the high efficiency hypersonic plasma spraying gun and the effects of hypersonic plasma jet on the sprayed particles. The optimised spraying process parameters for several ceramic powders such as Al 2 O 3 , Cr 2 O 3 , ZrO 2 , Cr 3 C 2 and Co-WC were listed. The properties and microstructure of the sprayed ceramic coatings were investigated. Nano Al 2 O 3 -TiO 2 ceramic coating sprayed by using the high efficiency hypersonic plasma spraying was also studied. Compared with the conventional air plasma spraying, high efficiency hypersonic plasma spraying improves greatly the ceramic coatings quality but at low cost. (orig.)

  16. Safe and high quality food production using low quality waters and improved irrigation systems and management

    DEFF Research Database (Denmark)

    Plauborg, Finn; Andersen, Mathias Neumann; Liu, Fulai

    2010-01-01

    uneven irrigation patterns can increase the water use efficiency as well as the quality of vegetable crops. Furthermore, recent innovations in the water treatment and irrigation industry have shown potential for the use of low quality water resources, such as reclaimed water or surface water in peri...

  17. High throughput electrospinning of high-quality nanofibers via an aluminum disk spinneret

    Science.gov (United States)

    Zheng, Guokuo

    In this work, a simple and efficient needleless high throughput electrospinning process using an aluminum disk spinneret with 24 holes is described. Electrospun mats produced by this setup consisted of fine fibers (nano-sized) of the highest quality while the productivity (yield) was many times that obtained from conventional single-needle electrospinning. The goal was to produce scaled-up amounts of the same or better quality nanofibers under variable concentration, voltage, and the working distance than those produced with the single needle lab setting. The fiber mats produced were either polymer or ceramic (such as molybdenum trioxide nanofibers). Through experimentation the optimum process conditions were defined to be: 24 kilovolt, a distance to collector of 15cm. More diluted solutions resulted in smaller diameter fibers. Comparing the morphologies of the nanofibers of MoO3 produced by both the traditional and the high throughput set up it was found that they were very similar. Moreover, the nanofibers production rate is nearly 10 times than that of traditional needle electrospinning. Thus, the high throughput process has the potential to become an industrial nanomanufacturing process and the materials processed by it may be used as filtration devices, in tissue engineering, and as sensors.

  18. Comparative analysis of core genome MLST and SNP typing within a European Salmonella serovar Enteritidis outbreak.

    Science.gov (United States)

    Pearce, Madison E; Alikhan, Nabil-Fareed; Dallman, Timothy J; Zhou, Zhemin; Grant, Kathie; Maiden, Martin C J

    2018-06-02

    Multi-country outbreaks of foodborne bacterial disease present challenges in their detection, tracking, and notification. As food is increasingly distributed across borders, such outbreaks are becoming more common. This increases the need for high-resolution, accessible, and replicable isolate typing schemes. Here we evaluate a core genome multilocus typing (cgMLST) scheme for the high-resolution reproducible typing of Salmonella enterica (S. enterica) isolates, by its application to a large European outbreak of S. enterica serovar Enteritidis. This outbreak had been extensively characterised using single nucleotide polymorphism (SNP)-based approaches. The cgMLST analysis was congruent with the original SNP-based analysis, the epidemiological data, and whole genome MLST (wgMLST) analysis. Combination of the cgMLST and epidemiological data confirmed that the genetic diversity among the isolates predated the outbreak, and was likely present at the infection source. There was consequently no link between country of isolation and genetic diversity, but the cgMLST clusters were congruent with date of isolation. Furthermore, comparison with publicly available Enteritidis isolate data demonstrated that the cgMLST scheme presented is highly scalable, enabling outbreaks to be contextualised within the Salmonella genus. The cgMLST scheme is therefore shown to be a standardised and scalable typing method, which allows Salmonella outbreaks to be analysed and compared across laboratories and jurisdictions. Copyright © 2018. Published by Elsevier B.V.

  19. Improving the quality of pork and pork products for the consumer : development of innovative, integrated, and sustainable food production chains of high quality pork products matching consumer demands

    NARCIS (Netherlands)

    Heimann, B.; Christensen, M.; Rosendal Rasmussen, S.; Bonneau, M.; Grunert, K.G.; Arnau, J.; Trienekens, J.H.; Oksbjerg, N.; Greef, de K.H.; Petersen, B.

    2012-01-01

    Improving the quality of pork and pork products for the consumer: development of innovative, integrated, and sustainable food production chains of high quality pork products matching consumer demands.

  20. Solar Radiation-Associated Adaptive SNP Genetic Differentiation in Wild Emmer Wheat, Triticum dicoccoides.

    Science.gov (United States)

    Ren, Jing; Chen, Liang; Jin, Xiaoli; Zhang, Miaomiao; You, Frank M; Wang, Jirui; Frenkel, Vladimir; Yin, Xuegui; Nevo, Eviatar; Sun, Dongfa; Luo, Ming-Cheng; Peng, Junhua

    2017-01-01

    Whole-genome scans with large number of genetic markers provide the opportunity to investigate local adaptation in natural populations and identify candidate genes under positive selection. In the present study, adaptation genetic differentiation associated with solar radiation was investigated using 695 polymorphic SNP markers in wild emmer wheat originated in a micro-site at Yehudiyya, Israel. The test involved two solar radiation niches: (1) sun, in-between trees; and (2) shade, under tree canopy, separated apart by a distance of 2-4 m. Analysis of molecular variance showed a small (0.53%) but significant portion of overall variation between the sun and shade micro-niches, indicating a non-ignorable genetic differentiation between sun and shade habitats. Fifty SNP markers showed a medium (0.05 ≤ F ST ≤ 0.15) or high genetic differentiation ( F ST > 0.15). A total of 21 outlier loci under positive selection were identified by using four different F ST -outlier testing algorithms. The markers and genome locations under positive selection are consistent with the known patterns of selection. These results suggested that genetic differentiation between sun and shade habitats is substantial, radiation-associated, and therefore ecologically determined. Hence, the results of this study reflected effects of natural selection through solar radiation on EST-related SNP genetic diversity, resulting presumably in different adaptive complexes at a micro-scale divergence. The present work highlights the evolutionary theory and application significance of solar radiation-driven natural selection in wheat improvement.

  1. A general SNP-based molecular barcode for Plasmodium falciparum identification and tracking

    Directory of Open Access Journals (Sweden)

    Rosen David

    2008-10-01

    Full Text Available Abstract Background Single nucleotide polymorphism (SNP genotyping provides the means to develop a practical, rapid, inexpensive assay that will uniquely identify any Plasmodium falciparum parasite using a small amount of DNA. Such an assay could be used to distinguish recrudescence from re-infection in drug trials, to monitor the frequency and distribution of specific parasites in a patient population undergoing drug treatment or vaccine challenge, or for tracking samples and determining purity of isolates in the laboratory during culture adaptation and sub-cloning, as well as routine passage. Methods A panel of twenty-four SNP markers has been identified that exhibit a high minor allele frequency (average MAF > 35%, for which robust TaqMan genotyping assays were constructed. All SNPs were identified through whole genome sequencing and MAF was estimated through Affymetrix array-based genotyping of a worldwide collection of parasites. These assays create a "molecular barcode" to uniquely identify a parasite genome. Results Using 24 such markers no two parasites known to be of independent origin have yet been found to have the same allele signature. The TaqMan genotyping assays can be performed on a variety of samples including cultured parasites, frozen whole blood, or whole blood spotted onto filter paper with a success rate > 99%. Less than 5 ng of parasite DNA is needed to complete a panel of 24 markers. The ability of this SNP panel to detect and identify parasites was compared to the standard molecular methods, MSP-1 and MSP-2 typing. Conclusion This work provides a facile field-deployable genotyping tool that can be used without special skills with standard lab equipment, and at reasonable cost that will unambiguously identify and track P. falciparum parasites both from patient samples and in the laboratory.

  2. Novel Quantitative Real-Time LCR for the Sensitive Detection of SNP Frequencies in Pooled DNA: Method Development, Evaluation and Application

    Science.gov (United States)

    Psifidi, Androniki; Dovas, Chrysostomos; Banos, Georgios

    2011-01-01

    Background Single nucleotide polymorphisms (SNP) have proven to be powerful genetic markers for genetic applications in medicine, life science and agriculture. A variety of methods exist for SNP detection but few can quantify SNP frequencies when the mutated DNA molecules correspond to a small fraction of the wild-type DNA. Furthermore, there is no generally accepted gold standard for SNP quantification, and, in general, currently applied methods give inconsistent results in selected cohorts. In the present study we sought to develop a novel method for accurate detection and quantification of SNP in DNA pooled samples. Methods The development and evaluation of a novel Ligase Chain Reaction (LCR) protocol that uses a DNA-specific fluorescent dye to allow quantitative real-time analysis is described. Different reaction components and thermocycling parameters affecting the efficiency and specificity of LCR were examined. Several protocols, including gap-LCR modifications, were evaluated using plasmid standard and genomic DNA pools. A protocol of choice was identified and applied for the quantification of a polymorphism at codon 136 of the ovine PRNP gene that is associated with susceptibility to a transmissible spongiform encephalopathy in sheep. Conclusions The real-time LCR protocol developed in the present study showed high sensitivity, accuracy, reproducibility and a wide dynamic range of SNP quantification in different DNA pools. The limits of detection and quantification of SNP frequencies were 0.085% and 0.35%, respectively. Significance The proposed real-time LCR protocol is applicable when sensitive detection and accurate quantification of low copy number mutations in DNA pools is needed. Examples include oncogenes and tumour suppressor genes, infectious diseases, pathogenic bacteria, fungal species, viral mutants, drug resistance resulting from point mutations, and genetically modified organisms in food. PMID:21283808

  3. High Yield Chemical Vapor Deposition Growth of High Quality Large-Area AB Stacked Bilayer Graphene

    Science.gov (United States)

    Liu, Lixin; Zhou, Hailong; Cheng, Rui; Yu, Woo Jong; Liu, Yuan; Chen, Yu; Shaw, Jonathan; Zhong, Xing; Huang, Yu; Duan, Xiangfeng

    2012-01-01

    Bernal stacked (AB stacked) bilayer graphene is of significant interest for functional electronic and photonic devices due to the feasibility to continuously tune its band gap with a vertical electrical field. Mechanical exfoliation can be used to produce AB stacked bilayer graphene flakes but typically with the sizes limited to a few micrometers. Chemical vapor deposition (CVD) has been recently explored for the synthesis of bilayer graphene but usually with limited coverage and a mixture of AB and randomly stacked structures. Herein we report a rational approach to produce large-area high quality AB stacked bilayer graphene. We show that the self-limiting effect of graphene growth on Cu foil can be broken by using a high H2/CH4 ratio in a low pressure CVD process to enable the continued growth of bilayer graphene. A high temperature and low pressure nucleation step is found to be critical for the formation of bilayer graphene nuclei with high AB stacking ratio. A rational design of a two-step CVD process is developed for the growth of bilayer graphene with high AB stacking ratio (up to 90 %) and high coverage (up to 99 %). The electrical transport studies demonstrated that devices made of the as-grown bilayer graphene exhibit typical characteristics of AB stacked bilayer graphene with the highest carrier mobility exceeding 4,000 cm2/V·s at room temperature, comparable to that of the exfoliated bilayer graphene. PMID:22906199

  4. Clonal diversity analysis using SNP microarray: a new prognostic tool for chronic lymphocytic leukemia.

    Science.gov (United States)

    Zhang, Linsheng; Znoyko, Iya; Costa, Luciano J; Conlin, Laura K; Daber, Robert D; Self, Sally E; Wolff, Daynna J

    2011-12-01

    Chronic lymphocytic leukemia (CLL) is a clinically heterogeneous disease. The methods currently used for monitoring CLL and determining conditions for treatment are limited in their ability to predict disease progression, patient survival, and response to therapy. Although clonal diversity and the acquisition of new chromosomal abnormalities during the disease course (clonal evolution) have been associated with disease progression, their prognostic potential has been underappreciated because cytogenetic and fluorescence in situ hybridization (FISH) studies have a restricted ability to detect genomic abnormalities and clonal evolution. We hypothesized that whole genome analysis using high resolution single nucleotide polymorphism (SNP) microarrays would be useful to detect diversity and infer clonal evolution to offer prognostic information. In this study, we used the Infinium Omni1 BeadChip (Illumina, San Diego, CA) array for the analysis of genetic variation and percent mosaicism in 25 non-selected CLL patients to explore the prognostic value of the assessment of clonal diversity in patients with CLL. We calculated the percentage of mosaicism for each abnormality by applying a mathematical algorithm to the genotype frequency data and by manual determination using the Simulated DNA Copy Number (SiDCoN) tool, which was developed from a computer model of mosaicism. At least one genetic abnormality was identified in each case, and the SNP data was 98% concordant with FISH results. Clonal diversity, defined as the presence of two or more genetic abnormalities with differing percentages of mosaicism, was observed in 12 patients (48%), and the diversity correlated with the disease stage. Clonal diversity was present in most cases of advanced disease (Rai stages III and IV) or those with previous treatment, whereas 9 of 13 patients without detected clonal diversity were asymptomatic or clinically stable. In conclusion, SNP microarray studies with simultaneous evaluation

  5. Consumers' expected quality and intention to purchase high quality pork meat.

    Science.gov (United States)

    Papanagiotou, P; Tzimitra-Kalogianni, I; Melfou, K

    2013-03-01

    Expected quality is believed to be one of the most important factors that influence consumers' intention to purchase food. The present study seeks to explore the concept of pork meat expected quality and compare it with self-stated consumer intention to purchase pork meat. The aim is attempted by means of a field research conducted in Greece, following a conjoint analytic procedure. Results show that quality expectations comply with intention to buy pork, in many aspects. However, several differences have been identified. More specifically, country of origin and marbling appear to be more important for respondents' purchase decisions than they are for their quality evaluations, while the opposite appears to be true for price. Finally, socio-demographic factors such as gender, level of education, place of purchase and consumption habits seem to influence perceptions. Copyright © 2012 Elsevier Ltd. All rights reserved.

  6. CGH and SNP array using DNA extracted from fixed cytogenetic preparations and long-term refrigerated bone marrow specimens

    Directory of Open Access Journals (Sweden)

    MacKinnon Ruth N

    2012-02-01

    Full Text Available Abstract Background The analysis of nucleic acids is limited by the availability of archival specimens and the quality and amount of the extracted material. Archived cytogenetic preparations are stored in many laboratories and are a potential source of total genomic DNA for array karyotyping and other applications. Array CGH using DNA from fixed cytogenetic preparations has been described, but it is not known whether it can be used for SNP arrays. Diagnostic bone marrow specimens taken during the assessment of hematological malignancies are also a potential source of DNA, but it is generally assumed that DNA must be extracted, or the specimen frozen, within a day or two of collection, to obtain DNA suitable for further analysis. We have assessed DNA extracted from these materials for both SNP array and array CGH. Results We show that both SNP array and array CGH can be performed on genomic DNA extracted from cytogenetic specimens stored in Carnoy's fixative, and from bone marrow which has been stored unfrozen, at 4°C, for at least 36 days. We describe a procedure for extracting a usable concentration of total genomic DNA from cytogenetic suspensions of low cellularity. Conclusions The ability to use these archival specimens for DNA-based analysis increases the potential for retrospective genetic analysis of clinical specimens. Fixed cytogenetic preparations and long-term refrigerated bone marrow both provide DNA suitable for array karyotyping, and may be suitable for a wider range of analytical procedures.

  7. Safe and High Quality Food Production using Low Quality Waters and Improved Irrigation Systems and Management, EU Project

    DEFF Research Database (Denmark)

    Plauborg, Finn; Jensen, Christian Richardt; Dalsgaard, Anders

    2009-01-01

    : the safety and quality of food products, and the increasing competition for clean freshwater. SAFIR is funded for the period 2005-2009 under the Food Quality and Safety thematic area of the EU 6th Framework Research Programme. The challenge for the next years will be to produce safe and high quality foods...... a multi-disciplinary team, with food safety and quality experts, engineers, agronomists and economists from17 research institutes and private companies in Europe, Israel and China working together. The project assesses potential risks to farmers. Coupled with farm management and economic models, a new...... intelligent tool for efficient and safe use and re-use of low-quality water are being developed. Already published results indicate water saving in the order of 25-30% in agricultural crops as potatoes and tomatoes are possible without yield reduction. Slightly treated waste water can be used safely when...

  8. rSNPBase 3.0: an updated database of SNP-related regulatory elements, element-gene pairs and SNP-based gene regulatory networks.

    Science.gov (United States)

    Guo, Liyuan; Wang, Jing

    2018-01-04

    Here, we present the updated rSNPBase 3.0 database (http://rsnp3.psych.ac.cn), which provides human SNP-related regulatory elements, element-gene pairs and SNP-based regulatory networks. This database is the updated version of the SNP regulatory annotation database rSNPBase and rVarBase. In comparison to the last two versions, there are both structural and data adjustments in rSNPBase 3.0: (i) The most significant new feature is the expansion of analysis scope from SNP-related regulatory elements to include regulatory element-target gene pairs (E-G pairs), therefore it can provide SNP-based gene regulatory networks. (ii) Web function was modified according to data content and a new network search module is provided in the rSNPBase 3.0 in addition to the previous regulatory SNP (rSNP) search module. The two search modules support data query for detailed information (related-elements, element-gene pairs, and other extended annotations) on specific SNPs and SNP-related graphic networks constructed by interacting transcription factors (TFs), miRNAs and genes. (3) The type of regulatory elements was modified and enriched. To our best knowledge, the updated rSNPBase 3.0 is the first data tool supports SNP functional analysis from a regulatory network prospective, it will provide both a comprehensive understanding and concrete guidance for SNP-related regulatory studies. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  9. Quality assessment and potential utilization of high amylolytic ...

    African Journals Online (AJOL)

    STORAGESEVER

    2008-12-03

    Dec 3, 2008 ... This study was carried out to compare the qualities of two acclaimed Nigerian amylolytic maize cultivars; SPMAT ... growing demand for usage as a gluten-free cereal. (Sweeny ... The grain was malted and the malting loss was calculated using the .... also confirmed that there was no significant difference in.

  10. Quality Alternative Certification Programs in Special Education Ensure High Retention

    Science.gov (United States)

    Karge, Belinda D.; McCabe, Marjorie

    2014-01-01

    Market driven alternative routes to teaching have evolved into a quality program option and not just an answer to the teacher shortage. Alternative certification is a viable means of recruiting, training, and certifying those who have a bachelor's degree and a strong desire to enter the field of teaching. California has been a leader in the…

  11. Innovation in Business Education: Developing a High Quality Online MBA

    Science.gov (United States)

    Roe, C. William; Toma, Alfred G.; Yallapragada, RamMohan R.

    2015-01-01

    Online degree programs were probably pioneered by for-profit universities such as University of Phoenix. Many online degree programs were initially considered low quality academic programs compared to traditional programs. Therefore, many public and private universities were slow to adopt the online programs. However, gradually more and more…

  12. Quality of life of people living with HIV/AIDS and on highly active ...

    African Journals Online (AJOL)

    Quality of life of people living with HIV/AIDS and on highly active ... the Short Form-36 Health Survey (SF-36) was used to measure quality of life among patients on ... instrument for use in Ethiopia to assess the quality of life of people living with ...

  13. Does High School Facility Quality Affect Student Achievement? A Two-Level Hierarchical Linear Model

    Science.gov (United States)

    Bowers, Alex J.; Urick, Angela

    2011-01-01

    The purpose of this study is to isolate the independent effects of high school facility quality on student achievement using a large, nationally representative U.S. database of student achievement and school facility quality. Prior research on linking school facility quality to student achievement has been mixed. Studies that relate overall…

  14. Single nucleotide polymorphism (SNP) detection on a magnetoresistive sensor

    DEFF Research Database (Denmark)

    Rizzi, Giovanni; Østerberg, Frederik Westergaard; Dufva, Martin

    2013-01-01

    We present a magnetoresistive sensor platform for hybridization assays and demonstrate its applicability on single nucleotide polymorphism (SNP) genotyping. The sensor relies on anisotropic magnetoresistance in a new geometry with a local negative reference and uses the magnetic field from...... the sensor bias current to magnetize magnetic beads in the vicinity of the sensor. The method allows for real-time measurements of the specific bead binding to the sensor surface during DNA hybridization and washing. Compared to other magnetic biosensing platforms, our approach eliminates the need...... for external electromagnets and thus allows for miniaturization of the sensor platform....

  15. SNP and haplotype mapping for genetic analysis in the rat

    Czech Academy of Sciences Publication Activity Database

    Saar, K.; Beck, A.; Bihoreau, M. T.; Birney, E.; Brocklebank, D.; Chen, Y.; Cuppen, E.; Demonchy, S.; Dopazo, J.; Flicek, P.; Foglio, M.; Fujiyama, A.; Gut, I. G.; Gauguier, D.; Guigo, R.; Guryev, V.; Heinig, M.; Hummel, O.; Jahn, N.; Klages, S.; Křen, Vladimír; Kube, M.; Kuhl, H.; Kuramoto, T.; Pravenec, Michal

    2008-01-01

    Roč. 40, č. 5 (2008), s. 560-566 ISSN 1061-4036 R&D Projects: GA MŠk(CZ) 1P05ME791; GA MŠk(CZ) 1M0520; GA MŠk(CZ) ME08006 Grant - others:HHMI(US) 55005624; -(XE) LSHG-CT-2005-019015 Institutional research plan: CEZ:AV0Z50110509 Source of funding: N - neverejné zdroje ; R - rámcový projekt EK Keywords : SNP * rat * complete map Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 30.259, year: 2008

  16. Manufacturing High-Quality Carbon Nanotubes at Lower Cost

    Science.gov (United States)

    Benavides, Jeanette M.; Lidecker, Henning

    2004-01-01

    A modified electric-arc welding process has been developed for manufacturing high-quality batches of carbon nanotubes at relatively low cost. Unlike in some other processes for making carbon nanotubes, metal catalysts are not used and, consequently, it is not necessary to perform extensive cleaning and purification. Also, unlike some other processes, this process is carried out at atmospheric pressure under a hood instead of in a closed, pressurized chamber; as a result, the present process can be implemented more easily. Although the present welding-based process includes an electric arc, it differs from a prior electric-arc nanotube-production process. The welding equipment used in this process includes an AC/DC welding power source with an integral helium-gas delivery system and circulating water for cooling an assembly that holds one of the welding electrodes (in this case, the anode). The cathode is a hollow carbon (optionally, graphite) rod having an outside diameter of 2 in. (approximately equal to 5.1 cm) and an inside diameter of 5/8 in. (approximately equal to 1.6 cm). The cathode is partly immersed in a water bath, such that it protrudes about 2 in. (about 5.1 cm) above the surface of the water. The bottom end of the cathode is held underwater by a clamp, to which is connected the grounding cable of the welding power source. The anode is a carbon rod 1/8 in. (approximately equal to 0.3 cm) in diameter. The assembly that holds the anode includes a thumbknob- driven mechanism for controlling the height of the anode. A small hood is placed over the anode to direct a flow of helium downward from the anode to the cathode during the welding process. A bell-shaped exhaust hood collects the helium and other gases from the process. During the process, as the anode is consumed, the height of the anode is adjusted to maintain an anode-to-cathode gap of 1 mm. The arc-welding process is continued until the upper end of the anode has been lowered to a specified height

  17. Numerical determination of injector design for high beam quality

    International Nuclear Information System (INIS)

    Boyd, J.K.

    1985-01-01

    The performance of a free electron laser strongly depends on the electron beam quality or brightness. The electron beam is transported into the free electron laser after it has been accelerated to the desired energy. Typically the maximum beam brightness produced by an accelerator is constrained by the beam brightness deliverd by the accelerator injector. Thus it is important to design the accelerator injector to yield the required electron beam brightness. The DPC (Darwin Particle Code) computer code has been written to numerically model accelerator injectors. DPC solves for the transport of a beam from emission through acceleration up to the full energy of the injector. The relativistic force equation is solved to determine particle orbits. Field equations are solved for self consistent electric and magnetic fields in the Darwin approximation. DPC has been used to investigate the beam quality consequences of A-K gap, accelerating stress, electrode configuration and axial magnetic field profile

  18. 'Radiooncology 2007: High quality of life, the ultimate goal'. Abstracts

    International Nuclear Information System (INIS)

    2007-01-01

    The 13th annual congress of Deutsche Gesellschaft fuer Radioonkologie e.V. discussed clinical radiotherapy, medical physics and radiation biology, as well as an extensive programme of working groups on radiology in medical technology, care, and office. The focus was on new equipment (from image-supported to image-guided radiotherapy) and new approaches of targeted tumour therapy. Aspects of life quality are coming to the fore and will get even more important in the future. (orig.)

  19. High image quality sub 100 picosecond gated framing camera development

    International Nuclear Information System (INIS)

    Price, R.H.; Wiedwald, J.D.

    1983-01-01

    A major challenge for laser fusion is the study of the symmetry and hydrodynamic stability of imploding fuel capsules. Framed x-radiographs of 10-100 ps duration, excellent image quality, minimum geometrical distortion (< 1%), dynamic range greater than 1000, and more than 200 x 200 pixels are required for this application. Recent progress on a gated proximity focused intensifier which meets these requirements is presented

  20. The High Flying Leadership Qualities: What Matters the Most

    Science.gov (United States)

    2016-04-01

    operational and functional background of its personnel steeped in both DoD and industry experience. Research Methodology Based on their experiences...DeLorean Motors, Levitz Furniture , Enron, and many other corporations like these learned what happens when key leadership qualities lose all lift...graduate of the Canadian Force Command and Staff College in Toronto, Ontario, Canada; and the U.S. Army War College in Carlisle Barracks

  1. Diversity in 113 cowpea [Vigna unguiculata (L) Walp] accessions assessed with 458 SNP markers.

    Science.gov (United States)

    Egbadzor, Kenneth F; Ofori, Kwadwo; Yeboah, Martin; Aboagye, Lawrence M; Opoku-Agyeman, Michael O; Danquah, Eric Y; Offei, Samuel K

    2014-01-01

    Single Nucleotide Polymorphism (SNP) markers were used in characterization of 113 cowpea accessions comprising of 108 from Ghana and 5 from abroad. Leaf tissues from plants cultivated at the University of Ghana were genotyped at KBioscience in the United Kingdom. Data was generated for 477 SNPs, out of which 458 revealed polymorphism. The results were used to analyze genetic dissimilarity among the accessions using Darwin 5 software. The markers discriminated among all of the cowpea accessions and the dissimilarity values which ranged from 0.006 to 0.63 were used for factorial plot. Unexpected high levels of heterozygosity were observed on some of the accessions. Accessions known to be closely related clustered together in a dendrogram drawn with WPGMA method. A maximum length sub-tree which comprised of 48 core accessions was constructed. The software package structure was used to separate accessions into three groups, and the programme correctly identified varieties that were known hybrids. The hybrids were those accessions with numerous heterozygous loci. The structure plot showed closely related accessions with similar genome patterns. The SNP markers were more efficient in discriminating among the cowpea germplasm than morphological, seed protein polymorphism and simple sequence repeat studies reported earlier on the same collection.

  2. Snpdat: Easy and rapid annotation of results from de novo snp discovery projects for model and non-model organisms

    Directory of Open Access Journals (Sweden)

    Doran Anthony G

    2013-02-01

    Full Text Available Abstract Background Single nucleotide polymorphisms (SNPs are the most abundant genetic variant found in vertebrates and invertebrates. SNP discovery has become a highly automated, robust and relatively inexpensive process allowing the identification of many thousands of mutations for model and non-model organisms. Annotating large numbers of SNPs can be a difficult and complex process. Many tools available are optimised for use with organisms densely sampled for SNPs, such as humans. There are currently few tools available that are species non-specific or support non-model organism data. Results Here we present SNPdat, a high throughput analysis tool that can provide a comprehensive annotation of both novel and known SNPs for any organism with a draft sequence and annotation. Using a dataset of 4,566 SNPs identified in cattle using high-throughput DNA sequencing we demonstrate the annotations performed and the statistics that can be generated by SNPdat. Conclusions SNPdat provides users with a simple tool for annotation of genomes that are either not supported by other tools or have a small number of annotated SNPs available. SNPdat can also be used to analyse datasets from organisms which are densely sampled for SNPs. As a command line tool it can easily be incorporated into existing SNP discovery pipelines and fills a niche for analyses involving non-model organisms that are not supported by many available SNP annotation tools. SNPdat will be of great interest to scientists involved in SNP discovery and analysis projects, particularly those with limited bioinformatics experience.

  3. Analytical and statistical consideration on the use of the ISAG-ICAR-SNP bovine panel for parentage control, using the Illumina BeadChip technology: example on the German Holstein population.

    Science.gov (United States)

    Schütz, Ekkehard; Brenig, Bertram

    2015-02-05

    Parentage control is moving from short tandem repeats- to single nucleotide polymorphism (SNP) systems. For SNP-based parentage control in cattle, the ISAG-ICAR Committee proposes a set of 100/200 SNPs but quality criteria are lacking. Regarding German Holstein-Friesian cattle with only a limited number of evaluated individuals, the exclusion probability is not well-defined. We propose a statistical procedure for excluding single SNPs from parentage control, based on case-by-case evaluation of the GenCall score, to minimize parentage exclusion, based on miscalled genotypes. Exclusion power of the ISAG-ICAR SNPs used for the German Holstein-Friesian population was adjusted based on the results of more than 25,000 individuals. Experimental data were derived from routine genomic selection analyses of the German Holstein-Friesian population using the Illumina BovineSNP50 v2 BeadChip (20,000 individuals) or the EuroG10K variant (7000 individuals). Averages and standard deviations of GenCall scores for the 200 SNPs of the ISAG-ICAR recommended panel were calculated and used to calculate the downward Z-value. Based on minor allelic frequencies in the Holstein-Friesian population, one minus exclusion probability was equal to 1.4×10⁻¹⁰ and 7.2×10⁻²⁶, with one and two parents, respectively. Two monomorphic SNPs from the 100-SNP ISAG-ICAR core-panel did not contribute. Simulation of 10,000 parentage control combinations, using the GenCall score data from both BeadChips, showed that with a Z-value greater than 3.66 only about 2.5% parentages were excluded, based on the ISAG-ICAR recommendations (core-panel: ≥ 90 SNPs for one, ≥ 85 SNPs for two parents). When applied to real data from 1750 single parentage assessments, the optimal threshold was determined to be Z = 5.0, with only 34 censored cases and reduction to four (0.2%) doubtful parentages. About 70 parentage exclusions due to weak genotype calls were avoided, whereas true exclusions (n = 34) were

  4. Water Quality: A Field-Based Quality Testing Program for Middle Schools and High Schools.

    Science.gov (United States)

    Massachusetts State Water Resources Authority, Boston.

    This manual contains background information, lesson ideas, procedures, data collection and reporting forms, suggestions for interpreting results, and extension activities to complement a water quality field testing program. Information on testing water temperature, water pH, dissolved oxygen content, biochemical oxygen demand, nitrates, total…

  5. SNP Analysis and Whole Exome Sequencing: Their Application in the Analysis of a Consanguineous Pedigree Segregating Ataxia

    Directory of Open Access Journals (Sweden)

    Sarah L. Nickerson

    2015-10-01

    Full Text Available Autosomal recessive cerebellar ataxia encompasses a large and heterogeneous group of neurodegenerative disorders. We employed single nucleotide polymorphism (SNP analysis and whole exome sequencing to investigate a consanguineous Maori pedigree segregating ataxia. We identified a novel mutation in exon 10 of the SACS gene: c.7962T>G p.(Tyr2654*, establishing the diagnosis of autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS. Our findings expand both the genetic and phenotypic spectrum of this rare disorder, and highlight the value of high-density SNP analysis and whole exome sequencing as powerful and cost-effective tools in the diagnosis of genetically heterogeneous disorders such as the hereditary ataxias.

  6. Real-World Solutions for Developing High-Quality PHP Frameworks and Applications

    CERN Document Server

    Bergmann, Sebastian

    2011-01-01

    Learn to develop high-quality applications and frameworks in PHP Packed with in-depth information and step-by-step guidance, this book escorts you through the process of creating, maintaining and extending sustainable software of high quality with PHP. World-renowned PHP experts present real-world case studies for developing high-quality applications and frameworks in PHP that can easily be adapted to changing business requirements. . They offer different approaches to solving  typical development and quality assurance problems that every developer needs to know and master.Details the process

  7. A SNP uncoupling Mina expression from the TGFβ signaling pathway.

    Science.gov (United States)

    Lian, Shang L; Mihi, Belgacem; Koyanagi, Madoka; Nakayama, Toshinori; Bix, Mark

    2018-03-01

    Mina is a JmjC family 2-oxoglutarate oxygenase with pleiotropic roles in cell proliferation, cancer, T cell differentiation, pulmonary inflammation, and intestinal parasite expulsion. Although Mina expression varies according to cell-type, developmental stage and activation state, its transcriptional regulation is poorly understood. Across inbred mouse strains, Mina protein level exhibits a bimodal distribution, correlating with inheritance of a biallelic haplotype block comprising 21 promoter/intron 1-region SNPs. We previously showed that heritable differences in Mina protein level are transcriptionally regulated. Accordingly, we decided to test the hypothesis that at least one of the promoter/intron 1-region SNPs perturbs a Mina cis-regulatory element (CRE). Here, we have comprehensively scanned for CREs across a Mina locus-spanning 26-kilobase genomic interval. We discovered 8 potential CREs and functionally validated 4 of these, the strongest of which (E2), residing in intron 1, contained a SNP whose BALB/c-but not C57Bl/6 allele-abolished both Smad3 binding and transforming growth factor beta (TGFβ) responsiveness. Our results demonstrate the TGFβ signaling pathway plays a critical role in regulating Mina expression and SNP rs4191790 controls heritable variation in Mina expression level, raising important questions regarding the evolution of an allele that uncouples Mina expression from the TGFβ signaling pathway. © 2017 The Authors. Immunity, Inflammation and Disease Published by John Wiley & Sons Ltd.

  8. Idea on patent ; It is high time to stress quality

    International Nuclear Information System (INIS)

    2012-03-01

    This book deals with patent stressing on the quality, which includes from idea to technical business, It's simple to register the computer program, why do patent lawyer appoint the patent attorney's office? construction of patent right range, a good patent and a bad patent, strong patent and weak patent. It doesn't allow for Dus to use as we like, each patent has different value, Let's write technical specifications, advice on talking for invention with a patent attorney's office and what kind of task do intellectual property division do?

  9. High-quality PWO crystals for the PANDA-EMC

    International Nuclear Information System (INIS)

    Novotny, R W; Bremer, D; Dormenev, V; Drexler, P; Eissner, T; Kuske, T; Moritz, M

    2011-01-01

    The paper provides a status report on the crystal production and quality control of a major part of the PbWO 4 crystals for the PANDA-EMC. The results confirm the excellent performance of the new generation of PWO-II. The mechanism of stimulated recovery provides an additional tool to recover radiation damage at room and low temperatures by applying an external infrared light source. Even on-line recovery can be considered if the photo sensor is insensitive in that particular wavelength region.

  10. Measurement system with high accuracy for laser beam quality.

    Science.gov (United States)

    Ke, Yi; Zeng, Ciling; Xie, Peiyuan; Jiang, Qingshan; Liang, Ke; Yang, Zhenyu; Zhao, Ming

    2015-05-20

    Presently, most of the laser beam quality measurement system collimates the optical path manually with low efficiency and low repeatability. To solve these problems, this paper proposed a new collimated method to improve the reliability and accuracy of the measurement results. The system accuracy controlled the position of the mirror to change laser beam propagation direction, which can realize the beam perpendicularly incident to the photosurface of camera. The experiment results show that the proposed system has good repeatability and the measuring deviation of M2 factor is less than 0.6%.

  11. Rehosting of Bacterial Chaperones for High-Quality Protein Production▿

    Science.gov (United States)

    Martínez-Alonso, Mónica; Toledo-Rubio, Verónica; Noad, Rob; Unzueta, Ugutz; Ferrer-Miralles, Neus; Roy, Polly; Villaverde, Antonio

    2009-01-01

    Coproduction of DnaK/DnaJ in Escherichia coli enhances solubility but promotes proteolytic degradation of their substrates, minimizing the yield of unstable polypeptides. Higher eukaryotes have orthologs of DnaK/DnaJ but lack the linked bacterial proteolytic system. By coexpression of DnaK and DnaJ in insect cells with inherently misfolding-prone recombinant proteins, we demonstrate simultaneous improvement of soluble protein yield and quality and proteolytic stability. Thus, undesired side effects of bacterial folding modulators can be avoided by appropriate rehosting in heterologous cell expression systems. PMID:19820142

  12. Health-Related Quality of Life in Children with High-Functioning Autism

    Science.gov (United States)

    Potvin, Marie-Christine; Snider, Laurie; Prelock, Patricia A.; Wood-Dauphinee, Sharon; Kehayia, Eva

    2015-01-01

    The health-related quality of life of school-aged children with high-functioning autism is poorly understood. The objectives of this study were to compare the health-related quality of life of children with high-functioning autism to that of typically developing peers and to compare child-self and parent-proxy reports of health-related quality of…

  13. Publishing high-quality climate data on the semantic web

    Science.gov (United States)

    Woolf, Andrew; Haller, Armin; Lefort, Laurent; Taylor, Kerry

    2013-04-01

    The effort over more than a decade to establish the semantic web [Berners-Lee et. al., 2001] has received a major boost in recent years through the Open Government movement. Governments around the world are seeking technical solutions to enable more open and transparent access to Public Sector Information (PSI) they hold. Existing technical protocols and data standards tend to be domain specific, and so limit the ability to publish and integrate data across domains (health, environment, statistics, education, etc.). The web provides a domain-neutral platform for information publishing, and has proven itself beyond expectations for publishing and linking human-readable electronic documents. Extending the web pattern to data (often called Web 3.0) offers enormous potential. The semantic web applies the basic web principles to data [Berners-Lee, 2006]: using URIs as identifiers (for data objects and real-world 'things', instead of documents) making the URIs actionable by providing useful information via HTTP using a common exchange standard (serialised RDF for data instead of HTML for documents) establishing typed links between information objects to enable linking and integration Leading examples of 'linked data' for publishing PSI may be found in both the UK (http://data.gov.uk/linked-data) and US (http://www.data.gov/page/semantic-web). The Bureau of Meteorology (BoM) is Australia's national meteorological agency, and has a new mandate to establish a national environmental information infrastructure (under the National Plan for Environmental Information, NPEI [BoM, 2012a]). While the initial approach is based on the existing best practice Spatial Data Infrastructure (SDI) architecture, linked-data is being explored as a technological alternative that shows great promise for the future. We report here the first trial of government linked-data in Australia under data.gov.au. In this initial pilot study, we have taken BoM's new high-quality reference surface

  14. Quality Improvement, Inventory Management, Lead Time Reduction and Production Scheduling in High-Mix Manufacturing Environments

    Science.gov (United States)

    2017-01-13

    Quality Improvement , Inventory Management, Lead Time Reduction and Production Scheduling in High-mix Manufacturing Environments by Sean Daigle B.S...Mechanical Engineering Chairman, Department Committee on Graduate Theses 2 Quality Improvement , Inventory Management, Lead Time Reduction and... Production Scheduling in High-mix Manufacturing Environments by Sean Daigle Submitted to the Department of Mechanical Engineering on January 13, 2017, in

  15. Optimization of nitridation conditions for high quality inter-polysilicon dielectric layers

    NARCIS (Netherlands)

    Klootwijk, J.H.; Bergveld, H.J.; van Kranenburg, H.; Woerlee, P.H.; Wallinga, Hans

    1996-01-01

    Nitridation of deposited high temperature oxides (HTO) was studied to form high quality inter-polysilicon dielectric layers for embedded non volatile memories. Good quality dielectric layers were obtained earlier by using an optimized deposition of polysilicon and by performing a post-dielectric

  16. Bridges to Excellence--recognizing high-quality care: analysis of physician quality and resource use.

    Science.gov (United States)

    Rosenthal, Meredith B; de Brantes, Francois S; Sinaiko, Anna D; Frankel, Matthew; Robbins, Russell D; Young, Sara

    2008-10-01

    To examine whether physicians who sought and received Bridges to Excellence (BTE) recognition performed better than similar physicians on a standardized set of population-based performance measures. Cross-sectional comparison of performance data. Using a claims dataset of all commercially insured members from 6 health plans in Massachusetts, we examined population-based measures of quality and resource use for physicians recognized by the BTE programs Physician Office Link and Diabetes Care Link, compared with nonrecognized physicians in the same specialties. Differences in performance were tested using generalized linear models. Physician Office Link-recognized physicians performed significantly better than their nonrecognized peers on measures of cervical cancer screening, mammography, and glycosylated hemoglobin testing. Diabetes Care Link-recognized physicians performed significantly better on all 4 diabetes process measures of quality, with the largest differences observed in microalbumin screening (17.7%). Patients of Physician Office Link-recognized physicians had a significantly greater percentage of their resource use accounted for by evaluation and management services (3.4%), and a smaller percentage accounted for by facility (-1.6%), inpatient ancillary (-0.1%), and nonmanagement outpatient services (-1.0%). After adjustment for patient age and sex, and case mix, Physician Office Link-recognized physicians had significantly fewer episodes per patient (0.13) and lower resource use per episode (dollars 130), but findings were mixed for Diabetes Care Link-recognized physicians. Our findings suggest that the BTE approach to ascertaining physician quality identifies physicians who perform better on claims-based quality measures and primary care physicians who use a less resource-intensive practice style.

  17. Academic coordination at university: Strategies for high quality education

    Directory of Open Access Journals (Sweden)

    Maria del Mar Durán Bellonch

    2009-08-01

    Full Text Available Most lecturers and professors involved in teaching School Management and Education Management courses have been engaged in developing some innovative actions to improve the training quality that we offer to students in the Pedagogy degree at the Autonomous University of Barcelona. These actions are aimed at increasing co-ordination among the teaching staff when designing and implementing the course curricula. Co-ordination meetings, exchanges of teaching experiences, discussions about what, how and when to teach the different contents, in which courses and at what level, methodological issues pointed out through technical description cards or the elaboration of study cases to be solved have become the basis of relevant actions during the last academic years. This paper explains each one of them, and provides useful information about the theoretical background, the process carried out, some of the results obtained, the output and the tools created.

  18. Possibilities of obtaining and controlling high-quality pressure castings

    Directory of Open Access Journals (Sweden)

    S. Pietrowski

    2011-07-01

    Full Text Available The paper presents the influence of the type of furnace charging melting, refining and modification silumins 226 and 231 on the porosity and microstructure of castings. It was shown that in order to reduce or eliminate the porosity of the castings is necessary to the refining ECOSAL-AL113 of liquid silumin both in the melting furnace, and in the ladle and an additional nitrogen, in the heat furnace modified and refining with nitrogen. To control the effects of refining and modifying the TDA method was used. It was found that based on crystal- lization curve can be qualitatively assess the gas porosity of the castings. In order to control and quality control silumins author developed a computer program using the method of TDA, which sets out: Rm, A5, HB and casting porosity P and the concentration of hydrogen in them. The program also informs the technological procedures to be performed for liquid silumin improper preparation.

  19. Generation and analysis of ESTs from the eastern oyster, Crassostrea virginica Gmelin and identification of microsatellite and SNP markers

    Directory of Open Access Journals (Sweden)

    Wallace Richard

    2007-06-01

    Full Text Available Abstract Background The eastern oyster, Crassostrea virginica (Gmelin 1791, is an economically important species cultured in many areas in North America. It is also ecologically important because of the impact of its filter feeding behaviour on water quality. Populations of C. virginica have been threatened by overfishing, habitat degradation, and diseases. Through genome research, strategies are being developed to reverse its population decline. However, large-scale expressed sequence tag (EST resources have been lacking for this species. Efficient generation of EST resources from this species has been hindered by a high redundancy of transcripts. The objectives of this study were to construct a normalized cDNA library for efficient EST analysis, to generate thousands of ESTs, and to analyze the ESTs for microsatellites and potential single nucleotide polymorphisms (SNPs. Results A normalized and subtracted C. virginica cDNA library was constructed from pooled RNA isolated from hemocytes, mantle, gill, gonad and digestive tract, muscle, and a whole juvenile oyster. A total of 6,528 clones were sequenced from this library generating 5,542 high-quality EST sequences. Cluster analysis indicated the presence of 635 contigs and 4,053 singletons, generating a total of 4,688 unique sequences. About 46% (2,174 of the unique ESTs had significant hits (E-value ≤ 1e-05 to the non-redundant protein database; 1,104 of which were annotated using Gene Ontology (GO terms. A total of 35 microsatellites were identified from the ESTs, with 18 having sufficient flanking sequences for primer design. A total of 6,533 putative SNPs were also identified using all existing and the newly generated EST resources of the eastern oysters. Conclusion A high quality normalized cDNA library was constructed. A total of 5,542 ESTs were generated representing 4,688 unique sequences. Putative microsatellite and SNP markers were identified. These genome resources provide the

  20. prediction of bread-making quality using size exclusion high

    African Journals Online (AJOL)

    ACSS

    Variation in the distribution of protein molecular weight in wheat (Triticum aestivum), influences ... with high G/G ratios in SDS-insoluble protein fraction were Sceptre x Nata and Kariega x Sceptre. ...... Molecular characterisation and dynamic.

  1. High-quality single crystals for neutron experiments

    Indian Academy of Sciences (India)

    studies and our collaborative research projects with other UK and international groups will be discussed. Keywords. Crystal growth; floating zone method; neutron scattering. ... of single crystals of new materials is a highly competitive business.

  2. A low-density SNP array for analyzing differential selection in freshwater and marine populations of threespine stickleback (Gasterosteus aculeatus).

    Science.gov (United States)

    Ferchaud, Anne-Laure; Pedersen, Susanne H; Bekkevold, Dorte; Jian, Jianbo; Niu, Yongchao; Hansen, Michael M

    2014-10-06

    The threespine stickleback (Gasterosteus aculeatus) has become an important model species for studying both contemporary and parallel evolution. In particular, differential adaptation to freshwater and marine environments has led to high differentiation between freshwater and marine stickleback populations at the phenotypic trait of lateral plate morphology and the underlying candidate gene Ectodysplacin (EDA). Many studies have focused on this trait and candidate gene, although other genes involved in marine-freshwater adaptation may be equally important. In order to develop a resource for rapid and cost efficient analysis of genetic divergence between freshwater and marine sticklebacks, we generated a low-density SNP (Single Nucleotide Polymorphism) array encompassing markers of chromosome regions under putative directional selection, along with neutral markers for background. RAD (Restriction site Associated DNA) sequencing of sixty individuals representing two freshwater and one marine population led to the identification of 33,993 SNP markers. Ninety-six of these were chosen for the low-density SNP array, among which 70 represented SNPs under putatively directional selection in freshwater vs. marine environments, whereas 26 SNPs were assumed to be neutral. Annotation of these regions revealed several genes that are candidates for affecting stickleback phenotypic variation, some of which have been observed in previous studies whereas others are new. We have developed a cost-efficient low-density SNP array that allows for rapid screening of polymorphisms in threespine stickleback. The array provides a valuable tool for analyzing adaptive divergence between freshwater and marine stickleback populations beyond the well-established candidate gene Ectodysplacin (EDA).

  3. Conclusive evidence for hexasomic inheritance in chrysanthemum based on analysis of a 183 k SNP array.

    Science.gov (United States)

    van Geest, Geert; Voorrips, Roeland E; Esselink, Danny; Post, Aike; Visser, Richard Gf; Arens, Paul

    2017-08-07

    Cultivated chrysanthemum is an outcrossing hexaploid (2n = 6× = 54) with a disputed mode of inheritance. In this paper, we present a single nucleotide polymorphism (SNP) selection pipeline that was used to design an Affymetrix Axiom array with 183 k SNPs from RNA sequencing data (1). With this array, we genotyped four bi-parental populations (with sizes of 405, 53, 76 and 37 offspring plants respectively), and a cultivar panel of 63 genotypes. Further, we present a method for dosage scoring in hexaploids from signal intensities of the array based on mixture models (2) and validation of selection steps in the SNP selection pipeline (3). The resulting genotypic data is used to draw conclusions on the mode of inheritance in chrysanthemum (4), and to make an inference on allelic expression bias (5). With use of the mixture model approach, we successfully called the dosage of 73,936 out of 183,130 SNPs (40.4%) that segregated in any of the bi-parental populations. To investigate the mode of inheritance, we analysed markers that segregated in the large bi-parental population (n = 405). Analysis of segregation of duplex x nulliplex SNPs resulted in evidence for genome-wide hexasomic inheritance. This evidence was substantiated by the absence of strong linkage between markers in repulsion, which indicated absence of full disomic inheritance. We present the success rate of SNP discovery out of RNA sequencing data as affected by different selection steps, among which SNP coverage over genotypes and use of different types of sequence read mapping software. Genomic dosage highly correlated with relative allele coverage from the RNA sequencing data, indicating that most alleles are expressed according to their genomic dosage. The large population, genotyped with a very large number of markers, is a unique framework for extensive genetic analyses in hexaploid chrysanthemum. As starting point, we show conclusive evidence for genome-wide hexasomic inheritance.

  4. A SNP resource for studying North American moose [version 1; referees: 2 approved, 1 approved with reservations

    Directory of Open Access Journals (Sweden)

    Theodore S. Kalbfleisch

    2018-01-01

    Full Text Available Background: Moose (Alces alces colonized the North American continent from Asia less than 15,000 years ago, and spread across the boreal forest regions of Canada and the northern United States (US.  Contemporary populations have low genetic diversity, due either to low number of individuals in the original migration (founder effect, and/or subsequent population bottlenecks in North America.  Genetic tests based on informative single nucleotide polymorphism (SNP markers are helpful in forensic and wildlife conservation activities, but have been difficult to develop for moose, due to the lack of a reference genome assembly and whole genome sequence (WGS data. Methods:  WGS data were generated for four individual moose from the US states of Alaska, Idaho, Wyoming, and Vermont with minimum and average genome coverage depths of 14- and 19-fold, respectively.  Cattle and sheep reference genomes were used for aligning sequence reads and identifying moose SNPs. Results:  Approximately 11% and 9% of moose WGS reads aligned to cattle and sheep genomes, respectively.  The reads clustered at genomic segments, where sequence identity between these species was greater than 95%.  In these segments, average mapped read depth was approximately 19-fold.  Sets of 46,005 and 36,934 high-confidence SNPs were identified from cattle and sheep comparisons, respectively, with 773 and 552 of those having minor allele frequency of 0.5 and conserved flanking sequences in all three species.  Among the four moose, heterozygosity and allele sharing of SNP genotypes were consistent with decreasing levels of moose genetic diversity from west to east.  A minimum set of 317 SNPs, informative across all four moose, was selected as a resource for future SNP assay design. Conclusions:  All SNPs and associated information are available, without restriction, to support development of SNP-based tests for animal identification, parentage determination, and estimating

  5. Switchgrass genomic diversity, ploidy, and evolution: novel insights from a network-based SNP discovery protocol.

    Directory of Open Access Journals (Sweden)

    Fei Lu

    Full Text Available Switchgrass (Panicum virgatum L. is a perennial grass that has been designated as an herbaceous model biofuel crop for the United States of America. To facilitate accelerated breeding programs of switchgrass, we developed both an association panel and linkage populations for genome-wide association study (GWAS and genomic selection (GS. All of the 840 individuals were then genotyped using genotyping by sequencing (GBS, generating 350 GB of sequence in total. As a highly heterozygous polyploid (tetraploid and octoploid species lacking a reference genome, switchgrass is highly intractable with earlier methodologies of single nucleotide polymorphism (SNP discovery. To access the genetic diversity of species like switchgrass, we developed a SNP discovery pipeline based on a network approach called the Universal Network-Enabled Analysis Kit (UNEAK. Complexities that hinder single nucleotide polymorphism discovery, such as repeats, paralogs, and sequencing errors, are easily resolved with UNEAK. Here, 1.2 million putative SNPs were discovered in a diverse collection of primarily upland, northern-adapted switchgrass populations. Further analysis of this data set revealed the fundamentally diploid nature of tetraploid switchgrass. Taking advantage of the high conservation of genome structure between switchgrass and foxtail millet (Setaria italica (L. P. Beauv., two parent-specific, synteny-based, ultra high-density linkage maps containing a total of 88,217 SNPs were constructed. Also, our results showed clear patterns of isolation-by-distance and isolation-by-ploidy in natural populations of switchgrass. Phylogenetic analysis supported a general south-to-north migration path of switchgrass. In addition, this analysis suggested that upland tetraploid arose from upland octoploid. All together, this study provides unparalleled insights into the diversity, genomic complexity, population structure, phylogeny, phylogeography, ploidy, and evolutionary dynamics

  6. Ubiquitin-conjugating enzyme E2-like gene associated to pathogen response in Concholepas concholepas: SNP identification and transcription expression.

    Science.gov (United States)

    Núñez-Acuña, Gustavo; Aguilar-Espinoza, Andrea; Chávez-Mardones, Jacqueline; Gallardo-Escárate, Cristian

    2012-10-01

    Ubiquitin-conjugated E2 enzyme (UBE2) is one of the main components of the proteasome degradation cascade. Previous studies have shown an increase of expression levels in individuals challenged to some pathogen organism such as virus and bacteria. The study was to characterize the immune response of UBE2 gene in the gastropod Concholepas concholepas through expression analysis and single nucleotide polymorphisms (SNP) discovery. Hence, UBE2 was identified from a cDNA library by 454 pyrosequencing, while SNP identification and validation were performed using De novo assembly and high resolution melting analysis. Challenge trials with Vibrio anguillarum was carried out to evaluate the relative transcript abundance of UBE2 gene from two to thirty-three hours post-treatment. The results showed a partial UBE2 sequence of 889 base pair (bp) with a partial coding region of 291 bp. SNP variation (A/C) was observed at the 546th position. Individuals challenged by V. anguillarum showed an overexpression of the UBE2 gene, the expression being significantly higher in homozygous individuals (AA) than (CC) or heterozygous individuals (A/C). This study contributes useful information relating to the UBE2 gene and its association with innate immune response in marine invertebrates. Copyright © 2012 Elsevier Ltd. All rights reserved.

  7. Quality

    International Nuclear Information System (INIS)

    Burnett, N.; Jeffries, J.; Mach, J.; Robson, M.; Pajot, D.; Harrigan, J.; Lebsack, T.; Mullen, D.; Rat, F.; Theys, P.

    1993-01-01

    What is quality? How do you achieve it? How do you keep it once you have got it. The answer for industry at large is the three-step hierarchy of quality control, quality assurance and Total quality Management. An overview is given of the history of quality movement, illustrated with examples from Schlumberger operations, as well as the oil industry's approach to quality. An introduction of the Schlumberger's quality-associated ClientLink program is presented. 15 figs., 4 ills., 16 refs

  8. SNP Discovery for mapping alien introgressions in wheat

    Science.gov (United States)

    2014-01-01

    Background Monitoring alien introgressions in crop plants is difficult due to the lack of genetic and molecular mapping information on the wild crop relatives. The tertiary gene pool of wheat is a very important source of genetic variability for wheat improvement against biotic and abiotic stresses. By exploring the 5Mg short arm (5MgS) of Aegilops geniculata, we can apply chromosome genomics for the discovery of SNP markers and their use for monitoring alien introgressions in wheat (Triticum aestivum L). Results The short arm of chromosome 5Mg of Ae. geniculata Roth (syn. Ae. ovata L.; 2n = 4x = 28, UgUgMgMg) was flow-sorted from a wheat line in which it is maintained as a telocentric chromosome. DNA of the sorted arm was amplified and sequenced using an Illumina Hiseq 2000 with ~45x coverage. The sequence data was used for SNP discovery against wheat homoeologous group-5 assemblies. A total of 2,178 unique, 5MgS-specific SNPs were discovered. Randomly selected samples of 59 5MgS-specific SNPs were tested (44 by KASPar assay and 15 by Sanger sequencing) and 84% were validated. Of the selected SNPs, 97% mapped to a chromosome 5Mg addition to wheat (the source of t5MgS), and 94% to 5Mg introgressed from a different accession of Ae. geniculata substituting for chromosome 5D of wheat. The validated SNPs also identified chromosome segments of 5MgS origin in a set of T5D-5Mg translocation lines; eight SNPs (25%) mapped to TA5601 [T5DL · 5DS-5MgS(0.75)] and three (8%) to TA5602 [T5DL · 5DS-5MgS (0.95)]. SNPs (gsnp_5ms83 and gsnp_5ms94), tagging chromosome T5DL · 5DS-5MgS(0.95) with the smallest introgression carrying resistance to leaf rust (Lr57) and stripe rust (Yr40), were validated in two released germplasm lines with Lr57 and Yr40 genes. Conclusion This approach should be widely applicable for the identification of species/genome-specific SNPs. The development of a large number of SNP markers will facilitate the precise introgression and

  9. SNP Discovery for mapping alien introgressions in wheat.

    Science.gov (United States)

    Tiwari, Vijay K; Wang, Shichen; Sehgal, Sunish; Vrána, Jan; Friebe, Bernd; Kubaláková, Marie; Chhuneja, Praveen; Doležel, Jaroslav; Akhunov, Eduard; Kalia, Bhanu; Sabir, Jamal; Gill, Bikram S

    2014-04-10

    Monitoring alien introgressions in crop plants is difficult due to the lack of genetic and molecular mapping information on the wild crop relatives. The tertiary gene pool of wheat is a very important source of genetic variability for wheat improvement against biotic and abiotic stresses. By exploring the 5Mg short arm (5MgS) of Aegilops geniculata, we can apply chromosome genomics for the discovery of SNP markers and their use for monitoring alien introgressions in wheat (Triticum aestivum L). The short arm of chromosome 5Mg of Ae. geniculata Roth (syn. Ae. ovata L.; 2n = 4x = 28, UgUgMgMg) was flow-sorted from a wheat line in which it is maintained as a telocentric chromosome. DNA of the sorted arm was amplified and sequenced using an Illumina Hiseq 2000 with ~45x coverage. The sequence data was used for SNP discovery against wheat homoeologous group-5 assemblies. A total of 2,178 unique, 5MgS-specific SNPs were discovered. Randomly selected samples of 59 5MgS-specific SNPs were tested (44 by KASPar assay and 15 by Sanger sequencing) and 84% were validated. Of the selected SNPs, 97% mapped to a chromosome 5Mg addition to wheat (the source of t5MgS), and 94% to 5Mg introgressed from a different accession of Ae. geniculata substituting for chromosome 5D of wheat. The validated SNPs also identified chromosome segments of 5MgS origin in a set of T5D-5Mg translocation lines; eight SNPs (25%) mapped to TA5601 [T5DL · 5DS-5MgS(0.75)] and three (8%) to TA5602 [T5DL · 5DS-5MgS (0.95)]. SNPs (gsnp_5ms83 and gsnp_5ms94), tagging chromosome T5DL · 5DS-5MgS(0.95) with the smallest introgression carrying resistance to leaf rust (Lr57) and stripe rust (Yr40), were validated in two released germplasm lines with Lr57 and Yr40 genes. This approach should be widely applicable for the identification of species/genome-specific SNPs. The development of a large number of SNP markers will facilitate the precise introgression and monitoring of alien segments in crop

  10. The LPL S447X cSNP is associated with decreased blood pressure and plasma triglycerides, and reduced risk of coronary artery disease

    NARCIS (Netherlands)

    Clee, S. M.; Loubser, O.; Collins, J.; Kastelein, J. J.; Hayden, M. R.

    2001-01-01

    Linkage of the lipoprotein lipase (LPL) gene to blood pressure levels has been reported. The LPL S447X single nucleotide polymorphism (cSNP) has been associated with decreased triglycerides (TG), increased high density lipoprotein cholesterol, and a decreased risk of coronary artery disease (CAD),

  11. Population structure of Atlantic Mackerel inferred from RAD-seq derived SNP markers: effects of sequence clustering parameters and hierarchical SNP selection

    KAUST Repository

    Rodrí guez-Ezpeleta, Naiara; Bradbury, Ian R.; Mendibil, Iñ aki; Á lvarez, Paula; Cotano, Unai; Irigoien, Xabier

    2016-01-01

    : the maximum number of mismatches allowed to merge reads into a locus and the relatedness of the individuals used for genotype calling and SNP selection. Our study resolves the population structure of the Atlantic mackerel, but, most importantly, provides

  12. High quality actively cooled plasma-facing components for fusion

    International Nuclear Information System (INIS)

    Nygren, R.E.

    1995-01-01

    This paper interweaves some suggestions for developing actively cooled plasma-facing components (PFCs) for future fusion devices, with supporting examples taken from the design, fabrication and operation of Tore Supra's Phase III outboard pump limiter (OPL). This actively cooled midplane limiter, designed for heat and particle removal during long-pulse operation, has been operated under essentially thermally steady state conditions. Testing to identify braze flaws, analysis of the impact of joining flaws on the thermal-hydraulic performance of the OPL, and the extensive calorimetry and IR thermography used to confirm and update safe operating limits for power handling of the OPL are reviewed. This experience suggests that, for PFCs in future fusion devices, flaw-tolerant designs are possible; analyses of the impacts of flaws on performance can provide criteria for quality assurance; and validating appropriate methods of inspection for such flaws early in the design development of PFCs is prudent. The need for in-service monitoring is also discussed. (orig.)

  13. Health care in small prisons: incorporating high-quality standards.

    Science.gov (United States)

    Rieder, Jean-Pierre; Casillas, Alejandra; Mary, Gérard; Secretan, Anne-Dominique; Gaspoz, Jean-Michel; Wolff, Hans

    2013-01-01

    In the past, health management in Geneva's six post-trial prisons had been variable and inconsistent. In 2008, the unit of penitentiary medicine of the Geneva University Hospitals was mandated to re-organize and provide health care at all six prison facilities. The specific aim of this paper is to outline the example as a practical solution to some of the common challenges in unifying the structure and process of health services across multiple small facilities, while meeting European prison health and local quality standards. Geneva's post-trial prisons are small and close to one another in geographical proximity - ideal conditions for the construction of a health mobile team (HMT). This multidisciplinary mobile team operated like a community ambulatory care model; it was progressively launched in all prison facilities in Geneva. The authors incorporated an implementation strategy where health providers partnered with prison and community stakeholders in the health delivery model's development and adaption process. The model's strategic initiatives are described along the following areas, in light of other international prison health activity and prior care models: access to a health care professional, equivalence of care, patient consent, confidentiality, humanitarian interventions, and professional competence and independence. From the perspective of the HMT members, the authors provide the "lessons learned" through this experience, especially to providers who are working on prison health services reform and coordination improvement. The paper particularly stresses the importance of partnering with community health stakeholders and prison staff, a key component to the approach.

  14. A high-quality catalog of the Drosophila melanogaster proteome

    DEFF Research Database (Denmark)

    Brunner, Erich; Ahrens, Christian H.; Mohanty, Sonaly

    2007-01-01

    % of the predicted Drosophila melanogaster proteome by detecting 9,124 proteins from 498,000 redundant and 72,281 distinct peptide identifications. This unprecedented high proteome coverage for a complex eukaryote was achieved by combining sample diversity, multidimensional biochemical fractionation and analysis...

  15. Bust economics: foragers choose high quality habitats in lean times

    Directory of Open Access Journals (Sweden)

    Sonny S. Bleicher

    2016-01-01

    Full Text Available In environments where food resources are spatially variable and temporarily impoverished, consumers that encounter habitat patches with different food density should focus their foraging initially where food density is highest before they move to patches where food density is lower. Increasing missed opportunity costs should drive individuals progressively to patches with lower food density as resources in the initially high food density patches deplete. To test these expectations, we assessed the foraging decisions of two species of dasyurid marsupials (dunnarts: Sminthopsis hirtipes and S. youngsoni during a deep drought, or bust period, in the Simpson Desert of central Australia. Dunnarts were allowed access to three patches containing different food densities using an interview chamber experiment. Both species exhibited clear preference for the high density over the lower food density patches as measured in total harvested resources. Similarly, when measuring the proportion of resources harvested within the patches, we observed a marginal preference for patches with initially high densities. Models analyzing behavioral choices at the population level found no differences in behavior between the two species, but models analyzing choices at the individual level uncovered some variation. We conclude that dunnarts can distinguish between habitat patches with different densities of food and preferentially exploit the most valuable. As our observations were made during bust conditions, experiments should be repeated during boom times to assess the foraging economics of dunnarts when environmental resources are high.

  16. Whole high-quality light environment for humans and plants

    Science.gov (United States)

    Sharakshane, Anton

    2017-11-01

    Plants sharing a single light environment on a spaceship with a human being and bearing a decorative function should look as natural and attractive as possible. And consequently they can be illuminated only with white light with a high color rendering index. Can lighting optimized for a human eye be effective and appropriate for plants? Spectrum-based effects have been compared under artificial lighting of plants by high-pressure sodium lamps and general-purpose white LEDs. It has been shown that for the survey sample phytochrome photo-equilibria does not depend significantly on the parameters of white LED light, while the share of phytoactive blue light grows significantly as the color temperature increases. It has been revealed that yield photon flux is proportional to luminous efficacy and increases as the color temperature decreases, general color rendering index Ra and the special color rendering index R14 (green leaf) increase. General-purpose white LED lamps with a color temperature of 2700 K, Ra > 90 and luminous efficacy of 100 lm/W are as efficient as the best high-pressure sodium lamps, and at a higher luminous efficacy their yield photon flux per joule is even bigger in proportion. Here we show that demand for high color rendering white LED light is not contradictory to the agro-technical objectives.

  17. Pacifiplex: an ancestry-informative SNP panel centred on Australia and the Pacific region.

    Science.gov (United States)

    Santos, Carla; Phillips, Christopher; Fondevila, Manuel; Daniel, Runa; van Oorschot, Roland A H; Burchard, Esteban G; Schanfield, Moses S; Souto, Luis; Uacyisrael, Jolame; Via, Marc; Carracedo, Ángel; Lareu, Maria V

    2016-01-01

    The analysis of human population variation is an area of considerable interest in the forensic, medical genetics and anthropological fields. Several forensic single nucleotide polymorphism (SNP) assays provide ancestry-informative genotypes in sensitive tests designed to work with limited DNA samples, including a 34-SNP multiplex differentiating African, European and East Asian ancestries. Although assays capable of differentiating Oceanian ancestry at a global scale have become available, this study describes markers compiled specifically for differentiation of Oceanian populations. A sensitive multiplex assay, termed Pacifiplex, was developed and optimized in a small-scale test applicable to forensic analyses. The Pacifiplex assay comprises 29 ancestry-informative marker SNPs (AIM-SNPs) selected to complement the 34-plex test, that in a combined set distinguish Africans, Europeans, East Asians and Oceanians. Nine Pacific region study populations were genotyped with both SNP assays, then compared to four reference population groups from the HGDP-CEPH human diversity panel. STRUCTURE analyses estimated population cluster membership proportions that aligned with the patterns of variation suggested for each study population's currently inferred demographic histories. Aboriginal Taiwanese and Philippine samples indicated high East Asian ancestry components, Papua New Guinean and Aboriginal Australians samples were predominantly Oceanian, while other populations displayed cluster patterns explained by the distribution of divergence amongst Melanesians, Polynesians and Micronesians. Genotype data from Pacifiplex and 34-plex tests is particularly well suited to analysis of Australian Aboriginal populations and when combined with Y and mitochondrial DNA variation will provide a powerful set of markers for ancestry inference applied to modern Australian demographic profiles. On a broader geographic scale, Pacifiplex adds highly informative data for inferring the ancestry

  18. Genome wide SNP discovery in flax through next generation sequencing of reduced representation libraries

    Directory of Open Access Journals (Sweden)

    Kumar Santosh

    2012-12-01

    Full Text Available Abstract Background Flax (Linum usitatissimum L. is a significant fibre and oilseed crop. Current flax molecular markers, including isozymes, RAPDs, AFLPs and SSRs are of limited use in the construction of high density linkage maps and for association mapping applications due to factors such as low reproducibility, intense labour requirements and/or limited numbers. We report here on the use of a reduced representation library strategy combined with next generation Illumina sequencing for rapid and large scale discovery of SNPs in eight flax genotypes. SNP discovery was performed through in silico analysis of the sequencing data against the whole genome shotgun sequence assembly of flax genotype CDC Bethune. Genotyping-by-sequencing of an F6-derived recombinant inbred line population provided validation of the SNPs. Results Reduced representation libraries of eight flax genotypes were sequenced on the Illumina sequencing platform resulting in sequence coverage ranging from 4.33 to 15.64X (genome equivalents. Depending on the relatedness of the genotypes and the number and length of the reads, between 78% and 93% of the reads mapped onto the CDC Bethune whole genome shotgun sequence assembly. A total of 55,465 SNPs were discovered with the largest number of SNPs belonging to the genotypes with the highest mapping coverage percentage. Approximately 84% of the SNPs discovered were identified in a single genotype, 13% were shared between any two genotypes and the remaining 3% in three or more. Nearly a quarter of the SNPs were found in genic regions. A total of 4,706 out of 4,863 SNPs discovered in Macbeth were validated using genotyping-by-sequencing of 96 F6 individuals from a recombinant inbred line population derived from a cross between CDC Bethune and Macbeth, corresponding to a validation rate of 96.8%. Conclusions Next generation sequencing of reduced representation libraries was successfully implemented for genome-wide SNP discovery from

  19. The influence of knowledge management implementation toward the quality of high schools

    Directory of Open Access Journals (Sweden)

    Hilda Ainissyifa

    2012-09-01

    Full Text Available The purpose of this study is to analyze the influence of knowledge management implementation toward the quality of high schools. This study was conducted among five high schools under an education foundation. The analysis models used in the study were correlation analysis and t-test. The respondents were used as the profession references are 86 teachers. The result of the study shows that knowledge management implementation has a positive and significant influence toward the quality of high schools.

  20. Honey bee-inspired algorithms for SNP haplotype reconstruction problem

    Science.gov (United States)

    PourkamaliAnaraki, Maryam; Sadeghi, Mehdi

    2016-03-01

    Reconstructing haplotypes from SNP fragments is an important problem in computational biology. There have been a lot of interests in this field because haplotypes have been shown to contain promising data for disease association research. It is proved that haplotype reconstruction in Minimum Error Correction model is an NP-hard problem. Therefore, several methods such as clustering techniques, evolutionary algorithms, neural networks and swarm intelligence approaches have been proposed in order to solve this problem in appropriate time. In this paper, we have focused on various evolutionary clustering techniques and try to find an efficient technique for solving haplotype reconstruction problem. It can be referred from our experiments that the clustering methods relying on the behaviour of honey bee colony in nature, specifically bees algorithm and artificial bee colony methods, are expected to result in more efficient solutions. An application program of the methods is available at the following link. http://www.bioinf.cs.ipm.ir/software/haprs/

  1. Grouping preprocess for haplotype inference from SNP and CNV data

    International Nuclear Information System (INIS)

    Shindo, Hiroyuki; Chigira, Hiroshi; Nagaoka, Tomoyo; Inoue, Masato; Kamatani, Naoyuki

    2009-01-01

    The method of statistical haplotype inference is an indispensable technique in the field of medical science. The authors previously reported Hardy-Weinberg equilibrium-based haplotype inference that could manage single nucleotide polymorphism (SNP) data. We recently extended the method to cover copy number variation (CNV) data. Haplotype inference from mixed data is important because SNPs and CNVs are occasionally in linkage disequilibrium. The idea underlying the proposed method is simple, but the algorithm for it needs to be quite elaborate to reduce the calculation cost. Consequently, we have focused on the details on the algorithm in this study. Although the main advantage of the method is accuracy, in that it does not use any approximation, its main disadvantage is still the calculation cost, which is sometimes intractable for large data sets with missing values.

  2. SNP-VISTA: An Interactive SNPs Visualization Tool

    Energy Technology Data Exchange (ETDEWEB)

    Shah, Nameeta; Teplitsky, Michael V.; Pennacchio, Len A.; Hugenholtz, Philip; Hamann, Bernd; Dubchak, Inna L.

    2005-07-05

    Recent advances in sequencing technologies promise better diagnostics for many diseases as well as better understanding of evolution of microbial populations. Single Nucleotide Polymorphisms(SNPs) are established genetic markers that aid in the identification of loci affecting quantitative traits and/or disease in a wide variety of eukaryotic species. With today's technological capabilities, it is possible to re-sequence a large set of appropriate candidate genes in individuals with a given disease and then screen for causative mutations.In addition, SNPs have been used extensively in efforts to study the evolution of microbial populations, and the recent application of random shotgun sequencing to environmental samples makes possible more extensive SNP analysis of co-occurring and co-evolving microbial populations. The program is available at http://genome.lbl.gov/vista/snpvista.

  3. Grouping preprocess for haplotype inference from SNP and CNV data

    Energy Technology Data Exchange (ETDEWEB)

    Shindo, Hiroyuki; Chigira, Hiroshi; Nagaoka, Tomoyo; Inoue, Masato [Department of Electrical Engineering and Bioscience, School of Advanced Science and Engineering, Waseda University, 3-4-1, Okubo, Shinjuku-ku, Tokyo 169-8555 (Japan); Kamatani, Naoyuki, E-mail: masato.inoue@eb.waseda.ac.j [Institute of Rheumatology, Tokyo Women' s Medical University, 10-22, Kawada-cho, Shinjuku-ku, Tokyo 162-0054 (Japan)

    2009-12-01

    The method of statistical haplotype inference is an indispensable technique in the field of medical science. The authors previously reported Hardy-Weinberg equilibrium-based haplotype inference that could manage single nucleotide polymorphism (SNP) data. We recently extended the method to cover copy number variation (CNV) data. Haplotype inference from mixed data is important because SNPs and CNVs are occasionally in linkage disequilibrium. The idea underlying the proposed method is simple, but the algorithm for it needs to be quite elaborate to reduce the calculation cost. Consequently, we have focused on the details on the algorithm in this study. Although the main advantage of the method is accuracy, in that it does not use any approximation, its main disadvantage is still the calculation cost, which is sometimes intractable for large data sets with missing values.

  4. Achieving high-quality care: a view from NICE.

    Science.gov (United States)

    Leng, Gillian; Partridge, Gemma

    2018-01-01

    The National Institute for Health and Care Excellence (NICE) was established in 1999 to provide evidence-based guidance. The task of producing guidance by reviewing primary research data and using an advisory committee to develop evidence-based recommendations, is not straightforward. Guidance production is, however, less challenging than the task of putting evidence-based recommendations into practice.NICE is very sensitive to this challenge as, since 1999, over 1500 pieces of NICE guidance have been published. A number of pieces of guidance relate to heart disease, including pharmaceutical agents, new medical technologies and clinical guidelines. Examples include guidelines on acute heart failure and atrial fibrillation, and advice on technologies including edoxaban and implantable cardioverter defibrillators.The research evidence is clear that a change in practice rarely comes about as a result of simply disseminating guidance on best practice. Simple dissemination is particularly ineffective if the guidance has not been produced by a well-respected, credible organisation. It is also clear from the literature that implementation is more successful when more than one approach is taken, and when there is alignment between efforts at organisational, local and national levels.At an organisational level, there should be support from the Board for quality improvement, with ongoing measurement of progress. Resources should be provided for targeted change programmes, particularly where new guidance suggests improvements are required. A systematic process for putting change in place should include identifying barriers to change, agreeing interventions to overcome the barriers and drive forward improvement and planning for implementation and evaluation. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

  5. Modern High Technology Solutions for Quality and Longterm Vegetable Preservation

    International Nuclear Information System (INIS)

    Nacheva, I.; Miteva, D.; Todorov, Y.; Loginovska, K.; Tsvetkov, Ts.

    2012-01-01

    In the publication the authors present the results of the applying of two modern technologies for long term and safe vegetable preservation – freeze-drying and gamma sterilization. The freeze-dried vegetables feature minimum moisture – from 2 – 5% and taste-aroma complex preserved to the highest degree. The carried out gamma sterilization ensures a high microbial purity of the vegetables and guarantees for their long term preservation - up to 5 years in polymer packing, under usual conditions

  6. High quality factor gigahertz frequencies in nanomechanical diamond resonators

    OpenAIRE

    Gaidarzhy, Alexei; Imboden, Matthias; Mohanty, Pritiraj; Rankin, Janet; Sheldon, Brian W.

    2007-01-01

    We report actuation and detection of gigahertz-range resonance frequencies in nano-crystalline diamond mechanical resonators. High order transverse vibration modes are measured in coupled-beam resonators exhibiting frequencies up to 1.441 GHz. The cantilever-array design of the resonators translates the gigahertz-range resonant motion of micron-long cantilever elements to the displacement of the central supporting structure. Use of nano-crystalline diamond further increases the frequency comp...

  7. A 48-plex autosomal SNP GenPlex™ assay for human individualization and relationship testing

    DEFF Research Database (Denmark)

    Tomas Mas, Carmen; Børsting, Claus; Morling, Niels

    2012-01-01

    SNPs are being increasingly used by forensic laboratories. Different platforms have been developed for SNP typing. We describe the GenPlex™ HID system protocol, a new SNP-typing platform developed by Applied Biosystems where 48 of the 52 SNPforID SNPs and amelogenin are included. The GenPlex™ HID...

  8. Performance of the SNPforID 52 SNP-plex assay in paternity testing

    DEFF Research Database (Denmark)

    Børsting, Claus; Sanchez, Juan Jose; Hansen, Hanna E

    2008-01-01

    (VNTRs). The typical PIs based on 15 STRs or seven VNTRs were 5-50 times higher than the typical PIs based on 52 SNPs. Six mutations in tandem repeats were detected among the randomly selected trios. In contrast, there was not found any mutations in the SNP loci. The results showed that the 52 SNP...

  9. Evaluation of the OvineSNP50 chip for use in four South African ...

    African Journals Online (AJOL)

    Relatively rapid and cost-effective genotyping using the OvineSNP50 chip holds great promise for the South African sheep industry and research partners. However, SNP ascertainment bias may influence inferences from the genotyping results of South African sheep breeds. Therefore, samples from Dorper, Namaqua ...

  10. Development and application of a 20K SNP array in potato

    NARCIS (Netherlands)

    Vos, Peter

    2016-01-01

    In this thesis the results are described of investigations of various application of genome wide SNP (single nucleotide polymorphism) markers. The set of SNP markers was identified by GBS (genotyping by sequencing) strategy. The resulting dataset of 129,156 SNPs across 83 tetraploid varieties was

  11. Exome sequencing and SNP analysis detect novel compound heterozygosity in fatty acid hydroxylase-associated neurodegeneration

    Science.gov (United States)

    Pierson, Tyler Mark; Simeonov, Dimitre R; Sincan, Murat; Adams, David A; Markello, Thomas; Golas, Gretchen; Fuentes-Fajardo, Karin; Hansen, Nancy F; Cherukuri, Praveen F; Cruz, Pedro; Blackstone, Craig; Tifft, Cynthia; Boerkoel, Cornelius F; Gahl, William A

    2012-01-01

    Fatty acid hydroxylase-associated neurodegeneration due to fatty acid 2-hydroxylase deficiency presents with a wide range of phenotypes including spastic paraplegia, leukodystrophy, and/or brain iron deposition. All previously described families with this disorder were consanguineous, with homozygous mutations in the probands. We describe a 10-year-old male, from a non-consanguineous family, with progressive spastic paraplegia, dystonia, ataxia, and cognitive decline associated with a sural axonal neuropathy. The use of high-throughput sequencing techniques combined with SNP array analyses revealed a novel paternally derived missense mutation and an overlapping novel maternally derived ∼28-kb genomic deletion in FA2H. This patient provides further insight into the consistent features of this disorder and expands our understanding of its phenotypic presentation. The presence of a sural nerve axonal neuropathy had not been previously associated with this disorder and so may extend the phenotype. PMID:22146942

  12. Design and synthesis of the superionic conductor Na10SnP2S12

    Science.gov (United States)

    Richards, William D.; Tsujimura, Tomoyuki; Miara, Lincoln J.; Wang, Yan; Kim, Jae Chul; Ong, Shyue Ping; Uechi, Ichiro; Suzuki, Naoki; Ceder, Gerbrand

    2016-03-01

    Sodium-ion batteries are emerging as candidates for large-scale energy storage due to their low cost and the wide variety of cathode materials available. As battery size and adoption in critical applications increases, safety concerns are resurfacing due to the inherent flammability of organic electrolytes currently in use in both lithium and sodium battery chemistries. Development of solid-state batteries with ionic electrolytes eliminates this concern, while also allowing novel device architectures and potentially improving cycle life. Here we report the computation-assisted discovery and synthesis of a high-performance solid-state electrolyte material: Na10SnP2S12, with room temperature ionic conductivity of 0.4 mS cm-1 rivalling the conductivity of the best sodium sulfide solid electrolytes to date. We also computationally investigate the variants of this compound where tin is substituted by germanium or silicon and find that the latter may achieve even higher conductivity.

  13. Design and synthesis of the superionic conductor Na10SnP2S12.

    Science.gov (United States)

    Richards, William D; Tsujimura, Tomoyuki; Miara, Lincoln J; Wang, Yan; Kim, Jae Chul; Ong, Shyue Ping; Uechi, Ichiro; Suzuki, Naoki; Ceder, Gerbrand

    2016-03-17

    Sodium-ion batteries are emerging as candidates for large-scale energy storage due to their low cost and the wide variety of cathode materials available. As battery size and adoption in critical applications increases, safety concerns are resurfacing due to the inherent flammability of organic electrolytes currently in use in both lithium and sodium battery chemistries. Development of solid-state batteries with ionic electrolytes eliminates this concern, while also allowing novel device architectures and potentially improving cycle life. Here we report the computation-assisted discovery and synthesis of a high-performance solid-state electrolyte material: Na10SnP2S12, with room temperature ionic conductivity of 0.4 mS cm(-1) rivalling the conductivity of the best sodium sulfide solid electrolytes to date. We also computationally investigate the variants of this compound where tin is substituted by germanium or silicon and find that the latter may achieve even higher conductivity.

  14. Health-related quality of life in children with high-functioning autism.

    Science.gov (United States)

    Potvin, Marie-Christine; Snider, Laurie; Prelock, Patricia A; Wood-Dauphinee, Sharon; Kehayia, Eva

    2015-01-01

    The health-related quality of life of school-aged children with high-functioning autism is poorly understood. The objectives of this study were to compare the health-related quality of life of children with high-functioning autism to that of typically developing peers and to compare child-self and parent-proxy reports of health-related quality of life of children. A cross-sectional study of children with high-functioning autism (n = 30) and peers (n = 31) was conducted using the Pediatric Quality of Life Inventory 4.0 Generic Core Scales. Children with high-functioning autism had significantly poorer health-related quality of life than peers whether reported by themselves (p children and parental scores suggested variance in points of view. This study specifically investigated health-related quality of life in children with high-functioning autism as compared to a sample of peers, from the child's perspective. It strengthens earlier findings that children with high-functioning autism experience poorer health-related quality of life than those without this disorder and points to the importance of clinicians working with families to identify areas in a child's life that promote or hinder their sense of well-being. © The Author(s) 2013.

  15. High oleic sunflower biodiesel: quality control and different purification methods

    Directory of Open Access Journals (Sweden)

    Pighinelli, Anna L.M.T.

    2011-06-01

    Full Text Available The objective of the present work is to evaluate the production of biodiesel using ethanol and sunflower oil. The extraction of the sunflower oil was evaluated first. An experimental design was used to estimate the influence of the independent variables grain temperature (25º to 110ºC and expeller rotation (85 to 119rpm on the crude oil. The best result obtained was 68.38%, achieved with a rotation from 100 to 115rpm, grain temperature ranging from 25º to 30ºC and moisture content of around 7%. The next study consisted of transesterification, evaluating the influence of the ethanol, oil molar ratio and the catalyst concentration (sodium methylate on the ester-rich phase yield. The highest yield was 98.39% obtained with a molar ratio of 9:1 and 3% catalyst. An experiment was then carried out on a small reactor and the biodiesel produced was purified by three different methods: acidified water, silica and distillation. The quality aspects of the purified biodiesel samples were evaluated according to the Brazilian specifications for biodiesel, and distillation was shown to be the best method of purification.

    El objetivo del presente trabajo es evaluar la producción de biodiesel usando etanol y aceite de girasol. La extracción del aceite de girasol fue evaluada primero. Un diseño experimental fue usado para estimar la influencia de las variables independientes: temperatura del grano (25º a 110ºC y rotación del expeller (85 a 119 rpm en la obtención del aceite crudo. El mejor resultado obtenido fue un 68,38%, conseguido con una rotación de 100 a 115 rpm, una temperatura del grano de 25º a 30ºC y un contenido de humedad de alrededor del 7%. El siguiente estudio mediante transesterificación, evaluó la influencia de la relación molar etanol: aceite y concentración de catalizador (metilato sódico en el rendimiento de la fase rica en esteres. El rendimiento más alto fue 98,39% obtenido con una relación molar de 9.1 y 3% de

  16. In silico SNP analysis of the breast cancer antigen NY-BR-1.

    Science.gov (United States)

    Kosaloglu, Zeynep; Bitzer, Julia; Halama, Niels; Huang, Zhiqin; Zapatka, Marc; Schneeweiss, Andreas; Jäger, Dirk; Zörnig, Inka

    2016-11-18

    Breast cancer is one of the most common malignancies with increasing incidences every year and a leading cause of death among women. Although early stage breast cancer can be effectively treated, there are limited numbers of treatment options available for patients with advanced and metastatic disease. The novel breast cancer associated antigen NY-BR-1 was identified by SEREX analysis and is expressed in the majority (>70%) of breast tumors as well as metastases, in normal breast tissue, in testis and occasionally in prostate tissue. The biological function and regulation of NY-BR-1 is up to date unknown. We performed an in silico analysis on the genetic variations of the NY-BR-1 gene using data available in public SNP databases and the tools SIFT, Polyphen and Provean to find possible functional SNPs. Additionally, we considered the allele frequency of the found damaging SNPs and also analyzed data from an in-house sequencing project of 55 breast cancer samples for recurring SNPs, recorded in dbSNP. Over 2800 SNPs are recorded in the dbSNP and NHLBI ESP databases for the NY-BR-1 gene. Of these, 65 (2.07%) are synonymous SNPs, 191 (6.09%) are non-synoymous SNPs, and 2430 (77.48%) are noncoding intronic SNPs. As a result, 69 non-synoymous SNPs were predicted to be damaging by at least two, and 16 SNPs were predicted as damaging by all three of the used tools. The SNPs rs200639888, rs367841401 and rs377750885 were categorized as highly damaging by all three tools. Eight damaging SNPs are located in the ankyrin repeat domain (ANK), a domain known for its frequent involvement in protein-protein interactions. No distinctive features could be observed in the allele frequency of the analyzed SNPs. Considering these results we expect to gain more insights into the variations of the NY-BR-1 gene and their possible impact on giving rise to splice variants and therefore influence the function of NY-BR-1 in healthy tissue as well as in breast cancer.

  17. A safe inexpensive method to isolate high quality plant and fungal ...

    African Journals Online (AJOL)

    STORAGESEVER

    2008-08-18

    Aug 18, 2008 ... quality DNA from plant and fungal species. This method uses potassium acetate to remove proteins and polysaccharides in an SDS extraction buffer. Further DNA purification is achieved using a low salt. CTAB treatment. This SDS/CTAB protocol was used to isolate high quality genomic DNA subject to.

  18. Development of a set of SNP markers present in expressed genes of the apple.

    Science.gov (United States)

    Chagné, David; Gasic, Ksenija; Crowhurst, Ross N; Han, Yuepeng; Bassett, Heather C; Bowatte, Deepa R; Lawrence, Timothy J; Rikkerink, Erik H A; Gardiner, Susan E; Korban, Schuyler S

    2008-11-01

    Molecular markers associated with gene coding regions are useful tools for bridging functional and structural genomics. Due to their high abundance in plant genomes, single nucleotide polymorphisms (SNPs) are present within virtually all genomic regions, including most coding sequences. The objective of this study was to develop a set of SNPs for the apple by taking advantage of the wealth of genomics resources available for the apple, including a large collection of expressed sequenced tags (ESTs). Using bioinformatics tools, a search for SNPs within an EST database of approximately 350,000 sequences developed from a variety of apple accessions was conducted. This resulted in the identification of a total of 71,482 putative SNPs. As the apple genome is reported to be an ancient polyploid, attempts were made to verify whether those SNPs detected in silico were attributable either to allelic polymorphisms or to gene duplication or paralogous or homeologous sequence variations. To this end, a set of 464 PCR primer pairs was designed, PCR was amplified using two subsets of plants, and the PCR products were sequenced. The SNPs retrieved from these sequences were then mapped onto apple genetic maps, including a newly constructed map of a Royal Gala x A689-24 cross and a Malling 9 x Robusta 5, map using a bin mapping strategy. The SNP genotyping was performed using the high-resolution melting (HRM) technique. A total of 93 new markers containing 210 coding SNPs were successfully mapped. This new set of SNP markers for the apple offers new opportunities for understanding the genetic control of important horticultural traits using quantitative trait loci (QTL) or linkage disequilibrium analysis. These also serve as useful markers for aligning physical and genetic maps, and as potential transferable markers across the Rosaceae family.

  19. Dual-Readout Calorimetry for High-Quality Energy

    CERN Multimedia

    During the past seven years, the DREAM collaboration has systematically investigated all factors that determine and limit the precision with which the properties of hadrons and jets can be measured in calorimeters. Using simultaneous detection of the deposited energy and the Cerenkov light produced in hadronic shower development ${(dual}$ ${readout}$), the fluctuations in the electromagnetic shower fraction could be measured event by event their effects on signal linearity, response function and energy resolution eliminated. Detailed measurement of the time structure of the signals made it possible to measure the contirbutions of nuclear evaporation neutrons to the signals and thus reduce the effects of fluctuations in "invisible energy". We are now embarking on the construction of a full-scale calorimeter which incorporates all these elements and which should make it possible to measure the four-vectors of both electrons, hadrons and jets with very high precision, in an instrument that can be simply calibrat...

  20. Export is necessary to maintain high quality supply

    International Nuclear Information System (INIS)

    Sirugue, S.

    2016-01-01

    Nuclear industry achieves about 20% of its turnover with the export of equipment and services but nuclear trade is submitted to specific constrains like non-proliferation policies. According to IAEA the world capacity of nuclear power is expected to double allowing the development of emerging countries while reducing CO_2 emissions. The French commercial offer focuses on the high-end market with the EPR reactor and an intermediate power range reactor ATMEA-1 designed with MHI (Mitsubishi Heavy Industries). AREVA is the unique world operator able to master the entire chain of spent fuel reprocessing thanks to the La Hague plant. In the framework of the rebuilding of the French nuclear industry, discussions are ongoing to achieve partnerships with foreign partners in exchange of shares in AREVA and AREVA NP. Today's main challenges of AREVA are to reduce EPR cost, to speed EPR construction and to benefit fully of the move into the digital age. (A.C.)

  1. Access High Quality Imagery from the NOAA View Portal

    Science.gov (United States)

    Pisut, D.; Powell, A. M.; Loomis, T.; Goel, V.; Mills, B.; Cowan, D.

    2013-12-01

    NOAA curates a vast treasure trove of environmental data, but one that is sometimes not easily accessed, especially for education, outreach, and media purposes. Traditional data portals in NOAA require extensive knowledge of the specific names of observation platforms, models, and analyses, along with nomenclature for variable outputs. A new website and web mapping service (WMS) from NOAA attempts to remedy such issues. The NOAA View data imagery portal provides a seamless entry point into data from across the agency: satellite, models, in-situ analysis, etc. The system provides the user with ability to browse, animate, and download high resolution (e.g., 4,000 x 2,000 pixel) imagery, Google Earth, and even proxy data files. The WMS architecture also allows the resources to be ingested into other software systems or applications.

  2. High Quality Rapeseed Products as Feed for Sensitive Monogastrics

    DEFF Research Database (Denmark)

    Frandsen, Heidi Blok

    in plants of the order Brassicales (former known as Capparales), which include rapeseed, rype (Brassica campestris L.) Indian mustard (Brassica juncea L.), broccoli (Brassica oleracea L.var. italica) and many other plants. Glucosinolates have been studied widely for their biologic effects ranging from...... by xenobiotica enzymes in the liver. The last study (manuscript IV) deals with the novel processing techniques, pulsed electric field (PEF) and high pressure treatment (HPT) and the processing effects on glucosinolates in broccoli. The largest effects were observed to be a result of the different handling...... of the plant materials prior to the process treatment. It was thus found that a great amount of the glucosinolate loss has occurred in the broccoli juice and purée prior to PEF processing. Only a minor loss was observed in broccoli flowers prior to processing, and HP treatment at 700 MPa for 10 min. was found...

  3. A customized pigmentation SNP array identifies a novel SNP associated with melanoma predisposition in the SLC45A2 gene.

    Directory of Open Access Journals (Sweden)

    Maider Ibarrola-Villava

    Full Text Available As the incidence of Malignant Melanoma (MM reflects an interaction between skin colour and UV exposure, variations in genes implicated in pigmentation and tanning response to UV may be associated with susceptibility to MM. In this study, 363 SNPs in 65 gene regions belonging to the pigmentation pathway have been successfully genotyped using a SNP array. Five hundred and ninety MM cases and 507 controls were analyzed in a discovery phase I. Ten candidate SNPs based on a p-value threshold of 0.01 were identified. Two of them, rs35414 (SLC45A2 and rs2069398 (SILV/CKD2, were statistically significant after conservative Bonferroni correction. The best six SNPs were further tested in an independent Spanish series (624 MM cases and 789 controls. A novel SNP located on the SLC45A2 gene (rs35414 was found to be significantly associated with melanoma in both phase I and phase II (P<0.0001. None of the other five SNPs were replicated in this second phase of the study. However, three SNPs in TYR, SILV/CDK2 and ADAMTS20 genes (rs17793678, rs2069398 and rs1510521 respectively had an overall p-value<0.05 when considering the whole DNA collection (1214 MM cases and 1296 controls. Both the SLC45A2 and the SILV/CDK2 variants behave as protective alleles, while the TYR and ADAMTS20 variants seem to function as risk alleles. Cumulative effects were detected when these four variants were considered together. Furthermore, individuals carrying two or more mutations in MC1R, a well-known low penetrance melanoma-predisposing gene, had a decreased MM risk if concurrently bearing the SLC45A2 protective variant. To our knowledge, this is the largest study on Spanish sporadic MM cases to date.

  4. Recycle food wastes into high quality fish feeds for safe and quality fish production.

    Science.gov (United States)

    Wong, Ming-Hung; Mo, Wing-Yin; Choi, Wai-Ming; Cheng, Zhang; Man, Yu-Bon

    2016-12-01

    The amount of food waste generated from modern societies is increasing, which has imposed a tremendous pressure on its treatment and disposal. Food waste should be treated as a valuable resource rather than waste, and turning it into fish feeds would be a viable alternative. This paper attempts to review the feasibility of using food waste to formulate feed pellets to culture a few freshwater fish species, such as grass carp, grey mullet, and tilapia, under polyculture mode (growing different species in the same pond). These species occupy different ecological niches, with different feeding modes (i.e., herbivorous, filter feeding, etc.), and therefore all the nutrients derived from the food waste could be efficiently recycled within the ecosystem. The problems facing environmental pollution and fish contamination; the past and present situation of inland fish culture (focusing on South China); upgrade of food waste based feed pellets by adding enzymes, vitamin-mineral premix, probiotics (yeast), prebiotics, and Chinese medicinal herbs into feeds; and potential health risks of fish cultivated by food waste based pellets are discussed, citing some local examples. It can be concluded that appropriate portions of different types of food waste could satisfy basic nutritional requirements of lower trophic level fish species such as grass carp and tilapia. Upgrading the fish pellets by adding different supplements mentioned above could further elevated the quality of feeds, leading to higher growth rates, and enhanced immunity of fish. Health risk assessments based on the major environmental contaminants (mercury, PAHs and DDTs) in fish flesh showed that fish fed food waste based pellets are safer for consumption, when compared with those fed commercial feed pellets. Copyright © 2016 Elsevier Ltd. All rights reserved.

  5. High-quality thorium TRISO fuel performance in HTGRs

    Energy Technology Data Exchange (ETDEWEB)

    Verfondern, Karl [Forschungszentrum Juelich GmbH (Germany); Allelein, Hans-Josef [Forschungszentrum Juelich GmbH (Germany); Technische Hochschule Aachen (Germany); Nabielek, Heinz; Kania, Michael J.

    2013-11-01

    Thorium as a nuclear fuel has received renewed interest, because of its widespread availability and the good irradiation performance of Th and mixed (Th,U) oxide compounds as fuels in nuclear power systems. Early HTGR development employed thorium together with high-enriched uranium (HEU). After 1980, HTGR fuel systems switched to low-enriched uranium (LEU). After completing fuel development for the AVR and the THTR with BISO coated particles, the German program expanded its efforts utilizing thorium and HEU TRISO coated particles in advanced HTGR concepts for process heat applications (PNP) and direct-cycle electricity production (HHT). The combination of a low-temperature isotropic (LTI) inner and outer pyrocarbon layers surrounding a strong, stable SiC layer greatly improved manufacturing conditions and the subsequent contamination and defective particle fractions in production fuel elements. In addition, this combination provided improved mechanical strength and a higher degree of solid fission product retention, not known previously with high-temperature isotropic (HTI) BISO coatings. The improved performance of the HEU (Th, U)O{sub 2} TRISO fuel system was successfully demonstrated in three primary areas of development: manufacturing, irradiation testing under normal operating conditions, and accident simulation testing. In terms of demonstrating performance for advanced HTGR applications, the experimental failure statistic from manufacture and irradiation testing are significantly below the coated particle requirements specified for PNP and HHT designs at the time. Covering a range to 1300 C in normal operations and 1600 C in accidents, with burnups to 13% FIMA and fast fluences to 8 x 10{sup 25} n/m{sup 2} (E> 16 fJ), the performance results exceed the design limits on manufacturing and operational requirements for the German HTR-Modul concept, which are 6.5 x 10{sup -5} for manufacturing, 2 x 10{sup -4} for normal operating conditions, and 5 x 10{sup -4

  6. High-quality thorium TRISO fuel performance in HTGRs

    International Nuclear Information System (INIS)

    Verfondern, Karl; Allelein, Hans-Josef; Nabielek, Heinz; Kania, Michael J.

    2013-01-01

    Thorium as a nuclear fuel has received renewed interest, because of its widespread availability and the good irradiation performance of Th and mixed (Th,U) oxide compounds as fuels in nuclear power systems. Early HTGR development employed thorium together with high-enriched uranium (HEU). After 1980, HTGR fuel systems switched to low-enriched uranium (LEU). After completing fuel development for the AVR and the THTR with BISO coated particles, the German program expanded its efforts utilizing thorium and HEU TRISO coated particles in advanced HTGR concepts for process heat applications (PNP) and direct-cycle electricity production (HHT). The combination of a low-temperature isotropic (LTI) inner and outer pyrocarbon layers surrounding a strong, stable SiC layer greatly improved manufacturing conditions and the subsequent contamination and defective particle fractions in production fuel elements. In addition, this combination provided improved mechanical strength and a higher degree of solid fission product retention, not known previously with high-temperature isotropic (HTI) BISO coatings. The improved performance of the HEU (Th, U)O 2 TRISO fuel system was successfully demonstrated in three primary areas of development: manufacturing, irradiation testing under normal operating conditions, and accident simulation testing. In terms of demonstrating performance for advanced HTGR applications, the experimental failure statistic from manufacture and irradiation testing are significantly below the coated particle requirements specified for PNP and HHT designs at the time. Covering a range to 1300 C in normal operations and 1600 C in accidents, with burnups to 13% FIMA and fast fluences to 8 x 10 25 n/m 2 (E> 16 fJ), the performance results exceed the design limits on manufacturing and operational requirements for the German HTR-Modul concept, which are 6.5 x 10 -5 for manufacturing, 2 x 10 -4 for normal operating conditions, and 5 x 10 -4 for accident conditions. These

  7. MDM2 gene SNP309 T/G and p53 gene SNP72 G/C do not influence diffuse large B-cell non-Hodgkin lymphoma onset or survival in central European Caucasians

    Directory of Open Access Journals (Sweden)

    Landt Olfert

    2008-04-01

    Full Text Available Abstract Background SNP309 T/G (rs2279744 causes higher levels of MDM2, the most important negative regulator of the p53 tumor suppressor. SNP72 G/C (rs1042522 gives rise to a p53 protein with a greatly reduced capacity to induce apoptosis. Both polymorphisms have been implicated in cancer. The SNP309 G-allele has recently been reported to accelerate diffuse large B-cell lymphoma (DLBCL formation in pre-menopausal women and suggested to constitute a genetic basis for estrogen affecting human tumorigenesis. Here we asked whether SNP309 and SNP72 are associated with DLBCL in women and are correlated with age of onset, diagnosis, or patient's survival. Methods SNP309 and SNP72 were PCR-genotyped in a case-control study that included 512 controls and 311 patients diagnosed with aggressive NHL. Of these, 205 were diagnosed with DLBCL. Results The age of onset was similar in men and women. The control and patients group showed similar SNP309 and SNP72 genotype frequencies. Importantly and in contrast to the previous findings, similar genotype frequencies were observed in female patients diagnosed by 51 years of age and those diagnosed later. Specifically, 3/20 female DLBCL patients diagnosed by 51 years of age were homozygous for SNP309 G and 2/20 DLBCL females in that age group were homozygous for SNP72 C. Neither SNP309 nor SNP72 had a significant influence on event-free and overall survival in multivariate analyses. Conclusion In contrast to the previous study on Ashkenazi Jewish Caucasians, DLBCL in pre-menopausal women of central European Caucasian ethnicity was not associated with SNP309 G. Neither SNP309 nor SNP72 seem to be correlated with age of onset, diagnosis, or survival of patients.

  8. Towards a high quality high school workforce: A longitudinal, demographic analysis of U.S. public school physics teachers

    OpenAIRE

    Gregory T. Rushton; David Rosengrant; Andrew Dewar; Lisa Shah; Herman E. Ray; Keith Sheppard; Lynn Watanabe

    2017-01-01

    Efforts to improve the number and quality of the high school physics teaching workforce have taken several forms, including those sponsored by professional organizations. Using a series of large-scale teacher demographic data sets from the National Center for Education Statistics (NCES), this study sought to investigate trends in teacher quality at the national level in the two and a half decades between 1987 and 2012. Specifically, we investigated (i) details about the degree backgrounds, ma...

  9. EXPERT-ANALITICAL MONITORING OF LEARNING PROCESS QUALITY IN HIGH SCHOOL

    Directory of Open Access Journals (Sweden)

    T. M. Korotun

    2010-10-01

    Full Text Available The technological model is proposed for monitoring process of learning process quality in high school compliant with current European and home standards. The mathematical methods are elaborated for diverse activities as to learning process objects quality determination unified support. They self-consistently combine: automatic expert evaluation with Bayesian net and Value tree models; Delphi technique enhancement; best practices for education quality assessment. Quality estimates’ consistency index is introduced for their choice and acceptability analysis. Its permanent increasing over monitoring stages is guaranteed. The tools for these stages’ automatic support are described.

  10. Timing of high-quality child care and cognitive, language, and preacademic development.

    Science.gov (United States)

    Li, Weilin; Farkas, George; Duncan, Greg J; Burchinal, Margaret R; Vandell, Deborah Lowe

    2013-08-01

    The effects of high- versus low-quality child care during 2 developmental periods (infant-toddlerhood and preschool) were examined using data from the National Institute of Child Health and Human Development Study of Early Child Care. Propensity score matching was used to account for differences in families who used different combinations of child care quality during the 2 developmental periods. Findings indicated that cognitive, language, and preacademic skills prior to school entry were highest among children who experienced high-quality care in both the infant-toddler and preschool periods, somewhat lower among children who experienced high-quality child care during only 1 of these periods, and lowest among children who experienced low-quality care during both periods. Irrespective of the care received during infancy-toddlerhood, high-quality preschool care was related to better language and preacademic outcomes at the end of the preschool period; high-quality infant-toddler care, irrespective of preschool care, was related to better memory skills at the end of the preschool period. (PsycINFO Database Record (c) 2013 APA, all rights reserved).

  11. An approach to high speed ship ride quality simulation

    Science.gov (United States)

    Malone, W. L.; Vickery, J. M.

    1975-01-01

    The high speeds attained by certain advanced surface ships result in a spectrum of motion which is higher in frequency than that of conventional ships. This fact along with the inclusion of advanced ride control features in the design of these ships resulted in an increased awareness of the need for ride criteria. Such criteria can be developed using data from actual ship operations in varied sea states or from clinical laboratory experiments. A third approach is to simulate ship conditions using measured or calculated ship motion data. Recent simulations have used data derived from a math model of Surface Effect Ship (SES) motion. The model in turn is based on equations of motion which have been refined with data from scale models and SES of up to 101 600-kg (100-ton) displacement. Employment of broad band motion emphasizes the use of the simulators as a design tool to evaluate a given ship configuration in several operational situations and also serves to provide data as to the overall effect of a given motion on crew performance and physiological status.

  12. The polymorphisms of P53 codon 72 and MDM2 SNP309 and renal cell carcinoma risk in a low arsenic exposure area

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Chao-Yuan [Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan (China); Department of Urology, National Taiwan University Hospital, College of Medicine National Taiwan University, Taipei, Taiwan (China); Su, Chien-Tien [Department of Family Medicine, Taipei Medical University Hospital, Taipei, Taiwan (China); Chu, Jan-Show [Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan (China); Department of Pathology, College of Medicine, Taipei Medical University, Taipei, Taiwan (China); Huang, Shu-Pin [Department of Urology, Kaohsiung Medical University Hospital, College of Medicine Kaohsiung Medical University, Kaohsiung, Taiwan (China); Pu, Yeong-Shiau [Department of Urology, National Taiwan University Hospital, College of Medicine National Taiwan University, Taipei, Taiwan (China); Yang, Hsiu-Yuan [School of Public Health, College of Public Health and Nutrition, Taipei Medical University, Taipei, Taiwan (China); Chung, Chi-Jung [Department of Medical Research, China Medical University Hospital, Taichung, Taiwan (China); Department of Health Risk Management, College of Public Health, China Medical University, Taichung, Taiwan (China); Wu, Chia-Chang [School of Public Health, College of Public Health and Nutrition, Taipei Medical University, Taipei, Taiwan (China); Department of Urology, Taipei Medical Universtiy-Shuang Ho Hospital, Taipei, Taiwan (China); Hsueh, Yu-Mei, E-mail: ymhsueh@tmu.edu.tw [School of Public Health, College of Public Health and Nutrition, Taipei Medical University, Taipei, Taiwan (China); Department of Public Health, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan (China)

    2011-12-15

    Our recent study demonstrated the increased risk of renal cell carcinoma (RCC) associated with high urinary total arsenic levels among people living in a low arsenic exposure area. Genomic instability is important in arsenic carcinogenesis. This study evaluated the relationship between the polymorphisms of p53, p21, and MDM2, which plays a role in gene stability, and the arsenic-related RCC risk. Here, we found that p53 Pro/Pro genotype and MDM2 SNP309 GG genotype significantly increased RCC risk compared to the p53 Arg/Arg genotype and MDM2 SNP309 TT genotype. RCC patients with the p53Arg/Arg genotype had a signicantly low percentage of inorganic arsenic, a low percentage of monomethylarsonic acid (MMA), and a high percentage of dimethylarsinic acid (DMA), which indicates efcient arsenic methylation capacity. Subjects with the p53 Arg/Pro + Pro/Pro genotype or MDM2 SNP309 TG + GG genotype, in conjunction with high urinary total arsenic ({>=} 14.02 {mu}g/L), had a signicantly higher RCC risk than those with the p53 Arg/Arg or MDM2 SNP309 TT genotypes and low urinary total arsenic. Taken together, this is the first study to show that a variant genotype of p53 Arg{sup 72}Pro or MDM2 SNP309 may modify the arsenic-related RCC risk even in a non-obvious arsenic exposure area. -- Highlights: Black-Right-Pointing-Pointer Subjects with p53 Pro/Pro or MDM2 GG genotype significantly increased RCC risk. Black-Right-Pointing-Pointer A significant multiplicative joint effect of p53 and p21 on RCC risk. Black-Right-Pointing-Pointer RCC patients with p53 Arg/Arg genotype had efficient arsenic methylation capacity. Black-Right-Pointing-Pointer Joint effect of p53 or MDM2 genotype and high urinary total arsenic on RCC risk.

  13. A functional SNP associated with atopic dermatitis controls cell type-specific methylation of the VSTM1 gene locus

    Directory of Open Access Journals (Sweden)

    Dilip Kumar

    2017-02-01

    Full Text Available Abstract Background Expression quantitative trait loci (eQTL databases represent a valuable resource to link disease-associated SNPs to specific candidate genes whose gene expression is significantly modulated by the SNP under investigation. We previously identified signal inhibitory receptor on leukocytes-1 (SIRL-1 as a powerful regulator of human innate immune cell function. While it is constitutively high expressed on neutrophils, on monocytes the SIRL-1 surface expression varies strongly between individuals. The underlying mechanism of regulation, its genetic control as well as potential clinical implications had not been explored yet. Methods Whole blood eQTL data of a Chinese cohort was used to identify SNPs regulating the expression of VSTM1, the gene encoding SIRL-1. The genotype effect was validated by flow cytometry (cell surface expression, correlated with electrophoretic mobility shift assay (EMSA, chromatin immunoprecipitation (ChIP and bisulfite sequencing (C-methylation and its functional impact studied the inhibition of reactive oxygen species (ROS. Results We found a significant association of a single CpG-SNP, rs612529T/C, located in the promoter of VSTM1. Through flow cytometry analysis we confirmed that primarily in the monocytes the protein level of SIRL-1 is strongly associated with genotype of this SNP. In monocytes, the T allele of this SNP facilitates binding of the transcription factors YY1 and PU.1, of which the latter has been recently shown to act as docking site for modifiers of DNA methylation. In line with this notion rs612529T associates with a complete demethylation of the VSTM1 promoter correlating with the allele-specific upregulation of SIRL-1 expression. In monocytes, this upregulation strongly impacts the IgA-induced production of ROS by these cells. Through targeted association analysis we found a significant Meta P value of 1.14 × 10–6 for rs612529 for association to atopic dermatitis (AD

  14. Identifying suitable substrates for high-quality graphene-based heterostructures

    Science.gov (United States)

    Banszerus, L.; Janssen, H.; Otto, M.; Epping, A.; Taniguchi, T.; Watanabe, K.; Beschoten, B.; Neumaier, D.; Stampfer, C.

    2017-06-01

    We report on a scanning confocal Raman spectroscopy study investigating the strain-uniformity and the overall strain and doping of high-quality chemical vapour deposited (CVD) graphene-based heterostuctures on a large number of different substrate materials, including hexagonal boron nitride (hBN), transition metal dichalcogenides, silicon, different oxides and nitrides, as well as polymers. By applying a hBN-assisted, contamination free, dry transfer process for CVD graphene, high-quality heterostructures with low doping densities and low strain variations are assembled. The Raman spectra of these pristine heterostructures are sensitive to substrate-induced doping and strain variations and are thus used to probe the suitability of the substrate material for potential high-quality graphene devices. We find that the flatness of the substrate material is a key figure for gaining, or preserving high-quality graphene.

  15. Production of high quality sodium iodide preparations labelled with carrier free iodine-125

    International Nuclear Information System (INIS)

    Abdukayumov, M.N.; Chistyakov, P.G.; Shilin, E.A.

    2001-01-01

    Work is related to the problem of high-quality Sodium Iodide preparation production and to the choice of the peptids iodination methods with the purpose of control test developing to determine the Biological activity of the above mentioned preparation

  16. The Role of Dosimetry in High-Quality EMI Risk Assessment

    National Research Council Canada - National Science Library

    2006-01-01

    The Final Proceedings for The role of EMF dosimetry in high quality risk assessment 13 September 2006 - 15 September 2006 In the last three decades the use of devices that emit electromagnetic fields (EMF...

  17. Diode pumped 1kHz high power Nd:YAG laser with excellent beam quality

    NARCIS (Netherlands)

    Godfried, Herman; Godfried, H.P; Offerhaus, Herman L.

    1997-01-01

    The design and operation of a one kilohertz diode pumped all solid-state Nd:YAG master oscillator power amplifier system with a phase conjugate mirror is presented. The setup allows high power scaling without reduction in beam quality.

  18. SNP Polymorphism Survey of the Parental Lines of ISRA Sorghum Breeding Program as Part of the Feed the Future

    Data.gov (United States)

    US Agency for International Development — Polymorphism of SNP Markers (single nucleotide polymorphisms) was assessed on 24 parental lines of the ISRA sorghum breeding program . About 1300 SNP have been used...

  19. Universal and rapid salt-extraction of high quality genomic DNA for PCR-based techniques.

    OpenAIRE

    Aljanabi, S M; Martinez, I

    1997-01-01

    A very simple, fast, universally applicable and reproducible method to extract high quality megabase genomic DNA from different organisms is described. We applied the same method to extract high quality complex genomic DNA from different tissues (wheat, barley, potato, beans, pear and almond leaves as well as fungi, insects and shrimps' fresh tissue) without any modification. The method does not require expensive and environmentally hazardous reagents and equipment. It can be performed even i...

  20. Development and Evaluation of a Barley 50k iSelect SNP Array

    Directory of Open Access Journals (Sweden)

    Micha M. Bayer

    2017-10-01

    Full Text Available High-throughput genotyping arrays continue to be an attractive, cost-effective alternative to sequencing based approaches. We have developed a new 50k Illumina Infinium iSelect genotyping array for barley, a cereal crop species of major international importance. The majority of SNPs on the array have been extracted from variants called in exome capture data of a wide range of European barley germplasm. We used the recently published barley pseudomolecule assembly to map the exome capture data, which allowed us to generate markers with accurate physical positions and detailed gene annotation. Markers from an existing and widely used barley 9k Infinium iSelect array were carried over onto the 50k chip for backward compatibility. The array design featured 49,267 SNP markers that converted into 44,040 working assays, of which 43,461 were scorable in GenomeStudio. Of the working assays, 6,251 are from the 9k iSelect platform. We validated the SNPs by comparing the genotype calls from the new array to legacy datasets. Rates of agreement averaged 98.1 and 93.9% respectively for the legacy 9k iSelect SNP set (Comadran et al., 2012 and the exome capture SNPs. To test the utility of the 50k chip for genetic mapping, we genotyped a segregating population derived from a Golden Promise × Morex cross (Liu et al., 2014 and mapped over 14,000 SNPs to genetic positions which showed a near exact correspondence to their known physical positions. Manual adjustment of the cluster files used by the interpreting software for genotype scoring improved results substantially, but migration of cluster files between sites led to a deterioration of results, suggesting that local adjustment of cluster files is required on a site-per-site basis. Information relating to the markers on the chip is available online at https://ics.hutton.ac.uk/50k.

  1. The use of citation indicators to identify and support high-quality research in Poland.

    Science.gov (United States)

    Pilc, Andrzej

    2008-01-01

    In large, mostly English-speaking countries, where the "critical mass" of scientists working in different subfields of science is achieved, the peer review system may be sufficient to assess the quality of scientific research. However, in smaller countries, outside the Anglo-American circle, it is important to introduce different systems to identify research of high quality. In Poland, a parametric system for assessing the quality of research has been introduced. It was largely based on the impact factor of scientific journals. While the use of this indicator to assess research quality is highly questionable, the implementation of the system in the Polish reality is even worse. Therefore it is important to change and improve the system currently used by the Ministry of Science and Higher Education to both evaluate and, more importantly, finance science in Poland. Here, a system based on three factors, i.e. the impact factor, the institutional h-index, and the institutional number of citations, is proposed. The scientific quality of institutions in Division VI: Medical Sciences of the Polish Academy of Sciences were evaluated and the results were compared with the existing system. Moreover, a method to identify high-quality researchers and institutions at the national level based on the quantity of highly cited papers is shown. Additionally, an attempt to identify the highest quality Polish research on an international level is proposed. This is based on the number of individual citations, the individual h-index, the number of publications, and the priority of the discovery.

  2. Expression Level of the DREB2-Type Gene, Identified with Amplifluor SNP Markers, Correlates with Performance, and Tolerance to Dehydration in Bread Wheat Cultivars from Northern Kazakhstan

    Science.gov (United States)

    Shavrukov, Yuri; Zhumalin, Aibek; Serikbay, Dauren; Botayeva, Makpal; Otemisova, Ainur; Absattarova, Aiman; Sereda, Grigoriy; Sereda, Sergey; Shvidchenko, Vladimir; Turbekova, Arysgul; Jatayev, Satyvaldy; Lopato, Sergiy; Soole, Kathleen; Langridge, Peter

    2016-01-01

    A panel of 89 local commercial cultivars of bread wheat was tested in field trials in the dry conditions of Northern Kazakhstan. Two distinct groups of cultivars (six cultivars in each group), which had the highest and the lowest grain yield under drought were selected for further experiments. A dehydration test conducted on detached leaves indicated a strong association between rates of water loss in plants from the first group with highest grain yield production in the dry environment relative to the second group. Modern high-throughput Amplifluor Single Nucleotide Polymorphism (SNP) technology was applied to study allelic variations in a series of drought-responsive genes using 19 SNP markers. Genotyping of an SNP in the TaDREB5 (DREB2-type) gene using the Amplifluor SNP marker KATU48 revealed clear allele distribution across the entire panel of wheat accessions, and distinguished between the two groups of cultivars with high and low yield under drought. Significant differences in expression levels of TaDREB5 were revealed by qRT-PCR. Most wheat plants from the first group of cultivars with high grain yield showed slight up-regulation in the TaDREB5 transcript in dehydrated leaves. In contrast, expression of TaDREB5 in plants from the second group of cultivars with low grain yield was significantly down-regulated. It was found that SNPs did not alter the amino acid sequence of TaDREB5 protein. Thus, a possible explanation is that alternative splicing and up-stream regulation of TaDREB5 may be affected by SNP, but these hypotheses require additional analysis (and will be the focus of future studies). PMID:27917186

  3. Expression level of the DREB2-type gene, identified with Amplifluor SNP markers, correlates with performance and tolerance to dehydration in bread wheat cultivars from Northern Kazakhstan

    Directory of Open Access Journals (Sweden)

    Yuri Shavrukov

    2016-11-01

    Full Text Available A panel of 89 local commercial cultivars of bread wheat was tested in field trials in the dry conditions of Northern Kazakhstan. Two distinct groups of cultivars (six cultivars in each group, which had the highest and the lowest grain yield under drought were selected for further experiments. A dehydration test conducted on detached leaves indicated a strong association between rates of water loss in plants from the first group with highest grain yield production in the dry environment relative to the second group. Modern high-throughput Amplifluor SNP technology was applied to study allelic variations in a series of drought-responsive genes using 19 SNP markers. Genotyping of an SNP in the TaDREB5 (DREB2-type gene using the Amplifluor SNP marker KATU48 revealed clear allele distribution across the entire panel of wheat accessions, and distinguished between the two groups of cultivars with high and low yield under drought. Significant differences in expression levels of TaDREB5 were revealed by qRT-PCR. Most wheat plants from the first group of cultivars with high grain yield showed strong up-regulation of TaDREB5 transcript in dehydrated leaves. In contrast, expression of TaDREB5 in plants from the second group of cultivars with low grain yield was significantly down-regulated. It was found that SNPs did not alter the amino acid sequence of TaDREB5 protein. Thus, a possible explanation is that alternative splicing and up-stream regulation of TaDREB5 may be affected by SNP, but these hypotheses require additional analysis (and will be the focus of future studies.

  4. SNP-based pathway enrichment analysis for genome-wide association studies

    Directory of Open Access Journals (Sweden)

    Potkin Steven G

    2011-04-01

    Full Text Available Abstract Background Recently we have witnessed a surge of interest in using genome-wide association studies (GWAS to discover the genetic basis of complex diseases. Many genetic variations, mostly in the form of single nucleotide polymorphisms (SNPs, have been identified in a wide spectrum of diseases, including diabetes, cancer, and psychiatric diseases. A common theme arising from these studies is that the genetic variations discovered by GWAS can only explain a small fraction of the genetic risks associated with the complex diseases. New strategies and statistical approaches are needed to address this lack of explanation. One such approach is the pathway analysis, which considers the genetic variations underlying a biological pathway, rather than separately as in the traditional GWAS studies. A critical challenge in the pathway analysis is how to combine evidences of association over multiple SNPs within a gene and multiple genes within a pathway. Most current methods choose the most significant SNP from each gene as a representative, ignoring the joint action of multiple SNPs within a gene. This approach leads to preferential identification of genes with a greater number of SNPs. Results We describe a SNP-based pathway enrichment method for GWAS studies. The method consists of the following two main steps: 1 for a given pathway, using an adaptive truncated product statistic to identify all representative (potentially more than one SNPs of each gene, calculating the average number of representative SNPs for the genes, then re-selecting the representative SNPs of genes in the pathway based on this number; and 2 ranking all selected SNPs by the significance of their statistical association with a trait of interest, and testing if the set of SNPs from a particular pathway is significantly enriched with high ranks using a weighted Kolmogorov-Smirnov test. We applied our method to two large genetically distinct GWAS data sets of schizophrenia, one

  5. Selection of process parameters for producing high quality defatted sesame flour at pilot scale.

    Science.gov (United States)

    Manikantan, M R; Sharma, Rajiv; Yadav, D N; Gupta, R K

    2015-03-01

    The present work was undertaken to study the effect of pearling duration, soaking time, steaming duration and drying temperature on the quality of sesame seeds and mechanically extracted partially defatted sesame cake. On the basis of quality attributes i.e. high protein, low crude fibre, low residual oil and low oxalic acid, the optimum process parameters were selected. The combination of 20 min of pearling duration, 15 min of soaking, 15 min of steaming at 100 kPa pressure and drying at 50 °C yielded high quality partially defatted protein rich sesame flour as compared to untreated defatted sesame flour. The developed high quality partially defatted protein rich sesame flour may be used in various food applications as a vital ingredient to increase the nutritional significance of the prepared foodstuffs.

  6. Two combinatorial optimization problems for SNP discovery using base-specific cleavage and mass spectrometry.

    Science.gov (United States)

    Chen, Xin; Wu, Qiong; Sun, Ruimin; Zhang, Louxin

    2012-01-01

    The discovery of single-nucleotide polymorphisms (SNPs) has important implications in a variety of genetic studies on human diseases and biological functions. One valuable approach proposed for SNP discovery is based on base-specific cleavage and mass spectrometry. However, it is still very challenging to achieve the full potential of this SNP discovery approach. In this study, we formulate two new combinatorial optimization problems. While both problems are aimed at reconstructing the sample sequence that would attain the minimum number of SNPs, they search over different candidate sequence spaces. The first problem, denoted as SNP - MSP, limits its search to sequences whose in silico predicted mass spectra have all their signals contained in the measured mass spectra. In contrast, the second problem, denoted as SNP - MSQ, limits its search to sequences whose in silico predicted mass spectra instead contain all the signals of the measured mass spectra. We present an exact dynamic programming algorithm for solving the SNP - MSP problem and also show that the SNP - MSQ problem is NP-hard by a reduction from a restricted variation of the 3-partition problem. We believe that an efficient solution to either problem above could offer a seamless integration of information in four complementary base-specific cleavage reactions, thereby improving the capability of the underlying biotechnology for sensitive and accurate SNP discovery.

  7. Interference of Homologous Sequences on the SNP Study of CYP2A13 Gene

    Directory of Open Access Journals (Sweden)

    Qinghua ZHOU

    2010-02-01

    Full Text Available Background and objective It has been proven that cytochrome P450 enzyme 2A13 (CYP2A13 played an important role in the association between single nucleotide polymorphisms (SNP and human diseases. Cytochrome P450 enzymes are a group of isoenzymes, whose sequence homology may interfere with the study for SNP. The aim of this study is to explore the interference on the SNP study of CYP2A13 caused by homologous sequences. Methods Taqman probe was applied to detect distribution of rs8192789 sites in 573 subjects, and BLAST method was used to analyze the amplified sequences. Partial sequences of CYP2A13 were emplified by PCR from 60 cases. The emplified sequences were TA cloned and sequenced. Results For rs8192789 loci in 573 cases, only 3 cases were TT, while the rest were CT heterozygotes, which was caused by homologous sequences. There are a large number of overlapping peaks in identical sequences of 60 cases, and the SNP of 101 amino acid site reported in the SNP database is not found. The cloned sequences are 247 bp, 235 bp fragments. Conclusion The homologous sequences may interfere the study for SNP of CYP2A13, and some SNP may not exist.

  8. Genetic Polymorphism of MDM2 SNP309 in Patients with Helicobacter Pylori-Associated Gastritis.

    Science.gov (United States)

    Tongtawee, Taweesak; Dechsukhum, Chavaboon; Leeanansaksiri, Wilairat; Kaewpitoon, Soraya; Kaewpitoon, Natthawut; Loyd, Ryan A; Matrakool, Likit; Panpimanmas, Sukij

    2015-01-01

    Helicobacter pylori plays an important role in gastric cancer, which has a relatively low inciduence in Thailand. MDM2 is a major negative regulator of p53, the key tumor suppressor involved in tumorigenesis of the majority of human cancers. Whether its expression might explain the relative lack of gastric cancer in Thailand was assessed here. This single-center study was conducted in the northeast region of Thailand. Gastric mucosa from 100 patients with Helicobacter pylori associated gastritis was analyzed for MDM2 SNP309 using real-time PCR hybridization (light-cycler) probes. In the total 100 Helicobacter pylori associated gastritis cases the incidence of SNP 309 T/T homozygous was 78 % with SNP309 G/T heterozygous found in 19% and SNP309 G/G homozygous in 3%. The result show SNP 309 T/T and SNP 309 G/T to be rather common in the Thai population. Our study indicates that the MDM2 SNP309 G/G homozygous genotype might be a risk factor for gastric cancer in Thailand and the fact that it is infrequent could explain to some extent the low incidence of gastric cancer in the Thai population.

  9. GenomeRunner web server: regulatory similarity and differences define the functional impact of SNP sets.

    Science.gov (United States)

    Dozmorov, Mikhail G; Cara, Lukas R; Giles, Cory B; Wren, Jonathan D

    2016-08-01

    The growing amount of regulatory data from the ENCODE, Roadmap Epigenomics and other consortia provides a wealth of opportunities to investigate the functional impact of single nucleotide polymorphisms (SNPs). Yet, given the large number of regulatory datasets, researchers are posed with a challenge of how to efficiently utilize them to interpret the functional impact of SNP sets. We developed the GenomeRunner web server to automate systematic statistical analysis of SNP sets within a regulatory context. Besides defining the functional impact of SNP sets, GenomeRunner implements novel regulatory similarity/differential analyses, and cell type-specific regulatory enrichment analysis. Validated against literature- and disease ontology-based approaches, analysis of 39 disease/trait-associated SNP sets demonstrated that the functional impact of SNP sets corresponds to known disease relationships. We identified a group of autoimmune diseases with SNPs distinctly enriched in the enhancers of T helper cell subpopulations, and demonstrated relevant cell type-specificity of the functional impact of other SNP sets. In summary, we show how systematic analysis of genomic data within a regulatory context can help interpreting the functional impact of SNP sets. GenomeRunner web server is freely available at http://www.integrativegenomics.org/ mikhail.dozmorov@gmail.com Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  10. Inter-laboratory evaluation of the EUROFORGEN Global ancestry-informative SNP panel by massively parallel sequencing using the Ion PGM™.

    Science.gov (United States)

    Eduardoff, M; Gross, T E; Santos, C; de la Puente, M; Ballard, D; Strobl, C; Børsting, C; Morling, N; Fusco, L; Hussing, C; Egyed, B; Souto, L; Uacyisrael, J; Syndercombe Court, D; Carracedo, Á; Lareu, M V; Schneider, P M; Parson, W; Phillips, C; Parson, W; Phillips, C

    2016-07-01

    The EUROFORGEN Global ancestry-informative SNP (AIM-SNPs) panel is a forensic multiplex of 128 markers designed to differentiate an individual's ancestry from amongst the five continental population groups of Africa, Europe, East Asia, Native America, and Oceania. A custom multiplex of AmpliSeq™ PCR primers was designed for the Global AIM-SNPs to perform massively parallel sequencing using the Ion PGM™ system. This study assessed individual SNP genotyping precision using the Ion PGM™, the forensic sensitivity of the multiplex using dilution series, degraded DNA plus simple mixtures, and the ancestry differentiation power of the final panel design, which required substitution of three original ancestry-informative SNPs with alternatives. Fourteen populations that had not been previously analyzed were genotyped using the custom multiplex and these studies allowed assessment of genotyping performance by comparison of data across five laboratories. Results indicate a low level of genotyping error can still occur from sequence misalignment caused by homopolymeric tracts close to the target SNP, despite careful scrutiny of candidate SNPs at the design stage. Such sequence misalignment required the exclusion of component SNP rs2080161 from the Global AIM-SNPs panel. However, the overall genotyping precision and sensitivity of this custom multiplex indicates the Ion PGM™ assay for the Global AIM-SNPs is highly suitable for forensic ancestry analysis with massively parallel sequencing. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  11. High Quality RNA Isolation from Leaf, Shell, Root Tissues and Callus of Hazelnut (Corylus avellana L.

    Directory of Open Access Journals (Sweden)

    Hossein Khosravi

    2017-12-01

    Full Text Available Extraction of high quality RNA is a critical step in molecular genetics studies. Hazelnut is one of the most important nuts plants in the world. The presence of the taxol and other taxanes in hazelnut plant necessitates explaining their biosynthesis pathway and identifying the candidate genes. Therefore, an easy and practical method is necessary for RNA extraction from hazelnuts. Hazelnut has high levels of phenolic compounds. High amounts of polyphenolic and polysaccharide compounds in plants could be causing problems in RNA extraction procedures.  To avoid these problems, a simple and efficient method can be used based on cetyltrimethylammonium bromide (CTAB extraction buffer and lithium chloride for extraction of high quality RNA from different parts of hazelnut plant. Using this method, a high-quality RNA sample (light absorbed in the A260/A280 was 2.04

  12. Development of a dense SNP-based linkage map of an apple rootstock progeny using the Malus Infinium whole genome genotyping array.

    Science.gov (United States)

    Antanaviciute, Laima; Fernández-Fernández, Felicidad; Jansen, Johannes; Banchi, Elisa; Evans, Katherine M; Viola, Roberto; Velasco, Riccardo; Dunwell, Jim M; Troggio, Michela; Sargent, Daniel J

    2012-05-25

    A whole-genome genotyping array has previously been developed for Malus using SNP data from 28 Malus genotypes. This array offers the prospect of high throughput genotyping and linkage map development for any given Malus progeny. To test the applicability of the array for mapping in diverse Malus genotypes, we applied the array to the construction of a SNP-based linkage map of an apple rootstock progeny. Of the 7,867 Malus SNP markers on the array, 1,823 (23.2%) were heterozygous in one of the two parents of the progeny, 1,007 (12.8%) were heterozygous in both parental genotypes, whilst just 2.8% of the 921 Pyrus SNPs were heterozygous. A linkage map spanning 1,282.2 cM was produced comprising 2,272 SNP markers, 306 SSR markers and the S-locus. The length of the M432 linkage map was increased by 52.7 cM with the addition of the SNP markers, whilst marker density increased from 3.8 cM/marker to 0.5 cM/marker. Just three regions in excess of 10 cM remain where no markers were mapped. We compared the positions of the mapped SNP markers on the M432 map with their predicted positions on the 'Golden Delicious' genome sequence. A total of 311 markers (13.7% of all mapped markers) mapped to positions that conflicted with their predicted positions on the 'Golden Delicious' pseudo-chromosomes, indicating the presence of paralogous genomic regions or mis-assignments of genome sequence contigs during the assembly and anchoring of the genome sequence. We incorporated data for the 2,272 SNP markers onto the map of the M432 progeny and have presented the most complete and saturated map of the full 17 linkage groups of M. pumila to date. The data were generated rapidly in a high-throughput semi-automated pipeline, permitting significant savings in time and cost over linkage map construction using microsatellites. The application of the array will permit linkage maps to be developed for QTL analyses in a cost-effective manner, and the identification of SNPs that have been

  13. Isolation of high quality RNA from pistachio (Pistacia vera L.) and other woody plants high in secondary metabolites.

    Science.gov (United States)

    Moazzam Jazi, Maryam; Rajaei, Saideh; Seyedi, Seyed Mahdi

    2015-10-01

    The quality and quantity of RNA are critical for successful downstream transcriptome-based studies such as microarrays and RNA sequencing (RNA-Seq). RNA isolation from woody plants, such as Pistacia vera, with very high amounts of polyphenols and polysaccharides is an enormous challenge. Here, we describe a highly efficient protocol that overcomes the limitations posed by poor quality and low yield of isolated RNA from pistachio and various recalcitrant woody plants. The key factors that resulted in a yield of 150 μg of high quality RNA per 200 mg of plant tissue include the elimination of phenol from the extraction buffer, raising the concentration of β-mercaptoethanol, long time incubation at 65 °C, and nucleic acid precipitation with optimized volume of NaCl and isopropyl alcohol. Also, the A260/A280 and A260/A230 of extracted RNA were about 1.9-2.1and 2.2-2.3, respectively, revealing the high purity. Since the isolated RNA passed highly stringent quality control standards for sensitive reactions, including RNA sequencing and real-time PCR, it can be considered as a reliable and cost-effective method for RNA extraction from woody plants.

  14. Sequential sentinel SNP Regional Association Plots (SSS-RAP): an approach for testing independence of SNP association signals using meta-analysis data.

    Science.gov (United States)

    Zheng, Jie; Gaunt, Tom R; Day, Ian N M

    2013-01-01

    Genome-Wide Association Studies (GWAS) frequently incorporate meta-analysis within their framework. However, conditional analysis of individual-level data, which is an established approach for fine mapping of causal sites, is often precluded where only group-level summary data are available for analysis. Here, we present a numerical and graphical approach, "sequential sentinel SNP regional association plot" (SSS-RAP), which estimates regression coefficients (beta) with their standard errors using the meta-analysis summary results directly. Under an additive model, typical for genes with small effect, the effect for a sentinel SNP can be transformed to the predicted effect for a possibly dependent SNP through a 2×2 2-SNP haplotypes table. The approach assumes Hardy-Weinberg equilibrium for test SNPs. SSS-RAP is available as a Web-tool (http://apps.biocompute.org.uk/sssrap/sssrap.cgi). To develop and illustrate SSS-RAP we analyzed lipid and ECG traits data from the British Women's Heart and Health Study (BWHHS), evaluated a meta-analysis for ECG trait and presented several simulations. We compared results with existing approaches such as model selection methods and conditional analysis. Generally findings were consistent. SSS-RAP represents a tool for testing independence of SNP association signals using meta-analysis data, and is also a convenient approach based on biological principles for fine mapping in group level summary data. © 2012 Blackwell Publishing Ltd/University College London.

  15. MDM2 promoter SNP344T>A (rs1196333 status does not affect cancer risk.

    Directory of Open Access Journals (Sweden)

    Stian Knappskog

    Full Text Available The MDM2 proto-oncogene plays a key role in central cellular processes like growth control and apoptosis, and the gene locus is frequently amplified in sarcomas. Two polymorphisms located in the MDM2 promoter P2 have been shown to affect cancer risk. One of these polymorphisms (SNP309T>G; rs2279744 facilitates Sp1 transcription factor binding to the promoter and is associated with increased cancer risk. In contrast, SNP285G>C (rs117039649, located 24 bp upstream of rs2279744, and in complete linkage disequilibrium with the SNP309G allele, reduces Sp1 recruitment and lowers cancer risk. Thus, fine tuning of MDM2 expression has proven to be of significant importance with respect to tumorigenesis. We assessed the potential functional effects of a third MDM2 promoter P2 polymorphism (SNP344T>A; rs1196333 located on the SNP309T allele. While in silico analyses indicated SNP344A to modulate TFAP2A, SPIB and AP1 transcription factor binding, we found no effect of SNP344 status on MDM2 expression levels. Assessing the frequency of SNP344A in healthy Caucasians (n = 2,954 and patients suffering from ovarian (n = 1,927, breast (n = 1,271, endometrial (n = 895 or prostatic cancer (n = 641, we detected no significant difference in the distribution of this polymorphism between any of these cancer forms and healthy controls (6.1% in healthy controls, and 4.9%, 5.0%, 5.4% and 7.2% in the cancer groups, respectively. In conclusion, our findings provide no evidence indicating that SNP344A may affect MDM2 transcription or cancer risk.

  16. SNP-based typing: a useful tool to study Bordetella pertussis populations.

    Directory of Open Access Journals (Sweden)

    Marjolein van Gent

    Full Text Available To monitor changes in Bordetella pertussis populations, mainly two typing methods are used; Pulsed-Field Gel Electrophoresis (PFGE and Multiple-Locus Variable-Number Tandem Repeat Analysis (MLVA. In this study, a single nucleotide polymorphism (SNP typing method, based on 87 SNPs, was developed and compared with PFGE and MLVA. The discriminatory indices of SNP typing, PFGE and MLVA were found to be 0.85, 0.95 and 0.83, respectively. Phylogenetic analysis, using SNP typing as Gold Standard, revealed false homoplasies in the PFGE and MLVA trees. Further, in contrast to the SNP-based tree, the PFGE- and MLVA-based trees did not reveal a positive correlation between root-to-tip distance and the isolation year of strains. Thus PFGE and MLVA do not allow an estimation of the relative age of the selected strains. In conclusion, SNP typing was found to be phylogenetically more informative than PFGE and more discriminative than MLVA. Further, in contrast to PFGE, it is readily standardized allowing interlaboratory comparisons. We applied SNP typing to study strains with a novel allele for the pertussis toxin promoter, ptxP3, which have a worldwide distribution and which have replaced the resident ptxP1 strains in the last 20 years. Previously, we showed that ptxP3 strains showed increased pertussis toxin expression and that their emergence was associated with increased notification in The Netherlands. SNP typing showed that the ptxP3 strains isolated in the Americas, Asia, Australia and Europe formed a monophyletic branch which recently diverged from ptxP1 strains. Two predominant ptxP3 SNP types were identified which spread worldwide. The widespread use of SNP typing will enhance our understanding of the evolution and global epidemiology of B. pertussis.

  17. SNP-Based Typing: A Useful Tool to Study Bordetella pertussis Populations

    Science.gov (United States)

    van der Heide, Han G. J.; Heuvelman, Kees J.; Kallonen, Teemu; He, Qiushui; Mertsola, Jussi; Advani, Abdolreza; Hallander, Hans O.; Janssens, Koen; Hermans, Peter W.; Mooi, Frits R.

    2011-01-01

    To monitor changes in Bordetella pertussis populations, mainly two typing methods are used; Pulsed-Field Gel Electrophoresis (PFGE) and Multiple-Locus Variable-Number Tandem Repeat Analysis (MLVA). In this study, a single nucleotide polymorphism (SNP) typing method, based on 87 SNPs, was developed and compared with PFGE and MLVA. The discriminatory indices of SNP typing, PFGE and MLVA were found to be 0.85, 0.95 and 0.83, respectively. Phylogenetic analysis, using SNP typing as Gold Standard, revealed false homoplasies in the PFGE and MLVA trees. Further, in contrast to the SNP-based tree, the PFGE- and MLVA-based trees did not reveal a positive correlation between root-to-tip distance and the isolation year of strains. Thus PFGE and MLVA do not allow an estimation of the relative age of the selected strains. In conclusion, SNP typing was found to be phylogenetically more informative than PFGE and more discriminative than MLVA. Further, in contrast to PFGE, it is readily standardized allowing interlaboratory comparisons. We applied SNP typing to study strains with a novel allele for the pertussis toxin promoter, ptxP3, which have a worldwide distribution and which have replaced the resident ptxP1 strains in the last 20 years. Previously, we showed that ptxP3 strains showed increased pertussis toxin expression and that their emergence was associated with increased notification in the Netherlands. SNP typing showed that the ptxP3 strains isolated in the Americas, Asia, Australia and Europe formed a monophyletic branch which recently diverged from ptxP1 strains. Two predominant ptxP3 SNP types were identified which spread worldwide. The widespread use of SNP typing will enhance our understanding of the evolution and global epidemiology of B. pertussis. PMID:21647370

  18. Analysis of apple beverages treated with high-power ultrasound: a quality function deployment approach.

    Science.gov (United States)

    Režek Jambrak, Anet; Šimunek, Marina; Grbeš, Franjo; Mandura, Ana; Djekic, Ilija

    2018-04-01

    The objective of this paper was to demonstrate application of quality function deployment in analysing effects of high power ultrasound on quality properties of apple juices and nectars. In order to develop a quality function deployment model, joint with instrumental analysis of treated samples, a field survey was performed to identify consumer preferences towards quality characteristics of juices/nectar. Based on field research, the three most important characteristics were 'taste' and 'aroma' with 28.5% of relative absolute weight importance, followed by 'odour' (16.9%). The quality function deployment model showed that the top three 'quality scores' for apple juice were treatments with amplitude 90 µm, 9 min treatment time and sample temperature 40 °C; 60 µm, 9 min, 60 °C; and 90 µm, 6 min, 40 °C. For nectars, the top three were treatments 120 µm, 9 min, 20 °C; 60 µm, 9 min, 60 °C; and A2.16 60 µm, 9 min, 20 °C. This type of quality model enables a more complex measure of large scale of different quality parameters. Its simplicity should be understood as its practical advantage and, as such, this tool can be a part of design quality when using novel preservation technologies. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

  19. Bullying as a risk for poor sleep quality among high school students in China.

    Directory of Open Access Journals (Sweden)

    Ying Zhou

    Full Text Available To determine whether involvement in bullying as a bully, victim, or bully-victim was associated with a higher risk of poor sleep quality among high school students in China.A cross-sectional study was conducted. A total of 23,877 high school students were surveyed in six cities in Guangdong Province. All students were asked to complete the adolescent health status questionnaire, which included the Chinese version of the Pittsburgh Sleep Quality Index (PSQI and bullying involvement. Descriptive statistics were used to evaluate sleep quality and the prevalence of school bullying. Multi-level logistic regression analyses were conducted to examine the association between being victimized and bullying others with sleep quality.Among the 23,877 students, 6,127 (25.66% reported having poor sleep quality, and 10.89% reported being involved in bullying behaviors. Of the respondents, 1,410 (5.91% were pure victims of bullying, 401 (1.68% were bullies and 784 (3.28% were bully-victims. Frequently being involved in bullying behaviors (being bullied or bullying others was related to increased risks of poor sleep quality compared with adolescents who were not involved in bullying behaviors. After adjusting for age, sex, and other confounding factors, the students who were being bullied (OR=2.05, 95%CI=1.81-2.32, bullied others (OR=2.30, 95%CI=1.85-2.86 or both (OR=2.58, 95%CI=2.20-3.03 were at a higher risk for poor sleep quality.Poor sleep quality among high school students is highly prevalent, and school bullying is prevalent among adolescents in China. The present results suggested that being involved in school bullying might be a risk factor for poor sleep quality among adolescents.

  20. Bullying as a risk for poor sleep quality among high school students in China.

    Science.gov (United States)

    Zhou, Ying; Guo, Lan; Lu, Ci-yong; Deng, Jian-xiong; He, Yuan; Huang, Jing-hui; Huang, Guo-liang; Deng, Xue-qing; Gao, Xue

    2015-01-01

    To determine whether involvement in bullying as a bully, victim, or bully-victim was associated with a higher risk of poor sleep quality among high school students in China. A cross-sectional study was conducted. A total of 23,877 high school students were surveyed in six cities in Guangdong Province. All students were asked to complete the adolescent health status questionnaire, which included the Chinese version of the Pittsburgh Sleep Quality Index (PSQI) and bullying involvement. Descriptive statistics were used to evaluate sleep quality and the prevalence of school bullying. Multi-level logistic regression analyses were conducted to examine the association between being victimized and bullying others with sleep quality. Among the 23,877 students, 6,127 (25.66%) reported having poor sleep quality, and 10.89% reported being involved in bullying behaviors. Of the respondents, 1,410 (5.91%) were pure victims of bullying, 401 (1.68%) were bullies and 784 (3.28%) were bully-victims. Frequently being involved in bullying behaviors (being bullied or bullying others) was related to increased risks of poor sleep quality compared with adolescents who were not involved in bullying behaviors. After adjusting for age, sex, and other confounding factors, the students who were being bullied (OR=2.05, 95%CI=1.81-2.32), bullied others (OR=2.30, 95%CI=1.85-2.86) or both (OR=2.58, 95%CI=2.20-3.03) were at a higher risk for poor sleep quality. Poor sleep quality among high school students is highly prevalent, and school bullying is prevalent among adolescents in China. The present results suggested that being involved in school bullying might be a risk factor for poor sleep quality among adolescents.

  1. Drop-out probabilities of IrisPlex SNP alleles

    DEFF Research Database (Denmark)

    Andersen, Jeppe Dyrberg; Tvedebrink, Torben; Mogensen, Helle Smidt

    2013-01-01

    In certain crime cases, information about a perpetrator's phenotype, including eye colour, may be a valuable tool if no DNA profile of any suspect or individual in the DNA database matches the DNA profile found at the crime scene. Often, the available DNA material is sparse and allelic drop-out...... of true alleles is possible. As part of the validation of the IrisPlex assay in our ISO17025 accredited, forensic genetic laboratory, we estimated the probability of drop-out of specific SNP alleles using 29 and 30 PCR cycles and 25, 50 and 100 Single Base Extension (SBE) cycles. We observed no drop-out...... when the amount of DNA was greater than 125 pg for 29 cycles of PCR and greater than 62 pg for 30 cycles of PCR. With the use of a logistic regression model, we estimated the allele specific probability of drop-out in heterozygote systems based on the signal strength of the observed allele...

  2. When high-volume PCI operators in high-volume hospitals move to lower volume hospitals-Do they still maintain high volume and quality of outcomes?

    Science.gov (United States)

    Lu, Tsung-Hsueh; Li, Sheng-Tun; Liang, Fu-Wen; Lee, Jo-Chi; Yin, Wei-Hsian

    2017-10-31

    The aim of this quasi-experimental study was to examine whether high-volume percutaneous coronary intervention (PCI) operators still maintain high volume and quality of outcomes when they moved to lower volume hospitals. Systematic reviews have indicated that high-volume PCI operators and hospitals have higher quality outcomes. However, little is known on whether high PCI volume and high quality outcomes are mainly due to operator characteristics (i.e., skill and experience) and is portable across organizations or whether it is due to hospital characteristics (i.e., equipment, team, and management system) and is less portable. We used Taiwan National Health Insurance claims data 2000-2012 to identify 98 high-volume PCI operators, 10 of whom moved from one hospital to another during the study period. We compared the PCI volume, risk-adjusted mortality ratio, and major adverse cardiovascular event (MACE) ratio before and after moving. Of the 10 high-volume operators who moved, 6 moved from high- to moderate- or low-volume hospitals, with median annual PCI volumes (interquartile range) of 130 (117-165) in prior hospitals and 54 (46-84) in subsequent hospitals (the hospital the operator moved to), and the remaining 4 moved from high to high-volume hospitals, with median annual PCI volumes (interquartile range) of 151 (133-162) in prior hospitals and 193 (178-239) in subsequent hospitals. No significant differences were observed in the risk-adjusted mortality ratios and MACE ratios between high-volume operators and matched controls before and after moving. High-volume operators cannot maintain high volume when they moved from high to moderate or low-volume hospitals; however, the quality of care is maintained. High PCI volume and high-quality outcomes are less portable and more hospital bound. © 2017 Wiley Periodicals, Inc.

  3. A Narrative Review of High-Quality Literature on the Effects of Resident Duty Hours Reforms.

    Science.gov (United States)

    Lin, Henry; Lin, Emery; Auditore, Stephanie; Fanning, Jon

    2016-01-01

    To summarize current high-quality studies evaluating the effect and efficacy of resident duty hours reforms (DHRs) on patient safety and resident education and well-being. The authors searched PubMed and Medline in August 2012 and again in May 2013 for literature (1987-2013) about the effects of DHRs. They assessed the quality of articles using the Medical Education Research Study Quality Instrument (MERSQI) scoring system. They considered randomized controlled trials (RCTs), partial RCTs, and all studies with a MERSQI score ≥ 14 to be "high-quality" methodology studies. A total of 72 high-quality studies met inclusion criteria. Most studies showed no change or slight improvement in mortality and complication rates after DHRs. Resident well-being was generally improved, but there was a perceived negative impact on education (knowledge acquisition, skills, and cognitive performance) following DHRs. Eleven high-quality studies assessed the impact of DHR interventions; all reported a neutral to positive impact. Seven high-quality studies assessed costs associated with DHRs and demonstrated an increase in hospital costs. The results of most studies that allow enough time for DHR interventions to take effect suggest a benefit to patient safety and resident well-being, but the effect on the quality of training remains unknown. Additional methodologically sound studies on the impact of DHRs are necessary. Priorities for future research include approaches to optimizing education and clinical proficiency and studies on the effect of intervention strategies on both education and patient safety. Such studies will provide additional information to help improve duty hours policies.

  4. Certifying leaders? high-quality management practices and healthy organisations: an ISO-9000 based standardisation approach.

    Science.gov (United States)

    Montano, Diego

    2016-08-05

    The present study proposes a set of quality requirements to management practices by taking into account the empirical evidence on their potential effects on health, the systemic nature of social organisations, and the current conceptualisations of management functions within the framework of comprehensive quality management systems. Systematic reviews and meta-analyses focusing on the associations between leadership and/or supervision and health in occupational settings are evaluated, and the core elements of an ISO 9001 standardisation approach are presented. Six major occupational health requirements to high-quality management practices are identified pertaining to communication processes, organisational justice, role clarity, decision making, social influence processes and management support. It is concluded that the quality of management practices may be improved by developing a quality management system of management practices that ensures not only conformity to product but also to occupational safety and health requirements. Further research may evaluate the practicability of the proposed approach.

  5. Modeling the Subjective Quality of Highly Contrasted Videos Displayed on LCD With Local Backlight Dimming

    DEFF Research Database (Denmark)

    Mantel, Claire; Bech, Søren; Korhonen, Jari

    2015-01-01

    Local backlight dimming is a technology aiming at both saving energy and improving visual quality on television sets. As the rendition of the image is specified locally, the numerical signal corresponding to the displayed image needs to be computed through a model of the display. This simulated...... signal can then be used as input to objective quality metrics. The focus of this paper is on determining which characteristics of locally backlit displays influence quality assessment. A subjective experiment assessing the quality of highly contrasted videos displayed with various local backlight......-dimming algorithms is set up. Subjective results are then compared with both objective measures and objective quality metrics using different display models. The first analysis indicates that the most significant objective features are temporal variations, power consumption (probably representing leakage...

  6. The effect of the amiodarone-warfarin interaction on anticoagulation quality in a single, high-quality anticoagulation center.

    Science.gov (United States)

    White, Ryan D; Riggs, Kyle W; Ege, Ed J; Petroski, Gregory F; Koerber, Scott M; Flaker, Greg

    2016-03-01

    Clinical trials have reported a low time in therapeutic range (TTR) in patients with atrial fibrillation treated with both warfarin andamiodarone. These trials included centers and countries with both high and low TTRs. What is the impact of amiodarone on the TTR in a single, high-quality anticoagulation clinic? TTR was assessed in amiodarone and nonamiodarone-treated patients from a University anticoagulation clinic. Baseline characteristics between patients ever-taking or never-taking amiodarone were similar, except more amiodarone patients were smokers (19.5 vs. 6.1%, P = 0.0031). The TTR calculated from 8901international normalized ratios (INRs) in 249 nonamiodarone patients with a mean follow-up of 34 ± 20 months (mean INR 36 ± 18) was 66 ± 16.6% compared with 61.3 ± 16.2% (P = 0.111) from 1455 INRs in 41 amiodarone-treated patients with a mean follow-up of 28 ± 20 months (mean INR 35 ± 22). Factors associated with a low TTR were male sex (P = 0.0013), smoker (P = 0.0048), and amiodarone use (P = 0.0374). A second on-treatment analysis, in which the TTR was calculated only during amiodarone therapy, resulted in similar findings; however, amiodarone did not emerge as a predictor of a low TTR. In 11 patients, the TTR prior to amiodarone (54.5 ± 22.2%) was not significantly different in the first 3 months (54.6 ± 33.4%) or after 3 months (67.2 ± 33.7%) of amiodarone. In a single high-quality anticoagulation center, anticoagulation quality, as measured by the TTR, can be comparable in amiodarone and nonamiodarone-treated patients.

  7. Combined microfluidization and ultrasonication: a synergistic protocol for high-efficient processing of SWCNT dispersions with high quality

    Energy Technology Data Exchange (ETDEWEB)

    Luo, Sida, E-mail: s.luo@buaa.edu.cn [Beihang University, School of Mechanical Engineering and Automation (China); Liu, Tao, E-mail: tliu@fsu.edu [Florida State University, High-Performance Materials Institute (United States); Wang, Yong; Li, Liuhe [Beihang University, School of Mechanical Engineering and Automation (China); Wang, Guantao; Luo, Yun [China University of Geosciences, Center of Safety Research, School of Engineering and Technology (China)

    2016-08-15

    High-efficient and large-scale production of high-quality CNT dispersions is necessary for meeting the future needs to develop various CNT-based electronic devices. Herein, we have designed novel processing protocols by combining conventional ultrasonication process with a new microfluidization technique to produce high-quality SWCNT dispersions with improved processing efficiency. To judge the quality of SWCNT dispersions, one critical factor is the degree of exfoliation, which could be quantified by both geometrical dimension of the exfoliated nanotubes and percentage of individual tubes in a given dispersion. In this paper, the synergistic effect of the combined protocols was systematically investigated through evaluating SWCNT dispersions with newly developed characterization techniques, namely preparative ultracentrifuge method (PUM) and simultaneous Raman scattering and photoluminescence spectroscopy (SRSPL). The results of both techniques draw similar conclusions that as compared with either of the processes operated separately, a low-pass microfluidization followed by a reasonable duration of ultrasonication could substantially improve the processing efficiency to produce high-quality SWCNT dispersions with averaged particle length and diameter as small as ~600 and ~2 nm, respectively.Graphical abstract.

  8. Towards a High Quality High School Workforce: A Longitudinal, Demographic Analysis of U.S. Public School Physics Teachers

    Science.gov (United States)

    Rushton, Gregory T.; Rosengrant, David; Dewar, Andrew; Shah, Lisa; Ray, Herman E.; Sheppard, Keith; Watanabe, Lynn

    2017-01-01

    Efforts to improve the number and quality of the high school physics teaching workforce have taken several forms, including those sponsored by professional organizations. Using a series of large-scale teacher demographic data sets from the National Center for Education Statistics (NCES), this study sought to investigate trends in teacher quality…

  9. Examining Relational Engagement across the Transition to High Schools in Three US High Schools Reformed to Improve Relationship Quality

    Science.gov (United States)

    Davis, Heather A.; Chang, Mei-Lin; Andrzejewski, Carey E.; Poirier, Ryan R.

    2014-01-01

    The purpose of this study was to examine changes in students' relational engagement across the transition to high school in three schools reformed to improve the quality of student-teacher relationships. In order to analyze this data we employed latent growth curve (LGC) modeling techniques (n = 637). We ran three LGC models on three…

  10. Development of a high-quality cut-off wall using electrophoresis

    International Nuclear Information System (INIS)

    Kawachi, T.; Murahashi, H.

    1991-01-01

    Techniques to build a high-quality cut-off wall have been developed for storage facilities of low-level radioactive waste (LLW) as an emergency measures to prevent leakages. The cut-off wall is highly impermeable, nucleid-adsorptive and have long-term durability. Electrophoresis is used to form impermeable membrane of bentonite as main features of the cut-off wall. First of all, laboratory tests have been conducted to study ways of building barriers on site and to collect data on the barriers properties. Afterwards, on-site construction tests of a high-quality cut-off wall have been carried out. In this paper, we describe the process and results on the studies of the high-quality cut-off wall using electrophoresis

  11. Analytical method for high resolution liquid chromatography for quality control French Macaw

    International Nuclear Information System (INIS)

    Garcia Penna, Caridad M; Torres Amaro, Leonid; Menendez Castillo, Rosa; Sanchez, Esther; Martinez Espinosa, Vivian; Gonzalez, Maria Lidia; Rodriguez, Carlos

    2007-01-01

    Was developed and validated an analytical method for high resolution liquid chromatography applicable to quality control of drugs dry French Macaw (Senna alata L. Roxb.) With ultraviolet detection at 340 nm. The method for high resolution liquid chromatography used to quantify the sennosides A and B, main components, was validated and proved to be specific, linear, precise and accurate. (Author)

  12. High quality factor GaAs microcavity with buried bullseye defects

    DEFF Research Database (Denmark)

    Winkler, K.; Gregersen, Niels; Hayrynen, T.

    2018-01-01

    The development of high quality factor solid-state microcavities with low mode volumes has paved the way towards on-chip cavity quantum electrodynamics experiments and the development of high-performance nanophotonic devices. Here, we report on the implementation of a new kind of solid...

  13. Quality and performance of laser cutting with a high power SM fiber laser

    DEFF Research Database (Denmark)

    Kristiansen, Morten; Selchau, Jacob; Olsen, F. O.

    2013-01-01

    The introduction of high power single mode fiber lasers allows for a beam of high power and a good beam quality factor (M2 ” 1.2), compared to the multimode fiber lasers often utilised in macro laser metal cutting. This paper describes fundamental studies of macro laser metal cutting with a singl...

  14. Effects of High School Students' Perceptions of School Life Quality on Their Academic Motivation Levels

    Science.gov (United States)

    Akin Kösterelioglu, Meltem; Kösterelioglu, Ilker

    2015-01-01

    This study aims to identify the effects of high school students' perceptions of school life quality on their academic motivation levels. The study was conducted on a sample of high school students (n = 2371) in Amasya Province in the fall semester of 2013-2014 academic year. Study sample was selected with the help of cluster sampling method. Data…

  15. Typing of 48 autosomal SNPs and amelogenin with GenPlex SNP genotyping system in forensic genetics

    DEFF Research Database (Denmark)

    Tomas Mas, Carmen; Stangegaard, Michael; Børsting, Claus

    2008-01-01

    , Somalia and Greenland were investigated with GenPlex using a Biomek 3000 (Beckman Coulter) robot. The results were compared to results obtained with an ISO 17025 accredited SNP typing assay based on single base extension (SBE). With the GenPlex SNP genotyping system, full SNP profiles were obtained in 97.......6% of the investigations. Perfect concordance was obtained in duplicate investigations and the SNP genotypes obtained with the GenPlex system were concordant with those of the accredited SBE based SNP typing system except for one result in rs901398 in one of 286 individuals most likely due to a mutation 6 bp downstream...

  16. Preliminary Study on the Single Nucleotide Polymorphism (SNP of XRCC1 Gene Identificationto Improve the Outcomes of Radiotherapy for Cervical Cancer

    Directory of Open Access Journals (Sweden)

    Devita Tetriana

    2015-09-01

    Full Text Available Cervical cancer is the most fatal disease among Indonesian women. In recognition of the substantial variation in the intrinsic response of individuals to radiation, an effort had been done to identify the genetic markers, primarily Single Nucleotide polymorphisms (SNPs, which are associated with responsiveness of cancer cells to radiation therapy. One of these SNPs is X-ray repair cross-complementing protein 1 (XRCC1 that is one of the most important genes in deoxyribonucleic acid (DNA repair pathways. Meta-analysis in the determination of the association of XRCC1 polymorphisms with cervical cancer revealed the potential role of XRCC1 polymorphisms in predicting cell response to radiotherapy.Our preliminary study with real-time polymerase chain reaction (RT-PCR showed that radiotherapy affected the XRCC1 gene analyzed in blood of cervical cancer patient. Other published study found three SNPs of XRCC1 (Arg194Trp, Arg280His, and Arg399Gln that cause amino acid substitutions. Arg194Trp is only SNPs that associated with high risk of cervical cancer but not others. Additionally, structure and function of this protein can be altered by functional SNPs, which may lead to the susceptibility of individuals to cancers. Anotherstudy found G399A polymorphisms. We concluded that SNP of this DNA repair genes have been found to be good predictors of efficacy of radiotherapy.Kanker serviks adalah penyakit yang paling fatal pada perempuan di Indonesia. Untuk memahami variasi substansial respon intrinsik individual terhadap radiasi, suatu usaha telah dilakukan untuk mengidentifikasi petanda genetik, terutama Single Nucleotide polymorphism (SNP, yang berkaitan dengan responsel kanker terhadap terapi radiasi. Satu dari SNP tersebut adalah X-ray repair cross-complementing protein 1 (XRCC1 yang merupakan satu dari gen paling penting dalam lajur perbaikan asam deoksiribonukleat (DNA. Meta-analysis dalam penentuan hubungan polimorfisme XRCC1 dengan kanker serviks

  17. High dose-rate brachytherapy source position quality assurance using radiochromic film

    International Nuclear Information System (INIS)

    Evans, M.D.C.; Devic, S.; Podgorsak, E.B.

    2007-01-01

    Traditionally, radiographic film has been used to verify high-dose-rate brachytherapy source position accuracy by co-registering autoradiographic and diagnostic images of the associated applicator. Filmless PACS-based clinics that do not have access to radiographic film and wet developers may have trouble performing this quality assurance test in a simple and practical manner. We describe an alternative method for quality assurance using radiochromic-type film. In addition to being easy and practical to use, radiochromic film has some advantages in comparison with traditional radiographic film when used for HDR brachytherapy quality assurance

  18. Production of high-quality polydisperse construction mixes for additive 3D technologies.

    Science.gov (United States)

    Gerasimov, M. D.; Brazhnik, Yu V.; Gorshkov, P. S.; Latyshev, S. S.

    2018-03-01

    The paper describes a new design of a mixer allowing production of high quality polydisperse powders, used in additive 3D technologies. A new principle of dry powder particle mixing is considered, implementing a possibility of a close-to-ideal distribution of such particles in common space. A mathematical model of the mixer is presented, allowing evaluating quality indicators of the produced mixture. Experimental results are shown and rational values of process parameters of the mixer are obtained.

  19. Teaching Surgical Procedures with Movies: Tips for High-quality Video Clips

    OpenAIRE

    Jacquemart, Mathieu; Bouletreau, Pierre; Breton, Pierre; Mojallal, Ali; Sigaux, Nicolas

    2016-01-01

    Summary: Video must now be considered as a precious tool for learning surgery. However, the medium does present production challenges, and currently, quality movies are not always accessible. We developed a series of 7 surgical videos and made them available on a publicly accessible internet website. Our videos have been viewed by thousands of people worldwide. High-quality educational movies must respect strategic and technical points to be reliable.

  20. Teaching Surgical Procedures with Movies: Tips for High-quality Video Clips.

    Science.gov (United States)

    Jacquemart, Mathieu; Bouletreau, Pierre; Breton, Pierre; Mojallal, Ali; Sigaux, Nicolas

    2016-09-01

    Video must now be considered as a precious tool for learning surgery. However, the medium does present production challenges, and currently, quality movies are not always accessible. We developed a series of 7 surgical videos and made them available on a publicly accessible internet website. Our videos have been viewed by thousands of people worldwide. High-quality educational movies must respect strategic and technical points to be reliable.