WorldWideScience

Sample records for bi-dimensional genome scan

  1. A bi-dimensional genome scan for prolificacy traits in pigs shows the existence of multiple epistatic QTL

    Directory of Open Access Journals (Sweden)

    Bidanel Jean P

    2009-12-01

    Full Text Available Abstract Background Prolificacy is the most important trait influencing the reproductive efficiency of pig production systems. The low heritability and sex-limited expression of prolificacy have hindered to some extent the improvement of this trait through artificial selection. Moreover, the relative contributions of additive, dominant and epistatic QTL to the genetic variance of pig prolificacy remain to be defined. In this work, we have undertaken this issue by performing one-dimensional and bi-dimensional genome scans for number of piglets born alive (NBA and total number of piglets born (TNB in a three generation Iberian by Meishan F2 intercross. Results The one-dimensional genome scan for NBA and TNB revealed the existence of two genome-wide highly significant QTL located on SSC13 (P SSC17 (P P P P P Conclusions The complex inheritance of prolificacy traits in pigs has been evidenced by identifying multiple additive (SSC13 and SSC17, dominant and epistatic QTL in an Iberian × Meishan F2 intercross. Our results demonstrate that a significant fraction of the phenotypic variance of swine prolificacy traits can be attributed to first-order gene-by-gene interactions emphasizing that the phenotypic effects of alleles might be strongly modulated by the genetic background where they segregate.

  2. Clinical applications of Genome Polymorphism Scans

    OpenAIRE

    Weber James L

    2006-01-01

    Abstract Applications of Genome Polymorphism Scans range from the relatively simple such as gender determination and confirmation of biological relationships, to the relatively complex such as determination of autozygosity and propagation of genetic information throughout pedigrees. Unlike nearly all other clinical DNA tests, the Scan is a universal test – it covers all people and all genes. In balance, I argue that the Genome Polymorphism Scan is the most powerful, affordable clinical DNA te...

  3. Genome-based peptide fingerprint scanning

    OpenAIRE

    Giddings, Michael C.; Shah, Atul A.; Gesteland, Ray; Moore, Barry

    2002-01-01

    We have implemented a method that identifies the genomic origins of sample proteins by scanning their peptide-mass fingerprint against the theoretical translation and proteolytic digest of an entire genome. Unlike previously reported techniques, this method requires no predefined ORF or protein annotations. Fixed-size windows along the genome sequence are scored by an equation accounting for the number of matching peptides, the number of missed enzymatic cleavages in each peptide, the number ...

  4. Clinical applications of Genome Polymorphism Scans

    Directory of Open Access Journals (Sweden)

    Weber James L

    2006-06-01

    Full Text Available Abstract Applications of Genome Polymorphism Scans range from the relatively simple such as gender determination and confirmation of biological relationships, to the relatively complex such as determination of autozygosity and propagation of genetic information throughout pedigrees. Unlike nearly all other clinical DNA tests, the Scan is a universal test – it covers all people and all genes. In balance, I argue that the Genome Polymorphism Scan is the most powerful, affordable clinical DNA test available today. Reviewers: This article was reviewed by Scott Weiss (nominated by Neil Smalheiser, Roberta Pagon (nominated by Jerzy Jurka and Val Sheffield (nominated by Neil Smalheiser.

  5. Genome-Wide Scan Reveals Mutation Associated with Melanoma

    Science.gov (United States)

    ... 1999 Spotlight on Research 2012 July 2012 (historical) Genome-Wide Scan Reveals Mutation Associated with Melanoma A ... out to see if a technology called whole genome sequencing would help them find other genetic risk ...

  6. Enhancer scanning to locate regulatory regions in genomic loci.

    Science.gov (United States)

    Buckley, Melissa; Gjyshi, Anxhela; Mendoza-Fandiño, Gustavo; Baskin, Rebekah; Carvalho, Renato S; Carvalho, Marcelo A; Woods, Nicholas T; Monteiro, Alvaro N A

    2016-01-01

    This protocol provides a rapid, streamlined and scalable strategy to systematically scan genomic regions for the presence of transcriptional regulatory regions that are active in a specific cell type. It creates genomic tiles spanning a region of interest that are subsequently cloned by recombination into a luciferase reporter vector containing the simian virus 40 promoter. Tiling clones are transfected into specific cell types to test for the presence of transcriptional regulatory regions. The protocol includes testing of different single-nucleotide polymorphism (SNP) alleles to determine their effect on regulatory activity. This procedure provides a systematic framework for identifying candidate functional SNPs within a locus during functional analysis of genome-wide association studies. This protocol adapts and combines previous well-established molecular biology methods to provide a streamlined strategy, based on automated primer design and recombinational cloning, allowing one to rapidly go from a genomic locus to a set of candidate functional SNPs in 8 weeks. PMID:26658467

  7. Controlling false discoveries in genome scans for selection.

    Science.gov (United States)

    François, Olivier; Martins, Helena; Caye, Kevin; Schoville, Sean D

    2016-01-01

    Population differentiation (PD) and ecological association (EA) tests have recently emerged as prominent statistical methods to investigate signatures of local adaptation using population genomic data. Based on statistical models, these genomewide testing procedures have attracted considerable attention as tools to identify loci potentially targeted by natural selection. An important issue with PD and EA tests is that incorrect model specification can generate large numbers of false-positive associations. Spurious association may indeed arise when shared demographic history, patterns of isolation by distance, cryptic relatedness or genetic background are ignored. Recent works on PD and EA tests have widely focused on improvements of test corrections for those confounding effects. Despite significant algorithmic improvements, there is still a number of open questions on how to check that false discoveries are under control and implement test corrections, or how to combine statistical tests from multiple genome scan methods. This tutorial study provides a detailed answer to these questions. It clarifies the relationships between traditional methods based on allele frequency differentiation and EA methods and provides a unified framework for their underlying statistical tests. We demonstrate how techniques developed in the area of genomewide association studies, such as inflation factors and linear mixed models, benefit genome scan methods and provide guidelines for good practice while conducting statistical tests in landscape and population genomic applications. Finally, we highlight how the combination of several well-calibrated statistical tests can increase the power to reject neutrality, improving our ability to infer patterns of local adaptation in large population genomic data sets. PMID:26671840

  8. A new approach for using genome scans to detect recent positive selection in the human genome.

    Directory of Open Access Journals (Sweden)

    Kun Tang

    2007-07-01

    Full Text Available Genome-wide scanning for signals of recent positive selection is essential for a comprehensive and systematic understanding of human adaptation. Here, we present a genomic survey of recent local selective sweeps, especially aimed at those nearly or recently completed. A novel approach was developed for such signals, based on contrasting the extended haplotype homozygosity (EHH profiles between populations. We applied this method to the genome single nucleotide polymorphism (SNP data of both the International HapMap Project and Perlegen Sciences, and detected widespread signals of recent local selection across the genome, consisting of both complete and partial sweeps. A challenging problem of genomic scans of recent positive selection is to clearly distinguish selection from neutral effects, given the high sensitivity of the test statistics to departures from neutral demographic assumptions and the lack of a single, accurate neutral model of human history. We therefore developed a new procedure that is robust across a wide range of demographic and ascertainment models, one that indicates that certain portions of the genome clearly depart from neutrality. Simulations of positive selection showed that our tests have high power towards strong selection sweeps that have undergone fixation. Gene ontology analysis of the candidate regions revealed several new functional groups that might help explain some important interpopulation differences in phenotypic traits.

  9. Genome scan for meat quality traits in Nelore beef cattle.

    Science.gov (United States)

    Tizioto, P C; Decker, J E; Taylor, J F; Schnabel, R D; Mudadu, M A; Silva, F L; Mourão, G B; Coutinho, L L; Tholon, P; Sonstegard, T S; Rosa, A N; Alencar, M M; Tullio, R R; Medeiros, S R; Nassu, R T; Feijó, G L D; Silva, L O C; Torres, R A; Siqueira, F; Higa, R H; Regitano, L C A

    2013-11-01

    Meat quality traits are economically important because they affect consumers' acceptance, which, in turn, influences the demand for beef. However, selection to improve meat quality is limited by the small numbers of animals on which meat tenderness can be evaluated due to the cost of performing shear force analysis and the resultant damage to the carcass. Genome wide-association studies for Warner-Bratzler shear force measured at different times of meat aging, backfat thickness, ribeye muscle area, scanning parameters [lightness, redness (a*), and yellowness] to ascertain color characteristics of meat and fat, water-holding capacity, cooking loss (CL), and muscle pH were conducted using genotype data from the Illumina BovineHD BeadChip array to identify quantitative trait loci (QTL) in all phenotyped Nelore cattle. Phenotype count for these animals ranged from 430 to 536 across traits. Meat quality traits in Nelore are controlled by numerous QTL of small effect, except for a small number of large-effect QTL identified for a*fat, CL, and pH. Genomic regions harboring these QTL and the pathways in which the genes from these regions act appear to differ from those identified in taurine cattle for meat quality traits. These results will guide future QTL mapping studies and the development of models for the prediction of genetic merit to implement genomic selection for meat quality in Nelore cattle.

  10. Genome-Wide Scan for Methylation Profiles in Keloids

    Directory of Open Access Journals (Sweden)

    Lamont R. Jones

    2015-01-01

    Full Text Available Keloids are benign fibroproliferative tumors of the skin which commonly occur after injury mainly in darker skinned patients. Medical treatment is fraught with high recurrence rates mainly because of an incomplete understanding of the biological mechanisms that lead to keloids. The purpose of this project was to examine keloid pathogenesis from the epigenome perspective of DNA methylation. Genome-wide profiling used the Infinium HumanMethylation450 BeadChip to interrogate DNA from 6 fresh keloid and 6 normal skin samples from 12 anonymous donors. A 3-tiered approach was used to call out genes most differentially methylated between keloid and normal. When compared to normal, of the 685 differentially methylated CpGs at Tier 3, 510 were hypomethylated and 175 were hypermethylated with 190 CpGs in promoter and 495 in nonpromoter regions. The 190 promoter region CpGs corresponded to 152 genes: 96 (63% were hypomethylated and 56 (37% hypermethylated. This exploratory genome-wide scan of the keloid methylome highlights a predominance of hypomethylated genomic landscapes, favoring nonpromoter regions. DNA methylation, as an additional mechanism for gene regulation in keloid pathogenesis, holds potential for novel treatments that reverse deleterious epigenetic changes. As an alternative mechanism for regulating genes, epigenetics may explain why gene mutations alone do not provide definitive mechanisms for keloid formation.

  11. Genome scan for linkage to Gilles de la Tourette syndrome

    Energy Technology Data Exchange (ETDEWEB)

    Barr, C.L.; Livingston, J.; Williamson, R. [and others

    1994-09-01

    Gilles de la Tourette Syndrome (TS) is a familial, neuropsychiatric disorder characterized by chronic, intermittent motor and vocal tics. In addition to tics, affected individuals frequently display symptoms such as attention-deficit hyperactivity disorder and/or obsessive compulsive disorder. Genetic analyses of family data have suggested that susceptibility to the disorder is most likely due to a single genetic locus with a dominant mode of transmission and reduced penetrance. In the search for genetic linkage for TS, we have collected well-characterized pedigrees with multiple affected individuals on whom extensive diagnostic evaluations have been done. The first stage of our study is to scan the genome systematically using a panel of uniformly spaced (10 to 20 cM), highly polymorphic, microsatellite markers on 5 families segregating TS. To date, 290 markers have been typed and 3,660 non-overlapping cM of the genome have been excluded for possible linkage under the assumption of genetic homogeneity. Because of the possibility of locus heterogeneity overall summed exclusion is not considered tantamount to absolute exclusion of a disease locus in that region. The results from each family are carefully evaluated and a positive lod score in a single family is followed up by typing closely linked markers. Linkage to TS was examined by two-point analysis using the following genetic model: single autosomal dominant gene with gene frequency .003 and maximum penetrance of .99. An age-of-onset correction is included using a linear function increasing from age 2 years to 21 years. A small rate of phenocopies is also incorporated into the model. Only individuals with TS or CMT according to DSM III-R criteria were regarded as affected for the purposes of this summary. Additional markers are being tested to provide coverage at 5 cM intervals. Moreover, we are currently analyzing the data non-parametrically using the Affected-Pedigree-Member Method of linkage analysis.

  12. Comparative analysis of whole genome structure of Streptococcus suis using whole genome PCR scanning

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    An outbreak associated with Streptococcus suis infection in humans emerged in Sichuan province, China in 2005. The outbreak is atypical for the apparent large number of human cases, high fatality rate and geographical spread. To determine whether the bacterium has changed, we compared both human and animal isolates from the Sichuan outbreak with those collected previously within China and in other countries using whole genome PCR scanning (WGPScaning) comparative sequencing of several known virulence factor genes and multilocus sequence typing (MLST) analysis. WGPScanning analysis showed that all primer pairs yielded PCR products of the expected sizes in all four strains tested. The nucleotide sequences of all the detected virulence factor genes are identical in the four strains and MLST results showed that the four isolates studied and reference strain all belonged to the ST1 com-plex. No new genetic changes were found in the genome structure of the isolates from this Sichuan outbreak.

  13. Comparative analysis of whole genome structure of Streptococcus suis using whole genome PCR scanning

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    An outbreak associated with Streptococcus suis infection in humans emerged in Sichuan province, China in 2005. The outbreak is atypical for the apparent large number of human cases, high fatality rate and geographical spread. To determine whether the bacterium has changed, we compared both human and animal isolates from the Sichuan outbreak with those collected previously within China and in other countries using whole genome PCR scanning (WGPScaning) comparative sequencing of several known virulence factor genes and multilocus sequence typing (MLST) analysis. WGPScanning analysis showed that all primer pairs yielded PCR products of the expected sizes in all four strains tested. The nucleotide sequences of all the detected virulence factor genes are identical in the four strains and MLST results showed that the four isolates studied and reference strain all belonged to the ST1 complex. No new genetic changes were found in the genome structure of the isolates from this Sichuan outbreak.

  14. An automated annotation tool for genomic DNA sequences using GeneScan and BLAST

    Indian Academy of Sciences (India)

    Andrew M. Lynn; Chakresh Kumar Jain; K. Kosalai; Pranjan Barman; Nupur Thakur; Harish Batra; Alok Bhattacharya

    2001-04-01

    Genomic sequence data are often available well before the annotated sequence is published. We present a method for analysis of genomic DNA to identify coding sequences using the GeneScan algorithm and characterize these resultant sequences by BLAST. The routines are used to develop a system for automated annotation of genome DNA sequences.

  15. Genome scan for parent-of-origin QTL effects on bovine growth and carcass traits

    NARCIS (Netherlands)

    Imumorin, I.G.; Kim, B.; Li, Y.; Koning, de D.J.; Arendonk, van J.A.M.; Donato, S.

    2011-01-01

    Parent-of-origin effects (POE) such as genomic imprinting influence growth and body composition in livestock, rodents, and humans. Here, we report the results of a genome scan to detect quantitative trait loci (QTL) with POE on growth and carcass traits in Angus × Brahman cattle crossbreds. We ident

  16. Genome Scan Meta-Analysis of Schizophrenia and Bipolar Disorder, Part II: Schizophrenia

    OpenAIRE

    Lewis, Cathryn M.; Levinson, Douglas F.; Wise, Lesley H.; Delisi, Lynn E.; Straub, Richard E.; Hovatta, Iiris; Williams, Nigel M.; Schwab, Sibylle G.; Pulver, Ann E; Faraone, Stephen V.; Brzustowicz, Linda M.; Kaufmann, Charles A.; Garver, David L.; Gurling, Hugh M.D.; Lindholm, Eva

    2003-01-01

    Schizophrenia is a common disorder with high heritability and a 10-fold increase in risk to siblings of probands. Replication has been inconsistent for reports of significant genetic linkage. To assess evidence for linkage across studies, rank-based genome scan meta-analysis (GSMA) was applied to data from 20 schizophrenia genome scans. Each marker for each scan was assigned to 1 of 120 30-cM bins, with the bins ranked by linkage scores (1 = most significant) and the ranks averaged across stu...

  17. Genomic scans for selective sweeps using SNP data

    DEFF Research Database (Denmark)

    Nielsen, Rasmus; Williamson, Scott; Kim, Yuseob;

    2005-01-01

    Detecting selective sweeps from genomic SNP data is complicated by the intricate ascertainment schemes used to discover SNPs, and by the confounding influence of the underlying complex demographics and varying mutation and recombination rates. Current methods for detecting selective sweeps have...... little or no robustness to the demographic assumptions and varying recombination rates, and provide no method for correcting for ascertainment biases. Here, we present several new tests aimed at detecting selective sweeps from genomic SNP data. Using extensive simulations, we show that a new parametric...... test, based on composite likelihood, has a high power to detect selective sweeps and is surprisingly robust to assumptions regarding recombination rates and demography (i.e., has low Type I error). Our new test also provides estimates of the location of the selective sweep(s) and the magnitude...

  18. Ab initio gene identification: prokaryote genome annotation with GeneScan and GLIMMER

    Indian Academy of Sciences (India)

    Gautam Aggarwal; Ramakrishna Ramaswamy

    2002-02-01

    We compare the annotation of three complete genomes using the ab initio methods of gene identification GeneScan and GLIMMER. The annotation given in GenBank, the standard against which these are compared, has been made using GeneMark. We find a number of novel genes which are predicted by both methods used here, as well as a number of genes that are predicted by GeneMark, but are not identified by either of the nonconsensus methods that we have used. The three organisms studied here are all prokaryotic species with fairly compact genomes. The Fourier measure forms the basis for an efficient non-consensus method for gene prediction, and the algorithm GeneScan exploits this measure. We have bench-marked this program as well as GLIMMER using 3 complete prokaryotic genomes. An effort has also been made to study the limitations of these techniques for complete genome analysis. GeneScan and GLIMMER are of comparable accuracy insofar as gene-identification is concerned, with sensitivities and specificities typically greater than 0.9. The number of false predictions (both positive and negative) is higher for GeneScan as compared to GLIMMER, but in a significant number of cases, similar results are provided by the two techniques. This suggests that there could be some as-yet unidentified additional genes in these three genomes, and also that some of the putative identifications made hitherto might require re-evaluation. All these cases are discussed in detail.

  19. Genome scan for parent-of-origin QTL effects on bovine growth and carcass traits

    OpenAIRE

    Ikhide G. Imumorin; Eun-Hee eKim; Yun-Mi eLee; Dirk-Jan eDe Koning; Johan eVan Arendonk; Marcos eDe Donato; Jeremy Francis Taylor; Jong-Joo eKim

    2011-01-01

    Parent-of-origin effects (POE) such as genomic imprinting influence growth and body composition in livestock, rodents and humans. Here, we report the results of a genome scan to detect quantitative trait loci (QTL) with POE on growth and carcass traits in Angus x Brahman cattle crossbreds. We identified 24 POE-QTL on 15 Bos taurus autosomes (BTAs) of which 6 were significant at 5% genome-wide level and 18 at the 5% chromosome-wide significance level. Six QTL were paternally expressed while 15...

  20. Meta-analysis of genome-wide linkage scans of attention deficit hyperactivity disorder

    NARCIS (Netherlands)

    Zhou, Kaixin; Dempfle, Astrid; Arcos-Burgos, Mauricio; Bakker, Steven C; Banaschewski, Tobias; Biederman, Joseph; Buitelaar, Jan; Castellanos, F Xavier; Doyle, Alysa; Ebstein, Richard P; Ekholm, Jenny; Forabosco, Paola; Franke, Barbara; Freitag, Christine; Friedel, Susann; Gill, Michael; Hebebrand, Johannes; Hinney, Anke; Jacob, Christian; Lesch, Klaus Peter; Loo, Sandra K; Lopera, Francisco; McCracken, James T; McGough, James J; Meyer, Jobst; Mick, Eric; Miranda, Ana; Muenke, Maximilian; Mulas, Fernando; Nelson, Stanley F; Nguyen, T Trang; Oades, Robert D; Ogdie, Matthew N; Palacio, Juan David; Pineda, David; Reif, Andreas; Renner, Tobias J; Roeyers, Herbert; Romanos, Marcel; Rothenberger, Aribert; Schäfer, Helmut; Sergeant, Joseph; Sinke, Richard J; Smalley, Susan L; Sonuga-Barke, Edmund; Steinhausen, Hans-Christoph; van der Meulen, Emma; Walitza, Susanne; Warnke, Andreas; Lewis, Cathryn M; Faraone, Stephen V; Asherson, Philip

    2008-01-01

    Genetic contribution to the development of attention deficit hyperactivity disorder (ADHD) is well established. Seven independent genome-wide linkage scans have been performed to map loci that increase the risk for ADHD. Although significant linkage signals were identified in some of the studies, th

  1. Whole genome scan to detect quantitative trait loci for bovine milk protein composition

    NARCIS (Netherlands)

    Schopen, G.C.B.; Koks, P.D.; Arendonk, van J.A.M.; Bovenhuis, H.; Visker, M.H.P.W.

    2009-01-01

    The objective of this study was to perform a whole genome scan to detect quantitative trait loci (QTL) for milk protein composition in 849 Holstein–Friesian cows originating from seven sires. One morning milk sample was analysed for the major milk proteins using capillary zone electrophoresis. A gen

  2. Genome-wide scans using archived neonatal dried blood spot samples

    Directory of Open Access Journals (Sweden)

    Wiuf Carsten

    2009-07-01

    Full Text Available Abstract Background Identification of disease susceptible genes requires access to DNA from numerous well-characterised subjects. Archived residual dried blood spot samples from national newborn screening programs may provide DNA from entire populations and medical registries the corresponding clinical information. The amount of DNA available in these samples is however rarely sufficient for reliable genome-wide scans, and whole-genome amplification may thus be necessary. This study assess the quality of DNA obtained from different amplification protocols by evaluating fidelity and robustness of the genotyping of 610,000 single nucleotide polymorphisms, using the Illumina Infinium HD Human610-Quad BeadChip. Whole-genome amplified DNA from 24 neonatal dried blood spot samples stored between 15 to 25 years was tested, and high-quality genomic DNA from 8 of the same individuals was used as reference. Results Using 3.2 mm disks from dried blood spot samples the optimal DNA-extraction and amplification protocol resulted in call-rates between 99.15% – 99.73% (mean 99.56%, N = 16, and conflicts with reference DNA in only three per 10,000 genotype calls. Conclusion Whole-genome amplified DNA from archived neonatal dried blood spot samples can be used for reliable genome-wide scans and is a cost-efficient alternative to collecting new samples.

  3. Combined amplification and hybridization techniques for genome scanning in vegetatively propagated crops

    International Nuclear Information System (INIS)

    A combination of PCR- and hybridization-based genome scanning techniques and sequence comparisons between non-coding chloroplast DNA flanking tRNA genes has been employed to screen Dioscorea species for intra- and interspecific genetic diversity. This methodology detected extensive polymorphisms within Dioscorea bulbifera L., and revealed taxonomic and phylogenetic relationships among cultivated Guinea yams varieties and their potential wild progenitors. Finally, screening of yam germplasm grown in Jamaica permitted reliable discrimination between all major cultivars. Genome scanning by micro satellite-primed PCR (MP-PCR) and random amplified polymorphic DNA (RAPD) analysis in combination with the novel random amplified micro satellite polymorphisms (RAMPO) hybridization technique has shown high potential for the genetic analysis of yams, and holds promise for other vegetatively propagated orphan crops. (author)

  4. Quantitative linkage genome scan for atopy in a large collection of Caucasian families

    DEFF Research Database (Denmark)

    Webb, BT; van den Oord, E; Akkari, A;

    2007-01-01

    Quantitative phenotypes correlated with a complex disorder offer increased power to detect linkage in comparison to affected-unaffected classifications. Asthma is a complex disorder characterized by periods of bronchial obstruction and increased bronchial hyper reactivity. In childhood and early...... report represents one of the biggest genome scans so far reported for asthma related phenotypes. This study also demonstrates the utility of increased sample sizes and quantitative phenotypes in linkage analysis of complex disorders....

  5. Genome-wide association scan for five major dimensions of personality

    OpenAIRE

    Terracciano, Antonio; Sanna, Serena; Uda, Manuela; Deiana, Barbara; Usala, Gianluca; Busonero, Fabio; Maschio, Andrea; Scally, Matthew; Patriciu, Nicholas; Chen, Wei-Min; Distel, Marijn A.; Slagboom, Eline P.; Boomsma, Dorret I.; Villafuerte, Sandra; Śliwerska, Elżbieta

    2008-01-01

    Personality traits are summarized by five broad dimensions with pervasive influences on major life outcomes, strong links to psychiatric disorders, and clear heritable components. To identify genetic variants associated with each of the five dimensions of personality we performed a genome wide association (GWA) scan of 3,972 individuals from a genetically isolated population within Sardinia, Italy. Based on analyses of 362,129 single nucleotide polymorphisms (SNPs) we found several strong sig...

  6. Testing the bi-dimensional effects of attitudes on behavioural intentions and subsequent behaviour.

    Science.gov (United States)

    Elliott, Mark A; Brewster, Sarah E; Thomson, James A; Malcolm, Carly; Rasmussen, Susan

    2015-11-01

    Attitudes are typically treated as unidimensional predictors of both behavioural intentions and subsequent behaviour. On the basis of previous research showing that attitudes comprise two independent, positive and negative dimensions, we hypothesized that attitudes would be bi-dimensional predictors of both behavioural intentions and subsequent behaviour. We focused on health-risk behaviours. We therefore also hypothesized that the positive dimension of attitude (evaluations of positive behavioural outcomes) would better predict both behavioural intentions and subsequent behaviour than would the negative dimension, consistent with the positivity bias/offset principle. In Study 1 (cross sectional design), N = 109 university students completed questionnaire measures of their intentions to binge-drink and the positive and negative dimensions of attitude. Consistent with the hypotheses, both attitude dimensions independently predicted behavioural intentions and the positive dimension was a significantly better predictor than was the negative dimension. The same pattern of findings emerged in Study 2 (cross sectional design; N = 186 university students) when we predicted intentions to binge-drink, smoke and consume a high-fat diet. Similarly, in Study 3 (prospective design; N = 1,232 speed limit offenders), both the positive and negative dimensions of attitude predicted subsequent (6-month post-baseline) speeding behaviour on two different road types and the positive dimension was the better predictor. The implications for understanding the motivation of behaviour and the development of behaviour-change interventions are discussed. PMID:25440892

  7. Modular data acquisition system based on transputer technology for bi-dimensional time coincidence counting

    International Nuclear Information System (INIS)

    We describe the rationale and the test of a modular Data AcQuisition system (DAQ) for bi-dimensional (X-Y) digital imaging, based on a 16 channel Time-to-Digital Converter (TDC) NIM module connected to a specially designed TRAnsputer Module (TRAM). TDC time resolution is 12.5 ns (LSB) with a 40 MHz clock, time range is 3.3 s (28 bits), for a maximum rate of 500 kHz/channel guaranteed. The TDC+TRAM pair is the basic unit that can be scaled in modules of 8X+8Y channels to meet the user's requirement for a larger number of X-Y channels to be considered simultaneously. TDC directly accesses the large RAM memory (32 Mbytes) of the INMOS T805 (20 MHz) transputer on the TRAM board. Each transputer in the modular system is a node of a ring network, whose root transputer node is hosted in a i386-based personal computer. After real-time data acquisition, a parallel reconstruction algorithm resolves time coincidences. Laboratory tests give a reconstruction time of 6.2 s for 1.28 105 events on 16 X+16 Y channels (2 TDC+2 TRAM), obtained in 1 s with a fluence of 5x104 events/mm2 (typically used in radiological imaging) on an area of 1.6x1.6 mm2. ((orig.))

  8. Non-random mate choice in humans: insights from a genome scan.

    Science.gov (United States)

    Laurent, R; Toupance, B; Chaix, R

    2012-02-01

    Little is known about the genetic factors influencing mate choice in humans. Still, there is evidence for non-random mate choice with respect to physical traits. In addition, some studies suggest that the Major Histocompatibility Complex may affect pair formation. Nowadays, the availability of high density genomic data sets gives the opportunity to scan the genome for signatures of non-random mate choice without prior assumptions on which genes may be involved, while taking into account socio-demographic factors. Here, we performed a genome scan to detect extreme patterns of similarity or dissimilarity among spouses throughout the genome in three populations of African, European American, and Mexican origins from the HapMap 3 database. Our analyses identified genes and biological functions that may affect pair formation in humans, including genes involved in skin appearance, morphogenesis, immunity and behaviour. We found little overlap between the three populations, suggesting that the biological functions potentially influencing mate choice are population specific, in other words are culturally driven. Moreover, whenever the same functional category of genes showed a significant signal in two populations, different genes were actually involved, which suggests the possibility of evolutionary convergences.

  9. Genome scan for nonadditive heterotic trait loci reveals mainly underdominant effects in Saccharomyces cerevisiae.

    Science.gov (United States)

    Laiba, Efrat; Glikaite, Ilana; Levy, Yael; Pasternak, Zohar; Fridman, Eyal

    2016-04-01

    The overdominant model of heterosis explains the superior phenotype of hybrids by synergistic allelic interaction within heterozygous loci. To map such genetic variation in yeast, we used a population doubling time dataset of Saccharomyces cerevisiae 16 × 16 diallel and searched for major contributing heterotic trait loci (HTL). Heterosis was observed for the majority of hybrids, as they surpassed their best parent growth rate. However, most of the local heterozygous loci identified by genome scan were surprisingly underdominant, i.e., reduced growth. We speculated that in these loci adverse effects on growth resulted from incompatible allelic interactions. To test this assumption, we eliminated these allelic interactions by creating hybrids with local hemizygosity for the underdominant HTLs, as well as for control random loci. Growth of hybrids was indeed elevated for most hemizygous to HTL genes but not for control genes, hence validating the results of our genome scan. Assessing the consequences of local heterozygosity by reciprocal hemizygosity and allele replacement assays revealed the influence of genetic background on the underdominant effects of HTLs. Overall, this genome-wide study on a multi-parental hybrid population provides a strong argument against single gene overdominance as a major contributor to heterosis, and favors the dominance complementation model.

  10. The lottery-panel task for bi-dimensional parameter-free elicitation of risk attitudes

    Directory of Open Access Journals (Sweden)

    García-Gallego, Aurora

    2012-03-01

    Full Text Available In this paper, we propose a simple task for eliciting attitudes toward risky choice, the Sabater-Grande and Georgantzís (SGG lottery-panel task, which consists in a series of lotteries constructed to compensate riskier options with higher risk-return trade-offs. Using Principal Component Analysis technique, we show that the SGG lotterypanel task is capable of capturing two dimensions of individual risky decision making: subjects’ average willingness to choose risky projects and their sensitivity towards variations in the return to risk. We report results from a large dataset obtained from the implementation of the SGG lottery-panel task and discuss regularities and the desirability of its bi-dimensionality both for describing behaviour under uncertainty and explaining behaviour in other contexts.

    En este trabajo proponemos una tarea sencilla que permite obtener la actitud frente a la toma de riesgo monetario, y que llamaremos tarea Sabater-Grande y Georgantzís (SGG de riesgo. Esta tarea consiste en una serie de loterías construidas para compensar las opciones de mayor riesgo con un mayor retorno. Utilizando la técnica de componentes principales, encontramos que la tarea SGG es capaz de capturar dos dimensiones de la toma de decisiones individuales: por un lado, la voluntad promedio de los sujetos de elegir proyectos arriesgados y, por otro, su sensibilidad hacia las variaciones en el retorno por riesgo. Presentamos los resultados de una gran muestra de datos obtenidos a partir de la implementación de la tarea SGG, y discutimos las regularidades y la conveniencia de su bidimensionalidad tanto para describir el comportamiento en condiciones de incertidumbre como para explicar el comportamiento humano en otros contextos.

  11. A genome-wide scan for Eysenckian personality dimensions in adolescent twin sibships: psychoticism, extraversion, neuroticism, and lie.

    Science.gov (United States)

    Gillespie, Nathan A; Zhu, Gu; Evans, David M; Medland, Sarah E; Wright, Margie J; Martin, Nick G

    2008-12-01

    We report the first genome-wide scan of adolescent personality. We conducted a genome-wide scan to detect linkage for measures of adolescent Psychoticism, Extraversion, Neuroticism, and Lie from the Junior Eysenck Personality Questionnaire. Data are based on 1,280 genotyped Australian adolescent twins and their siblings. The highest linkage peaks were found on chromosomes 16 and 19 for Neuroticism, on chromosomes 1, 7, 10, 13 m, and 18 for Psychoticism, and on chromosomes 2 and 3 for Extraversion.

  12. Genome Scan for Parent-of-Origin QTL Effects on Bovine Growth and Carcass Traits.

    Science.gov (United States)

    Imumorin, Ikhide G; Kim, Eun-Hee; Lee, Yun-Mi; De Koning, Dirk-Jan; van Arendonk, Johan A; De Donato, Marcos; Taylor, Jeremy F; Kim, Jong-Joo

    2011-01-01

    Parent-of-origin effects (POE) such as genomic imprinting influence growth and body composition in livestock, rodents, and humans. Here, we report the results of a genome scan to detect quantitative trait loci (QTL) with POE on growth and carcass traits in Angus × Brahman cattle crossbreds. We identified 24 POE-QTL on 15 Bos taurus autosomes (BTAs) of which six were significant at 5% genome-wide (GW) level and 18 at the 5% chromosome-wide (CW) significance level. Six QTL were paternally expressed while 15 were maternally expressed. Three QTL influencing post-weaning growth map to the proximal end of BTA2 (linkage region of 0-9 cM; genomic region of 5.0-10.8 Mb), for which only one imprinted ortholog is known so far in the human and mouse genomes, and therefore may potentially represent a novel imprinted region. The detected QTL individually explained 1.4 ∼ 5.1% of each trait's phenotypic variance. Comparative in silico analysis of bovine genomic locations show that 32 out of 1,442 known mammalian imprinted genes from human and mouse homologs map to the identified QTL regions. Although several of the 32 genes have been associated with quantitative traits in cattle, only two (GNAS and PEG3) have experimental proof of being imprinted in cattle. These results lend additional support to recent reports that POE on quantitative traits in mammals may be more common than previously thought, and strengthen the need to identify and experimentally validate cattle orthologs of imprinted genes so as to investigate their effects on quantitative traits.

  13. Genome scan for parent-of-origin QTL effects on bovine growth and carcass traits

    Directory of Open Access Journals (Sweden)

    Ikhide G. Imumorin

    2011-07-01

    Full Text Available Parent-of-origin effects (POE such as genomic imprinting influence growth and body composition in livestock, rodents and humans. Here, we report the results of a genome scan to detect quantitative trait loci (QTL with POE on growth and carcass traits in Angus x Brahman cattle crossbreds. We identified 24 POE-QTL on 15 Bos taurus autosomes (BTAs of which 6 were significant at 5% genome-wide level and 18 at the 5% chromosome-wide significance level. Six QTL were paternally expressed while 15 were maternally expressed. Three QTL influencing post-weaning growth map to the proximal end of BTA2 [linkage region of 0 – 9 cM; genomic region of 5.0 – 10.8 Mb], for which only one imprinted orthologue is known so far in the human and mouse genomes, and therefore may potentially represent a novel imprinted region. The detected QTL individually explained 1.4% ~ 5.1% of each trait’s phenotypic variance. Comparative in-silico analysis of bovine genomic locations show that 32 out of 1,442 known mammalian imprinted genes from human and mouse homologues map to the identified QTL regions. Although several of the 32 genes have been associated with quantitative traits in cattle, only 2 (GNAS and PEG3 have experimental proof of being imprinted in cattle. These results lend additional support to recent reports that POE on quantitative traits in mammals may be more common than previously thought, and strengthen the need to identify and experimentally validate cattle orthologues of imprinted genes so as to investigate their effects on quantitative traits.

  14. Genome Scan for Parent-of-Origin QTL Effects on Bovine Growth and Carcass Traits.

    Science.gov (United States)

    Imumorin, Ikhide G; Kim, Eun-Hee; Lee, Yun-Mi; De Koning, Dirk-Jan; van Arendonk, Johan A; De Donato, Marcos; Taylor, Jeremy F; Kim, Jong-Joo

    2011-01-01

    Parent-of-origin effects (POE) such as genomic imprinting influence growth and body composition in livestock, rodents, and humans. Here, we report the results of a genome scan to detect quantitative trait loci (QTL) with POE on growth and carcass traits in Angus × Brahman cattle crossbreds. We identified 24 POE-QTL on 15 Bos taurus autosomes (BTAs) of which six were significant at 5% genome-wide (GW) level and 18 at the 5% chromosome-wide (CW) significance level. Six QTL were paternally expressed while 15 were maternally expressed. Three QTL influencing post-weaning growth map to the proximal end of BTA2 (linkage region of 0-9 cM; genomic region of 5.0-10.8 Mb), for which only one imprinted ortholog is known so far in the human and mouse genomes, and therefore may potentially represent a novel imprinted region. The detected QTL individually explained 1.4 ∼ 5.1% of each trait's phenotypic variance. Comparative in silico analysis of bovine genomic locations show that 32 out of 1,442 known mammalian imprinted genes from human and mouse homologs map to the identified QTL regions. Although several of the 32 genes have been associated with quantitative traits in cattle, only two (GNAS and PEG3) have experimental proof of being imprinted in cattle. These results lend additional support to recent reports that POE on quantitative traits in mammals may be more common than previously thought, and strengthen the need to identify and experimentally validate cattle orthologs of imprinted genes so as to investigate their effects on quantitative traits. PMID:22303340

  15. Combined genome scans for body stature in 6,602 European twins

    DEFF Research Database (Denmark)

    Perola, Markus; Sammalisto, Sampo; Hiekkalinna, Tero;

    2007-01-01

    Twin cohorts provide a unique advantage for investigations of the role of genetics and environment in the etiology of variation in common complex traits by reducing the variance due to environment, age, and cohort differences. The GenomEUtwin (http://www.genomeutwin.org) consortium consists...... of eight twin cohorts (Australian, Danish, Dutch, Finnish, Italian, Norwegian, Swedish, and United Kingdom) with the total resource of hundreds of thousands of twin pairs. We performed quantitative trait locus (QTL) analysis of one of the most heritable human complex traits, adult stature (body height......) using genome-wide scans performed for 3,817 families (8,450 individuals) derived from twin cohorts from Australia, Denmark, Finland, Netherlands, Sweden, and United Kingdom with an approximate ten-centimorgan microsatellite marker map. The marker maps for different studies differed and they were...

  16. Genome-Wide Scan for Adaptive Divergence and Association with Population-Specific Covariates.

    Science.gov (United States)

    Gautier, Mathieu

    2015-12-01

    In population genomics studies, accounting for the neutral covariance structure across population allele frequencies is critical to improve the robustness of genome-wide scan approaches. Elaborating on the BayEnv model, this study investigates several modeling extensions (i) to improve the estimation accuracy of the population covariance matrix and all the related measures, (ii) to identify significantly overly differentiated SNPs based on a calibration procedure of the XtX statistics, and (iii) to consider alternative covariate models for analyses of association with population-specific covariables. In particular, the auxiliary variable model allows one to deal with multiple testing issues and, providing the relative marker positions are available, to capture some linkage disequilibrium information. A comprehensive simulation study was carried out to evaluate the performances of these different models. Also, when compared in terms of power, robustness, and computational efficiency to five other state-of-the-art genome-scan methods (BayEnv2, BayScEnv, BayScan, flk, and lfmm), the proposed approaches proved highly effective. For illustration purposes, genotyping data on 18 French cattle breeds were analyzed, leading to the identification of 13 strong signatures of selection. Among these, four (surrounding the KITLG, KIT, EDN3, and ALB genes) contained SNPs strongly associated with the piebald coloration pattern while a fifth (surrounding PLAG1) could be associated to morphological differences across the populations. Finally, analysis of Pool-Seq data from 12 populations of Littorina saxatilis living in two different ecotypes illustrates how the proposed framework might help in addressing relevant ecological issues in nonmodel species. Overall, the proposed methods define a robust Bayesian framework to characterize adaptive genetic differentiation across populations. The BayPass program implementing the different models is available at http://www1.montpellier.inra.fr/CBGP/software/baypass/.

  17. Genome-Wide Scan for Adaptive Divergence and Association with Population-Specific Covariates.

    Science.gov (United States)

    Gautier, Mathieu

    2015-12-01

    In population genomics studies, accounting for the neutral covariance structure across population allele frequencies is critical to improve the robustness of genome-wide scan approaches. Elaborating on the BayEnv model, this study investigates several modeling extensions (i) to improve the estimation accuracy of the population covariance matrix and all the related measures, (ii) to identify significantly overly differentiated SNPs based on a calibration procedure of the XtX statistics, and (iii) to consider alternative covariate models for analyses of association with population-specific covariables. In particular, the auxiliary variable model allows one to deal with multiple testing issues and, providing the relative marker positions are available, to capture some linkage disequilibrium information. A comprehensive simulation study was carried out to evaluate the performances of these different models. Also, when compared in terms of power, robustness, and computational efficiency to five other state-of-the-art genome-scan methods (BayEnv2, BayScEnv, BayScan, flk, and lfmm), the proposed approaches proved highly effective. For illustration purposes, genotyping data on 18 French cattle breeds were analyzed, leading to the identification of 13 strong signatures of selection. Among these, four (surrounding the KITLG, KIT, EDN3, and ALB genes) contained SNPs strongly associated with the piebald coloration pattern while a fifth (surrounding PLAG1) could be associated to morphological differences across the populations. Finally, analysis of Pool-Seq data from 12 populations of Littorina saxatilis living in two different ecotypes illustrates how the proposed framework might help in addressing relevant ecological issues in nonmodel species. Overall, the proposed methods define a robust Bayesian framework to characterize adaptive genetic differentiation across populations. The BayPass program implementing the different models is available at http://www1.montpellier

  18. Genome-wide scan of healthy human connectome discovers SPON1 gene variant influencing dementia severity

    Science.gov (United States)

    Jahanshad, Neda; Rajagopalan, Priya; Hua, Xue; Hibar, Derrek P.; Nir, Talia M.; Toga, Arthur W.; Jack, Clifford R.; Saykin, Andrew J.; Green, Robert C.; Weiner, Michael W.; Medland, Sarah E.; Montgomery, Grant W.; Hansell, Narelle K.; McMahon, Katie L.; de Zubicaray, Greig I.; Martin, Nicholas G.; Wright, Margaret J.; Thompson, Paul M.; Weiner, Michael; Aisen, Paul; Weiner, Michael; Aisen, Paul; Petersen, Ronald; Jack, Clifford R.; Jagust, William; Trojanowski, John Q.; Toga, Arthur W.; Beckett, Laurel; Green, Robert C.; Saykin, Andrew J.; Morris, John; Liu, Enchi; Green, Robert C.; Montine, Tom; Petersen, Ronald; Aisen, Paul; Gamst, Anthony; Thomas, Ronald G.; Donohue, Michael; Walter, Sarah; Gessert, Devon; Sather, Tamie; Beckett, Laurel; Harvey, Danielle; Gamst, Anthony; Donohue, Michael; Kornak, John; Jack, Clifford R.; Dale, Anders; Bernstein, Matthew; Felmlee, Joel; Fox, Nick; Thompson, Paul; Schuff, Norbert; Alexander, Gene; DeCarli, Charles; Jagust, William; Bandy, Dan; Koeppe, Robert A.; Foster, Norm; Reiman, Eric M.; Chen, Kewei; Mathis, Chet; Morris, John; Cairns, Nigel J.; Taylor-Reinwald, Lisa; Trojanowki, J.Q.; Shaw, Les; Lee, Virginia M.Y.; Korecka, Magdalena; Toga, Arthur W.; Crawford, Karen; Neu, Scott; Saykin, Andrew J.; Foroud, Tatiana M.; Potkin, Steven; Shen, Li; Khachaturian, Zaven; Frank, Richard; Snyder, Peter J.; Molchan, Susan; Kaye, Jeffrey; Quinn, Joseph; Lind, Betty; Dolen, Sara; Schneider, Lon S.; Pawluczyk, Sonia; Spann, Bryan M.; Brewer, James; Vanderswag, Helen; Heidebrink, Judith L.; Lord, Joanne L.; Petersen, Ronald; Johnson, Kris; Doody, Rachelle S.; Villanueva-Meyer, Javier; Chowdhury, Munir; Stern, Yaakov; Honig, Lawrence S.; Bell, Karen L.; Morris, John C.; Ances, Beau; Carroll, Maria; Leon, Sue; Mintun, Mark A.; Schneider, Stacy; Marson, Daniel; Griffith, Randall; Clark, David; Grossman, Hillel; Mitsis, Effie; Romirowsky, Aliza; deToledo-Morrell, Leyla; Shah, Raj C.; Duara, Ranjan; Varon, Daniel; Roberts, Peggy; Albert, Marilyn; Onyike, Chiadi; Kielb, Stephanie; Rusinek, Henry; de Leon, Mony J.; Glodzik, Lidia; De Santi, Susan; Doraiswamy, P. Murali; Petrella, Jeffrey R.; Coleman, R. Edward; Arnold, Steven E.; Karlawish, Jason H.; Wolk, David; Smith, Charles D.; Jicha, Greg; Hardy, Peter; Lopez, Oscar L.; Oakley, MaryAnn; Simpson, Donna M.; Porsteinsson, Anton P.; Goldstein, Bonnie S.; Martin, Kim; Makino, Kelly M.; Ismail, M. Saleem; Brand, Connie; Mulnard, Ruth A.; Thai, Gaby; Mc-Adams-Ortiz, Catherine; Womack, Kyle; Mathews, Dana; Quiceno, Mary; Diaz-Arrastia, Ramon; King, Richard; Weiner, Myron; Martin-Cook, Kristen; DeVous, Michael; Levey, Allan I.; Lah, James J.; Cellar, Janet S.; Burns, Jeffrey M.; Anderson, Heather S.; Swerdlow, Russell H.; Apostolova, Liana; Lu, Po H.; Bartzokis, George; Silverman, Daniel H.S.; Graff-Radford, Neill R.; Parfitt, Francine; Johnson, Heather; Farlow, Martin R.; Hake, Ann Marie; Matthews, Brandy R.; Herring, Scott; van Dyck, Christopher H.; Carson, Richard E.; MacAvoy, Martha G.; Chertkow, Howard; Bergman, Howard; Hosein, Chris; Black, Sandra; Stefanovic, Bojana; Caldwell, Curtis; Hsiung, Ging-Yuek Robin; Feldman, Howard; Mudge, Benita; Assaly, Michele; Kertesz, Andrew; Rogers, John; Trost, Dick; Bernick, Charles; Munic, Donna; Kerwin, Diana; Mesulam, Marek-Marsel; Lipowski, Kristina; Wu, Chuang-Kuo; Johnson, Nancy; Sadowsky, Carl; Martinez, Walter; Villena, Teresa; Turner, Raymond Scott; Johnson, Kathleen; Reynolds, Brigid; Sperling, Reisa A.; Johnson, Keith A.; Marshall, Gad; Frey, Meghan; Yesavage, Jerome; Taylor, Joy L.; Lane, Barton; Rosen, Allyson; Tinklenberg, Jared; Sabbagh, Marwan; Belden, Christine; Jacobson, Sandra; Kowall, Neil; Killiany, Ronald; Budson, Andrew E.; Norbash, Alexander; Johnson, Patricia Lynn; Obisesan, Thomas O.; Wolday, Saba; Bwayo, Salome K.; Lerner, Alan; Hudson, Leon; Ogrocki, Paula; Fletcher, Evan; Carmichael, Owen; Olichney, John; DeCarli, Charles; Kittur, Smita; Borrie, Michael; Lee, T.-Y.; Bartha, Rob; Johnson, Sterling; Asthana, Sanjay; Carlsson, Cynthia M.; Potkin, Steven G.; Preda, Adrian; Nguyen, Dana; Tariot, Pierre; Fleisher, Adam; Reeder, Stephanie; Bates, Vernice; Capote, Horacio; Rainka, Michelle; Scharre, Douglas W.; Kataki, Maria; Zimmerman, Earl A.; Celmins, Dzintra; Brown, Alice D.; Pearlson, Godfrey D.; Blank, Karen; Anderson, Karen; Saykin, Andrew J.; Santulli, Robert B.; Schwartz, Eben S.; Sink, Kaycee M.; Williamson, Jeff D.; Garg, Pradeep; Watkins, Franklin; Ott, Brian R.; Querfurth, Henry; Tremont, Geoffrey; Salloway, Stephen; Malloy, Paul; Correia, Stephen; Rosen, Howard J.; Miller, Bruce L.; Mintzer, Jacobo

    2013-01-01

    Aberrant connectivity is implicated in many neurological and psychiatric disorders, including Alzheimer’s disease and schizophrenia. However, other than a few disease-associated candidate genes, we know little about the degree to which genetics play a role in the brain networks; we know even less about specific genes that influence brain connections. Twin and family-based studies can generate estimates of overall genetic influences on a trait, but genome-wide association scans (GWASs) can screen the genome for specific variants influencing the brain or risk for disease. To identify the heritability of various brain connections, we scanned healthy young adult twins with high-field, high-angular resolution diffusion MRI. We adapted GWASs to screen the brain’s connectivity pattern, allowing us to discover genetic variants that affect the human brain’s wiring. The association of connectivity with the SPON1 variant at rs2618516 on chromosome 11 (11p15.2) reached connectome-wide, genome-wide significance after stringent statistical corrections were enforced, and it was replicated in an independent subsample. rs2618516 was shown to affect brain structure in an elderly population with varying degrees of dementia. Older people who carried the connectivity variant had significantly milder clinical dementia scores and lower risk of Alzheimer’s disease. As a posthoc analysis, we conducted GWASs on several organizational and topological network measures derived from the matrices to discover variants in and around genes associated with autism (MACROD2), development (NEDD4), and mental retardation (UBE2A) significantly associated with connectivity. Connectome-wide, genome-wide screening offers substantial promise to discover genes affecting brain connectivity and risk for brain diseases. PMID:23471985

  19. SARS CTL vaccine candidates; HLA supertype-, genome-wide scanning and biochemical validation

    DEFF Research Database (Denmark)

    Sylvester-Hvid, C; Nielsen, M; Lamberth, K;

    2004-01-01

    of the HLA supertypes and identified almost 100 potential vaccine candidates. These should be further validated in SARS survivors and used for vaccine formulation. We suggest that immunobioinformatics may become a fast and valuable tool in rational vaccine design.......An effective Severe Acute Respiratory Syndrome (SARS) vaccine is likely to include components that can induce specific cytotoxic T-lymphocyte (CTL) responses. The specificities of such responses are governed by human leukocyte antigen (HLA)-restricted presentation of SARS-derived peptide epitopes......-CoV) was isolated and full-length sequenced (Marra et al., Science 2003: 300: 1399-404). Here, we have combined advanced bioinformatics and high-throughput immunology to perform an HLA supertype-, genome-wide scan for SARS-specific CTL epitopes. The scan includes all nine human HLA supertypes in total covering >99...

  20. SARS CTL vaccine candidates; HLA supertype-, genome-wide scanning and biochemical validation

    DEFF Research Database (Denmark)

    Sylvester-Hvid, C.; Nielsen, Morten; Lamberth, K.;

    2004-01-01

    of the HLA supertypes and identified almost 100 potential vaccine candidates. These should be further validated in SARS survivors and used for vaccine formulation. We suggest that immunobioinformatics may become a fast and valuable tool in rational vaccine design.......An effective Severe Acute Respiratory Syndrome (SARS) vaccine is likely to include components that can induce specific cytotoxic T-lymphocyte (CTL) responses. The specificities of such responses are governed by human leukocyte antigen (HLA)-restricted presentation of SARS-derived peptide epitopes......-CoV) was isolated and full-length sequenced (Marra et al., Science 2003: 300: 1399404). Here, we have combined advanced bioinformatics and high-throughput immunology to perform an HLA supertype-, genome-wide scan for SARS-specific CTL epitopes. The scan includes all nine human HLA supertypes in total covering >99...

  1. Automated screening system for retinal health using bi-dimensional empirical mode decomposition and integrated index.

    Science.gov (United States)

    Acharya, U Rajendra; Mookiah, Muthu Rama Krishnan; Koh, Joel E W; Tan, Jen Hong; Bhandary, Sulatha V; Rao, A Krishna; Fujita, Hamido; Hagiwara, Yuki; Chua, Chua Kuang; Laude, Augustinus

    2016-08-01

    Posterior Segment Eye Diseases (PSED) namely Diabetic Retinopathy (DR), glaucoma and Age-related Macular Degeneration (AMD) are the prime causes of vision loss globally. Vision loss can be prevented, if these diseases are detected at an early stage. Structural abnormalities such as changes in cup-to-disc ratio, Hard Exudates (HE), drusen, Microaneurysms (MA), Cotton Wool Spots (CWS), Haemorrhages (HA), Geographic Atrophy (GA) and Choroidal Neovascularization (CNV) in PSED can be identified by manual examination of fundus images by clinicians. However, manual screening is labour-intensive, tiresome and time consuming. Hence, there is a need to automate the eye screening. In this work Bi-dimensional Empirical Mode Decomposition (BEMD) technique is used to decompose fundus images into 2D Intrinsic Mode Functions (IMFs) to capture variations in the pixels due to morphological changes. Further, various entropy namely Renyi, Fuzzy, Shannon, Vajda, Kapur and Yager and energy features are extracted from IMFs. These extracted features are ranked using Chernoff Bound and Bhattacharyya Distance (CBBD), Kullback-Leibler Divergence (KLD), Fuzzy-minimum Redundancy Maximum Relevance (FmRMR), Wilcoxon, Receiver Operating Characteristics Curve (ROC) and t-test methods. Further, these ranked features are fed to Support Vector Machine (SVM) classifier to classify normal and abnormal (DR, AMD and glaucoma) classes. The performance of the proposed eye screening system is evaluated using 800 (Normal=400 and Abnormal=400) digital fundus images and 10-fold cross validation method. Our proposed system automatically identifies normal and abnormal classes with an average accuracy of 88.63%, sensitivity of 86.25% and specificity of 91% using 17 optimal features ranked using CBBD and SVM-Radial Basis Function (RBF) classifier. Moreover, a novel Retinal Risk Index (RRI) is developed using two significant features to distinguish two classes using single number. Such a system helps to reduce eye

  2. HybGFS: a hybrid method for genome-fingerprint scanning

    Directory of Open Access Journals (Sweden)

    Sugiyama Naoyuki

    2006-10-01

    Full Text Available Abstract Background Protein identification based on mass spectrometry (MS has previously been performed using peptide mass fingerprinting (PMF or tandem MS (MS/MS database searching. However, these methods cannot identify proteins that are not already listed in existing databases. Moreover, the alternative approach of de novo sequencing requires costly equipment and the interpretation of complex MS/MS spectra. Thus, there is a need for novel high-throughput protein-identification methods that are independent of existing predefined protein databases. Results Here, we present a hybrid method for genome-fingerprint scanning, known as HybGFS. This technique combines genome sequence-based peptide MS/MS ion searching with liquid-chromatography elution-time (LC-ET prediction, to improve the reliability of identification. The hybrid method allows the simultaneous identification and mapping of proteins without a priori information about their coding sequences. The current study used standard LC-MS/MS data to query an in silico-generated six-reading-frame translation and the enzymatic digest of an entire genome. Used in conjunction with precursor/product ion-mass searching, the LC-ETs increased confidence in the peptide-identification process and reduced the number of false-positive matches. The power of this method was demonstrated using recombinant proteins from the Escherichia coli K12 strain. Conclusion The novel hybrid method described in this study will be useful for the large-scale experimental confirmation of genome coding sequences, without the need for transcriptome-level expression analysis or costly MS database searching.

  3. A genome scan for type 2 diabetes susceptibility loci in a genetically isolated population.

    Science.gov (United States)

    Permutt, M A; Wasson, J C; Suarez, B K; Lin, J; Thomas, J; Meyer, J; Lewitzky, S; Rennich, J S; Parker, A; DuPrat, L; Maruti, S; Chayen, S; Glaser, B

    2001-03-01

    A total of 896 individuals of Ashkenazi Jewish descent were ascertained in Israel from 267 multiplex families, including 472 sib-pairs affected with type 2 diabetes. A genome-wide scan with average marker spacing of 9.5 cM revealed five regions on four chromosomes (4q, 8q, 14q, and 20q) that exhibited nominal evidence for linkage (P families were ranked by BMI (in increasing order) did a subset attain nominal significance, and only for chromosome 4. The findings reported here lend credence to the hypothesis, now supported by four studies of Caucasian populations and most recently by a combined analysis of 1,852 pedigrees, that a type 2 diabetes susceptibility locus resides on chromosome 20q. This population, because of its unique genetic attributes, may facilitate identification of this and other genes contributing to type 2 diabetes. PMID:11246891

  4. Scanning for signatures of geographically restricted selection based on population genomics analysis

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Natural selection, as the driving force of human evolution, has direct impact on population differentiation. However, it is still unclear to what extent the genetic differentiation has been caused by natural selection. To explore this question, we performed a genome-wide scan with single nucleotide polymorphism (SNP) data from the International HapMap Project. Single locus FST analysis was applied to assess the frequency difference among populations in autosomes. Based on the empirical distribution of FST, we identified 12669 SNPs correlating to population differentiation and 1853 candidate genes subjected to geographic restricted natural selection. Further interpretation of gene ontogeny revealed 121 categories of biological process with the enrichments of candidate genes. Our results suggest that natural selection may play an important role in human population differentiation. In addition, our analysis provides new clues as well as research methods for our understanding of population differentiation and natural selection.

  5. Efficient strategies for genome scanning using maximum-likelihood affected-sib-pair analysis

    Energy Technology Data Exchange (ETDEWEB)

    Holmans, P.; Craddock, N. [Univ. of Wales College of Medicine, Cardiff (United Kingdom)

    1997-03-01

    Detection of linkage with a systematic genome scan in nuclear families including an affected sibling pair is an important initial step on the path to cloning susceptibility genes for complex genetic disorders, and it is desirable to optimize the efficiency of such studies. The aim is to maximize power while simultaneously minimizing the total number of genotypings and probability of type I error. One approach to increase efficiency, which has been investigated by other workers, is grid tightening: a sample is initially typed using a coarse grid of markers, and promising results are followed up by use of a finer grid. Another approach, not previously considered in detail in the context of an affected-sib-pair genome scan for linkage, is sample splitting: a portion of the sample is typed in the screening stage, and promising results are followed up in the whole sample. In the current study, we have used computer simulation to investigate the relative efficiency of two-stage strategies involving combinations of both grid tightening and sample splitting and found that the optimal strategy incorporates both approaches. In general, typing half the sample of affected pairs with a coarse grid of markers in the screening stage is an efficient strategy under a variety of conditions. If Hardy-Weinberg equilibrium holds, it is most efficient not to type parents in the screening stage. If Hardy-Weinberg equilibrium does not hold (e.g., because of stratification) failure to type parents in the first stage increases the amount of genotyping required, although the overall probability of type I error is not greatly increased, provided the parents are used in the final analysis. 23 refs., 4 figs., 5 tabs.

  6. A genome scan for quantitative trait loci affecting resistance to Trichostrongylus colubriformis in sheep.

    Science.gov (United States)

    Beh, K J; Hulme, D J; Callaghan, M J; Leish, Z; Lenane, I; Windon, R G; Maddox, J F

    2002-04-01

    A genome linkage scan was carried out using a resource flock of 1029 sheep in six half-sib families. The families were offspring of sires derived by crossing divergent lines of sheep selected for response to challenge with the intestinal parasitic nematode Trichostrongylus colubriformis. All animals in the resource flock were phenotypically assessed for worm resistance soon after weaning using a vaccination/challenge regime. After correcting for fixed effects using a least squares linear model the faecal egg count data obtained following the first challenge and the faecal egg count data obtained after the second challenge were designated Trait 1 and Trait 2, respectively. A total of 472 lambs drawn from the phenotypic extremes of the Trait 2 faecal egg count distribution were genotyped with a panel of 133 microsatellite markers covering all 26 sheep autosomes. Detection of quantitative trait loci (QTL) for each of the faecal egg count traits was determined using interval analysis with the Animap program with recombination rates between markers derived from an existing marker map. No chromosomal regions attained genome-wide significance for QTL influencing either of the traits. However, one region attained chromosome-wide significance and five other regions attained point-wise significance for the presence of QTL affecting parasite resistance.

  7. Genome-wide Scan of 29,141 African Americans Finds No Evidence of Directional Selection since Admixture

    OpenAIRE

    Bhatia, Gaurav; Tandon, Arti; Patterson, Nick; Aldrich, Melinda C.; Ambrosone, Christine B.; Amos, Christopher; Bandera, Elisa V.; Berndt, Sonja I.; Bernstein, Leslie; Blot, William J.; Bock, Cathryn H.; Caporaso, Neil; Casey, Graham; Deming, Sandra L.; Diver, W. Ryan

    2014-01-01

    The extent of recent selection in admixed populations is currently an unresolved question. We scanned the genomes of 29,141 African Americans and failed to find any genome-wide-significant deviations in local ancestry, indicating no evidence of selection influencing ancestry after admixture. A recent analysis of data from 1,890 African Americans reported that there was evidence of selection in African Americans after their ancestors left Africa, both before and after admixture. Selection afte...

  8. Whole genome scan to detect quantitative trait loci for bovine milk protein composition.

    Science.gov (United States)

    Schopen, G C B; Koks, P D; van Arendonk, J A M; Bovenhuis, H; Visker, M H P W

    2009-08-01

    The objective of this study was to perform a whole genome scan to detect quantitative trait loci (QTL) for milk protein composition in 849 Holstein-Friesian cows originating from seven sires. One morning milk sample was analysed for the major milk proteins using capillary zone electrophoresis. A genetic map was constructed with 1341 single nucleotide polymorphisms, covering 2829 centimorgans (cM) and 95% of the cattle genome. The chromosomal regions most significantly related to milk protein composition (P(genome) casein, alpha(S2)-casein, beta-casein and kappa-casein. The QTL on BTA11 was found at 124 cM, and affected beta-lactoglobulin, and the QTL on BTA14 was found at 0 cM, and affected protein percentage. The proportion of phenotypic variance explained by the QTL was 3.6% for beta-casein and 7.9% for kappa-casein on BTA6, 28.3% for beta-lactoglobulin on BTA11, and 8.6% for protein percentage on BTA14. The QTL affecting alpha(S2)-casein on BTA6 and 17 showed a significant interaction. We investigated the extent to which the detected QTL affecting milk protein composition could be explained by known polymorphisms in beta-casein, kappa-casein, beta-lactoglobulin and DGAT1 genes. Correction for these polymorphisms decreased the proportion of phenotypic variance explained by the QTL previously found on BTA6, 11 and 14. Thus, several significant QTL affecting milk protein composition were found, of which some QTL could partially be explained by polymorphisms in milk protein genes.

  9. A genome scan for quantitative trait loci affecting body conformation traits in Spanish Churra dairy sheep.

    Science.gov (United States)

    Gutiérrez-Gil, B; Alvarez, L; de la Fuente, L F; Sanchez, J P; San Primitivo, F; Arranz, J J

    2011-08-01

    A genome scan for chromosomal regions influencing body conformation traits was conducted for a population of Spanish Churra dairy sheep following a daughter design. A total of 739 ewes from 11 half-sib sire families were included in the study. The ewes were scored for the 5 linear traits used in the breeding scheme of the Churra breed to assess body conformation: stature, rear legs-rear view, foot angle, rump width, and general appearance. All the animals, including the 11 sires, were genotyped for 181 microsatellite markers evenly distributed across the 26 sheep autosomes. Using the yield deviations of the raw scores adjusted for fixed factors as phenotypic measurements, a quantitative trait loci (QTL) analysis was performed on the basis of a multi-marker regression method. Seven suggestive QTL were identified on chromosomes Ovis aries (OAR)2, OAR5, OAR16, OAR23, and OAR26, but none reached a genome-wise significance level. Putative QTL were identified for all of the traits analyzed, except for general appearance score. The suggestive QTL showing the highest test statistic influenced rear legs-rear view and was localized on OAR16, close to the growth hormone receptor coding gene, GHR. Some of the putative linkage associations reported here are consistent with previously reported QTL in cattle for similar traits. To the best of our knowledge, this study provides the first report of QTL for body conformation traits in dairy sheep; further studies will be needed to confirm and redefine the linkage associations reported herein. It is expected that future genome-wide association analyses of larger families will help identify genes underlying these putative genetic effects and provide useful markers for marker-assisted selection of such functional traits.

  10. Genome-wide scan of 29,141 African Americans finds no evidence of selection since admixture

    OpenAIRE

    Bhatia, Gaurav; Tandon, Arti; Aldrich, Melinda C.; Ambrosone, Christine B.; Amos, Christopher; Bandera, Elisa V.; Berndt, Sonja I.; Bernstein, Leslie; William J Blot; Bock, Cathryn H.; Caporaso, Neil; Casey, Graham; Deming, Sandra L.; Diver, W Ryan; Gapstur, Susan M

    2013-01-01

    We scanned through the genomes of 29,141 African Americans, searching for loci where the average proportion of African ancestry deviates significantly from the genome-wide average. We failed to find any genome-wide significant deviations, and conclude that any selection in African Americans since admixture is sufficiently weak that it falls below the threshold of our power to detect it using a large sample size. These results stand in contrast to the findings of a recent study of selection in...

  11. Magnetization reversal via a Stoner–Wohlfarth model with bi-dimensional angular distribution of easy axis

    International Nuclear Information System (INIS)

    A numerical extension of the simple Stoner–Wohlfarth model to the case of bi-dimensional angular distributions of easy axis is provided. The results are particularized in case of step-like, Gaussian-like and user defined distributions. In spite of its simplicity, the model can be applied to magnetically textured thin films and multilayers with in-plane magnetic anisotropy, independently on the texture source. Exemplifications are provided for a simple ferromagnetic textured FeCo film as well as for a FeMn/FeCo/Cu/FeCo spin valve structure. - Highlights: • Magnetic texture effects are included in the Stoner–Wohlfarth problem. • Step-like, Gaussian-like and user defined angular EADs are discussed. • The magnetic texture is obtained from the overall magnetization reversal. • Results beyond the OR method can be provided for complex systems

  12. Magnetization reversal via a Stoner–Wohlfarth model with bi-dimensional angular distribution of easy axis

    Energy Technology Data Exchange (ETDEWEB)

    Kuncser, A. [National Institute of Materials Physics, 105 bis Atomistilor Street, 077125 Bucharest-Magurele (Romania); Faculty of Physics, University of Bucharest, 405 Atomistilor Street, 077125 Bucharest-Magurele (Romania); Kuncser, V., E-mail: kuncser@infim.ro [National Institute of Materials Physics, 105 bis Atomistilor Street, 077125 Bucharest-Magurele (Romania)

    2015-12-01

    A numerical extension of the simple Stoner–Wohlfarth model to the case of bi-dimensional angular distributions of easy axis is provided. The results are particularized in case of step-like, Gaussian-like and user defined distributions. In spite of its simplicity, the model can be applied to magnetically textured thin films and multilayers with in-plane magnetic anisotropy, independently on the texture source. Exemplifications are provided for a simple ferromagnetic textured FeCo film as well as for a FeMn/FeCo/Cu/FeCo spin valve structure. - Highlights: • Magnetic texture effects are included in the Stoner–Wohlfarth problem. • Step-like, Gaussian-like and user defined angular EADs are discussed. • The magnetic texture is obtained from the overall magnetization reversal. • Results beyond the OR method can be provided for complex systems.

  13. Identifying signatures of natural selection in Tibetan and Andean populations using dense genome scan data.

    Directory of Open Access Journals (Sweden)

    Abigail Bigham

    2010-09-01

    Full Text Available High-altitude hypoxia (reduced inspired oxygen tension due to decreased barometric pressure exerts severe physiological stress on the human body. Two high-altitude regions where humans have lived for millennia are the Andean Altiplano and the Tibetan Plateau. Populations living in these regions exhibit unique circulatory, respiratory, and hematological adaptations to life at high altitude. Although these responses have been well characterized physiologically, their underlying genetic basis remains unknown. We performed a genome scan to identify genes showing evidence of adaptation to hypoxia. We looked across each chromosome to identify genomic regions with previously unknown function with respect to altitude phenotypes. In addition, groups of genes functioning in oxygen metabolism and sensing were examined to test the hypothesis that particular pathways have been involved in genetic adaptation to altitude. Applying four population genetic statistics commonly used for detecting signatures of natural selection, we identified selection-nominated candidate genes and gene regions in these two populations (Andeans and Tibetans separately. The Tibetan and Andean patterns of genetic adaptation are largely distinct from one another, with both populations showing evidence of positive natural selection in different genes or gene regions. Interestingly, one gene previously known to be important in cellular oxygen sensing, EGLN1 (also known as PHD2, shows evidence of positive selection in both Tibetans and Andeans. However, the pattern of variation for this gene differs between the two populations. Our results indicate that several key HIF-regulatory and targeted genes are responsible for adaptation to high altitude in Andeans and Tibetans, and several different chromosomal regions are implicated in the putative response to selection. These data suggest a genetic role in high-altitude adaption and provide a basis for future genotype/phenotype association

  14. Application of the Restriction Landmark Genome Scanning (RLGS Method for Analysis of Genetic Diversity between Asian and African Sorghum

    Directory of Open Access Journals (Sweden)

    Hisato Okuizumi*, Tomotsugu Noguchi, Tatsuya Saguchi,Takuma Fujita, Eri Nonaka, Shinsuke Yamanaka, Koffi Kombate, Subbarayan Sivakumar , Kulandaivelu Ganesamurthy, Yasufumi Murakami

    2010-07-01

    Full Text Available Restriction Landmark Genome Scanning (RLGS used to detect large numbers of restriction landmarks in a single experiment andapplied to analyze the genetic diversity of Asian and African sorghum accessions. This method is one of the genome analysistools based on the concept that restriction enzyme sites can serve as landmarks throughout a genome. RLGS uses direct endlabelingof the genomic DNA digested with a rare-cutting restriction enzyme and high-resolution two-dimensionalelectrophoresis. It has an advantage of providing precise information on a spot intensity that reflects the copy number ofrestriction landmarks and to visualize differences in methylation levels across the genome. RLGS becomes very useful for doingwhole genome scans that equals the work of thousands of polymerase chain reactions. A study was carried out using Sorghumaccessions collected from countries viz., Morocco, Nigeria, Sudan, South Africa, Japan, South Korea, and China. Onerepresentative sample was chosen from a country for analysis carried out at National Institute of Agrobiological Sciences(NIAS. Two dimensional spot images for seven accessions obtained and spot intensities were scanned. Totally, 119 spots weredetected of which 95 spots observed as polymorphic and 24 as non polymorphic. Unique presence and null spots werespecifically detected in all accessions taken for study. A total of 37 unique spots and 12 null spots, detected in this experiment.Principal Coordinate Analysis indicated, four African accessions scattered in the diagram were diverse and three Asianaccessions closely distributed with narrow diversity. The phylogenetic tree showed that Sudan and Nigerian accessions weredistant while Chinna, Japan and Korea accessions had close proximity

  15. A genome-wide association scan in admixed Latin Americans identifies loci influencing facial and scalp hair features

    OpenAIRE

    Adhikari, Kaustubh; Fontanil, Tania; Cal, Santiago; Mendoza-Revilla, Javier; Fuentes-Guajardo, Macarena; Chacón-Duque, Juan-Camilo; Al-Saadi, Farah; Johansson, Jeanette A.; Quinto-Sanchez, Mirsha; Acuña-Alonzo, Victor; Jaramillo, Claudia; Arias, William; Barquera Lozano, Rodrigo; Macín Pérez, Gastón; Gómez-Valdés, Jorge

    2016-01-01

    We report a genome-wide association scan in over 6,000 Latin Americans for features of scalp hair (shape, colour, greying, balding) and facial hair (beard thickness, monobrow, eyebrow thickness). We found 18 signals of association reaching genome-wide significance (P values 5 × 10(-8) to 3 × 10(-119)), including 10 novel associations. These include novel loci for scalp hair shape and balding, and the first reported loci for hair greying, monobrow, eyebrow and beard thickness. A newly identifi...

  16. A genome-wide association scan in admixed Latin Americans identifies loci influencing facial and scalp hair features

    OpenAIRE

    Adhikari, Kaustubh; Fontanil, Tania; Cal, Santiago; Mendoza-Revilla, Javier; Fuentes-Guajardo, Macarena; Chacón-Duque, Juan-Camilo; Al-Saadi, Farah; Johansson, Jeanette A.; Quinto-Sanchez, Mirsha; Acuña-Alonzo, Victor; Jaramillo, Claudia; Arias, William; Barquera Lozano, Rodrigo; Macín Pérez, Gastón; Gómez-Valdés, Jorge

    2016-01-01

    We report a genome-wide association scan in over 6,000 Latin Americans for features of scalp hair (shape, colour, greying, balding) and facial hair (beard thickness, monobrow, eyebrow thickness). We found 18 signals of association reaching genome-wide significance (P values 5 × 10−8 to 3 × 10−119), including 10 novel associations. These include novel loci for scalp hair shape and balding, and the first reported loci for hair greying, monobrow, eyebrow and beard thickness. A newly identified l...

  17. A genome scan for QTL affecting resistance to Haemonchus contortus in sheep.

    Science.gov (United States)

    Sallé, G; Jacquiet, P; Gruner, L; Cortet, J; Sauvé, C; Prévot, F; Grisez, C; Bergeaud, J P; Schibler, L; Tircazes, A; François, D; Pery, C; Bouvier, F; Thouly, J C; Brunel, J C; Legarra, A; Elsen, J M; Bouix, J; Rupp, R; Moreno, C R

    2012-12-01

    Gastrointestinal nematodes are one of the main health issues in sheep breeding. To identify loci affecting the resistance to Haemonchus contortus, a genome scan was carried out using 1,275 Romane × Martinik Black Belly backcross lambs. The entire population was challenged with Haemonchus contortus in 2 consecutive experimental infections, and fecal egg counts (FEC) and packed cell volumes were measured. A subgroup of 332 lambs with extreme FEC was necropsied to determine the total worm burden, length of female worms, sex ratio in the worm population, abomasal pH, and serum and mucosal G immunoglobulins (IgG) responses. Pepsinogen concentration was measured in another subset of 229 lambs. For QTL detection, 160 microsatellite markers were used as well as the Illumina OvineSNP50 BeadChip that provided 42,469 SNP markers after quality control. Linkage, association, and joint linkage and association analyses were performed with the QTLMAP software. Linkage disequilibrium (LD) was estimated within each pure breed, and association analyses were carried out either considering or not the breed origin of the haplotypes. Four QTL regions on sheep chromosomes (OAR)5, 12, 13, and 21 were identified as key players among many other QTL with small to moderate effects. A QTL on OAR21 affecting pepsinogen concentration exactly matched the pepsinogen (PGA5) locus. A 10-Mbp region affecting FEC after the 1st and 2nd infections was found on OAR12. The SNP markers outperformed microsatellites in the linkage analysis. Taking advantage of the LD helped to refine the locations of the QTL mapped on OAR5 and 13.

  18. Cross-laboratory validation of the OncoScan® FFPE Assay, a multiplex tool for whole genome tumour profiling

    OpenAIRE

    Foster, Joseph M.; Oumie, Assa; Togneri, Fiona S.; Vasques, Fabiana Ramos; Hau, Debra; Taylor, Morag; Tinkler-Hundal, Emma; Southward, Katie; Medlow, Paul; McGreeghan-Crosby, Keith; Halfpenny, Iris; McMullan, Dominic J.; Quirke, Phil; Keating, Katherine E; Griffiths, Mike

    2015-01-01

    Background Adoption of new technology in both basic research and clinical settings requires rigorous validation of analytical performance. The OncoScan® FFPE Assay is a multiplexing tool that offers genome-wide copy number and loss of heterozygosity detection, as well as identification of frequently tested somatic mutations. Methods In this study, 162 formalin fixed paraffin embedded samples, representing six different tumour types, were profiled in triplicate across three independent laborat...

  19. A scan statistic to extract causal gene clusters from case-control genome-wide rare CNV data

    Directory of Open Access Journals (Sweden)

    Scherer Stephen W

    2011-05-01

    Full Text Available Abstract Background Several statistical tests have been developed for analyzing genome-wide association data by incorporating gene pathway information in terms of gene sets. Using these methods, hundreds of gene sets are typically tested, and the tested gene sets often overlap. This overlapping greatly increases the probability of generating false positives, and the results obtained are difficult to interpret, particularly when many gene sets show statistical significance. Results We propose a flexible statistical framework to circumvent these problems. Inspired by spatial scan statistics for detecting clustering of disease occurrence in the field of epidemiology, we developed a scan statistic to extract disease-associated gene clusters from a whole gene pathway. Extracting one or a few significant gene clusters from a global pathway limits the overall false positive probability, which results in increased statistical power, and facilitates the interpretation of test results. In the present study, we applied our method to genome-wide association data for rare copy-number variations, which have been strongly implicated in common diseases. Application of our method to a simulated dataset demonstrated the high accuracy of this method in detecting disease-associated gene clusters in a whole gene pathway. Conclusions The scan statistic approach proposed here shows a high level of accuracy in detecting gene clusters in a whole gene pathway. This study has provided a sound statistical framework for analyzing genome-wide rare CNV data by incorporating topological information on the gene pathway.

  20. A genome-wide association scan in admixed Latin Americans identifies loci influencing facial and scalp hair features.

    Science.gov (United States)

    Adhikari, Kaustubh; Fontanil, Tania; Cal, Santiago; Mendoza-Revilla, Javier; Fuentes-Guajardo, Macarena; Chacón-Duque, Juan-Camilo; Al-Saadi, Farah; Johansson, Jeanette A; Quinto-Sanchez, Mirsha; Acuña-Alonzo, Victor; Jaramillo, Claudia; Arias, William; Barquera Lozano, Rodrigo; Macín Pérez, Gastón; Gómez-Valdés, Jorge; Villamil-Ramírez, Hugo; Hunemeier, Tábita; Ramallo, Virginia; Silva de Cerqueira, Caio C; Hurtado, Malena; Villegas, Valeria; Granja, Vanessa; Gallo, Carla; Poletti, Giovanni; Schuler-Faccini, Lavinia; Salzano, Francisco M; Bortolini, Maria-Cátira; Canizales-Quinteros, Samuel; Rothhammer, Francisco; Bedoya, Gabriel; Gonzalez-José, Rolando; Headon, Denis; López-Otín, Carlos; Tobin, Desmond J; Balding, David; Ruiz-Linares, Andrés

    2016-01-01

    We report a genome-wide association scan in over 6,000 Latin Americans for features of scalp hair (shape, colour, greying, balding) and facial hair (beard thickness, monobrow, eyebrow thickness). We found 18 signals of association reaching genome-wide significance (P values 5 × 10(-8) to 3 × 10(-119)), including 10 novel associations. These include novel loci for scalp hair shape and balding, and the first reported loci for hair greying, monobrow, eyebrow and beard thickness. A newly identified locus influencing hair shape includes a Q30R substitution in the Protease Serine S1 family member 53 (PRSS53). We demonstrate that this enzyme is highly expressed in the hair follicle, especially the inner root sheath, and that the Q30R substitution affects enzyme processing and secretion. The genome regions associated with hair features are enriched for signals of selection, consistent with proposals regarding the evolution of human hair. PMID:26926045

  1. A genome-wide association scan in admixed Latin Americans identifies loci influencing facial and scalp hair features.

    Science.gov (United States)

    Adhikari, Kaustubh; Fontanil, Tania; Cal, Santiago; Mendoza-Revilla, Javier; Fuentes-Guajardo, Macarena; Chacón-Duque, Juan-Camilo; Al-Saadi, Farah; Johansson, Jeanette A; Quinto-Sanchez, Mirsha; Acuña-Alonzo, Victor; Jaramillo, Claudia; Arias, William; Barquera Lozano, Rodrigo; Macín Pérez, Gastón; Gómez-Valdés, Jorge; Villamil-Ramírez, Hugo; Hunemeier, Tábita; Ramallo, Virginia; Silva de Cerqueira, Caio C; Hurtado, Malena; Villegas, Valeria; Granja, Vanessa; Gallo, Carla; Poletti, Giovanni; Schuler-Faccini, Lavinia; Salzano, Francisco M; Bortolini, Maria-Cátira; Canizales-Quinteros, Samuel; Rothhammer, Francisco; Bedoya, Gabriel; Gonzalez-José, Rolando; Headon, Denis; López-Otín, Carlos; Tobin, Desmond J; Balding, David; Ruiz-Linares, Andrés

    2016-03-01

    We report a genome-wide association scan in over 6,000 Latin Americans for features of scalp hair (shape, colour, greying, balding) and facial hair (beard thickness, monobrow, eyebrow thickness). We found 18 signals of association reaching genome-wide significance (P values 5 × 10(-8) to 3 × 10(-119)), including 10 novel associations. These include novel loci for scalp hair shape and balding, and the first reported loci for hair greying, monobrow, eyebrow and beard thickness. A newly identified locus influencing hair shape includes a Q30R substitution in the Protease Serine S1 family member 53 (PRSS53). We demonstrate that this enzyme is highly expressed in the hair follicle, especially the inner root sheath, and that the Q30R substitution affects enzyme processing and secretion. The genome regions associated with hair features are enriched for signals of selection, consistent with proposals regarding the evolution of human hair.

  2. A general and efficient method for estimating continuous IBD functions for use in genome scans for QTL

    Directory of Open Access Journals (Sweden)

    Carlborg Örjan

    2007-11-01

    Full Text Available Abstract Background Identity by descent (IBD matrix estimation is a central component in mapping of Quantitative Trait Loci (QTL using variance component models. A large number of algorithms have been developed for estimation of IBD between individuals in populations at discrete locations in the genome for use in genome scans to detect QTL affecting various traits of interest in experimental animal, human and agricultural pedigrees. Here, we propose a new approach to estimate IBD as continuous functions rather than as discrete values. Results Estimation of IBD functions improved the computational efficiency and memory usage in genome scanning for QTL. We have explored two approaches to obtain continuous marker-bracket IBD-functions. By re-implementing an existing and fast deterministic IBD-estimation method, we show that this approach results in IBD functions that produces the exact same IBD as the original algorithm, but with a greater than 2-fold improvement of the computational efficiency and a considerably lower memory requirement for storing the resulting genome-wide IBD. By developing a general IBD function approximation algorithm, we show that it is possible to estimate marker-bracket IBD functions from IBD matrices estimated at marker locations by any existing IBD estimation algorithm. The general algorithm provides approximations that lead to QTL variance component estimates that even in worst-case scenarios are very similar to the true values. The approach of storing IBD as polynomial IBD-function was also shown to reduce the amount of memory required in genome scans for QTL. Conclusion In addition to direct improvements in computational and memory efficiency, estimation of IBD-functions is a fundamental step needed to develop and implement new efficient optimization algorithms for high precision localization of QTL. Here, we discuss and test two approaches for estimating IBD functions based on existing IBD estimation algorithms. Our

  3. On the bi-dimensional variational decomposition applied to nonstationary vibration signals for rolling bearing crack detection in coal cutters

    Science.gov (United States)

    Jiang, Yu; Li, Zhixiong; Zhang, Chao; Hu, Chao; Peng, Z.

    2016-06-01

    This work aims to detect rolling bearing cracks using a variational approach. An original method that appropriately incorporates bi-dimensional variational mode decomposition (BVMD) into discriminant diffusion maps (DDM) is proposed to analyze the nonstationary vibration signals recorded from the cracked rolling bearings in coal cutters. The advantage of this variational decomposition based diffusion map (VDDM) method in comparison to the current DDM is that the intrinsic vibration mode of the crack can be filtered into a limited bandwidth in the frequency domain with an estimated central frequency, thus discarding the interference signal components in the vibration signals and significantly improving the crack detection performance. In addition, the VDDM is able to simultaneously process two-channel sensor signals to reduce information leakage. Experimental validation using rolling bearing crack vibration signals demonstrates that the VDDM separated the raw signals into four intrinsic modes, including one roller vibration mode, one roller cage vibration mode, one inner race vibration mode, and one outer race vibration mode. Hence, reliable fault features were extracted from the outer race vibration mode, and satisfactory crack identification performance was achieved. The comparison between the proposed VDDM and existing approaches indicated that the VDDM method was more efficient and reliable for crack detection in coal cutter rolling bearings. As an effective catalyst for rolling bearing crack detection, this newly proposed method is useful for practical applications.

  4. Family-Based Genome-Wide Association Scan of Attention-Deficit/Hyperactivity Disorder

    Science.gov (United States)

    Mick, Eric; Todorov, Alexandre; Smalley, Susan; Hu, Xiaolan; Loo, Sandra; Todd, Richard D.; Biederman, Joseph; Byrne, Deirdre; Dechairo, Bryan; Guiney, Allan; McCracken, James; McGough, James; Nelson, Stanley F.; Reiersen, Angela M.; Wilens, Timothy E.; Wozniak, Janet; Neale, Benjamin M.; Faraone, Stephen V.

    2010-01-01

    Objective: Genes likely play a substantial role in the etiology of attention-deficit/hyperactivity disorder (ADHD). However, the genetic architecture of the disorder is unknown, and prior genome-wide association studies (GWAS) have not identified a genome-wide significant association. We have conducted a third, independent, multisite GWAS of…

  5. Whole genome PCR scanning reveals the syntenic genome structure of toxigenic Vibrio cholerae strains in the O1/O139 population.

    Directory of Open Access Journals (Sweden)

    Bo Pang

    Full Text Available Vibrio cholerae is commonly found in estuarine water systems. Toxigenic O1 and O139 V. cholerae strains have caused cholera epidemics and pandemics, whereas the nontoxigenic strains within these serogroups only occasionally lead to disease. To understand the differences in the genome and clonality between the toxigenic and nontoxigenic strains of V. cholerae serogroups O1 and O139, we employed a whole genome PCR scanning (WGPScanning method, an rrn operon-mediated fragment rearrangement analysis and comparative genomic hybridization (CGH to analyze the genome structure of different strains. WGPScanning in conjunction with CGH revealed that the genomic contents of the toxigenic strains were conservative, except for a few indels located mainly in mobile elements. Minor nucleotide variation in orthologous genes appeared to be the major difference between the toxigenic strains. rrn operon-mediated rearrangements were infrequent in El Tor toxigenic strains tested using I-CeuI digested pulsed-field gel electrophoresis (PFGE analysis and PCR analysis based on flanking sequence of rrn operons. Using these methods, we found that the genomic structures of toxigenic El Tor and O139 strains were syntenic. The nontoxigenic strains exhibited more extensive sequence variations, but toxin coregulated pilus positive (TCP+ strains had a similar structure. TCP+ nontoxigenic strains could be subdivided into multiple lineages according to the TCP type, suggesting the existence of complex intermediates in the evolution of toxigenic strains. The data indicate that toxigenic O1 El Tor and O139 strains were derived from a single lineage of intermediates from complex clones in the environment. The nontoxigenic strains with non-El Tor type TCP may yet evolve into new epidemic clones after attaining toxigenic attributes.

  6. An international collaborative family-based whole genome quantitative trait linkage scan for myopic refractive error

    DEFF Research Database (Denmark)

    Abbott, Diana; Li, Yi-Ju; Guggenheim, Jeremy A;

    2012-01-01

    To investigate quantitative trait loci linked to refractive error, we performed a genome-wide quantitative trait linkage analysis using single nucleotide polymorphism markers and family data from five international sites....

  7. A Genome-Wide Scan for Breast Cancer Risk Haplotypes among African American Women

    OpenAIRE

    Song, Chi; Chen, Gary K.; Millikan, Robert C.; Ambrosone, Christine B.; John, Esther M; Bernstein, Leslie; Zheng, Wei; Jennifer J Hu; Ziegler, Regina G.; Nyante, Sarah; Bandera, Elisa V.; Sue A Ingles; Michael F. Press; Deming, Sandra L.; Rodriguez-Gil, Jorge L.

    2013-01-01

    Genome-wide association studies (GWAS) simultaneously investigating hundreds of thousands of single nucleotide polymorphisms (SNP) have become a powerful tool in the investigation of new disease susceptibility loci. Haplotypes are sometimes thought to be superior to SNPs and are promising in genetic association analyses. The application of genome-wide haplotype analysis, however, is hindered by the complexity of haplotypes themselves and sophistication in computation. We systematically analyz...

  8. The Application of Restriction Landmark Genome Scanning Method for Surveillance of Non-Mendelian Inheritance in F1 Hybrids

    Directory of Open Access Journals (Sweden)

    Tomoko Takamiya

    2009-01-01

    Full Text Available We analyzed inheritance of DNA methylation in reciprocal F1 hybrids (subsp. japonica cv. Nipponbare × subsp. indica cv. Kasalath of rice (Oryza sativa L. using restriction landmark genome scanning (RLGS, and detected differing RLGS spots between the parents and reciprocal F1 hybrids. MspI/HpaII restriction sites in the DNA from these different spots were suspected to be heterozygously methylated in the Nipponbare parent. These spots segregated in F1 plants, but did not segregate in selfed progeny of Nipponbare, showing non-Mendelian inheritance of the methylation status. As a result of RT-PCR and sequencing, a specific allele of the gene nearest to the methylated sites was expressed in reciprocal F1 plants, showing evidence of biased allelic expression. These results show the applicability of RLGS for scanning of non-Mendelian inheritance of DNA methylation and biased allelic expression.

  9. Genome-wide association scan meta-analysis identifies three loci influencing adiposity and fat distribution

    NARCIS (Netherlands)

    C.M. Lindgren (Cecilia); I.M. Heid (Iris); J.C. Randall (Joshua); C. Lamina (Claudia); V. Steinthorsdottir (Valgerdur); L. Qi (Lu); E.K. Speliotes (Elizabeth); G. Thorleifsson (Gudmar); C.J. Willer (Cristen); B.M. Herrera (Blanca); A.U. Jackson (Anne); N. Lim (Noha); P. Scheet (Paul); N. Soranzo (Nicole); N. Amin (Najaf); Y.S. Aulchenko (Yurii); J.C. Chambers (John); A. Drong (Alexander); J. Luan; H.N. Lyon (Helen); F. Rivadeneira Ramirez (Fernando); S. Sanna (Serena); N. Timpson (Nicholas); M.C. Zillikens (Carola); H.Z. Jing; P. Almgren (Peter); S. Bandinelli (Stefania); A.J. Bennett (Amanda); R.N. Bergman (Richard); L.L. Bonnycastle (Lori); S. Bumpstead (Suzannah); S.J. Chanock (Stephen); L. Cherkas (Lynn); P.S. Chines (Peter); L. Coin (Lachlan); C. Cooper (Charles); G. Crawford (Gabe); A. Doering (Angela); A. Dominiczak (Anna); A.S.F. Doney (Alex); S. Ebrahim (Shanil); P. Elliott (Paul); M.R. Erdos (Michael); K. Estrada Gil (Karol); L. Ferrucci (Luigi); G. Fischer (Guido); N.G. Forouhi (Nita); C. Gieger (Christian); H. Grallert (Harald); C.J. Groves (Christopher); S.M. Grundy (Scott); C. Guiducci (Candace); D. Hadley (David); A. Hamsten (Anders); A.S. Havulinna (Aki); A. Hofman (Albert); R. Holle (Rolf); J.W. Holloway (John); T. Illig (Thomas); B. Isomaa (Bo); L.C. Jacobs (Leonie); K. Jameson (Karen); P. Jousilahti (Pekka); F. Karpe (Fredrik); J. Kuusisto (Johanna); J. Laitinen (Jaana); G.M. Lathrop (Mark); D.A. Lawlor (Debbie); M. Mangino (Massimo); W.L. McArdle (Wendy); T. Meitinger (Thomas); M.A. Morken (Mario); A.P. Morris (Andrew); P. Munroe (Patricia); N. Narisu (Narisu); A. Nordström (Anna); B.A. Oostra (Ben); C.N.A. Palmer (Colin); F. Payne (Felicity); J. Peden (John); I. Prokopenko (Inga); F. Renström (Frida); A. Ruokonen (Aimo); V. Salomaa (Veikko); M.S. Sandhu (Manjinder); L.J. Scott (Laura); A. Scuteri (Angelo); K. Silander (Kaisa); K. Song (Kijoung); X. Yuan (Xin); H.M. Stringham (Heather); A.J. Swift (Amy); T. Tuomi (Tiinamaija); M. Uda (Manuela); P. Vollenweider (Peter); G. Waeber (Gérard); C. Wallace (Chris); G.B. Walters (Bragi); M.N. Weedon (Michael); J.C.M. Witteman (Jacqueline); C. Zhang (Cuilin); M. Caulfield (Mark); F.S. Collins (Francis); G.D. Smith; I.N.M. Day (Ian); P.W. Franks (Paul); A.T. Hattersley (Andrew); F.B. Hu (Frank); M.R. Jarvelin; A. Kong (Augustine); J.S. Kooner (Jaspal); M. Laakso (Markku); E. Lakatta (Edward); V. Mooser (Vincent); L. Peltonen (Leena Johanna); N.J. Samani (Nilesh); T.D. Spector (Timothy); D.P. Strachan (David); T. Tanaka (Toshiko); J. Tuomilehto (Jaakko); A.G. Uitterlinden (André); P. Tikka-Kleemola (Päivi); N.J. Wareham (Nick); H. Watkins (Hugh); D. Waterworth (Dawn); M. Boehnke (Michael); P. Deloukas (Panagiotis); L. Groop (Leif); D.J. Hunter (David); U. Thorsteinsdottir (Unnur); D. Schlessinger (David); H.E. Wichmann (Erich); T.M. Frayling (Timothy); G.R. Abecasis (Gonçalo); J.N. Hirschhorn (Joel); R.J.F. Loos (Ruth); J-A. Zwart (John-Anker); K.L. Mohlke (Karen); I. Barroso (Inês); M.I. McCarthy (Mark)

    2009-01-01

    textabstractTo identify genetic loci influencing central obesity and fat distribution, we performed a meta-analysis of 16 genome-wide association studies (GWAS, N = 38,580) informative for adult waist circumference (WC) and waist-hip ratio (WHR). We selected 26 SNPs for follow-up, for which the evid

  10. A genome-wide scan for common alleles affecting risk for autism

    NARCIS (Netherlands)

    Anney, Richard; Klei, Lambertus; Pinto, Dalila; Regan, Regina; Conroy, Judith; Magalhaes, Tiago R.; Correia, Catarina; Abrahams, Brett S.; Sykes, Nuala; Pagnamenta, Alistair T.; Almeida, Joana; Bacchelli, Elena; Bailey, Anthony J.; Baird, Gillian; Battaglia, Agatino; Berney, Tom; Bolshakova, Nadia; Boelte, Sven; Bolton, Patrick F.; Bourgeron, Thomas; Brennan, Sean; Brian, Jessica; Carson, Andrew R.; Casallo, Guillermo; Casey, Jillian; Chu, Su H.; Cochrane, Lynne; Corsello, Christina; Crawford, Emily L.; Crossett, Andrew; Dawson, Geraldine; de Jonge, Maretha; Delorme, Richard; Drmic, Irene; Duketis, Eftichia; Duque, Frederico; Estes, Annette; Farrar, Penny; Fernandez, Bridget A.; Folstein, Susan E.; Fombonne, Eric; Freitag, Christine M.; Gilbert, John; Gillberg, Christopher; Glessner, Joseph T.; Goldberg, Jeremy; Green, Jonathan; Guter, Stephen J.; Hakonarson, Hakon; Heron, Elizabeth A.; Hill, Matthew; Holt, Richard; Howe, Jennifer L.; Hughes, Gillian; Hus, Vanessa; Igliozzi, Roberta; Kim, Cecilia; Klauck, Sabine M.; Kolevzon, Alexander; Korvatska, Olena; Kustanovich, Vlad; Lajonchere, Clara M.; Lamb, Janine A.; Laskawiec, Magdalena; Leboyer, Marion; Le Couteur, Ann; Leventhal, Bennett L.; Lionel, Anath C.; Liu, Xiao-Qing; Lord, Catherine; Lotspeich, Linda; Lund, Sabata C.; Maestrini, Elena; Mahoney, William; Mantoulan, Carine; Marshall, Christian R.; McConachie, Helen; McDougle, Christopher J.; McGrath, Jane; McMahon, William M.; Melhem, Nadine M.; Merikangas, Alison; Migita, Ohsuke; Minshew, Nancy J.; Mirza, Ghazala K.; Munson, Jeff; Nelson, Stanley F.; Noakes, Carolyn; Noor, Abdul; Nygren, Gudrun; Oliveira, Guiomar; Papanikolaou, Katerina; Parr, Jeremy R.; Parrini, Barbara; Paton, Tara; Pickles, Andrew; Piven, Joseph; osey, David J.; Poustka, Annemarie; Poustka, Fritz; Prasad, Aparna; Ragoussis, Jiannis; Renshaw, Katy; Rickaby, Jessica; Roberts, Wendy; Roeder, Kathryn; Roge, Bernadette; Rutter, Michael L.; Bierut, Laura J.; Rice, John P.; Salt, Jeff; Sansom, Katherine; Sato, Daisuke; Segurado, Ricardo; Senman, Lili; Shah, Naisha; Sheffield, Val C.; Soorya, Latha; Sousa, Ines; Stoppioni, Vera; Strawbridge, Christina; Tancredi, Raffaella; Tansey, Katherine; Thiruvahindrapduram, Bhooma; Thompson, Ann P.; Thomson, Susanne; Tryfon, Ana; Tsiantis, John; Van Engeland, Herman; Vincent, John B.; Volkmar, Fred; Wallace, Simon; Wang, Kai; Wang, Zhouzhi; Wassink, Thomas H.; Wing, Kirsty; Wittemeyer, Kerstin; Wood, Shawn; Yaspan, Brian L.; Zurawiecki, Danielle; Zwaigenbaum, Lonnie; Betancur, Catalina; Buxbaum, Joseph D.; Cantor, Rita M.; Cook, Edwin H.; Coon, Hilary; Cuccaro, Michael L.; Gallagher, Louise; Geschwind, Daniel H.; Gill, Michael; Haines, Jonathan L.; Miller, Judith; Monaco, Anthony P.; Nurnberger, John I.; Paterson, Andrew D.; Pericak-Vance, Margaret A.; Schellenberg, Gerard D.; Scherer, Stephen W.; Sutcliffe, James S.; Szatmari, Peter; Vicente, Astrid M.; Vieland, Veronica J.; Wijsman, Ellen M.; Devlin, Bernie; Ennis, Sean; Hallmayer, Joachim

    2010-01-01

    Although autism spectrum disorders (ASDs) have a substantial genetic basis, most of the known genetic risk has been traced to rare variants, principally copy number variants (CNVs). To identify common risk variation, the Autism Genome Project (AGP) Consortium genotyped 1558 rigorously defined ASD fa

  11. A genome-wide scan for breast cancer risk haplotypes among African American women.

    Directory of Open Access Journals (Sweden)

    Chi Song

    Full Text Available Genome-wide association studies (GWAS simultaneously investigating hundreds of thousands of single nucleotide polymorphisms (SNP have become a powerful tool in the investigation of new disease susceptibility loci. Haplotypes are sometimes thought to be superior to SNPs and are promising in genetic association analyses. The application of genome-wide haplotype analysis, however, is hindered by the complexity of haplotypes themselves and sophistication in computation. We systematically analyzed the haplotype effects for breast cancer risk among 5,761 African American women (3,016 cases and 2,745 controls using a sliding window approach on the genome-wide scale. Three regions on chromosomes 1, 4 and 18 exhibited moderate haplotype effects. Furthermore, among 21 breast cancer susceptibility loci previously established in European populations, 10p15 and 14q24 are likely to harbor novel haplotype effects. We also proposed a heuristic of determining the significance level and the effective number of independent tests by the permutation analysis on chromosome 22 data. It suggests that the effective number was approximately half of the total (7,794 out of 15,645, thus the half number could serve as a quick reference to evaluating genome-wide significance if a similar sliding window approach of haplotype analysis is adopted in similar populations using similar genotype density.

  12. Efficient Haplotype Inference Algorithms in One Whole Genome Scan for Pedigree Data with Non-genotyped Founders

    Institute of Scientific and Technical Information of China (English)

    Yongxi Cheng; Hadi Sabaa; Zhipeng Cai; Randy Goebel; Guohui Lin

    2009-01-01

    An efficient rule-based algorithm is presented for haplotype inference from general pedigree genotype data, with the assumption of no recombination. This algorithm generalizes previous algorithms to handle the cases where some pedigree founders are not genotyped, provided that for each nuclear family at least one parent is genotyped and each non-genotyped founder appears in exactly one nuclear family. The importance of this generalization lies in that such cases frequently happen in real data, because some founders may have passed away and their genotype data can no longer be collected. The algorithm runs in O(m3n3) time, where m is the number of single nucleotide polymorphism (SNP) loci under consideration and n is the number of genotyped members in the pedigree. This zero-recombination haplotyping algorithm is extended to a maximum parsimoniously haplotyping algorithm in one whole genome scan to minimize the total number of breakpoint sites, or equivalently, the number of maximal zero-recombination chromosomal regions. We show that such a whole genome scan haplotyping algorithm can be implemented in O(m3n3) time in a novel incremental fashion,here m denotes the total number of SNP loci along the chromosome.

  13. Genome scan for quantitative trait loci influencing HDL levels: evidence for multilocus inheritance in familial combined hyperlipidemia.

    Science.gov (United States)

    Gagnon, France; Jarvik, Gail P; Badzioch, Michael D; Motulsky, Arno G; Brunzell, John D; Wijsman, Ellen M

    2005-09-01

    Several genome scans in search of high-density lipoprotein (HDL) quantitative trait loci (QTLs) have been performed. However, to date the actual identification of genes implicated in the regulation of common forms of HDL abnormalities remains unsuccessful. This may be due, in part, to the oligogenic and multivariate nature of HDL regulation, and potentially, pleiotropy affecting HDL and other lipid-related traits. Using a Bayesian Markov Chain Monte Carlo (MCMC) approach, we recently provided evidence of linkage of HDL level variation to the APOA1-C3-A4-A5 gene complex, in familial combined hyperlipidemia pedigrees, with an estimated number of two to three large QTLs remaining to be identified. We also presented results consistent with pleiotropy affecting HDL and triglycerides at the APOA1-C3-A4-A5 gene complex. Here we use the same MCMC analytic strategy, which allows for oligogenic trait models, as well as simultaneous incorporation of covariates, in the context of multipoint analysis. We now present results from a genome scan in search for the additional HDL QTLs in these pedigrees. We provide evidence of linkage for additional HDL QTLs on chromosomes 3p14 and 13q32, with results on chromosome 3 further supported by maximum parametric and variance component LOD scores of 3.0 and 2.6, respectively. Weaker evidence of linkage was also obtained for 7q32, 12q12, 14q31-32 and 16q23-24.

  14. A 2cM genome-wide scan of European Holstein cattle affected by classical BSE

    Directory of Open Access Journals (Sweden)

    Prasad Aparna

    2010-03-01

    Full Text Available Abstract Background Classical bovine spongiform encephalopathy (BSE is an acquired prion disease that is invariably fatal in cattle and has been implicated as a significant human health risk. Polymorphisms that alter the prion protein of sheep or humans have been associated with variations in transmissible spongiform encephalopathy susceptibility or resistance. In contrast, there is no strong evidence that non-synonymous mutations in the bovine prion gene (PRNP are associated with classical BSE disease susceptibility. However, two bovine PRNP insertion/deletion polymorphisms, one within the promoter region and the other in intron 1, have been associated with susceptibility to classical BSE. These associations do not explain the full extent of BSE susceptibility, and loci outside of PRNP appear to be associated with disease incidence in some cattle populations. To test for associations with BSE susceptibility, we conducted a genome wide scan using a panel of 3,072 single nucleotide polymorphism (SNP markers on 814 animals representing cases and control Holstein cattle from the United Kingdom BSE epidemic. Results Two sets of BSE affected Holstein cattle were analyzed in this study, one set with known family relationships and the second set of paired cases with controls. The family set comprises half-sibling progeny from six sires. The progeny from four of these sires had previously been scanned with microsatellite markers. The results obtained from the current analysis of the family set yielded both some supporting and new results compared with those obtained in the earlier study. The results revealed 27 SNPs representing 18 chromosomes associated with incidence of BSE disease. These results confirm a region previously reported on chromosome 20, and identify additional regions on chromosomes 2, 14, 16, 21 and 28. This study did not identify a significant association near the PRNP in the family sample set. The only association found in the PRNP

  15. Genome wide scan for quantitative trait loci affecting tick resistance in cattle (Bos taurus × Bos indicus

    Directory of Open Access Journals (Sweden)

    Guimarães Simone EF

    2010-04-01

    Full Text Available Abstract Background In tropical countries, losses caused by bovine tick Rhipicephalus (Boophilus microplus infestation have a tremendous economic impact on cattle production systems. Genetic variation between Bos taurus and Bos indicus to tick resistance and molecular biology tools might allow for the identification of molecular markers linked to resistance traits that could be used as an auxiliary tool in selection programs. The objective of this work was to identify QTL associated with tick resistance/susceptibility in a bovine F2 population derived from the Gyr (Bos indicus × Holstein (Bos taurus cross. Results Through a whole genome scan with microsatellite markers, we were able to map six genomic regions associated with bovine tick resistance. For most QTL, we have found that depending on the tick evaluation season (dry and rainy different sets of genes could be involved in the resistance mechanism. We identified dry season specific QTL on BTA 2 and 10, rainy season specific QTL on BTA 5, 11 and 27. We also found a highly significant genome wide QTL for both dry and rainy seasons in the central region of BTA 23. Conclusions The experimental F2 population derived from Gyr × Holstein cross successfully allowed the identification of six highly significant QTL associated with tick resistance in cattle. QTL located on BTA 23 might be related with the bovine histocompatibility complex. Further investigation of these QTL will help to isolate candidate genes involved with tick resistance in cattle.

  16. Genome-wide linkage scans for major depression in individuals with alcohol dependence

    OpenAIRE

    Kuo, Po-Hsiu; Neale, Michael C.; Walsh, Dermot; Patterson, Diana G.; Riley, Brien; Prescott, Carol A.; Kendler, Kenneth S.

    2010-01-01

    Major depression is more prevalent among individuals with alcoholism than in the general population. Twin studies have found a moderate degree of genetic correlation for alcohol dependence (AD) and major depression (MD), suggesting the existence of loci that confer susceptibility to both disorders. The aim of the present study was to conduct genome-wide linkage analyses to identify loci and to replicate prior evidence for linkage to MD, and to search for linkage regions that may confer risk t...

  17. Genome-Wide Scans Provide Evidence for Positive Selection of Genes Implicated in Lassa Fever

    OpenAIRE

    Andersen, Kristian G.; Shylakhter, Ilya; Tabrizi, Shervin; Grossman, Sharon Rachel; Happi, Christian Tientcha; Sabeti, Pardis Christine

    2012-01-01

    Rapidly evolving viruses and other pathogens can have an immense impact on human evolution as natural selection acts to increase the prevalence of genetic variants providing resistance to disease. With the emergence of large datasets of human genetic variation, we can search for signatures of natural selection in the human genome driven by such disease-causing microorganisms. Based on this approach, we have previously hypothesized that Lassa virus (LASV) may have been a driver of natural sele...

  18. Genome-wide scans provide evidence for positive selection of genes implicated in Lassa fever

    OpenAIRE

    Andersen, Kristian G.; Shylakhter, Ilya; Tabrizi, Shervin; Grossman, Sharon R.; Happi, Christian T; Sabeti, Pardis C.

    2012-01-01

    Rapidly evolving viruses and other pathogens can have an immense impact on human evolution as natural selection acts to increase the prevalence of genetic variants providing resistance to disease. With the emergence of large datasets of human genetic variation, we can search for signatures of natural selection in the human genome driven by such disease-causing microorganisms. Based on this approach, we have previously hypothesized that Lassa virus (LASV) may have been a driver of natural sele...

  19. Genome-wide scans provide evidence for positive selection of genes implicated in Lassa fever.

    Science.gov (United States)

    Andersen, Kristian G; Shylakhter, Ilya; Tabrizi, Shervin; Grossman, Sharon R; Happi, Christian T; Sabeti, Pardis C

    2012-03-19

    Rapidly evolving viruses and other pathogens can have an immense impact on human evolution as natural selection acts to increase the prevalence of genetic variants providing resistance to disease. With the emergence of large datasets of human genetic variation, we can search for signatures of natural selection in the human genome driven by such disease-causing microorganisms. Based on this approach, we have previously hypothesized that Lassa virus (LASV) may have been a driver of natural selection in West African populations where Lassa haemorrhagic fever is endemic. In this study, we provide further evidence for this notion. By applying tests for selection to genome-wide data from the International Haplotype Map Consortium and the 1000 Genomes Consortium, we demonstrate evidence for positive selection in LARGE and interleukin 21 (IL21), two genes implicated in LASV infectivity and immunity. We further localized the signals of selection, using the recently developed composite of multiple signals method, to introns and putative regulatory regions of those genes. Our results suggest that natural selection may have targeted variants giving rise to alternative splicing or differential gene expression of LARGE and IL21. Overall, our study supports the hypothesis that selective pressures imposed by LASV may have led to the emergence of particular alleles conferring resistance to Lassa fever, and opens up new avenues of research pursuit. PMID:22312054

  20. Genome-wide scans provide evidence for positive selection of genes implicated in Lassa fever

    Science.gov (United States)

    Andersen, Kristian G.; Shylakhter, Ilya; Tabrizi, Shervin; Grossman, Sharon R.; Happi, Christian T.; Sabeti, Pardis C.

    2012-01-01

    Rapidly evolving viruses and other pathogens can have an immense impact on human evolution as natural selection acts to increase the prevalence of genetic variants providing resistance to disease. With the emergence of large datasets of human genetic variation, we can search for signatures of natural selection in the human genome driven by such disease-causing microorganisms. Based on this approach, we have previously hypothesized that Lassa virus (LASV) may have been a driver of natural selection in West African populations where Lassa haemorrhagic fever is endemic. In this study, we provide further evidence for this notion. By applying tests for selection to genome-wide data from the International Haplotype Map Consortium and the 1000 Genomes Consortium, we demonstrate evidence for positive selection in LARGE and interleukin 21 (IL21), two genes implicated in LASV infectivity and immunity. We further localized the signals of selection, using the recently developed composite of multiple signals method, to introns and putative regulatory regions of those genes. Our results suggest that natural selection may have targeted variants giving rise to alternative splicing or differential gene expression of LARGE and IL21. Overall, our study supports the hypothesis that selective pressures imposed by LASV may have led to the emergence of particular alleles conferring resistance to Lassa fever, and opens up new avenues of research pursuit. PMID:22312054

  1. A genome-wide scan for selection signatures in Nellore cattle.

    Science.gov (United States)

    Somavilla, A L; Sonstegard, T S; Higa, R H; Rosa, A N; Siqueira, F; Silva, L O C; Torres Júnior, R A A; Coutinho, L L; Mudadu, M A; Alencar, M M; Regitano, L C A

    2014-12-01

    Brazilian Nellore cattle (Bos indicus) have been selected for growth traits for over more than four decades. In recent years, reproductive and meat quality traits have become more important because of increasing consumption, exports and consumer demand. The identification of genome regions altered by artificial selection can potentially permit a better understanding of the biology of specific phenotypes that are useful for the development of tools designed to increase selection efficiency. Therefore, the aims of this study were to detect evidence of recent selection signatures in Nellore cattle using extended haplotype homozygosity methodology and BovineHD marker genotypes (>777,000 single nucleotide polymorphisms) as well as to identify corresponding genes underlying these signals. Thirty-one significant regions (P meat quality, fatty acid profiles and immunity. In addition, 545 genes were identified in regions harboring selection signatures. Within this group, 58 genes were associated with growth, muscle and adipose tissue metabolism, reproductive traits or the immune system. Using relative extended haplotype homozygosity to analyze high-density single nucleotide polymorphism marker data allowed for the identification of regions potentially under artificial selection pressure in the Nellore genome, which might be used to better understand autozygosity and the effects of selection on the Nellore genome.

  2. A genome-wide scan for common alleles affecting risk for autism.

    LENUS (Irish Health Repository)

    Anney, Richard

    2010-10-15

    Although autism spectrum disorders (ASDs) have a substantial genetic basis, most of the known genetic risk has been traced to rare variants, principally copy number variants (CNVs). To identify common risk variation, the Autism Genome Project (AGP) Consortium genotyped 1558 rigorously defined ASD families for 1 million single-nucleotide polymorphisms (SNPs) and analyzed these SNP genotypes for association with ASD. In one of four primary association analyses, the association signal for marker rs4141463, located within MACROD2, crossed the genome-wide association significance threshold of P < 5 × 10(-8). When a smaller replication sample was analyzed, the risk allele at rs4141463 was again over-transmitted; yet, consistent with the winner\\'s curse, its effect size in the replication sample was much smaller; and, for the combined samples, the association signal barely fell below the P < 5 × 10(-8) threshold. Exploratory analyses of phenotypic subtypes yielded no significant associations after correction for multiple testing. They did, however, yield strong signals within several genes, KIAA0564, PLD5, POU6F2, ST8SIA2 and TAF1C.

  3. Genome-wide association scan suggests basis for microtia in Awassi sheep.

    Science.gov (United States)

    Jawasreh, K; Boettcher, P J; Stella, A

    2016-08-01

    Hereditary underdevelopment of the ear, a condition also known as microtia, has been observed in several sheep breeds as well as in humans and other species. Its genetic basis in sheep is unknown. The Awassi sheep, a breed native to southwest Asia, carries this phenotype and was targeted for molecular characterization via a genome-wide association study. DNA samples were collected from sheep in Jordan. Eight affected and 12 normal individuals were genotyped with the Illumina OvineSNP50(®) chip. Multilocus analyses failed to identify any genotypic association. In contrast, a single-locus analysis revealed a statistically significant association (P = 0.012, genome-wide) with a SNP at basepair 34 647 499 on OAR23. This marker is adjacent to the gene encoding transcription factor GATA-6, which has been shown to play a role in many developmental processes, including chondrogenesis. The lack of extended homozygosity in this region suggests a fairly ancient mutation, and the time of occurrence was estimated to be approximately 3000 years ago. Many of the earless sheep breeds may thus share the causative mutation, especially within the subgroup of fat-tailed, wool sheep. PMID:26990958

  4. A genome-wide scan for common alleles affecting risk for autism

    Science.gov (United States)

    Anney, Richard; Klei, Lambertus; Pinto, Dalila; Regan, Regina; Conroy, Judith; Magalhaes, Tiago R.; Correia, Catarina; Abrahams, Brett S.; Sykes, Nuala; Pagnamenta, Alistair T.; Almeida, Joana; Bacchelli, Elena; Bailey, Anthony J.; Baird, Gillian; Battaglia, Agatino; Berney, Tom; Bolshakova, Nadia; Bölte, Sven; Bolton, Patrick F.; Bourgeron, Thomas; Brennan, Sean; Brian, Jessica; Carson, Andrew R.; Casallo, Guillermo; Casey, Jillian; Chu, Su H.; Cochrane, Lynne; Corsello, Christina; Crawford, Emily L.; Crossett, Andrew; Dawson, Geraldine; de Jonge, Maretha; Delorme, Richard; Drmic, Irene; Duketis, Eftichia; Duque, Frederico; Estes, Annette; Farrar, Penny; Fernandez, Bridget A.; Folstein, Susan E.; Fombonne, Eric; Freitag, Christine M.; Gilbert, John; Gillberg, Christopher; Glessner, Joseph T.; Goldberg, Jeremy; Green, Jonathan; Guter, Stephen J.; Hakonarson, Hakon; Heron, Elizabeth A.; Hill, Matthew; Holt, Richard; Howe, Jennifer L.; Hughes, Gillian; Hus, Vanessa; Igliozzi, Roberta; Kim, Cecilia; Klauck, Sabine M.; Kolevzon, Alexander; Korvatska, Olena; Kustanovich, Vlad; Lajonchere, Clara M.; Lamb, Janine A.; Laskawiec, Magdalena; Leboyer, Marion; Le Couteur, Ann; Leventhal, Bennett L.; Lionel, Anath C.; Liu, Xiao-Qing; Lord, Catherine; Lotspeich, Linda; Lund, Sabata C.; Maestrini, Elena; Mahoney, William; Mantoulan, Carine; Marshall, Christian R.; McConachie, Helen; McDougle, Christopher J.; McGrath, Jane; McMahon, William M.; Melhem, Nadine M.; Merikangas, Alison; Migita, Ohsuke; Minshew, Nancy J.; Mirza, Ghazala K.; Munson, Jeff; Nelson, Stanley F.; Noakes, Carolyn; Noor, Abdul; Nygren, Gudrun; Oliveira, Guiomar; Papanikolaou, Katerina; Parr, Jeremy R.; Parrini, Barbara; Paton, Tara; Pickles, Andrew; Piven, Joseph; Posey, David J; Poustka, Annemarie; Poustka, Fritz; Prasad, Aparna; Ragoussis, Jiannis; Renshaw, Katy; Rickaby, Jessica; Roberts, Wendy; Roeder, Kathryn; Roge, Bernadette; Rutter, Michael L.; Bierut, Laura J.; Rice, John P.; Salt, Jeff; Sansom, Katherine; Sato, Daisuke; Segurado, Ricardo; Senman, Lili; Shah, Naisha; Sheffield, Val C.; Soorya, Latha; Sousa, Inês; Stoppioni, Vera; Strawbridge, Christina; Tancredi, Raffaella; Tansey, Katherine; Thiruvahindrapduram, Bhooma; Thompson, Ann P.; Thomson, Susanne; Tryfon, Ana; Tsiantis, John; Van Engeland, Herman; Vincent, John B.; Volkmar, Fred; Wallace, Simon; Wang, Kai; Wang, Zhouzhi; Wassink, Thomas H.; Wing, Kirsty; Wittemeyer, Kerstin; Wood, Shawn; Yaspan, Brian L.; Zurawiecki, Danielle; Zwaigenbaum, Lonnie; Betancur, Catalina; Buxbaum, Joseph D.; Cantor, Rita M.; Cook, Edwin H.; Coon, Hilary; Cuccaro, Michael L.; Gallagher, Louise; Geschwind, Daniel H.; Gill, Michael; Haines, Jonathan L.; Miller, Judith; Monaco, Anthony P.; Nurnberger, John I.; Paterson, Andrew D.; Pericak-Vance, Margaret A.; Schellenberg, Gerard D.; Scherer, Stephen W.; Sutcliffe, James S.; Szatmari, Peter; Vicente, Astrid M.; Vieland, Veronica J.; Wijsman, Ellen M.; Devlin, Bernie; Ennis, Sean; Hallmayer, Joachim

    2010-01-01

    Although autism spectrum disorders (ASDs) have a substantial genetic basis, most of the known genetic risk has been traced to rare variants, principally copy number variants (CNVs). To identify common risk variation, the Autism Genome Project (AGP) Consortium genotyped 1558 rigorously defined ASD families for 1 million single-nucleotide polymorphisms (SNPs) and analyzed these SNP genotypes for association with ASD. In one of four primary association analyses, the association signal for marker rs4141463, located within MACROD2, crossed the genome-wide association significance threshold of P < 5 × 10−8. When a smaller replication sample was analyzed, the risk allele at rs4141463 was again over-transmitted; yet, consistent with the winner's curse, its effect size in the replication sample was much smaller; and, for the combined samples, the association signal barely fell below the P < 5 × 10−8 threshold. Exploratory analyses of phenotypic subtypes yielded no significant associations after correction for multiple testing. They did, however, yield strong signals within several genes, KIAA0564, PLD5, POU6F2, ST8SIA2 and TAF1C. PMID:20663923

  5. Genome-wide association scan suggests basis for microtia in Awassi sheep.

    Science.gov (United States)

    Jawasreh, K; Boettcher, P J; Stella, A

    2016-08-01

    Hereditary underdevelopment of the ear, a condition also known as microtia, has been observed in several sheep breeds as well as in humans and other species. Its genetic basis in sheep is unknown. The Awassi sheep, a breed native to southwest Asia, carries this phenotype and was targeted for molecular characterization via a genome-wide association study. DNA samples were collected from sheep in Jordan. Eight affected and 12 normal individuals were genotyped with the Illumina OvineSNP50(®) chip. Multilocus analyses failed to identify any genotypic association. In contrast, a single-locus analysis revealed a statistically significant association (P = 0.012, genome-wide) with a SNP at basepair 34 647 499 on OAR23. This marker is adjacent to the gene encoding transcription factor GATA-6, which has been shown to play a role in many developmental processes, including chondrogenesis. The lack of extended homozygosity in this region suggests a fairly ancient mutation, and the time of occurrence was estimated to be approximately 3000 years ago. Many of the earless sheep breeds may thus share the causative mutation, especially within the subgroup of fat-tailed, wool sheep.

  6. A scan for positively selected genes in the genomes of humans and chimpanzees.

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    Rasmus Nielsen

    2005-06-01

    Full Text Available Since the divergence of humans and chimpanzees about 5 million years ago, these species have undergone a remarkable evolution with drastic divergence in anatomy and cognitive abilities. At the molecular level, despite the small overall magnitude of DNA sequence divergence, we might expect such evolutionary changes to leave a noticeable signature throughout the genome. We here compare 13,731 annotated genes from humans to their chimpanzee orthologs to identify genes that show evidence of positive selection. Many of the genes that present a signature of positive selection tend to be involved in sensory perception or immune defenses. However, the group of genes that show the strongest evidence for positive selection also includes a surprising number of genes involved in tumor suppression and apoptosis, and of genes involved in spermatogenesis. We hypothesize that positive selection in some of these genes may be driven by genomic conflict due to apoptosis during spermatogenesis. Genes with maximal expression in the brain show little or no evidence for positive selection, while genes with maximal expression in the testis tend to be enriched with positively selected genes. Genes on the X chromosome also tend to show an elevated tendency for positive selection. We also present polymorphism data from 20 Caucasian Americans and 19 African Americans for the 50 annotated genes showing the strongest evidence for positive selection. The polymorphism analysis further supports the presence of positive selection in these genes by showing an excess of high-frequency derived nonsynonymous mutations.

  7. A Genome Scan for Modifiers of Age at Onset in Huntington Disease: The HD MAPS Study

    OpenAIRE

    Li, Jian-Liang; Hayden, Michael R.; Almqvist, Elisabeth W.; Brinkman, Ryan R; Durr, Alexandra; Dodé, Catherine; Morrison, Patrick J.; Suchowersky, Oksana; Ross, Christopher A.; Margolis, Russell L.; Rosenblatt, Adam; Gómez-Tortosa, Estrella; Cabrero, David Mayo; Novelletto, Andrea; Frontali, Marina

    2003-01-01

    Huntington disease (HD) is caused by the expansion of a CAG repeat within the coding region of a novel gene on 4p16.3. Although the variation in age at onset is partly explained by the size of the expanded repeat, the unexplained variation in age at onset is strongly heritable (h2=0.56), which suggests that other genes modify the age at onset of HD. To identify these modifier loci, we performed a 10-cM density genomewide scan in 629 affected sibling pairs (295 pedigrees and 695 individuals), ...

  8. Whole-Genome Scans Provide Evidence of Adaptive Evolution in Malawian Plasmodium falciparum Isolates

    DEFF Research Database (Denmark)

    Ocholla, Harold; Preston, Mark D; Mipando, Mwapatsa;

    2014-01-01

    BACKGROUND:  Selection by host immunity and antimalarial drugs has driven extensive adaptive evolution in Plasmodium falciparum and continues to produce ever-changing landscapes of genetic variation. METHODS:  We performed whole-genome sequencing of 69 P. falciparum isolates from Malawi and used...... population genetics approaches to investigate genetic diversity and population structure and identify loci under selection. RESULTS:  High genetic diversity (π = 2.4 × 10(-4)), moderately high multiplicity of infection (2.7), and low linkage disequilibrium (500-bp) were observed in Chikhwawa District, Malawi......, an area of high malaria transmission. Allele frequency-based tests provided evidence of recent population growth in Malawi and detected potential targets of host immunity and candidate vaccine antigens. Comparison of the sequence variation between isolates from Malawi and those from 5 geographically...

  9. A genome-wide scan in affected sibling pairs with idiopathic recurrent miscarriage suggests genetic linkage

    DEFF Research Database (Denmark)

    Kolte, Astrid Marie; Nielsen, H S; Moltke, Ida;

    2011-01-01

    Previously, siblings of patients with idiopathic recurrent miscarriage (IRM) have been shown to have a higher risk of miscarriage. This study comprises two parts: (i) an epidemiological part, in which we introduce data on the frequency of miscarriage among 268 siblings of 244 patients with IRM and...... (ii) a genetic part presenting data from a genome-wide linkage study of 38 affected sibling pairs with IRM. All IRM patients (probands) had experienced three or more miscarriages and affected siblings two or more miscarriages. The sibling pairs were genotyped by the Affymetrix GeneChip 50K Xba......I platform and non-parametric linkage analysis was performed via the software package Merlin. We find that siblings of IRM patients exhibit a higher frequency of miscarriage than population controls regardless of age at the time of pregnancy. We identify chromosomal regions with LOD scores between 2.5 and 3...

  10. High Resolution Genomic Scans Reveal Genetic Architecture Controlling Alcohol Preference in Bidirectionally Selected Rat Model.

    Science.gov (United States)

    Lo, Chiao-Ling; Lossie, Amy C; Liang, Tiebing; Liu, Yunlong; Xuei, Xiaoling; Lumeng, Lawrence; Zhou, Feng C; Muir, William M

    2016-08-01

    Investigations on the influence of nature vs. nurture on Alcoholism (Alcohol Use Disorder) in human have yet to provide a clear view on potential genomic etiologies. To address this issue, we sequenced a replicated animal model system bidirectionally-selected for alcohol preference (AP). This model is uniquely suited to map genetic effects with high reproducibility, and resolution. The origin of the rat lines (an 8-way cross) resulted in small haplotype blocks (HB) with a corresponding high level of resolution. We sequenced DNAs from 40 samples (10 per line of each replicate) to determine allele frequencies and HB. We achieved ~46X coverage per line and replicate. Excessive differentiation in the genomic architecture between lines, across replicates, termed signatures of selection (SS), were classified according to gene and region. We identified SS in 930 genes associated with AP. The majority (50%) of the SS were confined to single gene regions, the greatest numbers of which were in promoters (284) and intronic regions (169) with the least in exon's (4), suggesting that differences in AP were primarily due to alterations in regulatory regions. We confirmed previously identified genes and found many new genes associated with AP. Of those newly identified genes, several demonstrated neuronal function involved in synaptic memory and reward behavior, e.g. ion channels (Kcnf1, Kcnn3, Scn5a), excitatory receptors (Grin2a, Gria3, Grip1), neurotransmitters (Pomc), and synapses (Snap29). This study not only reveals the polygenic architecture of AP, but also emphasizes the importance of regulatory elements, consistent with other complex traits. PMID:27490364

  11. Genomic Scans of Zygotic Disequilibrium and Epistatic SNPs in HapMap Phase III Populations.

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    Xin-Sheng Hu

    Full Text Available Previous theory indicates that zygotic linkage disequilibrium (LD is more informative than gametic or composite digenic LD in revealing natural population history. Further, the difference between the composite digenic and maximum zygotic LDs can be used to detect epistatic selection for fitness. Here we corroborate the theory by investigating genome-wide zygotic LDs in HapMap phase III human populations. Results show that non-Africa populations have much more significant zygotic LDs than do Africa populations. Africa populations (ASW, LWK, MKK, and YRI possess more significant zygotic LDs for the double-homozygotes (DAABB than any other significant zygotic LDs (DAABb, DAaBB, and DAaBb, while non-Africa populations generally have more significant DAaBb's than any other significant zygotic LDs (DAABB, DAABb, and DAaBB. Average r-squares for any significant zygotic LDs increase generally in an order of populations YRI, MKK, CEU, CHB, LWK, JPT, CHD, TSI, GIH, ASW, and MEX. Average r-squares are greater for DAABB and DAaBb than for DAaBB and DAABb in each population. YRI and MKK can be separated from LWK and ASW in terms of the pattern of average r-squares. All population divergences in zygotic LDs can be interpreted with the model of Out of Africa for modern human origins. We have also detected 19735-95921 SNP pairs exhibiting strong signals of epistatic selection in different populations. Gene-gene interactions for some epistatic SNP pairs are evident from empirical findings, but many more epistatic SNP pairs await evidence. Common epistatic SNP pairs rarely exist among all populations, but exist in distinct regions (Africa, Europe, and East Asia, which helps to understand geographical genomic medicine.

  12. Genome-wide scan of 29,141 African Americans finds no evidence of directional selection since admixture.

    Science.gov (United States)

    Bhatia, Gaurav; Tandon, Arti; Patterson, Nick; Aldrich, Melinda C; Ambrosone, Christine B; Amos, Christopher; Bandera, Elisa V; Berndt, Sonja I; Bernstein, Leslie; Blot, William J; Bock, Cathryn H; Caporaso, Neil; Casey, Graham; Deming, Sandra L; Diver, W Ryan; Gapstur, Susan M; Gillanders, Elizabeth M; Harris, Curtis C; Henderson, Brian E; Ingles, Sue A; Isaacs, William; De Jager, Phillip L; John, Esther M; Kittles, Rick A; Larkin, Emma; McNeill, Lorna H; Millikan, Robert C; Murphy, Adam; Neslund-Dudas, Christine; Nyante, Sarah; Press, Michael F; Rodriguez-Gil, Jorge L; Rybicki, Benjamin A; Schwartz, Ann G; Signorello, Lisa B; Spitz, Margaret; Strom, Sara S; Tucker, Margaret A; Wiencke, John K; Witte, John S; Wu, Xifeng; Yamamura, Yuko; Zanetti, Krista A; Zheng, Wei; Ziegler, Regina G; Chanock, Stephen J; Haiman, Christopher A; Reich, David; Price, Alkes L

    2014-10-01

    The extent of recent selection in admixed populations is currently an unresolved question. We scanned the genomes of 29,141 African Americans and failed to find any genome-wide-significant deviations in local ancestry, indicating no evidence of selection influencing ancestry after admixture. A recent analysis of data from 1,890 African Americans reported that there was evidence of selection in African Americans after their ancestors left Africa, both before and after admixture. Selection after admixture was reported on the basis of deviations in local ancestry, and selection before admixture was reported on the basis of allele-frequency differences between African Americans and African populations. The local-ancestry deviations reported by the previous study did not replicate in our very large sample, and we show that such deviations were expected purely by chance, given the number of hypotheses tested. We further show that the previous study's conclusion of selection in African Americans before admixture is also subject to doubt. This is because the FST statistics they used were inflated and because true signals of unusual allele-frequency differences between African Americans and African populations would be best explained by selection that occurred in Africa prior to migration to the Americas.

  13. Genome-wide Scan of 29,141 African Americans Finds No Evidence of Directional Selection since Admixture

    Science.gov (United States)

    Bhatia, Gaurav; Tandon, Arti; Patterson, Nick; Aldrich, Melinda C.; Ambrosone, Christine B.; Amos, Christopher; Bandera, Elisa V.; Berndt, Sonja I.; Bernstein, Leslie; Blot, William J.; Bock, Cathryn H.; Caporaso, Neil; Casey, Graham; Deming, Sandra L.; Diver, W. Ryan; Gapstur, Susan M.; Gillanders, Elizabeth M.; Harris, Curtis C.; Henderson, Brian E.; Ingles, Sue A.; Isaacs, William; De Jager, Phillip L.; John, Esther M.; Kittles, Rick A.; Larkin, Emma; McNeill, Lorna H.; Millikan, Robert C.; Murphy, Adam; Neslund-Dudas, Christine; Nyante, Sarah; Press, Michael F.; Rodriguez-Gil, Jorge L.; Rybicki, Benjamin A.; Schwartz, Ann G.; Signorello, Lisa B.; Spitz, Margaret; Strom, Sara S.; Tucker, Margaret A.; Wiencke, John K.; Witte, John S.; Wu, Xifeng; Yamamura, Yuko; Zanetti, Krista A.; Zheng, Wei; Ziegler, Regina G.; Chanock, Stephen J.; Haiman, Christopher A.; Reich, David; Price, Alkes L.

    2014-01-01

    The extent of recent selection in admixed populations is currently an unresolved question. We scanned the genomes of 29,141 African Americans and failed to find any genome-wide-significant deviations in local ancestry, indicating no evidence of selection influencing ancestry after admixture. A recent analysis of data from 1,890 African Americans reported that there was evidence of selection in African Americans after their ancestors left Africa, both before and after admixture. Selection after admixture was reported on the basis of deviations in local ancestry, and selection before admixture was reported on the basis of allele-frequency differences between African Americans and African populations. The local-ancestry deviations reported by the previous study did not replicate in our very large sample, and we show that such deviations were expected purely by chance, given the number of hypotheses tested. We further show that the previous study’s conclusion of selection in African Americans before admixture is also subject to doubt. This is because the FST statistics they used were inflated and because true signals of unusual allele-frequency differences between African Americans and African populations would be best explained by selection that occurred in Africa prior to migration to the Americas. PMID:25242497

  14. Evolutionary change driven by metal exposure as revealed by coding SNP genome scan in wild yellow perch (Perca flavescens).

    Science.gov (United States)

    Bélanger-Deschênes, Sébastien; Couture, Patrice; Campbell, Peter G C; Bernatchez, Louis

    2013-07-01

    Pollution can drive rapid evolutionary change in wild populations. This study targets functional polymorphisms of chronically metal-contaminated wild yellow perch (Perca flavescens). A de novo transcriptome scan contrasted subsets of individuals from clean (n = 16) and contaminated (n = 16) lakes to identify 87 candidate annotated coding SNPs. Candidate genotypes and liver [metal] were obtained in 10 populations (n = 1,052) and a genome scan distinguished outliers: one nuclear (cyclin G1 gene) and two mitochondrial (cytochrome b and NADH dehydrogenase subunit 2 genes) also displaying allelic correlation to mean population [cadmium]. Whole mtDNA and 17 kb surrounding cyclin G1 were characterised through 454 sequencing thus revealing two non-synonymous substitutions involving dissimilar amino acids. Based on associated functions and inter-population differentiation, contaminated perch may have been selected for fast life cycle completion (p53 pathway) and memorization impairment mitigation (long-term potentiation pathway). In accordance with predicted evolutionary trajectory for stressed and energy deprived organisms, adapted perch would not compensate for repair mechanism inhibition, instead reallocating energy towards growth and favouring inexpensive impairment mitigation adaptations over costly detoxification. Overall, 85 years of selection could have driven rapid, potentially adaptive evolution by selecting alleles increasing perch fitness in polluted environments. PMID:23722603

  15. Genome scan for locus involved in mandibular prognathism in pedigrees from China.

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    Qin Li

    Full Text Available BACKGROUND: It is well known that genetic components play an important role in the etiology of mandibular prognathism, but few susceptibility loci have been mapped. METHODOLOGY: In order to identify linkage regions for mandibular prognathism, we analyzed two Chinese pedigrees with 6,090 genome-wide single-nucleotide polymorphism (SNP markers from Illumina Linkage-12 DNA Analysis Kit (average spacing 0.58 cM. Multipoint parametric and non-parametric (model-free linkage analyses were used for the pedigrees. PRINCIPAL FINDING: The most statistically significant linkage results were with markers on chromosome 4 (LOD=3.166 and NPL=3.65 with rs 875864, 4p16.1, 8.38 cM. Candidate genes within the 4p16.1 include EVC, EVC2. CONCLUSION: We detected a novel suggestive linkage locus for mandibular prognathism in two Chinese pedigrees, and this linkage region provides target for susceptibility gene identification, a process that will provide important insights into the molecular and cellular basis of mandibular prognathism.

  16. Univariate/multivariate genome-wide association scans using data from families and unrelated samples.

    Directory of Open Access Journals (Sweden)

    Lei Zhang

    Full Text Available As genome-wide association studies (GWAS are becoming more popular, two approaches, among others, could be considered in order to improve statistical power for identifying genes contributing subtle to moderate effects to human diseases. The first approach is to increase sample size, which could be achieved by combining both unrelated and familial subjects together. The second approach is to jointly analyze multiple correlated traits. In this study, by extending generalized estimating equations (GEEs, we propose a simple approach for performing univariate or multivariate association tests for the combined data of unrelated subjects and nuclear families. In particular, we correct for population stratification by integrating principal component analysis and transmission disequilibrium test strategies. The proposed method allows for multiple siblings as well as missing parental information. Simulation studies show that the proposed test has improved power compared to two popular methods, EIGENSTRAT and FBAT, by analyzing the combined data, while correcting for population stratification. In addition, joint analysis of bivariate traits has improved power over univariate analysis when pleiotropic effects are present. Application to the Genetic Analysis Workshop 16 (GAW16 data sets attests to the feasibility and applicability of the proposed method.

  17. Genome-wide association scan meta-analysis identifies three Loci influencing adiposity and fat distribution.

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    Cecilia M Lindgren

    2009-06-01

    Full Text Available To identify genetic loci influencing central obesity and fat distribution, we performed a meta-analysis of 16 genome-wide association studies (GWAS, N = 38,580 informative for adult waist circumference (WC and waist-hip ratio (WHR. We selected 26 SNPs for follow-up, for which the evidence of association with measures of central adiposity (WC and/or WHR was strong and disproportionate to that for overall adiposity or height. Follow-up studies in a maximum of 70,689 individuals identified two loci strongly associated with measures of central adiposity; these map near TFAP2B (WC, P = 1.9x10(-11 and MSRA (WC, P = 8.9x10(-9. A third locus, near LYPLAL1, was associated with WHR in women only (P = 2.6x10(-8. The variants near TFAP2B appear to influence central adiposity through an effect on overall obesity/fat-mass, whereas LYPLAL1 displays a strong female-only association with fat distribution. By focusing on anthropometric measures of central obesity and fat distribution, we have identified three loci implicated in the regulation of human adiposity.

  18. A genome scan for quantitative trait loci affecting the Salmonella carrier-state in the chicken

    Directory of Open Access Journals (Sweden)

    Bumstead Nat

    2005-09-01

    Full Text Available Abstract Selection for increased resistance to Salmonella colonisation and excretion could reduce the risk of foodborne Salmonella infection. In order to identify potential loci affecting resistance, differences in resistance were identified between the N and 61 inbred lines and two QTL research performed. In an F2 cross, the animals were inoculated at one week of age with Salmonella enteritidis and cloacal swabs were carried out 4 and 5 wk post inoculation (thereafter called CSW4F2 and CSW4F2 and caecal contamination (CAECF2 was assessed 1 week later. The animals from the (N × 61 × N backcross were inoculated at six weeks of age with Salmonella typhimurium and cloacal swabs were studied from wk 1 to 4 (thereafter called CSW1BC to CSW4BC. A total of 33 F2 and 46 backcross progeny were selectively genotyped for 103 and 135 microsatellite markers respectively. The analysis used least-squares-based and non-parametric interval mapping. Two genome-wise significant QTL were observed on Chromosome 1 for CSW2BC and on Chromosome 2 for CSW4F2, and four suggestive QTL for CSW5F2 on Chromosome 2, for CSW5F2 and CSW2BC on chromosome 5 and for CAECF2 on chromosome 16. These results suggest new regions of interest and the putative role of SAL1.

  19. Genome-wide linkage scan for factors of metabolic syndrome in a Chinese population

    Directory of Open Access Journals (Sweden)

    Chan Juliana CN

    2010-02-01

    Full Text Available Abstract Background Shared genetic factors may contribute to the phenotypic clustering of different components of the metabolic syndrome (MES. This study aims to identify genetic loci that contribute to individual or multiple factors related to MES. Results We studied 478 normoglycemic subjects ascertained through 163 families participating in the Hong Kong Family Diabetes Study. Factor analysis on 15 MES-related traits yielded 6 factors including adiposity factor (body mass index, waist and hip circumferences, insulin factor (fasting insulin and insulin AUC during OGTT, glucose factor (fasting glucose and glucose AUC during OGTT, TC-LDLC factor (total cholesterol and LDL-cholesterol, blood pressure factor (systolic and diastolic blood pressure and TG-HDLC factor (triglycerides and HDL-cholesterol. Genome-wide linkage analyses were performed on these factors using variance component approach. Suggestive evidence for linkage (LOD = 1.24 - 2.46 were observed for adiposity factor (chromosome 1 at 187 cM, chromosome 9 at 34 cM and chromosome 17 at 10 cM, insulin factor (chromosome 2 at 128 cM, chromosome 5 at 21 cM and chromosome 12 at 7 cM, glucose factor (chromosome 7 at 155 cM, TC-LDLC factor (chromosome 7 at 151 cM and chromosome 13 at 15 cM and TG-HDLC factor (chromosome 7 at 155 cM. Conclusions In summary, our findings suggest the presence of susceptibility loci that influence either single (chromosomes 1, 2, 5, 9, 12, 13 and 17 or multiple factors (chromosome 7 for MES in Hong Kong Chinese without diabetes.

  20. A Genome Scan to Detect Quantitative Trait Loci for Economically Important Traits in Holstein Cattle Using Two Methods and a Dense Single Nucleotide Polymorphism Map

    NARCIS (Netherlands)

    Daetwyler, H.D.; Schenkel, F.S.; Sargolzaei, M.; Robinson, J.A.B.

    2008-01-01

    Genome scans for detection of bovine quantitative trait loci (QTL) were performed via variance component linkage analysis and linkage disequilibrium single-locus regression (LDRM). Four hundred eighty-four Holstein sires, of which 427 were from 10 grandsire families, were genotyped for 9,919 single

  1. Genome-wide scan for bovine milk-fat composition. I. Quantitative trait loci for short- and medium-chain fatty acids

    NARCIS (Netherlands)

    Stoop, W.M.; Schennink, A.; Visker, M.H.P.W.; Mullaart, E.; Arendonk, van J.A.M.; Bovenhuis, H.

    2009-01-01

    A genome-wide scan was performed to identify quantitative trait loci (QTL) for short- and medium-chain fatty acids (expressed in wt/wt %). Milk samples were available from 1,905 cows from 398 commercial herds in the Netherlands, and milk-fat composition was measured by gas chromatography. DNA was av

  2. Genome-wide scan for visceral leishmaniasis in mixed-breed dogs identifies candidate genes involved in T helper cells and macrophage signaling

    Science.gov (United States)

    We conducted a genome-wide scan for visceral leishmaniasis in mixed-breed dogs from a highly endemic area in Brazil using 149,648 single nucleotide polymorphism (SNP) markers genotyped in 20 cases and 28 controls. Using a mixed model approach, we found two candidate loci on canine autosomes 1 and 2....

  3. Genome scan identifies a locus affecting gamma-globin expression in human beta-cluster YAC transgenic mice

    Energy Technology Data Exchange (ETDEWEB)

    Lin, S.D.; Cooper, P.; Fung, J.; Weier, H.U.G.; Rubin, E.M.

    2000-03-01

    Genetic factors affecting post-natal g-globin expression - a major modifier of the severity of both b-thalassemia and sickle cell anemia, have been difficult to study. This is especially so in mice, an organism lacking a globin gene with an expression pattern equivalent to that of human g-globin. To model the human b-cluster in mice, with the goal of screening for loci affecting human g-globin expression in vivo, we introduced a human b-globin cluster YAC transgene into the genome of FVB mice . The b-cluster contained a Greek hereditary persistence of fetal hemoglobin (HPFH) g allele resulting in postnatal expression of human g-globin in transgenic mice. The level of human g-globin for various F1 hybrids derived from crosses between the FVB transgenics and other inbred mouse strains was assessed. The g-globin level of the C3HeB/FVB transgenic mice was noted to be significantly elevated. To map genes affecting postnatal g-globin expression, a 20 centiMorgan (cM) genome scan of a C3HeB/F VB transgenics [prime] FVB backcross was performed, followed by high-resolution marker analysis of promising loci. From this analysis we mapped a locus within a 2.2 cM interval of mouse chromosome 1 at a LOD score of 4.2 that contributes 10.4% of variation in g-globin expression level. Combining transgenic modeling of the human b-globin gene cluster with quantitative trait analysis, we have identified and mapped a murine locus that impacts on human g-globin expression in vivo.

  4. Genome-wide association scan shows genetic variants in the FTO gene are associated with obesity-related traits.

    Directory of Open Access Journals (Sweden)

    Angelo Scuteri

    2007-07-01

    Full Text Available The obesity epidemic is responsible for a substantial economic burden in developed countries and is a major risk factor for type 2 diabetes and cardiovascular disease. The disease is the result not only of several environmental risk factors, but also of genetic predisposition. To take advantage of recent advances in gene-mapping technology, we executed a genome-wide association scan to identify genetic variants associated with obesity-related quantitative traits in the genetically isolated population of Sardinia. Initial analysis suggested that several SNPs in the FTO and PFKP genes were associated with increased BMI, hip circumference, and weight. Within the FTO gene, rs9930506 showed the strongest association with BMI (p = 8.6 x10(-7, hip circumference (p = 3.4 x 10(-8, and weight (p = 9.1 x 10(-7. In Sardinia, homozygotes for the rare "G" allele of this SNP (minor allele frequency = 0.46 were 1.3 BMI units heavier than homozygotes for the common "A" allele. Within the PFKP gene, rs6602024 showed very strong association with BMI (p = 4.9 x 10(-6. Homozygotes for the rare "A" allele of this SNP (minor allele frequency = 0.12 were 1.8 BMI units heavier than homozygotes for the common "G" allele. To replicate our findings, we genotyped these two SNPs in the GenNet study. In European Americans (N = 1,496 and in Hispanic Americans (N = 839, we replicated significant association between rs9930506 in the FTO gene and BMI (p-value for meta-analysis of European American and Hispanic American follow-up samples, p = 0.001, weight (p = 0.001, and hip circumference (p = 0.0005. We did not replicate association between rs6602024 and obesity-related traits in the GenNet sample, although we found that in European Americans, Hispanic Americans, and African Americans, homozygotes for the rare "A" allele were, on average, 1.0-3.0 BMI units heavier than homozygotes for the more common "G" allele. In summary, we have completed a whole genome-association scan for

  5. Genome-wide scan for quantitative trait loci influencing LDL size and plasma triglyceride in familial hypertriglyceridemia.

    Science.gov (United States)

    Austin, Melissa A; Edwards, Karen L; Monks, Stephanie A; Koprowicz, Kent M; Brunzell, John D; Motulsky, Arno G; Mahaney, Michael C; Hixson, James E

    2003-11-01

    Small, dense LDLs and hypertriglyceridemia, two highly correlated and genetically influenced risk factors, are known to predict for risk of coronary heart disease. The objective of this study was to perform a whole-genome scan for linkage to LDL size and triglyceride (TG) levels in 26 kindreds with familial hypertriglyceridemia (FHTG). LDL size was estimated using gradient gel electrophoresis, and genotyping was performed for 355 autosomal markers with an average heterozygosity of 76% and an average spacing of 10.2 centimorgans (cMs). Using variance components linkage analysis, one possible linkage was found for LDL size [logarithm of odds (LOD) = 2.1] on chromosome 6, peak at 140 cM distal to marker F13A1 (closest marker D6S2436). With adjustment for TG and/or HDL cholesterol, the LOD scores were reduced, but remained in exactly the same location. For TG, LOD scores of 2.56 and 2.44 were observed at two locations on chromosome 15, with peaks at 29 and 61 cM distal to marker D15S822 (closest markers D15S643 and D15S211, respectively). These peaks were retained with adjustment for LDL size and/or HDL cholesterol. These findings, if confirmed, suggest that LDL particle size and plasma TG levels could be caused by two different genetic loci in FHTG.

  6. Genome-wide SNP-based linkage scan identifies a locus on 8q24 for an age-related hearing impairment trait

    DEFF Research Database (Denmark)

    Huyghe, J.R.; Laer, L. Van; Hendrickx, J.J.;

    2008-01-01

    conducted a genome-wide association as well as a linkage scan with high-density SNP microarrays. Because of the presence of genetic population substructure, association testing was stratified after which evidence was combined by meta-analysis. No association signals reaching genome-wide significance were...... results of a cross-sectional family-based genetic study employing audiometric data. By using principal component analysis, we were able to reduce the dimensionality of this multivariate phenotype while capturing most of the variation and retaining biologically important features of the audiograms. We...... detected. Linkage analysis identified a linkage peak on 8q24.13-q24.22 for a trait correlated to audiogram shape. The signal reached genome-wide significance, as assessed by simulations. This finding represents the first locus for an ARHI trait Udgivelsesdato: 2008/9/12...

  7. Genome-wide linkage scan and association study of PARL to the expression of LHON families in Thailand.

    Science.gov (United States)

    Phasukkijwatana, Nopasak; Kunhapan, Bussaraporn; Stankovich, Jim; Chuenkongkaew, Wanicha L; Thomson, Russell; Thornton, Timothy; Bahlo, Melanie; Mushiroda, Taisei; Nakamura, Yusuke; Mahasirimongkol, Surakameth; Tun, Aung Win; Srisawat, Chatchawan; Limwongse, Chanin; Peerapittayamongkol, Chayanon; Sura, Thanyachai; Suthammarak, Wichit; Lertrit, Patcharee

    2010-07-01

    Leber hereditary optic neuropathy (LHON) is the most common mitochondrially inherited disease causing blindness, preferentially in young adult males. Most of the patients carry the G11778A mitochondrial DNA (mtDNA) mutation. However, the marked incomplete penetrance and the gender bias indicate some additional genetic and/or environmental factors to disease expression. Herein, we first conducted a genome-wide linkage scan with 400 microsatellite markers in 9 large Thai LHON G11778A pedigrees. Using an affecteds-only nonparametric linkage analysis, 4 regions on chromosomes 3, 12, 13 and 18 showed Zlr scores greater than 2 (P 2 in 10 of 16 allele sharing models tested) was then expanded to include the region 3q26.2-3q28 covering SLC7A14 (3q26.2), MFN1 (3q26.32), MRPL47 (3q26.33), MCCC1 (3q27.1), PARL (3q27.1) and OPA1 (3q28-q29). All of these candidate genes were selected from the Maestro database and had known to be localized in mitochondria. Sixty tag SNPs were genotyped in 86 cases, 211 of their relatives and 32 unrelated Thai controls, by multiplex-PCR-based Invader assay. Analyses using a powerful association testing tool that adjusts for relatedness (the M(QLS) statistic) showed the most evidence of association between two SNPs, rs3749446 and rs1402000 (located in PARL presenilins-associated rhomboid-like) and LHON expression (both P = 8.8 x 10(-5)). The mitochondrial PARL protease has been recently known to play a role with a dynamin-related OPA1 protein in preventing apoptotic events by slowing down the release of cytochrome c out of mitochondrial cristae junctions. Moreover, PARL is required to activate the intramembranous proteolyses resulting in the degradation of an accumulated pro-apoptotic protein in the outer mitochondrial membrane. Under these circumstances, variants of PARL are suggested to influence cell death by apoptosis which has long been believed to intrigue the neurodegeneration of LHON.

  8. Additive and epistatic genome-wide association for growth and ultrasound scan measures of carcass-related traits in Brahman cattle.

    Science.gov (United States)

    Ali, A A; Khatkar, M S; Kadarmideen, H N; Thomson, P C

    2015-04-01

    Genome-wide association studies are routinely used to identify genomic regions associated with traits of interest. However, this ignores an important class of genomic associations, that of epistatic interactions. A genome-wide interaction analysis between single nucleotide polymorphisms (SNPs) using highly dense markers can detect epistatic interactions, but is a difficult task due to multiple testing and computational demand. However, It is important for revealing complex trait heredity. This study considers analytical methods that detect statistical interactions between pairs of loci. We investigated a three-stage modelling procedure: (i) a model without the SNP to estimate the variance components; (ii) a model with the SNP using variance component estimates from (i), thus avoiding iteration; and (iii) using the significant SNPs from (ii) for genome-wide epistasis analysis. We fitted these three-stage models to field data for growth and ultrasound measures for subcutaneous fat thickness in Brahman cattle. The study demonstrated the usefulness of modelling epistasis in the analysis of complex traits as it revealed extra sources of genetic variation and identified potential candidate genes affecting the concentration of insulin-like growth factor-1 and ultrasound scan measure of fat depth traits. Information about epistasis can add to our understanding of the complex genetic networks that form the fundamental basis of biological systems.

  9. Additive and epistatic genome-wide association for growth and ultrasound scan measures of carcass-related traits in Brahman cattle.

    Science.gov (United States)

    Ali, A A; Khatkar, M S; Kadarmideen, H N; Thomson, P C

    2015-04-01

    Genome-wide association studies are routinely used to identify genomic regions associated with traits of interest. However, this ignores an important class of genomic associations, that of epistatic interactions. A genome-wide interaction analysis between single nucleotide polymorphisms (SNPs) using highly dense markers can detect epistatic interactions, but is a difficult task due to multiple testing and computational demand. However, It is important for revealing complex trait heredity. This study considers analytical methods that detect statistical interactions between pairs of loci. We investigated a three-stage modelling procedure: (i) a model without the SNP to estimate the variance components; (ii) a model with the SNP using variance component estimates from (i), thus avoiding iteration; and (iii) using the significant SNPs from (ii) for genome-wide epistasis analysis. We fitted these three-stage models to field data for growth and ultrasound measures for subcutaneous fat thickness in Brahman cattle. The study demonstrated the usefulness of modelling epistasis in the analysis of complex traits as it revealed extra sources of genetic variation and identified potential candidate genes affecting the concentration of insulin-like growth factor-1 and ultrasound scan measure of fat depth traits. Information about epistasis can add to our understanding of the complex genetic networks that form the fundamental basis of biological systems. PMID:25754883

  10. A genome-wide scan of selective sweeps in two broiler chicken lines divergently selected for abdominal fat content

    Directory of Open Access Journals (Sweden)

    Zhang Hui

    2012-12-01

    Full Text Available Abstract Background Genomic regions controlling abdominal fatness (AF were studied in the Northeast Agricultural University broiler line divergently selected for AF. In this study, the chicken 60KSNP chip and extended haplotype homozygosity (EHH test were used to detect genome-wide signatures of AF. Results A total of 5357 and 5593 core regions were detected in the lean and fat lines, and 51 and 57 reached a significant level (PRB1, BBS7, MAOA, MAOB, EHBP1, LRP2BP, LRP1B, MYO7A, MYO9A and PRPSAP1, were detected. These genes may be important for AF deposition in chickens. Conclusions We provide a genome-wide map of selection signatures in the chicken genome, and make a contribution to the better understanding the mechanisms of selection for AF content in chickens. The selection for low AF in commercial breeding using this information will accelerate the breeding progress.

  11. Plasmodium falciparum genome-wide scans for positive selection, recombination hot spots and resistance to antimalarial drugs

    OpenAIRE

    Mu, Jianbing; Myers, Rachel A.; Jiang, Hongying; Liu, Shengfa; Ricklefs, Stacy; Waisberg, Michael; Chotivanich, Kesinee; Wilairata, Polrat; Krudsood, Srivicha; White, Nicholas J; Udomsangpetch, Rachanee; Cui, Liwang; Ho, May; Ou, Fengzheng; Li, Haibo

    2010-01-01

    Antimalarial drugs impose strong pressure on Plasmodium falciparum parasites and leave signatures of selection in the parasite genome 1,2. Search for signals of selection may lead to genes encoding drug or immune targets 3. The lack of high-throughput genotyping methods, inadequate knowledge of parasite population history, and time-consuming adaptations of parasites to in vitro culture have hampered genome-wide association studies (GWAS) of parasite traits. Here we report genotyping of DNA fr...

  12. Genomic scan of selective sweeps in thin and fat tail sheep breeds for identifying of candidate regions associated with fat deposition

    Directory of Open Access Journals (Sweden)

    Moradi Mohammad Hossein

    2012-02-01

    Full Text Available Abstract Background Identification of genomic regions that have been targets of selection for phenotypic traits is one of the most important and challenging areas of research in animal genetics. However, currently there are relatively few genomic regions identified that have been subject to positive selection. In this study, a genome-wide scan using ~50,000 Single Nucleotide Polymorphisms (SNPs was performed in an attempt to identify genomic regions associated with fat deposition in fat-tail breeds. This trait and its modification are very important in those countries grazing these breeds. Results Two independent experiments using either Iranian or Ovine HapMap genotyping data contrasted thin and fat tail breeds. Population differentiation using FST in Iranian thin and fat tail breeds revealed seven genomic regions. Almost all of these regions overlapped with QTLs that had previously been identified as affecting fat and carcass yield traits in beef and dairy cattle. Study of selection sweep signatures using FST in thin and fat tail breeds sampled from the Ovine HapMap project confirmed three of these regions located on Chromosomes 5, 7 and X. We found increased homozygosity in these regions in favour of fat tail breeds on chromosome 5 and X and in favour of thin tail breeds on chromosome 7. Conclusions In this study, we were able to identify three novel regions associated with fat deposition in thin and fat tail sheep breeds. Two of these were associated with an increase of homozygosity in the fat tail breeds which would be consistent with selection for mutations affecting fat tail size several thousand years after domestication.

  13. A genome scan for quantitative trait loci affecting growth-related traits in an F1 family of Asian seabass (Lates calcarifer

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    Yue Gen

    2006-10-01

    Full Text Available Abstract Background Body weight and length are economically important traits in foodfish species influenced by quantitative trait loci (QTL and environmental factors. It is usually difficult to dissect the genetic and environmental effects. Asian seabass (Lates calcarifer is an important marine foodfish species with a compact genome (~700 Mb. The recent construction of a first generation linkage map of Asian seabass with 240 microsatellites provides a good opportunity to determine the number and position of QTL, and the magnitude of QTL effects with a genome scan. Results We conducted a genome scan for QTL affecting body weight, standard length and condition factors in an F1 family containing 380 full-sib individuals from a breeding stock by using 97 microsatellites evenly covering 24 chromosomes. Interval mapping and multiple QTL model mapping detected five significant and 27 suggestive QTL on ten linkage groups (LGs. Among the five significant QTL detected, three (qBW2-a, qTL2-a and qSL2-a controlling body weight, total and standard length respectively, were mapped on the same region near Lca287 on LG2, and explained 28.8, 58.9 and 59.7% of the phenotypic variance. The other two QTL affecting body weight, qBW2-b and qBW3, were located on LG2 and 3, and accounted for 6.4 and 8.8% of the phenotypic variance. Suggestive QTL associated with condition factors are located on six different LGs. Conclusion This study presents the first example of QTL detection for growth-related traits in an F1 family of a marine foodfish species. The results presented here will enable further fine-mapping of these QTL for marker-assisted selection of the Asian seabass, eventually identifying individual genes responsible for growth-related traits.

  14. Genome-wide linkage scan for contraction velocity characteristics of knee musculature in the Leuven Genes for Muscular Strength Study

    OpenAIRE

    De Mars, Gunther; Windelinckx, An; Huygens, Wim; Peeters, Maarten W.; Beunen, Gaston P; Aerssens, Jeroen; Vlietinck, Robert; Thomis, Martine A. I.

    2008-01-01

    The torque-velocity relationship is known to be affected by ageing, decreasing its protective role in the prevention of falls. Interindividual variability in this torque-velocity relationship is partly determined by genetic factors (h2: 44–67%). As a first attempt, this genome-wide linkage study aimed to identify chromosomal regions linked to the torque-velocity relationship of the knee flexors and extensors. A selection of 283 informative male siblings (17–36 yr), belonging to 105 families, ...

  15. AFLP genome scan to detect genetic structure and candidate loci under selection for local adaptation of the invasive weed Mikania micrantha.

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    Ting Wang

    Full Text Available Why some species become successful invaders is an important issue in invasive biology. However, limited genomic resources make it very difficult for identifying candidate genes involved in invasiveness. Mikania micrantha H.B.K. (Asteraceae, one of the world's most invasive weeds, has adapted rapidly in response to novel environments since its introduction to southern China. In its genome, we expect to find outlier loci under selection for local adaptation, critical to dissecting the molecular mechanisms of invasiveness. An explorative amplified fragment length polymorphism (AFLP genome scan was used to detect candidate loci under selection in 28 M. micrantha populations across its entire introduced range in southern China. We also estimated population genetic parameters, bottleneck signatures, and linkage disequilibrium. In binary characters, such as presence or absence of AFLP bands, if all four character combinations are present, it is referred to as a character incompatibility. Since character incompatibility is deemed to be rare in populations with extensive asexual reproduction, a character incompatibility analysis was also performed in order to infer the predominant mating system in the introduced M. micrantha populations. Out of 483 AFLP loci examined using stringent significance criteria, 14 highly credible outlier loci were identified by Dfdist and Bayescan. Moreover, remarkable genetic variation, multiple introductions, substantial bottlenecks and character compatibility were found to occur in M. micrantha. Thus local adaptation at the genome level indeed exists in M. micrantha, and may represent a major evolutionary mechanism of successful invasion. Interactions between genetic diversity, multiple introductions, and reproductive modes contribute to increase the capacity of adaptive evolution.

  16. Whole-genome scan to detect quantitative trait loci associated with milk protein composition in 3 French dairy cattle breeds.

    Science.gov (United States)

    Sanchez, M P; Govignon-Gion, A; Ferrand, M; Gelé, M; Pourchet, D; Amigues, Y; Fritz, S; Boussaha, M; Capitan, A; Rocha, D; Miranda, G; Martin, P; Brochard, M; Boichard, D

    2016-10-01

    In the context of the PhénoFinLait project, a genome-wide analysis was performed to detect quantitative trait loci (QTL) that affect milk protein composition estimated using mid-infrared spectrometry in the Montbéliarde (MO), Normande (NO), and Holstein (HO) French dairy cattle breeds. The 6 main milk proteins (α-lactalbumin, β-lactoglobulin, and αS1-, αS2-, β-, and κ-caseins) expressed as grams per 100g of milk (% of milk) or as grams per 100g of protein (% of protein) were estimated in 848,068 test-day milk samples from 156,660 cows. Genotyping was performed for 2,773 MO, 2,673 NO, and 2,208 HO cows using the Illumina BovineSNP50 BeadChip (Illumina Inc., San Diego, CA). Individual test-day records were adjusted for environmental effects and then averaged per cow to define the phenotypes analyzed. Quantitative trait loci detection was performed within each breed using a linkage disequilibrium and linkage analysis approach. A total of 39 genomic regions distributed on 20 of the 29 Bos taurus autosomes (BTA) were significantly associated with milk protein composition at a genome-wide level of significance in at least 1 of the 3 breeds. The 9 most significant QTL were located on BTA2 (133 Mbp), BTA6 (38, 47, and 87 Mbp), BTA11 (103 Mbp), BTA14 (1.8 Mbp), BTA20 (32 and 58 Mbp), and BTA29 (8 Mbp). The BTA6 (87 Mbp), BTA11, and BTA20 (58 Mbp) QTL were found in all 3 breeds, and they had highly significant effects on κ-casein, β-lactoglobulin, and α-lactalbumin, expressed as a percentage of protein, respectively. Each of these QTL explained between 13% (BTA14) and 51% (BTA11) of the genetic variance of the trait. Many other QTL regions were also identified in at least one breed. They were located on 14 additional chromosomes (1, 3, 4, 5, 7, 15, 17, 19, 21, 22, 24, 25, 26, and 27), and they explained 2 to 8% of the genetic variance of 1 or more protein composition traits. Concordance analyses, performed between QTL status and sequence-derived polymorphisms from

  17. Evolution of the pygmy phenotype: evidence of positive selection fro genome-wide scans in African, Asian, and Melanesian pygmies.

    Science.gov (United States)

    Migliano, Andrea Bamberg; Romero, Irene Gallego; Metspalu, Mait; Leavesley, Matthew; Pagani, Luca; Antao, Tiago; Huang, Da-Wei; Sherman, Brad T; Siddle, Katharine; Scholes, Clarissa; Hudjashov, Georgi; Kaitokai, Elton; Babalu, Avis; Belatti, Maggie; Cagan, Alex; Hopkinshaw, Byrony; Shaw, Colin; Nelis, Mari; Metspalu, Ene; Mägi, Reedik; Lempicki, Richard A; Villems, Richard; Lahr, Marta Mirazon; Kivisild, Toomas

    2013-01-01

    Human pygmy populations inhabit different regions of the world, from Africa to Melanesia. In Asia, short-statured populations are often referred to as "negritos." Their short stature has been interpreted as a consequence of thermoregulatory, nutritional, and/or locomotory adaptations to life in tropical forests. A more recent hypothesis proposes that their stature is the outcome of a life history trade-off in high-mortality environments, where early reproduction is favored and, consequently, early sexual maturation and early growth cessation have coevolved. Some serological evidence of deficiencies in the growth hormone/insulin-like growth factor axis have been previously associated with pygmies' short stature. Using genome-wide single-nucleotide polymorphism genotype data, we first tested whether different negrito groups living in the Philippines and Papua New Guinea are closely related and then investigated genomic signals of recent positive selection in African, Asian, and Papuan pygmy populations. We found that negritos in the Philippines and Papua New Guinea are genetically more similar to their nonpygmy neighbors than to one another and have experienced positive selection at different genes. These results indicate that geographically distant pygmy groups are likely to have evolved their short stature independently. We also found that selection on common height variants is unlikely to explain their short stature and that different genes associated with growth, thyroid function, and sexual development are under selection in different pygmy groups.

  18. Single-Copy Nuclear Gene Primers for Streptanthus and Other Brassicaceae from Genomic Scans, Published Data, and ESTs

    Directory of Open Access Journals (Sweden)

    N. Ivalú Cacho

    2013-07-01

    Full Text Available Premise of the study: We report 11 primer sets for nine single-copy nuclear genes in Streptanthus and other Thelypodieae (Brassicaceae and their utility at tribal-level and species-level phylogenetics in this poorly resolved group. Methods and Results: We selected regions based on a cross-referenced matrix of previous studies and public Brassica expressed sequence tags. To design primers, we used alignments of low-depth-coverage Illumina sequencing of genomic DNA for two species of Brassica mapped onto Arabidopsis thaliana. We report several primer combinations for five regions that consistently amplified a single band and yielded high-quality sequences for at least 70% of the species assayed, and for four additional regions whose utility might be clade specific. Conclusions: Our primers will be useful in improving resolution at shallow depths across the Thelypodieae, and likely in other Brassicaceae.

  19. Sex-specific variability and a 'cage effect' independently mask a neuropathic pain quantitative trait locus detected in a whole genome scan.

    Science.gov (United States)

    Devor, Marshall; Gilad, Amit; Arbilly, Michal; Nissenbaum, Jonathan; Yakir, Benjamin; Raber, Pnina; Minert, Anne; Pisanté, Anne; Darvasi, Ariel

    2007-08-01

    Sex and environment may dramatically affect genetic studies, and thus should be carefully considered. Beginning with two inbred mouse strains with contrasting phenotype in the neuroma model of neuropathic pain (autotomy), we established a backcross population on which we conducted a genome-wide scan. The backcross population was partially maintained in small social groups and partially in isolation. The genome scan detected one previously reported quantitative trait locus (QTL) on chromosome 15 (pain1), but no additional QTLs were found. Interestingly, group caging introduced phenotypic noise large enough to completely mask the genetic effect of the chromosome 15 QTL. The reason appears to be that group-caging animals from the low-autotomy strain together with animals from the high-autotomy strain dramatically increases autotomy in the otherwise low-autotomy mice (males or females). The converse, suppression of pain behaviour in the high-autotomy strain when caged with the low-autotomy strain was also observed, but only in females. Even in isolated mice, the genetic effect of the chromosome 15 QTL was significant only in females. To determine why, we evaluated autotomy levels of females in 12 different inbred stains of mice and compared them to previously reported levels for males. Strikingly larger environmental variation was observed in males than in females for this pain phenotype. The high baseline variance in males can explain the difficulty in detecting the genetic effect, which was readily seen in females. Our study emphasizes the importance of sex and environment in the genetic analysis of pain.

  20. Genome-wide linkage scan for contraction velocity characteristics of knee musculature in the Leuven Genes for Muscular Strength Study.

    Science.gov (United States)

    De Mars, Gunther; Windelinckx, An; Huygens, Wim; Peeters, Maarten W; Beunen, Gaston P; Aerssens, Jeroen; Vlietinck, Robert; Thomis, Martine A I

    2008-09-17

    The torque-velocity relationship is known to be affected by ageing, decreasing its protective role in the prevention of falls. Interindividual variability in this torque-velocity relationship is partly determined by genetic factors (h(2): 44-67%). As a first attempt, this genome-wide linkage study aimed to identify chromosomal regions linked to the torque-velocity relationship of the knee flexors and extensors. A selection of 283 informative male siblings (17-36 yr), belonging to 105 families, was used to conduct a genome-wide SNP-based (Illumina Linkage IVb panel) multipoint linkage analysis for the torque-velocity relationship of the knee flexors and extensors. The strongest evidence for linkage was found at 15q23 for the torque-velocity slope of the knee extensors (TVSE). Other interesting linkage regions with LOD scores >2 were found at 7p12.3 [logarithm of the odds ratio (LOD) = 2.03, P = 0.0011] for the torque-velocity ratio of the knee flexors (TVRF), at 2q14.3 (LOD = 2.25, P = 0.0006) for TVSE, and at 4p14 and 18q23 for the torque-velocity ratio of the knee extensors TVRE (LOD = 2.23 and 2.08; P = 0.0007 and 0.001, respectively). We conclude that many small contributing genes are involved in causing variation in the torque-velocity relationship of the knee flexor and extensor muscles. Several earlier reported candidate genes for muscle strength and muscle mass and new candidates are harbored within or in close vicinity of the linkage regions reported in the present study. PMID:18682575

  1. Detecting loci under recent positive selection in dairy and beef cattle by combining different genome-wide scan methods.

    Directory of Open Access Journals (Sweden)

    Yuri Tani Utsunomiya

    Full Text Available As the methodologies available for the detection of positive selection from genomic data vary in terms of assumptions and execution, weak correlations are expected among them. However, if there is any given signal that is consistently supported across different methodologies, it is strong evidence that the locus has been under past selection. In this paper, a straightforward frequentist approach based on the Stouffer Method to combine P-values across different tests for evidence of recent positive selection in common variations, as well as strategies for extracting biological information from the detected signals, were described and applied to high density single nucleotide polymorphism (SNP data generated from dairy and beef cattle (taurine and indicine. The ancestral Bovinae allele state of over 440,000 SNP is also reported. Using this combination of methods, highly significant (P<3.17×10(-7 population-specific sweeps pointing out to candidate genes and pathways that may be involved in beef and dairy production were identified. The most significant signal was found in the Cornichon homolog 3 gene (CNIH3 in Brown Swiss (P = 3.82×10(-12, and may be involved in the regulation of pre-ovulatory luteinizing hormone surge. Other putative pathways under selection are the glucolysis/gluconeogenesis, transcription machinery and chemokine/cytokine activity in Angus; calpain-calpastatin system and ribosome biogenesis in Brown Swiss; and gangliosides deposition in milk fat globules in Gyr. The composite method, combined with the strategies applied to retrieve functional information, may be a useful tool for surveying genome-wide selective sweeps and providing insights in to the source of selection.

  2. A genome-wide association scan implicates DCHS2, RUNX2, GLI3, PAX1 and EDAR in human facial variation.

    Science.gov (United States)

    Adhikari, Kaustubh; Fuentes-Guajardo, Macarena; Quinto-Sánchez, Mirsha; Mendoza-Revilla, Javier; Camilo Chacón-Duque, Juan; Acuña-Alonzo, Victor; Jaramillo, Claudia; Arias, William; Lozano, Rodrigo Barquera; Pérez, Gastón Macín; Gómez-Valdés, Jorge; Villamil-Ramírez, Hugo; Hunemeier, Tábita; Ramallo, Virginia; Silva de Cerqueira, Caio C; Hurtado, Malena; Villegas, Valeria; Granja, Vanessa; Gallo, Carla; Poletti, Giovanni; Schuler-Faccini, Lavinia; Salzano, Francisco M; Bortolini, Maria-Cátira; Canizales-Quinteros, Samuel; Cheeseman, Michael; Rosique, Javier; Bedoya, Gabriel; Rothhammer, Francisco; Headon, Denis; González-José, Rolando; Balding, David; Ruiz-Linares, Andrés

    2016-01-01

    We report a genome-wide association scan for facial features in ∼6,000 Latin Americans. We evaluated 14 traits on an ordinal scale and found significant association (P values<5 × 10(-8)) at single-nucleotide polymorphisms (SNPs) in four genomic regions for three nose-related traits: columella inclination (4q31), nose bridge breadth (6p21) and nose wing breadth (7p13 and 20p11). In a subsample of ∼3,000 individuals we obtained quantitative traits related to 9 of the ordinal phenotypes and, also, a measure of nasion position. Quantitative analyses confirmed the ordinal-based associations, identified SNPs in 2q12 associated to chin protrusion, and replicated the reported association of nasion position with SNPs in PAX3. Strongest association in 2q12, 4q31, 6p21 and 7p13 was observed for SNPs in the EDAR, DCHS2, RUNX2 and GLI3 genes, respectively. Associated SNPs in 20p11 extend to PAX1. Consistent with the effect of EDAR on chin protrusion, we documented alterations of mandible length in mice with modified Edar funtion. PMID:27193062

  3. A genome-wide association scan implicates DCHS2, RUNX2, GLI3, PAX1 and EDAR in human facial variation

    Science.gov (United States)

    Adhikari, Kaustubh; Fuentes-Guajardo, Macarena; Quinto-Sánchez, Mirsha; Mendoza-Revilla, Javier; Camilo Chacón-Duque, Juan; Acuña-Alonzo, Victor; Jaramillo, Claudia; Arias, William; Lozano, Rodrigo Barquera; Pérez, Gastón Macín; Gómez-Valdés, Jorge; Villamil-Ramírez, Hugo; Hunemeier, Tábita; Ramallo, Virginia; Silva de Cerqueira, Caio C.; Hurtado, Malena; Villegas, Valeria; Granja, Vanessa; Gallo, Carla; Poletti, Giovanni; Schuler-Faccini, Lavinia; Salzano, Francisco M.; Bortolini, Maria- Cátira; Canizales-Quinteros, Samuel; Cheeseman, Michael; Rosique, Javier; Bedoya, Gabriel; Rothhammer, Francisco; Headon, Denis; González-José, Rolando; Balding, David; Ruiz-Linares, Andrés

    2016-01-01

    We report a genome-wide association scan for facial features in ∼6,000 Latin Americans. We evaluated 14 traits on an ordinal scale and found significant association (P values<5 × 10−8) at single-nucleotide polymorphisms (SNPs) in four genomic regions for three nose-related traits: columella inclination (4q31), nose bridge breadth (6p21) and nose wing breadth (7p13 and 20p11). In a subsample of ∼3,000 individuals we obtained quantitative traits related to 9 of the ordinal phenotypes and, also, a measure of nasion position. Quantitative analyses confirmed the ordinal-based associations, identified SNPs in 2q12 associated to chin protrusion, and replicated the reported association of nasion position with SNPs in PAX3. Strongest association in 2q12, 4q31, 6p21 and 7p13 was observed for SNPs in the EDAR, DCHS2, RUNX2 and GLI3 genes, respectively. Associated SNPs in 20p11 extend to PAX1. Consistent with the effect of EDAR on chin protrusion, we documented alterations of mandible length in mice with modified Edar funtion. PMID:27193062

  4. A genome-wide scan study identifies a single nucleotide substitution in ASIP associated with white versus non-white coat-colour variation in sheep (Ovis aries).

    Science.gov (United States)

    Li, M-H; Tiirikka, T; Kantanen, J

    2014-02-01

    In sheep, coat colour (and pattern) is one of the important traits of great biological, economic and social importance. However, the genetics of sheep coat colour has not yet been fully clarified. We conducted a genome-wide association study of sheep coat colours by genotyping 47 303 single-nucleotide polymorphisms (SNPs) in the Finnsheep population in Finland. We identified 35 SNPs associated with all the coat colours studied, which cover genomic regions encompassing three known pigmentation genes (TYRP1, ASIP and MITF) in sheep. Eighteen of these associations were confirmed in further tests between white versus non-white individuals, but none of the 35 associations were significant in the analysis of only non-white colours. Across the tests, the s66432.1 in ASIP showed significant association (P=4.2 × 10(-11) for all the colours; P=2.3 × 10(-11) for white versus non-white colours) with the variation in coat colours and strong linkage disequilibrium with other significant variants surrounding the ASIP gene. The signals detected around the ASIP gene were explained by differences in white versus non-white alleles. Further, a genome scan for selection for white coat pigmentation identified a strong and striking selection signal spanning ASIP. Our study identified the main candidate gene for the coat colour variation between white and non-white as ASIP, an autosomal gene that has been directly implicated in the pathway regulating melanogenesis. Together with ASIP, the two other newly identified genes (TYRP1 and MITF) in the Finnsheep, bordering associated SNPs, represent a new resource for enriching sheep coat-colour genetics and breeding.

  5. Genome-wide scan on total serum IgE levels identifies FCER1A as novel susceptibility locus.

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    Stephan Weidinger

    2008-08-01

    Full Text Available High levels of serum IgE are considered markers of parasite and helminth exposure. In addition, they are associated with allergic disorders, play a key role in anti-tumoral defence, and are crucial mediators of autoimmune diseases. Total IgE is a strongly heritable trait. In a genome-wide association study (GWAS, we tested 353,569 SNPs for association with serum IgE levels in 1,530 individuals from the population-based KORA S3/F3 study. Replication was performed in four independent population-based study samples (total n = 9,769 individuals. Functional variants in the gene encoding the alpha chain of the high affinity receptor for IgE (FCER1A on chromosome 1q23 (rs2251746 and rs2427837 were strongly associated with total IgE levels in all cohorts with P values of 1.85 x 10(-20 and 7.08 x 10(-19 in a combined analysis, and in a post-hoc analysis showed additional associations with allergic sensitization (P = 7.78 x 10(-4 and P = 1.95 x 10(-3. The "top" SNP significantly influenced the cell surface expression of FCER1A on basophils, and genome-wide expression profiles indicated an interesting novel regulatory mechanism of FCER1A expression via GATA-2. Polymorphisms within the RAD50 gene on chromosome 5q31 were consistently associated with IgE levels (P values 6.28 x 10(-7-4.46 x 10(-8 and increased the risk for atopic eczema and asthma. Furthermore, STAT6 was confirmed as susceptibility locus modulating IgE levels. In this first GWAS on total IgE FCER1A was identified and replicated as new susceptibility locus at which common genetic variation influences serum IgE levels. In addition, variants within the RAD50 gene might represent additional factors within cytokine gene cluster on chromosome 5q31, emphasizing the need for further investigations in this intriguing region. Our data furthermore confirm association of STAT6 variation with serum IgE levels.

  6. Meta-analysis of genome-wide scans for human adult stature identifies novel Loci and associations with measures of skeletal frame size.

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    Nicole Soranzo

    2009-04-01

    Full Text Available Recent genome-wide (GW scans have identified several independent loci affecting human stature, but their contribution through the different skeletal components of height is still poorly understood. We carried out a genome-wide scan in 12,611 participants, followed by replication in an additional 7,187 individuals, and identified 17 genomic regions with GW-significant association with height. Of these, two are entirely novel (rs11809207 in CATSPER4, combined P-value = 6.1x10(-8 and rs910316 in TMED10, P-value = 1.4x10(-7 and two had previously been described with weak statistical support (rs10472828 in NPR3, P-value = 3x10(-7 and rs849141 in JAZF1, P-value = 3.2x10(-11. One locus (rs1182188 at GNA12 identifies the first height eQTL. We also assessed the contribution of height loci to the upper- (trunk and lower-body (hip axis and femur skeletal components of height. We find evidence for several loci associated with trunk length (including rs6570507 in GPR126, P-value = 4x10(-5 and rs6817306 in LCORL, P-value = 4x10(-4, hip axis length (including rs6830062 at LCORL, P-value = 4.8x10(-4 and rs4911494 at UQCC, P-value = 1.9x10(-4, and femur length (including rs710841 at PRKG2, P-value = 2.4x10(-5 and rs10946808 at HIST1H1D, P-value = 6.4x10(-6. Finally, we used conditional analyses to explore a possible differential contribution of the height loci to these different skeletal size measurements. In addition to validating four novel loci controlling adult stature, our study represents the first effort to assess the contribution of genetic loci to three skeletal components of height. Further statistical tests in larger numbers of individuals will be required to verify if the height loci affect height preferentially through these subcomponents of height.

  7. Non-additive genome-wide association scan reveals a new gene associated with habitual coffee consumption.

    Science.gov (United States)

    Pirastu, Nicola; Kooyman, Maarten; Robino, Antonietta; van der Spek, Ashley; Navarini, Luciano; Amin, Najaf; Karssen, Lennart C; Van Duijn, Cornelia M; Gasparini, Paolo

    2016-01-01

    Coffee is one of the most consumed beverages world-wide and one of the primary sources of caffeine intake. Given its important health and economic impact, the underlying genetics of its consumption has been widely studied. Despite these efforts, much has still to be uncovered. In particular, the use of non-additive genetic models may uncover new information about the genetic variants driving coffee consumption. We have conducted a genome-wide association study in two Italian populations using additive, recessive and dominant models for analysis. This has uncovered a significant association in the PDSS2 gene under the recessive model that has been replicated in an independent cohort from the Netherlands (ERF). The identified gene has been shown to negatively regulate the expression of the caffeine metabolism genes and can thus be linked to coffee consumption. Further bioinformatics analysis of eQTL and histone marks from Roadmap data has evidenced a possible role of the identified SNPs in regulating PDSS2 gene expression through enhancers present in its intron. Our results highlight a novel gene which regulates coffee consumption by regulating the expression of the genes linked to caffeine metabolism. Further studies will be needed to clarify the biological mechanism which links PDSS2 and coffee consumption. PMID:27561104

  8. Genome-wide scan for serum ghrelin detects linkage on chromosome 1p36 in Hispanic children: results from the Viva La Familia study.

    Science.gov (United States)

    Voruganti, V Saroja; Göring, Harald H H; Diego, Vincent P; Cai, Guowen; Mehta, Nitesh R; Haack, Karin; Cole, Shelley A; Butte, Nancy F; Comuzzie, Anthony G

    2007-10-01

    This study was conducted to investigate genetic influence on serum ghrelin and its relationship with adiposity-related phenotypes in Hispanic children (n=1030) from the Viva La Familia study (VFS). Anthropometric measurements and levels of serum ghrelin were estimated and genetic analyses conducted according to standard procedures. Mean age, body mass index (BMI), and serum ghrelin were 11+/-0.13 y, 25+/-0.24 kg/m2 and 38+/-0.5 ng/mL, respectively. Significant heritabilities (p<0.001) were obtained for BMI, weight, fat mass, percent fat, waist circumference, waist-to-height ratio, and ghrelin. Bivariate analyses of ghrelin with adiposity traits showed significant negative genetic correlations (p<0.0001) with weight, BMI, fat mass, percent fat, waist circumference, and waist-to-height ratio. A genome-wide scan for ghrelin detected significant linkage on chromosome 1p36.2 between STR markers D1S2697 and D1S199 (LOD=3.2). The same region on chromosome 1 was the site of linkage for insulin (LOD=3.3), insulinlike growth factor binding protein 1 (IGFBP1) (LOD=3.4), homeostatic model assessment method (HOMA) (LOD=2.9), and C-peptide (LOD=2.0). Several family-based studies have reported linkages for obesity-related phenotypes in the region of 1p36. These results indicate the importance of this region in relation to adiposity in children from the VFS.

  9. A genome-wide admixture scan identifies MYH9 as a candidate locus associated with non-diabetic end stage renal disease in African Americans

    Science.gov (United States)

    Linda Kao, WH; Klag, Michael J; Meoni, Lucy A; Reich, David; Berthier-Schaad, Yvette; Li, Man; Coresh, Josef; Patterson, Nick; Tandon, Arti; Powe, Neil R; Fink, Nancy E; Sadler, John H; Weir, Matthew R; Abboud, Hanna E; Adler, Sharon; Divers, Jasmin; Iyengar, Sudha K; Freedman, Barry I; Kimmel, Paul L; Knowler, William C; Kohn, Orly F; Kramp, Kristopher; Leehey, David J; Nicholas, Susanne; Pahl, Madeleine; Schelling, Jeffrey R; Sedor, John R; Thornley-Brown, Denyse; Winkler, Cheryl A; Smith, Michael W.; Parekh, Rulan S.

    2008-01-01

    End stage renal disease (ESRD) has a four times higher incidence in African Americans compared to European Americans. This led to the hypothesis that susceptibility alleles for ESRD have a higher frequency in West African than European gene pool. We performed a genome-wide admixture scan in 1,372 ESRD cases and 806 controls and demonstrated a highly significant association between excess African ancestry and non-diabetic ESRD (LOD 5.70) but not diabetic ESRD (LOD 0.47) on chromosome 22q12. Each copy of the European ancestral allele conferred a relative risk of 0.50 (95% credible interval 0.39 – 0.63) compared to African ancestry. Multiple common SNPs (allele frequency ranging from 0.2 to 0.6) in the gene that encodes non-muscle myosin heavy chain type II isoform A (MYH9) were associated with 2-4 times greater risk of non-diabetic ESRD and accounted for a large proportion of the excess risk of ESRD observed in African compared to European Americans. PMID:18794854

  10. When genetic distance matters: Measuring genetic differentiation at microsatellite loci in whole-genome scans of recent and incipient mosquito species

    Science.gov (United States)

    Wang, Rui; Zheng, Liangbiao; Touré, Yeya T.; Dandekar, Thomas; Kafatos, Fotis C.

    2001-01-01

    Genetic distance measurements are an important tool to differentiate field populations of disease vectors such as the mosquito vectors of malaria. Here, we have measured the genetic differentiation between Anopheles arabiensis and Anopheles gambiae, as well as between proposed emerging species of the latter taxon, in whole genome scans by using 23–25 microsatellite loci. In doing so, we have reviewed and evaluated the advantages and disadvantages of standard parameters of genetic distance, FST, RST, (δμ)2, and D. Further, we have introduced new parameters, D′ and DK, which have well defined statistical significance tests and complement the standard parameters to advantage. D′ is a modification of D, whereas DK is a measure of covariance based on Pearson's correlation coefficient. We find that A. gambiae and A. arabiensis are closely related at most autosomal loci but appear to be distantly related on the basis of X-linked chromosomal loci within the chromosomal Xag inversion. The M and S molecular forms of A. gambiae are practically indistinguishable but differ significantly at two microsatellite loci from the proximal region of the X, outside the Xag inversion. At one of these loci, both M and S molecular forms differ significantly from A. arabiensis, but remarkably, at the other locus, A. arabiensis is indistinguishable from the M molecular form of A. gambiae. These data support the recent proposal of genetically differentiated M and S molecular forms of A. gambiae. PMID:11553812

  11. Combined effect of tobacco smoking and alcohol drinking in the risk of head and neck cancers: a re-analysis of case-control studies using bi-dimensional spline models.

    Science.gov (United States)

    Dal Maso, Luigino; Torelli, Nicola; Biancotto, Elisa; Di Maso, Matteo; Gini, Andrea; Franchin, Gianni; Levi, Fabio; La Vecchia, Carlo; Serraino, Diego; Polesel, Jerry

    2016-04-01

    The synergistic effect of tobacco smoking and alcohol consumption on the risk of head and neck cancers has been mainly investigated as a cross-product of categorical exposure, thus leading to loss of information. We propose a bi-dimensional logistic spline model to investigate the interacting dose-response relationship of two continuous exposures (i.e., ethanol intake and tobacco smoking) on the risk of head and neck cancers, representing results through three-dimensional graphs. This model was applied to a pool of hospital-based case-control studies on head and neck cancers conducted in Italy and in the Vaud Swiss Canton between 1982 and 2000, including 1569 cases and 3147 controls. Among never drinkers and for all levels of ethanol intake, the risk of head and neck cancers steeply increased with increasing smoking intensity, starting from 1 cigarette/day. The risk associated to ethanol intake increased with incrementing exposure among smokers, and a threshold effect at approximately 50 g/day emerged among never smokers. Compared to abstainers from both tobacco and alcohol consumption, the combined exposure to ethanol and/or cigarettes led to a steep increase of cancer risk up to a 35-fold higher risk (95 % confidence interval 27.30-43.61) among people consuming 84 g/day of ethanol and 10 cigarettes/day. The highest risk was observed at the highest levels of alcohol and tobacco consumption. Our findings confirmed a combined effect of tobacco smoking and alcohol drinking on head and neck cancers risk, providing evidence that bi-dimensional spline models could be a feasible and flexible method to explore the pattern of risks associated to two interacting continuous-exposure variables.

  12. Combined effect of tobacco smoking and alcohol drinking in the risk of head and neck cancers: a re-analysis of case-control studies using bi-dimensional spline models.

    Science.gov (United States)

    Dal Maso, Luigino; Torelli, Nicola; Biancotto, Elisa; Di Maso, Matteo; Gini, Andrea; Franchin, Gianni; Levi, Fabio; La Vecchia, Carlo; Serraino, Diego; Polesel, Jerry

    2016-04-01

    The synergistic effect of tobacco smoking and alcohol consumption on the risk of head and neck cancers has been mainly investigated as a cross-product of categorical exposure, thus leading to loss of information. We propose a bi-dimensional logistic spline model to investigate the interacting dose-response relationship of two continuous exposures (i.e., ethanol intake and tobacco smoking) on the risk of head and neck cancers, representing results through three-dimensional graphs. This model was applied to a pool of hospital-based case-control studies on head and neck cancers conducted in Italy and in the Vaud Swiss Canton between 1982 and 2000, including 1569 cases and 3147 controls. Among never drinkers and for all levels of ethanol intake, the risk of head and neck cancers steeply increased with increasing smoking intensity, starting from 1 cigarette/day. The risk associated to ethanol intake increased with incrementing exposure among smokers, and a threshold effect at approximately 50 g/day emerged among never smokers. Compared to abstainers from both tobacco and alcohol consumption, the combined exposure to ethanol and/or cigarettes led to a steep increase of cancer risk up to a 35-fold higher risk (95 % confidence interval 27.30-43.61) among people consuming 84 g/day of ethanol and 10 cigarettes/day. The highest risk was observed at the highest levels of alcohol and tobacco consumption. Our findings confirmed a combined effect of tobacco smoking and alcohol drinking on head and neck cancers risk, providing evidence that bi-dimensional spline models could be a feasible and flexible method to explore the pattern of risks associated to two interacting continuous-exposure variables. PMID:25855002

  13. A genome-wide association scan on the levels of markers of inflammation in Sardinians reveals associations that underpin its complex regulation.

    Directory of Open Access Journals (Sweden)

    Silvia Naitza

    2012-01-01

    Full Text Available Identifying the genes that influence levels of pro-inflammatory molecules can help to elucidate the mechanisms underlying this process. We first conducted a two-stage genome-wide association scan (GWAS for the key inflammatory biomarkers Interleukin-6 (IL-6, the general measure of inflammation erythrocyte sedimentation rate (ESR, monocyte chemotactic protein-1 (MCP-1, and high-sensitivity C-reactive protein (hsCRP in a large cohort of individuals from the founder population of Sardinia. By analysing 731,213 autosomal or X chromosome SNPs and an additional ∼1.9 million imputed variants in 4,694 individuals, we identified several SNPs associated with the selected quantitative trait loci (QTLs and replicated all the top signals in an independent sample of 1,392 individuals from the same population. Next, to increase power to detect and resolve associations, we further genotyped the whole cohort (6,145 individuals for 293,875 variants included on the ImmunoChip and MetaboChip custom arrays. Overall, our combined approach led to the identification of 9 genome-wide significant novel independent signals-5 of which were identified only with the custom arrays-and provided confirmatory evidence for an additional 7. Novel signals include: for IL-6, in the ABO gene (rs657152, p = 2.13×10(-29; for ESR, at the HBB (rs4910472, p = 2.31×10(-11 and UCN119B/SPPL3 (rs11829037, p = 8.91×10(-10 loci; for MCP-1, near its receptor CCR2 (rs17141006, p = 7.53×10(-13 and in CADM3 (rs3026968, p = 7.63×10(-13; for hsCRP, within the CRP gene (rs3093077, p = 5.73×10(-21, near DARC (rs3845624, p = 1.43×10(-10, UNC119B/SPPL3 (rs11829037, p = 1.50×10(-14, and ICOSLG/AIRE (rs113459440, p = 1.54×10(-08 loci. Confirmatory evidence was found for IL-6 in the IL-6R gene (rs4129267; for ESR at CR1 (rs12567990 and TMEM57 (rs10903129; for MCP-1 at DARC (rs12075; and for hsCRP at CRP (rs1205, HNF1A (rs225918, and APOC-I (rs4420638. Our

  14. A Genome-Wide Association Scan on the Levels of Markers of Inflammation in Sardinians Reveals Associations That Underpin Its Complex Regulation

    Science.gov (United States)

    Naitza, Silvia; Porcu, Eleonora; Steri, Maristella; Taub, Dennis D.; Mulas, Antonella; Xiao, Xiang; Strait, James; Dei, Mariano; Lai, Sandra; Busonero, Fabio; Maschio, Andrea; Usala, Gianluca; Zoledziewska, Magdalena; Sidore, Carlo; Zara, Ilenia; Pitzalis, Maristella; Loi, Alessia; Virdis, Francesca; Piras, Roberta; Deidda, Francesca; Whalen, Michael B.; Crisponi, Laura; Concas, Antonio; Podda, Carlo; Uzzau, Sergio; Scheet, Paul; Longo, Dan L.; Lakatta, Edward; Abecasis, Gonçalo R.; Cao, Antonio; Schlessinger, David; Uda, Manuela

    2012-01-01

    Identifying the genes that influence levels of pro-inflammatory molecules can help to elucidate the mechanisms underlying this process. We first conducted a two-stage genome-wide association scan (GWAS) for the key inflammatory biomarkers Interleukin-6 (IL-6), the general measure of inflammation erythrocyte sedimentation rate (ESR), monocyte chemotactic protein-1 (MCP-1), and high-sensitivity C-reactive protein (hsCRP) in a large cohort of individuals from the founder population of Sardinia. By analysing 731,213 autosomal or X chromosome SNPs and an additional ∼1.9 million imputed variants in 4,694 individuals, we identified several SNPs associated with the selected quantitative trait loci (QTLs) and replicated all the top signals in an independent sample of 1,392 individuals from the same population. Next, to increase power to detect and resolve associations, we further genotyped the whole cohort (6,145 individuals) for 293,875 variants included on the ImmunoChip and MetaboChip custom arrays. Overall, our combined approach led to the identification of 9 genome-wide significant novel independent signals—5 of which were identified only with the custom arrays—and provided confirmatory evidence for an additional 7. Novel signals include: for IL-6, in the ABO gene (rs657152, p = 2.13×10−29); for ESR, at the HBB (rs4910472, p = 2.31×10−11) and UCN119B/SPPL3 (rs11829037, p = 8.91×10−10) loci; for MCP-1, near its receptor CCR2 (rs17141006, p = 7.53×10−13) and in CADM3 (rs3026968, p = 7.63×10−13); for hsCRP, within the CRP gene (rs3093077, p = 5.73×10−21), near DARC (rs3845624, p = 1.43×10−10), UNC119B/SPPL3 (rs11829037, p = 1.50×10−14), and ICOSLG/AIRE (rs113459440, p = 1.54×10−08) loci. Confirmatory evidence was found for IL-6 in the IL-6R gene (rs4129267); for ESR at CR1 (rs12567990) and TMEM57 (rs10903129); for MCP-1 at DARC (rs12075); and for hsCRP at CRP (rs1205), HNF1A (rs225918), and APOC-I (rs

  15. The Finland–United States Investigation of Non–Insulin-Dependent Diabetes Mellitus Genetics (FUSION) Study. II. An Autosomal Genome Scan for Diabetes-Related Quantitative-Trait Loci

    OpenAIRE

    Watanabe, Richard M; Ghosh, Soumitra; Langefeld, Carl D.; Valle, Timo T.; Hauser, Elizabeth R; Magnuson, Victoria L.; Mohlke, Karen L.; Silander, Kaisa; Ally, Delphine S.; Chines, Peter; Blaschak-Harvan, Jillian; Douglas, Julie A.; Duren, William L.; Epstein, Michael P.; Fingerlin, Tasha E.

    2000-01-01

    Type 2 diabetes mellitus is a complex disorder encompassing multiple metabolic defects. We report results from an autosomal genome scan for type 2 diabetes–related quantitative traits in 580 Finnish families ascertained for an affected sibling pair and analyzed by the variance components-based quantitative-trait locus (QTL) linkage approach. We analyzed diabetic and nondiabetic subjects separately, because of the possible impact of disease on the traits of interest. In diabetic individuals, o...

  16. Nuclear Scans

    Science.gov (United States)

    Nuclear scans use radioactive substances to see structures and functions inside your body. They use a special ... images. Most scans take 20 to 45 minutes. Nuclear scans can help doctors diagnose many conditions, including ...

  17. Coincident linkage of type 2 diabetes, metabolic syndrome, and measures of cardiovascular disease in a genome scan of the diabetes heart study.

    Science.gov (United States)

    Bowden, Donald W; Rudock, Megan; Ziegler, Julie; Lehtinen, Allison B; Xu, Jianzhao; Wagenknecht, Lynne E; Herrington, David; Rich, Stephen S; Freedman, Barry I; Carr, J Jeffrey; Langefeld, Carl D

    2006-07-01

    Cardiovascular disease (CVD) is a major contributor to morbidity and mortality in type 2 diabetes, but the relationship between CVD and type 2 diabetes is not well understood. The Diabetes Heart Study is a study of type 2 diabetes-enriched families extensively phenotyped for measures of CVD, type 2 diabetes, and metabolic syndrome. A total of 977 Caucasian subjects from 358 pedigrees (575 type 2 diabetic relative pairs) with at least two individuals with type 2 diabetes and, where possible, unaffected siblings were included in a genome scan. Qualitative traits evaluated in this analysis are with or without the presence of coronary calcified plaque (CCP) and with or without carotid calcified plaque (CarCP) measured by electrocardiogram-gated helical computed tomography. In addition, prevalent CVD was measured using two definitions: CVD1, based on self-reported history of clinical CVD (393 subjects), and CVD2, defined as CVD1 and/or CCP >400 (606 subjects). These discrete traits (type 2 diabetes, metabolic syndrome, CVD1, CVD2, CCP, and CarCP) frequently coincide in the same individuals with concordance ranging from 42.9 to 99%. Multipoint nonparametric linkage analysis revealed evidence for coincident mapping of each trait (type 2 diabetes, metabolic syndrome, CVD1, CVD2, CCP, and CarCP) to three different genomic regions: a broad region on chromosome 3 (70-160 cM; logarithm of odds [LOD] scores ranging between 1.15 and 2.71), chromosome 4q31 (peak LOD 146 cM; LOD scores ranging between 0.90 and 2.41), and on chromosome 14p (peak LOD 23 cM; LOD scores ranging between 1.43 and 2.31). Ordered subset analysis (OSA) suggests that the linked chromosome 3 region consists of at least two separate loci on 3p and 3q. In addition, OSA based on lipid measures and other traits identify family subsets with significantly stronger evidence of linkage (e.g., CVD2 on chromosome 3 at 87 cM subsetting on low HDL with an initial LOD of 2.19 is maximized to an LOD of 7.04 in a subset of

  18. A novel method, digital genome scanning detects KRAS gene amplification in gastric cancers: involvement of overexpressed wild-type KRAS in downstream signaling and cancer cell growth

    Directory of Open Access Journals (Sweden)

    Yanagihara Kazuyoshi

    2009-06-01

    Full Text Available Abstract Background Gastric cancer is the third most common malignancy affecting the general population worldwide. Aberrant activation of KRAS is a key factor in the development of many types of tumor, however, oncogenic mutations of KRAS are infrequent in gastric cancer. We have developed a novel quantitative method of analysis of DNA copy number, termed digital genome scanning (DGS, which is based on the enumeration of short restriction fragments, and does not involve PCR or hybridization. In the current study, we used DGS to survey copy-number alterations in gastric cancer cells. Methods DGS of gastric cancer cell lines was performed using the sequences of 5000 to 15000 restriction fragments. We screened 20 gastric cancer cell lines and 86 primary gastric tumors for KRAS amplification by quantitative PCR, and investigated KRAS amplification at the DNA, mRNA and protein levels by mutational analysis, real-time PCR, immunoblot analysis, GTP-RAS pull-down assay and immunohistochemical analysis. The effect of KRAS knock-down on the activation of p44/42 MAP kinase and AKT and on cell growth were examined by immunoblot and colorimetric assay, respectively. Results DGS analysis of the HSC45 gastric cancer cell line revealed the amplification of a 500-kb region on chromosome 12p12.1, which contains the KRAS gene locus. Amplification of the KRAS locus was detected in 15% (3/20 of gastric cancer cell lines (8–18-fold amplification and 4.7% (4/86 of primary gastric tumors (8–50-fold amplification. KRAS mutations were identified in two of the three cell lines in which KRAS was amplified, but were not detected in any of the primary tumors. Overexpression of KRAS protein correlated directly with increased KRAS copy number. The level of GTP-bound KRAS was elevated following serum stimulation in cells with amplified wild-type KRAS, but not in cells with amplified mutant KRAS. Knock-down of KRAS in gastric cancer cells that carried amplified wild

  19. A novel method, digital genome scanning detects KRAS gene amplification in gastric cancers: involvement of overexpressed wild-type KRAS in downstream signaling and cancer cell growth

    International Nuclear Information System (INIS)

    Gastric cancer is the third most common malignancy affecting the general population worldwide. Aberrant activation of KRAS is a key factor in the development of many types of tumor, however, oncogenic mutations of KRAS are infrequent in gastric cancer. We have developed a novel quantitative method of analysis of DNA copy number, termed digital genome scanning (DGS), which is based on the enumeration of short restriction fragments, and does not involve PCR or hybridization. In the current study, we used DGS to survey copy-number alterations in gastric cancer cells. DGS of gastric cancer cell lines was performed using the sequences of 5000 to 15000 restriction fragments. We screened 20 gastric cancer cell lines and 86 primary gastric tumors for KRAS amplification by quantitative PCR, and investigated KRAS amplification at the DNA, mRNA and protein levels by mutational analysis, real-time PCR, immunoblot analysis, GTP-RAS pull-down assay and immunohistochemical analysis. The effect of KRAS knock-down on the activation of p44/42 MAP kinase and AKT and on cell growth were examined by immunoblot and colorimetric assay, respectively. DGS analysis of the HSC45 gastric cancer cell line revealed the amplification of a 500-kb region on chromosome 12p12.1, which contains the KRAS gene locus. Amplification of the KRAS locus was detected in 15% (3/20) of gastric cancer cell lines (8–18-fold amplification) and 4.7% (4/86) of primary gastric tumors (8–50-fold amplification). KRAS mutations were identified in two of the three cell lines in which KRAS was amplified, but were not detected in any of the primary tumors. Overexpression of KRAS protein correlated directly with increased KRAS copy number. The level of GTP-bound KRAS was elevated following serum stimulation in cells with amplified wild-type KRAS, but not in cells with amplified mutant KRAS. Knock-down of KRAS in gastric cancer cells that carried amplified wild-type KRAS resulted in the inhibition of cell growth and

  20. CT Scans

    Science.gov (United States)

    ... cross-sectional pictures of your body. Doctors use CT scans to look for Broken bones Cancers Blood clots Signs of heart disease Internal bleeding During a CT scan, you lie still on a table. The table ...

  1. Thyroid scan

    Science.gov (United States)

    ... PET scan Skin nodules Thyroid cancer Thyroid cancer - medullary carcinoma Thyroid cancer - papillary carcinoma Toxic nodular goiter ... Topics Hyperthyroidism Hypothyroidism Nuclear Scans Thyroid Cancer Thyroid Diseases Thyroid Tests Browse the Encyclopedia A.D.A. ...

  2. Genome-Wide Association Scan Identifies a Risk Locus for Preeclampsia on 2q14, Near the Inhibin, Beta B Gene

    OpenAIRE

    Johnson, Matthew P.; Shaun P Brennecke; East, Christine E.; Göring, Harald H. H.; Kent, Jack W.; Thomas D Dyer; Said, Joanne M.; Roten, Linda T; Iversen, Ann-Charlotte; Abraham, Lawrence J.; Heinonen, Seppo; Kajantie, Eero; Kere, Juha; Kivinen, Katja; Pouta, Anneli

    2012-01-01

    Elucidating the genetic architecture of preeclampsia is a major goal in obstetric medicine. We have performed a genome-wide association study (GWAS) for preeclampsia in unrelated Australian individuals of Caucasian ancestry using the Illumina OmniExpress-12 BeadChip to successfully genotype 648,175 SNPs in 538 preeclampsia cases and 540 normal pregnancy controls. Two SNP associations (rs7579169, p = 3.58×10−7, OR = 1.57; rs12711941, p = 4.26×10−7, OR = 1.56) satisfied our genome-wide signific...

  3. Genome-wide association scan identifies a risk locus for preeclampsia on 2q14, near the inhibin, beta B gene

    OpenAIRE

    Johnson, Matthew P.; Shaun P Brennecke; East, Christine; Göring, Harald H. H.; Kent, Jack W.; Thomas D Dyer; Said, Joanne M.; Roten, Linda Tømmerdal; Iversen, Ann-Charlotte; Abraham, Lawrence J.; Heinonen, Seppo; Kajantie, Eero; Kere, Juha; Kivinen, Katja; Pouta, Anneli

    2012-01-01

    Elucidating the genetic architecture of preeclampsia is a major goal in obstetric medicine. We have performed a genome-wide association study (GWAS) for preeclampsia in unrelated Australian individuals of Caucasian ancestry using the Illumina OmniExpress-12 BeadChip to successfully genotype 648,175 SNPs in 538 preeclampsia cases and 540 normal pregnancy controls. Two SNP associations (rs7579169, p = 3.58×10−7, OR = 1.57; rs12711941, p = 4.26×10−7, OR = 1.56) satisfied our genome-wide signific...

  4. SHEsisEpi, a GPU-enhanced genome-wide SNP-SNP interaction scanning algorithm, efficiently reveals the risk genetic epistasis in bipolar disorder

    Institute of Scientific and Technical Information of China (English)

    Xiaohan Hu; Qiang Liu; Zhao Zhang; Zhiqiang Li; Shilin Wang; Lin He; Yongyong Shi

    2010-01-01

    @@ Dear Editor, We developed a GPU-based analytical method, named as SHEsisEpi, which purely focuses on risk epistasis in a genome-wide association study (GWAS) of complex traits, excluding the contamination of marginal effects caused by single-locus association. We analyzed the Wellcome Trust Case Control Consortium's (WTCCC)GWAS data of bipolar disorder (BPD) with 500K SNPs.

  5. The importance of context to the genetic architecture of diabetes-related traits is revealed in a genome-wide scan of a LG/J × SM/J murine model.

    Science.gov (United States)

    Lawson, Heather A; Lee, Arthur; Fawcett, Gloria L; Wang, Bing; Pletscher, L Susan; Maxwell, Taylor J; Ehrich, Thomas H; Kenney-Hunt, Jane P; Wolf, Jason B; Semenkovich, Clay F; Cheverud, James M

    2011-04-01

    Variations in diabetic phenotypes are caused by complex interactions of genetic effects, environmental factors, and the interplay between the two. We tease apart these complex interactions by examining genome-wide genetic and epigenetic effects on diabetes-related traits among different sex, diet, and sex-by-diet cohorts in a Mus musculus model. We conducted a genome-wide scan for quantitative trait loci that affect serum glucose and insulin levels and response to glucose stress in an F(16) Advanced Intercross Line of the LG/J and SM/J intercross (Wustl:LG,SM-G16). Half of each sibship was fed a high-fat diet and half was fed a relatively low-fat diet. Context-dependent genetic (additive and dominance) and epigenetic (parent-of-origin imprinting) effects were characterized by partitioning animals into sex, diet, and sex-by-diet cohorts. We found that different cohorts often have unique genetic effects at the same loci, and that genetic signals can be masked or erroneously assigned to specific cohorts if they are not considered individually. Our data demonstrate that the effects of genes on complex trait variation are highly context-dependent and that the same genomic sequence can affect traits differently depending on an individual's sex and/or dietary environment. Our results have important implications for studies of complex traits in humans.

  6. Using Regulatory and Epistatic Networks to Extend the Findings of a Genome Scan: Identifying the Gene Drivers of Pigmentation in Merino Sheep

    OpenAIRE

    Elsa García-Gámez; Antonio Reverter; Vicki Whan; McWilliam, Sean M.; Juan José Arranz; James Kijas

    2011-01-01

    Extending genome wide association analysis by the inclusion of gene expression data may assist in the dissection of complex traits. We examined piebald, a pigmentation phenotype in both human and Merino sheep, by analysing multiple data types using a systems approach. First, a case control analysis of 49,034 ovine SNP was performed which confirmed a multigenic basis for the condition. We combined these results with gene expression data from five tissue types analysed with a skin-specific micr...

  7. Genome scans reveal candidate domestication and improvement genes in cultivated sunflower, as well as post-domestication introgression with wild relatives.

    Science.gov (United States)

    Baute, Gregory J; Kane, Nolan C; Grassa, Christopher J; Lai, Zhao; Rieseberg, Loren H

    2015-04-01

    The development of modern crops typically involves both selection and hybridization, but to date most studies have focused on the former. In the present study, we explore how both processes, and their interactions, have molded the genome of the cultivated sunflower (Helianthus annuus), a globally important oilseed. To identify genes targeted by selection during the domestication and improvement of sunflower, and to detect post-domestication hybridization with wild species, we analyzed transcriptome sequences of 80 genotypes, including wild, landrace, and modern lines of H. annuus, as well as two cross-compatible wild relatives, Helianthus argophyllus and Helianthus petiolaris. Outlier analyses identified 122 and 15 candidate genes associated with domestication and improvement, respectively. As in several previous studies, genes putatively involved in oil biosynthesis were the most extreme outliers. Additionally, several promising associations were observed with previously mapped quantitative trait loci (QTLs), such as branching. Admixture analyses revealed that all the modern cultivar genomes we examined contained one or more introgressions from wild populations, with every chromosome having evidence of introgression in at least one modern line. Cumulatively, introgressions cover c. 10% of the cultivated sunflower genome. Surprisingly, introgressions do not avoid candidate domestication genes, probably because of the reintroduction of branching.

  8. Genome scans reveal candidate domestication and improvement genes in cultivated sunflower, as well as post-domestication introgression with wild relatives.

    Science.gov (United States)

    Baute, Gregory J; Kane, Nolan C; Grassa, Christopher J; Lai, Zhao; Rieseberg, Loren H

    2015-04-01

    The development of modern crops typically involves both selection and hybridization, but to date most studies have focused on the former. In the present study, we explore how both processes, and their interactions, have molded the genome of the cultivated sunflower (Helianthus annuus), a globally important oilseed. To identify genes targeted by selection during the domestication and improvement of sunflower, and to detect post-domestication hybridization with wild species, we analyzed transcriptome sequences of 80 genotypes, including wild, landrace, and modern lines of H. annuus, as well as two cross-compatible wild relatives, Helianthus argophyllus and Helianthus petiolaris. Outlier analyses identified 122 and 15 candidate genes associated with domestication and improvement, respectively. As in several previous studies, genes putatively involved in oil biosynthesis were the most extreme outliers. Additionally, several promising associations were observed with previously mapped quantitative trait loci (QTLs), such as branching. Admixture analyses revealed that all the modern cultivar genomes we examined contained one or more introgressions from wild populations, with every chromosome having evidence of introgression in at least one modern line. Cumulatively, introgressions cover c. 10% of the cultivated sunflower genome. Surprisingly, introgressions do not avoid candidate domestication genes, probably because of the reintroduction of branching. PMID:25641359

  9. Using an Inbred Horse Breed in a High Density Genome-Wide Scan for Genetic Risk Factors of Insect Bite Hypersensitivity (IBH)

    Science.gov (United States)

    Velie, Brandon D.; Shrestha, Merina; Franҫois, Liesbeth; Schurink, Anouk; Tesfayonas, Yohannes G.; Stinckens, Anneleen; Blott, Sarah; Ducro, Bart J.; Mikko, Sofia; Thomas, Ruth; Swinburne, June E.; Sundqvist, Marie; Eriksson, Susanne; Buys, Nadine; Lindgren, Gabriella

    2016-01-01

    While susceptibility to hypersensitive reactions is a common problem amongst humans and animals alike, the population structure of certain animal species and breeds provides a more advantageous route to better understanding the biology underpinning these conditions. The current study uses Exmoor ponies, a highly inbred breed of horse known to frequently suffer from insect bite hypersensitivity, to identify genomic regions associated with a type I and type IV hypersensitive reaction. A total of 110 cases and 170 controls were genotyped on the 670K Axiom Equine Genotyping Array. Quality control resulted in 452,457 SNPs and 268 individuals being tested for association. Genome-wide association analyses were performed using the GenABEL package in R and resulted in the identification of two regions of interest on Chromosome 8. The first region contained the most significant SNP identified, which was located in an intron of the DCC netrin 1 receptor gene. The second region identified contained multiple top SNPs and encompassed the PIGN, KIAA1468, TNFRSF11A, ZCCHC2, and PHLPP1 genes. Although additional studies will be needed to validate the importance of these regions in horses and the relevance of these regions in other species, the knowledge gained from the current study has the potential to be a step forward in unraveling the complex nature of hypersensitive reactions. PMID:27070818

  10. Genome-wide association scan identifies a risk locus for preeclampsia on 2q14, near the inhibin, beta B gene.

    Directory of Open Access Journals (Sweden)

    Matthew P Johnson

    Full Text Available Elucidating the genetic architecture of preeclampsia is a major goal in obstetric medicine. We have performed a genome-wide association study (GWAS for preeclampsia in unrelated Australian individuals of Caucasian ancestry using the Illumina OmniExpress-12 BeadChip to successfully genotype 648,175 SNPs in 538 preeclampsia cases and 540 normal pregnancy controls. Two SNP associations (rs7579169, p = 3.58×10(-7, OR = 1.57; rs12711941, p = 4.26×10(-7, OR = 1.56 satisfied our genome-wide significance threshold (modified Bonferroni p0.92. We attempted to provide evidence of a putative regulatory role for these SNPs using bioinformatic analyses and found that they all reside within regions of low sequence conservation and/or low complexity, suggesting functional importance is low. We also explored the mRNA expression in decidua of genes ±500 kb of INHBB and found a nominally significant correlation between a transcript encoded by the EPB41L5 gene, ∼250 kb centromeric to INHBB, and preeclampsia (p = 0.03. We were unable to replicate the associations shown by the significant GWAS SNPs in case-control cohorts from Norway and Finland, leading us to conclude that it is more likely that these SNPs are in LD with as yet unidentified causal variant(s.

  11. Genome-wide association scan identifies a risk locus for preeclampsia on 2q14, near the inhibin, beta B gene.

    Science.gov (United States)

    Johnson, Matthew P; Brennecke, Shaun P; East, Christine E; Göring, Harald H H; Kent, Jack W; Dyer, Thomas D; Said, Joanne M; Roten, Linda T; Iversen, Ann-Charlotte; Abraham, Lawrence J; Heinonen, Seppo; Kajantie, Eero; Kere, Juha; Kivinen, Katja; Pouta, Anneli; Laivuori, Hannele; Austgulen, Rigmor; Blangero, John; Moses, Eric K

    2012-01-01

    Elucidating the genetic architecture of preeclampsia is a major goal in obstetric medicine. We have performed a genome-wide association study (GWAS) for preeclampsia in unrelated Australian individuals of Caucasian ancestry using the Illumina OmniExpress-12 BeadChip to successfully genotype 648,175 SNPs in 538 preeclampsia cases and 540 normal pregnancy controls. Two SNP associations (rs7579169, p = 3.58×10(-7), OR = 1.57; rs12711941, p = 4.26×10(-7), OR = 1.56) satisfied our genome-wide significance threshold (modified Bonferroni p0.92). We attempted to provide evidence of a putative regulatory role for these SNPs using bioinformatic analyses and found that they all reside within regions of low sequence conservation and/or low complexity, suggesting functional importance is low. We also explored the mRNA expression in decidua of genes ±500 kb of INHBB and found a nominally significant correlation between a transcript encoded by the EPB41L5 gene, ∼250 kb centromeric to INHBB, and preeclampsia (p = 0.03). We were unable to replicate the associations shown by the significant GWAS SNPs in case-control cohorts from Norway and Finland, leading us to conclude that it is more likely that these SNPs are in LD with as yet unidentified causal variant(s). PMID:22432041

  12. MRI Scans

    Science.gov (United States)

    Magnetic resonance imaging (MRI) uses a large magnet and radio waves to look at organs and structures inside your body. Health care professionals use MRI scans to diagnose a variety of conditions, from ...

  13. CT scan

    Science.gov (United States)

    ... come from a CT scan. Some people have allergies to contrast dye. Let your doctor know if you have ... vein contains iodine. If you have an iodine allergy, a type of contrast may cause nausea or vomiting , sneezing , itching , or ...

  14. The Finland–United States Investigation of Non–Insulin-Dependent Diabetes Mellitus Genetics (FUSION) Study. I. An Autosomal Genome Scan for Genes That Predispose to Type 2 Diabetes

    OpenAIRE

    Ghosh, Soumitra; Watanabe, Richard M; Valle, Timo T.; Hauser, Elizabeth R; Magnuson, Victoria L.; Langefeld, Carl D.; Ally, Delphine S.; Mohlke, Karen L.; Silander, Kaisa; Kohtamäki, Kimmo; Chines, Peter; Balow, Jr., James; Birznieks, Gunther; Chang, Jennie; Eldridge, William

    2000-01-01

    We performed a genome scan at an average resolution of 8 cM in 719 Finnish sib pairs with type 2 diabetes. Our strongest results are for chromosome 20, where we observe a weighted maximum LOD score (MLS) of 2.15 at map position 69.5 cM from pter and secondary weighted LOD-score peaks of 2.04 at 56.5 cM and 1.99 at 17.5 cM. Our next largest MLS is for chromosome 11 (MLS = 1.75 at 84.0 cM), followed by chromosomes 2 (MLS = 0.87 at 5.5 cM), 10 (MLS = 0.77 at 75.0 cM), and 6 (MLS = 0.61 at 112.5 ...

  15. Quantitative trait loci involved in sex determination and body growth in the gilthead sea bream (Sparus aurata L. through targeted genome scan.

    Directory of Open Access Journals (Sweden)

    Dimitrios Loukovitis

    Full Text Available Among vertebrates, teleost fish exhibit a considerably wide range of sex determination patterns that may be influenced by extrinsic parameters. However even for model fish species like the zebrafish Danio rerio the precise mechanisms involved in primary sex determination have not been studied extensively. The zebrafish, a gonochoristic species, is lacking discernible sex chromosomes and the sex of juvenile fish is difficult to determine. Sequential protandrous hermaphrodite species provide distinct determination of the gender and allow studying the sex determination process by looking at the mechanism of sex reversal. This is the first attempt to understand the genetic basis of phenotypic variation for sex determination and body weight in a sequential protandrous hermaphrodite species, the gilthead sea bream (Sparus aurata. This work demonstrates a fast and efficient strategy for Quantitative Trait Loci (QTL detection in the gilthead sea bream, a non-model but target hermaphrodite fish species. Therefore a comparative mapping approach was performed to query syntenies against two other Perciformes, the European sea bass (Dicentrarchus labrax, a gonochoristic species and the Asian sea bass (Lates calcarifer a protandrous hermaphrodite. In this manner two significant QTLs, one QTL affecting both body weight and sex and one QTL affecting sex, were detected on the same linkage group. The co-segregation of the two QTLs provides a genomic base to the observed genetic correlation between these two traits in sea bream as well as in other teleosts. The identification of QTLs linked to sex reversal and growth, will contribute significantly to a better understanding of the complex nature of sex determination in S. aurata where most individuals reverse to the female sex at the age of two years through development and maturation of the ovarian portion of the gonad and regression of the testicular area. [Genomic sequences reported in this manuscript have been

  16. Genome-wide linkage scan to identify loci associated with type 2 diabetes and blood lipid phenotypes in the Sikh Diabetes Study.

    Directory of Open Access Journals (Sweden)

    Dharambir K Sanghera

    Full Text Available In this investigation, we have carried out an autosomal genome-wide linkage analysis to map genes associated with type 2 diabetes (T2D and five quantitative traits of blood lipids including total cholesterol, high-density lipoprotein (HDL cholesterol, low-density lipoprotein (LDL cholesterol, very low-density lipoprotein (VLDL cholesterol, and triglycerides in a unique family-based cohort from the Sikh Diabetes Study (SDS. A total of 870 individuals (526 male/344 female from 321 families were successfully genotyped using 398 polymorphic microsatellite markers with an average spacing of 9.26 cM on the autosomes. Results of non-parametric multipoint linkage analysis using S(all statistics (implemented in Merlin did not reveal any chromosomal region to be significantly associated with T2D in this Sikh cohort. However, linkage analysis for lipid traits using QTL-ALL analysis revealed promising linkage signals with p≤0.005 for total cholesterol, LDL cholesterol, and HDL cholesterol at chromosomes 5p15, 9q21, 10p11, 10q21, and 22q13. The most significant signal (p = 0.0011 occurred at 10q21.2 for HDL cholesterol. We also observed linkage signals for total cholesterol at 22q13.32 (p = 0.0016 and 5p15.33 (p = 0.0031 and for LDL cholesterol at 10p11.23 (p = 0.0045. Interestingly, some of linkage regions identified in this Sikh population coincide with plausible candidate genes reported in recent genome-wide association and meta-analysis studies for lipid traits. Our study provides the first evidence of linkage for loci associated with quantitative lipid traits at four chromosomal regions in this Asian Indian population from Punjab. More detailed examination of these regions with more informative genotyping, sequencing, and functional studies should lead to rapid detection of novel targets of therapeutic importance.

  17. Using regulatory and epistatic networks to extend the findings of a genome scan: identifying the gene drivers of pigmentation in merino sheep.

    Science.gov (United States)

    García-Gámez, Elsa; Reverter, Antonio; Whan, Vicki; McWilliam, Sean M; Arranz, Juan José; Kijas, James

    2011-01-01

    Extending genome wide association analysis by the inclusion of gene expression data may assist in the dissection of complex traits. We examined piebald, a pigmentation phenotype in both human and Merino sheep, by analysing multiple data types using a systems approach. First, a case control analysis of 49,034 ovine SNP was performed which confirmed a multigenic basis for the condition. We combined these results with gene expression data from five tissue types analysed with a skin-specific microarray. Promoter sequence analysis of differentially expressed genes allowed us to reverse-engineer a regulatory network. Likewise, by testing two-loci models derived from all pair-wise comparisons across piebald-associated SNP, we generated an epistatic network. At the intersection of both networks, we identified thirteen genes with insulin-like growth factor binding protein 7 (IGFBP7), platelet-derived growth factor alpha (PDGFRA) and the tetraspanin platelet activator CD9 at the kernel of the intersection. Further, we report a number of differentially expressed genes in regions containing highly associated SNP including ATRN, DOCK7, FGFR1OP, GLI3, SILV and TBX15. The application of network theory facilitated co-analysis of genetic variation with gene expression, recapitulated aspects of the known molecular biology of skin pigmentation and provided insights into the transcription regulation and epistatic interactions involved in piebald Merino sheep.

  18. A genome scan for quantitative trait loci affecting grain yield and its components of maize both in single-and two-locus levels

    Institute of Scientific and Technical Information of China (English)

    YAN Jianbing; TANG Hua; HUANG Yiqin; ZHENG Yonglian; SUBHASH Chander; LI Jiansheng

    2006-01-01

    By adding thirty-one markers in the previous linkage map, a new genetic linkage map containing 205 markers was constructed, spanning a total of 2305.4 cM with an average interval of 11.2 cM. The genotypic errors in the whole genome were detected by the statistical method and removed manually. The precision of the linkage map was improved significantly. Main and epistatic QTL were detected by R/qtl, and main QTL were confirmed and refined by multiple interval mapping (MIM). Finally, MIM detected seven QTL for rows number, and five QTL for each grain yield, kernels per row and 100-kernel weight. The contribution to genetic variations of QTL varied from 35.3% for grain yield to 61.5% for rows number. Only kernels per row exhibited significant epistatic interactions between QTL. Twenty-four epistatic QTL were detected which distributed on almost all the ten chromosomes. About two-third epistatic QTL were observed between main QTL and another locus, which had no significant effects. These results indicate rather clearly that there are a number of QTL affecting trait expressions, not directly but indirectly through interactions with other loci. Thus, epistatic QTL effects may play a crucial role, if not more important than main QTL effects, in the genetic variation for the measured traits in present study.

  19. Using regulatory and epistatic networks to extend the findings of a genome scan: identifying the gene drivers of pigmentation in merino sheep.

    Directory of Open Access Journals (Sweden)

    Elsa García-Gámez

    Full Text Available Extending genome wide association analysis by the inclusion of gene expression data may assist in the dissection of complex traits. We examined piebald, a pigmentation phenotype in both human and Merino sheep, by analysing multiple data types using a systems approach. First, a case control analysis of 49,034 ovine SNP was performed which confirmed a multigenic basis for the condition. We combined these results with gene expression data from five tissue types analysed with a skin-specific microarray. Promoter sequence analysis of differentially expressed genes allowed us to reverse-engineer a regulatory network. Likewise, by testing two-loci models derived from all pair-wise comparisons across piebald-associated SNP, we generated an epistatic network. At the intersection of both networks, we identified thirteen genes with insulin-like growth factor binding protein 7 (IGFBP7, platelet-derived growth factor alpha (PDGFRA and the tetraspanin platelet activator CD9 at the kernel of the intersection. Further, we report a number of differentially expressed genes in regions containing highly associated SNP including ATRN, DOCK7, FGFR1OP, GLI3, SILV and TBX15. The application of network theory facilitated co-analysis of genetic variation with gene expression, recapitulated aspects of the known molecular biology of skin pigmentation and provided insights into the transcription regulation and epistatic interactions involved in piebald Merino sheep.

  20. A genome-wide scan reveals important roles of DNA methylation in human longevity by regulating age-related disease genes.

    Directory of Open Access Journals (Sweden)

    Fu-Hui Xiao

    Full Text Available It is recognized that genetic factors contribute to human longevity. Besides the hypothesis of existence of longevity genes, another suggests that a lower frequency of risk alleles decreases the incidence of age-related diseases in the long-lived people. However, the latter finds no support from recent genetic studies. Considering the crucial role of epigenetic modification in gene regulation, we then hypothesize that suppressing disease-related genes in longevity individuals is likely achieved by epigenetic modification, e.g. DNA methylation. To test this hypothesis, we investigated the genome-wide methylation profile in 4 Chinese female centenarians and 4 middle-aged controls using methyl-DNA immunoprecipitation sequencing. 626 differentially methylated regions (DMRs were observed between both groups. Interestingly, genes with these DMRs were enriched in age-related diseases, including type-2 diabetes, cardiovascular disease, stroke and Alzheimer's disease. This pattern remains rather stable after including methylomes of two white individuals. Further analyses suggest that the observed DMRs likely have functional roles in regulating disease-associated gene expressions, with some genes [e.g. caspase 3 (CASP3] being down-regulated whereas the others [i.e. interleukin 1 receptor, type 2 (IL1R2] up-regulated. Therefore, our study suggests that suppressing the disease-related genes via epigenetic modification is an important contributor to human longevity.

  1. Scan Statistics

    CERN Document Server

    Glaz, Joseph

    2009-01-01

    Suitable for graduate students and researchers in applied probability and statistics, as well as for scientists in biology, computer science, pharmaceutical science and medicine, this title brings together a collection of chapters illustrating the depth and diversity of theory, methods and applications in the area of scan statistics.

  2. Perineal scanning.

    Science.gov (United States)

    Jeanty, P; d'Alton, M; Romero, R; Hobbins, J C

    1986-10-01

    Although various techniques have been described to aid in the ultrasound diagnosis of placenta previa and incompetent cervix, these maneuvers depend on the precise identification of the internal cervical os, a feat which is notoriously difficult to accomplish consistently. In an attempt to get a closer view of the cervix we tried another approach. This simple technique of perineal scanning has the potential to help considerably with these problems. PMID:3530265

  3. Methylation and downregulated expression of mac25/insulin-like growth factor binding protein-7 is associated with liver tumorigenesis in SV40T/t antigen transgenic mice, screened by restriction landmark genomic scanning for methylation (RLGS-M).

    Science.gov (United States)

    Komatsu, S; Okazaki, Y; Tateno, M; Kawai, J; Konno, H; Kusakabe, M; Yoshiki, A; Muramatsu, M; Held, W A; Hayashizaki, Y

    2000-01-01

    Restriction landmark genomic scanning for methylation (RLGS-M) was used to detect alterations in DNA methylation associated with murine SV40 T/t antigen-induced hepatocarcinogenesis. An altered locus/spot (S130) was cloned and found to correspond to sequences in the 5' flanking region and 5' portion of the cDNA for the murine mac25/insulin-like growth factor binding protein-7 (Igfbp-7) gene. IGFBPs are believed to be capable of binding insulin, Igf1, and Igf2 and modulating mitogenic effects. Previous studies have shown that Igf2 has an important role in promoting liver tumorigenesis. Quantitative PCR was used to access the methylation status of the NotI site just 5' to the coding region and the expression level of the mac25/igfbp-7 gene. The results indicated that the degree of methylation was inversely related to the expression level and is consistent with a role for DNA methylation in silencing mac25/Igfbp-7 gene expression and function for mac25/Igfbp-7 as a tumor suppressor gene. PMID:10623583

  4. Handheld scanning probes for optical coherence tomography: developments, applications, and perspectives

    Science.gov (United States)

    Duma, V.-F.; Demian, D.; Sinescu, C.; Cernat, R.; Dobre, G.; Negrutiu, M. L.; Topala, F. I.; Hutiu, Gh.; Bradu, A.; Podoleanu, A. G.

    2016-03-01

    We present the handheld scanning probes that we have recently developed in our current project for biomedical imaging in general and for Optical Coherence Tomography (OCT) in particular. OCT is an established, but dynamic imagistic technique based on laser interferometry, which offers micrometer resolutions and millimeters penetration depths. With regard to existing devices, the newly developed handheld probes are simple, light and relatively low cost. Their design is described in detail to allow for the reproduction in any lab, including for educational purposes. Two probes are constructed almost entirely from off-the-shelf components, while a third, final variant is constructed with dedicated components, in an ergonomic design. The handheld probes have uni-dimensional (1D) galvanometer scanners therefore they achieve transversal sections through the biological sample investigated - in contrast to handheld probes equipped with bi-dimensional (2D) scanners that can also achieve volumetric (3D) reconstructions of the samples. These latter handheld probes are therefore also discussed, as well as the possibility to equip them with galvanometer 2D scanners or with Risley prisms. For galvanometer scanners the optimal scanning functions studied in a series of previous works are pointed out; these functions offer a higher temporal efficiency/duty cycle of the scanning process, as well as artifact-free OCT images. The testing of the handheld scanning probes in dental applications is presented, for metal ceramic prosthesis and for teeth.

  5. Helix Scan: A Scan Design for Diagnosis

    Institute of Scientific and Technical Information of China (English)

    WANG Fei; HU Yu; LI Xiaowei

    2007-01-01

    Scan design is a widely used design-for-testability technique to improve test quality and efficiency. For the scan-designed circuit, test and diagnosis of the scan chain and the circuit is an important process for silicon debug and yield learning. However, conventional scan designs and diagnosis methods abort the subsequent diagnosis process after diagnosing the scan chain if the scan chain is faulty. In this work, we propose a design-for-diagnosis scan strategy called helix scan and a diagnosis algorithm to address this issue. Unlike previous proposed methods, helix scan has the capability to carry on the diagnosis process without losing information when the scan chain is faulty. What is more, it simplifies scan chain diagnosis and achieves high diagnostic resolution as well as accuracy. Experimental results demonstrate the effectiveness of our design.

  6. Heart PET scan

    Science.gov (United States)

    ... nuclear medicine scan; Heart positron emission tomography; Myocardial PET scan ... A PET scan requires a small amount of radioactive material (tracer). This tracer is given through a vein (IV), ...

  7. Coronary Calcium Scan

    Science.gov (United States)

    ... the NHLBI on Twitter. What Is a Coronary Calcium Scan? A coronary calcium scan is a test ... you have calcifications in your coronary arteries. Coronary Calcium Scan Figure A shows the position of the ...

  8. Scan BIST with biased scan test signals

    Institute of Scientific and Technical Information of China (English)

    XIANG Dong; CHEN MingJing; SUN JiaGuang

    2008-01-01

    The conventional test-per-scan built-in self-test (BIST) scheme needs a number of shift cycles followed by one capture cycle.Fault effects received by the scan flip-flops are shifted out while shifting in the next test vector like scan testing.Unlike deterministic testing,it is unnecessary to apply a complete test vector to the scan chains.A new scan-based BIST scheme is proposed by properly controlling the test signals of the scan chains,Different biased random values are assigned to the test signals of scan flip-flops in separate scan chains.Capture cycles can be inserted at any clock cycle if necessary.A new testability estimation procedure according to the proposed testing scheme is presented.A greedy procedure is proposed to select a weight for each scan chain.Experimental results show that the proposed method can improve test effectiveness of scan-based BIST greatly,and most circuits can obtain complete fault coverage or very close to complete fault coverage.

  9. Conventional cerebrospinal fluid scanning

    Energy Technology Data Exchange (ETDEWEB)

    Schicha, H.

    1985-06-01

    Conventional cerebrospinal fluid scanning (CSF scanning) today is mainly carried out in addition to computerized tomography to obtain information about liquor flow kinetics. Especially in patients with communicating obstructive hydrocephalus, CSF scanning is clinically useful for the decision for shunt surgery. In patients with intracranial cysts, CSF scanning can provide information about liquor circulation. Further indications for CSF scanning include the assessment of shunt patency especially in children, as well as the detection and localization of cerebrospinal fluid leaks.

  10. Rapid Frequency Scan EPR

    OpenAIRE

    Tseitlin, Mark; Rinard, George A.; Quine, Richard W.; Eaton, Sandra S.; Eaton, Gareth R.

    2011-01-01

    In rapid frequency scan EPR with triangular scans, sufficient time must be allowed to insure that the magnetization in the x,y plane decays to baseline at the end of the scan, which typically is about 5 T2 after the spins are excited. To permit relaxation of signals excited toward the extremes of the scan the total scan time required may be much longer than 5 T2. However, with periodic, saw-tooth excitation, the slow-scan EPR spectrum can be recovered by Fourier deconvolution of data recorded...

  11. RBC nuclear scan

    Science.gov (United States)

    ... page: //medlineplus.gov/ency/article/003835.htm RBC nuclear scan To use the sharing features on this page, please enable JavaScript. An RBC nuclear scan uses small amounts of radioactive material to ...

  12. Pulmonary ventilation/perfusion scan

    Science.gov (United States)

    V/Q scan; Ventilation/perfusion scan; Lung ventilation/perfusion scan ... A pulmonary ventilation/perfusion scan is actually two tests. They may be done separately or together. During the perfusion scan, a health care ...

  13. Pulmonary ventilation/perfusion scan

    Science.gov (United States)

    V/Q scan; Ventilation/perfusion scan; Lung ventilation/perfusion scan ... A pulmonary ventilation/perfusion scan is actually two tests. They may be done separately or together. During the perfusion scan, a health ...

  14. Rapid frequency scan EPR.

    Science.gov (United States)

    Tseitlin, Mark; Rinard, George A; Quine, Richard W; Eaton, Sandra S; Eaton, Gareth R

    2011-08-01

    In rapid frequency scan EPR with triangular scans, sufficient time must be allowed to insure that the magnetization in the x, y plane decays to baseline at the end of the scan, which typically is about 5T(2) after the spins are excited. To permit relaxation of signals excited toward the extremes of the scan the total scan time required may be much longer than 5T(2). However, with periodic, saw-tooth excitation, the slow-scan EPR spectrum can be recovered by Fourier deconvolution of data recorded with a total scan period of 5T(2), even if some spins are excited later in the scan. This scan time is similar to polyphase excitation methods. The peak power required for either polyphase excitation or rapid frequency scans is substantially smaller than for pulsed EPR. The use of an arbitrary waveform generator (AWG) and cross loop resonator facilitated implementation of the rapid frequency scan experiments reported here. The use of constant continuous low B(1), periodic excitation waveform, and constant external magnetic field is similar to polyphase excitation, but could be implemented without the AWG that is required for polyphase excitation. PMID:21664848

  15. Line-scanning, stage scanning confocal microscope

    Science.gov (United States)

    Carucci, John A.; Stevenson, Mary; Gareau, Daniel

    2016-03-01

    We created a line-scanning, stage scanning confocal microscope as part of a new procedure: video assisted micrographic surgery (VAMS). The need for rapid pathological assessment of the tissue on the surface of skin excisions very large since there are 3.5 million new skin cancers diagnosed annually in the United States. The new design presented here is a confocal microscope without any scanning optics. Instead, a line is focused in space and the sample, which is flattened, is physically translated such that the line scans across its face in a direction perpendicular to the line its self. The line is 6mm long and the stage is capable of scanning 50 mm, hence the field of view is quite large. The theoretical diffraction-limited resolution is 0.7um lateral and 3.7um axial. However, in this preliminary report, we present initial results that are a factor of 5-7 poorer in resolution. The results are encouraging because they demonstrate that the linear array detector measures sufficient signal from fluorescently labeled tissue and also demonstrate the large field of view achievable with VAMS.

  16. Radionucleotide scanning in osteomyelitis

    International Nuclear Information System (INIS)

    Radionucleotide bone scanning can be an excellent adjunct to the standard radiograph and clinical findings in the diagnosis of osteomyelitis. Bone scans have the ability to detect osteomyelitis far in advance of the standard radiograph. The sequential use of technetium and gallium has been useful in differentiating cellulitis and osteomyelitis. Serial scanning with technetium and gallium may be used to monitor the response of osteomyelitis to antibiotic therapy

  17. Domestication genomics: evidence from animals.

    Science.gov (United States)

    Wang, Guo-Dong; Xie, Hai-Bing; Peng, Min-Sheng; Irwin, David; Zhang, Ya-Ping

    2014-02-01

    Animal domestication has far-reaching significance for human society. The sequenced genomes of domesticated animals provide critical resources for understanding the genetic basis of domestication. Various genomic analyses have shed a new light on the mechanism of artificial selection and have allowed the mapping of genes involved in important domestication traits. Here, we summarize the published genomes of domesticated animals that have been generated over the past decade, as well as their origins, from a phylogenomic point of view. This review provides a general description of the genomic features encountered under a two-stage domestication process. We also introduce recent findings for domestication traits based on results from genome-wide association studies and selective-sweep scans for artificially selected genomic regions. Particular attention is paid to issues relating to the costs of domestication and the convergent evolution of genes between domesticated animals and humans.

  18. Getting a CAT Scan

    Medline Plus

    Full Text Available ... Crushes What's a Booger? Getting a CAT Scan (Video) KidsHealth > For Kids > Getting a CAT Scan (Video) Print A A A Text Size en español Obtención de una tomografía computada (video) CAT stands for "computerized axial tomography." Translated, that ...

  19. Getting a CAT Scan

    Medline Plus

    Full Text Available ... Here's Help White House Lunch Recipes Getting a CAT Scan (Video) KidsHealth > For Kids > Getting a CAT Scan (Video) Print A A A Text Size en español Obtención de una tomografía computada (video) CAT stands for "computerized axial tomography." Translated, that means ...

  20. Frequency scanning microstrip antennas

    DEFF Research Database (Denmark)

    Danielsen, Magnus; Jørgensen, Rolf

    1979-01-01

    The principles of using radiating microstrip resonators as elements in a frequency scanning antenna array are described. The resonators are cascade-coupled. This gives a scan of the main lobe due to the phase-shift in the resonator in addition to that created by the transmission line phase...

  1. Abdominal CT scan

    Science.gov (United States)

    ... than regular x-rays. Many x-rays or CT scans over time may increase your risk for cancer. However, the risk from any one scan is small. Talk to your doctor about this risk and the benefit of the test for getting a correct diagnosis ...

  2. Environmental Scanning Report.

    Science.gov (United States)

    Truckee Meadows Community Coll., Sparks, NV.

    This report describes Truckee Meadows Community College's (Nevada) environmental scanning process and results. The college decided that environmental scanning and forecasting techniques should be used to plan for both short-term and long-term external factors that impact programs, enrollment, and budgets. Strategic goals include: (1) keeping pace…

  3. Optical Scanning Applications.

    Science.gov (United States)

    Wagner, Hans

    The successful use of optical scanning at the University of the Pacific (UOP) indicates that such techniques can simplify a number of administrative data processing tasks. Optical scanning is regularly used at UOP to assist with data processing in the areas of admissions, registration and grade reporting and also has applications for other tasks…

  4. Knee CT scan

    Science.gov (United States)

    Risks of CT scans include: Exposure to radiation Allergy to contrast dye CT scans give off more radiation than ... injected contrast dye. The most common type of contrast contains ... you have this an iodine allergy. If you need to have this kind of ...

  5. Getting a CAT Scan

    Medline Plus

    Full Text Available ... Dictionary of Medical Words En Español What Other Kids Are Reading Movie: Digestive System Winter Sports: Sledding, ... Booger? Getting a CAT Scan (Video) KidsHealth > For Kids > Getting a CAT Scan (Video) Print A A ...

  6. Getting a CAT Scan

    Medline Plus

    Full Text Available ... Skiing, Snowboarding, Skating Crushes What's a Booger? Getting a CAT Scan (Video) KidsHealth > For Kids > Getting a CAT Scan (Video) Print A A A Text Size en español Obtención de ...

  7. Getting a CAT Scan

    Medline Plus

    Full Text Available ... Snowboarding, Skating Crushes What's a Booger? Getting a CAT Scan (Video) KidsHealth > For Kids > Getting a CAT Scan (Video) Print A A A Text Size en español Obtención de una tomografía computada (video) CAT stands for "computerized axial tomography." Translated, that means ...

  8. Thermal image filtering by bi-dimensional empirical mode decomposition

    Science.gov (United States)

    Gavriloaia, Bogdan-Mihai; Vizireanu, Constantin-Radu; Fratu, Octavian; Mara, Constantin; Vizireanu, Dragos-Nicolae; Preda, Radu; Gavriloaia, Gheorghe

    2015-02-01

    The abnormal function of cells can be detected by anatomic or physiological registrations. Most of modern approaches, as ultrasound, RMN or CT, show anatomic parametric modifications of tissues or organs. They highlight areas with a larger diameter 1 cm. In the case of skin or superficial cancers, local temperature is different, and it can be put out by thermal imager. Medical imaging is a leading role in modern diagnosis for abnormal or normal tissues or organs. Some information has to be improved for a better diagnosis by reducing or removing some unwanted information like noise affecting image texture. The traditional technologies for medical image enhancement use spatial or frequency domain methods, but whole image processing will hide both partial and specific information for human signals. A particular kind of medical images is represented by thermal imaging. Recently, these images were used for skin or superficial cancers diagnosis, but very clear outlines of certain alleged affected areas need to be shown. Histogram equalization cannot highlights the edges and control the effects of enhancement. A new filtering method was introduced by Huang by using the empirical mode decomposition, EMD. An improved filtering method for thermal images, based on EMD, is presented in this paper, and permits to analyze nonlinear and non-stationary data by the adaptive decomposition into intrinsic mode surfaces. The results, evaluated by SNR ratios, are compared with other filtering methods.

  9. Scanning with Iodine-125

    International Nuclear Information System (INIS)

    The use of I125 as I125-iodide for scanning of the thyroid and of thyroid carcinoma métastasés and as I125-labelled Rose Bengal for scanning of the liver has been investigated in our laboratories. In some patients, the thyroid scans and the scans of thyroid carcinoma metastases were repeated with I131. The liver scans were repeated with colloidal Au198. Cold nodules in the thyroid which could not be detected with I131 were clearly seen with I125. Anterior métastasés in the lungs could be differentiated from posterior métastasés with I125, while with I131 this was not possible. Using the same doses of radioactivity the background with I131 was much higher and could not be eliminated, as this would have reduced the counting rate over the lesions to levels which could not be detected. Some of the photoscans and mechanical scans of livers carried out with colloidal Au198 could not be interpreted. However, ''cold'' lesions were clearly seen on the scans of the same livers with I125-labelled Rose Bengal. (author)

  10. The conical scan radiometer

    Science.gov (United States)

    Prosch, T.; Hennings, D.

    1982-07-01

    A satellite-borne conical scan radiometer (CSR) is proposed, offering multiangular and multispectral measurements of Earth radiation fields, including the total radiances, which are not available from conventional radiometers. Advantages of the CSR for meteorological studies are discussed. In comparison to conventional cross track scanning instruments, the CSR is unique with respect to the selected picture element size which is kept constant by means of a specially shaped detector matrix at all scan angles. The conical scan mode offers the chance to improve angular sampling. Angular sampling gaps of previous satellite-borne radiometers can be interpolated and complemented by CSR data. Radiances are measured through 10 radiometric channels which are selected to study cloudiness, water vapor, ozone, surface albedo, ground and mean stratospheric temperature, and aerosols.

  11. Pediatric CT Scans

    Science.gov (United States)

    The Radiation Epidemiology Branch and collaborators have initiated a retrospective cohort study to evaluate the relationship between radiation exposure from CT scans conducted during childhood and adolescence and the subsequent development of cancer.

  12. Pelvic CT scan

    Science.gov (United States)

    ... Abscess (collection of pus) Bladder stones Broken bone Cancer Diverticulitis ... scans over time may increase your risk of cancer. But the risk from any ... to contrast dye. Let your provider know if you have ever ...

  13. Sinus CT scan

    Science.gov (United States)

    ... may be due to: Birth defects Bone fractures Cancer Polyps in the sinuses Sinus infection (sinusitis) ... scans over time may increase your risk for cancer. However, the risk ... to contrast dye. Let your provider know if you have ever ...

  14. Cancer genomics

    DEFF Research Database (Denmark)

    Norrild, Bodil; Guldberg, Per; Ralfkiær, Elisabeth Methner

    2007-01-01

    Almost all cells in the human body contain a complete copy of the genome with an estimated number of 25,000 genes. The sequences of these genes make up about three percent of the genome and comprise the inherited set of genetic information. The genome also contains information that determines whe...

  15. Scanning ultrafast electron microscopy

    OpenAIRE

    Yang, Ding-Shyue; Mohammed, Omar F.; Zewail, Ahmed H.

    2010-01-01

    Progress has been made in the development of four-dimensional ultrafast electron microscopy, which enables space-time imaging of structural dynamics in the condensed phase. In ultrafast electron microscopy, the electrons are accelerated, typically to 200 keV, and the microscope operates in the transmission mode. Here, we report the development of scanning ultrafast electron microscopy using a field-emission-source configuration. Scanning of pulses is made in the single-electron mode, for whic...

  16. Advanced Network Scanning

    Directory of Open Access Journals (Sweden)

    Ashiqur Rahman

    2016-07-01

    Full Text Available Network scanning is à procedure for identifying active hosts on a network, either for the purpose of attacking them or for network security assessment. Scanning procedures, such as ping sweeps and port scans, return information about which IP addresses map to live hosts that are active on the Internet and what services they offer. Another scanning method, inverse mapping, returns information about what IP addresses do not map to live hosts; this enables an attacker to make assumptions about viable addresses. Scanning is one of three components of intelligence gathering for an attacker. In the foot printing phase, the attacker creates a profile of the target organization, with information such as its domain name system (DNS and e-mail servers, and its IP address range. Most of this information is available online. In the scanning phase, the attacker finds information about the specific IP addresses that can be accessed over the Internet, their operating systems, the system architecture, and the services running on each computer. In the enumeration phase, the attacker gathers information such as network user and group names, routing tables, and Simple Network Management Protocol (SNMP data

  17. Lung Ventilation/Perfusion Scan

    Science.gov (United States)

    ... two types of scans: ventilation and perfusion. The ventilation scan shows where air flows in your lungs. The perfusion scan shows where blood flows in your lungs. Both scans use radioisotopes (a low-risk radioactive substance). For the ventilation scan, you ...

  18. Scanning Probe Microscopy and Spectroscopy

    Science.gov (United States)

    Wiesendanger, Roland

    1994-09-01

    Preface; List of acronyms; Introduction; Part I. Experimental Methods and Theoretical Background of Scanning Probe Microscopy and Spectroscopy: 1. Scanning tunnelling microscopy; 2. Scanning force microscopy; 3. Related scanning probe techniques; Part II. Applications of Scanning Probe Microscopy and Spectroscopy: 4. Condensed matter physics; 5. Chemistry; 6. Organic materials; 7. Metrology and standards; 8. Nanotechnology; References; Index.

  19. Lung scans and malignancy

    International Nuclear Information System (INIS)

    An experience of pulmonary isotope scanning carried out with mercury 197 labelled mercury chloride and acetate, cobalt 57-labelled bleomycin, and Cu67 and Cu64 labelled copper citrate was presented. The scans were carried out with various isotopes supplied by the French Atomic Energy Authority, and gave comparable results, which may be summarised as follows: increased uptake in more than 90% of cases of carcinoma, absent uptake in all cases of benign tumour, frequent increased uptake in acute or advanced inflammatory lesions, absence of uptake, very commonly, in tuberculoma and chronic lesions with scar formation. Radio-isotope scan using Cu67 labelled copper citrate permitted discrimination of malignant tumours (increased fixation which showed up best at the 24th hour) from inflammatory lesions (increased fixation which was reduced on the 24th hour). The positive or negative character of the fixation in a given lesions remains the same, whatever the isotope used in our experience

  20. Adaptive Optical Scanning Holography

    Science.gov (United States)

    Tsang, P. W. M.; Poon, Ting-Chung; Liu, J.-P.

    2016-01-01

    Optical Scanning Holography (OSH) is a powerful technique that employs a single-pixel sensor and a row-by-row scanning mechanism to capture the hologram of a wide-view, three-dimensional object. However, the time required to acquire a hologram with OSH is rather lengthy. In this paper, we propose an enhanced framework, which is referred to as Adaptive OSH (AOSH), to shorten the holographic recording process. We have demonstrated that the AOSH method is capable of decreasing the acquisition time by up to an order of magnitude, while preserving the content of the hologram favorably. PMID:26916866

  1. Bone scan in rheumatology

    International Nuclear Information System (INIS)

    In this chapter a revision is made concerning different uses of bone scan in rheumatic diseases. These include reflex sympathetic dystrophy, osteomyelitis, spondyloarthropaties, metabolic bone diseases, avascular bone necrosis and bone injuries due to sports. There is as well some comments concerning pediatric pathology and orthopedics. (authors). 19 refs., 9 figs

  2. Scan This Book!

    Science.gov (United States)

    Albanese, Andrew Richard

    2007-01-01

    In this article, the author presents an interview with Brewster Kahle, leader of the Open Content Alliance (OCA). OCA book scan program is an alternative to Google's library project that aims to make books accessible online. In this interview, Kahle discusses his views on the challenges of getting books on the Web, on Google's library…

  3. Lung gallium scan

    Science.gov (United States)

    ... Critical Care, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA. Also reviewed by David Zieve, MD, MHA, Isla Ogilvie, PhD, and the A.D.A.M. Editorial team. Related MedlinePlus Health Topics Lung Diseases Nuclear Scans Sarcoidosis Browse the Encyclopedia A.D.A. ...

  4. Surface micromachined scanning mirrors

    DEFF Research Database (Denmark)

    Mattsson, Kent Erik

    1992-01-01

    Both aluminum cantilever and torsional scanning mirrors have been fabricated and their static and dynamic properties are studied experimentally and theoretically. The experiments showed resonance frequencies in the range of 163 k-Hz - 632 kHz for cantilever beams with Q values between 5 and 11. T...

  5. Scanning bubble chamber pictures

    CERN Multimedia

    1974-01-01

    These were taken at the 2 m hydrogen bubble chamber. The photo shows an early Shiva system where the pre-measurements needed to qualify the event were done manually (cf photo 7408136X). The scanning tables were located in bld. 12. Gilberte Saulmier sits on foreground, Inge Arents at centre.

  6. Energy Scan program

    Directory of Open Access Journals (Sweden)

    Poniatowska Katarzyna M.

    2014-04-01

    Full Text Available Femtoscopy of two non-identical particles in heavy ion collisions enables one to study the space-time asymmetry in the particle's emission process. Theoretical studies based on EPOS model performed for collision energies from the Beam Energy Scan program in STAR allow us to investigate the dependence of source sizes and dynamics effects. Obtained information will enable us to predict the collective behaviour of femtoscopic particle's source.

  7. Forensic Scanning Electron Microscope

    Science.gov (United States)

    Keeley, R. H.

    1983-03-01

    The scanning electron microscope equipped with an x-ray spectrometer is a versatile instrument which has many uses in the investigation of crime and preparation of scientific evidence for the courts. Major applications include microscopy and analysis of very small fragments of paint, glass and other materials which may link an individual with a scene of crime, identification of firearms residues and examination of questioned documents. Although simultaneous observation and chemical analysis of the sample is the most important feature of the instrument, other modes of operation such as cathodoluminescence spectrometry, backscattered electron imaging and direct x-ray excitation are also exploited. Marks on two bullets or cartridge cases can be compared directly by sequential scanning with a single beam or electronic linkage of two instruments. Particles of primer residue deposited on the skin and clothing when a gun is fired can be collected on adhesive tape and identified by their morphology and elemental composition. It is also possible to differentiate between the primer residues of different types of ammunition. Bullets may be identified from the small fragments left behind as they pass through the body tissues. In the examination of questioned documents the scanning electron microscope is used to establish the order in which two intersecting ink lines were written and to detect traces of chemical markers added to the security inks on official documents.

  8. Linking the genomes of nonmodel teleosts through comparative genomics.

    Science.gov (United States)

    Sarropoulou, E; Nousdili, D; Magoulas, A; Kotoulas, G

    2008-01-01

    Recently the genomes of two more teleost species have been released: the medaka (Oryzias latipes), and the three-spined stickleback (Gasterosteus aculateus). The rapid developments in genomics of fish species paved the way to new and valuable research in comparative genetics and genomics. With the accumulation of information in model species, the genetic and genomic characterization of nonmodel, but economically important species, is now feasible. Furthermore, comparison of low coverage gene maps of aquacultured fish species against fully sequenced fish species will enhance the efficiency of candidate genes identification projected for quantitative trait loci (QTL) scans for traits of commercial interest. This study shows the syntenic relationship between the genomes of six different teleost species, including three fully sequenced model species: Tetraodon nigroviridis, Oryzias latipes, Gasterosteus aculateus, and three marine species of commercial and evolutionary interest: Sparus aurata, Dicentrarchus labrax, Oreochromis spp. All three commercial fish species belong to the order Perciformes, which is the richest in number of species (approximately 10,000) but poor in terms of available genomic information and tools. Syntenic relationships were established by using 800 EST and microsatellites sequences successfully mapped on the RH map of seabream. Comparison to the stickleback genome produced most positive BLAT hits (58%) followed by medaka (32%) and Tetraodon (30%). Thus, stickleback was used as the major stepping stone to compare seabass and tilapia to seabream. In addition to the significance for the aquaculture industry, this approach can encompass important ecological and evolutionary implications. PMID:18297360

  9. Visualization in Scanning

    International Nuclear Information System (INIS)

    Scanning is essentially a method of making the unknown known, and for the vast majority of scanning work this means making the invisible visible. Visualization is developed as a process involving a model of eye and brain function, display performance and counter performance combined with the spatial frequency components in the object scanned. The performance of a scanner or gamma camera depends in part on its display system and experiments have been performed to determine the fractional change in count-rate which can be perceived by the eye from colour, photoscan and cathode-ray tube displays, for both circular and line sources of radioactivity. For circular sources, colour and photoscan displays are capable of making 10% increases in count-rate perceptible in backgrounds ranging from 5 to 100 counts/s for sources of 1 to 4 cm diameter, whilst cathode-ray tube and black-mark displays show only 20% at best. The results for line sources are also given. In testing for the statistical significance of count-rate differences on a scan, the counts are usually compared for equal areas. On this basis the cathode-ray tube display is only able to show five standard deviations of difference whereas colour and photoscan displays show from 2.5 to 3 standard deviations, levels not usually accepted statistically as significant. It is suggested that if the eye examines the areas surrounding the area of interest then the significance of a count-rate difference may be established more accurately and in general will be increased, thereby accounting for the visualization of apparently 'insignificant' regions. This theory is used to predict the areas of count density which should be visually perceived in the presence of noise, and extended to consider practical display conditions, which have been described in this paper. The performance of a scanner can be considered in terms of its modulation transfer function (derived from a line spread function). Fourier analysis has been performed

  10. Ultrafast scanning tunneling microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Botkin, D.A. [California Univ., Berkeley, CA (United States). Dept. of Physics]|[Lawrence Berkeley Lab., CA (United States)

    1995-09-01

    I have developed an ultrafast scanning tunneling microscope (USTM) based on uniting stroboscopic methods of ultrafast optics and scanned probe microscopy to obtain nanometer spatial resolution and sub-picosecond temporal resolution. USTM increases the achievable time resolution of a STM by more than 6 orders of magnitude; this should enable exploration of mesoscopic and nanometer size systems on time scales corresponding to the period or decay of fundamental excitations. USTM consists of a photoconductive switch with subpicosecond response time in series with the tip of a STM. An optical pulse from a modelocked laser activates the switch to create a gate for the tunneling current, while a second laser pulse on the sample initiates a dynamic process which affects the tunneling current. By sending a large sequence of identical pulse pairs and measuring the average tunnel current as a function of the relative time delay between the pulses in each pair, one can map the time evolution of the surface process. USTM was used to measure the broadband response of the STM`s atomic size tunnel barrier in frequencies from tens to hundreds of GHz. The USTM signal amplitude decays linearly with the tunnel junction conductance, so the spatial resolution of the time-resolved signal is comparable to that of a conventional STM. Geometrical capacitance of the junction does not appear to play an important role in the measurement, but a capacitive effect intimately related to tunneling contributes to the measured signals and may limit the ultimate resolution of the USTM.

  11. Nuclear Medicine Scans for Cancer

    Science.gov (United States)

    ... My ACS » Your Local Offices Close + - Text Size Nuclear Medicine Scans for Cancer Other names for these ... inflammation, or cancer. Use of monoclonal antibodies in nuclear scans A special type of antibody made in ...

  12. Scanned-cantilever atomic force microscope with large scanning range

    Institute of Scientific and Technical Information of China (English)

    Jintao Yang; Wendong Xu

    2006-01-01

    A scanned-cantilever atomic force microscope (AFM) with large scanning range is proposed, which adopts a new design named laser spot tracking. The scanned-cantilever AFM uses the separate flexure x-y scanner and z scanner instead of the conventional piezoelectric tube scanner. The closed-loop control and integrated capacitive sensors of these scanners can insure that the images of samples have excellent linearity and stability. According to the experimental results, the scanned-cantilever AFM can realize maximal 100 × 100 (μm) scanning range, and 1-nm resolution in z direction, which can meet the requirements of large scale sample testing.

  13. Quadrature wavelength scanning interferometry.

    Science.gov (United States)

    Moschetti, Giuseppe; Forbes, Alistair; Leach, Richard K; Jiang, Xiang; O'Connor, Daniel

    2016-07-10

    A novel method to double the measurement range of wavelength scanning interferometery (WSI) is described. In WSI the measured optical path difference (OPD) is affected by a sign ambiguity, that is, from an interference signal it is not possible to distinguish whether the OPD is positive or negative. The sign ambiguity can be resolved by measuring an interference signal in quadrature. A method to obtain a quadrature interference signal for WSI is described, and a theoretical analysis of the advantages is reported. Simulations of the advantages of the technique and of signal errors due to nonideal quadrature are discussed. The analysis and simulation are supported by experimental measurements to show the improved performances. PMID:27409307

  14. A Scanning Cavity Microscope

    CERN Document Server

    Mader, Matthias; Hänsch, Theodor W; Hunger, David

    2014-01-01

    Imaging of the optical properties of individual nanosystems beyond fluorescence can provide a wealth of information. However, the minute signals for absorption and dispersion are challenging to observe, and only specialized techniques requiring sophisticated noise rejection are available. Here we use signal enhancement in a scanning optical microcavity to demonstrate ultra-sensitive imaging. Harnessing multiple interactions of probe light with a sample within an optical resonator, we achieve a 1700-fold signal enhancement compared to diffraction-limited microscopy. We demonstrate quantitative imaging of the extinction cross section of gold nanoparticles with a sensitivity below 1 nm2, we show a method to improve spatial resolution potentially below the diffraction limit by using higher order cavity modes, and we present measurements of the birefringence and extinction contrast of gold nanorods. The demonstrated simultaneous enhancement of absorptive and dispersive signals promises intriguing potential for opt...

  15. Telescopic horizon scanning.

    Science.gov (United States)

    Koenderink, Jan

    2014-12-20

    The problem of "distortionless" viewing with terrestrial telescopic systems (mainly "binoculars") remains problematic. The so called "globe effect" is only partially counteracted in modern designs. Theories addressing the phenomenon have never reached definitive closure. In this paper, we show that exact distortionless viewing with terrestrial telescopic systems is not possible in general, but that it is in principle possible in-very frequent in battle field and marine applications-the case of horizon scanning. However, this involves cylindrical optical elements. For opto-electronic systems, a full solution is more readily feasible. The solution involves a novel interpretation of the relevant constraints and objectives. For final design decisions, it is not necessary to rely on a corpus of psychophysical (or ergonomic) data, although one has to decide whether the instrument is intended as an extension of the eye or as a "pictorial" device. PMID:25608206

  16. Micro scanning probes

    CERN Document Server

    Niblock, T

    2001-01-01

    This thesis covers the design methodology, theory, modelling, fabrication and evaluation of a Micro-Scanning-Probe. The device is a thermally actuated bimorph quadrapod fabricated using Micro Electro Mechanical Systems technology. A quadrapod is a structure with four arms, in this case a planar structure with the four arms forming a cross which is dry etched out of a silicon diaphragm. Each arm has a layer of aluminium deposited on it forming a bimorph. Through heating each arm actuation is achieved in the plane of the quadrapod and the direction normal to it. Fabrication of the device has required the development of bulk micromachining techniques to handle post CMOS fabricated wafers and the patterning of thickly sputtered aluminium in bulk micro machined cavities. CMOS fabrication techniques were used to incorporate diodes onto the quadrapod arms for temperature measurement of the arms. Fine tungsten and silicon tips have also been fabricated to allow tunnelling between the tip and the platform at the centr...

  17. Fluorescence in situ hybridization on human metaphase chromosomes detected by near-field scanning optical microscopy

    NARCIS (Netherlands)

    Moers, M.H.P.; Kalle, W.H.J.; Ruiter, A.G.T.; Wiegant, J.C.A.G.; Raap, A.K.; Greve, J.; Grooth, de B.G.; Hulst, van N.F.

    1996-01-01

    Fluorescence in situ hybridization o­n human metaphase chromosomes is detected by near-field scanning optical microscopy. This combination of cytochemical and scanning probe techniques enables the localization and identification of several fluorescently labelled genomic DNA fragments o­n a single ch

  18. Scan mirrors relay for high resolution laser scanning systems

    Science.gov (United States)

    Kessler, David

    2014-09-01

    Two dimensional beam deflection is often required in medical laser scanning systems such as OCT or confocal microscopy. Commonly two linear galvo mirrors are used for performance in terms of their large apertures and scan angles. The galvo mirrors are placed at the vicinity of entrance pupil of the scan lens with a "displacement distance" separating them. This distance limits the scan fields and/or reduces the effective aperture of the scan lens. Another option is to use a beam or pupil relay, and image one galvo mirror onto the other. However, beam (or pupil) relays are notoriously complicated, expensive and can add significant aberrations. This paper discusses a simple, all reflective, diffraction limited, color corrected, beam relay, capable of large scan angles and large deflecting mirrors. The design is based on a unique combination of an Offner configuration with a Schmidt aspheric corrector. The design is highly corrected up to large scan mirrors and large scan angles down to milliwaves of aberrations. It allows significantly larger scan field and or scan lenses with higher numerical aperture as compared with scanners using galvos separated by the displacement distance. While this relay is of exceptionally high performance, it has one element located where the beam is focused which may present a problem for high power lasers. Thus modifications of the above design are introduced where the beam is focused in mid air thus making it usable for high power systems such including laser marking and fabrication systems.

  19. Listeria Genomics

    Science.gov (United States)

    Cabanes, Didier; Sousa, Sandra; Cossart, Pascale

    The opportunistic intracellular foodborne pathogen Listeria monocytogenes has become a paradigm for the study of host-pathogen interactions and bacterial adaptation to mammalian hosts. Analysis of L. monocytogenes infection has provided considerable insight into how bacteria invade cells, move intracellularly, and disseminate in tissues, as well as tools to address fundamental processes in cell biology. Moreover, the vast amount of knowledge that has been gathered through in-depth comparative genomic analyses and in vivo studies makes L. monocytogenes one of the most well-studied bacterial pathogens. This chapter provides an overview of progress in the exploration of genomic, transcriptomic, and proteomic data in Listeria spp. to understand genome evolution and diversity, as well as physiological aspects of metabolism used by bacteria when growing in diverse environments, in particular in infected hosts.

  20. Enhancer Identification through Comparative Genomics

    Energy Technology Data Exchange (ETDEWEB)

    Visel, Axel; Bristow, James; Pennacchio, Len A.

    2006-10-01

    With the availability of genomic sequence from numerousvertebrates, a paradigm shift has occurred in the identification ofdistant-acting gene regulatory elements. In contrast to traditionalgene-centric studies in which investigators randomly scanned genomicfragments that flank genes of interest in functional assays, the modernapproach begins electronically with publicly available comparativesequence datasets that provide investigators with prioritized lists ofputative functional sequences based on their evolutionary conservation.However, although a large number of tools and resources are nowavailable, application of comparative genomic approaches remains far fromtrivial. In particular, it requires users to dynamically consider thespecies and methods for comparison depending on the specific biologicalquestion under investigation. While there is currently no single generalrule to this end, it is clear that when applied appropriately,comparative genomic approaches exponentially increase our power ingenerating biological hypotheses for subsequent experimentaltesting.

  1. Cephalopod genomics

    DEFF Research Database (Denmark)

    Albertin, Caroline B.; Bonnaud, Laure; Brown, C. Titus;

    2012-01-01

    The Cephalopod Sequencing Consortium (CephSeq Consortium) was established at a NESCent Catalysis Group Meeting, ``Paths to Cephalopod Genomics-Strategies, Choices, Organization,'' held in Durham, North Carolina, USA on May 24-27, 2012. Twenty-eight participants representing nine countries (Austria...... active in sequencing, assembling and annotating genomes, agreed on a set of cephalopod species of particular importance for initial sequencing and developed strategies and an organization (CephSeq Consortium) to promote this sequencing. The conclusions and recommendations of this meeting are described...

  2. Genome Sequencing

    DEFF Research Database (Denmark)

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

    The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based on transcr......The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...

  3. Radionuclide brain scanning

    International Nuclear Information System (INIS)

    At one stage of medical imaging development, radionuclide brain scanning was the only technique available for imaging of the brain. Advent of CT and MRI pushed it to the background. It regained some of the grounds lost to ''allied advances'' with the introduction of brain perfusion radiopharmaceuticals. Positron emission tomography is a promising functional imaging modality that at present will remain as a research tool in special centres in developed countries. However, clinically useful developments will gradually percolate from PET to SPECT. The non-nuclear imaging methods are totally instrument dependent; they are somewhat like escalators, which can go that far and no further. Nuclear imaging has an unlimited scope for advance because of the new developments in radiopharmaceuticals. As the introduction of a radiopharmaceutical is less costly than buying new instruments, the recent advances in nuclear imaging are gradually perfusing through the developing countries also. Therefore, it is essential to follow very closely PET developments because what is research today might become routine tomorrow

  4. LANL Robotic Vessel Scanning

    Energy Technology Data Exchange (ETDEWEB)

    Webber, Nels W. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-11-25

    Los Alamos National Laboratory in J-1 DARHT Operations Group uses 6ft spherical vessels to contain hazardous materials produced in a hydrodynamic experiment. These contaminated vessels must be analyzed by means of a worker entering the vessel to locate, measure, and document every penetration mark on the vessel. If the worker can be replaced by a highly automated robotic system with a high precision scanner, it will eliminate the risks to the worker and provide management with an accurate 3D model of the vessel presenting the existing damage with the flexibility to manipulate the model for better and more in-depth assessment.The project was successful in meeting the primary goal of installing an automated system which scanned a 6ft vessel with an elapsed time of 45 minutes. This robotic system reduces the total time for the original scope of work by 75 minutes and results in excellent data accumulation and transmission to the 3D model imaging program.

  5. Ancient genomics

    DEFF Research Database (Denmark)

    Der Sarkissian, Clio; Allentoft, Morten Erik; Avila Arcos, Maria del Carmen;

    2015-01-01

    , archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when...

  6. Herbarium genomics

    DEFF Research Database (Denmark)

    Bakker, Freek T.; Lei, Di; Yu, Jiaying;

    2016-01-01

    Herbarium genomics is proving promising as next-generation sequencing approaches are well suited to deal with the usually fragmented nature of archival DNA. We show that routine assembly of partial plastome sequences from herbarium specimens is feasible, from total DNA extracts and with specimens...

  7. Genome cartography: charting the apicomplexan genome.

    Science.gov (United States)

    Kissinger, Jessica C; DeBarry, Jeremy

    2011-08-01

    Genes reside in particular genomic contexts that can be mapped at many levels. Historically, 'genetic maps' were used primarily to locate genes. Recent technological advances in the determination of genome sequences have made the analysis and comparison of whole genomes possible and increasingly tractable. What do we see if we shift our focus from gene content (the 'inventory' of genes contained within a genome) to the composition and organization of a genome? This review examines what has been learned about the evolution of the apicomplexan genome as well as the significance and impact of genomic location on our understanding of the eukaryotic genome and parasite biology.

  8. Hyperchromatic laser scanning cytometry

    Science.gov (United States)

    Tárnok, Attila; Mittag, Anja

    2007-02-01

    In the emerging fields of high-content and high-throughput single cell analysis for Systems Biology and Cytomics multi- and polychromatic analysis of biological specimens has become increasingly important. Combining different technologies and staining methods polychromatic analysis (i.e. using 8 or more fluorescent colors at a time) can be pushed forward to measure anything stainable in a cell, an approach termed hyperchromatic cytometry. For cytometric cell analysis microscope based Slide Based Cytometry (SBC) technologies are ideal as, unlike flow cytometry, they are non-consumptive, i.e. the analyzed sample is fixed on the slide. Based on the feature of relocation identical cells can be subsequently reanalyzed. In this manner data on the single cell level after manipulation steps can be collected. In this overview various components for hyperchromatic cytometry are demonstrated for a SBC instrument, the Laser Scanning Cytometer (Compucyte Corp., Cambridge, MA): 1) polychromatic cytometry, 2) iterative restaining (using the same fluorochrome for restaining and subsequent reanalysis), 3) differential photobleaching (differentiating fluorochromes by their different photostability), 4) photoactivation (activating fluorescent nanoparticles or photocaged dyes), and 5) photodestruction (destruction of FRET dyes). With the intelligent combination of several of these techniques hyperchromatic cytometry allows to quantify and analyze virtually all components of relevance on the identical cell. The combination of high-throughput and high-content SBC analysis with high-resolution confocal imaging allows clear verification of phenotypically distinct subpopulations of cells with structural information. The information gained per specimen is only limited by the number of available antibodies and by sterical hindrance.

  9. Re-scan confocal microscopy: scanning twice for better resolution

    NARCIS (Netherlands)

    G.M.R. De Luca; R.M.P. Breedijk; R.A.J. Brandt; C.H.C. Zeelenberg; B.E. de Jong; W. Timmermans; L.N. Azar; R.A. Hoebe; S. Stallinga; E.M.M. Manders

    2013-01-01

    We present a new super-resolution technique, Re-scan Confocal Microscopy (RCM), based on standard confocal microscopy extended with an optical (re-scanning) unit that projects the image directly on a CCD-camera. This new microscope has improved lateral resolution and strongly improved sensitivity wh

  10. Scanning tunneling microscopy II further applications and related scanning techniques

    CERN Document Server

    Güntherodt, Hans-Joachim

    1995-01-01

    Scanning Tunneling Microscopy II, like its predecessor, presents detailed and comprehensive accounts of the basic principles and broad range of applications of STM and related scanning probe techniques. The applications discussed in this volume come predominantly from the fields of electrochemistry and biology. In contrast to those described in STM I, these studies may be performed in air and in liquids. The extensions of the basic technique to map other interactions are described in chapters on scanning force microscopy, magnetic force microscopy, and scanning near-field optical microscopy, together with a survey of other related techniques. Also described here is the use of a scanning proximal probe for surface modification. Together, the two volumes give a comprehensive account of experimental aspects of STM. They provide essential reading and reference material for all students and researchers involved in this field. In this second edition the text has been updated and new methods are discussed.

  11. Scanning tunneling microscopy II further applications and related scanning techniques

    CERN Document Server

    Güntherodt, Hans-Joachim

    1992-01-01

    Scanning Tunneling Microscopy II, like its predecessor, presents detailed and comprehensive accounts of the basic principles and broad range of applications of STM and related scanning probe techniques. The applications discussed in this volume come predominantly from the fields of electrochemistry and biology. In contrast to those described in Vol. I, these sudies may be performed in air and in liquids. The extensions of the basic technique to map other interactions are described inchapters on scanning force microscopy, magnetic force microscopy, scanning near-field optical microscopy, together with a survey of other related techniques. Also described here is the use of a scanning proximal probe for surface modification. Togehter, the two volumes give a comprehensive account of experimental aspcets of STM. They provide essentialreading and reference material for all students and researchers involvedin this field.

  12. Citrus Genomics

    OpenAIRE

    Talon, Manuel; Gmitter, Fred G.Jr.

    2008-01-01

    Citrus is one of the most widespread fruit crops globally, with great economic and health value. It is among the most difficult plants to improve through traditional breeding approaches. Currently, there is risk of devastation by diseases threatening to limit production and future availability to the human population. As technologies rapidly advance in genomic science, they are quickly adapted to address the biological challenges of the citrus plant system and the world's industries. The hist...

  13. Bone Densitometry (Bone Density Scan)

    Science.gov (United States)

    ... of DXA Bone Densitometry? What is a Bone Density Scan (DXA)? Bone density scanning, also called dual-energy x-ray absorptiometry ( ... is today's established standard for measuring bone mineral density (BMD). An x-ray (radiograph) is a noninvasive ...

  14. The function genomics study

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    @@ Genomics is a biology term appeared ten years ago, used to describe the researches of genomic mapping, sequencing, and structure analysis, etc. Genomics, the first journal for publishing papers on genomics research was born in 1986. In the past decade, the concept of genomics has been widely accepted by scientists who are engaging in biology research. Meanwhile, the research scope of genomics has been extended continuously, from simple gene mapping and sequencing to function genomics study. To reflect the change, genomics is divided into two parts now, the structure genomics and the function genomics.

  15. Visualization for genomics: the Microbial Genome Viewer.

    NARCIS (Netherlands)

    Kerkhoven, R.; Enckevort, F.H.J. van; Boekhorst, J.; Molenaar, D.; Siezen, R.J.

    2004-01-01

    SUMMARY: A Web-based visualization tool, the Microbial Genome Viewer, is presented that allows the user to combine complex genomic data in a highly interactive way. This Web tool enables the interactive generation of chromosome wheels and linear genome maps from genome annotation data stored in a My

  16. Dating the age of admixture via wavelet transform analysis of genome-wide data

    NARCIS (Netherlands)

    I. Pugach (Irina); R. Matveyev (Rostislav); A. Wollstein (Andreas); M.H. Kayser (Manfred); M. Stoneking (Mark)

    2011-01-01

    textabstractWe describe a PCA-based genome scan approach to analyze genome-wide admixture structure, and introduce wavelet transform analysis as a method for estimating the time of admixture. We test the wavelet transform method with simulations and apply it to genome-wide SNP data from eight admixe

  17. Re-scan confocal microscopy: scanning twice for better resolution.

    Science.gov (United States)

    De Luca, Giulia M R; Breedijk, Ronald M P; Brandt, Rick A J; Zeelenberg, Christiaan H C; de Jong, Babette E; Timmermans, Wendy; Azar, Leila Nahidi; Hoebe, Ron A; Stallinga, Sjoerd; Manders, Erik M M

    2013-01-01

    We present a new super-resolution technique, Re-scan Confocal Microscopy (RCM), based on standard confocal microscopy extended with an optical (re-scanning) unit that projects the image directly on a CCD-camera. This new microscope has improved lateral resolution and strongly improved sensitivity while maintaining the sectioning capability of a standard confocal microscope. This simple technology is typically useful for biological applications where the combination high-resolution and high-sensitivity is required.

  18. Establishing an Environmental Scanning Process.

    Science.gov (United States)

    Morrison, James L.

    1985-01-01

    A formal environmental scanning system designed to identify emerging issues, events, or trends threatening or bringing opportunity to an institution is discussed that uses a committee to systematically collect and analyze data from a variety of sources. (MSE)

  19. Scanning electron microscopy of biomaterials

    OpenAIRE

    McKinlay, K.J.; Scotchford, C A; Grant, D M; Oliver, J M; King, John R.; Brown, Paul D.

    2004-01-01

    A comparison of conventional high vacuum scanning electron microscopy (HVSEM), environmental SEM (ESEM) and confocal laser scanning microscopy (CLSM) in the assessment of cell-material interactions is made. The processing of cells cultured for conventional HVSEM leads to the loss of morphological features that are retained when using ESEM. The use of ESEM in conjunction with CLSM of the labeled cytoskeleton gives an indication of changes to the cell morphology as a consequence of incubation t...

  20. Pairagon+N-SCAN_EST: a model-based gene annotation pipeline

    DEFF Research Database (Denmark)

    Arumugam, Manimozhiyan; Wei, Chaochun; Brown, Randall H;

    2006-01-01

    This paper describes Pairagon+N-SCAN_EST, a gene annotation pipeline that uses only native alignments. For each expressed sequence it chooses the best genomic alignment. Systems like ENSEMBL and ExoGean rely on trans alignments, in which expressed sequences are aligned to the genomic loci...... of putative homologs. Trans alignments contain a high proportion of mismatches, gaps, and/or apparently unspliceable introns, compared to alignments of cDNA sequences to their native loci. The Pairagon+N-SCAN_EST pipeline's first stage is Pairagon, a cDNA-to-genome alignment program based on a Pair......HMM probability model. This model relies on prior knowledge, such as the fact that introns must begin with GT, GC, or AT and end with AG or AC. It produces very precise alignments of high quality cDNA sequences. In the genomic regions between Pairagon's cDNA alignments, the pipeline combines EST alignments...

  1. Whole Genome Sequencing

    Science.gov (United States)

    ... you want to learn. Search form Search Whole Genome Sequencing You are here Home Testing & Services Testing ... the full story, click here . What is whole genome sequencing? Whole genome sequencing is the mapping out ...

  2. Genomes on ice.

    Science.gov (United States)

    Parkhill, Julian

    2016-03-01

    This month's Genome Watch discusses the analysis of a Helicobacter pylori genome from the preserved Copper-Age mummy known as the Iceman and how ancient genomes shed light on the history of bacterial pathogens. PMID:26853114

  3. Environmental Scanning and the Information Manager.

    Science.gov (United States)

    Newsome, James; McInerney, Claire

    1990-01-01

    Discusses nine components of an environmental scanning model: selecting the scanning team; selecting resources to scan; choosing criteria for scanning; scanning the resources; identifying signals of new issues; selecting key events/issues; monitoring and analyzing events/issues; disseminating information; and deciding on appropriate organizational…

  4. Interesting bone scans - unusual findings

    Energy Technology Data Exchange (ETDEWEB)

    Dobson, M.; Wadhwa, S.S.; Mansberg, R.; Fernandes, V.B. [Wollongong Hospital, Wollongong, NSW (Australia)

    1997-12-01

    A 59-year-old female with carcinoma of the colon and known liver metastatic disease was referred for bone scan to evaluate for bone metastases. Although no bone metastases were found, there was abnormal uptake noted in the liver corresponding to a metastatic calcified lesion. The only other findings were of degenerative disease in the cervical spine, right shoulder and small joints of the hands. A 69-year-old male with carcinoma of the prostate and right side low back pain was referred for bone scan. No focal abnormalities to suggest metastatic disease were identified; findings within the cervical spine, lumber spine and knees were presumed secondary to degenerative disease. Intermittent pain persisted and the patient was referred for a repeat bone scan six months later. Previous scan findings of degenerative disease and no metastatic disease were confirmed; however, closer inspection revealed an enlarged right kidney with significant retention of tracer in the pelvicalyceal system suggesting possible obstruction. A Retrograde pyelogram was performed, and no obvious obstruction demonstrated. As bone scan findings were very suggestive of obstruction, a DTPA scan with lasix was performed showing a dilated right collecting system with no functional obstruction. Given the degree of dilation, it is possible that the patient experiences intermittent PUJ obstruction causing his symptoms. A 33-year-old male with insulin dependent diabetes mellitus and viral arthritis was referred for a bone scan. A three phase revealed increased uptake in the region of the knee and leR proximal tibia. Delayed whole body images revealed multiple focal areas of osteoblastic activity in the leR tibia. Abnormal uptake was also seen in the upper third of the leR femur. The remainder of the skeletal survey was normal. X-ray correlation of the leR tibia and femoral findings was undertaken. Combinating unilateral changes on bone scan and X-ray although very suggestive of sclerotic polyostotic

  5. The boundary-scan handbook

    CERN Document Server

    Parker, Kenneth P

    2016-01-01

    Aimed at electronics industry professionals, this 4th edition of the Boundary Scan Handbook describes recent changes to the IEEE1149.1 Standard Test Access Port and Boundary-Scan Architecture. This updated edition features new chapters on the possible effects of the changes on the work of the practicing test engineers and the new 1149.8.1 standard. Anyone needing to understand the basics of boundary scan and its practical industrial implementation will need this book. Provides an overview of the recent changes to the 1149.1 standard and the effect of the changes on the work of test engineers;   Explains the new IEEE 1149.8.1 subsidiary standard and applications;   Describes the latest updates on the supplementary IEEE testing standards. In particular, addresses: IEEE Std 1149.1                      Digital Boundary-Scan IEEE Std 1149.4                      Analog Boundary-Scan IEEE Std 1149.6                      Advanced I/O Testing IEEE Std 1149.8.1           �...

  6. Rodent malaria parasites : genome organization & comparative genomics

    NARCIS (Netherlands)

    Kooij, Taco W.A.

    2006-01-01

    The aim of the studies described in this thesis was to investigate the genome organization of rodent malaria parasites (RMPs) and compare the organization and gene content of the genomes of RMPs and the human malaria parasite P. falciparum. The release of the complete genome sequence of P. falciparu

  7. Broad scan linkage analysis in a large Tourette family pedigree

    Energy Technology Data Exchange (ETDEWEB)

    Peiffer, A.; Leppert, M. [Univ. of Utah Health Sciences Center, Salt Lake City, UT (United States); Wetering, B.J.M. van der [Univ. Hospital Rotterdam (Netherlands)

    1994-09-01

    Attempts to find a gene causing Tourette syndrome (TS) using linkage analysis have been unsuccessful even though as much as 65% of the autosomal genetic map has been excluded by the pooled results from several laboratories collaborating worldwide. One reason for this failure may be the misclassification of affection status of marry-in spouses. Specifically, we have found that six unrelated spouses in our Utah TS pedigree suffer from TS, obsessive-compulsive disorder or chronic motor tics. In light of these findings we decided to conduct a complete genomic scan from this Utah kindred with polymorphic markers in three related sibships in which there was no assortative mating. A linkage study assuming autosomal dominant inheritance was done using tetranucleotide repeat markers developed at the University of Utah. We selected markers that were less than 300 bp in size and that gave a heterozygosity of over 70% upon analysis in 4 CEPH families. Results to date with 95 markers run at an interval of 30 cM (covering 61% of the genome) show no evidence of linkage. We intend to extend the coverage to 100% of the genome. Pending completion of this scan, failure to provide evidence of linkage in our TS pedigree might then be attributed to phenotypic misclassification or erroneous assumptions regarding the genetic model of transmission.

  8. Mutation scanning of peach floral genes

    Directory of Open Access Journals (Sweden)

    Wilde H Dayton

    2011-05-01

    Full Text Available Abstract Background Mutation scanning technology has been used to develop crop species with improved traits. Modifications that improve screening throughput and sensitivity would facilitate the targeted mutation breeding of crops. Technical innovations for high-resolution melting (HRM analysis are enabling the clinic-based screening for human disease gene polymorphism. We examined the application of two HRM modifications, COLD-PCR and QMC-PCR, to the mutation scanning of genes in peach, Prunus persica. The targeted genes were the putative floral regulators PpAGAMOUS and PpTERMINAL FLOWER I. Results HRM analysis of PpAG and PpTFL1 coding regions in 36 peach cultivars found one polymorphic site in each gene. PpTFL1 and PpAG SNPs were used to examine approaches to increase HRM throughput. Cultivars with SNPs could be reliably detected in pools of twelve genotypes. COLD-PCR was found to increase the sensitivity of HRM analysis of pooled samples, but worked best with small amplicons. Examination of QMC-PCR demonstrated that primary PCR products for further analysis could be produced from variable levels of genomic DNA. Conclusions Natural SNPs in exons of target peach genes were discovered by HRM analysis of cultivars from a southeastern US breeding program. For detecting natural or induced SNPs in larger populations, HRM efficiency can be improved by increasing sample pooling and template production through approaches such as COLD-PCR and QMC-PCR. Technical advances developed to improve clinical diagnostics can play a role in the targeted mutation breeding of crops.

  9. Scanning Terahertz Heterodyne Imaging Systems

    Science.gov (United States)

    Siegel, Peter; Dengler, Robert

    2007-01-01

    Scanning terahertz heterodyne imaging systems are now at an early stage of development. In a basic scanning terahertz heterodyne imaging system, (see Figure 1) two far-infrared lasers generate beams denoted the local-oscillator (LO) and signal that differ in frequency by an amount, denoted the intermediate frequency (IF), chosen to suit the application. The LO beam is sent directly to a mixer as one of two inputs. The signal beam is focused to a spot on or in the specimen. After transmission through or reflection from the specimen, the beams are focused to a spot on a terahertz mixer, which extracts the IF outputs. The specimen is mounted on a translation stage, by means of which the focal spot is scanned across the specimen to build up an image.

  10. Calculation of Uniform of Beam Scanning

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    For the electron beam application, it is always scanned by a dipole magnet. The uniform of the scanning has great influence for some application, such as the irradiation of the thyristor. There are two methods for improving the scanning uniform:

  11. What Is a Nuclear Heart Scan?

    Science.gov (United States)

    ... from the NHLBI on Twitter. What Is a Nuclear Heart Scan? A nuclear heart scan is a test that provides important ... use it to create pictures of your heart. Nuclear heart scans are used for three main purposes: ...

  12. Children, CT Scan and Radiation

    OpenAIRE

    Morteza Bajoghli; Farshad Bajoghli; Nazila Tayari; Reza Rouzbahani

    2010-01-01

    Children are more sensitive to radiation than adults. Computer-ized tomography (CT) consists of 25 % of all medical imaging. It was estimated that more than 2% of all carcinomas in the USA are due to CT scans. There is an ongoing focus on the reduction of CT scan radiation dose. Awareness about risk-benefits of CT has increased. Reduction of radiological exam is an important issue because the accumulation effects of radiation can be hazardous. In addition, proper protocol should be followed f...

  13. RPC High Voltage Scan 2015

    CERN Document Server

    CMS Collaboration

    2016-01-01

    During the LS1 the CMS RPC system has been upgraded with 144 new chambers installed on the forth endcap stations. An annual HV (RPC efficiency vs HV) scan for the entire RPC system has been performed during the Run2 data taking period in 2015. The obtained results have been compared to the HV scans performed in 2011 and 2012. No significant differences are observed in the compared results. The optimal HV working points for the newly installed chambers have been evaluated for the first time with collision data.

  14. Producing colour pictures from SCAN

    International Nuclear Information System (INIS)

    The computer code SCAN.TSK has been written for use on the Interdata 7/32 minicomputer which will convert the pictures produced by the SCAN program into colour pictures on a colour graphics VDU. These colour pictures are a more powerful aid to detecting errors in the MONK input data than the normal lineprinter pictures. This report is intended as a user manual for using the program on the Interdata 7/32, and describes the method used to produce the pictures and gives examples of JCL, input data and of the pictures that can be produced. (U.K.)

  15. Identifying Synonymous Regulatory Elements in Vertebrate Genomes

    Energy Technology Data Exchange (ETDEWEB)

    Ovcharenko, I; Nobrega, M A

    2005-02-07

    Synonymous gene regulation, defined as driving shared temporal and/or spatial expression of groups of genes, is likely predicated on genomic elements that contain similar modules of certain transcription factor binding sites (TFBS). We have developed a method to scan vertebrate genomes for evolutionary conserved modules of TFBS in a predefined configuration, and created a tool, named SynoR that identify synonymous regulatory elements (SREs) in vertebrate genomes. SynoR performs de novo identification of SREs utilizing known patterns of TFBS in active regulatory elements (REs) as seeds for genome scans. Layers of multiple-species conservation allow the use of differential phylogenetic sequence conservation filters in the search of SREs and the results are displayed as to provide an extensive annotation of genes containing detected REs. Gene Ontology categories are utilized to further functionally classify the identified genes, and integrated GNF Expression Atlas 2 data allow the cataloging of tissue-specificities of the predicted SREs. We illustrate how this new tool can be used to establish a linkage between human diseases and noncoding genomic content. SynoR is publicly available at http://synor.dcode.org.

  16. Funding Opportunity: Genomic Data Centers

    Science.gov (United States)

    Funding Opportunity CCG, Funding Opportunity Center for Cancer Genomics, CCG, Center for Cancer Genomics, CCG RFA, Center for cancer genomics rfa, genomic data analysis network, genomic data analysis network centers,

  17. Localizing Test Power Consumption for Scan Testing

    Institute of Scientific and Technical Information of China (English)

    XIANG Dong; LI Kai-wei

    2005-01-01

    A two stage scan architecture is proposed to do low powerand low test application cost scan testing. The first stage includes multiple scan chains, where each scan chain is driven by a primary input. Each scan flip-flop in the multiple scan chains drives a group of scan flip-flops. The scan flip-flop in the multiple scan chain and the scan flipflop driven by it are assigned the same values for all test vectors. Scan flip-flops in the multiple scan chains and those in the second stage use separate clock signals, but the design for testability technqiue needs only one clock. The proposed scan architecture localizes test power consumption to the multiple scan chains during test application. Test signals assigned to scan flip-flops in the multiple scan chains are applied to the scan flip-flops in the second stage after the test vector has been applied to the multiple scan chains. This technique can make test power consumption very small.

  18. Enabling functional genomics with genome engineering.

    Science.gov (United States)

    Hilton, Isaac B; Gersbach, Charles A

    2015-10-01

    Advances in genome engineering technologies have made the precise control over genome sequence and regulation possible across a variety of disciplines. These tools can expand our understanding of fundamental biological processes and create new opportunities for therapeutic designs. The rapid evolution of these methods has also catalyzed a new era of genomics that includes multiple approaches to functionally characterize and manipulate the regulation of genomic information. Here, we review the recent advances of the most widely adopted genome engineering platforms and their application to functional genomics. This includes engineered zinc finger proteins, TALEs/TALENs, and the CRISPR/Cas9 system as nucleases for genome editing, transcription factors for epigenome editing, and other emerging applications. We also present current and potential future applications of these tools, as well as their current limitations and areas for future advances. PMID:26430154

  19. Genome Mapping in Plant Comparative Genomics.

    Science.gov (United States)

    Chaney, Lindsay; Sharp, Aaron R; Evans, Carrie R; Udall, Joshua A

    2016-09-01

    Genome mapping produces fingerprints of DNA sequences to construct a physical map of the whole genome. It provides contiguous, long-range information that complements and, in some cases, replaces sequencing data. Recent advances in genome-mapping technology will better allow researchers to detect large (>1kbp) structural variations between plant genomes. Some molecular and informatics complications need to be overcome for this novel technology to achieve its full utility. This technology will be useful for understanding phenotype responses due to DNA rearrangements and will yield insights into genome evolution, particularly in polyploids. In this review, we outline recent advances in genome-mapping technology, including the processes required for data collection and analysis, and applications in plant comparative genomics.

  20. Genome-wide prediction, display and refinement of binding sites with information theory-based models

    Directory of Open Access Journals (Sweden)

    Leeder J Steven

    2003-09-01

    Full Text Available Abstract Background We present Delila-genome, a software system for identification, visualization and analysis of protein binding sites in complete genome sequences. Binding sites are predicted by scanning genomic sequences with information theory-based (or user-defined weight matrices. Matrices are refined by adding experimentally-defined binding sites to published binding sites. Delila-Genome was used to examine the accuracy of individual information contents of binding sites detected with refined matrices as a measure of the strengths of the corresponding protein-nucleic acid interactions. The software can then be used to predict novel sites by rescanning the genome with the refined matrices. Results Parameters for genome scans are entered using a Java-based GUI interface and backend scripts in Perl. Multi-processor CPU load-sharing minimized the average response time for scans of different chromosomes. Scans of human genome assemblies required 4–6 hours for transcription factor binding sites and 10–19 hours for splice sites, respectively, on 24- and 3-node Mosix and Beowulf clusters. Individual binding sites are displayed either as high-resolution sequence walkers or in low-resolution custom tracks in the UCSC genome browser. For large datasets, we applied a data reduction strategy that limited displays of binding sites exceeding a threshold information content to specific chromosomal regions within or adjacent to genes. An HTML document is produced listing binding sites ranked by binding site strength or chromosomal location hyperlinked to the UCSC custom track, other annotation databases and binding site sequences. Post-genome scan tools parse binding site annotations of selected chromosome intervals and compare the results of genome scans using different weight matrices. Comparisons of multiple genome scans can display binding sites that are unique to each scan and identify sites with significantly altered binding strengths

  1. Exploring Other Genomes: Bacteria.

    Science.gov (United States)

    Flannery, Maura C.

    2001-01-01

    Points out the importance of genomes other than the human genome project and provides information on the identified bacterial genomes Pseudomonas aeuroginosa, Leprosy, Cholera, Meningitis, Tuberculosis, Bubonic Plague, and plant pathogens. Considers the computer's use in genome studies. (Contains 14 references.) (YDS)

  2. Developing an Environmental Scanning System.

    Science.gov (United States)

    Morrison, James L.

    A step-by-step approach is provided for developing an environmental scanning system for colleges and universities to assist them in planning for the future. The objectives of such a system are to detect social, scientific, economic, technical, and political interactions important to the organization; define potential threats and opportunities from…

  3. Environmental Scanning, Vancouver Community College.

    Science.gov (United States)

    Yao, Min

    This 1994 environmental scanning report from Vancouver Community College (VCC) reviews the expected effects of the separation of VCC into a new Vancouver Community College and Langara College (LC). The report examines the projected service area student-intake capacity; student characteristics; population growth trends; other postsecondary…

  4. Technical aspects of CT scanning.

    Science.gov (United States)

    Maravilla, K R; Pastel, M S

    1978-01-01

    The advent of computed tomography (CT) has initiated a technological revolution which continues to the present time. A brief review of basic principles of CT scanning is presented, and the evolution of modern CT scanner systems is traced. Some early indications of future trends are also presented.

  5. Broadband antenna with frequency scanning

    Directory of Open Access Journals (Sweden)

    A. A. Shekaturin

    2014-06-01

    Full Text Available Relevance of this study. The main advantage of frequency scanning is simplicity of implementation. At this point, multifunctional usage of microwave modules is an urgent task, as well as their maximum simpler and cheaper. Antenna design and operation. The study is aimed at providing electric antenna with frequency scanning. It was based on the log-periodic antenna due to its wideband and negotiation capability over the entire operating frequency range. For this distribution line is bent in an arc of a circle in a plane blade while vibrators are arranged along the radius. Computer modeling of antennas with frequency scanning. Modeled with a non-mechanical motion antenna beam emitters representing system for receiving a radio frequency signal on mobile objects calculated for 1.8 GHz ... 4.2 GHz. The simulation was performed in a software environment for numerical modeling of electromagnetic «Feko 5.5». Analysis of the interaction of radiation is based on the method of moments. Findings. The result of this work is to propose a new design of the antenna with a frequency scanning method as agreed in a wide frequency range. In the studied technical solution provided by the rotation of NAM in the frequency range, and the matching of the antenna to the feed line is maintained. Application of this type of antennas on the proposed technical solution in communication systems will improve the communication reliability by maintaining coordination in the frequency range

  6. Introduction to scanning tunneling microscopy

    CERN Document Server

    Chen, C Julian

    2008-01-01

    The scanning tunneling and the atomic force microscope, both capable of imaging individual atoms, were crowned with the Physics Nobel Prize in 1986, and are the cornerstones of nanotechnology today. This is a thoroughly updated version of this 'bible' in the field.

  7. Unexpected cross-species contamination in genome sequencing projects

    Directory of Open Access Journals (Sweden)

    Samier Merchant

    2014-11-01

    Full Text Available The raw data from a genome sequencing project sometimes contains DNA from contaminating organisms, which may be introduced during sample collection or sequence preparation. In some instances, these contaminants remain in the sequence even after assembly and deposition of the genome into public databases. As a result, searches of these databases may yield erroneous and confusing results. We used efficient microbiome analysis software to scan the draft assembly of domestic cow, Bos taurus, and identify 173 small contigs that appeared to derive from microbial contaminants. In the course of verifying these findings, we discovered that one genome, Neisseria gonorrhoeae TCDC-NG08107, although putatively a complete genome, contained multiple sequences that actually derived from the cow and sheep genomes. Our findings illustrate the need to carefully validate findings of anomalous DNA that rely on comparisons to either draft or finished genomes.

  8. GENOMIC MEDICINE

    Directory of Open Access Journals (Sweden)

    Ignacio Briceño Balcázar

    2011-03-01

    Full Text Available Until the twilight of the 20th century, genetics was a branch of medicine applied to diseases of rare occurrence. The advent of the human genome sequence and the possibility of studying it at affordable costs for patients and healthcare institutions, has permitted its application in high-priority diseases like cancer, cardiovascular disease, diabetes, and Alzheimer’s, among others.There is great potential in predictive and preventive medicine, through studying polymorphic genetic variants associated to risks for different diseases. Currently, clinical laboratories offer studies of over 30,000 variants associated with susceptibilities, to which individuals can access without much difficulty because a medical prescription is not required. These exams permit conducting a specific plan of preventive medicine. For example, upon the possibility of finding a deleterious mutation in the BRCA1 and BRCA2 genes, the patient can prevent the breast cancer by mastectomy or chemoprophylaxis and in the presence of polymorphisms associated to cardiovascular risk preventive action may be undertaken through changes in life style (diet, exercise, etc..Legal aspects are also present in this new conception of medicine. For example, currently there is legislation for medications to indicate on their labels the different responses such medication can offer regarding the genetic variants of the patients, given that similar doses may provoke adverse reactions in an individual, while for another such dosage may be insufficient. This scenario would allow verifying the polymorphisms of drug response prior to administering medications like anticoagulants, hyperlipidemia treatments, or chemotherapy, among others.We must specially mention recessive diseases, produced by the presence of two alleles of a mutated gene, which are inherited from the mother, as well as the father. By studying the mutations, we may learn if a couple is at risk of bearing children with the disease

  9. Genomic Medicine

    Directory of Open Access Journals (Sweden)

    Ignacio Briceño Balcázar

    2011-04-01

    Full Text Available Until the twilight of the 20th century, genetics was a branch of medicine applied to diseases of rare occurrence.  The advent of the human genome sequence and the possibility of studying it at affordable costs for patients and healthcare institutions, has permitted its application in high-priority diseases like cancer, cardiovascular disease, diabetes, and Alzheimer’s, among others. There is great potential in predictive and preventive medicine, through studying polymorphic genetic variants associated to risks for different diseases. Currently, clinical laboratories offer studies of over 30,000 variants associated with susceptibilities, to which individuals can access without much difficulty because a medical prescription is not required. These exams permit conducting a specific plan of preventive medicine.  For example, upon the possibility of finding a deleterious mutation in the BRCA1 and BRCA2 genes, the patient can prevent the breast cancer by mastectomy or chemoprophylaxis and in the presence of polymorphisms associated to cardiovascular risk preventive action may be undertaken through changes in life style (diet, exercise, etc.. Legal aspects are also present in this new conception of medicine.  For example, currently there is legislation for medications to indicate on their labels the different responses such medication can offer regarding the genetic variants of the patients, given that similar doses may provoke adverse reactions in an individual, while for another such dosage may be insufficient. This scenario would allow verifying the polymorphisms of drug response prior to administering medications like anticoagulants, hyperlipidemia treatments, or chemotherapy, among others. We must specially mention recessive diseases, produced by the presence of two alleles of a mutated gene, which are inherited from the mother, as well as the father. By studying the mutations, we may learn if a couple is at risk of bearing children with the

  10. Genomes and evolutionary genomics of animals

    Institute of Scientific and Technical Information of China (English)

    Luting SONG; Wen WANG

    2013-01-01

    Alongside recent advances and booming applications of DNA sequencing technologies,a great number of complete genome sequences for animal species are available to researchers.Hundreds of animals have been involved in whole genome sequencing,and at least 87 non-human animal species' complete or draft genome sequences have been published since 1998.Based on these technological advances and the subsequent accumulation of large quantity of genomic data,evolutionary genomics has become one of the most rapidly advancing disciplines in biology.Scientists now can perform a number of comparative and evolutionary genomic studies for animals,to identify conserved genes or other functional elements among species,genomic elements that confer animals their own specific characteristics and new phenotypes for adaptation.This review deals with the current genomic and evolutionary research on non-human animals,and displays a comprehensive landscape of genomes and the evolutionary genomics of non-human animals.It is very helpful to a better understanding of the biology and evolution of the myriad forms within the animal kingdom [Current Zoology 59 (1):87-98,2013].

  11. Genome Maps, a new generation genome browser

    Science.gov (United States)

    Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

    2013-01-01

    Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org. PMID:23748955

  12. Genome Maps, a new generation genome browser.

    Science.gov (United States)

    Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

    2013-07-01

    Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org. PMID:23748955

  13. Genome Maps, a new generation genome browser.

    Science.gov (United States)

    Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

    2013-07-01

    Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org.

  14. Control on Electron Beam Scanning Track

    Institute of Scientific and Technical Information of China (English)

    王学东; 姚舜

    2004-01-01

    In order to use electron beam as a movable welding heat source and whose energy distribution along its moving trace can be controlled, a method of electron beam scanning track and scanning mode control was put forward. Based on it, the electron beam scanning track and scanning mode can be edited at will according to actual requirements, and the energy input of each point of the scanning track can be controlled. In addition, the scanning frequency and points control, real time adjusting of the scanning track etc. were explained. This method can be used in electron beam brazing, surface modification, surface heat treatment etc.

  15. Children, CT scan and radiation

    Directory of Open Access Journals (Sweden)

    Morteza Bajoghli

    2010-01-01

    Full Text Available Children are more sensitive to radiation than adults. Computer-ized tomography (CT consists of 25 % of all medical imaging. It was estimated that more than 2% of all carcinomas in the USA are due to CT scans. There is an ongoing focus on the reduction of CT scan radiation dose. Awareness about risk-benefits of CT has increased. Reduction of radiological exam is an important issue because the accumulation effects of radiation can be hazardous. In addition, proper protocol should be followed for diagnostic pro-cedures of ionization radiation and computerized tomography. Effective radiation dose should range from 0.8 to 10.5 millisievert. The same protocol should be followed in different hospitals as well. Basic principles of radiation protection should be monitored. As much as possible, both technician and radiologist must be pre-sent during computerized tomography for children, and MRI and ultrasound should be replaced if possible.

  16. /sup 67/Ga lung scan

    Energy Technology Data Exchange (ETDEWEB)

    Niden, A.H.; Mishkin, F.S.; Khurana, M.M.L.; Pick, R.

    1977-03-21

    Twenty-three patients with clinical signs of pulmonary embolic disease and lung infiltrates were studied to determine the value of gallium citrate /sup 67/Ga lung scan in differentiating embolic from inflammatory lung disease. In 11 patients without angiographically proved embolism, only seven had corresponding ventilation-perfusion defects compatible with inflammatory disease. In seven of these 11 patients, the /sup 67/Ga concentration indicated inflammatory disease. In the 12 patients with angiographically proved embolic disease, six had corresponding ventilation-perfusion defects compatible with inflammatory disease. None had an accumulation of /sup 67/Ga in the area of pulmonary infiltrate. Thus, ventilation-perfusion lung scans are of limited value when lung infiltrates are present. In contrast, the accumulation of /sup 67/Ga in the lung indicates an inflammatory process. Gallium imaging can help select those patients with lung infiltrates who need angiography.

  17. Seismic scanning tunneling macroscope - Theory

    KAUST Repository

    Schuster, Gerard T.

    2012-09-01

    We propose a seismic scanning tunneling macroscope (SSTM) that can detect the presence of sub-wavelength scatterers in the near-field of either the source or the receivers. Analytic formulas for the time reverse mirror (TRM) profile associated with a single scatterer model show that the spatial resolution limit to be, unlike the Abbe limit of λ/2, independent of wavelength and linearly proportional to the source-scatterer separation as long as the point scatterer is in the near-field region; if the sub-wavelength scatterer is a spherical impedance discontinuity then the resolution will also be limited by the radius of the sphere. Therefore, superresolution imaging can be achieved as the scatterer approaches the source. This is analogous to an optical scanning tunneling microscope that has sub-wavelength resolution. Scaled to seismic frequencies, it is theoretically possible to extract 100 Hz information from 20 Hz data by imaging of near-field seismic energy.

  18. Micro computed tomography (CT) scanned anatomical gateway to insect pest bioinformatics

    Science.gov (United States)

    An international collaboration to establish an interactive Digital Video Library for a Systems Biology Approach to study the Asian citrus Psyllid and psyllid genomics/proteomics interactions is demonstrated. Advances in micro-CT, digital computed tomography (CT) scan uses X-rays to make detailed pic...

  19. Differential scanning calorimetry of coal

    Science.gov (United States)

    Gold, P. I.

    1978-01-01

    Differential scanning calorimetry studies performed during the first year of this project demonstrated the occurrence of exothermic reactions associated with the production of volatile matter in or near the plastic region. The temperature and magnitude of the exothermic peak were observed to be strongly affected by the heating rate, sample mass and, to a lesser extent, by sample particle size. Thermal properties also were found to be influenced by oxidation of the coal sample due to weathering effects.

  20. Octreotide scanning for carcinoid tumours.

    OpenAIRE

    Critchley, M

    1997-01-01

    The somatostatin analogue octreotide may be used in the diagnosis of carcinoid and other neuroendocrine tumours. Radionuclide scanning following intravenous injection of 111Indium-labelled octreotide (111In-DTPA-pentetreotide) provides a sensitive, non-invasive method of localising somatostatin-positive tumours. The technique may also be used to identify patients who may respond to 'cold' octreotide therapy and to monitor therapeutic efficacy.

  1. 3D scanning with Kinect

    OpenAIRE

    Novak, David

    2012-01-01

    This paper describes the procedures and technologies used for scanning and three-dimensional reconstruction of objects using the optical scanner Kinect. Theoretical backgrounds of basic computer graphics, projective geometry, optics and graphical reconstruction were studied for better understanding of this field of computer science. A part of the content also describes the structure and operating of the Kinect and is used as a theoretical basis for implementing a new framework for three-di...

  2. Genomic Encyclopedia of Fungi

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor

    2012-08-10

    Genomes of fungi relevant to energy and environment are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 150 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such parts suggested by comparative genomics and functional analysis in these areas are presented here.

  3. JGI Fungal Genomics Program

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor V.

    2011-03-14

    Genomes of energy and environment fungi are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 50 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such 'parts' suggested by comparative genomics and functional analysis in these areas are presented here

  4. New Snail Mail Scanning Service

    CERN Multimedia

    2012-01-01

    Modernisation does not stop at the CERN postal service (GS/PS). “With more and more digitisation and the prevalence of e-mail throughout the site, we were hoping to provide more timely delivery of letters and make further saving in resources”, said Tueri Datta, head of GS/PS.   Instead of the standard delivery to your P.O. box, the CERN postal service will digitally scan all letters and books up to 100 pages on reception. These scans will subsequently be sent via e-mail to the corresponding recipient as PDF (Portable Data Format - you will need to install “Acrobat Reader” on your PC). Express mail will be handled with priority. Users without a valid CERN mailbox can register at mail.scan.service@cern.ch in order to have their letters read to them via the phone line (we are currently investigating whether we can use the voices of the last five DGs).   This service will start on 1st April 2012 on the Meyrin site and will gradually replace th...

  5. Mechanically scanned deployable antenna study

    Science.gov (United States)

    1983-03-01

    The conceptual design of a Mechanically Scanned Deployable Antenna which is launched by the STS (Space Shuttle) to provide radiometric brightness temperature maps of the Earth and oceans at selected frequency bands in the frequency range of 1.4 GHz to 11 GHz is presented. Unlike previous scanning radiometric systems, multiple radiometers for each frequency are required in order to fill in the resolution cells across the swath created by the 15 meter diameter spin stabilized system. This multiple beam radiometric system is sometimes designated as a ""whiskbroom'' system in that it combines the techniques of the scanning and ""pushbroom'' type systems. The definition of the feed system including possible feed elements and location, determination of the fundamental reflector feed offset geometry including offset angles and f/D ratio, preliminary estimates of the beam efficiency of the feed reflector system, a summary of reflector mesh losses at the proposed radiometric frequency bands, an overall conceptual configuration design and preliminary structural and thermal analyses are included.

  6. Genomic Data Commons | Office of Cancer Genomics

    Science.gov (United States)

    The NCI’s Center for Cancer Genomics launches the Genomic Data Commons (GDC), a unified data sharing platform for the cancer research community. The mission of the GDC is to enable data sharing across the entire cancer research community, to ultimately support precision medicine in oncology.

  7. Phytophthora genomics: the plant destroyers' genome decoded

    NARCIS (Netherlands)

    Govers, F.; Gijzen, M.

    2006-01-01

    The year 2004 was an exciting one for the Phytophthora research community. The United States Department of Energy Joint Genome Institute (JGI) completed the draft genome sequence of two Phytophthora species, Phytophthora sojae and Phytophthora ramorum. In August of that year over 50 people gathered

  8. Comparative Genome Analysis and Genome Evolution

    NARCIS (Netherlands)

    Snel, Berend

    2003-01-01

    This thesis described a collection of bioinformatic analyses on complete genome sequence data. We have studied the evolution of gene content and find that vertical inheritance dominates over horizontal gene trasnfer, even to the extent that we can use the gene content to make genome phylogenies. Usi

  9. Genomic Data Commons launches

    Science.gov (United States)

    The Genomic Data Commons (GDC), a unified data system that promotes sharing of genomic and clinical data between researchers, launched today with a visit from Vice President Joe Biden to the operations center at the University of Chicago.

  10. Rat Genome Database (RGD)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Rat Genome Database (RGD) is a collaborative effort between leading research institutions involved in rat genetic and genomic research to collect, consolidate,...

  11. Bipolar affective puerperal psychosis- genome-wide significant evidence for linkage to chromosome 16.

    OpenAIRE

    Corvin, Aiden; Gill, Michael

    2007-01-01

    OBJECTIVE: Vulnerability to the triggering of bipolar episodes by childbirth aggregates in families and may define a genetically relevant subtype of bipolar disorder. The authors conducted a search by systematic whole genome linkage scan for loci influencing vulnerability to bipolar affective puerperal psychosis. METHOD: The authors selected families with bipolar disorder from their previous bipolar disorder genome scan, in which there was at least one family member with a manic or psychotic ...

  12. An Adaptive Algorithm to Detect Port Scans

    Institute of Scientific and Technical Information of China (English)

    单蓉胜; 李小勇; 李建华

    2004-01-01

    Detection of port scan is an important component in a network intrusion detection and prevention system. Traditional statistical methods can be easily evaded by stealthy scans and are prone to DeS attacks. This paper presents a new mechanism termed PSD(port scan detection), which is based on TCP packet anomaly evaluation. By learning the port distribution and flags of TCP packets arriving at the protected hosts, PSD can compute the anomaly score of each packet and effectively detect port scans including slow scans and stealthy scans. Experiments show that PSD has high detection accuracy and low detection latency.

  13. Aperture scanning Fourier ptychographic microscopy

    Science.gov (United States)

    Ou, Xiaoze; Chung, Jaebum; Horstmeyer, Roarke; Yang, Changhuei

    2016-01-01

    Fourier ptychographic microscopy (FPM) is implemented through aperture scanning by an LCOS spatial light modulator at the back focal plane of the objective lens. This FPM configuration enables the capturing of the complex scattered field for a 3D sample both in the transmissive mode and the reflective mode. We further show that by combining with the compressive sensing theory, the reconstructed 2D complex scattered field can be used to recover the 3D sample scattering density. This implementation expands the scope of application for FPM and can be beneficial for areas such as tissue imaging and wafer inspection. PMID:27570705

  14. ABS: Sequence alignment by scanning

    KAUST Repository

    Bonny, Mohamed Talal

    2011-08-01

    Sequence alignment is an essential tool in almost any computational biology research. It processes large database sequences and considered to be high consumers of computation time. Heuristic algorithms are used to get approximate but fast results. We introduce fast alignment algorithm, called Alignment By Scanning (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the well-known alignment algorithms, the FASTA (which is heuristic) and the \\'Needleman-Wunsch\\' (which is optimal). The proposed algorithm achieves up to 76% enhancement in alignment score when it is compared with the FASTA Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

  15. Genomics of Sorghum

    OpenAIRE

    Paterson, Andrew H.

    2008-01-01

    Sorghum (Sorghum bicolor (L.) Moench) is a subject of plant genomics research based on its importance as one of the world's leading cereal crops, a biofuels crop of high and growing importance, a progenitor of one of the world's most noxious weeds, and a botanical model for many tropical grasses with complex genomes. A rich history of genome analysis, culminating in the recent complete sequencing of the genome of a leading inbred, provides a foundation for invigorating progress toward relatin...

  16. Exploiting the genome

    Energy Technology Data Exchange (ETDEWEB)

    Block, S. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Cornwall, J. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Dyson, F. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Koonin, S. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Lewis, N. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Schwitters, R. [The MITRE Corporation, McLean, VA (US). JASON Program Office

    1998-09-11

    In 1997, JASON conducted a DOE-sponsored study of the human genome project with special emphasis on the areas of technology, quality assurance and quality control, and informatics. The present study has two aims: first, to update the 1997 Report in light of recent developments in genome sequencing technology, and second, to consider possible roles for the DOE in the ''post-genomic" era, following acquisition of the complete human genome sequence.

  17. Whole Genome Selection

    Science.gov (United States)

    Whole genome selection (WGS) is an approach to using DNA markers that are distributed throughout the entire genome. Genes affecting most economically-important traits are distributed throughout the genome and there are relatively few that have large effects with many more genes with progressively sm...

  18. Chicken's Genome Decoded

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    @@ After completing the work on mapping chicken genome sequence and chicken genome variation in early March, 2004, two international research consortiums have made significant progress in reading the maps, shedding new light on the studies into the first bird as well as the first agricultural animal that has its genome sequenced and analyzed in the world.

  19. Public Health Genomics

    OpenAIRE

    Lavinha, João

    2012-01-01

    Professional genomic and molecular medicine and consumer genetics. The health field concept and the public health wheel. The enterprise of Public Health Genomics (PHGEN). Genetic exceptionalism. Ethical benchmarks. Introduction and use of genome-based knowledge in the health services. Stakeholder involvement.

  20. Ebolavirus comparative genomics

    DEFF Research Database (Denmark)

    Jun, Se-Ran; Leuze, Michael R.; Nookaew, Intawat;

    2015-01-01

    The 2014 Ebola outbreak in West Africa is the largest documented for this virus. To examine the dynamics of this genome, we compare more than 100 currently available ebolavirus genomes to each other and to other viral genomes. Based on oligomer frequency analysis, the family Filoviridae forms...

  1. Contrasting signals of positive selection in genes involved in human skin-color variation from tests based on SNP scans and resequencing

    NARCIS (Netherlands)

    J.M. de Gruijter (Johanna); O. Lao Grueso (Oscar); M. Vermeulen (Mark); Y. Xue (Yali); C. Woodwark (Cara); C.J. Gillson (Christopher); A.J. Coffey (Alison); Q. Ayub (Qasim); S.Q. Mehdi (Qasim); M.H. Kayser (Manfred); C. Tyler-Smith (Chris)

    2011-01-01

    textabstractBackground: Numerous genome-wide scans conducted by genotyping previously ascertained single-nucleotide polymorphisms (SNPs) have provided candidate signatures for positive selection in various regions of the human genome, including in genes involved in pigmentation traits. However, it i

  2. Using Environmental Scans in Educational Needs Assessment.

    Science.gov (United States)

    Hatch, Terry F.; Pearson, Thomas G.

    1998-01-01

    Presents advantages and disadvantages of environmental scanning for assessing the context of professional continuing education. Provides a checklist for evaluating the quality and usefulness of information sources. Addresses the ethics of scanning. (SK)

  3. Three-dimensional scanning confocal laser microscope

    Science.gov (United States)

    Anderson, R. Rox; Webb, Robert H.; Rajadhyaksha, Milind

    1999-01-01

    A confocal microscope for generating an image of a sample includes a first scanning element for scanning a light beam along a first axis, and a second scanning element for scanning the light beam at a predetermined amplitude along a second axis perpendicular to the first axis. A third scanning element scans the light beam at a predetermined amplitude along a third axis perpendicular to an imaging plane defined by the first and second axes. The second and third scanning element are synchronized to scan at the same frequency. The second and third predetermined amplitudes are percentages of their maximum amplitudes. A selector determines the second and third predetermined amplitudes such that the sum of the percentages is equal to one-hundred percent.

  4. Electronically-Scanned Fourier-Transform Spectrometer

    Science.gov (United States)

    Breckinridge, J. B.; Ocallaghan, F. G.

    1984-01-01

    Instrument efficient, lightweight, and stable. Fourier-transform spectrometer configuration uses electronic, instead of mechanical, scanning. Configuration insensitive to vibration-induced sampling errors introduced into mechanically scanned systems.

  5. Genome-wide effects of long-term divergent selection.

    Directory of Open Access Journals (Sweden)

    Anna M Johansson

    2010-11-01

    Full Text Available To understand the genetic mechanisms leading to phenotypic differentiation, it is important to identify genomic regions under selection. We scanned the genome of two chicken lines from a single trait selection experiment, where 50 generations of selection have resulted in a 9-fold difference in body weight. Analyses of nearly 60,000 SNP markers showed that the effects of selection on the genome are dramatic. The lines were fixed for alternative alleles in more than 50 regions as a result of selection. Another 10 regions displayed strong evidence for ongoing differentiation during the last 10 generations. Many more regions across the genome showed large differences in allele frequency between the lines, indicating that the phenotypic evolution in the lines in 50 generations is the result of an exploitation of standing genetic variation at 100s of loci across the genome.

  6. The Genomic Medicine Game.

    Science.gov (United States)

    Tran, Elvis; de Andrés-Galiana, Enrique J; Benitez, Sonia; Martin-Sanchez, Fernando; Lopez-Campos, Guillermo H

    2016-01-01

    With advancements in genomics technology, health care has been improving and new paradigms of medicine such as genomic medicine have evolved. The education of clinicians, researchers and students to face the challenges posed by these new approaches, however, has been often lagging behind. From this the Genomic Medicine Game, an educational tool, was created for the purpose of conceptualizing the key components of Genomic Medicine. A number of phenotype-genotype associations were found through a literature review, which was used to be a base for the concepts the Genomic Medicine Game would focus on. Built in Java, the game was successfully tested with promising results. PMID:27577486

  7. A genome blogger manifesto

    Directory of Open Access Journals (Sweden)

    Corpas Manuel

    2012-10-01

    Full Text Available Abstract Cheap prices for genomic testing have revolutionized consumers’ access to personal genomics. Exploration of personal genomes poses significant challenges for customers wishing to learn beyond provider customer reports. A vibrant community has spontaneously appeared blogging experiences and data as a way to learn about their personal genomes. No set of values has publicly been described to date encapsulating ideals and code of conduct for this community. Here I present a first attempt to address this vacuum based on my own personal experiences as genome blogger.

  8. Statistics of genome architecture

    International Nuclear Information System (INIS)

    The main statistical distributions applicable to the analysis of genome architecture and genome tracks are briefly discussed and critically assessed. Although the observed features in distributions of element lengths can be equally well fitted by the different statistical approximations, the interpretation of observed regularities may strongly depend on the chosen scheme. We discuss the possible evolution scenarios and describe the main characteristics obtained with different distributions. The expression for the assessment of levels in hierarchical chromatin folding is derived and the quantitative measure of genome architecture inhomogeneity is suggested. This theory provides the ground for the regular statistical study of genome architecture and genome tracks.

  9. GENOME-WIDE ASSOCIATION ANALYSIS IDENTIFIES LOCI FOR PRODUCTIVE TRAITS IN JERSEY BREED

    Science.gov (United States)

    A major objective of genomic research in dairy cattle at present is to identify, map, and characterize individual quantitative trait loci (QTL) that affects production traits. A genome scan was conducted in the US Jersey population to identify QTL affecting milk, fat and protein production. Data use...

  10. Issue Scanning: Finding the Future...Maybe.

    Science.gov (United States)

    Plog, Michael; Sweeney, Jim; Weiss, Barry

    Issue Scanning, sometimes called Environmental Scanning, is used in many business, government, educational, and nonprofit organizations. The technique is supposed to monitor the "pulse" of the external environment. The scanning process should lessen the randomness of the information used in decision making, and it should alert managers to trends…

  11. Genome-wide association analysis of milk yield traits in Nordic Red Cattle using imputed whole genome sequence variants

    DEFF Research Database (Denmark)

    Iso-Touru, T; Sahana, G; Guldbrandtsen, B;

    2016-01-01

    variants behind them. In this study, we used whole genome sequence level data from 4280 progeny tested Nordic Red Cattle bulls to scan the genome for loci affecting milk, fat and protein yields. RESULTS: Using a genome-wise significance threshold, regions on Bos taurus chromosomes 5, 14, 23, 25 and 26 were...... traits via biological networks. CONCLUSION: This is the first time when whole genome sequence data is utilized to study genomic regions affecting milk production in the Nordic Red Cattle population. Sequence level data offers the possibility to study quantitative traits in detail but still cannot......BACKGROUND: The Nordic Red Cattle consisting of three different populations from Finland, Sweden and Denmark are under a joint breeding value estimation system. The long history of recording of production and health traits offers a great opportunity to study production traits and identify causal...

  12. Two-dimensional DNA displays for comparisons of bacterial genomes

    Directory of Open Access Journals (Sweden)

    Malloff Chad

    2003-01-01

    Full Text Available We have developed two whole genome-scanning techniques to aid in the discovery of polymorphisms as well as horizontally acquired genes in prokaryotic organisms. First, two-dimensional bacterial genomic display (2DBGD was developed using restriction enzyme fragmentation to separate genomic DNA based on size, and then employing denaturing gradient gel electrophoresis (DGGE in the second dimension to exploit differences in sequence composition. This technique was used to generate high-resolution displays that enable the direct comparison of > 800 genomic fragments simultaneously and can be adapted for the high-throughput comparison of bacterial genomes. 2DBGDs are capable of detecting acquired and altered DNA, however, only in very closely related strains. If used to compare more distantly related strains (e.g. different species within a genus numerous small changes (i.e. small deletions and point mutations unrelated to the interesting phenotype, would encumber the comparison of 2DBGDs. For this reason a second method, bacterial comparative genomic hybridization (BCGH, was developed to directly compare bacterial genomes to identify gain or loss of genomic DNA. BCGH relies on performing 2DBGD on a pooled sample of genomic DNA from 2 strains to be compared and subsequently hybridizing the resulting 2DBGD blot separately with DNA from each individual strain. Unique spots (hybridization signals represent foreign DNA. The identification of novel DNA is easily achieved by excising the DNA from a dried gel followed by subsequent cloning and sequencing. 2DBGD and BCGH thus represent novel high resolution genome scanning techniques for directly identifying altered and/or acquired DNA.

  13. Causes of genome instability

    DEFF Research Database (Denmark)

    Langie, Sabine A S; Koppen, Gudrun; Desaulniers, Daniel;

    2015-01-01

    Genome instability is a prerequisite for the development of cancer. It occurs when genome maintenance systems fail to safeguard the genome's integrity, whether as a consequence of inherited defects or induced via exposure to environmental agents (chemicals, biological agents and radiation). Thus......, genome instability can be defined as an enhanced tendency for the genome to acquire mutations; ranging from changes to the nucleotide sequence to chromosomal gain, rearrangements or loss. This review raises the hypothesis that in addition to known human carcinogens, exposure to low dose of other...... chemicals present in our modern society could contribute to carcinogenesis by indirectly affecting genome stability. The selected chemicals with their mechanisms of action proposed to indirectly contribute to genome instability are: heavy metals (DNA repair, epigenetic modification, DNA damage signaling...

  14. A fluorescence scanning electron microscope

    Directory of Open Access Journals (Sweden)

    Takaaki Kanemaru

    2010-01-01

    Full Text Available Fluorescence techniques are widely used in biological research to examine molecular localization, while electron microscopy can provide unique ultrastructural information. To date, correlative images from both fluorescence and electron microscopy have been obtained separately using two different instruments, i.e. a fluorescence microscope (FM and an electron microscope (EM. In the current study, a scanning electron microscope (SEM (JEOL JXA8600 M was combined with a fluorescence digital camera microscope unit and this hybrid instrument was named a fluorescence SEM (FL-SEM. In the labeling of FL-SEM samples, both Fluolid, which is an organic EL dye, and Alexa Fluor, were employed. We successfully demonstrated that the FL-SEM is a simple and practical tool for correlative fluorescence and electron microscopy.

  15. QUANTITATIVE CONFOCAL LASER SCANNING MICROSCOPY

    Directory of Open Access Journals (Sweden)

    Merete Krog Raarup

    2011-05-01

    Full Text Available This paper discusses recent advances in confocal laser scanning microscopy (CLSM for imaging of 3D structure as well as quantitative characterization of biomolecular interactions and diffusion behaviour by means of one- and two-photon excitation. The use of CLSM for improved stereological length estimation in thick (up to 0.5 mm tissue is proposed. The techniques of FRET (Fluorescence Resonance Energy Transfer, FLIM (Fluorescence Lifetime Imaging Microscopy, FCS (Fluorescence Correlation Spectroscopy and FRAP (Fluorescence Recovery After Photobleaching are introduced and their applicability for quantitative imaging of biomolecular (co-localization and trafficking in live cells described. The advantage of two-photon versus one-photon excitation in relation to these techniques is discussed.

  16. Scanning ARM Cloud Radar Handbook

    Energy Technology Data Exchange (ETDEWEB)

    Widener, K; Bharadwaj, N; Johnson, K

    2012-06-18

    The scanning ARM cloud radar (SACR) is a polarimetric Doppler radar consisting of three different radar designs based on operating frequency. These are designated as follows: (1) X-band SACR (X-SACR); (2) Ka-band SACR (Ka-SACR); and (3) W-band SACR (W-SACR). There are two SACRs on a single pedestal at each site where SACRs are deployed. The selection of the operating frequencies at each deployed site is predominantly determined by atmospheric attenuation at the site. Because RF attenuation increases with atmospheric water vapor content, ARM's Tropical Western Pacific (TWP) sites use the X-/Ka-band frequency pair. The Southern Great Plains (SGP) and North Slope of Alaska (NSA) sites field the Ka-/W-band frequency pair. One ARM Mobile Facility (AMF1) has a Ka/W-SACR and the other (AMF2) has a X/Ka-SACR.

  17. Scanning strategies for imaging arrays

    CERN Document Server

    Kovács, A

    2008-01-01

    Large-format (sub)millimeter wavelength imaging arrays are best operated in scanning observing modes rather than traditional position-switched (chopped) modes. The choice of observing mode is critical for isolating source signals from various types of noise interference, especially for ground-based instrumentation operating under a bright atmosphere. Ideal observing strategies can combat 1/f noise, resist instrumental defects, sensitively recover emission on large scales, and provide an even field coverage -- all under feasible requirements of telescope movement. This work aims to guide the design of observing patterns that maximize scientific returns. It also compares some of the popular choices of observing modes for (sub)millimeter imaging, such as random, Lissajous, billiard, spiral, On-The-Fly (OTF), DREAM, chopped and stare patterns. Many of the conclusions are also applicable other imaging applications and imaging in one dimension (e.g. spectroscopic observations).

  18. Scanning laser polarimetry in glaucoma

    Directory of Open Access Journals (Sweden)

    Tanuj Dada

    2014-01-01

    Full Text Available Glaucoma is an acquired progressive optic neuropathy which is characterized by changes in the optic nerve head and retinal nerve fiber layer (RNFL. White-on-white perimetry is the gold standard for the diagnosis of glaucoma. However, it can detect defects in the visual field only after the loss of as many as 40% of the ganglion cells. Hence, the measurement of RNFL thickness has come up. Optical coherence tomography and scanning laser polarimetry (SLP are the techniques that utilize the evaluation of RNFL for the evaluation of glaucoma. SLP provides RNFL thickness measurements based upon the birefringence of the retinal ganglion cell axons. We have reviewed the published literature on the use of SLP in glaucoma. This review elucidates the technological principles, recent developments and the role of SLP in the diagnosis and monitoring of glaucomatous optic neuropathy, in the light of scientific evidence so far.

  19. Dating the age of admixture via wavelet transform analysis of genome-wide data.

    Science.gov (United States)

    Pugach, Irina; Matveyev, Rostislav; Wollstein, Andreas; Kayser, Manfred; Stoneking, Mark

    2011-01-01

    We describe a PCA-based genome scan approach to analyze genome-wide admixture structure, and introduce wavelet transform analysis as a method for estimating the time of admixture. We test the wavelet transform method with simulations and apply it to genome-wide SNP data from eight admixed human populations. The wavelet transform method offers better resolution than existing methods for dating admixture, and can be applied to either SNP or sequence data from humans or other species. PMID:21352535

  20. Dating the age of admixture via wavelet transform analysis of genome-wide data

    OpenAIRE

    Pugach, Irina; Matveyev, Rostislav; Wollstein, Andreas; Kayser, Manfred; Stoneking, Mark

    2011-01-01

    textabstractWe describe a PCA-based genome scan approach to analyze genome-wide admixture structure, and introduce wavelet transform analysis as a method for estimating the time of admixture. We test the wavelet transform method with simulations and apply it to genome-wide SNP data from eight admixed human populations. The wavelet transform method offers better resolution than existing methods for dating admixture, and can be applied to either SNP or sequence data from humans or other species.

  1. The utility of bone scans in rheumatology

    International Nuclear Information System (INIS)

    Full text: Introduction: Bone scans are the commonest diagnostic imaging services requested by Australian rheumatologists. Medicare figures suggest that an average rheumatologist orders about $50 000 (AUS) of bone scans annually. Aims: To ascertain the reasons why rheumatologists request bone scans and how it affects their patient management. Methods: A two-part prospective survey was administered before and after every bone scan ordered by four rheumatologists over a six-month period in 1996. Results: A total of 136 bone scans were requested (66.2% whole body; 33.8% regional; 6% SPECT). The primary indications for scanning were (1) to confirm a clinical diagnosis (38%); (2) to exclude a diagnosis (34%); (3) to localize site of pain (17%); and (4) to assist in management (6%). The common diseases that rheumatologists were attempting to confirm/exclude with bone scanning were inflammatory arthritis, malignancy, and fracture. However, the commonest provisional and final diagnosis was soft tissue rheumatism (18%) followed by inflammatory arthritis (15%) and osteoarthritis (11%). In 24% of patients with a provisional diagnosis of soft tissue rheumatism the diagnosis was changed by the bone scan. The scan was successful in excluding a diagnosis in 88 per cent where this was the primary indication for the test. It was successful in confirming a diagnosis in 79 per cent where this was the primary indication. In 32 per cent the bone scan altered the clinical diagnosis and in 43 per cent it altered management. The bone scan result prevented further investigations in 60 per cent. Conclusions: The commonest pre-scan and post-scan diagnosis is soft tissue rheumatism. Rheumatologists predominantly request bone scanning to confirm or exclude their clinical suspicion of inflammatory arthritis, malignancy, and fracture. Bone scans were successful in achieving these objectives in at least 79 per cent of cases

  2. Development in Rice Genome Research Based on Accurate Genome Sequence

    OpenAIRE

    2008-01-01

    Rice is one of the most important crops in the world. Although genetic improvement is a key technology for the acceleration of rice breeding, a lack of genome information had restricted efforts in molecular-based breeding until the completion of the high-quality rice genome sequence, which opened new opportunities for research in various areas of genomics. The syntenic relationship of the rice genome to other cereal genomes makes the rice genome invaluable for understanding how cereal genomes...

  3. Handbook of optical and laser scanning

    CERN Document Server

    Marshall, Gerald F

    2011-01-01

    From its initial publication titled Laser Beam Scanning in 1985 to Handbook of Optical and Laser Scanning, now in its second edition, this reference has kept professionals and students at the forefront of optical scanning technology. Carefully and meticulously updated in each iteration, the book continues to be the most comprehensive scanning resource on the market. It examines the breadth and depth of subtopics in the field from a variety of perspectives. The Second Edition covers: Technologies such as piezoelectric devices Applications of laser scanning such as Ladar (laser radar) Underwater

  4. Whole-exome/genome sequencing and genomics.

    Science.gov (United States)

    Grody, Wayne W; Thompson, Barry H; Hudgins, Louanne

    2013-12-01

    As medical genetics has progressed from a descriptive entity to one focused on the functional relationship between genes and clinical disorders, emphasis has been placed on genomics. Genomics, a subelement of genetics, is the study of the genome, the sum total of all the genes of an organism. The human genome, which is contained in the 23 pairs of nuclear chromosomes and in the mitochondrial DNA of each cell, comprises >6 billion nucleotides of genetic code. There are some 23,000 protein-coding genes, a surprisingly small fraction of the total genetic material, with the remainder composed of noncoding DNA, regulatory sequences, and introns. The Human Genome Project, launched in 1990, produced a draft of the genome in 2001 and then a finished sequence in 2003, on the 50th anniversary of the initial publication of Watson and Crick's paper on the double-helical structure of DNA. Since then, this mass of genetic information has been translated at an ever-increasing pace into useable knowledge applicable to clinical medicine. The recent advent of massively parallel DNA sequencing (also known as shotgun, high-throughput, and next-generation sequencing) has brought whole-genome analysis into the clinic for the first time, and most of the current applications are directed at children with congenital conditions that are undiagnosable by using standard genetic tests for single-gene disorders. Thus, pediatricians must become familiar with this technology, what it can and cannot offer, and its technical and ethical challenges. Here, we address the concepts of human genomic analysis and its clinical applicability for primary care providers.

  5. Mosaic Structure Of Foot-And-Mouth Disease Virus Genomes

    Science.gov (United States)

    We report the results of a simple pairwise scanning analysis designed to identify inter-serotype recombination events applied to genome data from 144 isolates of foot-and-mouth disease virus (FMDV) representing all seven serotypes. We identify large numbers of candidate recombinant fragments from a...

  6. Spatial heterodyne scanning laser confocal holographic microscopy

    CERN Document Server

    Liu, Changgeng

    2016-01-01

    Scanning laser confocal holographic microscopy using a spatial heterodyne detection method is presented. Spatial heterodyne detection technique employs a Mach-Zehnder interferometer with the reference beam frequency shifted by two acousto-optic modulators (AOM) relative to the object beam frequency. Different from the traditional temporal heterodyne detection technique in which hundreds temporal samples are taken at each scanning point to achieve the complex signal, the spatial heterodyne detection technique generates spatial interference fringes by use of a linear tempo-spatial relation provided by galvanometer scanning in a typical line-scanning confocal microscope or for the slow-scanning on one dimension in a point-scanning confocal microscope, thereby significantly reducing sampling rate and increasing the signal to noise ratio under the same illumination compared to the traditional temporal heterodyne counterpart. The proposed spatial heterodyne detection scheme applies to both line-scanning and point-s...

  7. Bone scanning in severe external otitis

    Energy Technology Data Exchange (ETDEWEB)

    Levin, W.J.; Shary, J.H. 3d.; Nichols, L.T.; Lucente, F.E.

    1986-11-01

    Technetium99 Methylene Diphosphate bone scanning has been considered an early valuable tool to diagnose necrotizing progressive malignant external otitis. However, to our knowledge, no formal studies have actually compared bone scans of otherwise young, healthy patients with severe external otitis to scans of patients with clinical presentation of malignant external otitis. Twelve patients with only severe external otitis were studied with Technetium99 Diphosphate and were compared to known cases of malignant otitis. All scans were evaluated by two neuroradiologists with no prior knowledge of the clinical status of the patients. Nine of the 12 patients had positive bone scans with many scans resembling those reported with malignant external otitis. Interestingly, there was no consistent correlation between the severity of clinical presentation and the amount of Technetium uptake. These findings suggest that a positive bone scan alone should not be interpreted as indicative of malignant external otitis.

  8. Scanning Tunneling Optical Resonance Microscopy

    Science.gov (United States)

    Bailey, Sheila; Wilt, Dave; Raffaelle, Ryne; Gennett, Tom; Tin, Padetha; Lau, Janice; Castro, Stephanie; Jenkins, Philip; Scheiman, Dave

    2003-01-01

    Scanning tunneling optical resonance microscopy (STORM) is a method, now undergoing development, for measuring optoelectronic properties of materials and devices on the nanoscale by means of a combination of (1) traditional scanning tunneling microscopy (STM) with (2) tunable laser spectroscopy. In STORM, an STM tip probing a semiconductor is illuminated with modulated light at a wavelength in the visible-to-near-infrared range and the resulting photoenhancement of the tunneling current is measured as a function of the illuminating wavelength. The photoenhancement of tunneling current occurs when the laser photon energy is sufficient to excite charge carriers into the conduction band of the semiconductor. Figure 1 schematically depicts a proposed STORM apparatus. The light for illuminating the semiconductor specimen at the STM would be generated by a ring laser that would be tunable across the wavelength range of interest. The laser beam would be chopped by an achromatic liquid-crystal modulator. A polarization-maintaining optical fiber would couple the light to the tip/sample junction of a commercial STM. An STM can be operated in one of two modes: constant height or constant current. A STORM apparatus would be operated in the constant-current mode, in which the height of the tip relative to the specimen would be varied in order to keep the tunneling current constant. In this mode, a feedback control circuit adjusts the voltage applied to a piezoelectric actuator in the STM that adjusts the height of the STM tip to keep the tunneling current constant. The exponential relationship between the tunneling current and tip-to-sample distance makes it relatively easy to implement this mode of operation. The choice of method by which the photoenhanced portion of the tunneling current would be measured depends on choice of the frequency at which the input illumination would be modulated (chopped). If the frequency of modulation were low enough (typically < 10 Hz) that the

  9. Bioinformatics decoding the genome

    CERN Document Server

    CERN. Geneva; Deutsch, Sam; Michielin, Olivier; Thomas, Arthur; Descombes, Patrick

    2006-01-01

    Extracting the fundamental genomic sequence from the DNA From Genome to Sequence : Biology in the early 21st century has been radically transformed by the availability of the full genome sequences of an ever increasing number of life forms, from bacteria to major crop plants and to humans. The lecture will concentrate on the computational challenges associated with the production, storage and analysis of genome sequence data, with an emphasis on mammalian genomes. The quality and usability of genome sequences is increasingly conditioned by the careful integration of strategies for data collection and computational analysis, from the construction of maps and libraries to the assembly of raw data into sequence contigs and chromosome-sized scaffolds. Once the sequence is assembled, a major challenge is the mapping of biologically relevant information onto this sequence: promoters, introns and exons of protein-encoding genes, regulatory elements, functional RNAs, pseudogenes, transposons, etc. The methodological ...

  10. State of cat genomics.

    Science.gov (United States)

    O'Brien, Stephen J; Johnson, Warren; Driscoll, Carlos; Pontius, Joan; Pecon-Slattery, Jill; Menotti-Raymond, Marilyn

    2008-06-01

    Our knowledge of cat family biology was recently expanded to include a genomics perspective with the completion of a draft whole genome sequence of an Abyssinian cat. The utility of the new genome information has been demonstrated by applications ranging from disease gene discovery and comparative genomics to species conservation. Patterns of genomic organization among cats and inbred domestic cat breeds have illuminated our view of domestication, revealing linkage disequilibrium tracks consequent of breed formation, defining chromosome exchanges that punctuated major lineages of mammals and suggesting ancestral continental migration events that led to 37 modern species of Felidae. We review these recent advances here. As the genome resources develop, the cat is poised to make a major contribution to many areas in genetics and biology.

  11. CT scanning: patterns of use and dose

    International Nuclear Information System (INIS)

    CT scanning is a relatively high-dose procedure. In spite of the use of magnetic resonance imaging, with faster CT scanners and helical techniques CT is becoming more common. There are few data from practice in the United States regarding the age and sex distribution of patients receiving CT scans, what type of scan and how many scans they receive, or how much radiation dose CT scans contribute. We reviewed over 33 700 consecutive CT examinations done at our institution in 1998 and 1999. Information on the types of scans as well as the age and sex distribution of the patients was determined. Between 1990 and 1999, CT examinations in our institution increased from 6.1% to 11.1% of all radiology procedures. Nineteen per cent of all patients seen in our department in the last year had at least one CT scan and more than half had multiple scans on the same day. Thirty-six per cent of all patients had a prior CT examination done on an earlier date. The male/female ratio of patients was 56/44. Studies of children age 0-15 years comprised 11.2% of scans. The highest percentage of scans was done in the 36-50-year-old age group. CT scanning accounted for 67% of the effective dose from diagnostic radiology. In most large hospitals in the United States CT scanning probably accounts for more than 10% of diagnostic radiology examinations and about two-thirds of the radiation dose. Most patients have multiple scan sequences. Studies done on children are probably more common than previously thought. (author)

  12. Physician Assistant Genomic Competencies.

    Science.gov (United States)

    Goldgar, Constance; Michaud, Ed; Park, Nguyen; Jenkins, Jean

    2016-09-01

    Genomic discoveries are increasingly being applied to the clinical care of patients. All physician assistants (PAs) need to acquire competency in genomics to provide the best possible care for patients within the scope of their practice. In this article, we present an updated version of PA genomic competencies and learning outcomes in a framework that is consistent with the current medical education guidelines and the collaborative nature of PAs in interprofessional health care teams. PMID:27490287

  13. Genome packaging in viruses

    OpenAIRE

    Sun, Siyang; Rao, Venigalla B.; Rossmann, Michael G.

    2010-01-01

    Genome packaging is a fundamental process in a viral life cycle. Many viruses assemble preformed capsids into which the genomic material is subsequently packaged. These viruses use a packaging motor protein that is driven by the hydrolysis of ATP to condense the nucleic acids into a confined space. How these motor proteins package viral genomes had been poorly understood until recently, when a few X-ray crystal structures and cryo-electron microscopy structures became available. Here we discu...

  14. Querying genomic databases

    Energy Technology Data Exchange (ETDEWEB)

    Baehr, A.; Hagstrom, R.; Joerg, D.; Overbeek, R.

    1991-09-01

    A natural-language interface has been developed that retrieves genomic information by using a simple subset of English. The interface spares the biologist from the task of learning database-specific query languages and computer programming. Currently, the interface deals with the E. coli genome. It can, however, be readily extended and shows promise as a means of easy access to other sequenced genomic databases as well.

  15. Chromium and Genomic Stability

    OpenAIRE

    Wise, Sandra S.; Wise, John Pierce

    2011-01-01

    Many metals serve as micronutrients which protect against genomic instability. Chromium is most abundant in its trivalent and hexavalent forms. Trivalent chromium has historically been considered an essential element, though recent data indicate that while it can have pharmacological effects and value, it is not essential. There are no data indicating that trivalent chromium promotes genomic stability and, instead may promote genomic instability. Hexavalent chromium is widely accepted as high...

  16. The Genome Atlas Resource

    OpenAIRE

    Azam Qureshi, Matloob; Rotenberg, Eva; Stærfeldt, Hans Henrik; Hansson, Lena; Ussery, David

    2010-01-01

    Abstract. The Genome Atlas is a resource for addressing the challenges of synchronising prokaryotic genomic sequence data from multiple public repositories. This resource can integrate bioinformatic analyses in various data format and quality. Existing open source tools have been used together with scripts and algorithms developed in a variety of programming languages at the Centre for Biological Sequence Analysis in order to create a three-tier software application for genome analysis. The r...

  17. The Classical Isotropic bi-Dimensional Oscilator in the Eisenhart Formulation of Classical Mechanics

    Directory of Open Access Journals (Sweden)

    U. Percoco

    2007-01-01

    Full Text Available De acuerdo con la Teoría de la Relatividad General, el movimi en- to de partículas por acción de su inercia y la gravedad es desc rito por geodésicas en el espacio-tiempo. Utilizamos la formulació n Geométrica de Eisenhart de la Mecánica Clásica para establecer una corres pondencia en- tre geodésicas y trayectorias en el espacio de fases del osci lador clásico isótropo. Se presentan los vectores de Killing y las constan tes de movimien- to asociadas, se comparan con las constantes de movimiento n o noetheriano calculadas por S. Hojman y colaboradores.

  18. Between two fern genomes.

    Science.gov (United States)

    Sessa, Emily B; Banks, Jo Ann; Barker, Michael S; Der, Joshua P; Duffy, Aaron M; Graham, Sean W; Hasebe, Mitsuyasu; Langdale, Jane; Li, Fay-Wei; Marchant, D Blaine; Pryer, Kathleen M; Rothfels, Carl J; Roux, Stanley J; Salmi, Mari L; Sigel, Erin M; Soltis, Douglas E; Soltis, Pamela S; Stevenson, Dennis W; Wolf, Paul G

    2014-01-01

    Ferns are the only major lineage of vascular plants not represented by a sequenced nuclear genome. This lack of genome sequence information significantly impedes our ability to understand and reconstruct genome evolution not only in ferns, but across all land plants. Azolla and Ceratopteris are ideal and complementary candidates to be the first ferns to have their nuclear genomes sequenced. They differ dramatically in genome size, life history, and habit, and thus represent the immense diversity of extant ferns. Together, this pair of genomes will facilitate myriad large-scale comparative analyses across ferns and all land plants. Here we review the unique biological characteristics of ferns and describe a number of outstanding questions in plant biology that will benefit from the addition of ferns to the set of taxa with sequenced nuclear genomes. We explain why the fern clade is pivotal for understanding genome evolution across land plants, and we provide a rationale for how knowledge of fern genomes will enable progress in research beyond the ferns themselves. PMID:25324969

  19. Fungal Genomics Program

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor

    2012-03-12

    The JGI Fungal Genomics Program aims to scale up sequencing and analysis of fungal genomes to explore the diversity of fungi important for energy and the environment, and to promote functional studies on a system level. Combining new sequencing technologies and comparative genomics tools, JGI is now leading the world in fungal genome sequencing and analysis. Over 120 sequenced fungal genomes with analytical tools are available via MycoCosm (www.jgi.doe.gov/fungi), a web-portal for fungal biologists. Our model of interacting with user communities, unique among other sequencing centers, helps organize these communities, improves genome annotation and analysis work, and facilitates new larger-scale genomic projects. This resulted in 20 high-profile papers published in 2011 alone and contributing to the Genomics Encyclopedia of Fungi, which targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts). Our next grand challenges include larger scale exploration of fungal diversity (1000 fungal genomes), developing molecular tools for DOE-relevant model organisms, and analysis of complex systems and metagenomes.

  20. Modulation transfer function of bar code scanning

    Science.gov (United States)

    Tang, Hong; Milster, Tom D.

    1998-09-01

    Bar code scanners are ubiquitous in supermarkets. As a bar code is passed over a scanner, a laser beam scans across the bar code. The scattered light is modulated by the reflectivity of the bars and spaces of the bar code. The bar code scanning process can be described as a 1D convolution of the scanning laser profile and the bar code reflectivity function. The modulation transfer function (MTF) of bar code scanning is the Fourier transform of the marginal profile of the laser beam. The properties of the MTF of bar code scanning is similar to that of an incoherent imaging system. Measurements of the MTF of bar code scanning at one focus position are presented. The experimental results are then discussed.

  1. Small-Scale Duplications Play a Significant Role in Rice Genome Evolution

    Institute of Scientific and Technical Information of China (English)

    GUO Xin-yi; XU Guo-hua; ZHANG Yang; HU Wei-min; FAN Long-jiang

    2005-01-01

    Genes are continually being created by the processes of genome duplication (ohnolog) and gene duplication (paralog)Whole-genome duplications have been found to be widespread in plant species and play an important role in plant evolution. Clearly un-overlapping duplicated blocks of whole-genome duplications can be detected in the genome of sequenced rice (Oryza sativa).Syntenic ohnolog pairs (ohnologues) of the whole-genome duplications in rice were identified based on their syntenic duplicate lines.The paralogs of ohnologues were further scanned using multi-round reciprocal BLAST best-hit searching (E<e-14). The results indicated that an average of 0.55 sister paralogs could be found for every ohnologue in rice. These results suggest that small-scale duplications, as well as whole-genome duplications, play a significant role in the two duplicated rice genomes.

  2. Genome position specific priors for genomic prediction

    DEFF Research Database (Denmark)

    Brøndum, Rasmus Froberg; Su, Guosheng; Lund, Mogens Sandø;

    2012-01-01

    Background The accuracy of genomic prediction is highly dependent on the size of the reference population. For small populations, including information from other populations could improve this accuracy. The usual strategy is to pool data from different populations; however, this has not proven...... as successful as hoped for with distantly related breeds. BayesRS is a novel approach to share information across populations for genomic predictions. The approach allows information to be captured even where the phase of SNP alleles and casual mutation alleles are reversed across populations, or the actual...... casual mutation is different between the populations but affects the same gene. Proportions of a four-distribution mixture for SNP effects in segments of fixed size along the genome are derived from one population and set as location specific prior proportions of distributions of SNP effects...

  3. Parallel scanning probe arrays: their applications

    Directory of Open Access Journals (Sweden)

    Chang Liu

    2008-01-01

    Full Text Available Since the invention of the scanning tunneling microscope (STM1 and the atomic force microscope (AFM2, the field of scanning probe microscopy (SPM instruments has grown steadily and has had a profound influence in materials research, chemistry, biology, nanotechnology, and electronics3,4. Today, scanning probe instruments are used for metrology, characterization5, detection6, manipulation7, patterning8,9, and material modification. A wide range of scanning probe applications are available, taking advantage of various modes of tip–substrate interactions, including force, optics10,11, electrochemistry12, electromagnetics, electrostatics, thermal and mass transfer13,14, and vibration15,16.

  4. Human Digital Modeling & Hand Scanning Lab

    Data.gov (United States)

    Federal Laboratory Consortium — This laboratory incorporates specialized scanning equipment, computer workstations and software applications for the acquisition and analysis of digitized models of...

  5. Selected papers on laser scanning and recording

    Science.gov (United States)

    Beiser, L.

    Previously published papers concerned with laser scanning and recording techniques are presented. Subjects treated include laser beam information scanning and recording, laser scanning techniques, system design considerations for laser scanning, laser noise, reliability, resolution, and dynamic range, and optical data storage systems. Consideration is given to the components and media for developing laser scanning and recording systems, in particular the laser, the optics, the scanner, and the storage media. Topics discussed include basic and operational multichannel acoustooptic operation; galvanometer and analog compensations; motor and control systems; angle measurement of scanner by interferometry, preheat-aided laser recording, creating multidimensional scan using a single rotating component, digital techniques in high resolution analog scanning and recording; laser scanning parameters and latitudes in laser xerography; optical video disc technology; focus error detection in optical data storage systems, holographic laser scanners for nonimpact printing; and techniques in optical strobe recording. Laser beam recording, techniques, film recorder systems, laser scanner applicaations, the optimization of printing speed and printout quality of laser beam printers, an internal drum laser scanning plate exposure system, and an ultra-high resolution graphic data terminal are described.

  6. Influence of scanning strategies on the accuracy of digital intraoral scanning systems.

    Science.gov (United States)

    Ender, A; Mehl, A

    2013-01-01

    The digital intraoral impression is a central part in today's CAD/CAM dentistry. With its possibilities, new treatment options for the patient is provided and the prosthetic workflow is accelerated. Nowadays, the major issue with intraoral scanning systems is to gain more accuracy especially for larger scan areas and to simplify clinical handling for the dentist. The aim of this study was to investigate different scanning strategies regardingtheir accuracy with full arch scans in an in-vitro study design. A reference master model was used for the digital impressions with the Lava COS, the Cerec Bluecam and a powderfree intraoral scanning system, Cadent iTero. The trueness and precision of each scanning protocol was measured. Lava COS provides the a trueness of 45.8 microm with the scanning protocol recommended from the manufacturer. A different scanning protocol shows significantly lower accuracy (trueness +/- 90.2 microm). Cerec Bluecam also benefits from an optimal scanning protocol with a trueness of +/- 23.3 microm compared to +/- 52.5 microm with a standard protocol. The powderfree impression system Cadent iTero shows also a high accurate full-arch scan with a trueness of +/- 35.0 microm and a precision of +/- 30.9 microm. With the current intraoral scanning systems, full arch dental impressions are possible with a high accuracy, if adequate scan strategies are used. The powderfree scanning system provides the same level of accuracy compared to scanning systems with surface pretreatment. PMID:23641661

  7. Influence of scanning strategies on the accuracy of digital intraoral scanning systems.

    Science.gov (United States)

    Ender, A; Mehl, A

    2013-01-01

    The digital intraoral impression is a central part in today's CAD/CAM dentistry. With its possibilities, new treatment options for the patient is provided and the prosthetic workflow is accelerated. Nowadays, the major issue with intraoral scanning systems is to gain more accuracy especially for larger scan areas and to simplify clinical handling for the dentist. The aim of this study was to investigate different scanning strategies regardingtheir accuracy with full arch scans in an in-vitro study design. A reference master model was used for the digital impressions with the Lava COS, the Cerec Bluecam and a powderfree intraoral scanning system, Cadent iTero. The trueness and precision of each scanning protocol was measured. Lava COS provides the a trueness of 45.8 microm with the scanning protocol recommended from the manufacturer. A different scanning protocol shows significantly lower accuracy (trueness +/- 90.2 microm). Cerec Bluecam also benefits from an optimal scanning protocol with a trueness of +/- 23.3 microm compared to +/- 52.5 microm with a standard protocol. The powderfree impression system Cadent iTero shows also a high accurate full-arch scan with a trueness of +/- 35.0 microm and a precision of +/- 30.9 microm. With the current intraoral scanning systems, full arch dental impressions are possible with a high accuracy, if adequate scan strategies are used. The powderfree scanning system provides the same level of accuracy compared to scanning systems with surface pretreatment.

  8. Genome-Scale Models

    DEFF Research Database (Denmark)

    Bergdahl, Basti; Sonnenschein, Nikolaus; Machado, Daniel;

    2016-01-01

    An introduction to genome-scale models, how to build and use them, will be given in this chapter. Genome-scale models have become an important part of systems biology and metabolic engineering, and are increasingly used in research, both in academica and in industry, both for modeling chemical...

  9. Estimation of genome length

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The genome length is a fundamental feature of a species. This note outlined the general concept and estimation method of the physical and genetic length. Some formulae for estimating the genetic length were derived in detail. As examples, the genome genetic length of Pinus pinaster Ait. and the genetic length of chromosome Ⅵ of Oryza sativa L. were estimated from partial linkage data.

  10. Genomics for Weed Science

    Science.gov (United States)

    Numerous genomic-based studies have provided insight to the physiological and evolutionary processes involved in developmental and environmental processes of model plants such as arabidopsis and rice. However, far fewer efforts have been attempted to use genomic resources to study physiological and ...

  11. Genetics and Genomics

    Science.gov (United States)

    Good progress is being made on genetics and genomics of sugar beet, however it is in process and the tools are now being generated and some results are being analyzed. The GABI BeetSeq project released a first draft of the sugar beet genome of KWS2320, a dihaploid (see http://bvseq.molgen.mpg.de/Gen...

  12. Unlocking the bovine genome

    Science.gov (United States)

    The draft genome sequence of cattle (Bos taurus) has now been analyzed by the Bovine Genome Sequencing and Analysis Consortium and the Bovine HapMap Consortium, which together represent an extensive collaboration involving more than 300 scientists from 25 different countries. ...

  13. Safeguarding genome integrity

    DEFF Research Database (Denmark)

    Sørensen, Claus Storgaard; Syljuåsen, Randi G

    2012-01-01

    Mechanisms that preserve genome integrity are highly important during the normal life cycle of human cells. Loss of genome protective mechanisms can lead to the development of diseases such as cancer. Checkpoint kinases function in the cellular surveillance pathways that help cells to cope with DNA...

  14. National Human Genome Research Institute

    Science.gov (United States)

    ... Director Organization Reports & Publications Español The National Human Genome Research Institute conducts genetic and genomic research, funds ... study, led by researchers at the National Human Genome Research Institute and the Eunice Kennedy Shriver National ...

  15. A novel method for identifying polymorphic transposable elements via scanning of high-throughput short reads.

    Science.gov (United States)

    Kang, Houxiang; Zhu, Dan; Lin, Runmao; Opiyo, Stephen Obol; Jiang, Ning; Shiu, Shin-Han; Wang, Guo-Liang

    2016-06-01

    Identification of polymorphic transposable elements (TEs) is important because TE polymorphism creates genetic diversity and influences the function of genes in the host genome. However, de novo scanning of polymorphic TEs remains a challenge. Here, we report a novel computational method, called PTEMD (polymorphic TEs and their movement detection), for de novo discovery of genome-wide polymorphic TEs. PTEMD searches highly identical sequences using reads supported breakpoint evidences. Using PTEMD, we identified 14 polymorphic TE families (905 sequences) in rice blast fungus Magnaporthe oryzae, and 68 (10,618 sequences) in maize. We validated one polymorphic TE family experimentally, MoTE-1; all MoTE-1 family members are located in different genomic loci in the three tested isolates. We found that 57.1% (8 of 14) of the PTEMD-detected polymorphic TE families in M. oryzae are active. Furthermore, our data indicate that there are more polymorphic DNA transposons in maize than their counterparts of retrotransposons despite the fact that retrotransposons occupy largest fraction of genomic mass. We demonstrated that PTEMD is an effective tool for identifying polymorphic TEs in M. oryzae and maize genomes. PTEMD and the genome-wide polymorphic TEs in M. oryzae and maize are publically available at http://www.kanglab.cn/blast/PTEMD_V1.02.htm. PMID:27098848

  16. Genomic Prediction in Barley

    DEFF Research Database (Denmark)

    Edriss, Vahid; Cericola, Fabio; Jensen, Jens D;

    Genomic prediction uses markers (SNPs) across the whole genome to predict individual breeding values at an early growth stage potentially before large scale phenotyping. One of the applications of genomic prediction in plant breeding is to identify the best individual candidate lines to contribute...... to next generation. The main goal of this study was to see the potential of using genomic prediction in a commercial Barley breeding program. The data used in this study was from Nordic Seed company which is located in Denmark. Around 350 advanced lines were genotyped with 9K Barely chip from...... Illumina. Traits used in this study were grain yield, plant height and heading date. Heading date is number days it takes after 1st June for plant to head. Heritabilities were 0.33, 0.44 and 0.48 for yield, height and heading, respectively for the average of nine plots. The GBLUP model was used for genomic...

  17. Genomic Prediction in Barley

    DEFF Research Database (Denmark)

    Edriss, Vahid; Cericola, Fabio; Jensen, Jens D;

    2015-01-01

    Genomic prediction uses markers (SNPs) across the whole genome to predict individual breeding values at an early growth stage potentially before large scale phenotyping. One of the applications of genomic prediction in plant breeding is to identify the best individual candidate lines to contribute...... to next generation. The main goal of this study was to see the potential of using genomic prediction in a commercial Barley breeding program. The data used in this study was from Nordic Seed company which is located in Denmark. Around 350 advanced lines were genotyped with 9K Barely chip from...... Illumina. Traits used in this study were grain yield, plant height and heading date. Heading date is number days it takes after 1st June for plant to head. Heritabilities were 0.33, 0.44 and 0.48 for yield, height and heading, respectively for the average of nine plots. The GBLUP model was used for genomic...

  18. Two Methods of Whole-Genome Amplification Enable Accurate Genotyping Across a 2320-SNP Linkage Panel

    OpenAIRE

    Barker, David L.; Hansen, Mark S. T.; Faruqi, A. Fawad; Giannola, Diane; Irsula, Orlando R.; Lasken, Roger S; Latterich, Martin; Makarov, Vladimir; Oliphant, Arnold; Pinter, Jonathon H.; Shen, Richard; Sleptsova, Irina; Ziehler, William; Lai, Eric

    2004-01-01

    Comprehensive genome scans involving many thousands of SNP assays will require significant amounts of genomic DNA from each sample. We report two successful methods for amplifying whole-genomic DNA prior to SNP analysis, multiple displacement amplification, and OmniPlex technology. We determined the coverage of amplification by analyzing a SNP linkage marker set that contained 2320 SNP markers spread across the genome at an average distance of 2.5 cM. We observed a concordance of >99.8% in ge...

  19. Search for Genomic Alterations in Monozygotic Twins Discordant for Cleft Lip and/or Palate

    DEFF Research Database (Denmark)

    Kimani, Jane W; Yoshiura, Koh-Ichiro; Shi, Min;

    2009-01-01

    consisting of 1,536 SNPs, to scan for genomic alterations in a sample of monozygotic twin pairs with discordant cleft lip and/or palate phenotypes. Paired analysis for deletions, amplifications and loss of heterozygosity, along with sequence verification of SNPs with discordant genotype calls did not reveal...... any genomic discordance between twin pairs in lymphocyte DNA samples. Our results demonstrate that postzygotic genomic alterations are not a common cause of monozygotic twin discordance for isolated cleft lip and/or palate. However, rare or balanced genomic alterations, tissue-specific events...

  20. A model for enterprises’ environmental scanning

    OpenAIRE

    Tudor NISTORESCU; Catalin Mihail BARBU

    2006-01-01

    Today’s environment determines companies to use scanning activities in order to seize the opportunities and to avoid the threats. Individual factors and organizational factors influence the scanning behavior. The examination of the environment can be presented in a model based on environment analyzability and organizational intrusiveness.

  1. Spatial scan statistics using elliptic windows

    DEFF Research Database (Denmark)

    Christiansen, Lasse Engbo; Andersen, Jens Strodl; Wegener, Henrik Caspar;

    The spatial scan statistic is widely used to search for clusters in epidemiologic data. This paper shows that the usually applied elimination of secondary clusters as implemented in SatScan is sensitive to smooth changes in the shape of the clusters. We present an algorithm for generation of set...

  2. Spatial scan statistics using elliptic windows

    DEFF Research Database (Denmark)

    Christiansen, Lasse Engbo; Andersen, Jens Strodl; Wegener, Henrik Caspar;

    2006-01-01

    The spatial scan statistic is widely used to search for clusters. This article shows that the usually applied elimination of secondary clusters as implemented in SatScan is sensitive to smooth changes in the shape of the clusters. We present an algorithm for generation of a set of confocal elliptic...

  3. Security scanning of Web sites at CERN

    CERN Multimedia

    IT Department

    2010-01-01

    As of early 2010, the CERN Computer Security Team will start regular scanning of all Web sites and Web applications at CERN, visible on the Internet, or on the General Purpose Network (office network). The goal of this scanning is to improve the quality of CERN Web sites. All deficits found will be reported by e-mail to the relevant Web site owners, and must be fixed in a timely manner. Web site owners may also request one-off scans of their Web site or Web application, by sending an e-mail to Computer.Security@cern.ch. These Web scans are designed to limit the impact on the scanned Web sites. Nevertheless, in very rare cases scans may cause undesired side-effects, e.g. generate a large number of log entries, or cause particularly badly designed or less robust Web applications to crash. If a Web site is affected by these security scans, it will also be susceptible to any more aggressive scan that can be performed any time by a malicious attacker. Such Web applications should be fixed, and also additionally...

  4. Environmental Scanning Practices for Rural Colleges.

    Science.gov (United States)

    Friedel, Janice Nahra; Lapin, Joel D.

    1995-01-01

    Discusses the importance of environmental scanning in the planning efforts of rural community colleges. Reviews basic techniques and terminology and suggests sources of data. Argues that environmental scanning allows rural colleges to inexpensively forecast change, identify implications for the organization, and plan preferred responses to shape…

  5. Environmental Scanning Is Vital to Strategic Planning.

    Science.gov (United States)

    Poole, Molly Linda

    1991-01-01

    Educators involved in strategic planning can use environmental scanning techniques to anticipate social, economic, political, and technological changes that will affect their schools. Compared to more traditional data gathering, environmental scanning is wider in scope and more concerned with anticipating the future and studying the interaction of…

  6. A Student-Built Scanning Tunneling Microscope

    Science.gov (United States)

    Ekkens, Tom

    2015-01-01

    Many introductory and nanotechnology textbooks discuss the operation of various microscopes including atomic force (AFM), scanning tunneling (STM), and scanning electron microscopes (SEM). In a nanotechnology laboratory class, students frequently utilize microscopes to obtain data without a thought about the detailed operation of the tool itself.…

  7. Scanning electron microscopy - application and techniques

    International Nuclear Information System (INIS)

    The application of the scanning electron microscope, and other image forming scanning systems (STEM and the nuclear microprobe), to a range of nuclear reactor problems is described. Particular attention is given to the solution of fracture problems. Autoradiography, electron spectroscopy, and an investigation of irradiation damage in boron carbide using the transmission electron microscope are also described. (author)

  8. Towards high-speed scanning tunneling microscopy

    NARCIS (Netherlands)

    Tabak, Femke Chantal

    2013-01-01

    In this thesis, two routes towards high-speed scanning tunneling microscopy (STM) are described. The first possibility for high-speed scanning that is discussed is the use of MEMS (Micro-Electro Mechanical Systems) devices as high-speed add-ons in STM microscopes. The functionality of these devices

  9. Live ultrasound volume reconstruction using scout scanning

    Science.gov (United States)

    Meyer, Amelie; Lasso, Andras; Ungi, Tamas; Fichtinger, Gabor

    2015-03-01

    Ultrasound-guided interventions often necessitate scanning of deep-seated anatomical structures that may be hard to visualize. Visualization can be improved using reconstructed 3D ultrasound volumes. High-resolution 3D reconstruction of a large area during clinical interventions is challenging if the region of interest is unknown. We propose a two-stage scanning method allowing the user to perform quick low-resolution scouting followed by high-resolution live volume reconstruction. Scout scanning is accomplished by stacking 2D tracked ultrasound images into a low-resolution volume. Then, within a region of interest defined in the scout scan, live volume reconstruction can be performed by continuous scanning until sufficient image density is achieved. We implemented the workflow as a module of the open-source 3D Slicer application, within the SlicerIGT extension and building on the PLUS toolkit. Scout scanning is performed in a few seconds using 3 mm spacing to allow region of interest definition. Live reconstruction parameters are set to provide good image quality (0.5 mm spacing, hole filling enabled) and feedback is given during live scanning by regularly updated display of the reconstructed volume. Use of scout scanning may allow the physician to identify anatomical structures. Subsequent live volume reconstruction in a region of interest may assist in procedures such as targeting needle interventions or estimating brain shift during surgery.

  10. The white blood cell scan in orthopedics

    Energy Technology Data Exchange (ETDEWEB)

    Propst-Proctor, S.L.; Dillingham, M.F.; McDougall, I.R.; Goodwin, D.

    1982-08-01

    A new nuclear scanning technique was found more specific for bone, joint, and soft tissue infections than any previously described scanning technique. The leukocyte scan, whereby a patient's own cells are labeled with a radioactive tagging agent (/sup 111/In oxine), can distinguish an active infectious process from other pain-inducing conditions. Ninety-seven /sup 111/In labeled autologous leukocyte scans were performed in 88 patients. The findings in 17 of 40 patients scanned for possible acute osteomyelitis, six of nine for suspected septic arthritis, and six for possible soft tissue infections, were positive. Subsequent clinical courses verified the infectious nature of these processes in all patients. Patients who had chronic osteomyelitis (14), bony metastases (four patients), heterotopic ossification (three), and degenerative arthritis (two) demonstrated negative findings. Of the seven patients scanned for acute long-bone fractures, one demonstrated positive findings. Nine scans demonstrated positive findings without determined causes. The leukocyte scan is a useful addition to the diagnostic tools of the orthopedic surgeon.

  11. A Scanning Microwave Radar and Radiometer

    DEFF Research Database (Denmark)

    Skou, Niels

    1995-01-01

    The Scanning Microwave Radar and Radiometer (SMRR) is a line scanner featuring a combined radar and radiometer system operating around 35 and 94 GHz. The layout of the SMRR is shown. The 2 offset antenna parabolas scan in synchronism, the receiver antenna has the highest gain in order to ensure...

  12. Camera Systems Rapidly Scan Large Structures

    Science.gov (United States)

    2013-01-01

    Needing a method to quickly scan large structures like an aircraft wing, Langley Research Center developed the line scanning thermography (LST) system. LST works in tandem with a moving infrared camera to capture how a material responds to changes in temperature. Princeton Junction, New Jersey-based MISTRAS Group Inc. now licenses the technology and uses it in power stations and industrial plants.

  13. Computed tomography scanning during a traumatic resuscitation

    NARCIS (Netherlands)

    L.F.M. Beenen; R. Adams; R.W. Koster; T. Otto

    2011-01-01

    In cardiopulmonary resuscitation, computed tomography (CT) imaging could be of decisive importance to therapeutic strategy making but is yet unavailable because of incompatibility of CT scanning and manual chest compressions. In this report, we describe a case in which CT scanning was performed on a

  14. Optimal stimulation settings for CMAP scan registrations

    NARCIS (Netherlands)

    E.M. Maathuis (Ellen); R.D. Henderson (Robert); J. Drenthen (Judith); N.M. Hutchinson (Nicole); J.R. Daube (Jasper); J.H. Blok (Joleen); G.H. Visser (Gerhard Henk)

    2012-01-01

    textabstractBackground: The CMAP (Compound Muscle Action Potential) scan is a non-invasive electrodiagnostic tool, which provides a quick and visual assessment of motor unit potentials as electrophysiological components that together constitute the CMAP. The CMAP scan records the electrical activity

  15. Phytozome Comparative Plant Genomics Portal

    Energy Technology Data Exchange (ETDEWEB)

    Goodstein, David; Batra, Sajeev; Carlson, Joseph; Hayes, Richard; Phillips, Jeremy; Shu, Shengqiang; Schmutz, Jeremy; Rokhsar, Daniel

    2014-09-09

    The Dept. of Energy Joint Genome Institute is a genomics user facility supporting DOE mission science in the areas of Bioenergy, Carbon Cycling, and Biogeochemistry. The Plant Program at the JGI applies genomic, analytical, computational and informatics platforms and methods to: 1. Understand and accelerate the improvement (domestication) of bioenergy crops 2. Characterize and moderate plant response to climate change 3. Use comparative genomics to identify constrained elements and infer gene function 4. Build high quality genomic resource platforms of JGI Plant Flagship genomes for functional and experimental work 5. Expand functional genomic resources for Plant Flagship genomes

  16. Scanning tunneling microscope assembly, reactor, and system

    Science.gov (United States)

    Tao, Feng; Salmeron, Miquel; Somorjai, Gabor A

    2014-11-18

    An embodiment of a scanning tunneling microscope (STM) reactor includes a pressure vessel, an STM assembly, and three spring coupling objects. The pressure vessel includes a sealable port, an interior, and an exterior. An embodiment of an STM system includes a vacuum chamber, an STM reactor, and three springs. The three springs couple the STM reactor to the vacuum chamber and are operable to suspend the scanning tunneling microscope reactor within the interior of the vacuum chamber during operation of the STM reactor. An embodiment of an STM assembly includes a coarse displacement arrangement, a piezoelectric fine displacement scanning tube coupled to the coarse displacement arrangement, and a receiver. The piezoelectric fine displacement scanning tube is coupled to the coarse displacement arrangement. The receiver is coupled to the piezoelectric scanning tube and is operable to receive a tip holder, and the tip holder is operable to receive a tip.

  17. Theory of second optimization for scan experiment

    CERN Document Server

    Mo, X H

    2015-01-01

    The optimal design of scan experiment is of great significance both for scientific research and from economical viewpoint. Two approaches, one has recourse to the sampling technique and the other resorts to the analytical proof, are adopted to figure out the optimized scan scheme for the relevant parameters. The final results indicate that for $n$ parameters scan experiment, $n$ energy points are necessary and sufficient for optimal determination of these $n$ parameters; each optimal position can be acquired by single parameter scan (sampling method), or by analysis of auxiliary function (analytic method); the luminosity allocation among the points can be determined analytically with respect to the relative importance between parameters. By virtue of the second optimization theory established in this paper, it is feasible to accommodate the perfectly optimal scheme for any scan experiment.

  18. MR guided spatial normalization of SPECT scans

    International Nuclear Information System (INIS)

    Full text: In SPECT population studies where magnetic resonance (MR) scans are also available, the higher resolution of the MR scans allows for an improved spatial normalization of the SPECT scans. In this approach, the SPECT images are first coregistered to their corresponding MR images by a linear (affine) transformation which is calculated using SPM's mutual information maximization algorithm. Non-linear spatial normalization maps are then computed either directly from the MR scans using SPM's built in spatial normalization algorithm, or, from segmented TI MR images using DARTEL, an advanced diffeomorphism based spatial normalization algorithm. We compare these MR based methods to standard SPECT based spatial normalization for a population of 27 fibromyalgia patients and 25 healthy controls with spin echo T1 scans. We identify significant perfusion deficits in prefrontal white matter in FM patients, with the DARTEL based spatial normalization procedure yielding stronger statistics than the standard SPECT based spatial normalization. (author)

  19. Genome instability and aging.

    Science.gov (United States)

    Vijg, Jan; Suh, Yousin

    2013-01-01

    Genome instability has long been implicated as the main causal factor in aging. Somatic cells are continuously exposed to various sources of DNA damage, from reactive oxygen species to UV radiation to environmental mutagens. To cope with the tens of thousands of chemical lesions introduced into the genome of a typical cell each day, a complex network of genome maintenance systems acts to remove damage and restore the correct base pair sequence. Occasionally, however, repair is erroneous, and such errors, as well as the occasional failure to correctly replicate the genome during cell division, are the basis for mutations and epimutations. There is now ample evidence that mutations accumulate in various organs and tissues of higher animals, including humans, mice, and flies. What is not known, however, is whether the frequency of these random changes is sufficient to cause the phenotypic effects generally associated with aging. The exception is cancer, an age-related disease caused by the accumulation of mutations and epimutations. Here, we first review current concepts regarding the relationship between DNA damage, repair, and mutation, as well as the data regarding genome alterations as a function of age. We then describe a model for how randomly induced DNA sequence and epigenomic variants in the somatic genomes of animals can result in functional decline and disease in old age. Finally, we discuss the genetics of genome instability in relation to longevity to address the importance of alterations in the somatic genome as a causal factor in aging and to underscore the opportunities provided by genetic approaches to develop interventions that attenuate genome instability, reduce disease risk, and increase life span. PMID:23398157

  20. Center for Cancer Genomics | Office of Cancer Genomics

    Science.gov (United States)

    The Center for Cancer Genomics (CCG) was established to unify the National Cancer Institute's activities in cancer genomics, with the goal of advancing genomics research and translating findings into the clinic to improve the precise diagnosis and treatment of cancers. In addition to promoting genomic sequencing approach

  1. Human Genome Project

    Energy Technology Data Exchange (ETDEWEB)

    Block, S. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Cornwall, J. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Dally, W. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Dyson, F. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Fortson, N. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Joyce, G. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Kimble, H. J. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Lewis, N. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Max, C. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Prince, T. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Schwitters, R. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Weinberger, P. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Woodin, W. H. [The MITRE Corporation, McLean, VA (US). JASON Program Office

    1998-01-04

    The study reviews Department of Energy supported aspects of the United States Human Genome Project, the joint National Institutes of Health/Department of Energy program to characterize all human genetic material, to discover the set of human genes, and to render them accessible for further biological study. The study concentrates on issues of technology, quality assurance/control, and informatics relevant to current effort on the genome project and needs beyond it. Recommendations are presented on areas of the genome program that are of particular interest to and supported by the Department of Energy.

  2. Genomic taxonomy of vibrios

    Directory of Open Access Journals (Sweden)

    Iida Tetsuya

    2009-10-01

    Full Text Available Abstract Background Vibrio taxonomy has been based on a polyphasic approach. In this study, we retrieve useful taxonomic information (i.e. data that can be used to distinguish different taxonomic levels, such as species and genera from 32 genome sequences of different vibrio species. We use a variety of tools to explore the taxonomic relationship between the sequenced genomes, including Multilocus Sequence Analysis (MLSA, supertrees, Average Amino Acid Identity (AAI, genomic signatures, and Genome BLAST atlases. Our aim is to analyse the usefulness of these tools for species identification in vibrios. Results We have generated four new genome sequences of three Vibrio species, i.e., V. alginolyticus 40B, V. harveyi-like 1DA3, and V. mimicus strains VM573 and VM603, and present a broad analyses of these genomes along with other sequenced Vibrio species. The genome atlas and pangenome plots provide a tantalizing image of the genomic differences that occur between closely related sister species, e.g. V. cholerae and V. mimicus. The vibrio pangenome contains around 26504 genes. The V. cholerae core genome and pangenome consist of 1520 and 6923 genes, respectively. Pangenomes might allow different strains of V. cholerae to occupy different niches. MLSA and supertree analyses resulted in a similar phylogenetic picture, with a clear distinction of four groups (Vibrio core group, V. cholerae-V. mimicus, Aliivibrio spp., and Photobacterium spp.. A Vibrio species is defined as a group of strains that share > 95% DNA identity in MLSA and supertree analysis, > 96% AAI, ≤ 10 genome signature dissimilarity, and > 61% proteome identity. Strains of the same species and species of the same genus will form monophyletic groups on the basis of MLSA and supertree. Conclusion The combination of different analytical and bioinformatics tools will enable the most accurate species identification through genomic computational analysis. This endeavour will culminate in

  3. Genomic signal processing

    CERN Document Server

    Shmulevich, Ilya

    2007-01-01

    Genomic signal processing (GSP) can be defined as the analysis, processing, and use of genomic signals to gain biological knowledge, and the translation of that knowledge into systems-based applications that can be used to diagnose and treat genetic diseases. Situated at the crossroads of engineering, biology, mathematics, statistics, and computer science, GSP requires the development of both nonlinear dynamical models that adequately represent genomic regulation, and diagnostic and therapeutic tools based on these models. This book facilitates these developments by providing rigorous mathema

  4. Human Genome Program

    Energy Technology Data Exchange (ETDEWEB)

    1993-01-01

    The DOE Human Genome program has grown tremendously, as shown by the marked increase in the number of genome-funded projects since the last workshop held in 1991. The abstracts in this book describe the genome research of DOE-funded grantees and contractors and invited guests, and all projects are represented at the workshop by posters. The 3-day meeting includes plenary sessions on ethical, legal, and social issues pertaining to the availability of genetic data; sequencing techniques, informatics support; and chromosome and cDNA mapping and sequencing.

  5. Genomic taxonomy of vibrios

    DEFF Research Database (Denmark)

    Thompson, Cristiane C.; Vicente, Ana Carolina P.; Souza, Rangel C.;

    2009-01-01

    BACKGROUND: Vibrio taxonomy has been based on a polyphasic approach. In this study, we retrieve useful taxonomic information (i.e. data that can be used to distinguish different taxonomic levels, such as species and genera) from 32 genome sequences of different vibrio species. We use a variety...... analytical and bioinformatics tools will enable the most accurate species identification through genomic computational analysis. This endeavour will culminate in the birth of the online genomic taxonomy whereby researchers and end-users of taxonomy will be able to identify their isolates through a web...

  6. The Genome Atlas Resource

    DEFF Research Database (Denmark)

    Azam Qureshi, Matloob; Rotenberg, Eva; Stærfeldt, Hans Henrik;

    2010-01-01

    Abstract. The Genome Atlas is a resource for addressing the challenges of synchronising prokaryotic genomic sequence data from multiple public repositories. This resource can integrate bioinformatic analyses in various data format and quality. Existing open source tools have been used together...... with scripts and algorithms developed in a variety of programming languages at the Centre for Biological Sequence Analysis in order to create a three-tier software application for genome analysis. The results are made available via a web interface developed in Java, PHP and Perl CGI. User...

  7. Bone scan in inflammatory osseous disease

    International Nuclear Information System (INIS)

    The /sup 99m/Tc-phosphate bone scan has become a sensitive, reliable, and safe method for evaluating the patient with suspected inflammatory disease of bone. The scan may become positive as early as the first 24 hr after the symptoms and 10-14 days before roentgenographic changes occur. It can be used to differentiate successfully a variety of diseases from osteomyelitis, and in conjunction with 67Ga-citrate scan has become a mainstay in the work-up of the patient with infectious disease. Applications of the bone scan to infectious diseases in pediatric practice are especially helpful, since these diseases are common problems in this age group. Increased experience with the /sup 99m/Tc-phosphate bone scan has already defined several areas of ''limitations'' in evaluating inflammatory disease. ''Cold'' defects, negative scans in early stages of osteomyelitis, and ''extended uptake'' may all pose problems in interpretation, but careful correlation of the bone scan results with clinical history and physical findings, blood cultures, and roentgenography will significantly reduce these problems

  8. Tumor scanning with 57Co-bleomycin

    International Nuclear Information System (INIS)

    The clinical application of 57Co-bleomycin as a tumor scanning radiopharmaceutical was firstly reported by Nouel and Maeda respectively. The authors conducted studies on the diagnostic significance of this tumor scanning agent and presented the results obtained in 40 patients with malignant and non malignant lesions. Six hours and 24 hours after the injection of 500 μCi of 57Co-bleomycin, scintigrams were taken with a 3-inch scintiscanner. Positive scans were found in 20 out of 36 patients with various malignant tumors. Of 20 patients with lung cancer, positive scans were obtained in 17 cases (85%) and of 6 with breast cancer, 3 cases showed positive scans. False negative scans were obtained in another 10 cases of malignant tumors (3 cases of thyroid carcinoma, 4 cases of hepatoma, and 1 case each of gastric carcinoma, peritoneal carcinomatosis, and reticulum cell sarcoma). Of 4 patients with non malignant disease, one case of pulmonary tuberculosis showed a positive scan. In 8 cases of lung cancer and 6 of breast cancer, the relationship between the size of the excised tumor and the scintigram findings was studied. The smallest tumors detected by scintigram were 2 cm in lung cancer and 3.2 cm in breast cancer. (author)

  9. Feedback Effects in Combined Fast-Scan Cyclic Voltammetry-Scanning Electrochemical Microscopy

    OpenAIRE

    Schrock, Daniel S.; Wipf, David O.; Baur, John E.

    2007-01-01

    Fast-scan cyclic voltammetry at scan rates between 5 and 1000 Vs−1 was performed at the tip of a scanning electrochemical microscope immersed in a solution of redox mediator. The effect of conducting and insulating substrates on the voltammetric signal was investigated as a function of scan rate and tip-substrate distance. It was found that diffusional interactions between the tip and the substrate are greatest at lower scan rates and on the reverse sweep of the voltammogram. At the fastest s...

  10. Bone scan in diagnosis of infectious osteoarthritis

    International Nuclear Information System (INIS)

    Bone scan with Technetium 99m is harmless method of evaluation of skeletal lesions. It is safe in pediatrics age group and it can be used in early diagnosis of infectious osteoarthritis. Bone scan differentiate osteomyelitis from cellulitis, and also it may help in diagnosis of subclinical involvement of rheumatoid arthritis, benign and malignant bone tumors, stress fractures and periostitis. We report results of bone scan in 30 pediatrics patients as follow: osteomyelitis 9 cases, cellulitis 4 cases, infectious arthritis 7 cases, tuberculous osteoarthritis 2 cases, rheumatoid arthritis 2 cases, and other different diseases 9 cases

  11. Bone scan in diagnosis of infectious osteoarthritis

    International Nuclear Information System (INIS)

    Bone scan with Technetium 99m is harmless method of evaluation of skeletal lesions. It is safe in pediatrics age group and it can be used in early diagnosis of infectious osteo-arthritis. Bone scan differentiate osteomyelitis from cellulitis, and also it may help in diagnosis of subclinical involvement of rheumatoid arthritis, benign and malignant bone tumors, stress fractures and periostitis. We report results of bone scan in 30 pediatric patients as follows: osteomyelitis 9 cases, cellulitis 4 cases, infectious arthritis 4 cases, tuberculous osteoarthritis 2 cases, rheumatoid arthritis 2 cases and other different diseases 9 cases

  12. CT scan for suspected acute appendicitis

    OpenAIRE

    Widlus, David M.

    2012-01-01

    Appendicitis is common with a 7% lifetime risk for an individual in the United States. Mean age at diagnosis is 22 years old. While frequently clinically obvious, by 2006, more than 90% of patients diagnosed with appendicitis had a CT scan of the abdomen and pelvis performed. Use of CT scans has allowed a decrease in false-negative rate at appendectomy to under 10% from a rate of approximately 20% before routine use of CT scan. In addition, the rate of perforation has decreased from nearly 30...

  13. Reconstruction the KROKUS scanning measuring projector

    International Nuclear Information System (INIS)

    Modernized scanning measuring projector, designated for primary scanning of films from bubble chambers is described. Detailed consideration is given to electronic circuit for controlling film-pulling mechanism in three modes: slow pulling, fast pulling and start-stop conditions. Controle unit for scanning device contains the following basic elements: the circuit of controlling by operating elements, photorelay circuit, phase shifting unit and supply unit of projector lamps and electric drive. The maximal image dimension on the screen - 400X600 mm. Film-pulling mechanism enables to load both 35 and 50 mm films

  14. pMSSM scans in ATLAS

    CERN Document Server

    Heinrich, Lukas; The ATLAS collaboration

    2016-01-01

    Multidimensional scans of the pMSSM have been used in ATLAS to assess the experiment sensitivity to classess of models usually not well represented by simplified models. Such scans require a well defined approach in generating signal events and deciding which ones should be passed through the CPU-intensive detector simulation and for which ones the sensitivity can be instead parametrised. They also impose challenges in deciding how the experiment sensitivity should be summarised. The talk will discuss in detail hos such large-scale scans have been approached by ATLAS, touching upon recent results obtained.

  15. Genome-specificity of triplet periodicity of prokaryotic genomes

    International Nuclear Information System (INIS)

    Authors have found that triplet periodicity (TP) is more similar inside genome than between genomes and that TP distribution inside genome corresponds to hypothesis which imply common TP pattern for majority of sequences inside a genome. To test the specificity of TP, the classification of the gene has been carried out to detect the belonging to one genome of the pair. For most pairs, the classification accuracy was more than 85%

  16. Lophotrochozoan mitochondrial genomes

    Energy Technology Data Exchange (ETDEWEB)

    Valles, Yvonne; Boore, Jeffrey L.

    2005-10-01

    Progress in both molecular techniques and phylogeneticmethods has challenged many of the interpretations of traditionaltaxonomy. One example is in the recognition of the animal superphylumLophotrochozoa (annelids, mollusks, echiurans, platyhelminthes,brachiopods, and other phyla), although the relationships within thisgroup and the inclusion of some phyla remain uncertain. While much ofthis progress in phylogenetic reconstruction has been based on comparingsingle gene sequences, we are beginning to see the potential of comparinglarge-scale features of genomes, such as the relative order of genes.Even though tremendous progress is being made on the sequencedetermination of whole nuclear genomes, the dataset of choice forgenome-level characters for many animals across a broad taxonomic rangeremains mitochondrial genomes. We review here what is known aboutmitochondrial genomes of the lophotrochozoans and discuss the promisethat this dataset will enable insight into theirrelationships.

  17. The genomics of adaptation.

    Science.gov (United States)

    Radwan, Jacek; Babik, Wiesław

    2012-12-22

    The amount and nature of genetic variation available to natural selection affect the rate, course and outcome of evolution. Consequently, the study of the genetic basis of adaptive evolutionary change has occupied biologists for decades, but progress has been hampered by the lack of resolution and the absence of a genome-level perspective. Technological advances in recent years should now allow us to answer many long-standing questions about the nature of adaptation. The data gathered so far are beginning to challenge some widespread views of the way in which natural selection operates at the genomic level. Papers in this Special Feature of Proceedings of the Royal Society B illustrate various aspects of the broad field of adaptation genomics. This introductory article sets up a context and, on the basis of a few selected examples, discusses how genomic data can advance our understanding of the process of adaptation.

  18. Epidemiology & Genomics Research Program

    Science.gov (United States)

    The Epidemiology and Genomics Research Program, in the National Cancer Institute's Division of Cancer Control and Population Sciences, funds research in human populations to understand the determinants of cancer occurrence and outcomes.

  19. The genomics of adaptation.

    Science.gov (United States)

    Radwan, Jacek; Babik, Wiesław

    2012-12-22

    The amount and nature of genetic variation available to natural selection affect the rate, course and outcome of evolution. Consequently, the study of the genetic basis of adaptive evolutionary change has occupied biologists for decades, but progress has been hampered by the lack of resolution and the absence of a genome-level perspective. Technological advances in recent years should now allow us to answer many long-standing questions about the nature of adaptation. The data gathered so far are beginning to challenge some widespread views of the way in which natural selection operates at the genomic level. Papers in this Special Feature of Proceedings of the Royal Society B illustrate various aspects of the broad field of adaptation genomics. This introductory article sets up a context and, on the basis of a few selected examples, discusses how genomic data can advance our understanding of the process of adaptation. PMID:23097510

  20. The genome editing revolution

    DEFF Research Database (Denmark)

    Stella, Stefano; Montoya, Guillermo

    2016-01-01

    the previously available DNA binding templates, zinc fingers and meganucleases. Recently, the area experimented a quantum leap because of the introduction of the clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein (Cas) system (clustered regularly interspaced short palindromic...... sequence). This ribonucleoprotein complex protects bacteria from invading DNAs, and it was adapted to be used in genome editing. The CRISPR ribonucleic acid (RNA) molecule guides to the specific DNA site the Cas9 nuclease to cleave the DNA target. Two years and more than 1000 publications later, the CRISPR......-Cas system has become the main tool for genome editing in many laboratories. Currently the targeted genome editing technology has been used in many fields and may be a possible approach for human gene therapy. Furthermore, it can also be used to modifying the genomes of model organisms for studying human...

  1. Yeast genome sequencing:

    DEFF Research Database (Denmark)

    Piskur, Jure; Langkjær, Rikke Breinhold

    2004-01-01

    For decades, unicellular yeasts have been general models to help understand the eukaryotic cell and also our own biology. Recently, over a dozen yeast genomes have been sequenced, providing the basis to resolve several complex biological questions. Analysis of the novel sequence data has shown...... of closely related species helps in gene annotation and to answer how many genes there really are within the genomes. Analysis of non-coding regions among closely related species has provided an example of how to determine novel gene regulatory sequences, which were previously difficult to analyse because...... they are short and degenerate and occupy different positions. Comparative genomics helps to understand the origin of yeasts and points out crucial molecular events in yeast evolutionary history, such as whole-genome duplication and horizontal gene transfer(s). In addition, the accumulating sequence data provide...

  2. Mouse genome database 2016.

    Science.gov (United States)

    Bult, Carol J; Eppig, Janan T; Blake, Judith A; Kadin, James A; Richardson, Joel E

    2016-01-01

    The Mouse Genome Database (MGD; http://www.informatics.jax.org) is the primary community model organism database for the laboratory mouse and serves as the source for key biological reference data related to mouse genes, gene functions, phenotypes and disease models with a strong emphasis on the relationship of these data to human biology and disease. As the cost of genome-scale sequencing continues to decrease and new technologies for genome editing become widely adopted, the laboratory mouse is more important than ever as a model system for understanding the biological significance of human genetic variation and for advancing the basic research needed to support the emergence of genome-guided precision medicine. Recent enhancements to MGD include new graphical summaries of biological annotations for mouse genes, support for mobile access to the database, tools to support the annotation and analysis of sets of genes, and expanded support for comparative biology through the expansion of homology data.

  3. Mouse Genome Informatics (MGI)

    Data.gov (United States)

    U.S. Department of Health & Human Services — MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human...

  4. The Lotus japonicus genome

    DEFF Research Database (Denmark)

    This book provides insights into some of the key achievements made in the study of Lotus japonicus (birdsfoot trefoil), as well as a timely overview of topics that are pertinent for future developments in legume genomics. Key topics covered include endosymbiosis, development, hormone regulation......, carbon/nitrogen and secondary metabolism, as well as advances made in high-throughput genomic and genetic approaches. Research focusing on model plants has underpinned the recent growth in plant genomics and genetics and provided a basis for investigations of major crop species. In the legume family...... Fabaceae, groundbreaking genetic and genomic research has established a significant body of knowledge on Lotus japonicus, which was adopted as a model species more than 20 years ago. The diverse nature of legumes means that such research has a wide potential and agricultural impact, for example...

  5. Genetical Genomics for Evolutionary Studies

    NARCIS (Netherlands)

    Prins, J.C.P.; Smant, G.; Jansen, R.C.

    2012-01-01

    enetical genomics combines acquired high-throughput genomic data with genetic analysis. In this chapter, we discuss the application of genetical genomics for evolutionary studies, where new high-throughput molecular technologies are combined with mapping quantitative trait loci (QTL) on the genome i

  6. An Introduction to Genome Annotation.

    Science.gov (United States)

    Campbell, Michael S; Yandell, Mark

    2015-12-17

    Genome projects have evolved from large international undertakings to tractable endeavors for a single lab. Accurate genome annotation is critical for successful genomic, genetic, and molecular biology experiments. These annotations can be generated using a number of approaches and available software tools. This unit describes methods for genome annotation and a number of software tools commonly used in gene annotation.

  7. Molluscan Evolutionary Genomics

    Energy Technology Data Exchange (ETDEWEB)

    Simison, W. Brian; Boore, Jeffrey L.

    2005-12-01

    In the last 20 years there have been dramatic advances in techniques of high-throughput DNA sequencing, most recently accelerated by the Human Genome Project, a program that has determined the three billion base pair code on which we are based. Now this tremendous capability is being directed at other genome targets that are being sampled across the broad range of life. This opens up opportunities as never before for evolutionary and organismal biologists to address questions of both processes and patterns of organismal change. We stand at the dawn of a new 'modern synthesis' period, paralleling that of the early 20th century when the fledgling field of genetics first identified the underlying basis for Darwin's theory. We must now unite the efforts of systematists, paleontologists, mathematicians, computer programmers, molecular biologists, developmental biologists, and others in the pursuit of discovering what genomics can teach us about the diversity of life. Genome-level sampling for mollusks to date has mostly been limited to mitochondrial genomes and it is likely that these will continue to provide the best targets for broad phylogenetic sampling in the near future. However, we are just beginning to see an inroad into complete nuclear genome sequencing, with several mollusks and other eutrochozoans having been selected for work about to begin. Here, we provide an overview of the state of molluscan mitochondrial genomics, highlight a few of the discoveries from this research, outline the promise of broadening this dataset, describe upcoming projects to sequence whole mollusk nuclear genomes, and challenge the community to prepare for making the best use of these data.

  8. The human genome project

    International Nuclear Information System (INIS)

    The Human Genome Project is a massive international research project, costing 3 to 5 billion dollars and expected to take 15 years, which will identify the all the genes in the human genome - i.e. the complete sequence of bases in human DNA. The prize will be the ability to identify genes causing or predisposing to disease, and in some cases the development of gene therapy, but this new knowledge will raise important ethical issues

  9. Cryptosporidium parvum Genome Project

    OpenAIRE

    Abrahamsen, Mitchell S.

    2001-01-01

    A lack of basic understanding of parasite biology has been a limiting factor in designing effective means of treating and preventing disease caused by Cryptosporidium parvum. Since the genomic DNA sequence encodes all of the heritable information responsible for development, disease pathogenesis, virulence, species permissiveness and immune resistance, a comprehensive knowledge of the C. parvum genome will provide the necessary information required for cost-effective and target...

  10. Decoding the human genome

    CERN Document Server

    CERN. Geneva. Audiovisual Unit; Antonerakis, S E

    2002-01-01

    Decoding the Human genome is a very up-to-date topic, raising several questions besides purely scientific, in view of the two competing teams (public and private), the ethics of using the results, and the fact that the project went apparently faster and easier than expected. The lecture series will address the following chapters: Scientific basis and challenges. Ethical and social aspects of genomics.

  11. Human Genome Annotation

    Science.gov (United States)

    Gerstein, Mark

    A central problem for 21st century science is annotating the human genome and making this annotation useful for the interpretation of personal genomes. My talk will focus on annotating the 99% of the genome that does not code for canonical genes, concentrating on intergenic features such as structural variants (SVs), pseudogenes (protein fossils), binding sites, and novel transcribed RNAs (ncRNAs). In particular, I will describe how we identify regulatory sites and variable blocks (SVs) based on processing next-generation sequencing experiments. I will further explain how we cluster together groups of sites to create larger annotations. Next, I will discuss a comprehensive pseudogene identification pipeline, which has enabled us to identify >10K pseudogenes in the genome and analyze their distribution with respect to age, protein family, and chromosomal location. Throughout, I will try to introduce some of the computational algorithms and approaches that are required for genome annotation. Much of this work has been carried out in the framework of the ENCODE, modENCODE, and 1000 genomes projects.

  12. Human social genomics.

    Directory of Open Access Journals (Sweden)

    Steven W Cole

    2014-08-01

    Full Text Available A growing literature in human social genomics has begun to analyze how everyday life circumstances influence human gene expression. Social-environmental conditions such as urbanity, low socioeconomic status, social isolation, social threat, and low or unstable social status have been found to associate with differential expression of hundreds of gene transcripts in leukocytes and diseased tissues such as metastatic cancers. In leukocytes, diverse types of social adversity evoke a common conserved transcriptional response to adversity (CTRA characterized by increased expression of proinflammatory genes and decreased expression of genes involved in innate antiviral responses and antibody synthesis. Mechanistic analyses have mapped the neural "social signal transduction" pathways that stimulate CTRA gene expression in response to social threat and may contribute to social gradients in health. Research has also begun to analyze the functional genomics of optimal health and thriving. Two emerging opportunities now stand to revolutionize our understanding of the everyday life of the human genome: network genomics analyses examining how systems-level capabilities emerge from groups of individual socially sensitive genomes and near-real-time transcriptional biofeedback to empirically optimize individual well-being in the context of the unique genetic, geographic, historical, developmental, and social contexts that jointly shape the transcriptional realization of our innate human genomic potential for thriving.

  13. Automated genome mining for natural products

    Directory of Open Access Journals (Sweden)

    Zajkowski James

    2009-06-01

    Full Text Available Abstract Background Discovery of new medicinal agents from natural sources has largely been an adventitious process based on screening of plant and microbial extracts combined with bioassay-guided identification and natural product structure elucidation. Increasingly rapid and more cost-effective genome sequencing technologies coupled with advanced computational power have converged to transform this trend toward a more rational and predictive pursuit. Results We have developed a rapid method of scanning genome sequences for multiple polyketide, nonribosomal peptide, and mixed combination natural products with output in a text format that can be readily converted to two and three dimensional structures using conventional software. Our open-source and web-based program can assemble various small molecules composed of twenty standard amino acids and twenty two other chain-elongation intermediates used in nonribosomal peptide systems, and four acyl-CoA extender units incorporated into polyketides by reading a hidden Markov model of DNA. This process evaluates and selects the substrate specificities along the assembly line of nonribosomal synthetases and modular polyketide synthases. Conclusion Using this approach we have predicted the structures of natural products from a diverse range of bacteria based on a limited number of signature sequences. In accelerating direct DNA to metabolomic analysis, this method bridges the interface between chemists and biologists and enables rapid scanning for compounds with potential therapeutic value.

  14. Electron Beam Scanning in Industrial Applications

    Science.gov (United States)

    Jongen, Yves; Herer, Arnold

    1996-05-01

    Scanned electron beams are used within many industries for applications such as sterilization of medical disposables, crosslinking of wire and cables insulating jackets, polymerization and degradation of resins and biomaterials, modification of semiconductors, coloration of gemstones and glasses, removal of oxides from coal plant flue gasses, and the curing of advanced composites and other molded forms. X-rays generated from scanned electron beams make yet other applications, such as food irradiation, viable. Typical accelerators for these applications range in beam energy from 0.5MeV to 10 MeV, with beam powers between 5 to 500kW and scanning widths between 20 and 300 cm. Since precise control of dose delivery is required in many of these applications, the integration of beam characteristics, product conveyance, and beam scanning mechanisms must be well understood and optimized. Fundamental issues and some case examples are presented.

  15. Indium-111 leukocyte scanning and fracture healing

    International Nuclear Information System (INIS)

    This study was undertaken to determine the specificity of indium-111 leukocyte scans for osteomyelitis when fractures are present. Midshaft tibial osteotomies were performed in 14 New Zealand white rabbits, seven of which were infected postoperatively with Staphylococcus aureus per Norden's protocol. All 14 rabbits were scanned following injection with 75 microCi of indium 111 at 72 h after osteotomy and at weekly intervals for 4 weeks. Before the rabbits were killed, the fracture sites were cultured to document the presence or absence of infection. The results of all infected osteotomy sites were positive, whereas no positive scans were found in the noninfected osteotomies. We concluded from this study that uncomplicated fracture healing does not result in a positive indium-111 leukocyte scan

  16. A Scanning Quantum Cryogenic Atom Microscope

    CERN Document Server

    Yang, Fan; Taylor, Stephen F; Turner, Richard W; Lev, Benjamin L

    2016-01-01

    Microscopic imaging of local magnetic fields provides a window into the organizing principles of complex and technologically relevant condensed matter materials. However, a wide variety of intriguing strongly correlated and topologically nontrivial materials exhibit poorly understood phenomena outside the detection capability of state-of-the-art high-sensitivity, high-resolution scanning probe magnetometers. We introduce a quantum-noise-limited scanning probe magnetometer that can operate from room-to-cryogenic temperatures with unprecedented DC-field sensitivity and micron-scale resolution. The Scanning Quantum Cryogenic Atom Microscope (SQCRAMscope) employs a magnetically levitated atomic Bose-Einstein condensate (BEC), thereby providing immunity to conductive and blackbody radiative heating. The SQCRAMscope has a noise floor of 300 pT and provides a 100x improvement in magnetic flux sensitivity over previous atomic scanning probe magnetometers. These capabilities are carefully benchmarked by imaging magnet...

  17. Probe microscopy: Scanning below the cell surface

    Science.gov (United States)

    Sahin, Ozgur

    2008-08-01

    Conventional atomic force microscopy probes only the surface of specimens. A related technique called scanning near-field ultrasonic holography can now image nanoparticles buried below the surfaces of cells, which could prove useful in nanotoxicology.

  18. Noncontact dimensional measurement system using holographic scanning

    Science.gov (United States)

    Sagan, Stephen F.; Rosso, Robert S.; Rowe, David M.

    1997-07-01

    Holographic scanning systems have been used for years in point-of-sale bar code scanners and other low resolution applications. These simple scanning systems could not successfully provide the accuracy and precision required to measure, inspect and control the production of today's high tech optical fibers, medical extrusions and electrical cables. A new class of instruments for the precision measurement of industrial processes has been created by the development of systems with a unique combination of holographic optical elements that can compensate for the wavelength drift in laser diodes, the application of proprietary post-processing algorithms, and the advancements in replication methods to fabricate low cost holographic scanning discs. These systems have improved upon the performance of traditional polygon mirror scanners. This paper presents the optical configuration and design features that have been incorporated into a holographic scanning inspection system that provides higher productivity, increased product quality and lower production costs for many manufacturers.

  19. EO Scanned Micro-LADAR Project

    Data.gov (United States)

    National Aeronautics and Space Administration — In this SBIR program we will develop, design and build new scanning based micro-ladar sensors with unprecedented small size, weight, and power (SWaP), thereby...

  20. Intelligent Classification and Visualization of Network Scans

    Energy Technology Data Exchange (ETDEWEB)

    Chen, L; Muelder, C; Ma, K; Bartoletti, A

    2007-03-01

    Network scans are a common first step in a network intrusion attempt. In order to gain information about a potential network intrusion, it is beneficial to analyze these network scans. Statistical methods such as wavelet scalogram analysis have been used along with visualization techniques in previous methods. However, applying these statistical methods to reduce the data causes a substantial amount of data loss. This paper presents a study of using associative memory learning techniques to directly compare network scans in order to create a classification which can be used by itself or in conjunction with existing visualization techniques to better characterize the sources of these scans. This produces an integrated system of visual and intelligent analysis which is applicable to real world data.

  1. EO Scanned Micro-LADAR Project

    Data.gov (United States)

    National Aeronautics and Space Administration — In this phase II SBIR we will design, build, test, and deliver new scanning based micro-ladar sensors with unprecedented small size, weight, and power (SWaP),...

  2. Nanoscale thermometry by scanning thermal microscopy

    Science.gov (United States)

    Menges, Fabian; Riel, Heike; Stemmer, Andreas; Gotsmann, Bernd

    2016-07-01

    Measuring temperature is a central challenge in nanoscience and technology. Addressing this challenge, we report the development of a high-vacuum scanning thermal microscope and a method for non-equilibrium scanning probe thermometry. The microscope is built inside an electromagnetically shielded, temperature-stabilized laboratory and features nanoscopic spatial resolution at sub-nanoWatt heat flux sensitivity. The method is a dual signal-sensing technique inferring temperature by probing a total steady-state heat flux simultaneously to a temporally modulated heat flux signal between a self-heated scanning probe sensor and a sample. Contact-related artifacts, which so far limit the reliability of nanoscopic temperature measurements by scanning thermal microscopy, are minimized. We characterize the microscope's performance and demonstrate the benefits of the new thermometry approach by studying hot spots near lithographically defined constrictions in a self-heated metal interconnect.

  3. Scan matching SLAM in underwater environments

    OpenAIRE

    Mallios, Angelos; Ridao Rodríguez, Pere; Ribas Romagós, David; Hernàndez Bes, Emili

    2014-01-01

    This paper proposes a pose-based algorithm to solve the full simultaneous localization and mapping problem for autonomous underwater vehicle (AUV) navigating in unknown and possibly unstructured environments. The proposed method first estimates the local path traveled by the robot while forming the acoustic image (scan) with range data coming from a mono-beam rotating sonar head, providing position estimates for correcting the distortions that the vehicle motion produces in the scans. Then, c...

  4. Towards high-speed scanning tunneling microscopy

    OpenAIRE

    Tabak, Femke Chantal

    2013-01-01

    In this thesis, two routes towards high-speed scanning tunneling microscopy (STM) are described. The first possibility for high-speed scanning that is discussed is the use of MEMS (Micro-Electro Mechanical Systems) devices as high-speed add-ons in STM microscopes. The functionality of these devices is shown using finite-element simulations, combined with measurements of their resonance frequency and actuation range. Tip deposition was done using EBID (Electron-Beam Induced Deposition) which a...

  5. Scanning probe microscopy on new dental alloys

    Science.gov (United States)

    Reusch, B.; Geis-Gerstorfer, J.; Ziegler, C.

    Surface analytical methods such as scanning force microscopy (SFM), scanning electron microscopy (SEM) and X-ray photoelectron spectroscopy (XPS) were used to determine the surface properties of amalgam substitutes as tooth filling materials. In particular the corrosion and the passivation behavior of new gallium restorative materials were studied. To give relevant practical data, the measurements were performed with and without the alloys being stored in artificial saliva to simulate physiological oral conditions.

  6. Optimal stimulation settings for CMAP scan registrations

    OpenAIRE

    Maathuis Ellen M; Henderson Robert D; Drenthen Judith; Hutchinson Nicole M; Daube Jasper R; Blok Joleen H; Visser Gerhard H

    2012-01-01

    Abstract Background The CMAP (Compound Muscle Action Potential) scan is a non-invasive electrodiagnostic tool, which provides a quick and visual assessment of motor unit potentials as electrophysiological components that together constitute the CMAP. The CMAP scan records the electrical activity of the muscle (CMAP) in response to transcutaneous stimulation of the motor nerve with gradual changes in stimulus intensity. Large MUs, including those that result from collateral reinnervation, appe...

  7. Evolution of small prokaryotic genomes

    OpenAIRE

    Martínez-Cano, David J.; Reyes-Prieto, Mariana; Martínez-Romero, Esperanza; Partida-Martínez, Laila P.; Latorre, Amparo; Moya, Andrés; Delaye, Luis

    2015-01-01

    As revealed by genome sequencing, the biology of prokaryotes with reduced genomes is strikingly diverse. These include free-living prokaryotes with ∼800 genes as well as endosymbiotic bacteria with as few as ∼140 genes. Comparative genomics is revealing the evolutionary mechanisms that led to these small genomes. In the case of free-living prokaryotes, natural selection directly favored genome reduction, while in the case of endosymbiotic prokaryotes neutral processes played a more prominent ...

  8. Evolution of small prokaryotic genomes

    OpenAIRE

    David José Martínez-Cano; Mariana eReyes-Prieto; Esperanza eMartinez-Romero; Laila Pamela Partida-Martinez; Amparo eLatorre; Andres eMoya; Luis eDelaye

    2015-01-01

    As revealed by genome sequencing, the biology of prokaryotes with reduced genomes is strikingly diverse. These include free-living prokaryotes with ~800 genes as well as endosymbiotic bacteria with as few as ~140 genes. Comparative genomics is revealing the evolutionary mechanisms that led to these small genomes. In the case of free-living prokaryotes, natural selection directly favored genome reduction, while in the case of endosymbiotic prokaryotes neutral processes played a more prominent ...

  9. Role of bone scan in rheumatic disease

    Energy Technology Data Exchange (ETDEWEB)

    Choi, Yun Young [Hanyang University College of Medicine, Seoul (Korea, Republic of)

    2003-06-01

    Rheumatic diseases can be categorized by pathology into several specific types of musculoskeletal problems, including synovitis (e.g. rheumatoid arthritis), enthesopathy (e.g. ankylosing spondylitis) and cartilage degeneration (e.g. osteoarthritis). Skeletal radiographs have contributed to the diagnosis of these articular diseases, and some disease entities need typical radiographic changes as a factor of the diagnostic criteria. However, they sometimes show normal radiographic findings in the early stage of disease, when there is demineralization of less than 30-50%. Bone scans have also been used in arthritis, but not widely because the findings are nonspecific and it is thought that bone scans do not add significant information to routine radiography. Bone scans do however play a different role than simple radiography, and it is a complementary imaging method in the course of management of arthritis. The image quality of bone scans can be improved by obtaining regional views and images under al pin-hole collimator, and through a variety of scintigraphic techniques including the three phase bone scan and bone SPECT. Therefore, bone scans could improve the diagnostic value, and answer multiple clinical questions, based on the pathophysiology of various forms of arthritis.

  10. MEMS-based fast scanning probe microscopes

    International Nuclear Information System (INIS)

    Scanning probe microscopy is a frequently used nanometer-scale surface investigation technique. Unfortunately, its applicability is limited by the relatively low image acquisition speed, typically seconds to minutes per image. Higher imaging speeds are desirable for rapid inspection of samples and for the study of a range of dynamic surface processes, such as catalysis and crystal growth. We have designed a new high-speed scanning probe microscope (SPM) based on micro-electro mechanical systems (MEMS). MEMS are small, typically micrometer size devices that can be designed to perform the scanning motion required in an SPM system. These devices can be optimized to have high resonance frequencies (up to the MHz range) and have very low mass (10-11 kg). Therefore, MEMS can perform fast scanning motion without exciting resonances in the mechanical loop of the SPM, and hence scan the surface without causing the image distortion from which conventional piezo scanners suffer. We have designed a MEMS z-scanner which we have integrated in commercial AFM (atomic force microscope) and STM (scanning tunneling microscope) setups. We show the first successful AFM experiments.

  11. Feedback effects in combined fast-scan cyclic voltammetry-scanning electrochemical microscopy.

    Science.gov (United States)

    Schrock, Daniel S; Wipf, David O; Baur, John E

    2007-07-01

    Fast-scan cyclic voltammetry at scan rates between 5 and 1000 V s(-1) was performed at the tip of a scanning electrochemical microscope immersed in a solution of redox mediator. The effect of conducting and insulating substrates on the voltammetric signal was investigated as a function of scan rate and tip-substrate distance. It was found that diffusional interactions between the tip and the substrate are greatest at lower scan rates and on the reverse sweep of the voltammogram. At the fastest scan rates used, the tip could be brought to with 1 microm of the substrate without appreciable perturbation of the voltammogram. By selecting scan rates and tip-substrate distances such that feedback effects were negligible, it was possible to image the diffusion layer of a 10 microm Pt substrate electrode. With the tip placed 1 microm above a biological cell, tip-substrate diffusional interactions were greatly diminished at a scan rate of 100 V s(-1) and absent at a scan rate of 1000 V s(-1). These results suggest conditions can be selected that allow chemical imaging of substrates without the feedback interactions typically encountered in scanning electrochemical microscopy. PMID:17550230

  12. WheatGenome.info: A Resource for Wheat Genomics Resource.

    Science.gov (United States)

    Lai, Kaitao

    2016-01-01

    An integrated database with a variety of Web-based systems named WheatGenome.info hosting wheat genome and genomic data has been developed to support wheat research and crop improvement. The resource includes multiple Web-based applications, which are implemented as a variety of Web-based systems. These include a GBrowse2-based wheat genome viewer with BLAST search portal, TAGdb for searching wheat second generation genome sequence data, wheat autoSNPdb, links to wheat genetic maps using CMap and CMap3D, and a wheat genome Wiki to allow interaction between diverse wheat genome sequencing activities. This portal provides links to a variety of wheat genome resources hosted at other research organizations. This integrated database aims to accelerate wheat genome research and is freely accessible via the web interface at http://www.wheatgenome.info/ . PMID:26519407

  13. Rumen microbial genomics

    International Nuclear Information System (INIS)

    Full text: Improving plant cell wall (fiber) degradation remains one of the highest priority goals for all livestock enterprises, whether it is the intensively managed dairy herds in the United States, or the nomadic cattle herds in sub-Saharan Africa. The North American Consortium for Genomics of Fibrolytic Ruminal Bacteria was created in 2000 to promote the sequencing and comparative analysis of rumen microbial genomes. High throughput genome sequencing offers the potential to obtain a complete blueprint for the lifestyle of a specific microbe, and to assess its genetic potential in a functional and comparative fashion. So far, a combination of funds from U.S. Department of Agriculture's (USDA's) Initiative for Future Agriculture and Food Systems and the National Science Foundation (USDA-NSF) Microbe Sequencing Program has supported the sequencing of three rumen bacterial genomes to closure. Genome closure and annotation is complete for Fibrobacter succinogenes, and the Ruminococcus albus and Prevotella ruminicola genomes should be completed during 2004. In addition to these sequencing projects, Consortium members have used subtractive hybridization methods to characterize the genomic differences among the sequenced genomes and the genomes of additional strains and species of ruminal bacteria. A database has also been developed by bioinformaticians at The Institute for Genomic Research (www.tigr.org), which will contain the sequence information arising from this project, as well as in silico tools for genome examination. Accordingly, our Consortium will have provided a comprehensive suite of resources and tools useful to microbiologists and animal scientists throughout the world, especially those interested in the conversion of cellulose-rich materials into useful commodities, such as meat, milk and draught animal power. The inherent value associated with whole genome sequencing is already apparent for the F. succinogenes project. The genome sequence has revealed

  14. Scan path entropy and Arrow plots: Capturing scanning behavior of multiple observers

    Directory of Open Access Journals (Sweden)

    Ignace T C Hooge

    2013-12-01

    Full Text Available Designers of visual communication material want their material to attract and retain attention. In marketing research, heat maps, dwell time, and time to AOI first hit are often used as evaluation parameters. Here we present two additional measures 1 scan path entropy to quantify gaze guidance and 2 the arrow plot to visualize the average scan path. Both are based on string representations of scan paths. The latter also incorporates transition matrices and time required for 50% of the observers to first hit AOIs (T50. The new measures were tested in an eye tracking study (48 observers, 39 advertisements. Scan path entropy is a sensible measure for gaze guidance and the new visualization method reveals aspects of the average scan path and gives a better indication in what order global scanning takes place.

  15. Scan path entropy and arrow plots: capturing scanning behavior of multiple observers.

    Science.gov (United States)

    Hooge, Ignace; Camps, Guido

    2013-01-01

    Designers of visual communication material want their material to attract and retain attention. In marketing research, heat maps, dwell time, and time to AOI first hit are often used as evaluation parameters. Here we present two additional measures (1) "scan path entropy" to quantify gaze guidance and (2) the "arrow plot" to visualize the average scan path. Both are based on string representations of scan paths. The latter also incorporates transition matrices and time required for 50% of the observers to first hit AOIs (T50). The new measures were tested in an eye tracking study (48 observers, 39 advertisements). Scan path entropy is a sensible measure for gaze guidance and the new visualization method reveals aspects of the average scan path and gives a better indication in what order global scanning takes place. PMID:24399993

  16. Genomes to Proteomes

    Energy Technology Data Exchange (ETDEWEB)

    Panisko, Ellen A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Grigoriev, Igor [USDOE Joint Genome Inst., Walnut Creek, CA (United States); Daly, Don S. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Webb-Robertson, Bobbie-Jo [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Baker, Scott E. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2009-03-01

    Biologists are awash with genomic sequence data. In large part, this is due to the rapid acceleration in the generation of DNA sequence that occurred as public and private research institutes raced to sequence the human genome. In parallel with the large human genome effort, mostly smaller genomes of other important model organisms were sequenced. Projects following on these initial efforts have made use of technological advances and the DNA sequencing infrastructure that was built for the human and other organism genome projects. As a result, the genome sequences of many organisms are available in high quality draft form. While in many ways this is good news, there are limitations to the biological insights that can be gleaned from DNA sequences alone; genome sequences offer only a bird's eye view of the biological processes endemic to an organism or community. Fortunately, the genome sequences now being produced at such a high rate can serve as the foundation for other global experimental platforms such as proteomics. Proteomic methods offer a snapshot of the proteins present at a point in time for a given biological sample. Current global proteomics methods combine enzymatic digestion, separations, mass spectrometry and database searching for peptide identification. One key aspect of proteomics is the prediction of peptide sequences from mass spectrometry data. Global proteomic analysis uses computational matching of experimental mass spectra with predicted spectra based on databases of gene models that are often generated computationally. Thus, the quality of gene models predicted from a genome sequence is crucial in the generation of high quality peptide identifications. Once peptides are identified they can be assigned to their parent protein. Proteins identified as expressed in a given experiment are most useful when compared to other expressed proteins in a larger biological context or biochemical pathway. In this chapter we will discuss the automatic

  17. Combining p-values in large scale genomics experiments

    OpenAIRE

    Dmitri V Zaykin; Zhivotovsky, Lev A.; Czika, Wendy; Shao, Susan; Wolfinger, Russell D.

    2007-01-01

    In large-scale genomics experiments involving thousands of statistical tests, such as association scans and microarray expression experiments, a key question is: Which of the L tests represent true associations (TAs)? The traditional way to control false findings is via individual adjustments. In the presence of multiple TAs, p-value combination methods offer certain advantages. Both Fisher’s and Lancaster’s combination methods use an inverse gamma transformation. We identify the relation of ...

  18. Emerging Paradigms in Genomics-Based Crop Improvement

    Directory of Open Access Journals (Sweden)

    Abhishek Bohra

    2013-01-01

    Full Text Available Next generation sequencing platforms and high-throughput genotyping assays have remarkably expedited the pace of development of genomic tools and resources for several crops. Complementing the technological developments, conceptual shifts have also been witnessed in designing experimental populations. Availability of second generation mapping populations encompassing multiple alleles, multiple traits, and extensive recombination events is radically changing the phenomenon of classical QTL mapping. Additionally, the rising molecular breeding approaches like marker assisted recurrent selection (MARS that are able to harness several QTLs are of particular importance in obtaining a “designed” genotype carrying the most desirable combinations of favourable alleles. Furthermore, rapid generation of genome-wide marker data coupled with easy access to precise and accurate phenotypic screens enable large-scale exploitation of LD not only to discover novel QTLs via whole genome association scans but also to practise genomic estimated breeding value (GEBV-based selection of genotypes. Given refinements being experienced in analytical methods and software tools, the multiparent populations will be the resource of choice to undertake genome wide association studies (GWAS, multiparent MARS, and genomic selection (GS. With this, it is envisioned that these high-throughput and high-power molecular breeding methods would greatly assist in exploiting the enormous potential underlying breeding by design approach to facilitate accelerated crop improvement.

  19. Bone scans in nasopharyngeal carcinoma: local experience

    International Nuclear Information System (INIS)

    Introduction: Nasopharyngeal carcinoma (NPC) tops the list of malignancy in Malaysia and ranks first in male malignancy in the state of Sarawak. The majority of the NPC patients presented in the advanced stages and often with distal metastasis usually to the bones. In our local hospital is the new practice of bone scan using Tc99 started last year. Over a period of 9 months from July 2003 to March 2004, 41 NPC patients had the bone scans and our experience in these are reviewed and presented. Method: The NPC patients are selected consecutively including both new and treated patients. The scanner used is Siemen E.cam plus and Technecium (Tc99) the radio-active isotope used. The scan images are read and reported by qualified and trained Radiologists. The bone scans are requested from the ENT Specialist of the ENT department of the Hospital. The bone scan reports are checked by the ENT Specialists and the decisions made as to clinical correlation and further definitive imaging studies. Results: 41 NPC patients were included in the studies, 29 newly diagnosed and bone-canned before treatment started and 12 treated of which 3 being diagnosed having recurrent NPC. Of the 29 newly diagnosed patients, one was found true positive bone scan having increased radio-tracer uptake and confirmed Xray imagings. 3 of the treated patients had true positive bone scan with increased radio-tracer uptake and confirmed Xray imagings. Hence a total of 4 out of the 41 patients (9.8%) had bone metastasis on positive bone scans. Of the 29 newly diagnosed patients, 14 were found false positive bone scan having increased radio-tracer uptake but no confirmed X ray imagings. 4 of the treated patients had false positive bone scan with increased radio-tracer uptake but no confirmed X ray imagings. Hence a total of 18 out of the 41 patients (44%) had no bone metastasis on positive bone scans. There were 6 patients with symptoms referable to the bones' distal to the head and 2 had true positive bone

  20. Genome position specific priors for genomic prediction

    Directory of Open Access Journals (Sweden)

    Brøndum Rasmus

    2012-10-01

    Full Text Available Abstract Background The accuracy of genomic prediction is highly dependent on the size of the reference population. For small populations, including information from other populations could improve this accuracy. The usual strategy is to pool data from different populations; however, this has not proven as successful as hoped for with distantly related breeds. BayesRS is a novel approach to share information across populations for genomic predictions. The approach allows information to be captured even where the phase of SNP alleles and casuative mutation alleles are reversed across populations, or the actual casuative mutation is different between the populations but affects the same gene. Proportions of a four-distribution mixture for SNP effects in segments of fixed size along the genome are derived from one population and set as location specific prior proportions of distributions of SNP effects for the target population. The model was tested using dairy cattle populations of different breeds: 540 Australian Jersey bulls, 2297 Australian Holstein bulls and 5214 Nordic Holstein bulls. The traits studied were protein-, fat- and milk yield. Genotypic data was Illumina 777K SNPs, real or imputed. Results Results showed an increase in accuracy of up to 3.5% for the Jersey population when using BayesRS with a prior derived from Australian Holstein compared to a model without location specific priors. The increase in accuracy was however lower than was achieved when reference populations were combined to estimate SNP effects, except in the case of fat yield. The small size of the Jersey validation set meant that these improvements in accuracy were not significant using a Hotelling-Williams t-test at the 5% level. An increase in accuracy of 1-2% for all traits was observed in the Australian Holstein population when using a prior derived from the Nordic Holstein population compared to using no prior information. These improvements were significant (P

  1. Pose-based SLAM with probabilistic scan matching algorithm using a mechanical scanned imaging sonar

    OpenAIRE

    Mallios, Angelos; Ridao Rodríguez, Pere; Hernàndez Bes, Emili; Ribas Romagós, David; Maurelli, Francesco; Petillot, Yvan R.

    2009-01-01

    This paper proposes a pose-based algorithm to solve the full SLAM problem for an autonomous underwater vehicle (AUV), navigating in an unknown and possibly unstructured environment. The technique incorporate probabilistic scan matching with range scans gathered from a mechanical scanning imaging sonar (MSIS) and the robot dead-reckoning displacements estimated from a Doppler velocity log (DVL) and a motion reference unit (MRU). The proposed method utilizes two extended Kalman filters (EKF). T...

  2. Pose-based slam with probabilistic scan matching algorithm using a mechanical scanned imaging sonar

    OpenAIRE

    Mallios, Angelos; Ridao, Pere; Hernández, Emili; Ribas, David

    2010-01-01

    This paper proposes a pose-based algorithm to solve the full SLAM problem for an Autonomous Underwater Vehicle (AUV), navigating in an unknown and possibly unstructured environment. The technique incorporate probabilistic scan matching with range scans gathered from a Mechanical Scanned Imaging Sonar (MSIS) and the robot dead-reckoning displacements estimated from a Doppler Velocity Log (DVL) and a Motion Reference Unit (MRU). The raw data from the sensors are processed and ...

  3. Scanning a DNA molecule for bound proteins using hybrid magnetic and optical tweezers.

    Directory of Open Access Journals (Sweden)

    Marijn T J van Loenhout

    Full Text Available The functional state of the genome is determined by its interactions with proteins that bind, modify, and move along the DNA. To determine the positions and binding strength of proteins localized on DNA we have developed a combined magnetic and optical tweezers apparatus that allows for both sensitive and label-free detection. A DNA loop, that acts as a scanning probe, is created by looping an optically trapped DNA tether around a DNA molecule that is held with magnetic tweezers. Upon scanning the loop along the λ-DNA molecule, EcoRI proteins were detected with ~17 nm spatial resolution. An offset of 33 ± 5 nm for the detected protein positions was found between back and forwards scans, corresponding to the size of the DNA loop and in agreement with theoretical estimates. At higher applied stretching forces, the scanning loop was able to remove bound proteins from the DNA, showing that the method is in principle also capable of measuring the binding strength of proteins to DNA with a force resolution of 0.1 pN/[Formula: see text]. The use of magnetic tweezers in this assay allows the facile preparation of many single-molecule tethers, which can be scanned one after the other, while it also allows for direct control of the supercoiling state of the DNA molecule, making it uniquely suitable to address the effects of torque on protein-DNA interactions.

  4. Effects of scanning orientation on outlier formation in 3D laser scanning of reflective surfaces

    Science.gov (United States)

    Wang, Yutao; Feng, Hsi-Yung

    2016-06-01

    Inspecting objects with reflective surfaces using 3D laser scanning is a demanded but challenging part inspection task due to undesirable specular reflections, which produce extensive outliers in the scanned point cloud. These outliers need to be removed in order to alleviate subsequent data processing issues. Many existing automatic outlier removal methods do not detect outliers according to the outlier formation properties. As a result, these methods only offer limited capabilities in removing extensive and complex outliers from scanning objects with reflective surfaces. This paper reports an empirical study which experimentally investigates the outlier formation characteristics in relation to the scanning orientation of the laser probe. The objective is to characterize the scanning orientation effects on outlier formation in order to facilitate the development of an effective outlier detection and removal method. Such an experimental investigation was hardly done before. It has been found in this work that scanning orientation can directly affect outlier extensity and occurrence in 3D laser scanning. A general guidance on proper scan path planning can then be provided with an aim to reduce the occurrence of outliers. Further, the observed dependency of outlier formation on scanning orientation can be exploited to facilitate effective and automatic outlier detection and removal.

  5. Scanning-time evaluation of Digimarc Barcode

    Science.gov (United States)

    Gerlach, Rebecca; Pinard, Dan; Weaver, Matt; Alattar, Adnan

    2015-03-01

    This paper presents a speed comparison between the use of Digimarc® Barcodes and the Universal Product Code (UPC) for customer checkout at point of sale (POS). The recently introduced Digimarc Barcode promises to increase the speed of scanning packaged goods at POS. When this increase is exploited by workforce optimization systems, the retail industry could potentially save billions of dollars. The Digimarc Barcode is based on Digimarc's watermarking technology, and it is imperceptible, very robust, and does not require any special ink, material, or printing processes. Using an image-based scanner, a checker can quickly scan consumer packaged goods (CPG) embedded with the Digimarc Barcode without the need to reorient the packages with respect to the scanner. Faster scanning of packages saves money and enhances customer satisfaction. It reduces the length of the queues at checkout, reduces the cost of cashier labor, and makes self-checkout more convenient. This paper quantifies the increase in POS scanning rates resulting from the use of the Digimarc Barcode versus the traditional UPC. It explains the testing methodology, describes the experimental setup, and analyzes the obtained results. It concludes that the Digimarc Barcode increases number of items per minute (IPM) scanned at least 50% over traditional UPC.

  6. Scanning of Bone Marrow in Haematopoietic Disorders

    International Nuclear Information System (INIS)

    Scanning can help evaluate size and distribution of the haematopoietic marrow, a difficult task by aspiration or biopsy. With the 61-hole focusing gold-tungsten Oak Ridge National Laboratory Scanner, the marrow organ has been clearly delineated by means of intravenous colloidal Au198, it being known that reticulo-endothelial function in the marrow correlates with areas of haematopoiesis. Patients with normal haematopoiesis and with a variety of blood disorders such as focal marrow lesions, acute and chronic leukaemia, polycythaemiavera, myelofibrosis, multiple myeloma, and lymphoma have been scanned. Because of the reticulo-endothelial activity in liver and spleen, the marrow pattern is obscured in the mid-trunk. Vertebral bodies, intervertebral discs, pelvis and long bones are outlined, and, in the thorax, the sternum and thoracic vertebrae. Focal lesions have also been found. Because of respiratory motion, individual ribs are not seen. In expanded marrow, the knee region can be shown, including the joint space. It has been possible to correlate these scans with aspiration biopsy and with linear scans. Because relatively large doses of Au198 are required, other isotopes are being investigated. An improved whole- body scanner is being tested for more practical scans. (author)

  7. Automated planning of MRI neuro scans

    Science.gov (United States)

    Young, Stewart; Bystrov, Daniel; Netsch, Thomas; Bergmans, Rene; van Muiswinkel, Arianne; Visser, Fredy; Sprigorum, Rudolf; Gieseke, Jürgen

    2006-03-01

    In clinical MRI examinations, the geometry of diagnostic scans is defined in an initial planning phase. The operator plans the scan volumes (off-centre, angulation, field-of-view) with respect to patient anatomy in 'scout' images. Often multiple plans are required within a single examination, distracting attention from the patient waiting in the scanner. A novel and robust method is described for automated planning of neurological MRI scans, capable of handling strong shape deviations from healthy anatomy. The expert knowledge required to position scan geometries is learned from previous example plans, allowing site-specific styles to be readily taken into account. The proposed method first fits an anatomical model to the scout data, and then new scan geometries are positioned with respect to extracted landmarks. The accuracy of landmark extraction was measured to be comparable to the inter-observer variability, and automated plans are shown to be highly consistent with those created by expert operators using clinical data. The results of the presented evaluation demonstrate the robustness and applicability of the proposed approach, which has the potential to significantly improve clinical workflow.

  8. About infrared scanning of photovoltaic solar plant

    Science.gov (United States)

    Kauppinen, T.; Panouillot, P.-E.; Siikanen, S.; Athanasakou, E.; Baltas, P.; Nikopoulous, B.

    2015-05-01

    The paper is discussing about infrared scanning of PV solar plants. It is important that the performance of each solar panel and cell is verified. One new possibility compared to traditional ground-based scanning (handheld camera) is the utilization of UAV (Unmanned Aerial Vehicle). In this paper results from a PV solar Plant in Western Greece are introduced. The nominal power of the solar plants were 0, 9 MW and 2 MW and they were scanned both by a ground-controlled drone and by handheld equipment. It is essential to know all the factors effecting to results and also the time of scanning is important. The results done from the drone and from ground-based scanning are compared; also results from various altitudes and time of day are discussed. The UAV (Unmanned Aerial Vehicle/RPAS (Remote Piloted Aircraft Systems) will give an excellent opportunity to monitor various targets which are impossible or difficult to access from the ground. Compared to fixed-wing and helicopter-based platforms it will give advantages but also this technology has limitations. One limitation is the weight of the equipment and the short operational range and short flight time. Also valid procedures must be created for different solutions in the future. The most important thing, as in all infrared thermography applications, is the proper interpretation of results.

  9. The application of genomic technologies to investigate the inheritance of economically important traits in goats

    OpenAIRE

    Marcel Amills

    2014-01-01

    Goat genomics has evolved at a low pace because of a lack of molecular tools and sufficient investment. Whilst thousands and hundreds of quantitative trait loci (QTL) have been identified in cattle and sheep, respectively, about nine genome scans have been performed in goats dealing with traits as conformation, growth, fiber quality, resistance to nematodes, and milk yield and composition. In contrast, a great effort has been devoted to the characterization of candidate genes and their associ...

  10. The discrepancies in the results of bioinformatics tools for genomic structural annotation

    Science.gov (United States)

    Pawełkowicz, Magdalena; Nowak, Robert; Osipowski, Paweł; Rymuszka, Jacek; Świerkula, Katarzyna; Wojcieszek, Michał; Przybecki, Zbigniew

    2014-11-01

    A major focus of sequencing project is to identify genes in genomes. However it is necessary to define the variety of genes and the criteria for identifying them. In this work we present discrepancies and dependencies from the application of different bioinformatic programs for structural annotation performed on the cucumber data set from Polish Consortium of Cucumber Genome Sequencing. We use Fgenesh, GenScan and GeneMark to automated structural annotation, the results have been compared to reference annotation.

  11. Genomics of Salmonella Species

    Science.gov (United States)

    Canals, Rocio; McClelland, Michael; Santiviago, Carlos A.; Andrews-Polymenis, Helene

    Progress in the study of Salmonella survival, colonization, and virulence has increased rapidly with the advent of complete genome sequencing and higher capacity assays for transcriptomic and proteomic analysis. Although many of these techniques have yet to be used to directly assay Salmonella growth on foods, these assays are currently in use to determine Salmonella factors necessary for growth in animal models including livestock animals and in in vitro conditions that mimic many different environments. As sequencing of the Salmonella genome and microarray analysis have revolutionized genomics and transcriptomics of salmonellae over the last decade, so are new high-throughput sequencing technologies currently accelerating the pace of our studies and allowing us to approach complex problems that were not previously experimentally tractable.

  12. Domestication and plant genomes.

    Science.gov (United States)

    Tang, Haibao; Sezen, Uzay; Paterson, Andrew H

    2010-04-01

    The techniques of plant improvement have been evolving with the advancement of technology, progressing from crop domestication by Neolithic humans to scientific plant breeding, and now including DNA-based genotyping and genetic engineering. Archeological findings have shown that early human ancestors often unintentionally selected for and finally fixed a few major domestication traits over time. Recent advancement of molecular and genomic tools has enabled scientists to pinpoint changes to specific chromosomal regions and genetic loci that are responsible for dramatic morphological and other transitions that distinguish crops from their wild progenitors. Extensive studies in a multitude of additional crop species, facilitated by rapid progress in sequencing and resequencing(s) of crop genomes, will further our understanding of the genomic impact from both the unusual population history of cultivated plants and millennia of human selection.

  13. Methods for detection of subtle mutations in cancer genomes

    DEFF Research Database (Denmark)

    Dahl, Christina; Ralfkiaer, Ulrik; Guldberg, Per

    2006-01-01

    With the realization that cancer is a genetic disease, detection of mutations in genomic DNA has become an important discipline in many areas of cancer research. Although the publication of the human genome sequence and the immense technological advancements have facilitated the analysis of cancer...... genomes, detection of mutations in tumor specimens may still be challenging and fraught with technical problems. In this review, we describe current technologies for detection of small DNA mutations, including mutation scanning techniques to search for unknown mutations, and diagnostic techniques...... to detect known cancer mutations. We outline the principles of the different techniques and discuss their advantages and limitations. We also discuss critical issues that must be considered before choosing methodology, including sensitivity, specificity, limit of detection, throughput and cost, quantity...

  14. Brief Guide to Genomics: DNA, Genes and Genomes

    Science.gov (United States)

    ... de genómica A Brief Guide to Genomics DNA, Genes and Genomes Deoxyribonucleic acid (DNA) is the chemical ... needed to build the entire human body. A gene traditionally refers to the unit of DNA that ...

  15. Scanning fluorescence detector for high-throughput DNA genotyping

    Science.gov (United States)

    Rusch, Terry L.; Petsinger, Jeremy; Christensen, Carl; Vaske, David A.; Brumley, Robert L., Jr.; Luckey, John A.; Weber, James L.

    1996-04-01

    A new scanning fluorescence detector (SCAFUD) was developed for high-throughput genotyping of short tandem repeat polymorphisms (STRPs). Fluorescent dyes are incorporated into relatively short DNA fragments via polymerase chain reaction (PCR) and are separated by electrophoresis in short, wide polyacrylamide gels (144 lanes with well to read distances of 14 cm). Excitation light from an argon laser with primary lines at 488 and 514 nm is introduced into the gel through a fiber optic cable, dichroic mirror, and 40X microscope objective. Emitted fluorescent light is collected confocally through a second fiber. The confocal head is translated across the bottom of the gel at 0.5 Hz. The detection unit utilizes dichroic mirrors and band pass filters to direct light with 10 - 20 nm bandwidths to four photomultiplier tubes (PMTs). PMT signals are independently amplified with variable gain and then sampled at a rate of 2500 points per scan using a computer based A/D board. LabView software (National Instruments) is used for instrument operation. Currently, three fluorescent dyes (Fam, Hex and Rox) are simultaneously detected with peak detection wavelengths of 543, 567, and 613 nm, respectively. The detection limit for fluorescein-labeled primers is about 100 attomoles. Planned SCAFUD upgrades include rearrangement of laser head geometry, use of additional excitation lasers for simultaneous detection of more dyes, and the use of detector arrays instead of individual PMTs. Extensive software has been written for automatic analysis of SCAFUD images. The software enables background subtraction, band identification, multiple- dye signal resolution, lane finding, band sizing and allele calling. Whole genome screens are currently underway to search for loci influencing such complex diseases as diabetes, asthma, and hypertension. Seven production SCAFUDs are currently in operation. Genotyping output for the coming year is projected to be about one million total genotypes (DNA

  16. Genomics in Cardiovascular Disease

    OpenAIRE

    Roberts, Robert; Marian, A.J.; Dandona, Sonny; Alexandre F R Stewart

    2013-01-01

    A paradigm shift towards biology occurred in the 1990’s subsequently catalyzed by the sequencing of the human genome in 2000. The cost of DNA sequencing has gone from millions to thousands of dollars with sequencing of one’s entire genome costing only $1,000. Rapid DNA sequencing is being embraced for single gene disorders, particularly for sporadic cases and those from small families. Transmission of lethal genes such as associated with Huntington’s disease can, through in-vitro fertilizatio...

  17. Precision genome editing

    DEFF Research Database (Denmark)

    Steentoft, Catharina; Bennett, Eric P; Schjoldager, Katrine Ter-Borch Gram;

    2014-01-01

    of glycobiology, primarily due to their low efficiencies, with resultant failure to impose substantial phenotypic consequences upon the final glycosylation products. Here, we review novel nuclease-based precision genome editing techniques enabling efficient and stable gene editing, including gene disruption...... by introducing single or double-stranded breaks at a defined genomic sequence. We here compare and contrast the different techniques and summarize their current applications, highlighting cases from the field of glycobiology as well as pointing to future opportunities. The emerging potential of precision gene...

  18. Conductivity map from scanning tunneling potentiometry.

    Science.gov (United States)

    Zhang, Hao; Li, Xianqi; Chen, Yunmei; Durand, Corentin; Li, An-Ping; Zhang, X-G

    2016-08-01

    We present a novel method for extracting two-dimensional (2D) conductivity profiles from large electrochemical potential datasets acquired by scanning tunneling potentiometry of a 2D conductor. The method consists of a data preprocessing procedure to reduce/eliminate noise and a numerical conductivity reconstruction. The preprocessing procedure employs an inverse consistent image registration method to align the forward and backward scans of the same line for each image line followed by a total variation (TV) based image restoration method to obtain a (nearly) noise-free potential from the aligned scans. The preprocessed potential is then used for numerical conductivity reconstruction, based on a TV model solved by accelerated alternating direction method of multiplier. The method is demonstrated on a measurement of the grain boundary of a monolayer graphene, yielding a nearly 10:1 ratio for the grain boundary resistivity over bulk resistivity.

  19. RADSCAN - A novel conically scanning tracking feed

    Science.gov (United States)

    Sullivan, A.

    The SCR-584 radar, which was developed as one of the first tracking systems at the beginning of 1942, used a conically scanning technique. A unique conically scanned feed, called RADSCAN, which has but one moving part and no rotary joint, has now been developed by an American company. A pair of stationary orthogonal printed circuit dipoles are used to excite the TE11 mode in the rotating circular waveguide. The displacement of the phase center of the circular waveguide from the boresight axis causes the conical scanning. The single-channel monopulse technique is discussed, and a comparison of RADSCAN and the single channel monopulse is conducted. Attention is given to aspects of reliability, low-angle tracking, beam crossover variation with frequency, cross talk, error modulation, and boresight shift with frequency.

  20. PET scanning in plastic and reconstructive surgery

    International Nuclear Information System (INIS)

    In this report we highlight the use of position emission tomography (PET) scan in plastic and reconstructive surgery. PET scanning is a very important tool in plastic surgery oncology (melanoma, soft-tissue sarcomas and bone sarcomas, head and neck cancer, peripheral nerve sheath tumors of the extremities and breast cancer after breast esthetic surgery), as diagnosis, staging, treatment planning and follow-up of cancer patients is based on imaging. PET scanning seems also to be useful as a flap monitoring system as well as an infection's imaging tool, for example in the management of diabetic foot ulcer. PET also contributes to the understanding of pathophysiology of keloids which remain a therapeutic challenge. (author)

  1. Parallel line scanning ophthalmoscope for retinal imaging.

    Science.gov (United States)

    Vienola, Kari V; Damodaran, Mathi; Braaf, Boy; Vermeer, Koenraad A; de Boer, Johannes F

    2015-11-15

    A parallel line scanning ophthalmoscope (PLSO) is presented using a digital micromirror device (DMD) for parallel confocal line imaging of the retina. The posterior part of the eye is illuminated using up to seven parallel lines, which were projected at 100 Hz. The DMD offers a high degree of parallelism in illuminating the retina compared to traditional scanning laser ophthalmoscope systems utilizing scanning mirrors. The system operated at the shot-noise limit with a signal-to-noise ratio of 28 for an optical power measured at the cornea of 100 μW. To demonstrate the imaging capabilities of the system, the macula and the optic nerve head of a healthy volunteer were imaged. Confocal images show good contrast and lateral resolution with a 10°×10° field of view. PMID:26565868

  2. Human performance in radiological survey scanning

    International Nuclear Information System (INIS)

    The probability of detecting residual contamination in the field using portable radiological survey instruments depends not only on the sensitivity of the instrumentation used in scanning, but also on the surveyor's performance. This report provides a basis for taking human performance into account in determining the minimum level of activity detectable by scanning. A theoretical framework was developed (based on signal detection theory) which allows influences on surveyors to be anticipated and understood, and supports a quantitative assessment of performance. The performance of surveyors under controlled yet realistic field conditions was examined to gain insight into the task and to develop means of quantifying performance. Then, their performance was assessed under laboratory conditions to quantify more precisely their ability to make the required discriminations. The information was used to characterize surveyors' performance in the scanning task and to provide a basis for predicting levels of radioactivity that are likely to be detectable under various conditions by surveyors using portable survey instruments

  3. Neutron scanning system for nondestructive testing

    International Nuclear Information System (INIS)

    Presented are the methods of nondestructive testing, based on neutron passing, outlet from the reactor, through the samples. Considered are possibilities of the neutron-spectrometric method of nondestructive sample analysis. Given is a description of half-automatic neutron scanning system, presupposed for investigation of nonirradiated, as well as irradiated samples. Described are the assemblies of the scanning device, mechanical relative aperture selector and crystalline monochromator for the purposes of nondestructive testing by the neutron-spectrometric method within 0.01-50 eV neutron energy range. The scanning device makes it possible to investigate a sample 1200 mm long and up to 15 mm in diameter with longitudinal transmission step of 0.5 mm and 0.1 mm accuracy of the transverse device. The equipment neutron spectra, measured by division chamber on the mechanical selector and the scaning results on the crystalline monochromator are given for illustrating the device operation

  4. Scanning microfluorometry in intravital microvascular research.

    Science.gov (United States)

    Witte, S

    1989-01-01

    Our own development of fluorometric scanning techniques in intravital microscopy of the microcirculation is described. Very tiny amount of fluorometric substances are detected with a high temporal and locational resolution. The everted small intestinal mesentery of the rat serves as a model. We have given a detailed description of the microscopes used, the optical systems, the conditions of measurement of the microfluorometry, the scanning techniques and the evaluation of the measurement data. The present state of technical development detects 10(-12) g of a fluorochromed plasma protein in 8 ms in a measurement field of 2 microns 2. The four-digit measurement data of a scanning line of 200 microns length in 0.25 micron locational resolution are registered in about 2 s.

  5. Conductivity map from scanning tunneling potentiometry

    Science.gov (United States)

    Zhang, Hao; Li, Xianqi; Chen, Yunmei; Durand, Corentin; Li, An-Ping; Zhang, X.-G.

    2016-08-01

    We present a novel method for extracting two-dimensional (2D) conductivity profiles from large electrochemical potential datasets acquired by scanning tunneling potentiometry of a 2D conductor. The method consists of a data preprocessing procedure to reduce/eliminate noise and a numerical conductivity reconstruction. The preprocessing procedure employs an inverse consistent image registration method to align the forward and backward scans of the same line for each image line followed by a total variation (TV) based image restoration method to obtain a (nearly) noise-free potential from the aligned scans. The preprocessed potential is then used for numerical conductivity reconstruction, based on a TV model solved by accelerated alternating direction method of multiplier. The method is demonstrated on a measurement of the grain boundary of a monolayer graphene, yielding a nearly 10:1 ratio for the grain boundary resistivity over bulk resistivity.

  6. Investigation into scanning tunnelling luminescence microscopy

    CERN Document Server

    Manson-Smith, S K

    2001-01-01

    This work reports on the development of a scanning tunnelling luminescence (STL) microscope and its application to the study of Ill-nitride semiconductor materials used in the production of light emitting devices. STL microscopy is a technique which uses the high resolution topographic imaging capabilities of the scanning tunnelling microscope (STM) to generate high resolution luminescence images. The STM tunnelling current acts as a highly localised source of electrons (or holes) which generates luminescence in certain materials. Light generated at the STM tunnelling junction is collected concurrently with the height variation of the tunnelling probe as it is scanned across a sample surface, producing simultaneous topographic and luminescence images. Due to the very localised excitation source, high resolution luminescence images can be obtained. Spectroscopic resolution can be obtained by using filters. Additionally, the variation of luminescence intensity with tunnel current and with bias voltage can provi...

  7. Proximity Scanning Transmission Electron Microscopy/Spectroscopy

    CERN Document Server

    Hwang, Ing-Shouh

    2016-01-01

    Here a new microscopic method is proposed to image and characterize very thin samples like few-layer materials, organic molecules, and nanostructures with nanometer or sub-nanometer resolution using electron beams of energies lower than 20 eV. The microscopic technique achieves high resolution through the proximity (or near-field) effect, as in scanning tunneling microscopy (STM), while it also allows detection of transmitted electrons for imaging and spectroscopy, as in scanning transmission electron microscopy (STEM). This proximity transmission electron microscopy (PSTEM) does not require any lens to focus the electron beam. It also allows detailed characterization of the interaction of low-energy electron with materials. PSTEM can operate in a way very similar to scanning tunneling microscopy, which provides high-resolution imaging of geometric and electronic structures of the sample surface. In addition, it allows imaging and characterization of the interior structures of the sample based on the detected...

  8. Tree Height Growth Measurement with Single-Scan Airborne, Static Terrestrial and Mobile Laser Scanning

    Directory of Open Access Journals (Sweden)

    Yi Lin

    2012-09-01

    Full Text Available This study explores the feasibility of applying single-scan airborne, static terrestrial and mobile laser scanning for improving the accuracy of tree height growth measurement. Specifically, compared to the traditional works on forest growth inventory with airborne laser scanning, two issues are regarded: “Can the new technique characterize the height growth for each individual tree?” and “Can this technique refine the minimum growth-discernable temporal interval further?” To solve these two puzzles, the sampling principles of the three laser scanning modes were first examined, and their error sources against the task of tree-top capturing were also analyzed. Next, the three-year growths of 58 Nordic maple trees (Crimson King for test were intermittently surveyed with one type of laser scanning each time and then analyzed by statistics. The evaluations show that the height growth of each individual tree still cannot be reliably characterized even by single-scan terrestrial laser scanning, and statistical analysis is necessary in this scenario. After Gaussian regression, it is found that the minimum temporal interval with distinguishable tree height growths can be refined into one month based on terrestrial laser scanning, far better than the two years deduced in the previous works based on airborne laser scanning. The associated mean growth was detected to be about 0.12 m. Moreover, the parameter of tree height generally under-estimated by airborne and even mobile laser scanning can be relatively revised by means of introducing static terrestrial laser scanning data. Overall, the effectiveness of the proposed technique is primarily validated.

  9. Forward scanning in verbal working memory updating.

    Science.gov (United States)

    Kessler, Yoav; Oberauer, Klaus

    2015-12-01

    Effective use of working memory (WM) for high-level cognitive tasks requires coordinating two conflicting requirements: robust maintenance and rapid updating. Models of WM suggest that these demands are coordinated by a gate between perceptual input and WM. Previous work with a letter-updating paradigm (Kessler & Oberauer, Journal of Experimental Psychology: Learning, Memory, and Cognition, 40, 738-754, 2014) supported a scanning and gate-switching (SGS) model of WM updating. The present work provides further evidence for the SGS model. Participants were required to keep track of the last letter that appeared in each of a row of frames on the screen. On each updating step, a variable subset of letters in varying positions in the row had to be updated. The SGS model assumes that on each updating step, participants scan through the memory set sequentially, opening the gate when a letter requires updating, and closing the gate when the next letter needs to be maintained. As is predicted by the SGS model, the reaction times for each updating step increased with the number of updated items and with the number of gate switches. In addition, the present experiment provides direct evidence supporting the scanning assumption of the model. Hebrew-speaking participants performed the task with either Hebrew or English letter stimuli, in different blocks. As was predicted, the scanning direction of the stimulus set was from left to right in English and from right to left in Hebrew. The SGS model fit the data only when the scanning direction was taken into account, establishing the role of item-based forward scanning during WM updating. PMID:25962687

  10. A genome-wide association scan (GWAS) for mean telomere length within the COGS project

    DEFF Research Database (Denmark)

    Pooley, Karen A; Bojesen, Stig E; Weischer, Maren;

    2013-01-01

    Mean telomere length (TL) in blood cells is heritable and has been reported to be associated with risks of several diseases, including cancer. We conducted a meta-analysis of three GWAS for TL (total n=2240) and selected 1629 variants for replication via the "iCOGS" custom genotyping array. All ∼...

  11. A genome-wide scan for signatures of directional selection in domesticated pigs

    NARCIS (Netherlands)

    Moon, S.; Kim, T.H.; Lee, K.T.; Kwak, W.; Lee, T.; Lee, S.W.; Kim, M.J.; Cho, K.; Kim, N.; Chung, W.H.; Sung, S.; Park, T.; Cho, S.; Groenen, M.A.M.; Nielsen, R.; Kim, Y.; Kim, H.

    2015-01-01

    Background: Animal domestication involved drastic phenotypic changes driven by strong artificial selection and also resulted in new populations of breeds, established by humans. This study aims to identify genes that show evidence of recent artificial selection during pig domestication. Results: Who

  12. A genome-wide association scan on estrogen receptor-negative breast cancer

    NARCIS (Netherlands)

    J. Li (Jingmei); M.K. Humphreys (Manjeet); H. Darabi (Hatef); G. Rosin (Gustaf); U. Hannelius (Ulf); T. Heikinen (Tuomas); K. Aittomäki (Kristiina); C. Blomqvist (Carl); P.D.P. Pharoah (Paul); A.M. Dunning (Alison); S. Ahmed (Shahana); M.J. Hooning (Maartje); A. Hollestelle (Antoinette); R.A. Oldenburg (Rogier); L. Alfredsson (Lars); A. Palotie (Aarno); L. Peltonen-Palotie (Leena); A. Irwanto (Astrid); H.Q. Low (Hui); G.H.K. Teoh (Garrett); A. Thalamuthu (Anbupalam); J. Kere (Juha); M. D'Amato (Mauro); D.F. Easton (Douglas); H. Nevanlinna (Heli); J. Liu (Jianjun); K. Czene (Kamila); A.S. Hall (Alistair)

    2010-01-01

    textabstractIntroduction: Breast cancer is a heterogeneous disease and may be characterized on the basis of whether estrogen receptors (ER) are expressed in the tumour cells. ER status of breast cancer is important clinically, and is used both as a prognostic indicator and treatment predictor. In th

  13. HybGFS: a hybrid method for genome-fingerprint scanning

    OpenAIRE

    Sugiyama Naoyuki; Masuda Takeshi; Yachie Nozomu; Shinoda Kosaku; Sugimoto Masahiro; Soga Tomoyoshi; Tomita Masaru

    2006-01-01

    Abstract Background Protein identification based on mass spectrometry (MS) has previously been performed using peptide mass fingerprinting (PMF) or tandem MS (MS/MS) database searching. However, these methods cannot identify proteins that are not already listed in existing databases. Moreover, the alternative approach of de novo sequencing requires costly equipment and the interpretation of complex MS/MS spectra. Thus, there is a need for novel high-throughput protein-identification methods t...

  14. A Scan for Positively Selected Genes in the Genomes of Humans and Chimpanzees

    DEFF Research Database (Denmark)

    Nielsen, Rasmus; Bustamente, Carlos; Clark, Andrew G.;

    2005-01-01

    Since the divergence of humans and chimpanzees about 5 million years ago, these species have undergone a remarkable evolution with drastic divergence in anatomy and cognitive abilities. At the molecular level, despite the small overall magnitude of DNA sequence divergence, we might expect...

  15. Quantitative linkage genome scan for atopy in a large collection of Caucasian families

    DEFF Research Database (Denmark)

    Webb, BT; van den Oord, E; Akkari, A;

    2007-01-01

    Quantitative phenotypes correlated with a complex disorder offer increased power to detect linkage in comparison to affected-unaffected classifications. Asthma is a complex disorder characterized by periods of bronchial obstruction and increased bronchial hyper reactivity. In childhood and early ...

  16. Genome Scan of Diabrotica virgifera virgifera for Genetic Variation Associated with Crop Rotation Tolerance

    Science.gov (United States)

    Crop rotation has been a valuable technique for control of the western corn rootworm, Diabrotica virgifera virgifera, for almost a century. However, during the last two decades, crop rotation has ceased to be effective in an expanding area of the United States Corn Belt. This failure appears to be d...

  17. Genome Scan Detects Quantitative Trait Loci Affecting Female Fertility Traits in Danish and Swedish Holstein Cattle

    DEFF Research Database (Denmark)

    Höglund, Johanna Karolina; Guldbrandtsen, B; Su, G;

    2009-01-01

    microsatellite markers. Single trait breeding values were used for 12 traits relating to female fertility and female reproductive disorders. Data were analyzed by least squares regression analysis within and across families. Twenty-six QTL were detected on 17 different chromosomes. The best evidence was found......Data from the joint Nordic breeding value prediction for Danish and Swedish Holstein grandsire families were used to locate quantitative trait loci (QTL) for female fertility traits in Danish and Swedish Holstein cattle. Up to 36 Holstein grandsires with over 2,000 sons were genotyped for 416...

  18. A genome-wide scan in families with maturity-onset diabetes of the young

    DEFF Research Database (Denmark)

    Frayling, Timothy M; Lindgren, Cecilia M; Chevre, Jean Claude;

    2003-01-01

    Maturity-onset diabetes of the young (MODY) is a heterogeneous single gene disorder characterized by non-insulin-dependent diabetes, an early onset and autosomal dominant inheritance. Mutations in six genes have been shown to cause MODY. Approximately 15-20% of families fitting MODY criteria do...

  19. A genome-wide association scan in pig identifies novel regions associated with feed efficiency trait

    DEFF Research Database (Denmark)

    Sahana, Goutam; Kadlecová, Veronika; Hornshøj, Henrik;

    2013-01-01

    probability more than or equal to 0.05, i.e. Bayes factor ≥ 10. Thirteen SNPs were identified both by LMM and BVS. These 13 SNPs were located on four chromosomes 4, 7, 8 and 14. Hypoxia inducible factor 1, alpha subunit inhibitor (HIF1AN) and Ladybird homeobox 1 (LBX1) are two possible candidate genes...

  20. Dexter: Data Extractor for scanned graphs

    Science.gov (United States)

    Demleitner, Markus

    2011-12-01

    The NASA Astrophysics Data System (ADS) now holds 1.3 million scanned pages, containing numerous plots and figures for which the original data sets are lost or inaccessible. The availability of scans of the figures can significantly ease the regeneration of the data sets. For this purpose, the ADS has developed Dexter, a Java applet that supports the user in this process. Dexter's basic functionality is to let the user manually digitize a plot by marking points and defining the coordinate transformation from the logical to the physical coordinate system. Advanced features include automatic identification of axes, tracing lines and finding points matching a template.

  1. MEMS scanning micromirror for optical coherence tomography.

    Science.gov (United States)

    Strathman, Matthew; Liu, Yunbo; Keeler, Ethan G; Song, Mingli; Baran, Utku; Xi, Jiefeng; Sun, Ming-Ting; Wang, Ruikang; Li, Xingde; Lin, Lih Y

    2015-01-01

    This paper describes an endoscopic-inspired imaging system employing a micro-electromechanical system (MEMS) micromirror scanner to achieve beam scanning for optical coherence tomography (OCT) imaging. Miniaturization of a scanning mirror using MEMS technology can allow a fully functional imaging probe to be contained in a package sufficiently small for utilization in a working channel of a standard gastroesophageal endoscope. This work employs advanced image processing techniques to enhance the images acquired using the MEMS scanner to correct non-idealities in mirror performance. The experimental results demonstrate the effectiveness of the proposed technique.

  2. Scanning evanescent electro-magnetic microscope

    Science.gov (United States)

    Xiang, Xiao-Dong; Gao, Chen

    2001-01-01

    A novel scanning microscope is described that uses near-field evanescent electromagnetic waves to probe sample properties. The novel microscope is capable of high resolution imaging and quantitative measurements of the electrical properties of the sample. The inventive scanning evanescent wave electromagnetic microscope (SEMM) can map dielectric constant, tangent loss, conductivity, complex electrical impedance, and other electrical parameters of materials. The quantitative map corresponds to the imaged detail. The novel microscope can be used to measure electrical properties of both dielectric and electrically conducting materials.

  3. Gallium-67 citrate scan in extrapulmonary tuberculosis

    Energy Technology Data Exchange (ETDEWEB)

    Lin Wanyu [Taichung Veterans General Hospital (Taiwan). Dept. of Nuclear Medicine; Hsieh Jihfang [Chi-Mei Foundation Hospital, Tainan (Taiwan)

    1999-07-01

    Aim: Whole-body gallium scan was performed to evaluate the usefulness of gallium scan for detecting extrapulmonary tuberculosis (TB) lesions. Methods: Thirty-seven patients with extrapulmonary TB were included in this study. Four patients were found to have two lesions. Totally, 41 lesions were identified, including 19 TB arthritis, 8 spinal TB, 5 TB meningitis, 3 TB lymphadenopathy, 2 TB pericarditis, 1 TB peritonitis, 1 intestinal TB, 1 skin TB and 1 renal TB. Results: Of the 41 extrapulmonary TB lesions, gallium scan detected 32 lesions with a sensitivity of 78%. All the patients with TB meningitis showed negative gallium scan. When the five cases of TB meningitis were excluded, the detection sensitivity of gallium scan increased to 88.9% (32/36). Conclusion: Our data revealed that gallium scan is a convenient and useful method for evaluating extrapulmonary TB lesions other than TB-meningitis. We suggest that gallium scan be included in the clinical routine for patients with suspected extrapulmonary TB. (orig.) [German] Ziel: Es wurden Ganzkoerper-Gallium-Szintigramme angefertigt, um den Nutzen der Gallium-Szintigraphie zur Erfassung von extrapulmonalen Tuberkuloseherden (TB) zu erfassen. Methoden: 37 Patienten mit extrapulmonaler TB wurden eingeschlossen. 4 Patienten hatten 2 Laesionen. Insgesamt wurden 41 Laesionen identifiziert, hierunter 19 TB-Arthritis, 8 spinale TB, 5 TB-Meningitis, 3 TB-Lymphadenopathie, 2 TB-Perikarditis, 1 TB-Peritonitis, 1 intestinale TB, 1 Haut-TB und eine Nieren-TB. Ergebnisse: Von den 41 extrapulmonalen TB-Herden erfasste die Gallium-Szintigraphie 32 Herde mit einer Sensitivitaet von 78%. Alle Patienten mit TB-Meningitis zeigten einen negativen Gallium-Scan. Wenn die 5 Faelle mit TB-Meningitis ausgeschlossen wurden, stieg die Sensitivititaet der Gallium-Szintigraphie auf 88,9% (32/36). Schlussfolgerung: Die Daten zeigen, dass die Gallium-Szintigraphie eine einfache und nuetzliche Methode zur Erfassung extrapulmonaler TB-Herde ist

  4. Deploying scanning lidars at coastal sites

    DEFF Research Database (Denmark)

    Courtney, Michael; Simon, Elliot

    This report presents the concept of scanning lidars placed at coastal sites in order to measure the near-coastal (offshore) wind resource. In particular, the site requirements for such scanning lidars are examined in the context of the siting choices made for the RUNE project. It is seen...... that the most desirable sites are away from sand dunes and with some significant elevation above the sea surface, such as at the top of a cliff. Coastal planning restrictions in Denmark are quite restrictive and it was important to allow sufficient time to obtain permission from the relevant authorities...

  5. Bone scanning in Shin Splint evaluation

    International Nuclear Information System (INIS)

    Jogging is increasingly popular; in U.S.A., in 1979 more than 25 millions people were considered joggers. Lesions of the locomotive system of the lower limbs are very frequent in athletes and the Shin Splint syndrome, for one, is very frequent. However this precise clinical entity, usually X-Ray negative, is ill-known. A bone scan study in a series of 30 athletes suffering from Shin Splints is presented. The bone scans being positive and typical were highly useful in confirming the clinical diagnosis. Moreover, follow-up studies were done in a number of these patients and results correlated well with the clinical evolution

  6. The low specificity of postoperative perfusion lung scan defects.

    OpenAIRE

    I Walker; Aukland, P; Hirsh, J.; Coates, G.; Cockshott, P; Taylor, R; Hull, R.

    1981-01-01

    Ventilation and perfusion lung scans were performed preoperatively and postoperatively in 169 patients and classified blindly according to preset criteria. Perfusion lung scan abnormalities were present in 25 (15%) of the preoperative scans and 42 (25%) of the postoperative scans; 16 (38%) of the 42 abnormal postoperative scans were identical to the preoperative scans. Perfusion defects indicating a "high probability" of pulmonary embolism (lobar or segmental defects) were present in 5 preope...

  7. Tick Genomics: The Ixodes genome project and beyond

    Science.gov (United States)

    Ticks and mites (subphylum Chelicerata; subclass Acari) are important pests of animals and plants worldwide. The Ixodes scapularis (black-legged tick) genome sequencing project marks the beginning of the genomics era for the field of acarology. This project is the first to sequence the genome of a...

  8. Exploring functional elements and genomic variation in the noncoding genome

    NARCIS (Netherlands)

    van Heesch, S.A.A.C.

    2014-01-01

    Gene expression regulation is a delicate process that depends on multiple aspects including genome structure and transcription factor binding to DNA elements. The majority of our genome consists of noncoding DNA, which was shown to be crucial in providing the correct context for genome function. Alt

  9. Scanning probe image wizard: A toolbox for automated scanning probe microscopy data analysis

    Science.gov (United States)

    Stirling, Julian; Woolley, Richard A. J.; Moriarty, Philip

    2013-11-01

    We describe SPIW (scanning probe image wizard), a new image processing toolbox for SPM (scanning probe microscope) images. SPIW can be used to automate many aspects of SPM data analysis, even for images with surface contamination and step edges present. Specialised routines are available for images with atomic or molecular resolution to improve image visualisation and generate statistical data on surface structure.

  10. The Scanning Theremin Microscope: A Model Scanning Probe Instrument for Hands-On Activities

    Science.gov (United States)

    Quardokus, Rebecca C.; Wasio, Natalie A.; Kandel, S. Alex

    2014-01-01

    A model scanning probe microscope, designed using similar principles of operation to research instruments, is described. Proximity sensing is done using a capacitance probe, and a mechanical linkage is used to scan this probe across surfaces. The signal is transduced as an audio tone using a heterodyne detection circuit analogous to that used in…

  11. A Successive Scans Method of Adjusting Scan-Time for Injection Electroluminescent Display Panels

    Institute of Scientific and Technical Information of China (English)

    OU Peng; YANG Gang; JIANG Quan; WANG Jun; HU Jian-Hua; WU Qi-Peng; LUO Kai-Jun

    2011-01-01

    @@ Aiming at the problem of luminance uniformity for injection electroluminescent display panels, we present a new scan method for display panels according to successive scans theory.First, on the basis of the number of pixels requiring light emitting in one frame period, we adjust the scan time for each row.Secondly, for ensuring image transmission synchronization, the frame period must to be a constant.We adopt a 64 × 32 LED display panel as an example to expound the new scan method and we obtain the good result that the reduce amplitude of luminance non-uniformity is 31.34% and the increase amplitude of the average luminance value is 7.8258%.%Aiming at the problem of luminance uniformity for injection electroluminescent display panels,we present a new scan method for display panets according to successive scans theory.First,on the basis of the number of pixels requiring light emitting in one frame period,we adjust the scan time for each row.Secondly,for ensuring image transmission synchronization,the frame period must to be a constant.We adopt a 64×32 LED display panel as an example to expound the new scan method and we odtain the good result that the reduce amplitude of luminance non-uniformity is 31.34% and the increase amplitude of the average luminance value is 7.8258%.

  12. Genome Statute and Legislation Database

    Science.gov (United States)

    ... Database Welcome to the Genome Statute and Legislation Database The Genome Statute and Legislation Database is comprised ... the National Society of Genetic Counselors . Search the Database Search Tips You may select one or more ...

  13. Illuminating the Druggable Genome (IDG)

    Data.gov (United States)

    Federal Laboratory Consortium — Results from the Human Genome Project revealed that the human genome contains 20,000 to 25,000 genes. A gene contains (encodes) the information that each cell uses...

  14. RIKEN mouse genome encyclopedia.

    Science.gov (United States)

    Hayashizaki, Yoshihide

    2003-01-01

    We have been working to establish the comprehensive mouse full-length cDNA collection and sequence database to cover as many genes as we can, named Riken mouse genome encyclopedia. Recently we are constructing higher-level annotation (Functional ANnoTation Of Mouse cDNA; FANTOM) not only with homology search based annotation but also with expression data profile, mapping information and protein-protein database. More than 1,000,000 clones prepared from 163 tissues were end-sequenced to classify into 159,789 clusters and 60,770 representative clones were fully sequenced. As a conclusion, the 60,770 sequences contained 33,409 unique. The next generation of life science is clearly based on all of the genome information and resources. Based on our cDNA clones we developed the additional system to explore gene function. We developed cDNA microarray system to print all of these cDNA clones, protein-protein interaction screening system, protein-DNA interaction screening system and so on. The integrated database of all the information is very useful not only for analysis of gene transcriptional network and for the connection of gene to phenotype to facilitate positional candidate approach. In this talk, the prospect of the application of these genome resourced should be discussed. More information is available at the web page: http://genome.gsc.riken.go.jp/.

  15. Genetics, genomics and fertility

    Science.gov (United States)

    In order to enhance the sustainability of dairy businesses, new management tools are needed to increase the fertility of dairy cattle. Genomic selection has been successfully used by AI studs to screen potential sires and significantly decrease the generation interval of bulls. Buoyed by the success...

  16. The tomato genome

    Science.gov (United States)

    The tomato genome sequence was undertaken at a time when state-of-the-art sequencing methodologies were undergoing a transition to co-called next generation methodologies. The result was an international consortium undertaking a strategy merging both old and new approaches. Because biologists were...

  17. The UCSC Ebola Genome Portal

    OpenAIRE

    Haeussler, Maximilian; Karolchik, Donna; Clawson, Hiram; Raney, Brian J.; Rosenbloom, Kate R.; Fujita, Pauline A.; Hinrichs, Angie S.; Speir, Matthew L; Eisenhart, Chris; Zweig, Ann S.; Haussler, David; Kent, W. James

    2014-01-01

    Background: With the Ebola epidemic raging out of control in West Africa, there has been a flurry of research into the Ebola virus, resulting in the generation of much genomic data. Methods: In response to the clear need for tools that integrate multiple strands of research around molecular sequences, we have created the University of California Santa Cruz (UCSC) Ebola Genome Browser, an adaptation of our popular UCSC Genome Browser web tool, which can be used to view the Ebola virus genome s...

  18. Challenges in global genomics education

    Directory of Open Access Journals (Sweden)

    Ashwini de Abrew

    2014-12-01

    Full Text Available In spite of high expectations for the integration of genomics into medicine, it is not clear that health providers are competent to appropriately use new genomic approaches. The issue is further complicated by differences across the globe in terms of educational systems, access to genomic technologies, and priorities in health care. In this commentary we will review some of the major challenges in educating the health provider workforce about genomic medicine.

  19. Statistical Challenges in Functional Genomics

    OpenAIRE

    Sebastiani, Paola; Gussoni, Emanuela; Kohane, Isaac S.; Ramoni, Marco F

    2003-01-01

    On February 12, 2001 the Human Genome Project announced the completion of a draft physical map of the human genome---the genetic blueprint for a human being. Now the challenge is to annotate this map by understanding the functions of genes and their interplay with proteins and the environment to create complex, dynamic living systems. This is the goal of functional genomics. Recent technological advances enable biomedical investigators to observe the genome of entire orga...

  20. Observability of Parabolic Systems under Scanning Sensors

    OpenAIRE

    Khapalov, A. Y.

    1991-01-01

    This paper continues the investigations in SDS on observability issues motivated by environmental monitoring and related problems. Here the author introduces a specific class of scanning sensors that ensure solvability of the problem and can further lead to numerically robust techniques.