WorldWideScience

Sample records for quantitative genetic analysis

  1. Event History Analysis in Quantitative Genetics

    DEFF Research Database (Denmark)

    Maia, Rafael Pimentel

    Event history analysis is a clas of statistical methods specially designed to analyze time-to-event characteristics, e.g. the time until death. The aim of the thesis was to present adequate multivariate versions of mixed survival models that properly represent the genetic aspects related to a given...... time-to-event characteristic of interest. Real genetic longevity studies based on female animals of different species (sows, dairy cows, and sheep) exemplifies the use of the methods. Moreover these studies allow to understand som genetic mechanisms related to the lenght of the productive life...

  2. Developments in statistical analysis in quantitative genetics

    DEFF Research Database (Denmark)

    Sorensen, Daniel

    2009-01-01

    A remarkable research impetus has taken place in statistical genetics since the last World Conference. This has been stimulated by breakthroughs in molecular genetics, automated data-recording devices and computer-intensive statistical methods. The latter were revolutionized by the bootstrap and ...

  3. Segregation Analysis on Genetic System of Quantitative Traits in Plants

    Institute of Scientific and Technical Information of China (English)

    Gai Junyi

    2006-01-01

    Based on the traditional polygene inheritance model of quantitative traits,the author suggests the major gene and polygene mixed inheritance model.The model was considered as a general one,while the pure major gene and pure polygene inheritance model was a specific case of the general model.Based on the proposed theory,the author established the segregation analysis procedure to study the genetic system of quantitative traits of plants.At present,this procedure can be used to evaluate the genetic effect of individual major genes (up to two to three major genes),the collective genetic effect of polygene,and their heritability value.This paper introduces how to establish the procedure,its main achievements,and its applications.An example is given to illustrate the steps,methods,and effectiveness of the procedure.

  4. Quantitative genetic analysis of injury liability in infants and toddlers

    Energy Technology Data Exchange (ETDEWEB)

    Phillips, K.; Matheny, A.P. Jr. [Univ. of Louisville Medical School, KY (United States)

    1995-02-27

    A threshold model of latent liability was applied to infant and toddler twin data on total count of injuries sustained during the interval from birth to 36 months of age. A quantitative genetic analysis of estimated twin correlations in injury liability indicated strong genetic dominance effects, but no additive genetic variance was detected. Because interpretations involving overdominance have little research support, the results may be due to low order epistasis or other interaction effects. Boys had more injuries than girls, but this effect was found only for groups whose parents were prompted and questioned in detail about their children`s injuries. Activity and impulsivity are two behavioral predictors of childhood injury, and the results are discussed in relation to animal research on infant and adult activity levels, and impulsivity in adult humans. Genetic epidemiological approaches to childhood injury should aid in targeting higher risk children for preventive intervention. 30 refs., 4 figs., 3 tabs.

  5. Advancing genetic theory and application by metabolic quantitative trait loci analysis.

    Science.gov (United States)

    Kliebenstein, Danielj

    2009-06-01

    This review describes recent advances in the analysis of metabolism using quantitative genetics. It focuses on how recent metabolic quantitative trait loci (QTL) studies enhance our understanding of the genetic architecture underlying naturally variable phenotypes and the impact of this fundamental research on agriculture, specifically crop breeding. In particular, the role of whole-genome duplications in generating quantitative genetic variation within a species is highlighted and the potential uses of this phenomenon presented. Additionally, the review describes how new observations from metabolic QTL mapping analyses are helping to shape and expand the concepts of genetic epistasis.

  6. A quantitative genetic analysis of intermediate asthma phenotypes

    DEFF Research Database (Denmark)

    Thomsen, S.F.; Ferreira, M.A.R.; Kyvik, K.O.

    2009-01-01

    to the observed data using maximum likelihood methods. RESULTS: Additive genetic factors explained 67% of the variation in FeNO, 43% in airway responsiveness, 22% in airway obstruction, and 81% in serum total IgE. In general, traits had genetically and environmentally distinct variance structures. The most...

  7. Developmental quantitative genetic analysis of body weights and morphological traits in the turbot, Scophthalmusmaximus

    Institute of Scientific and Technical Information of China (English)

    WANG Xinan; MA Aijun; MA Deyou

    2015-01-01

    In order to elucidate the genetic mechanism of growth traits in turbot during ontogeny, developmental genetic analysis of the body weights, total lengths, standard lengths and body heights of turbots was conducted by mixed genetic models with additive-dominance effects, based on complete diallel crosses with four different strains of Scophthalmus maximus from Denmark, Norway, Britain, and France. Unconditional genetic analysis revealed that the unconditional additive effects for the four traits were more significant than unconditional dominance effects, meanwhile, the alternative expressions were also observed between the additive and dominant effects for body weights, total lengths and standard lengths. Conditional analysis showed that the developmental periods with active gene expression for body weights, total lengths, standard lengths and body heights were 15–18, 15 and 21–24, 15 and 24, and 21 and 27 months of age, respectively. The proportions of unconditional/conditional variances indicated that the narrow-sense heritabilities of body weights, total lengths and standard lengths were all increased systematically. The accumulative effects of genes controlling the four quantitative traits were mainly additive effects, suggesting that the selection is more efficient for the genetic improvement of turbots. The conditional genetic procedure is a useful tool to understand the expression of genes controlling developmental quantitative traits at a specific developmental period (t-1→t) during ontogeny. It is also important to determine the appropriate developmental period (t-1→t) for trait measurement in developmental quantitative genetic analysis in fish.

  8. Quantitative analysis of terahertz spectra for illicit drugs using adaptive-range micro-genetic algorithm

    Science.gov (United States)

    Chen, Yi; Ma, Yong; Lu, Zheng; Peng, Bei; Chen, Qin

    2011-08-01

    In the field of anti-illicit drug applications, many suspicious mixture samples might consist of various drug components—for example, a mixture of methamphetamine, heroin, and amoxicillin—which makes spectral identification very difficult. A terahertz spectroscopic quantitative analysis method using an adaptive range micro-genetic algorithm with a variable internal population (ARVIPɛμGA) has been proposed. Five mixture cases are discussed using ARVIPɛμGA driven quantitative terahertz spectroscopic analysis in this paper. The devised simulation results show agreement with the previous experimental results, which suggested that the proposed technique has potential applications for terahertz spectral identifications of drug mixture components. The results show agreement with the results obtained using other experimental and numerical techniques.

  9. The Genetic Architecture of Quantitative Traits Cannot Be Inferred from Variance Component Analysis

    Science.gov (United States)

    Huang, Wen; Mackay, Trudy F. C.

    2016-01-01

    Classical quantitative genetic analyses estimate additive and non-additive genetic and environmental components of variance from phenotypes of related individuals without knowing the identities of quantitative trait loci (QTLs). Many studies have found a large proportion of quantitative trait variation can be attributed to the additive genetic variance (VA), providing the basis for claims that non-additive gene actions are unimportant. In this study, we show that arbitrarily defined parameterizations of genetic effects seemingly consistent with non-additive gene actions can also capture the majority of genetic variation. This reveals a logical flaw in using the relative magnitudes of variance components to indicate the relative importance of additive and non-additive gene actions. We discuss the implications and propose that variance component analyses should not be used to infer the genetic architecture of quantitative traits. PMID:27812106

  10. The Genetic Architecture of Quantitative Traits Cannot Be Inferred from Variance Component Analysis.

    Directory of Open Access Journals (Sweden)

    Wen Huang

    2016-11-01

    Full Text Available Classical quantitative genetic analyses estimate additive and non-additive genetic and environmental components of variance from phenotypes of related individuals without knowing the identities of quantitative trait loci (QTLs. Many studies have found a large proportion of quantitative trait variation can be attributed to the additive genetic variance (VA, providing the basis for claims that non-additive gene actions are unimportant. In this study, we show that arbitrarily defined parameterizations of genetic effects seemingly consistent with non-additive gene actions can also capture the majority of genetic variation. This reveals a logical flaw in using the relative magnitudes of variance components to indicate the relative importance of additive and non-additive gene actions. We discuss the implications and propose that variance component analyses should not be used to infer the genetic architecture of quantitative traits.

  11. Quantitative genetic analysis of chlorophyll a fluorescence parameters in maize in the field environments

    Institute of Scientific and Technical Information of China (English)

    Domagojimi; Hrvoje Lepedu; Vlatka Jurkovi; Jasenka Antunovi; Vera Cesar

    2014-01-01

    Chlorophyl fluorescence transient from initial to maximum fluorescence (“P”step) throughout two intermedi-ate steps (“J”and“I”) (JIP-test) is considered a reliable early quantitative indicator of stress in plants. The JIP-test is particularly useful for crop plants when applied in variable field environments. The aim of the present study was to conduct a quantitative trait loci (QTL) analysis for nine JIP-test parameters in maize during flowering in four field environ-ments differing in weather conditions. QTL analysis and identification of putative candidate genes might help to explain the genetic relationship between photosynthesis and different field scenarios in maize plants. The JIP-test param-eters were analyzed in the intermated B73 ? Mo17 (IBM) maize population of 205 recombinant inbred lines. A set of 2,178 molecular markers across the whole maize genome was used for QTL analysis revealing 10 significant QTLs for seven JIP-test parameters, of which five were co-localized when combined over the four environments indicating polygenic inheritance and pleiotropy. Our results demonstrate that QTL analysis of chlorophyl fluorescence parameters was capable of detecting one pleiotropic locus on chromosome 7, coinciding with the gene gst23 that may be associated with efficient photosynthe-sis under different field scenarios.

  12. Genetic programming:  a novel method for the quantitative analysis of pyrolysis mass spectral data.

    Science.gov (United States)

    Gilbert, R J; Goodacre, R; Woodward, A M; Kell, D B

    1997-11-01

    A technique for the analysis of multivariate data by genetic programming (GP) is described, with particular reference to the quantitative analysis of orange juice adulteration data collected by pyrolysis mass spectrometry (PyMS). The dimensionality of the input space was reduced by ranking variables according to product moment correlation or mutual information with the outputs. The GP technique as described gives predictive errors equivalent to, if not better than, more widespread methods such as partial least squares and artificial neural networks but additionally can provide a means for easing the interpretation of the correlation between input and output variables. The described application demonstrates that by using the GP method for analyzing PyMS data the adulteration of orange juice with 10% sucrose solution can be quantified reliably over a 0-20% range with an RMS error in the estimate of ∼1%.

  13. Quantitative Genetic Analysis of Biomass and Wood Chemistry of Populus under Different Nitrogen Levels

    Energy Technology Data Exchange (ETDEWEB)

    Novaes, E.; Osorio, L.; Drost, D. R.; Miles, B. L.; Boaventura-Novaes, C. R. D.; Benedict, C.; Dervinis, C.; Yu, Q.; Sykes, R.; Davis, M.; Martin, T. A.; Peter, G. F.; Kirst, M.

    2009-01-01

    The genetic control of carbon allocation and partitioning in woody perennial plants is poorly understood despite its importance for carbon sequestration, biofuels and other wood-based industries. It is also unclear how environmental cues, such as nitrogen availability, impact the genes that regulate growth, biomass allocation and wood composition in trees. We phenotyped 396 clonally replicated genotypes of an interspecific pseudo-backcross pedigree of Populus for wood composition and biomass traits in above- and below-ground organs. The loci that regulate growth, carbon allocation and partitioning under two nitrogen conditions were identified, defining the contribution of environmental cues to their genetic control. Sixty-three quantitative trait loci were identified for the 20 traits analyzed. The majority of quantitative trait loci are specific to one of the two nitrogen treatments, demonstrating significant nitrogen-dependent genetic control. A highly significant genetic correlation was observed between plant growth and lignin/cellulose composition, and quantitative trait loci co-localization identified the genomic position of potential pleiotropic regulators. Pleiotropic loci linking higher growth rates to wood with less lignin are excellent targets to engineer tree germplasm improved for pulp, paper and cellulosic ethanol production. The causative genes are being identified with a genetical genomics approach.

  14. A Creative Helicobacter pylori Diagnosis Scheme Based on Multiple Genetic Analysis System: Qualification and Quantitation.

    Science.gov (United States)

    Zhou, Lifang; Zhao, Fuju; Hu, Binjie; Fang, Yi; Miao, Yingxin; Huang, Yiqin; Ji, Da'nian; Zhang, Jinghao; Xu, Lingli; Zhang, Yanmei; Bao, Zhijun; Zhao, Hu

    2015-10-01

    Currently, several diagnostic assays for Helicobacter pylori (H. pylori) are available, but each has some limitations. Further, a high-flux quantitative assay is required to assist clinical diagnosis and monitor the effectiveness of therapy and novel vaccine candidates. Three hundred and eighty-seven adult patients [nonulcer dyspepsia (NUD) 295, peptic ulcer disease (PUD) 77, gastric cancer (GC) 15] were enrolled for gastrointestinal endoscopies. Three biopsy samples from gastric antrum were collected for the following tests: culture, rapid urease test (RUT), histopathology, conventional polymerase chain reaction (PCR), and Multiple Genetic Analysis System (MGAS). The diagnostic capability of H. pylori for all methods was evaluated through the receiver operating characteristic (ROC) curves. Based on the gold standard, the sensitivity and specificity of MGAS were 92.9 and 92.4%, and positive predict value (PPV) and negative predict value (NPV) were 96.0 and 87.1%, respectively. All the above parameters of MGAS were higher than that of culture (except its specificity), RUT and histopathology, and nearly closed to that of conventional PCR. The area under curve (AUC) was 0.7575 (Culture), 0.8870 (RUT), 0.9000 (Histopathology), 0.9496 (Conventional PCR), and 0.9277 (MGAS). No significant statistical difference was observed for the H. pylori DNA load in different disease groups (p = .067). In contrast, a statistically significant difference in the H. pylori DNA copy number was observed based on age (p = .043) and gender (p = .021). The data showed that MGAS performed well in detecting H. pylori infection. Furthermore, the quantitative analysis showed that the load of H. pylori was significantly different within both age and gender groups. These results suggested that MGAS could be a potential alternative method for clinical detection and monitoring of the effectiveness of H. pylori therapy. © 2015 John Wiley & Sons Ltd.

  15. Genetic modifier loci of mouse Mfrp(rd6) identified by quantitative trait locus analysis.

    Science.gov (United States)

    Won, Jungyeon; Charette, Jeremy R; Philip, Vivek M; Stearns, Timothy M; Zhang, Weidong; Naggert, Jürgen K; Krebs, Mark P; Nishina, Patsy M

    2014-01-01

    The identification of genes that modify pathological ocular phenotypes in mouse models may improve our understanding of disease mechanisms and lead to new treatment strategies. Here, we identify modifier loci affecting photoreceptor cell loss in homozygous Mfrp(rd6) mice, which exhibit a slowly progressive photoreceptor degeneration. A cohort of 63 F2 homozygous Mfrp(rd6) mice from a (B6.C3Ga-Mfrp(rd6)/J × CAST/EiJ) F1 intercross exhibited a variable number of cell bodies in the retinal outer nuclear layer at 20 weeks of age. Mice were genotyped with a panel of single nucleotide polymorphism markers, and genotypes were correlated with phenotype by quantitative trait locus (QTL) analysis to map modifier loci. A genome-wide scan revealed a statistically significant, protective candidate locus on CAST/EiJ Chromosome 1 and suggestive modifier loci on Chromosomes 6 and 11. Multiple regression analysis of a three-QTL model indicated that the modifier loci on Chromosomes 1 and 6 together account for 26% of the observed phenotypic variation, while the modifier locus on Chromosome 11 explains only an additional 4%. Our findings indicate that the severity of the Mfrp(rd6) retinal degenerative phenotype in mice depends on the strain genetic background and that a significant modifier locus on CAST/EiJ Chromosome 1 protects against Mfrp(rd6)-associated photoreceptor loss.

  16. EVOLUTION AND EXTINCTION IN A CHANGING ENVIRONMENT: A QUANTITATIVE-GENETIC ANALYSIS.

    Science.gov (United States)

    Bürger, Reinhard; Lynch, Michael

    1995-02-01

    Because of the ubiquity of genetic variation for quantitative traits, virtually all populations have some capacity to respond evolutionarily to selective challenges. However, natural selection imposes demographic costs on a population, and if these costs are sufficiently large, the likelihood of extinction will be high. We consider how the mean time to extinction depends on selective pressures (rate and stochasticity of environmental change, and strength of selection), population parameters (carrying capacity, and reproductive capacity), and genetics (rate of polygenic mutation). We assume that in a randomly mating, finite population subject to density-dependent population growth, individual fitness is determined by a single quantitative-genetic character under Gaussian stabilizing selection with the optimum phenotype exhibiting directional change, or random fluctuations, or both. The quantitative trait is determined by a finite number of freely recombining, mutationally equivalent, additive loci. The dynamics of evolution and extinction are investigated, assuming that the population is initially under mutation-selection-drift balance. Under this model, in a directionally changing environment, the mean phenotype lags behind the optimum, but on the average evolves parallel to it. The magnitude of the lag determines the vulnerability to extinction. In finite populations, stochastic variation in the genetic variance can be quite pronounced, and bottlenecks in the genetic variance temporarily can impair the population's adaptive capacity enough to cause extinction when it would otherwise be unlikely in an effectively infinite population. We find that maximum sustainable rates of evolution or, equivalently, critical rates of environmental change, may be considerably less than 10% of a phenotypic standard deviation per generation. © 1995 The Society for the Study of Evolution.

  17. Establishment of Quantitative Analysis Method for Genetically Modified Maize Using a Reference Plasmid and Novel Primers

    Science.gov (United States)

    Moon, Gi-Seong; Shin, Weon-Sun

    2012-01-01

    For the quantitative analysis of genetically modified (GM) maize in processed foods, primer sets and probes based on the 35S promoter (p35S), nopaline synthase terminator (tNOS), p35S-hsp70 intron, and zSSIIb gene encoding starch synthase II for intrinsic control were designed. Polymerase chain reaction (PCR) products (80~101 bp) were specifically amplified and the primer sets targeting the smaller regions (80 or 81 bp) were more sensitive than those targeting the larger regions (94 or 101 bp). Particularly, the primer set 35F1-R1 for p35S targeting 81 bp of sequence was even more sensitive than that targeting 101 bp of sequence by a 3-log scale. The target DNA fragments were also specifically amplified from all GM labeled food samples except for one item we tested when 35F1-R1 primer set was applied. A reference plasmid pGMmaize (3 kb) including the smaller PCR products for p35S, tNOS, p35S-hsp70 intron, and the zSSIIb gene was constructed for real-time PCR (RT-PCR). The linearity of standard curves was confirmed by using diluents ranging from 2×101~105 copies of pGMmaize and the R2 values ranged from 0.999~1.000. In the RT-PCR, the detection limit using the novel primer/probe sets was 5 pg of genomic DNA from MON810 line indicating that the primer sets targeting the smaller regions (80 or 81 bp) could be used for highly sensitive detection of foreign DNA fragments from GM maize in processed foods. PMID:24471096

  18. Quantitative Genetic Analysis for Yield and Yield Components in Boro Rice (Oryza sativa L.

    Directory of Open Access Journals (Sweden)

    Supriyo CHAKRABORTY

    2010-03-01

    Full Text Available Twenty-nine genotypes of boro rice (Oryza sativa L. were grown in a randomized block design with three replications in plots of 4m x 1m with a crop geometry of 20 cm x 20 cm between November-April, in Regional Agricultural Research Station, Nagaon, India. Quantitative data were collected on five randomly selected plants of each genotype per replication for yield/plant, and six other yield components, namely plant height, panicles/plant, panicle length, effective grains/panicle, 100 grain weight and harvest index. Mean values of the characters for each genotype were used for analysis of variance and covariance to obtain information on genotypic and phenotypic correlation along with coheritability between two characters. Path analyses were carried out to estimate the direct and indirect effects of boro rice�s yield components. The objective of the study was to identify the characters that mostly influence the yield for increasing boro rice productivity through breeding program. Correlation analysis revealed significant positive genotypic correlation of yield/plant with plant height (0.21, panicles/plant (0.53, panicle length (0.53, effective grains/panicle (0.57 and harvest index (0.86. Path analysis based on genotypic correlation coefficients elucidated high positive direct effect of harvest index (0.8631, panicle length (0.2560 and 100 grain weight (0.1632 on yield/plant with a residual effect of 0.33. Plant height and panicles/plant recorded high positive indirect effect on yield/plant via harvest index whereas effective grains/panicle on yield/plant via harvest index and panicle length. Results of the present study suggested that five component characters, namely harvest index, effective grains/plant, panicle length, panicles/plant and plant height influenced the yield of boro rice. A genotype with higher magnitude of these component characters could be either selected from the existing genotypes or evolved by breeding program for genetic

  19. Quantitative genetics of disease traits.

    Science.gov (United States)

    Wray, N R; Visscher, P M

    2015-04-01

    John James authored two key papers on the theory of risk to relatives for binary disease traits and the relationship between parameters on the observed binary scale and an unobserved scale of liability (James Annals of Human Genetics, 1971; 35: 47; Reich, James and Morris Annals of Human Genetics, 1972; 36: 163). These two papers are John James' most cited papers (198 and 328 citations, November 2014). They have been influential in human genetics and have recently gained renewed popularity because of their relevance to the estimation of quantitative genetics parameters for disease traits using SNP data. In this review, we summarize the two early papers and put them into context. We show recent extensions of the theory for ascertained case-control data and review recent applications in human genetics.

  20. Calculation of measurement uncertainty in quantitative analysis of genetically modified organisms using intermediate precision--a practical approach.

    Science.gov (United States)

    Zel, Jana; Gruden, Kristina; Cankar, Katarina; Stebih, Dejan; Blejec, Andrej

    2007-01-01

    Quantitative characterization of nucleic acids is becoming a frequently used method in routine analysis of biological samples, one use being the detection of genetically modified organisms (GMOs). Measurement uncertainty is an important factor to be considered in these analyses, especially where precise thresholds are set in regulations. Intermediate precision, defined as a measure between repeatability and reproducibility, is a parameter describing the real situation in laboratories dealing with quantitative aspects of molecular biology methods. In this paper, we describe the top-down approach to calculating measurement uncertainty, using intermediate precision, in routine GMO testing of food and feed samples. We illustrate its practicability in defining compliance of results with regulations. The method described is also applicable to other molecular methods for a variety of laboratory diagnostics where quantitative characterization of nucleic acids is needed.

  1. Development of quantitative duplex real-time PCR method for screening analysis of genetically modified maize.

    Science.gov (United States)

    Oguchi, Taichi; Onishi, Mari; Minegishi, Yasutaka; Kurosawa, Yasunori; Kasahara, Masaki; Akiyama, Hiroshi; Teshima, Reiko; Futo, Satoshi; Furui, Satoshi; Hino, Akihiro; Kitta, Kazumi

    2009-06-01

    A duplex real-time PCR method was developed for quantitative screening analysis of GM maize. The duplex real-time PCR simultaneously detected two GM-specific segments, namely the cauliflower mosaic virus (CaMV) 35S promoter (P35S) segment and an event-specific segment for GA21 maize which does not contain P35S. Calibration was performed with a plasmid calibrant specially designed for the duplex PCR. The result of an in-house evaluation suggested that the analytical precision of the developed method was almost equivalent to those of simplex real-time PCR methods, which have been adopted as ISO standard methods for the analysis of GMOs in foodstuffs and have also been employed for the analysis of GMOs in Japan. In addition, this method will reduce both the cost and time requirement of routine GMO analysis by half. The high analytical performance demonstrated in the current study would be useful for the quantitative screening analysis of GM maize. We believe the developed method will be useful for practical screening analysis of GM maize, although interlaboratory collaborative studies should be conducted to confirm this.

  2. Quantitative genetic analysis of retinal degeneration in the blind cavefish Astyanax mexicanus.

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    Kelly E O'Quin

    Full Text Available The retina is the light-sensitive tissue of the eye that facilitates vision. Mutations within genes affecting eye development and retinal function cause a host of degenerative visual diseases, including retinitis pigmentosa and anophthalmia/microphthalmia. The characin fish Astyanax mexicanus includes both eyed (surface fish and eyeless (cavefish morphs that initially develop eyes with normal retina; however, early in development, the eyes of cavefish degenerate. Since both surface and cave morphs are members of the same species, they serve as excellent evolutionary mutant models with which to identify genes causing retinal degeneration. In this study, we crossed the eyed and eyeless forms of A. mexicanus and quantified the thickness of individual retinal layers among 115 F(2 hybrid progeny. We used next generation sequencing (RAD-seq and microsatellite mapping to construct a dense genetic map of the Astyanax genome, scan for quantitative trait loci (QTL affecting retinal thickness, and identify candidate genes within these QTL regions. The map we constructed for Astyanax includes nearly 700 markers assembled into 25 linkage groups. Based on our scans with this map, we identified four QTL, one each associated with the thickness of the ganglion, inner nuclear, outer plexiform, and outer nuclear layers of the retina. For all but one QTL, cavefish alleles resulted in a clear reduction in the thickness of the affected layer. Comparative mapping of genetic markers within each QTL revealed that each QTL corresponds to an approximately 35 Mb region of the zebrafish genome. Within each region, we identified several candidate genes associated with the function of each affected retinal layer. Our study is the first to examine Astyanax retinal degeneration in the context of QTL mapping. The regions we identify serve as a starting point for future studies on the genetics of retinal degeneration and eye disease using the evolutionary mutant model Astyanax.

  3. Next generation quantitative genetics in plants.

    Science.gov (United States)

    Jiménez-Gómez, José M

    2011-01-01

    Most characteristics in living organisms show continuous variation, which suggests that they are controlled by multiple genes. Quantitative trait loci (QTL) analysis can identify the genes underlying continuous traits by establishing associations between genetic markers and observed phenotypic variation in a segregating population. The new high-throughput sequencing (HTS) technologies greatly facilitate QTL analysis by providing genetic markers at genome-wide resolution in any species without previous knowledge of its genome. In addition HTS serves to quantify molecular phenotypes, which aids to identify the loci responsible for QTLs and to understand the mechanisms underlying diversity. The constant improvements in price, experimental protocols, computational pipelines, and statistical frameworks are making feasible the use of HTS for any research group interested in quantitative genetics. In this review I discuss the application of HTS for molecular marker discovery, population genotyping, and expression profiling in QTL analysis.

  4. GENES - a software package for analysis in experimental statistics and quantitative genetics

    Directory of Open Access Journals (Sweden)

    Cosme Damião Cruz

    2013-06-01

    Full Text Available GENES is a software package used for data analysis and processing with different biometricmodels and is essential in genetic studies applied to plant and animal breeding. It allows parameterestimation to analyze biologicalphenomena and is fundamental for the decision-making process andpredictions of success and viability of selection strategies. The program can be downloaded from theInternet (http://www.ufv.br/dbg/genes/genes.htm orhttp://www.ufv.br/dbg/biodata.htm and is available inPortuguese, English and Spanish. Specific literature (http://www.livraria.ufv.br/ and a set of sample filesare also provided, making GENES easy to use. The software is integrated into the programs MS Word, MSExcel and Paint, ensuring simplicity and effectiveness indata import and export ofresults, figures and data.It is also compatible with the free software R and Matlab, through the supply of useful scripts available forcomplementary analyses in different areas, including genome wide selection, prediction of breeding valuesand use of neural networks in genetic improvement.

  5. Quantitative genetic analysis indicates natural selection on leaf phenotypes across wild tomato species (Solanum sect. Lycopersicon; Solanaceae).

    Science.gov (United States)

    Muir, Christopher D; Pease, James B; Moyle, Leonie C

    2014-12-01

    Adaptive evolution requires both raw genetic material and an accessible path of high fitness from one fitness peak to another. In this study, we used an introgression line (IL) population to map quantitative trait loci (QTL) for leaf traits thought to be associated with adaptation to precipitation in wild tomatoes (Solanum sect. Lycopersicon; Solanaceae). A QTL sign test showed that several traits likely evolved under directional natural selection. Leaf traits correlated across species do not share a common genetic basis, consistent with a scenario in which selection maintains trait covariation unconstrained by pleiotropy or linkage disequilibrium. Two large effect QTL for stomatal distribution colocalized with key genes in the stomatal development pathway, suggesting promising candidates for the molecular bases of adaptation in these species. Furthermore, macroevolutionary transitions between vastly different stomatal distributions may not be constrained when such large-effect mutations are available. Finally, genetic correlations between stomatal traits measured in this study and data on carbon isotope discrimination from the same ILs support a functional hypothesis that the distribution of stomata affects the resistance to CO2 diffusion inside the leaf, a trait implicated in climatic adaptation in wild tomatoes. Along with evidence from previous comparative and experimental studies, this analysis indicates that leaf traits are an important component of climatic niche adaptation in wild tomatoes and demonstrates that some trait transitions between species could have involved few, large-effect genetic changes, allowing rapid responses to new environmental conditions.

  6. Quantitative criteria for improving performance of buccal DNA for high-throughput genetic analysis

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    Woo Jessica G

    2012-08-01

    Full Text Available Abstract Background DNA from buccal brush samples is being used for high-throughput analyses in a variety of applications, but the impact of sample type on genotyping success and downstream statistical analysis remains unclear. The objective of the current study was to determine laboratory predictors of genotyping failure among buccal DNA samples, and to evaluate the successfully genotyped results with respect to analytic quality control metrics. Sample and genotyping characteristics were compared between buccal and blood samples collected in the population-based Genetic and Environmental Risk Factors for Hemorrhagic Stroke (GERFHS study (https://gerfhs.phs.wfubmc.edu/public/index.cfm. Results Seven-hundred eight (708 buccal and 142 blood DNA samples were analyzed for laboratory-based and analysis metrics. Overall genotyping failure rates were not statistically different between buccal (11.3% and blood (7.0%, p = 0.18 samples; however, both the Contrast Quality Control (cQC rate and the dynamic model (DM call rates were lower among buccal DNA samples (p  Conclusions We identified a buccal sample characteristic, a ratio of ds/total DNA

  7. Interlaboratory validation of quantitative duplex real-time PCR method for screening analysis of genetically modified maize.

    Science.gov (United States)

    Takabatake, Reona; Koiwa, Tomohiro; Kasahara, Masaki; Takashima, Kaori; Futo, Satoshi; Minegishi, Yasutaka; Akiyama, Hiroshi; Teshima, Reiko; Oguchi, Taichi; Mano, Junichi; Furui, Satoshi; Kitta, Kazumi

    2011-01-01

    To reduce the cost and time required to routinely perform the genetically modified organism (GMO) test, we developed a duplex quantitative real-time PCR method for a screening analysis simultaneously targeting an event-specific segment for GA21 and Cauliflower Mosaic Virus 35S promoter (P35S) segment [Oguchi et al., J. Food Hyg. Soc. Japan, 50, 117-125 (2009)]. To confirm the validity of the method, an interlaboratory collaborative study was conducted. In the collaborative study, conversion factors (Cfs), which are required to calculate the GMO amount (%), were first determined for two real-time PCR instruments, the ABI PRISM 7900HT and the ABI PRISM 7500. A blind test was then conducted. The limit of quantitation for both GA21 and P35S was estimated to be 0.5% or less. The trueness and precision were evaluated as the bias and reproducibility of the relative standard deviation (RSD(R)). The determined bias and RSD(R) were each less than 25%. We believe the developed method would be useful for the practical screening analysis of GM maize.

  8. Genetic analysis identifies quantitative trait loci controlling rosette mineral concentrations in Arabidopsis thaliana under drought

    NARCIS (Netherlands)

    Ghandilyan, A.; Barboza, L.; Tisne, S.; Granier, C.; Reymond, M.; Koornneef, M.; Schat, H.; Aarts, M.G.M.

    2009-01-01

    • Rosettes of 25 Arabidopsis thaliana accessions and an Antwerp-1 (An-1) × Landsberg erecta (Ler) population of recombinant inbred lines (RILs) grown in optimal watering conditions (OWC) and water deficit conditions (WDC) were analysed for mineral concentrations to identify genetic loci involved in

  9. Theory and Practice in Quantitative Genetics

    DEFF Research Database (Denmark)

    Posthuma, Daniëlle; Beem, A Leo; de Geus, Eco J C

    2003-01-01

    With the rapid advances in molecular biology, the near completion of the human genome, the development of appropriate statistical genetic methods and the availability of the necessary computing power, the identification of quantitative trait loci has now become a realistic prospect for quantitative...... geneticists. We briefly describe the theoretical biometrical foundations underlying quantitative genetics. These theoretical underpinnings are translated into mathematical equations that allow the assessment of the contribution of observed (using DNA samples) and unobserved (using known genetic relationships......) genetic variation to population variance in quantitative traits. Several statistical models for quantitative genetic analyses are described, such as models for the classical twin design, multivariate and longitudinal genetic analyses, extended twin analyses, and linkage and association analyses. For each...

  10. Quantitative genetic studies of antisocial behaviour.

    Science.gov (United States)

    Viding, Essi; Larsson, Henrik; Jones, Alice P

    2008-08-12

    This paper will broadly review the currently available twin and adoption data on antisocial behaviour (AB). It is argued that quantitative genetic research can make a significant contribution to further the understanding of how AB develops. Genetically informative study designs are particularly useful for investigating several important questions such as whether: the heritability estimates vary as a function of assessment method or gender; the relative importance of genetic and environmental influences varies for different types of AB; the environmental risk factors are truly environmental; and genetic vulnerability influences susceptibility to environmental risk. While the current data are not yet directly translatable for prevention and treatment programmes, quantitative genetic research has concrete translational potential. Quantitative genetic research can supplement neuroscience research in informing about different subtypes of AB, such as AB coupled with callous-unemotional traits. Quantitative genetic research is also important in advancing the understanding of the mechanisms by which environmental risk operates.

  11. Quantitative investment analysis

    CERN Document Server

    DeFusco, Richard

    2007-01-01

    In the "Second Edition" of "Quantitative Investment Analysis," financial experts Richard DeFusco, Dennis McLeavey, Jerald Pinto, and David Runkle outline the tools and techniques needed to understand and apply quantitative methods to today's investment process.

  12. Strategies for MCMC computation in quantitative genetics

    DEFF Research Database (Denmark)

    Waagepetersen, Rasmus; Ibánez, N.; Sorensen, Daniel

    2006-01-01

    Given observations of a trait and a pedigree for a group of animals, the basic model in quantitative genetics is a linear mixed model with genetic random effects. The correlation matrix of the genetic random effects is determined by the pedigree and is typically very highdimensional...

  13. Parallel imaging of Drosophila embryos for quantitative analysis of genetic perturbations of the Ras pathway

    Directory of Open Access Journals (Sweden)

    Yogesh Goyal

    2017-07-01

    Full Text Available The Ras pathway patterns the poles of the Drosophila embryo by downregulating the levels and activity of a DNA-binding transcriptional repressor Capicua (Cic. We demonstrate that the spatiotemporal pattern of Cic during this signaling event can be harnessed for functional studies of mutations in the Ras pathway in human diseases. Our approach relies on a new microfluidic device that enables parallel imaging of Cic dynamics in dozens of live embryos. We found that although the pattern of Cic in early embryos is complex, it can be accurately approximated by a product of one spatial profile and one time-dependent amplitude. Analysis of these functions of space and time alone reveals the differential effects of mutations within the Ras pathway. Given the highly conserved nature of Ras-dependent control of Cic, our approach provides new opportunities for functional analysis of multiple sequence variants from developmental abnormalities and cancers.

  14. Theory and practice in quantitative genetics.

    Science.gov (United States)

    Posthuma, Daniëlle; Beem, A Leo; de Geus, Eco J C; van Baal, G Caroline M; von Hjelmborg, Jacob B; Iachine, Ivan; Boomsma, Dorret I

    2003-10-01

    With the rapid advances in molecular biology, the near completion of the human genome, the development of appropriate statistical genetic methods and the availability of the necessary computing power, the identification of quantitative trait loci has now become a realistic prospect for quantitative geneticists. We briefly describe the theoretical biometrical foundations underlying quantitative genetics. These theoretical underpinnings are translated into mathematical equations that allow the assessment of the contribution of observed (using DNA samples) and unobserved (using known genetic relationships) genetic variation to population variance in quantitative traits. Several statistical models for quantitative genetic analyses are described, such as models for the classical twin design, multivariate and longitudinal genetic analyses, extended twin analyses, and linkage and association analyses. For each, we show how the theoretical biometrical model can be translated into algebraic equations that may be used to generate scripts for statistical genetic software packages, such as Mx, Lisrel, SOLAR, or MERLIN. For using the former program a web-library (available from http://www.psy.vu.nl/mxbib) has been developed of freely available scripts that can be used to conduct all genetic analyses described in this paper.

  15. Quantitative Trait Locus and Genetical Genomics Analysis Identifies Putatively Causal Genes for Fecundity and Brooding in the Chicken

    Directory of Open Access Journals (Sweden)

    Martin Johnsson

    2016-02-01

    Full Text Available Life history traits such as fecundity are important to evolution because they make up components of lifetime fitness. Due to their polygenic architectures, such traits are difficult to investigate with genetic mapping. Therefore, little is known about their molecular basis. One possible way toward finding the underlying genes is to map intermediary molecular phenotypes, such as gene expression traits. We set out to map candidate quantitative trait genes for egg fecundity in the chicken by combining quantitative trait locus mapping in an advanced intercross of wild by domestic chickens with expression quantitative trait locus mapping in the same birds. We measured individual egg fecundity in 232 intercross chickens in two consecutive trials, the second one aimed at measuring brooding. We found 12 loci for different aspects of egg fecundity. We then combined the genomic confidence intervals of these loci with expression quantitative trait loci from bone and hypothalamus in the same intercross. Overlaps between egg loci and expression loci, and trait–gene expression correlations identify 29 candidates from bone and five from hypothalamus. The candidate quantitative trait genes include fibroblast growth factor 1, and mitochondrial ribosomal proteins L42 and L32. In summary, we found putative quantitative trait genes for egg traits in the chicken that may have been affected by regulatory variants under chicken domestication. These represent, to the best of our knowledge, some of the first candidate genes identified by genome-wide mapping for life history traits in an avian species.

  16. Quantitative Trait Locus and Genetical Genomics Analysis Identifies Putatively Causal Genes for Fecundity and Brooding in the Chicken.

    Science.gov (United States)

    Johnsson, Martin; Jonsson, Kenneth B; Andersson, Leif; Jensen, Per; Wright, Dominic

    2015-12-04

    Life history traits such as fecundity are important to evolution because they make up components of lifetime fitness. Due to their polygenic architectures, such traits are difficult to investigate with genetic mapping. Therefore, little is known about their molecular basis. One possible way toward finding the underlying genes is to map intermediary molecular phenotypes, such as gene expression traits. We set out to map candidate quantitative trait genes for egg fecundity in the chicken by combining quantitative trait locus mapping in an advanced intercross of wild by domestic chickens with expression quantitative trait locus mapping in the same birds. We measured individual egg fecundity in 232 intercross chickens in two consecutive trials, the second one aimed at measuring brooding. We found 12 loci for different aspects of egg fecundity. We then combined the genomic confidence intervals of these loci with expression quantitative trait loci from bone and hypothalamus in the same intercross. Overlaps between egg loci and expression loci, and trait-gene expression correlations identify 29 candidates from bone and five from hypothalamus. The candidate quantitative trait genes include fibroblast growth factor 1, and mitochondrial ribosomal proteins L42 and L32. In summary, we found putative quantitative trait genes for egg traits in the chicken that may have been affected by regulatory variants under chicken domestication. These represent, to the best of our knowledge, some of the first candidate genes identified by genome-wide mapping for life history traits in an avian species.

  17. MaGelLAn 1.0: a software to facilitate quantitative and population genetic analysis of maternal inheritance by combination of molecular and pedigree information.

    Science.gov (United States)

    Ristov, Strahil; Brajkovic, Vladimir; Cubric-Curik, Vlatka; Michieli, Ivan; Curik, Ino

    2016-09-10

    Identification of genes or even nucleotides that are responsible for quantitative and adaptive trait variation is a difficult task due to the complex interdependence between a large number of genetic and environmental factors. The polymorphism of the mitogenome is one of the factors that can contribute to quantitative trait variation. However, the effects of the mitogenome have not been comprehensively studied, since large numbers of mitogenome sequences and recorded phenotypes are required to reach the adequate power of analysis. Current research in our group focuses on acquiring the necessary mitochondria sequence information and analysing its influence on the phenotype of a quantitative trait. To facilitate these tasks we have produced software for processing pedigrees that is optimised for maternal lineage analysis. We present MaGelLAn 1.0 (maternal genealogy lineage analyser), a suite of four Python scripts (modules) that is designed to facilitate the analysis of the impact of mitogenome polymorphism on quantitative trait variation by combining molecular and pedigree information. MaGelLAn 1.0 is primarily used to: (1) optimise the sampling strategy for molecular analyses; (2) identify and correct pedigree inconsistencies; and (3) identify maternal lineages and assign the corresponding mitogenome sequences to all individuals in the pedigree, this information being used as input to any of the standard software for quantitative genetic (association) analysis. In addition, MaGelLAn 1.0 allows computing the mitogenome (maternal) effective population sizes and probability of mitogenome (maternal) identity that are useful for conservation management of small populations. MaGelLAn is the first tool for pedigree analysis that focuses on quantitative genetic analyses of mitogenome data. It is conceived with the purpose to significantly reduce the effort in handling and preparing large pedigrees for processing the information linked to maternal lines. The software source

  18. Quantitative genetic studies of antisocial behaviour

    OpenAIRE

    Viding, Essi; Larsson, Henrik; Jones, Alice P.

    2008-01-01

    This paper will broadly review the currently available twin and adoption data on antisocial behaviour (AB). It is argued that quantitative genetic research can make a significant contribution to further the understanding of how AB develops. Genetically informative study designs are particularly useful for investigating several important questions such as whether: the heritability estimates vary as a function of assessment method or gender; the relative importance of genetic and environmental ...

  19. Array-CGH and quantitative PCR genetic analysis in a case with bilateral hypoplasia of pulmonary arteries and lungs and simultaneous unilateral renal agenesis.

    Science.gov (United States)

    Hussein, Kais; Steinemann, Doris; Scholz, Henrike; Menkhaus, Ralf; Feist, Henning; Kreipe, Hans

    2010-08-18

    We describe the clinical course and have characterised anatomically and genetically a unique case of a newborn with bilateral hypoplasia of pulmonary arteries, consecutive extremely hypoplastic lung tissue and associated unilateral renal agenesis. Intrauterine oxygenation by the placenta seemed to have allowed normotrophic body maturity but immediately after delivery, in the third trimester, progressive hypoxemia developed and the newborn succumbed to acute respiratory failure. Genetic analysis by array-based comparative genomic hybridisation and quantitative PCR revealed duplication of 1p21, which, however, might not be the disease causing aberration. This case might represent an extreme form of previously reported, rare cases with simultaneous dysorganogenesis of lungs and kidneys.

  20. Evolutionary quantitative genetics of nonlinear developmental systems.

    Science.gov (United States)

    Morrissey, Michael B

    2015-08-01

    In quantitative genetics, the effects of developmental relationships among traits on microevolution are generally represented by the contribution of pleiotropy to additive genetic covariances. Pleiotropic additive genetic covariances arise only from the average effects of alleles on multiple traits, and therefore the evolutionary importance of nonlinearities in development is generally neglected in quantitative genetic views on evolution. However, nonlinearities in relationships among traits at the level of whole organisms are undeniably important to biology in general, and therefore critical to understanding evolution. I outline a system for characterizing key quantitative parameters in nonlinear developmental systems, which yields expressions for quantities such as trait means and phenotypic and genetic covariance matrices. I then develop a system for quantitative prediction of evolution in nonlinear developmental systems. I apply the system to generating a new hypothesis for why direct stabilizing selection is rarely observed. Other uses will include separation of purely correlative from direct and indirect causal effects in studying mechanisms of selection, generation of predictions of medium-term evolutionary trajectories rather than immediate predictions of evolutionary change over single generation time-steps, and the development of efficient and biologically motivated models for separating additive from epistatic genetic variances and covariances.

  1. Multivariate Quantitative Chemical Analysis

    Science.gov (United States)

    Kinchen, David G.; Capezza, Mary

    1995-01-01

    Technique of multivariate quantitative chemical analysis devised for use in determining relative proportions of two components mixed and sprayed together onto object to form thermally insulating foam. Potentially adaptable to other materials, especially in process-monitoring applications in which necessary to know and control critical properties of products via quantitative chemical analyses of products. In addition to chemical composition, also used to determine such physical properties as densities and strengths.

  2. Multivariate Quantitative Chemical Analysis

    Science.gov (United States)

    Kinchen, David G.; Capezza, Mary

    1995-01-01

    Technique of multivariate quantitative chemical analysis devised for use in determining relative proportions of two components mixed and sprayed together onto object to form thermally insulating foam. Potentially adaptable to other materials, especially in process-monitoring applications in which necessary to know and control critical properties of products via quantitative chemical analyses of products. In addition to chemical composition, also used to determine such physical properties as densities and strengths.

  3. Whole genome approaches to quantitative genetics.

    Science.gov (United States)

    Visscher, Peter M

    2009-06-01

    Apart from parent-offspring pairs and clones, relative pairs vary in the proportion of the genome that they share identical by descent. In the past, quantitative geneticists have used the expected value of sharing genes by descent to estimate genetic parameters and predict breeding values. With the possibility to genotype individuals for many markers across the genome it is now possible to empirically estimate the actual relationship between relatives. We review some of the theory underlying the variation in genetic identity, show applications to estimating genetic variance for height in humans and discuss other applications.

  4. Construction of a genetic linkage map of Thlaspi caerulescens and quantitative trait loci analysis of zinc accumulation.

    Science.gov (United States)

    Assunção, Ana G L; Pieper, Bjorn; Vromans, Jaap; Lindhout, Pim; Aarts, Mark G M; Schat, Henk

    2006-01-01

    Zinc (Zn) hyperaccumulation seems to be a constitutive species-level trait in Thlaspi caerulescens. When compared under conditions of equal Zn availability, considerable variation in the degree of hyperaccumulation is observed among accessions originating from different soil types. This variation offers an excellent opportunity for further dissection of the genetics of this trait. A T. caerulescens intraspecific cross was made between a plant from a nonmetallicolous accession [Lellingen (LE)], characterized by relatively high Zn accumulation, and a plant from a calamine accession [La Calamine (LC)], characterized by relatively low Zn accumulation. Zinc accumulation in roots and shoots segregated in the F3 population. This population was used to construct an LE/LC amplified fragment length polymorphism (AFLP)-based genetic linkage map and to map quantitative trait loci (QTL) for Zn accumulation. Two QTL were identified for root Zn accumulation, with the trait-enhancing alleles being derived from each of the parents, and explaining 21.7 and 16.6% of the phenotypic variation observed in the mapping population. Future development of more markers, based on Arabidopsis orthologous genes localized in the QTL regions, will allow fine-mapping and map-based cloning of the genes underlying the QTL.

  5. Quantitative Hydrocarbon Surface Analysis

    Science.gov (United States)

    Douglas, Vonnie M.

    2000-01-01

    The elimination of ozone depleting substances, such as carbon tetrachloride, has resulted in the use of new analytical techniques for cleanliness verification and contamination sampling. The last remaining application at Rocketdyne which required a replacement technique was the quantitative analysis of hydrocarbons by infrared spectrometry. This application, which previously utilized carbon tetrachloride, was successfully modified using the SOC-400, a compact portable FTIR manufactured by Surface Optics Corporation. This instrument can quantitatively measure and identify hydrocarbons from solvent flush of hardware as well as directly analyze the surface of metallic components without the use of ozone depleting chemicals. Several sampling accessories are utilized to perform analysis for various applications.

  6. Genetic variability, heritability and genetic advance of quantitative ...

    African Journals Online (AJOL)

    ONOS

    2010-05-10

    May 10, 2010 ... clusters/plant, number of pods/plant, number of seeds/pod, yield/plant and 100 seed weight of black gram in M2 ... Key words: Genetic variability, gamma rays, quantitative traits, black gram. ... MATERIALS AND METHODS.

  7. MR brain image analysis in dementia: From quantitative imaging biomarkers to ageing brain models and imaging genetics.

    Science.gov (United States)

    Niessen, Wiro J

    2016-10-01

    MR brain image analysis has constantly been a hot topic research area in medical image analysis over the past two decades. In this article, it is discussed how the field developed from the construction of tools for automatic quantification of brain morphology, function, connectivity and pathology, to creating models of the ageing brain in normal ageing and disease, and tools for integrated analysis of imaging and genetic data. The current and future role of the field in improved understanding of the development of neurodegenerative disease is discussed, and its potential for aiding in early and differential diagnosis and prognosis of different types of dementia. For the latter, the use of reference imaging data and reference models derived from large clinical and population imaging studies, and the application of machine learning techniques on these reference data, are expected to play a key role. Copyright © 2016 Elsevier B.V. All rights reserved.

  8. The quantitative genetics of phenotypic robustness.

    Directory of Open Access Journals (Sweden)

    Hunter B Fraser

    Full Text Available Phenotypic robustness, or canalization, has been extensively investigated both experimentally and theoretically. However, it remains unknown to what extent robustness varies between individuals, and whether factors buffering environmental variation also buffer genetic variation. Here we introduce a quantitative genetic approach to these issues, and apply this approach to data from three species. In mice, we find suggestive evidence that for hundreds of gene expression traits, robustness is polymorphic and can be genetically mapped to discrete genomic loci. Moreover, we find that the polymorphisms buffering genetic variation are distinct from those buffering environmental variation. In fact, these two classes have quite distinct mechanistic bases: environmental buffers of gene expression are predominantly sex-specific and trans-acting, whereas genetic buffers are not sex-specific and often cis-acting. Data from studies of morphological and life-history traits in plants and yeast support the distinction between polymorphisms buffering genetic and environmental variation, and further suggest that loci buffering different types of environmental variation do overlap with one another. These preliminary results suggest that naturally occurring polymorphisms affecting phenotypic robustness could be abundant, and that these polymorphisms may generally buffer either genetic or environmental variation, but not both.

  9. Construction of measurement uncertainty profiles for quantitative analysis of genetically modified organisms based on interlaboratory validation data.

    Science.gov (United States)

    Macarthur, Roy; Feinberg, Max; Bertheau, Yves

    2010-01-01

    A method is presented for estimating the size of uncertainty associated with the measurement of products derived from genetically modified organisms (GMOs). The method is based on the uncertainty profile, which is an extension, for the estimation of uncertainty, of a recent graphical statistical tool called an accuracy profile that was developed for the validation of quantitative analytical methods. The application of uncertainty profiles as an aid to decision making and assessment of fitness for purpose is also presented. Results of the measurement of the quantity of GMOs in flour by PCR-based methods collected through a number of interlaboratory studies followed the log-normal distribution. Uncertainty profiles built using the results generally give an expected range for measurement results of 50-200% of reference concentrations for materials that contain at least 1% GMO. This range is consistent with European Network of GM Laboratories and the European Union (EU) Community Reference Laboratory validation criteria and can be used as a fitness for purpose criterion for measurement methods. The effect on the enforcement of EU labeling regulations is that, in general, an individual analytical result needs to be 1.8% to demonstrate noncompliance with a labeling threshold of 0.9%.

  10. Quantitative analysis of fatty-acid-based biofuels produced by wild-type and genetically engineered cyanobacteria by gas chromatography-mass spectrometry.

    Science.gov (United States)

    Guan, Wenna; Zhao, Hui; Lu, Xuefeng; Wang, Cong; Yang, Menglong; Bai, Fali

    2011-11-11

    Simple and rapid quantitative determination of fatty-acid-based biofuels is greatly important for the study of genetic engineering progress for biofuels production by microalgae. Ideal biofuels produced from biological systems should be chemically similar to petroleum, like fatty-acid-based molecules including free fatty acids, fatty acid methyl esters, fatty acid ethyl esters, fatty alcohols and fatty alkanes. This study founded a gas chromatography-mass spectrometry (GC-MS) method for simultaneous quantification of seven free fatty acids, nine fatty acid methyl esters, five fatty acid ethyl esters, five fatty alcohols and three fatty alkanes produced by wild-type Synechocystis PCC 6803 and its genetically engineered strain. Data obtained from GC-MS analyses were quantified using internal standard peak area comparisons. The linearity, limit of detection (LOD) and precision (RSD) of the method were evaluated. The results demonstrated that fatty-acid-based biofuels can be directly determined by GC-MS without derivation. Therefore, rapid and reliable quantitative analysis of fatty-acid-based biofuels produced by wild-type and genetically engineered cyanobacteria can be achieved using the GC-MS method founded in this work. Copyright © 2011 Elsevier B.V. All rights reserved.

  11. The genetic basis of adaptive population differentiation: A quantitative trait locus analysis of fitness traits in two wild barley populations from contrasting habitats

    NARCIS (Netherlands)

    Verhoeven, K.J.F.; Vanhala, T.K.; Biere, A.; Nevo, E.; Damme, van J.M.M.

    2004-01-01

    We used a quantitative trait locus (QTL) approach to study the genetic basis of population differentiation in wild barley, Hordeum spontaneum. Several ecotypes are recognized in this model species, and population genetic studies and reciprocal transplant experiments have indicated the role of local

  12. Genetic Variation, Heritability, and Diversity Analysis of Upland Rice (Oryza sativa L. Genotypes Based on Quantitative Traits

    Directory of Open Access Journals (Sweden)

    Mst. Tuhina-Khatun

    2015-01-01

    Full Text Available Upland rice is important for sustainable crop production to meet future food demands. The expansion in area of irrigated rice faces limitations due to water scarcity resulting from climate change. Therefore, this research aimed to identify potential genotypes and suitable traits of upland rice germplasm for breeding programmes. Forty-three genotypes were evaluated in a randomised complete block design with three replications. All genotypes exhibited a wide and significant variation for 22 traits. The highest phenotypic and genotypic coefficient of variation was recorded for the number of filled grains/panicle and yields/plant (g. The highest heritability was found for photosynthetic rate, transpiration rate, stomatal conductance, intercellular CO2, and number of filled grains/panicle and yields/plant (g. Cluster analysis based on 22 traits grouped the 43 rice genotypes into five clusters. Cluster II was the largest and consisted of 20 genotypes mostly originating from the Philippines. The first four principle components of 22 traits accounted for about 72% of the total variation and indicated a wide variation among the genotypes. The selected best trait of the number of filled grains/panicle and yields/plant (g, which showed high heritability and high genetic advance, could be used as a selection criterion for hybridisation programmes in the future.

  13. Genetic Variation, Heritability, and Diversity Analysis of Upland Rice (Oryza sativa L.) Genotypes Based on Quantitative Traits.

    Science.gov (United States)

    Tuhina-Khatun, Mst; Hanafi, Mohamed M; Rafii Yusop, Mohd; Wong, M Y; Salleh, Faezah M; Ferdous, Jannatul

    2015-01-01

    Upland rice is important for sustainable crop production to meet future food demands. The expansion in area of irrigated rice faces limitations due to water scarcity resulting from climate change. Therefore, this research aimed to identify potential genotypes and suitable traits of upland rice germplasm for breeding programmes. Forty-three genotypes were evaluated in a randomised complete block design with three replications. All genotypes exhibited a wide and significant variation for 22 traits. The highest phenotypic and genotypic coefficient of variation was recorded for the number of filled grains/panicle and yields/plant (g). The highest heritability was found for photosynthetic rate, transpiration rate, stomatal conductance, intercellular CO₂, and number of filled grains/panicle and yields/plant (g). Cluster analysis based on 22 traits grouped the 43 rice genotypes into five clusters. Cluster II was the largest and consisted of 20 genotypes mostly originating from the Philippines. The first four principle components of 22 traits accounted for about 72% of the total variation and indicated a wide variation among the genotypes. The selected best trait of the number of filled grains/panicle and yields/plant (g), which showed high heritability and high genetic advance, could be used as a selection criterion for hybridisation programmes in the future.

  14. Complex genetic interactions in a quantitative trait locus.

    Directory of Open Access Journals (Sweden)

    Himanshu Sinha

    2006-02-01

    Full Text Available Whether in natural populations or between two unrelated members of a species, most phenotypic variation is quantitative. To analyze such quantitative traits, one must first map the underlying quantitative trait loci. Next, and far more difficult, one must identify the quantitative trait genes (QTGs, characterize QTG interactions, and identify the phenotypically relevant polymorphisms to determine how QTGs contribute to phenotype. In this work, we analyzed three Saccharomyces cerevisiae high-temperature growth (Htg QTGs (MKT1, END3, and RHO2. We observed a high level of genetic interactions among QTGs and strain background. Interestingly, while the MKT1 and END3 coding polymorphisms contribute to phenotype, it is the RHO2 3'UTR polymorphisms that are phenotypically relevant. Reciprocal hemizygosity analysis of the Htg QTGs in hybrids between S288c and ten unrelated S. cerevisiae strains reveals that the contributions of the Htg QTGs are not conserved in nine other hybrids, which has implications for QTG identification by marker-trait association. Our findings demonstrate the variety and complexity of QTG contributions to phenotype, the impact of genetic background, and the value of quantitative genetic studies in S. cerevisiae.

  15. Quantitative genetic analysis of brain size variation in sticklebacks: support for the mosaic model of brain evolution.

    Science.gov (United States)

    Noreikiene, Kristina; Herczeg, Gábor; Gonda, Abigél; Balázs, Gergely; Husby, Arild; Merilä, Juha

    2015-07-07

    The mosaic model of brain evolution postulates that different brain regions are relatively free to evolve independently from each other. Such independent evolution is possible only if genetic correlations among the different brain regions are less than unity. We estimated heritabilities, evolvabilities and genetic correlations of relative size of the brain, and its different regions in the three-spined stickleback (Gasterosteus aculeatus). We found that heritabilities were low (average h(2) = 0.24), suggesting a large plastic component to brain architecture. However, evolvabilities of different brain parts were moderate, suggesting the presence of additive genetic variance to sustain a response to selection in the long term. Genetic correlations among different brain regions were low (average rG = 0.40) and significantly less than unity. These results, along with those from analyses of phenotypic and genetic integration, indicate a high degree of independence between different brain regions, suggesting that responses to selection are unlikely to be severely constrained by genetic and phenotypic correlations. Hence, the results give strong support for the mosaic model of brain evolution. However, the genetic correlation between brain and body size was high (rG = 0.89), suggesting a constraint for independent evolution of brain and body size in sticklebacks.

  16. Integration of molecular genetic technology with quantitative genetic technology for maximizing the speed of genetic improvement

    Institute of Scientific and Technical Information of China (English)

    Jack; C.M.; DEKKERS

    2005-01-01

    To date,most genetic progress for quantita-tive traits in livestock has been made by selec-tion on phenotype or on estimates of breedingvalues(BBV)derived from phenotype,withoutknowledge of the number of genes that affect thetrait or the effects of each gene.In this quantita-tive genetic approach to genetic improvement,the genetic architecture of traits of interest hasessentially been treated as a‘black box’.De-spite this,the substantial rates of genetic im-provement that have been and continue to be a-chie...

  17. Quantitative-genetic analysis of wing form and bilateral asymmetry in isochromosomal lines of Drosophila subobscura using Procrustes methods

    Indian Academy of Sciences (India)

    Pedro Fernández Iriarte; Walkiria Céspedes; Mauro Santos

    2003-12-01

    Fluctuating asymmetry (FA) is often used as a measure of underlying developmental instability (DI), motivated by the idea that morphological variance is maladaptive. Whether or not DI has evolutionary potential is a highly disputed topic, marred by methodological problems and fuzzy prejudices. We report here some results from an ongoing study of the effects of karyotype, homozygosity and temperature on wing form and bilateral asymmetry using isochromosomal lines of Drosophila subobscura. Our approach uses the recently developed methodologies in geometric morphometrics to analyse shape configurations of landmarks within the standard statistical framework employed in studies of bilateral asymmetries, and we have extended these methods to partition the individual variation and the variation in asymmetries into genetic and environmental causal components. The analyses revealed temperature-dependent expression of genetic variation for wing size and wing shape, directional asymmetry (DA) of wing size, increased asymmetries at suboptimal temperature, and a transition from FA to DA in males as a result of increase in the rearing temperature. No genetic variation was generally detected for FA in our samples, but these are preliminary results because no crosses between lines were carried out and, therefore, the contribution of dominance was not taken into account. In addition, only a subset of the standing genetic variation was represented in the experiments.

  18. Factor analysis in the Genetics of Asthma International Network family study identifies five major quantitative asthma phenotypes

    NARCIS (Netherlands)

    Pillai, S. G.; Tang, Y.; van den Oord, E.; Klotsman, M.; Barnes, K.; Carlsen, K.; Gerritsen, J.; Lenney, W.; Silverman, M.; Sly, P.; Sundy, J.; Tsanakas, J.; von Berg, A.; Whyte, M.; Ortega, H. G.; Anderson, W. H.; Helms, P. J.

    2008-01-01

    Background Asthma is a clinically heterogeneous disease caused by a complex interaction between genetic susceptibility and diverse environmental factors. In common with other complex diseases the lack of a standardized scheme to evaluate the phenotypic variability poses challenges in identifying the

  19. Interacting personalities: behavioural ecology meets quantitative genetics.

    Science.gov (United States)

    Dingemanse, Niels J; Araya-Ajoy, Yimen G

    2015-02-01

    Behavioural ecologists increasingly study behavioural variation within and among individuals in conjunction, thereby integrating research on phenotypic plasticity and animal personality within a single adaptive framework. Interactions between individuals (cf. social environments) constitute a major causative factor of behavioural variation at both of these hierarchical levels. Social interactions give rise to complex 'interactive phenotypes' and group-level emergent properties. This type of phenotype has intriguing evolutionary implications, warranting a cohesive framework for its study. We detail here how a reaction-norm framework might be applied to usefully integrate social environment theory developed in behavioural ecology and quantitative genetics. The proposed emergent framework facilitates firm integration of social environments in adaptive research on phenotypic characters that vary within and among individuals.

  20. A common genetic determinism for sensitivities to soil water deficit and evaporative demand: meta-analysis of quantitative trait Loci and introgression lines of maize.

    Science.gov (United States)

    Welcker, Claude; Sadok, Walid; Dignat, Grégoire; Renault, Morgan; Salvi, Silvio; Charcosset, Alain; Tardieu, François

    2011-10-01

    Evaporative demand and soil water deficit equally contribute to water stress and to its effect on plant growth. We have compared the genetic architectures of the sensitivities of maize (Zea mays) leaf elongation rate with evaporative demand and soil water deficit. The former was measured via the response to leaf-to-air vapor pressure deficit in well-watered plants, the latter via the response to soil water potential in the absence of evaporative demand. Genetic analyses of each sensitivity were performed over 21 independent experiments with (1) three mapping populations, with temperate or tropical materials, (2) one population resulting from the introgression of a tropical drought-tolerant line in a temperate line, and (3) two introgression libraries genetically independent from mapping populations. A very large genetic variability was observed for both sensitivities. Some lines maintained leaf elongation at very high evaporative demand or water deficit, while others stopped elongation in mild conditions. A complex architecture arose from analyses of mapping populations, with 19 major meta-quantitative trait loci involving strong effects and/or more than one mapping population. A total of 68% of those quantitative trait loci affected sensitivities to both evaporative demand and soil water deficit. In introgressed lines, 73% of the tested genomic regions affected both sensitivities. To our knowledge, this study is the first genetic demonstration that hydraulic processes, which drive the response to evaporative demand, also have a large contribution to the genetic variability of plant growth under water deficit in a large range of genetic material.

  1. Quantitative EEG and Current Source Density Analysis of Combined Antiepileptic Drugs and Dopaminergic Agents in Genetic Epilepsy: Two Case Studies.

    Science.gov (United States)

    Emory, Hamlin; Wells, Christopher; Mizrahi, Neptune

    2015-07-01

    Two adolescent females with absence epilepsy were classified, one as attention deficit and the other as bipolar disorder. Physical and cognitive exams identified hypotension, bradycardia, and cognitive dysfunction. Their initial electroencephalograms (EEGs) were considered slightly slow, but within normal limits. Quantitative EEG (QEEG) data included relative theta excess and low alpha mean frequencies. A combined treatment of antiepileptic drugs with a catecholamine agonist/reuptake inhibitor was sequentially used. Both patients' physical and cognitive functions improved and they have remained seizure free. The clinical outcomes were correlated with statistically significant changes in QEEG measures toward normal Z-scores in both anterior and posterior regions. In addition, low resolution electromagnetic tomography (LORETA) Z-scored source correlation analyses of the initial and treated QEEG data showed normalized patterns, supporting a neuroanatomic resolution. This study presents preliminary evidence for a neurophysiologic approach to patients with absence epilepsy and comorbid disorders and may provide a method for further research.

  2. A Study of Mercury Methylation Genetics: Qualitative and Quantitative Analysis of hgcAB in Pure Culture

    Science.gov (United States)

    Christensen, G. A.; Wymore, A. M.; King, A. J.; Podar, M.; Hurt, R. A., Jr.; Santillan, E. F. U.; Gilmour, C. C.; Brandt, C. C.; Brown, S. D.; Palumbo, A. V.; Elias, D. A.

    2015-12-01

    Two proteins (HgcA and HgcB) have been determined to be essential for mercury (Hg)-methylation and either one alone is not sufficient for this process. Detection and quantification of these genes to determine at risk environments is critical. Universal degenerate polymerase chain reaction (PCR) primers spanning hgcAB were developed to ascertain organismal diversity and validate that both genes were present as an established prerequisite for Hg-methylation. To confirm this approach, an extensive set of pure cultures with published genomes (including methylators and non-methylators: 13 Deltaproteobacteria, 9 Firmicutes, and 10 methanogenic Archaea) were assayed with the newly designed universal hgcAB primer set. A single band within an agarose gel was observed for the majority of the cultures with known hgcAB and confirmed via Sanger sequencing. For environmental applications, once the potential for Hg-methylation is established from PCR amplification with the universal hgcAB primer set, quantification of clade-specific hgcAB gene abundance is desirable. We developed quantitative polymerase chain reaction (qPCR) degenerate primers targeting hgcA from each of the three dominate clades (Deltaproteobacteria, Firmicutes and methanogenic Archaea) known to be associated with anaerobic Hg-methylation. The qPCR primers amplify virtually all hgcA positive cultures overall and are specific for their designed clade. Finally, to ensure the procedure is robust and sensitive in complex environmental matrices, cells from all clades were mixed in different combinations and ratios to assess qPCR primer specificity. The development and validation of these high fidelity quantitative molecular tools now allows for rapid and accurate risk management assessment in any environment.

  3. Quantitative Techniques in Volumetric Analysis

    Science.gov (United States)

    Zimmerman, John; Jacobsen, Jerrold J.

    1996-12-01

    Quantitative Techniques in Volumetric Analysis is a visual library of techniques used in making volumetric measurements. This 40-minute VHS videotape is designed as a resource for introducing students to proper volumetric methods and procedures. The entire tape, or relevant segments of the tape, can also be used to review procedures used in subsequent experiments that rely on the traditional art of quantitative analysis laboratory practice. The techniques included are: Quantitative transfer of a solid with a weighing spoon Quantitative transfer of a solid with a finger held weighing bottle Quantitative transfer of a solid with a paper strap held bottle Quantitative transfer of a solid with a spatula Examples of common quantitative weighing errors Quantitative transfer of a solid from dish to beaker to volumetric flask Quantitative transfer of a solid from dish to volumetric flask Volumetric transfer pipet A complete acid-base titration Hand technique variations The conventional view of contemporary quantitative chemical measurement tends to focus on instrumental systems, computers, and robotics. In this view, the analyst is relegated to placing standards and samples on a tray. A robotic arm delivers a sample to the analysis center, while a computer controls the analysis conditions and records the results. In spite of this, it is rare to find an analysis process that does not rely on some aspect of more traditional quantitative analysis techniques, such as careful dilution to the mark of a volumetric flask. Figure 2. Transfer of a solid with a spatula. Clearly, errors in a classical step will affect the quality of the final analysis. Because of this, it is still important for students to master the key elements of the traditional art of quantitative chemical analysis laboratory practice. Some aspects of chemical analysis, like careful rinsing to insure quantitative transfer, are often an automated part of an instrumental process that must be understood by the

  4. A census of cells in time: quantitative genetics meets developmental biology.

    Science.gov (United States)

    Chitwood, Daniel H; Sinha, Neelima R

    2013-02-01

    Quantitative genetics has become a popular method for determining the genetic basis of natural variation. Combined with genomic methods, it provides a tool for discerning the genetic basis of gene expression. So-called genetical genomics approaches yield a wealth of genomic information, but by necessity, because of cost and time, fail to resolve the differences between organs, tissues, and/or cell types. Similarly, quantitative approaches in development that might potentially address these issues are seldom applied to quantitative genetics. We discuss recent advances in cell type-specific isolation methods, the quantitative analysis of phenotype, and developmental modeling that are compatible with quantitative genetics and, with time, promise to bridge the gap between these two powerful disciplines yielding unprecedented biological insight.

  5. Genetic analysis of ecological relevant morphological variability in Plantago lanceolata L. : 2. Localisation and organisation of quantitative trait loci.

    Science.gov (United States)

    Wolff, K

    1987-04-01

    Morphological variability was analysed in an F2-generation derived from crosses between two ecotypes of Plantago lanceolata L. Six allozyme loci, localised in five linkage groups, were used as markers. For two marker loci, Got-2 and Gpi-1, segregations did not fit monogenic ratios. In the linkage groups to which these two loci belonged, male sterility genes appeared to be present. In these crosses, male sterility (type 3, as described by Van Damme 1983) may be determined by two recessive loci located in the linkage groups of Got-2 and of Gpi-1. Many correlations of morphological and life history characters with allozyme markers were observed. The quantitative trait loci did not appear to be concentrated in major gene complexes. Often many loci were involved, sometimes with effects opposite to those expected from the population values. Main effects of the linkage groups appeared to be more important than interaction effects in determining variability. It also appeared that there is a positive correlation between the number of heterozygous allozyme loci and generative growth.

  6. Introduction to Focus Issue: Quantitative Approaches to Genetic Networks

    Science.gov (United States)

    Albert, Réka; Collins, James J.; Glass, Leon

    2013-06-01

    All cells of living organisms contain similar genetic instructions encoded in the organism's DNA. In any particular cell, the control of the expression of each different gene is regulated, in part, by binding of molecular complexes to specific regions of the DNA. The molecular complexes are composed of protein molecules, called transcription factors, combined with various other molecules such as hormones and drugs. Since transcription factors are coded by genes, cellular function is partially determined by genetic networks. Recent research is making large strides to understand both the structure and the function of these networks. Further, the emerging discipline of synthetic biology is engineering novel gene circuits with specific dynamic properties to advance both basic science and potential practical applications. Although there is not yet a universally accepted mathematical framework for studying the properties of genetic networks, the strong analogies between the activation and inhibition of gene expression and electric circuits suggest frameworks based on logical switching circuits. This focus issue provides a selection of papers reflecting current research directions in the quantitative analysis of genetic networks. The work extends from molecular models for the binding of proteins, to realistic detailed models of cellular metabolism. Between these extremes are simplified models in which genetic dynamics are modeled using classical methods of systems engineering, Boolean switching networks, differential equations that are continuous analogues of Boolean switching networks, and differential equations in which control is based on power law functions. The mathematical techniques are applied to study: (i) naturally occurring gene networks in living organisms including: cyanobacteria, Mycoplasma genitalium, fruit flies, immune cells in mammals; (ii) synthetic gene circuits in Escherichia coli and yeast; and (iii) electronic circuits modeling genetic networks

  7. Revised sections F7.5 (quantitative amino acid analysis) and F7.6 (qualitative amino acid analysis): American College of Medical Genetics Standards and Guidelines for Clinical Genetics Laboratories, 2003.

    Science.gov (United States)

    Grier, Robert E; Gahl, William A; Cowan, Tina; Bernardini, Isa; McDowell, Geraldine A; Rinaldo, Piero

    2004-01-01

    Determination of plasma amino acid levels has become a key piece of information in the diagnosis and clinical management of a group of metabolic genetic disorders. Appropriate laboratory methodologies have been published for amino acid analysis, yet there is a need for direction for the laboratory in performing this testing. The following guidelines were generated by a working group of the American College of Medical Genetics Laboratory Quality Assurance Committee. Based upon a body of knowledge and professional experience, these guidelines and standards are to be the benchmark for performance of amino acid analysis for clinical interpretation.

  8. Quantitative Risk Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Helms, J. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2017-02-10

    The US energy sector is vulnerable to multiple hazards including both natural disasters and malicious attacks from an intelligent adversary. The question that utility owners, operators and regulators face is how to prioritize their investments to mitigate the risks from a hazard that can have the most impact on the asset of interest. In order to be able to understand their risk landscape and develop a prioritized mitigation strategy, they must quantify risk in a consistent way across all hazards their asset is facing. Without being able to quantitatively measure risk, it is not possible to defensibly prioritize security investments or evaluate trade-offs between security and functionality. Development of a methodology that will consistently measure and quantify risk across different hazards is needed.

  9. From classical genetics to quantitative genetics to systems biology: modeling epistasis.

    Directory of Open Access Journals (Sweden)

    David L Aylor

    2008-03-01

    Full Text Available Gene expression data has been used in lieu of phenotype in both classical and quantitative genetic settings. These two disciplines have separate approaches to measuring and interpreting epistasis, which is the interaction between alleles at different loci. We propose a framework for estimating and interpreting epistasis from a classical experiment that combines the strengths of each approach. A regression analysis step accommodates the quantitative nature of expression measurements by estimating the effect of gene deletions plus any interaction. Effects are selected by significance such that a reduced model describes each expression trait. We show how the resulting models correspond to specific hierarchical relationships between two regulator genes and a target gene. These relationships are the basic units of genetic pathways and genomic system diagrams. Our approach can be extended to analyze data from a variety of experiments, multiple loci, and multiple environments.

  10. Monotowns: A Quantitative Analysis

    Directory of Open Access Journals (Sweden)

    Shastitko Andrei

    2016-06-01

    Full Text Available The authors propose an empirical analysis of the current situation in monotowns. The study questions the perceived seriousness of the ‘monotown problem’ as well as the actual challenges it presents. The authors use a cluster analysis to divide monotowns into groups for further structural comparison. The structural differences in the available databases limit the possibilities of empirical analysis. Hence, alternative approaches are required. The authors consider possible reasons for the limitations identified. Special attention is paid to the monotowns that were granted the status of advanced development territories. A comparative analysis makes it possible to study their general characteristics and socioeconomic indicators. The authors apply the theory of opportunistic behaviour to describe potential problems caused by the lack of unified criteria for granting monotowns the status of advanced development territories. The article identifies the main stakeholders and the character of their interaction; it desc ribes a conceptual model built on the principal/agent interactions, and identifies the parametric space of mutually beneficial cooperation. The solution to the principal/agent problem suggested in the article contributes to the development of an alternative approach to the current situation and a rational approach to overcoming the ‘monotown problem’.

  11. [The study of tomato fruit weight quantitative trait locus and its application in genetics teaching].

    Science.gov (United States)

    Wang, Haiyan

    2015-08-01

    The classical research cases, which have greatly promoted the development of genetics in history, can be combined with the content of courses in genetics teaching to train students' ability of scientific thinking and genetic analysis. The localization and clone of gene controlling tomato fruit weight is a pioneer work in quantitative trait locus (QTL) studies and represents a complete process of QTL research in plants. Application of this integrated case in genetics teaching, which showed a wonderful process of scientific discovery and the fascination of genetic research, has inspired students' interest in genetics and achieved a good teaching effect.

  12. The quantitative genetics of disgust sensitivity.

    Science.gov (United States)

    Sherlock, James M; Zietsch, Brendan P; Tybur, Joshua M; Jern, Patrick

    2016-02-01

    [Correction Notice: An Erratum for this article was reported in Vol 16(1) of Emotion (see record 2015-57029-001). In the article, the name of author Joshua M. Tybur was misspelled as Joshua M. Tyber. All versions of this article have been corrected.] Response sensitivity to common disgust elicitors varies considerably among individuals. The sources of these individual differences are largely unknown. In the current study, we use a large sample of female identical and nonidentical twins (N = 1,041 individuals) and their siblings (N = 170) to estimate the proportion of variation due to genetic effects, the shared environment, and other (residual) sources across multiple domains of disgust sensitivity. We also investigate the genetic and environmental influences on the covariation between the different disgust domains. Twin modeling revealed that approximately half of the variation in pathogen, sexual, and moral disgust is due to genetic effects. An independent pathways twin model also revealed that sexual and pathogen disgust sensitivity were influenced by unique sources of genetic variation, while also being significantly affected by a general genetic factor underlying all 3 disgust domains. Moral disgust sensitivity, in contrast, did not exhibit domain-specific genetic variation. These findings are discussed in light of contemporary evolutionary approaches to disgust sensitivity.

  13. A century after Fisher: time for a new paradigm in quantitative genetics.

    Science.gov (United States)

    Nelson, Ronald M; Pettersson, Mats E; Carlborg, Örjan

    2013-12-01

    Quantitative genetics traces its roots back through more than a century of theory, largely formed in the absence of directly observable genotype data, and has remained essentially unchanged for decades. By contrast, molecular genetics arose from direct observations and is currently undergoing rapid changes, making the amount of available data ever greater. Thus, the two disciplines are disparate both in their origins and their current states, yet they address the same fundamental question: how does the genotype affect the phenotype? The rapidly accumulating genomic data necessitate sophisticated analysis, but many of the current tools are adaptations of methods designed during the early days of quantitative genetics. We argue here that the present analysis paradigm in quantitative genetics is at its limits in regards to unraveling complex traits and it is necessary to re-evaluate the direction that genetic research is taking for the field to realize its full potential.

  14. International collaborative study of the endogenous reference gene, sucrose phosphate synthase (SPS), used for qualitative and quantitative analysis of genetically modified rice.

    Science.gov (United States)

    Jiang, Lingxi; Yang, Litao; Zhang, Haibo; Guo, Jinchao; Mazzara, Marco; Van den Eede, Guy; Zhang, Dabing

    2009-05-13

    One rice ( Oryza sativa ) gene, sucrose phosphate synthase (SPS), has been proven to be a suitable endogenous reference gene for genetically modified (GM) rice detection in a previous study. Herein are the reported results of an international collaborative ring trial for validation of the SPS gene as an endogenous reference gene and its optimized qualitative and quantitative polymerase chain reaction (PCR) systems. A total of 12 genetically modified organism (GMO) detection laboratories from seven countries participated in the ring trial and returned their results. The validated results confirmed the species specificity of the method through testing 10 plant genomic DNAs, low heterogeneity, and a stable single-copy number of the rice SPS gene among 7 indica varieties and 5 japonica varieties. The SPS qualitative PCR assay was validated with a limit of detection (LOD) of 0.1%, which corresponded to about 230 copies of haploid rice genomic DNA, while the limit of quantification (LOQ) for the quantitative PCR system was about 23 copies of haploid rice genomic DNA, with acceptable PCR efficiency and linearity. Furthermore, the bias between the test and true values of eight blind samples ranged from 5.22 to 26.53%. Thus, we believe that the SPS gene is suitable for use as an endogenous reference gene for the identification and quantification of GM rice and its derivates.

  15. Data-driven encoding for quantitative genetic trait prediction.

    Science.gov (United States)

    He, Dan; Wang, Zhanyong; Parida, Laxmi

    2015-01-01

    Given a set of biallelic molecular markers, such as SNPs, with genotype values on a collection of plant, animal or human samples, the goal of quantitative genetic trait prediction is to predict the quantitative trait values by simultaneously modeling all marker effects. Quantitative genetic trait prediction is usually represented as linear regression models which require quantitative encodings for the genotypes: the three distinct genotype values, corresponding to one heterozygous and two homozygous alleles, are usually coded as integers, and manipulated algebraically in the model. Further, epistasis between multiple markers is modeled as multiplication between the markers: it is unclear that the regression model continues to be effective under this. In this work we investigate the effects of encodings to the quantitative genetic trait prediction problem. We first showed that different encodings lead to different prediction accuracies, in many test cases. We then proposed a data-driven encoding strategy, where we encode the genotypes according to their distribution in the phenotypes and we allow each marker to have different encodings. We show in our experiments that this encoding strategy is able to improve the performance of the genetic trait prediction method and it is more helpful for the oligogenic traits, whose values rely on a relatively small set of markers. To the best of our knowledge, this is the first paper that discusses the effects of encodings to the genetic trait prediction problem.

  16. Genetic analysis of environmental variation

    NARCIS (Netherlands)

    Hill, W.G.; Mulder, H.A.

    2010-01-01

    Environmental variation (VE) in a quantitative trait – variation in phenotype that cannot be explained by genetic variation or identifiable genetic differences – can be regarded as being under some degree of genetic control. Such variation may be either between repeated expressions of the same trait

  17. Genetic analysis of environmental variation

    NARCIS (Netherlands)

    Hill, W.G.; Mulder, H.A.

    2010-01-01

    Environmental variation (VE) in a quantitative trait – variation in phenotype that cannot be explained by genetic variation or identifiable genetic differences – can be regarded as being under some degree of genetic control. Such variation may be either between repeated expressions of the same trait

  18. Genetic toxicology at the crossroads-from qualitative hazard evaluation to quantitative risk assessment.

    Science.gov (United States)

    White, Paul A; Johnson, George E

    2016-05-01

    Applied genetic toxicology is undergoing a transition from qualitative hazard identification to quantitative dose-response analysis and risk assessment. To facilitate this change, the Health and Environmental Sciences Institute (HESI) Genetic Toxicology Technical Committee (GTTC) sponsored a workshop held in Lancaster, UK on July 10-11, 2014. The event included invited speakers from several institutions and the contents was divided into three themes-1: Point-of-departure Metrics for Quantitative Dose-Response Analysis in Genetic Toxicology; 2: Measurement and Estimation of Exposures for Better Extrapolation to Humans and 3: The Use of Quantitative Approaches in Genetic Toxicology for human health risk assessment (HHRA). A host of pertinent issues were discussed relating to the use of in vitro and in vivo dose-response data, the development of methods for in vitro to in vivo extrapolation and approaches to use in vivo dose-response data to determine human exposure limits for regulatory evaluations and decision-making. This Special Issue, which was inspired by the workshop, contains a series of papers that collectively address topics related to the aforementioned themes. The Issue includes contributions that collectively evaluate, describe and discuss in silico, in vitro, in vivo and statistical approaches that are facilitating the shift from qualitative hazard evaluation to quantitative risk assessment. The use and application of the benchmark dose approach was a central theme in many of the workshop presentations and discussions, and the Special Issue includes several contributions that outline novel applications for the analysis and interpretation of genetic toxicity data. Although the contents of the Special Issue constitutes an important step towards the adoption of quantitative methods for regulatory assessment of genetic toxicity, formal acceptance of quantitative methods for HHRA and regulatory decision-making will require consensus regarding the

  19. Quantitative analysis of glycated proteins.

    Science.gov (United States)

    Priego-Capote, Feliciano; Ramírez-Boo, María; Finamore, Francesco; Gluck, Florent; Sanchez, Jean-Charles

    2014-02-07

    The proposed protocol presents a comprehensive approach for large-scale qualitative and quantitative analysis of glycated proteins (GP) in complex biological samples including biological fluids and cell lysates such as plasma and red blood cells. The method, named glycation isotopic labeling (GIL), is based on the differential labeling of proteins with isotopic [(13)C6]-glucose, which supports quantitation of the resulting glycated peptides after enzymatic digestion with endoproteinase Glu-C. The key principle of the GIL approach is the detection of doublet signals for each glycated peptide in MS precursor scanning (glycated peptide with in vivo [(12)C6]- and in vitro [(13)C6]-glucose). The mass shift of the doublet signals is +6, +3 or +2 Da depending on the peptide charge state and the number of glycation sites. The intensity ratio between doublet signals generates quantitative information of glycated proteins that can be related to the glycemic state of the studied samples. Tandem mass spectrometry with high-energy collisional dissociation (HCD-MS2) and data-dependent methods with collision-induced dissociation (CID-MS3 neutral loss scan) are used for qualitative analysis.

  20. Genetic architecture of quantitative traits and complex diseases.

    Science.gov (United States)

    Fu, Wenqing; O'Connor, Timothy D; Akey, Joshua M

    2013-12-01

    More than 150 years after Mendel discovered the laws of heredity, the genetic architecture of phenotypic variation remains elusive. Here, we discuss recent progress in deciphering how genotypes map onto phenotypes, sources of genetic complexity, and how model organisms are illuminating general principles about the relationship between genetic and phenotypic variation. Moreover, we highlight insights gleaned from large-scale sequencing studies in humans, and how this knowledge informs outstanding questions about the genetic architecture of quantitative traits and complex diseases. Finally, we articulate how the confluence of technologies enabling whole-genome sequencing, comprehensive phenotyping, and high-throughput functional assays of polymorphisms will facilitate a more principled and mechanistic understanding of the genetic architecture of phenotypic variation.

  1. Genetic mapping of quantitative phenotypic traits in Saccharomyces cerevisiae.

    Science.gov (United States)

    Swinnen, Steve; Thevelein, Johan M; Nevoigt, Elke

    2012-03-01

    Saccharomyces cerevisiae has become a favorite production organism in industrial biotechnology presenting new challenges to yeast engineers in terms of introducing advantageous traits such as stress tolerances. Exploring subspecies diversity of S. cerevisiae has identified strains that bear industrially relevant phenotypic traits. Provided that the genetic basis of such phenotypic traits can be identified inverse engineering allows the targeted modification of production strains. Most phenotypic traits of interest in S. cerevisiae strains are quantitative, meaning that they are controlled by multiple genetic loci referred to as quantitative trait loci (QTL). A straightforward approach to identify the genetic basis of quantitative traits is QTL mapping which aims at the allocation of the genetic determinants to regions in the genome. The application of high-density oligonucleotide arrays and whole-genome re-sequencing to detect genetic variations between strains has facilitated the detection of large numbers of molecular markers thus allowing high-resolution QTL mapping over the entire genome. This review focuses on the basic principle and state of the art of QTL mapping in S. cerevisiae. Furthermore we discuss several approaches developed during the last decade that allow down-scaling of the regions identified by QTL mapping to the gene level. We also emphasize the particular challenges of QTL mapping in nonlaboratory strains of S. cerevisiae.

  2. Quantitative Genetics in the Era of Molecular Genetics: Learning Abilities and Disabilities as an Example

    Science.gov (United States)

    Haworth, Claire M. A.; Plomin, Robert

    2010-01-01

    Objective: To consider recent findings from quantitative genetic research in the context of molecular genetic research, especially genome-wide association studies. We focus on findings that go beyond merely estimating heritability. We use learning abilities and disabilities as examples. Method: Recent twin research in the area of learning…

  3. The nature of quantitative genetic variation for Drosophila longevity.

    Science.gov (United States)

    Mackay, Trudy F C

    2002-01-01

    Longevity is a typical quantitative trait: the continuous variation in life span observed in natural populations is attributable to genetic variation at multiple quantitative trait loci (QTL), environmental sensitivity of QTL alleles, and truly continuous environmental variation. To begin to understand the genetic architecture of longevity at the level of individual QTL, we have mapped QTL for Drosophila life span that segregate between two inbred strains that were not selected for longevity. A mapping population of 98 recombinant inbred lines (RIL) was derived from these strains, and life span of virgin male and female flies measured under control culture conditions, chronic heat and cold stress, heat shock and starvation stress, and high and low density larval environments. The genotypes of the RIL were determined for polymorphic roo transposable element insertion sites, and life span QTL were mapped using composite interval mapping methods. A minimum of 19 life span QTL were detected by recombination mapping. The life span QTL exhibited strong genotype by sex, genotype by environment, and genotype by genotype (epistatic) interactions. These interactions complicate mapping efforts, but evolutionary theory predicts such properties of segregating QTL alleles. Quantitative deficiency mapping of four longevity QTL detected in the control environment by recombination mapping revealed a minimum of 11 QTL in these regions. Clearly, longevity is a complex quantitative trait. In the future, linkage disequilibrium mapping can be used to determine which candidate genes in a QTL region correspond to the genetic loci affecting variation in life span, and define the QTL alleles at the molecular level.

  4. Joint association analysis of bivariate quantitative and qualitative traits.

    Science.gov (United States)

    Yuan, Mengdie; Diao, Guoqing

    2011-11-29

    Univariate genome-wide association analysis of quantitative and qualitative traits has been investigated extensively in the literature. In the presence of correlated phenotypes, it is more intuitive to analyze all phenotypes simultaneously. We describe an efficient likelihood-based approach for the joint association analysis of quantitative and qualitative traits in unrelated individuals. We assume a probit model for the qualitative trait, under which an unobserved latent variable and a prespecified threshold determine the value of the qualitative trait. To jointly model the quantitative and qualitative traits, we assume that the quantitative trait and the latent variable follow a bivariate normal distribution. The latent variable is allowed to be correlated with the quantitative phenotype. Simultaneous modeling of the quantitative and qualitative traits allows us to make more precise inference on the pleiotropic genetic effects. We derive likelihood ratio tests for the testing of genetic effects. An application to the Genetic Analysis Workshop 17 data is provided. The new method yields reasonable power and meaningful results for the joint association analysis of the quantitative trait Q1 and the qualitative trait disease status at SNPs with not too small MAF.

  5. Quantitative genetic activity graphical profiles for use in chemical evaluation

    Energy Technology Data Exchange (ETDEWEB)

    Waters, M.D. [Environmental Protection Agency, Washington, DC (United States); Stack, H.F.; Garrett, N.E.; Jackson, M.A. [Environmental Health Research and Testing, Inc., Research Triangle Park, NC (United States)

    1990-12-31

    A graphic approach, terms a Genetic Activity Profile (GAP), was developed to display a matrix of data on the genetic and related effects of selected chemical agents. The profiles provide a visual overview of the quantitative (doses) and qualitative (test results) data for each chemical. Either the lowest effective dose or highest ineffective dose is recorded for each agent and bioassay. Up to 200 different test systems are represented across the GAP. Bioassay systems are organized according to the phylogeny of the test organisms and the end points of genetic activity. The methodology for producing and evaluating genetic activity profile was developed in collaboration with the International Agency for Research on Cancer (IARC). Data on individual chemicals were compiles by IARC and by the US Environmental Protection Agency (EPA). Data are available on 343 compounds selected from volumes 1-53 of the IARC Monographs and on 115 compounds identified as Superfund Priority Substances. Software to display the GAPs on an IBM-compatible personal computer is available from the authors. Structurally similar compounds frequently display qualitatively and quantitatively similar profiles of genetic activity. Through examination of the patterns of GAPs of pairs and groups of chemicals, it is possible to make more informed decisions regarding the selection of test batteries to be used in evaluation of chemical analogs. GAPs provided useful data for development of weight-of-evidence hazard ranking schemes. Also, some knowledge of the potential genetic activity of complex environmental mixtures may be gained from an assessment of the genetic activity profiles of component chemicals. The fundamental techniques and computer programs devised for the GAP database may be used to develop similar databases in other disciplines. 36 refs., 2 figs.

  6. Genetic Architectures of Quantitative Variation in RNA Editing Pathways.

    Science.gov (United States)

    Gu, Tongjun; Gatti, Daniel M; Srivastava, Anuj; Snyder, Elizabeth M; Raghupathy, Narayanan; Simecek, Petr; Svenson, Karen L; Dotu, Ivan; Chuang, Jeffrey H; Keller, Mark P; Attie, Alan D; Braun, Robert E; Churchill, Gary A

    2016-02-01

    RNA editing refers to post-transcriptional processes that alter the base sequence of RNA. Recently, hundreds of new RNA editing targets have been reported. However, the mechanisms that determine the specificity and degree of editing are not well understood. We examined quantitative variation of site-specific editing in a genetically diverse multiparent population, Diversity Outbred mice, and mapped polymorphic loci that alter editing ratios globally for C-to-U editing and at specific sites for A-to-I editing. An allelic series in the C-to-U editing enzyme Apobec1 influences the editing efficiency of Apob and 58 additional C-to-U editing targets. We identified 49 A-to-I editing sites with polymorphisms in the edited transcript that alter editing efficiency. In contrast to the shared genetic control of C-to-U editing, most of the variable A-to-I editing sites were determined by local nucleotide polymorphisms in proximity to the editing site in the RNA secondary structure. Our results indicate that RNA editing is a quantitative trait subject to genetic variation and that evolutionary constraints have given rise to distinct genetic architectures in the two canonical types of RNA editing.

  7. Genome-scan analysis for genetic mapping of quantitative trait loci underlying birth weight and onset of puberty in doe kids (Capra hircus).

    Science.gov (United States)

    Esmailizadeh, A K

    2014-12-01

    The objective of this study was to locate quantitative trait loci (QTL) causing variation in birth weight and age of puberty of doe kids in a population of Rayini cashmere goats. Four hundred and thirty kids from five half-sib families were genotyped for 116 microsatellite markers located on the caprine autosomes. The traits recorded were birth weight of the male and female kids, body weight at puberty, average daily gain from birth to age of puberty and age at puberty of the doe kids. QTL analysis was conducted using the least squares interval mapping approach. Linkage analysis indicated significant QTL for birth weight on Capra hircus chromosomes (CHI) 4, 5, 6, 18 and 21. Five QTL located on CHI 5, 14 and 29 were associated with age at puberty. Across-family analysis revealed evidence for overlapping QTL affecting birth weight (78 cM), body weight at puberty (72 cM), average daily gain from birth to age of puberty (72 cM) and age at puberty (76 cM) on CHI 5 and overlapping QTL controlling body weight at puberty and age at puberty on CHI 14 at 18-19 cM. The proportion of the phenotypic variance explained by the detected QTL ranged between 7.9% and 14.4%. Confirming some of the previously reported results for birth weight and growth QTL in goats, this study identified more QTL for these traits and is the first report of QTL for onset of puberty in doe kids.

  8. Genetic Basis of Differential Heat Resistance between Two Species of Congeneric Freshwater Snails: Insights from Quantitative Proteomics and Base Substitution Rate Analysis.

    Science.gov (United States)

    Mu, Huawei; Sun, Jin; Fang, Ling; Luan, Tiangang; Williams, Gray A; Cheung, Siu Gin; Wong, Chris K C; Qiu, Jian-Wen

    2015-10-02

    We compared the heat tolerance, proteomic responses to heat stress, and adaptive sequence divergence in the invasive snail Pomacea canaliculata and its noninvasive congener Pomacea diffusa. The LT50 of P. canaliculata was significantly higher than that of P. diffusa. More than 3350 proteins were identified from the hepatopancreas of the snails exposed to acute and chronic thermal stress using iTRAQ-coupled mass spectrometry. Acute exposure (3 h exposure at 37 °C with 25 °C as control) resulted in similar numbers (27 in P. canaliculata and 23 in P. diffusa) of differentially expressed proteins in the two species. Chronic exposure (3 weeks of exposure at 35 °C with 25 °C as control) caused differential expression of more proteins (58 in P. canaliculata and 118 in P. diffusa), with many of them related to restoration of damaged molecules, ubiquitinating dysfunctional molecules, and utilization of energy reserves in both species; but only in P. diffusa was there a shift from carbohydrate to lipid catabolism. Analysis of orthologous genes encoding the differentially expressed proteins revealed two genes having clear evidence of positive selection (Ka/Ks > 1) and seven candidates for more detailed analysis of positive selection (Ka/Ks between 0.5 and 1). These nine genes are related to energy metabolism, cellular oxidative homeostasis, signaling, and binding processes. Overall, the proteomic and base substitution rate analyses indicate genetic basis of differential resistance to heat stress between the two species, and such differences could affect their further range expansion in a warming climate.

  9. Submarine Pipeline Routing Risk Quantitative Analysis

    Institute of Scientific and Technical Information of China (English)

    徐慧; 于莉; 胡云昌; 王金英

    2004-01-01

    A new method for submarine pipeline routing risk quantitative analysis was provided, and the study was developed from qualitative analysis to quantitative analysis.The characteristics of the potential risk of the submarine pipeline system were considered, and grey-mode identification theory was used. The study process was composed of three parts: establishing the indexes system of routing risk quantitative analysis, establishing the model of grey-mode identification for routing risk quantitative analysis, and establishing the standard of mode identification result. It is shown that this model can directly and concisely reflect the hazard degree of the routing through computing example, and prepares the routing selection for the future.

  10. Genetic influences on attention deficit hyperactivity disorder symptoms from age 2 to 3: A quantitative and molecular genetic investigation

    Directory of Open Access Journals (Sweden)

    Saudino Kimberly J

    2010-12-01

    Full Text Available Abstract Background A twin study design was used to assess the degree to which additive genetic variance influences ADHD symptom scores across two ages during infancy. A further objective in the study was to observe whether genetic association with a number of candidate markers reflects results from the quantitative genetic analysis. Method We have studied 312 twin pairs at two time-points, age 2 and age 3. A composite measure of ADHD symptoms from two parent-rating scales: The Child Behavior Checklist/1.5 - 5 years (CBCL hyperactivity scale and the Revised Rutter Parent Scale for Preschool Children (RRPSPC was used for both quantitative and molecular genetic analyses. Results At ages 2 and 3 ADHD symptoms are highly heritable (h2 = 0.79 and 0.78, respectively with a high level of genetic stability across these ages. However, we also observe a significant level of genetic change from age 2 to age 3. There are modest influences of non-shared environment at each age independently (e2 = 0.22 and 0.21, respectively, with these influences being largely age-specific. In addition, we find modest association signals in DAT1 and NET1 at both ages, along with suggestive specific effects of 5-HTT and DRD4 at age 3. Conclusions ADHD symptoms are heritable at ages 2 and 3. Additive genetic variance is largely shared across these ages, although there are significant new effects emerging at age 3. Results from our genetic association analysis reflect these levels of stability and change and, more generally, suggest a requirement for consideration of age-specific genotypic effects in future molecular studies.

  11. A comparison of strategies for Markov chain Monte Carlo computation in quantitative genetics

    DEFF Research Database (Denmark)

    Waagepetersen, Rasmus; Ibánez-Escriche, Noelia; Sorensen, Daniel

    2008-01-01

    In quantitative genetics, Markov chain Monte Carlo (MCMC) methods are indispensable for statistical inference in non-standard models like generalized linear models with genetic random effects or models with genetically structured variance heterogeneity. A particular challenge for MCMC applications...

  12. Automated identification of pathways from quantitative genetic interaction data

    Science.gov (United States)

    Battle, Alexis; Jonikas, Martin C; Walter, Peter; Weissman, Jonathan S; Koller, Daphne

    2010-01-01

    High-throughput quantitative genetic interaction (GI) measurements provide detailed information regarding the structure of the underlying biological pathways by reporting on functional dependencies between genes. However, the analytical tools for fully exploiting such information lag behind the ability to collect these data. We present a novel Bayesian learning method that uses quantitative phenotypes of double knockout organisms to automatically reconstruct detailed pathway structures. We applied our method to a recent data set that measures GIs for endoplasmic reticulum (ER) genes, using the unfolded protein response as a quantitative phenotype. The results provided reconstructions of known functional pathways including N-linked glycosylation and ER-associated protein degradation. It also contained novel relationships, such as the placement of SGT2 in the tail-anchored biogenesis pathway, a finding that we experimentally validated. Our approach should be readily applicable to the next generation of quantitative GI data sets, as assays become available for additional phenotypes and eventually higher-level organisms. PMID:20531408

  13. Quantitative genetic-interaction mapping in mammalian cells

    Science.gov (United States)

    Roguev, Assen; Talbot, Dale; Negri, Gian Luca; Shales, Michael; Cagney, Gerard; Bandyopadhyay, Sourav; Panning, Barbara; Krogan, Nevan J

    2013-01-01

    Mapping genetic interactions (GIs) by simultaneously perturbing pairs of genes is a powerful tool for understanding complex biological phenomena. Here we describe an experimental platform for generating quantitative GI maps in mammalian cells using a combinatorial RNA interference strategy. We performed ~11,000 pairwise knockdowns in mouse fibroblasts, focusing on 130 factors involved in chromatin regulation to create a GI map. Comparison of the GI and protein-protein interaction (PPI) data revealed that pairs of genes exhibiting positive GIs and/or similar genetic profiles were predictive of the corresponding proteins being physically associated. The mammalian GI map identified pathways and complexes but also resolved functionally distinct submodules within larger protein complexes. By integrating GI and PPI data, we created a functional map of chromatin complexes in mouse fibroblasts, revealing that the PAF complex is a central player in the mammalian chromatin landscape. PMID:23407553

  14. Quantitative Genetic Interactions Reveal Layers of Biological Modularity

    Science.gov (United States)

    Beltrao, Pedro; Cagney, Gerard; Krogan, Nevan J.

    2010-01-01

    In the past, biomedical research has embraced a reductionist approach, primarily focused on characterizing the individual components that comprise a system of interest. Recent technical developments have significantly increased the size and scope of data describing biological systems. At the same time, advances in the field of systems biology have evoked a broader view of how the underlying components are interconnected. In this essay, we discuss how quantitative genetic interaction mapping has enhanced our view of biological systems, allowing a deeper functional interrogation at different biological scales. PMID:20510918

  15. Quantitative trait locus mapping reveals complex genetic architecture of quantitative virulence in the wheat pathogen Zymoseptoria tritici.

    Science.gov (United States)

    Stewart, Ethan L; Croll, Daniel; Lendenmann, Mark H; Sanchez-Vallet, Andrea; Hartmann, Fanny E; Palma-Guerrero, Javier; Ma, Xin; McDonald, Bruce A

    2016-11-21

    We conducted a comprehensive analysis of virulence in the fungal wheat pathogen Zymoseptoria tritici using quantitative trait locus (QTL) mapping. High-throughput phenotyping based on automated image analysis allowed the measurement of pathogen virulence on a scale and with a precision that was not previously possible. Across two mapping populations encompassing more than 520 progeny, 540 710 pycnidia were counted and their sizes and grey values were measured. A significant correlation was found between pycnidia size and both spore size and number. Precise measurements of percentage leaf area covered by lesions provided a quantitative measure of host damage. Combining these large and accurate phenotypic datasets with a dense panel of restriction site-associated DNA sequencing (RADseq) genetic markers enabled us to genetically dissect pathogen virulence into components related to host damage and those related to pathogen reproduction. We showed that different components of virulence can be under separate genetic control. Large- and small-effect QTLs were identified for all traits, with some QTLs specific to mapping populations, cultivars and traits and other QTLs shared among traits within the same mapping population. We associated the presence of four accessory chromosomes with small, but significant, increases in several virulence traits, providing the first evidence for a meaningful function associated with accessory chromosomes in this organism. A large-effect QTL involved in host specialization was identified on chromosome 7, leading to the identification of candidate genes having a large effect on virulence.

  16. The Quantitative Basis of the Arabidopsis Innate Immune System to Endemic Pathogens Depends on Pathogen Genetics.

    Directory of Open Access Journals (Sweden)

    Jason A Corwin

    2016-02-01

    Full Text Available The most established model of the eukaryotic innate immune system is derived from examples of large effect monogenic quantitative resistance to pathogens. However, many host-pathogen interactions involve many genes of small to medium effect and exhibit quantitative resistance. We used the Arabidopsis-Botrytis pathosystem to explore the quantitative genetic architecture underlying host innate immune system in a population of Arabidopsis thaliana. By infecting a diverse panel of Arabidopsis accessions with four phenotypically and genotypically distinct isolates of the fungal necrotroph B. cinerea, we identified a total of 2,982 genes associated with quantitative resistance using lesion area and 3,354 genes associated with camalexin production as measures of the interaction. Most genes were associated with resistance to a specific Botrytis isolate, which demonstrates the influence of pathogen genetic variation in analyzing host quantitative resistance. While known resistance genes, such as receptor-like kinases (RLKs and nucleotide-binding site leucine-rich repeat proteins (NLRs, were found to be enriched among associated genes, they only account for a small fraction of the total genes associated with quantitative resistance. Using publically available co-expression data, we condensed the quantitative resistance associated genes into co-expressed gene networks. GO analysis of these networks implicated several biological processes commonly connected to disease resistance, including defense hormone signaling and ROS production, as well as novel processes, such as leaf development. Validation of single gene T-DNA knockouts in a Col-0 background demonstrate a high success rate (60% when accounting for differences in environmental and Botrytis genetic variation. This study shows that the genetic architecture underlying host innate immune system is extremely complex and is likely able to sense and respond to differential virulence among pathogen

  17. Prediction of quantitative phenotypes based on genetic networks: a case study in yeast sporulation

    Directory of Open Access Journals (Sweden)

    Shen Li

    2010-09-01

    Full Text Available Abstract Background An exciting application of genetic network is to predict phenotypic consequences for environmental cues or genetic perturbations. However, de novo prediction for quantitative phenotypes based on network topology is always a challenging task. Results Using yeast sporulation as a model system, we have assembled a genetic network from literature and exploited Boolean network to predict sporulation efficiency change upon deleting individual genes. We observe that predictions based on the curated network correlate well with the experimentally measured values. In addition, computational analysis reveals the robustness and hysteresis of the yeast sporulation network and uncovers several patterns of sporulation efficiency change caused by double gene deletion. These discoveries may guide future investigation of underlying mechanisms. We have also shown that a hybridized genetic network reconstructed from both temporal microarray data and literature is able to achieve a satisfactory prediction accuracy of the same quantitative phenotypes. Conclusions This case study illustrates the value of predicting quantitative phenotypes based on genetic network and provides a generic approach.

  18. Comparative genetic analysis of quantitative traits in sunflower (Helianthus annuus L.). 2. Characterisation of QTL involved in developmental and agronomic traits.

    Science.gov (United States)

    Bert, P-F; Jouan, I; Tourvieille de Labrouhe, D; Serre, F; Philippon, J; Nicolas, P; Vear, F

    2003-06-01

    Seed weight and oil content are important properties of cultivated sunflower under complex genetic and environmental control, and associated with morphological and developmental characteristics such as plant height or flowering dates. Using a genetic map with 290 markers for a cross between two inbred sunflower lines and 2 years of observations on F3 families, QTL controlling seed weight, oil content, plant height, plant lodging, flowering dates, maturity dates and delay from flowering to maturity were detected. QTL detected were compared between the F2 and F3 generations and between the 2 years of testing for the F3 families in 1997 and 1999. Some of the QTL controlling seed weight overlapped with those controlling oil content. Several other co-localisations of QTL controlling developmental or morphological characteristics were observed and the relationships between the traits were also shown by correlation analyses. The relationships between all these traits and with resistance to Sclerotinia sclerotiorum and Diaporthe helianthi are discussed.

  19. Genetic diversity analysis based on molecular marker and quantitative traits of the response of different tomato (Lycopersicon esculentum Mill. cultivars to drought stress

    Directory of Open Access Journals (Sweden)

    Metwali Ehab M.R.

    2016-01-01

    Full Text Available The drought tolerance of tomato (Lycopersicon esculentum Mill. is a trait needing urgent improvement due to recent climate changes and limited water availability. We therefore conducted a greenhouse screening experiment to identify tomato cultivars with improved drought tolerance. Several sensitivity and tolerance indices were computed based on morphological markers. With the aim of establishing a correlation to these markers, a total of 16 inter-simple sequence repeat (ISSR primers were used, the genetic diversity among cultivars was elucidated and clustering the cultivars into groups based on their molecular profiles was performed. The obtained results indicated that selection indices, such as geometric mean productivity (GMP, mean productivity (MP, tolerance index (TOL,and stress tolerance index (STI, represented suitable indices for screening the drought tolerance of tomato cultivars. An interesting correlation of the ISSR analyses to these morphological findings was established according to 83 detectable fragments derived from 10 primers. The highest value of the effective multiplex ratio (EMR and marker index (MI was detected for primer INC7 followed by INC1. Based on Jaccard's similarity coefficients, the genetic distance of the genotypes varied from 0.702 to 0.942 with a mean value of 0.882. The results showed a clear-cut separation of the 15 tomato cultivars due to their genetic variability, making them a valuable genetic source for their incorporation into potential breeding programs. Molecular data were in good agreement with the results as regards selection indices, and both of them will be useful tools for improvement of the tomato germplasm.

  20. A strategy to apply quantitative epistasis analysis on developmental traits.

    Science.gov (United States)

    Labocha, Marta K; Yuan, Wang; Aleman-Meza, Boanerges; Zhong, Weiwei

    2017-05-15

    Genetic interactions are keys to understand complex traits and evolution. Epistasis analysis is an effective method to map genetic interactions. Large-scale quantitative epistasis analysis has been well established for single cells. However, there is a substantial lack of such studies in multicellular organisms and their complex phenotypes such as development. Here we present a method to extend quantitative epistasis analysis to developmental traits. In the nematode Caenorhabditis elegans, we applied RNA interference on mutants to inactivate two genes, used an imaging system to quantitatively measure phenotypes, and developed a set of statistical methods to extract genetic interactions from phenotypic measurement. Using two different C. elegans developmental phenotypes, body length and sex ratio, as examples, we showed that this method could accommodate various metazoan phenotypes with performances comparable to those methods in single cell growth studies. Comparing with qualitative observations, this method of quantitative epistasis enabled detection of new interactions involving subtle phenotypes. For example, several sex-ratio genes were found to interact with brc-1 and brd-1, the orthologs of the human breast cancer genes BRCA1 and BARD1, respectively. We confirmed the brc-1 interactions with the following genes in DNA damage response: C34F6.1, him-3 (ortholog of HORMAD1, HORMAD2), sdc-1, and set-2 (ortholog of SETD1A, SETD1B, KMT2C, KMT2D), validating the effectiveness of our method in detecting genetic interactions. We developed a reliable, high-throughput method for quantitative epistasis analysis of developmental phenotypes.

  1. Quantitative analysis of saccadic search strategy

    NARCIS (Netherlands)

    Over, E.A.B.

    2007-01-01

    This thesis deals with the quantitative analysis of saccadic search strategy. The goal of the research presented was twofold: 1) to quantify overall characteristics of fixation location and saccade direction, and 2) to identify search strategies, with the use of a quantitative description of eye mov

  2. Quantitative analysis of saccadic search strategy

    NARCIS (Netherlands)

    Over, E.A.B.

    2007-01-01

    This thesis deals with the quantitative analysis of saccadic search strategy. The goal of the research presented was twofold: 1) to quantify overall characteristics of fixation location and saccade direction, and 2) to identify search strategies, with the use of a quantitative description of eye

  3. Genetic mapping and quantitative trait loci analysis for disease resistance using F2 and F5 generation-based genetic maps derived from 'Tifrunner' x'GT-C20' in peanut

    Science.gov (United States)

    One mapping population derived from Tifrunner × GT-C20 has shown great potential in developing a high dense genetic map and identification of QTLs for important disease resistance, Tomato spotted wilt virus (TSWV) and leaf spot (LS). Both F2 and F5 generation-based genetic maps were constructed prev...

  4. Quantitative Analysis of Face Symmetry.

    Science.gov (United States)

    Tamir, Abraham

    2015-06-01

    The major objective of this article was to report quantitatively the degree of human face symmetry for reported images taken from the Internet. From the original image of a certain person that appears in the center of each triplet, 2 symmetric combinations were constructed that are based on the left part of the image and its mirror image (left-left) and on the right part of the image and its mirror image (right-right). By applying a computer software that enables to determine length, surface area, and perimeter of any geometric shape, the following measurements were obtained for each triplet: face perimeter and area; distance between the pupils; mouth length; its perimeter and area; nose length and face length, usually below the ears; as well as the area and perimeter of the pupils. Then, for each of the above measurements, the value C, which characterizes the degree of symmetry of the real image with respect to the combinations right-right and left-left, was calculated. C appears on the right-hand side below each image. A high value of C indicates a low symmetry, and as the value is decreasing, the symmetry is increasing. The magnitude on the left relates to the pupils and compares the difference between the area and perimeter of the 2 pupils. The major conclusion arrived at here is that the human face is asymmetric to some degree; the degree of asymmetry is reported quantitatively under each portrait.

  5. Combining microarrays and genetic analysis

    NARCIS (Netherlands)

    Alberts, Rudi; Fu, Jingyuan; Swertz, Morris A.; Lubbers, L. Alrik; Albers, Casper J.; Jansen, Ritsert C.

    2005-01-01

    Gene expression can be studied at a genome-wide scale with the aid of modern microarray technologies. Expression profiling of tens to hundreds of individuals in a genetic population can reveal the consequences of genetic variation. In this paper it is argued that the design and analysis of such a

  6. Combining microarrays and genetic analysis

    NARCIS (Netherlands)

    Alberts, Rudi; Fu, Jingyuan; Swertz, Morris A.; Lubbers, L. Alrik; Albers, Casper J.; Jansen, Ritsert C.

    2005-01-01

    Gene expression can be studied at a genome-wide scale with the aid of modern microarray technologies. Expression profiling of tens to hundreds of individuals in a genetic population can reveal the consequences of genetic variation. In this paper it is argued that the design and analysis of such a st

  7. Genetic diversity among exotic cotton accessions as for qualitative and quantitative traits.

    Science.gov (United States)

    de Carvalho, L P; Farias, F J C; Rodrigues, J I S; Suassuna, N D; Teodoro, P E

    2017-02-08

    Studying genetic diversity among a group of genotypes is important in genetic breeding because identifying hybrid combinations of greater heterotic effect also increases the chance of obtaining plants with favorable allele combinations in an intra-population selection program. The objective of this study was to compare different types of long and extra-long staple cotton and their genetic diversity in relation to the fiber traits and some agronomic traits in order to grant breeding programs. Diversity analysis among 29 cotton accessions based on qualitative and quantitative traits and joint including qualitative and quantitative traits was performed. Analysis based on qualitative and quantitative traits and joint met the accessions in three, two, and three groups, respectively. The cross between genotypes Giza 59 and Pima unknown was the most promising to generate segregating populations, comprising simultaneously resistance (based on molecular markers) to blue disease and bacterial blight, partial resistance to root-knot nematode, smaller size, in addition to good fiber characteristics. These populations can be used in recurrent selection programs as donors of alleles for development of long-staple cotton genotypes.

  8. Quantitative genetic bases of anthocyanin variation in grape (Vitis vinifera L. ssp. sativa) berry: a quantitative trait locus to quantitative trait nucleotide integrated study.

    Science.gov (United States)

    Fournier-Level, Alexandre; Le Cunff, Loïc; Gomez, Camila; Doligez, Agnès; Ageorges, Agnès; Roux, Catherine; Bertrand, Yves; Souquet, Jean-Marc; Cheynier, Véronique; This, Patrice

    2009-11-01

    The combination of QTL mapping studies of synthetic lines and association mapping studies of natural diversity represents an opportunity to throw light on the genetically based variation of quantitative traits. With the positional information provided through quantitative trait locus (QTL) mapping, which often leads to wide intervals encompassing numerous genes, it is now feasible to directly target candidate genes that are likely to be responsible for the observed variation in completely sequenced genomes and to test their effects through association genetics. This approach was performed in grape, a newly sequenced genome, to decipher the genetic architecture of anthocyanin content. Grapes may be either white or colored, ranging from the lightest pink to the darkest purple tones according to the amount of anthocyanin accumulated in the berry skin, which is a crucial trait for both wine quality and human nutrition. Although the determinism of the white phenotype has been fully identified, the genetic bases of the quantitative variation of anthocyanin content in berry skin remain unclear. A single QTL responsible for up to 62% of the variation in the anthocyanin content was mapped on a Syrah x Grenache F(1) pseudo-testcross. Among the 68 unigenes identified in the grape genome within the QTL interval, a cluster of four Myb-type genes was selected on the basis of physiological evidence (VvMybA1, VvMybA2, VvMybA3, and VvMybA4). From a core collection of natural resources (141 individuals), 32 polymorphisms revealed significant association, and extended linkage disequilibrium was observed. Using a multivariate regression method, we demonstrated that five polymorphisms in VvMybA genes except VvMybA4 (one retrotransposon, three single nucleotide polymorphisms and one 2-bp insertion/deletion) accounted for 84% of the observed variation. All these polymorphisms led to either structural changes in the MYB proteins or differences in the VvMybAs promoters. We concluded that

  9. Quantitative analysis of Boehm's GC

    Institute of Scientific and Technical Information of China (English)

    GUAN Xue-tao; ZHANG Yuan-rui; GOU Xiao-gang; CHENG Xu

    2003-01-01

    The term garbage collection describes the automated process of finding previously allocated memorythatis no longer in use in order to make the memory available to satisfy subsequent allocation requests. Wehave reviewed existing papers and implementations of GC, and especially analyzed Boehm' s C codes, which isa real-time mark-sweep GC running under Linux and ANSI C standard. In this paper, we will quantitatively an-alyze the performance of different configurations of Boehm' s collector subjected to different workloads. Reportedmeasurements demonstrate that a refined garbage collector is a viable alternative to traditional explicit memorymanagement techniques, even for low-level languages. It is more a trade-off for certain system than an all-or-nothing proposition.

  10. Quantitative analysis of qualitative images

    Science.gov (United States)

    Hockney, David; Falco, Charles M.

    2005-03-01

    We show optical evidence that demonstrates artists as early as Jan van Eyck and Robert Campin (c1425) used optical projections as aids for producing their paintings. We also have found optical evidence within works by later artists, including Bermejo (c1475), Lotto (c1525), Caravaggio (c1600), de la Tour (c1650), Chardin (c1750) and Ingres (c1825), demonstrating a continuum in the use of optical projections by artists, along with an evolution in the sophistication of that use. However, even for paintings where we have been able to extract unambiguous, quantitative evidence of the direct use of optical projections for producing certain of the features, this does not mean that paintings are effectively photographs. Because the hand and mind of the artist are intimately involved in the creation process, understanding these complex images requires more than can be obtained from only applying the equations of geometrical optics.

  11. Cancer detection by quantitative fluorescence image analysis.

    Science.gov (United States)

    Parry, W L; Hemstreet, G P

    1988-02-01

    Quantitative fluorescence image analysis is a rapidly evolving biophysical cytochemical technology with the potential for multiple clinical and basic research applications. We report the application of this technique for bladder cancer detection and discuss its potential usefulness as an adjunct to methods used currently by urologists for the diagnosis and management of bladder cancer. Quantitative fluorescence image analysis is a cytological method that incorporates 2 diagnostic techniques, quantitation of nuclear deoxyribonucleic acid and morphometric analysis, in a single semiautomated system to facilitate the identification of rare events, that is individual cancer cells. When compared to routine cytopathology for detection of bladder cancer in symptomatic patients, quantitative fluorescence image analysis demonstrated greater sensitivity (76 versus 33 per cent) for the detection of low grade transitional cell carcinoma. The specificity of quantitative fluorescence image analysis in a small control group was 94 per cent and with the manual method for quantitation of absolute nuclear fluorescence intensity in the screening of high risk asymptomatic subjects the specificity was 96.7 per cent. The more familiar flow cytometry is another fluorescence technique for measurement of nuclear deoxyribonucleic acid. However, rather than identifying individual cancer cells, flow cytometry identifies cellular pattern distributions, that is the ratio of normal to abnormal cells. Numerous studies by others have shown that flow cytometry is a sensitive method to monitor patients with diagnosed urological disease. Based upon results in separate quantitative fluorescence image analysis and flow cytometry studies, it appears that these 2 fluorescence techniques may be complementary tools for urological screening, diagnosis and management, and that they also may be useful separately or in combination to elucidate the oncogenic process, determine the biological potential of tumors

  12. WOMBAT: a tool for mixed model analyses in quantitative genetics by restricted maximum likelihood (REML).

    Science.gov (United States)

    Meyer, Karin

    2007-11-01

    WOMBAT is a software package for quantitative genetic analyses of continuous traits, fitting a linear, mixed model; estimates of covariance components and the resulting genetic parameters are obtained by restricted maximum likelihood. A wide range of models, comprising numerous traits, multiple fixed and random effects, selected genetic covariance structures, random regression models and reduced rank estimation are accommodated. WOMBAT employs up-to-date numerical and computational methods. Together with the use of efficient compilers, this generates fast executable programs, suitable for large scale analyses. Use of WOMBAT is illustrated for a bivariate analysis. The package consists of the executable program, available for LINUX and WINDOWS environments, manual and a set of worked example, and can be downloaded free of charge from (http://agbu. une.edu.au/~kmeyer/wombat.html).

  13. Quantitative autistic trait measurements index background genetic risk for ASD in Hispanic families.

    Science.gov (United States)

    Page, Joshua; Constantino, John Nicholas; Zambrana, Katherine; Martin, Eden; Tunc, Ilker; Zhang, Yi; Abbacchi, Anna; Messinger, Daniel

    2016-01-01

    Recent studies have indicated that quantitative autistic traits (QATs) of parents reflect inherited liabilities that may index background genetic risk for clinical autism spectrum disorder (ASD) in their offspring. Moreover, preferential mating for QATs has been observed as a potential factor in concentrating autistic liabilities in some families across generations. Heretofore, intergenerational studies of QATs have focused almost exclusively on Caucasian populations-the present study explored these phenomena in a well-characterized Hispanic population. The present study examined QAT scores in siblings and parents of 83 Hispanic probands meeting research diagnostic criteria for ASD, and 64 non-ASD controls, using the Social Responsiveness Scale-2 (SRS-2). Ancestry of the probands was characterized by genotype, using information from 541,929 single nucleotide polymorphic markers. In families of Hispanic children with an ASD diagnosis, the pattern of quantitative trait correlations observed between ASD-affected children and their first-degree relatives (ICCs on the order of 0.20), between unaffected first-degree relatives in ASD-affected families (sibling/mother ICC = 0.36; sibling/father ICC = 0.53), and between spouses (mother/father ICC = 0.48) were in keeping with the influence of transmitted background genetic risk and strong preferential mating for variation in quantitative autistic trait burden. Results from analysis of ancestry-informative genetic markers among probands in this sample were consistent with that from other Hispanic populations. Quantitative autistic traits represent measurable indices of inherited liability to ASD in Hispanic families. The accumulation of autistic traits occurs within generations, between spouses, and across generations, among Hispanic families affected by ASD. The occurrence of preferential mating for QATs-the magnitude of which may vary across cultures-constitutes a mechanism by which background genetic liability

  14. Estimation of genetic parameters and their sampling variances for quantitative traits in the type 2 modified augmented design

    Institute of Scientific and Technical Information of China (English)

    Frank M. You; Qijian Song; Gaofeng Jia; Yanzhao Cheng; Scott Duguid; Helen Booker; Sylvie Cloutier

    2016-01-01

    The type 2 modified augmented design (MAD2) is an efficient unreplicated experimental design used for evaluating large numbers of lines in plant breeding and for assessing genetic variation in a population. Statistical methods and data adjustment for soil heterogeneity have been previously described for this design. In the absence of replicated test genotypes in MAD2, their total variance cannot be partitioned into genetic and error components as required to estimate heritability and genetic correlation of quantitative traits, the two conventional genetic parameters used for breeding selection. We propose a method of estimating the error variance of unreplicated genotypes that uses replicated controls, and then of estimating the genetic parameters. Using the Delta method, we also derived formulas for estimating the sampling variances of the genetic parameters. Computer simulations indicated that the proposed method for estimating genetic parameters and their sampling variances was feasible and the reliability of the estimates was positively associated with the level of heritability of the trait. A case study of estimating the genetic parameters of three quantitative traits, iodine value, oil content, and linolenic acid content, in a biparental recombinant inbred line population of flax with 243 individuals, was conducted using our statistical models. A joint analysis of data over multiple years and sites was suggested for genetic parameter estimation. A pipeline module using SAS and Perl was developed to facilitate data analysis and appended to the previously developed MAD data analysis pipeline (http://probes.pw.usda.gov/bioinformatics_ tools/MADPipeline/index.html).

  15. Estimation of genetic parameters and their sampling variances for quantitative traits in the type 2 modified augmented design

    Institute of Scientific and Technical Information of China (English)

    Frank M.You; Qijian Song; Gaofeng Jia; Yanzhao Cheng; Scott Duguid; Helen Booker; Sylvie Cloutier

    2016-01-01

    The type 2 modified augmented design(MAD2) is an efficient unreplicated experimental design used for evaluating large numbers of lines in plant breeding and for assessing genetic variation in a population. Statistical methods and data adjustment for soil heterogeneity have been previously described for this design. In the absence of replicated test genotypes in MAD2, their total variance cannot be partitioned into genetic and error components as required to estimate heritability and genetic correlation of quantitative traits, the two conventional genetic parameters used for breeding selection. We propose a method of estimating the error variance of unreplicated genotypes that uses replicated controls, and then of estimating the genetic parameters. Using the Delta method, we also derived formulas for estimating the sampling variances of the genetic parameters.Computer simulations indicated that the proposed method for estimating genetic parameters and their sampling variances was feasible and the reliability of the estimates was positively associated with the level of heritability of the trait. A case study of estimating the genetic parameters of three quantitative traits, iodine value, oil content, and linolenic acid content, in a biparental recombinant inbred line population of flax with 243 individuals, was conducted using our statistical models. A joint analysis of data over multiple years and sites was suggested for genetic parameter estimation. A pipeline module using SAS and Perl was developed to facilitate data analysis and appended to the previously developed MAD data analysis pipeline(http://probes.pw.usda.gov/bioinformatics_ tools/MADPipeline/index.html).

  16. Estimation of genetic parameters and their sampling variances for quantitative traits in the type 2 modified augmented design

    Directory of Open Access Journals (Sweden)

    Frank M. You

    2016-04-01

    Full Text Available The type 2 modified augmented design (MAD2 is an efficient unreplicated experimental design used for evaluating large numbers of lines in plant breeding and for assessing genetic variation in a population. Statistical methods and data adjustment for soil heterogeneity have been previously described for this design. In the absence of replicated test genotypes in MAD2, their total variance cannot be partitioned into genetic and error components as required to estimate heritability and genetic correlation of quantitative traits, the two conventional genetic parameters used for breeding selection. We propose a method of estimating the error variance of unreplicated genotypes that uses replicated controls, and then of estimating the genetic parameters. Using the Delta method, we also derived formulas for estimating the sampling variances of the genetic parameters. Computer simulations indicated that the proposed method for estimating genetic parameters and their sampling variances was feasible and the reliability of the estimates was positively associated with the level of heritability of the trait. A case study of estimating the genetic parameters of three quantitative traits, iodine value, oil content, and linolenic acid content, in a biparental recombinant inbred line population of flax with 243 individuals, was conducted using our statistical models. A joint analysis of data over multiple years and sites was suggested for genetic parameter estimation. A pipeline module using SAS and Perl was developed to facilitate data analysis and appended to the previously developed MAD data analysis pipeline (http://probes.pw.usda.gov/bioinformatics_ tools/MADPipeline/index.html.

  17. A comparison of strategies for Markov chain Monte Carlo computation in quantitative genetics

    DEFF Research Database (Denmark)

    Waagepetersen, Rasmus; Ibánez-Escriche, Noelia; Sorensen, Daniel

    2008-01-01

    In quantitative genetics, Markov chain Monte Carlo (MCMC) methods are indispensable for statistical inference in non-standard models like generalized linear models with genetic random effects or models with genetically structured variance heterogeneity. A particular challenge for MCMC applications...... in quantitative genetics is to obtain efficient updates of the high-dimensional vectors of genetic random effects and the associated covariance parameters. We discuss various strategies to approach this problem including reparameterization, Langevin-Hastings updates, and updates based on normal approximations....... The methods are compared in applications to Bayesian inference for three data sets using a model with genetically structured variance heterogeneity...

  18. Structural model analysis of multiple quantitative traits.

    Directory of Open Access Journals (Sweden)

    Renhua Li

    2006-07-01

    Full Text Available We introduce a method for the analysis of multilocus, multitrait genetic data that provides an intuitive and precise characterization of genetic architecture. We show that it is possible to infer the magnitude and direction of causal relationships among multiple correlated phenotypes and illustrate the technique using body composition and bone density data from mouse intercross populations. Using these techniques we are able to distinguish genetic loci that affect adiposity from those that affect overall body size and thus reveal a shortcoming of standardized measures such as body mass index that are widely used in obesity research. The identification of causal networks sheds light on the nature of genetic heterogeneity and pleiotropy in complex genetic systems.

  19. Factors affecting the development of genetic testing service by using quantitative SWOT analysis%定量态势分析法分析我国基因检测服务发展影响因素的研究

    Institute of Scientific and Technical Information of China (English)

    包鹤龄; 王红漫

    2011-01-01

    目的 研究我国以基因组技术为基础的基因检测服务发展影响因素及发展策略.方法 通过目的 抽样的方法选择基因组学和基因检测领域相关专家,对11名专家进行深入访谈并设计问卷,通过调查问卷获取25名专家的数据信息,态势分析法、层次分析法、内部因素评价矩阵和外部因素评价矩阵相结合的定量态势分析法进行数据分析,随机一致性比率(CR)检验逻辑一致性(CR<10%).结果 共确定15项关键影响因素,其中重要性排在前三位的分别是法律与市场规范缺失、国家已出台政策扶持和缺少知识产权保护,权重分别为0.099、0.091和0.087,国内基因检测服务发展处于战略态势图的第三象限.结论 国内基因检测服务发展宜采取防御性战略,回避外部威胁,克服自身缺点,降低基因检测所带来的风险.%Objective To analyze the factors affecting the development of genome technology-based genetic testing services. Methods Purposive sampling was used to select experts in the field of genome or genetic testing. Following interview with 11 experts,data was obtained from 25 individuals and analyzed by using quantitative SWOT analysis, including the concept of SWOT method, Analytic Hierarchy Process,Internal Factor Evaluation ( IFE ) Matrix, and External Factor Evaluation ( EFE ) Matrix. Consistent ratio (CR) was chosen to test the logic. Results Of the 15 critical affecting factors, the weighting coefficient of deficiency of laws and market regulations, state supporting policies, and lack of intellectual property protection was 0. 099,0. 091 and 0. 087, respectively. The development of genetic testing services was found in the third quadrant of SWOT analysis. Conclusion These findings suggest that defensive strategy should be taken to improve genetic testing services and to reduce the risk of genetic testing.

  20. Quantitative histogram analysis of images

    Science.gov (United States)

    Holub, Oliver; Ferreira, Sérgio T.

    2006-11-01

    A routine for histogram analysis of images has been written in the object-oriented, graphical development environment LabVIEW. The program converts an RGB bitmap image into an intensity-linear greyscale image according to selectable conversion coefficients. This greyscale image is subsequently analysed by plots of the intensity histogram and probability distribution of brightness, and by calculation of various parameters, including average brightness, standard deviation, variance, minimal and maximal brightness, mode, skewness and kurtosis of the histogram and the median of the probability distribution. The program allows interactive selection of specific regions of interest (ROI) in the image and definition of lower and upper threshold levels (e.g., to permit the removal of a constant background signal). The results of the analysis of multiple images can be conveniently saved and exported for plotting in other programs, which allows fast analysis of relatively large sets of image data. The program file accompanies this manuscript together with a detailed description of two application examples: The analysis of fluorescence microscopy images, specifically of tau-immunofluorescence in primary cultures of rat cortical and hippocampal neurons, and the quantification of protein bands by Western-blot. The possibilities and limitations of this kind of analysis are discussed. Program summaryTitle of program: HAWGC Catalogue identifier: ADXG_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADXG_v1_0 Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Computers: Mobile Intel Pentium III, AMD Duron Installations: No installation necessary—Executable file together with necessary files for LabVIEW Run-time engine Operating systems or monitors under which the program has been tested: WindowsME/2000/XP Programming language used: LabVIEW 7.0 Memory required to execute with typical data:˜16MB for starting and ˜160MB used for

  1. Entering the second century of maize quantitative genetics

    Science.gov (United States)

    Maize is the most widely grown cereal in the world. In addition to its role in global agriculture, it has also long served as a model organism for genetic research. Maize stands at a genetic crossroads, as it has access to all the tools available for plant genetics but exhibits a genetic architectur...

  2. Quantitative estimation of activity and quality for collections of functional genetic elements.

    Science.gov (United States)

    Mutalik, Vivek K; Guimaraes, Joao C; Cambray, Guillaume; Mai, Quynh-Anh; Christoffersen, Marc Juul; Martin, Lance; Yu, Ayumi; Lam, Colin; Rodriguez, Cesar; Bennett, Gaymon; Keasling, Jay D; Endy, Drew; Arkin, Adam P

    2013-04-01

    The practice of engineering biology now depends on the ad hoc reuse of genetic elements whose precise activities vary across changing contexts. Methods are lacking for researchers to affordably coordinate the quantification and analysis of part performance across varied environments, as needed to identify, evaluate and improve problematic part types. We developed an easy-to-use analysis of variance (ANOVA) framework for quantifying the performance of genetic elements. For proof of concept, we assembled and analyzed combinations of prokaryotic transcription and translation initiation elements in Escherichia coli. We determined how estimation of part activity relates to the number of unique element combinations tested, and we show how to estimate expected ensemble-wide part activity from just one or two measurements. We propose a new statistic, biomolecular part 'quality', for tracking quantitative variation in part performance across changing contexts.

  3. Spotsizer: High-throughput quantitative analysis of microbial growth

    Science.gov (United States)

    Jeffares, Daniel C.; Arzhaeva, Yulia; Bähler, Jürg

    2017-01-01

    Microbial colony growth can serve as a useful readout in assays for studying complex genetic interactions or the effects of chemical compounds. Although computational tools for acquiring quantitative measurements of microbial colonies have been developed, their utility can be compromised by inflexible input image requirements, non-trivial installation procedures, or complicated operation. Here, we present the Spotsizer software tool for automated colony size measurements in images of robotically arrayed microbial colonies. Spotsizer features a convenient graphical user interface (GUI), has both single-image and batch-processing capabilities, and works with multiple input image formats and different colony grid types. We demonstrate how Spotsizer can be used for high-throughput quantitative analysis of fission yeast growth. The user-friendly Spotsizer tool provides rapid, accurate, and robust quantitative analyses of microbial growth in a high-throughput format. Spotsizer is freely available at https://data.csiro.au/dap/landingpage?pid=csiro:15330 under a proprietary CSIRO license. PMID:27712582

  4. Validation of PCR methods for quantitation of genetically modified plants in food.

    Science.gov (United States)

    Hübner, P; Waiblinger, H U; Pietsch, K; Brodmann, P

    2001-01-01

    For enforcement of the recently introduced labeling threshold for genetically modified organisms (GMOs) in food ingredients, quantitative detection methods such as quantitative competitive (QC-PCR) and real-time PCR are applied by official food control laboratories. The experiences of 3 European food control laboratories in validating such methods were compared to describe realistic performance characteristics of quantitative PCR detection methods. The limit of quantitation (LOQ) of GMO-specific, real-time PCR was experimentally determined to reach 30-50 target molecules, which is close to theoretical prediction. Starting PCR with 200 ng genomic plant DNA, the LOQ depends primarily on the genome size of the target plant and ranges from 0.02% for rice to 0.7% for wheat. The precision of quantitative PCR detection methods, expressed as relative standard deviation (RSD), varied from 10 to 30%. Using Bt176 corn containing test samples and applying Bt176 specific QC-PCR, mean values deviated from true values by -7to 18%, with an average of 2+/-10%. Ruggedness of real-time PCR detection methods was assessed in an interlaboratory study analyzing commercial, homogeneous food samples. Roundup Ready soybean DNA contents were determined in the range of 0.3 to 36%, relative to soybean DNA, with RSDs of about 25%. Taking the precision of quantitative PCR detection methods into account, suitable sample plans and sample sizes for GMO analysis are suggested. Because quantitative GMO detection methods measure GMO contents of samples in relation to reference material (calibrants), high priority must be given to international agreements and standardization on certified reference materials.

  5. Christhin: Quantitative Analysis of Thin Layer Chromatography

    CERN Document Server

    Barchiesi, Maximiliano; Renaudo, Carlos; Rossi, Pablo; Pramparo, María de Carmen; Nepote, Valeria; Grosso, Nelson Ruben; Gayol, María Fernanda

    2012-01-01

    Manual for Christhin 0.1.36 Christhin (Chromatography Riser Thin) is software developed for the quantitative analysis of data obtained from thin-layer chromatographic techniques (TLC). Once installed on your computer, the program is very easy to use, and provides data quickly and accurately. This manual describes the program, and reading should be enough to use it properly.

  6. Quantitative texture analysis of electrodeposited line patterns

    DEFF Research Database (Denmark)

    Pantleon, Karen; Somers, Marcel A.J.

    2005-01-01

    Free-standing line patterns of Cu and Ni were manufactured by electrochemical deposition into lithographically prepared patterns. Electrodeposition was carried out on top of a highly oriented Au-layer physically vapor deposited on glass. Quantitative texture analysis carried out by means of x...

  7. Quantitative texture analysis of electrodeposited line patterns

    DEFF Research Database (Denmark)

    Pantleon, Karen; Somers, Marcel A.J.

    2005-01-01

    Free-standing line patterns of Cu and Ni were manufactured by electrochemical deposition into lithographically prepared patterns. Electrodeposition was carried out on top of a highly oriented Au-layer physically vapor deposited on glass. Quantitative texture analysis carried out by means of x...

  8. Quantitative analysis of arm movement smoothness

    Science.gov (United States)

    Szczesna, Agnieszka; Błaszczyszyn, Monika

    2017-07-01

    The paper deals with the problem of motion data quantitative smoothness analysis. We investigated values of movement unit, fluidity and jerk for healthy and paralyzed arm of patients with hemiparesis after stroke. Patients were performing drinking task. To validate the approach, movement of 24 patients were captured using optical motion capture system.

  9. Seniors' Online Communities: A Quantitative Content Analysis

    Science.gov (United States)

    Nimrod, Galit

    2010-01-01

    Purpose: To examine the contents and characteristics of seniors' online communities and to explore their potential benefits to older adults. Design and Methods: Quantitative content analysis of a full year's data from 14 leading online communities using a novel computerized system. The overall database included 686,283 messages. Results: There was…

  10. A quantitative approach to scar analysis.

    Science.gov (United States)

    Khorasani, Hooman; Zheng, Zhong; Nguyen, Calvin; Zara, Janette; Zhang, Xinli; Wang, Joyce; Ting, Kang; Soo, Chia

    2011-02-01

    Analysis of collagen architecture is essential to wound healing research. However, to date no consistent methodologies exist for quantitatively assessing dermal collagen architecture in scars. In this study, we developed a standardized approach for quantitative analysis of scar collagen morphology by confocal microscopy using fractal dimension and lacunarity analysis. Full-thickness wounds were created on adult mice, closed by primary intention, and harvested at 14 days after wounding for morphometrics and standard Fourier transform-based scar analysis as well as fractal dimension and lacunarity analysis. In addition, transmission electron microscopy was used to evaluate collagen ultrastructure. We demonstrated that fractal dimension and lacunarity analysis were superior to Fourier transform analysis in discriminating scar versus unwounded tissue in a wild-type mouse model. To fully test the robustness of this scar analysis approach, a fibromodulin-null mouse model that heals with increased scar was also used. Fractal dimension and lacunarity analysis effectively discriminated unwounded fibromodulin-null versus wild-type skin as well as healing fibromodulin-null versus wild-type wounds, whereas Fourier transform analysis failed to do so. Furthermore, fractal dimension and lacunarity data also correlated well with transmission electron microscopy collagen ultrastructure analysis, adding to their validity. These results demonstrate that fractal dimension and lacunarity are more sensitive than Fourier transform analysis for quantification of scar morphology. Copyright © 2011 American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.

  11. Multiple mating but not recombination causes quantitative increase in offspring genetic diversity for varying genetic architectures.

    Directory of Open Access Journals (Sweden)

    Olav Rueppell

    Full Text Available Explaining the evolution of sex and recombination is particularly intriguing for some species of eusocial insects because they display exceptionally high mating frequencies and genomic recombination rates. Explanations for both phenomena are based on the notion that both increase colony genetic diversity, with demonstrated benefits for colony disease resistance and division of labor. However, the relative contributions of mating number and recombination rate to colony genetic diversity have never been simultaneously assessed. Our study simulates colonies, assuming different mating numbers, recombination rates, and genetic architectures, to assess their worker genotypic diversity. The number of loci has a strong negative effect on genotypic diversity when the allelic effects are inversely scaled to locus number. In contrast, dominance, epistasis, lethal effects, or limiting the allelic diversity at each locus does not significantly affect the model outcomes. Mating number increases colony genotypic variance and lowers variation among colonies with quickly diminishing returns. Genomic recombination rate does not affect intra- and inter-colonial genotypic variance, regardless of mating frequency and genetic architecture. Recombination slightly increases the genotypic range of colonies and more strongly the number of workers with unique allele combinations across all loci. Overall, our study contradicts the argument that the exceptionally high recombination rates cause a quantitative increase in offspring genotypic diversity across one generation. Alternative explanations for the evolution of high recombination rates in social insects are therefore needed. Short-term benefits are central to most explanations of the evolution of multiple mating and high recombination rates in social insects but our results also apply to other species.

  12. EvolQG - An R package for evolutionary quantitative genetics [version 2; referees: 1 approved, 2 approved with reservations

    Directory of Open Access Journals (Sweden)

    Diogo Melo

    2016-06-01

    Full Text Available We present an open source package for performing evolutionary quantitative genetics analyses in the R environment for statistical computing. Evolutionary theory shows that evolution depends critically on the available variation in a given population. When dealing with many quantitative traits this variation is expressed in the form of a covariance matrix, particularly the additive genetic covariance matrix or sometimes the phenotypic matrix, when the genetic matrix is unavailable and there is evidence the phenotypic matrix is sufficiently similar to the genetic matrix. Given this mathematical representation of available variation, the EvolQG package provides functions for calculation of relevant evolutionary statistics; estimation of sampling error; corrections for this error; matrix comparison via correlations, distances and matrix decomposition; analysis of modularity patterns; and functions for testing evolutionary hypotheses on taxa diversification.

  13. Attitudes towards genetic testing: analysis of contradictions

    DEFF Research Database (Denmark)

    Jallinoja, P; Hakonen, A; Aro, A R

    1998-01-01

    A survey study was conducted among 1169 people to evaluate attitudes towards genetic testing in Finland. Here we present an analysis of the contradictions detected in people's attitudes towards genetic testing. This analysis focuses on the approval of genetic testing as an individual choice...... and on the confidence in control of the process of genetic testing and its implications. Our analysis indicated that some of the respondents have contradictory attitudes towards genetic testing. It is proposed that contradictory attitudes towards genetic testing should be given greater significance both in scientific...... studies on attitudes towards genetic testing as well as in the health care context, e.g. in genetic counselling....

  14. Multiple quantitative trait analysis using bayesian networks.

    Science.gov (United States)

    Scutari, Marco; Howell, Phil; Balding, David J; Mackay, Ian

    2014-09-01

    Models for genome-wide prediction and association studies usually target a single phenotypic trait. However, in animal and plant genetics it is common to record information on multiple phenotypes for each individual that will be genotyped. Modeling traits individually disregards the fact that they are most likely associated due to pleiotropy and shared biological basis, thus providing only a partial, confounded view of genetic effects and phenotypic interactions. In this article we use data from a Multiparent Advanced Generation Inter-Cross (MAGIC) winter wheat population to explore Bayesian networks as a convenient and interpretable framework for the simultaneous modeling of multiple quantitative traits. We show that they are equivalent to multivariate genetic best linear unbiased prediction (GBLUP) and that they are competitive with single-trait elastic net and single-trait GBLUP in predictive performance. Finally, we discuss their relationship with other additive-effects models and their advantages in inference and interpretation. MAGIC populations provide an ideal setting for this kind of investigation because the very low population structure and large sample size result in predictive models with good power and limited confounding due to relatedness.

  15. Complex pedigree analysis to detect quantitative trait loci in dairy cattle.

    NARCIS (Netherlands)

    Bink, M.C.A.M.

    1998-01-01

    In dairy cattle, many quantitative traits of economic importance show phenotypic variation. For breeding purposes the analysis of this phenotypic variation and uncovering the contribution of genetic factors is very important. Usually, the individual gene effects contributing to the quantitative gene

  16. Functional genomics bridges the gap between quantitative genetics and molecular biology.

    Science.gov (United States)

    Lappalainen, Tuuli

    2015-10-01

    Deep characterization of molecular function of genetic variants in the human genome is becoming increasingly important for understanding genetic associations to disease and for learning to read the regulatory code of the genome. In this paper, I discuss how recent advances in both quantitative genetics and molecular biology have contributed to understanding functional effects of genetic variants, lessons learned from eQTL studies, and future challenges in this field.

  17. Quantitative genetics of functional characters in Drosophila melanogaster populations subjected to laboratory selection

    Indian Academy of Sciences (India)

    Henrique Teotónio; Margarida Matos; Michael R. Rose

    2004-12-01

    What are the genetics of phenotypes other than fitness, in outbred populations? To answer this question, the quantitative-genetic basis of divergence was characterized for outbred Drosophila melanogaster populations that had previously undergone selection to enhance characters related to fitness. Line-cross analysis using first-generation and second-generation hybrids from reciprocal crosses was conducted for two types of cross, each replicated fivefold. One type of cross was between representatives of the ancestral population, a set of five populations maintained for several hundred generations on a two-week discrete-generation life cycle and a set of five populations adapted to starvation stress. The other type of cross was between the same set of ancestral-representative populations and another set of five populations selected for accelerated development from egg to egg. Developmental time from egg to eclosion, starvation resistance, dry body weight and fecundity at day 14 from egg were fit to regression models estimating single-locus additive and dominant effects, maternal and paternal effects, and digenic additive and dominance epistatic effects. Additive genetic variation explained most of the differences between populations, with additive maternal and cytoplasmic effects also commonly found. Both within-locus and between-locus dominance effects were inferred in some cases, as well as one instance of additive epistasis. Some of these effects may have been caused by linkage disequilibrium. We conclude with a brief discussion concerning the relationship of the genetics of population differentiation to adaptation.

  18. Quantitative image analysis of celiac disease.

    Science.gov (United States)

    Ciaccio, Edward J; Bhagat, Govind; Lewis, Suzanne K; Green, Peter H

    2015-03-07

    We outline the use of quantitative techniques that are currently used for analysis of celiac disease. Image processing techniques can be useful to statistically analyze the pixular data of endoscopic images that is acquired with standard or videocapsule endoscopy. It is shown how current techniques have evolved to become more useful for gastroenterologists who seek to understand celiac disease and to screen for it in suspected patients. New directions for focus in the development of methodology for diagnosis and treatment of this disease are suggested. It is evident that there are yet broad areas where there is potential to expand the use of quantitative techniques for improved analysis in suspected or known celiac disease patients.

  19. Quantitative image analysis of celiac disease

    Science.gov (United States)

    Ciaccio, Edward J; Bhagat, Govind; Lewis, Suzanne K; Green, Peter H

    2015-01-01

    We outline the use of quantitative techniques that are currently used for analysis of celiac disease. Image processing techniques can be useful to statistically analyze the pixular data of endoscopic images that is acquired with standard or videocapsule endoscopy. It is shown how current techniques have evolved to become more useful for gastroenterologists who seek to understand celiac disease and to screen for it in suspected patients. New directions for focus in the development of methodology for diagnosis and treatment of this disease are suggested. It is evident that there are yet broad areas where there is potential to expand the use of quantitative techniques for improved analysis in suspected or known celiac disease patients. PMID:25759524

  20. Using Qualitative Hazard Analysis to Guide Quantitative Safety Analysis

    Science.gov (United States)

    Shortle, J. F.; Allocco, M.

    2005-01-01

    Quantitative methods can be beneficial in many types of safety investigations. However, there are many difficulties in using quantitative m ethods. Far example, there may be little relevant data available. This paper proposes a framework for using quantitative hazard analysis to prioritize hazard scenarios most suitable for quantitative mziysis. The framework first categorizes hazard scenarios by severity and likelihood. We then propose another metric "modeling difficulty" that desc ribes the complexity in modeling a given hazard scenario quantitatively. The combined metrics of severity, likelihood, and modeling difficu lty help to prioritize hazard scenarios for which quantitative analys is should be applied. We have applied this methodology to proposed concepts of operations for reduced wake separation for airplane operatio ns at closely spaced parallel runways.

  1. Influence analysis in quantitative trait loci detection.

    Science.gov (United States)

    Dou, Xiaoling; Kuriki, Satoshi; Maeno, Akiteru; Takada, Toyoyuki; Shiroishi, Toshihiko

    2014-07-01

    This paper presents systematic methods for the detection of influential individuals that affect the log odds (LOD) score curve. We derive general formulas of influence functions for profile likelihoods and introduce them into two standard quantitative trait locus detection methods-the interval mapping method and single marker analysis. Besides influence analysis on specific LOD scores, we also develop influence analysis methods on the shape of the LOD score curves. A simulation-based method is proposed to assess the significance of the influence of the individuals. These methods are shown useful in the influence analysis of a real dataset of an experimental population from an F2 mouse cross. By receiver operating characteristic analysis, we confirm that the proposed methods show better performance than existing diagnostics.

  2. Quantitative resilience analysis through control design.

    Energy Technology Data Exchange (ETDEWEB)

    Sunderland, Daniel; Vugrin, Eric D.; Camphouse, Russell Chris (Sandia National Laboratories, Carlsbad, NM)

    2009-09-01

    Critical infrastructure resilience has become a national priority for the U. S. Department of Homeland Security. System resilience has been studied for several decades in many different disciplines, but no standards or unifying methods exist for critical infrastructure resilience analysis. Few quantitative resilience methods exist, and those existing approaches tend to be rather simplistic and, hence, not capable of sufficiently assessing all aspects of critical infrastructure resilience. This report documents the results of a late-start Laboratory Directed Research and Development (LDRD) project that investigated the development of quantitative resilience through application of control design methods. Specifically, we conducted a survey of infrastructure models to assess what types of control design might be applicable for critical infrastructure resilience assessment. As a result of this survey, we developed a decision process that directs the resilience analyst to the control method that is most likely applicable to the system under consideration. Furthermore, we developed optimal control strategies for two sets of representative infrastructure systems to demonstrate how control methods could be used to assess the resilience of the systems to catastrophic disruptions. We present recommendations for future work to continue the development of quantitative resilience analysis methods.

  3. Genotype-by-environment interaction in genetic mapping of multiple quantitative trait loci

    NARCIS (Netherlands)

    Jansen, R.C.; Ooijen, J.W. van; Stam, P.; Lister, C.; Dean, C.

    1995-01-01

    The interval mapping method is widely used for the genetic mapping of quantitative trait loci (QTLs), though true resolution of quantitative variation into QTLs is hampered with this method. Separation of QTLs is troublesome, because single-QTL is models are fitted. Further, genotype-by-environment

  4. Genetic mapping of quantitative trait loci in plants - a novel statistical approach.

    NARCIS (Netherlands)

    Jansen, R.C.

    1995-01-01

    Quantitative variation is a feature of many important traits such as yield, quality and disease resistance in crop plants and farm animals, and diseases in humans. The genetic mapping, understanding and manipulation of quantitative trait loci (QTLs) are therefore of prime importance. Only by using g

  5. Integrating Quantitative Genetics and Practical Aspects in a Fish Breeding Network in Denmark

    DEFF Research Database (Denmark)

    Meier, Kristian; Sørensen, Anders Christian; Norberg, Elise;

    simulations are given to show how different practical aspects of a breeding plan can be optimized. By combining quantitative genetic theory with current breeding practice we are able to optimize different breeding plans increasing genetic gain while controlling the level of inbreeding and building up...

  6. Contribution and perspectives of quantitative genetics to plant breeding in Brazil

    Directory of Open Access Journals (Sweden)

    Fernando Henrique Ribeiro Barrozo Toledo

    2012-12-01

    Full Text Available The purpose of this article is to show how quantitative genetics has contributed to the huge genetic progress obtained inplant breeding in Brazil in the last forty years. The information obtained through quantitative genetics has given Brazilian breedersthe possibility of responding to innumerable questions in their work in a much more informative way, such as the use or not of hybridcultivars, which segregating population to use, which breeding method to employ, alternatives for improving the efficiency of selectionprograms, and how to handle the data of progeny and/or cultivars evaluations to identify the most stable ones and thus improverecommendations.

  7. Genetic mapping of quantitative trait loci (QTLs) with effects on ...

    African Journals Online (AJOL)

    SERVER

    2008-02-05

    Feb 5, 2008 ... 2Department of Crop Protection and Environmental Biology, ... identify genetic loci associated with the expression of resistance to FTh. ... indicated that resistance to FTh may be controlled by ... population or to pyramid resistance into new populations. .... environment and human health (Eigenbrode and.

  8. A bivariate quantitative genetic model for a threshold trait and a survival trait

    Directory of Open Access Journals (Sweden)

    Damgaard Lars

    2006-11-01

    Full Text Available Abstract Many of the functional traits considered in animal breeding can be analyzed as threshold traits or survival traits with examples including disease traits, conformation scores, calving difficulty and longevity. In this paper we derive and implement a bivariate quantitative genetic model for a threshold character and a survival trait that are genetically and environmentally correlated. For the survival trait, we considered the Weibull log-normal animal frailty model. A Bayesian approach using Gibbs sampling was adopted in which model parameters were augmented with unobserved liabilities associated with the threshold trait. The fully conditional posterior distributions associated with parameters of the threshold trait reduced to well known distributions. For the survival trait the two baseline Weibull parameters were updated jointly by a Metropolis-Hastings step. The remaining model parameters with non-normalized fully conditional distributions were updated univariately using adaptive rejection sampling. The Gibbs sampler was tested in a simulation study and illustrated in a joint analysis of calving difficulty and longevity of dairy cattle. The simulation study showed that the estimated marginal posterior distributions covered well and placed high density to the true values used in the simulation of data. The data analysis of calving difficulty and longevity showed that genetic variation exists for both traits. The additive genetic correlation was moderately favorable with marginal posterior mean equal to 0.37 and 95% central posterior credibility interval ranging between 0.11 and 0.61. Therefore, this study suggests that selection for improving one of the two traits will be beneficial for the other trait as well.

  9. A bivariate quantitative genetic model for a threshold trait and a survival trait.

    Science.gov (United States)

    Damgaard, Lars Holm; Korsgaard, Inge Riis

    2006-01-01

    Many of the functional traits considered in animal breeding can be analyzed as threshold traits or survival traits with examples including disease traits, conformation scores, calving difficulty and longevity. In this paper we derive and implement a bivariate quantitative genetic model for a threshold character and a survival trait that are genetically and environmentally correlated. For the survival trait, we considered the Weibull log-normal animal frailty model. A Bayesian approach using Gibbs sampling was adopted in which model parameters were augmented with unobserved liabilities associated with the threshold trait. The fully conditional posterior distributions associated with parameters of the threshold trait reduced to well known distributions. For the survival trait the two baseline Weibull parameters were updated jointly by a Metropolis-Hastings step. The remaining model parameters with non-normalized fully conditional distributions were updated univariately using adaptive rejection sampling. The Gibbs sampler was tested in a simulation study and illustrated in a joint analysis of calving difficulty and longevity of dairy cattle. The simulation study showed that the estimated marginal posterior distributions covered well and placed high density to the true values used in the simulation of data. The data analysis of calving difficulty and longevity showed that genetic variation exists for both traits. The additive genetic correlation was moderately favorable with marginal posterior mean equal to 0.37 and 95% central posterior credibility interval ranging between 0.11 and 0.61. Therefore, this study suggests that selection for improving one of the two traits will be beneficial for the other trait as well.

  10. Inspection, visualisation and analysis of quantitative proteomics data

    OpenAIRE

    Gatto, Laurent

    2016-01-01

    Material Quantitative Proteomics and Data Analysis Course. 4 - 5 April 2016, Queen Hotel, Chester, UK Table D - Inspection, visualisation and analysis of quantitative proteomics data, Laurent Gatto (University of Cambridge)

  11. Quantitative genetics theory for non-inbred populations in linkage disequilibrium

    Directory of Open Access Journals (Sweden)

    José Marcelo Soriano Viana

    2004-01-01

    Full Text Available Although linkage disequilibrium, epistasis and inbreeding are common phenomena in genetic systems that control quantitative traits, theory development and analysis are very complex, especially when they are considered together. The objective of this study is to offer additional quantitative genetics theory to define and analyze, in relation to non-inbred cross pollinating populations, components of genotypic variance, heritabilities and predicted gains, assuming linkage disequilibrium and absence of epistasis. The genotypic variance and its components, additive and due to dominance genetic variances, are invariant over the generations only in regard to completely linked genes and to those in equilibrium. When the population is structured in half-sib families, the additive variance in the parents' generation and the genotypic variance in the population can be estimated. When the population is structured in full-sib families, none of the components of genotypic variance can be estimated. The narrow sense heritability level at plant level can be estimated from the parent-offspring or mid parent-offspring regression. When there is dominance, the narrow sense heritability estimate in the in F2 is biased due to linkage disequilibrium when estimated by the Warner method, but not when estimated by means of the plant F2-family F3 regression. The bias is proportional to the number of pairs of linked genes, without independent assortment, and to the degree of dominance, and tends to be positive when genes in the coupling phase predominate or negative and of higher value when genes in the repulsion phase predominate. Linkage disequilibrium is also cause of bias in estimates of the narrow sense heritabilities at full-sib family mean and at plant within half-sib and full-sib families levels. Generally, the magnitude of the bias is proportional to the number of pairs of genes in disequilibrium and to the frequency of recombining gametes.

  12. Functional Maps of Protein Complexes from Quantitative Genetic Interaction Data

    OpenAIRE

    Sourav Bandyopadhyay; Ryan Kelley; Krogan, Nevan J.; Trey Ideker

    2008-01-01

    Recently, a number of advanced screening technologies have allowed for the comprehensive quantification of aggravating and alleviating genetic interactions among gene pairs. In parallel, TAP-MS studies (tandem affinity purification followed by mass spectroscopy) have been successful at identifying physical protein interactions that can indicate proteins participating in the same molecular complex. Here, we propose a method for the joint learning of protein complexes and their functional relat...

  13. Arthritis Genetics Analysis Aids Drug Discovery

    Science.gov (United States)

    ... Matters NIH Research Matters January 13, 2014 Arthritis Genetics Analysis Aids Drug Discovery An international research team ... may play a role in triggering the disease. Genetic factors are also thought to play a role. ...

  14. Partial least squares modeling and genetic algorithm optimization in quantitative structure-activity relationships.

    Science.gov (United States)

    Hasegawa, K; Funatsu, K

    2000-01-01

    Quantitative structure-activity relationship (QSAR) studies based on chemometric techniques are reviewed. Partial least squares (PLS) is introduced as a novel robust method to replace classical methods such as multiple linear regression (MLR). Advantages of PLS compared to MLR are illustrated with typical applications. Genetic algorithm (GA) is a novel optimization technique which can be used as a search engine in variable selection. A novel hybrid approach comprising GA and PLS for variable selection developed in our group (GAPLS) is described. The more advanced method for comparative molecular field analysis (CoMFA) modeling called GA-based region selection (GARGS) is described as well. Applications of GAPLS and GARGS to QSAR and 3D-QSAR problems are shown with some representative examples. GA can be hybridized with nonlinear modeling methods such as artificial neural networks (ANN) for providing useful tools in chemometric and QSAR.

  15. Quantitative analysis of spirality in elliptical galaxies

    CERN Document Server

    Dojcsak, Levente

    2013-01-01

    We use an automated galaxy morphology analysis method to quantitatively measure the spirality of galaxies classified manually as elliptical. The data set used for the analysis consists of 60,518 galaxy images with redshift obtained by the Sloan Digital Sky Survey (SDSS) and classified manually by Galaxy Zoo, as well as the RC3 and NA10 catalogues. We measure the spirality of the galaxies by using the Ganalyzer method, which transforms the galaxy image to its radial intensity plot to detect galaxy spirality that is in many cases difficult to notice by manual observation of the raw galaxy image. Experimental results using manually classified elliptical and S0 galaxies with redshift <0.3 suggest that galaxies classified manually as elliptical and S0 exhibit a nonzero signal for the spirality. These results suggest that the human eye observing the raw galaxy image might not always be the most effective way of detecting spirality and curves in the arms of galaxies.

  16. Quantitative laryngeal electromyography: turns and amplitude analysis.

    Science.gov (United States)

    Statham, Melissa McCarty; Rosen, Clark A; Nandedkar, Sanjeev D; Munin, Michael C

    2010-10-01

    Laryngeal electromyography (LEMG) is primarily a qualitative examination, with no standardized approach to interpretation. The objectives of our study were to establish quantitative norms for motor unit recruitment in controls and to compare with interference pattern analysis in patients with unilateral vocal fold paralysis (VFP). Retrospective case-control study We performed LEMG of the thyroarytenoid-lateral cricoarytenoid muscle complex (TA-LCA) in 21 controls and 16 patients with unilateral VFP. Our standardized protocol used a concentric needle electrode with subjects performing variable force TA-LCA contraction. To quantify the interference pattern density, we measured turns and mean amplitude per turn for ≥10 epochs (each 500 milliseconds). Logarithmic regression analysis between amplitude and turns was used to calculate slope and intercept. Standard deviation was calculated to further define the confidence interval, enabling generation of a linear-scale graphical "cloud" of activity containing ≥90% of data points for controls and patients. Median age of controls and patients was similar (50.7 vs. 48.5 years). In controls, TA-LCA amplitude with variable contraction ranged from 145-1112 μV, and regression analysis comparing mean amplitude per turn to root-mean-square amplitude demonstrated high correlation (R = 0.82). In controls performing variable contraction, median turns per second was significantly higher compared to patients (450 vs. 290, P = .002). We first present interference pattern analysis in the TA-LCA in healthy adults and patients with unilateral VFP. Our findings indicate that motor unit recruitment can be quantitatively measured within the TA-LCA. Additionally, patients with unilateral VFP had significantly reduced turns when compared with controls.

  17. Genetic analysis of bleeding disorders.

    Science.gov (United States)

    Edison, E; Konkle, B A; Goodeve, A C

    2016-07-01

    Molecular genetic analysis of inherited bleeding disorders has been practised for over 30 years. Technological changes have enabled advances, from analyses using extragenic linked markers to next-generation DNA sequencing and microarray analysis. Two approaches for genetic analysis are described, each suiting their environment. The Christian Medical Centre in Vellore, India, uses conformation-sensitive gel electrophoresis mutation screening of multiplexed PCR products to identify candidate mutations, followed by Sanger sequencing confirmation of variants identified. Specific analyses for F8 intron 1 and 22 inversions are also undertaken. The MyLifeOurFuture US project between the American Thrombosis and Hemostasis Network, the National Hemophilia Foundation, Bloodworks Northwest and Biogen uses molecular inversion probes (MIP) to capture target exons, splice sites plus 5' and 3' sequences and to detect F8 intron 1 and 22 inversions. This allows screening for all F8 and F9 variants in one sequencing run of multiple samples (196 or 392). Sequence variants identified are subsequently confirmed by a diagnostic laboratory. After having identified variants in genes of interest through these processes, a systematic procedure determining their likely pathogenicity should be applied. Several scientific societies have prepared guidelines. Systematic analysis of the available evidence facilitates reproducible scoring of likely pathogenicity. Documentation of frequency in population databases of variant prevalence and in locus-specific mutation databases can provide initial information on likely pathogenicity. Whereas null mutations are often pathogenic, missense and splice site variants often require in silico analyses to predict likely pathogenicity and using an accepted suite of tools can help standardize their documentation.

  18. Microsatellite data analysis for population genetics.

    Science.gov (United States)

    Kim, Kyung Seok; Sappington, Thomas W

    2013-01-01

    Theories and analytical tools of population genetics have been widely applied for addressing various questions in the fields of ecological genetics, conservation biology, and any context where the role of dispersal or gene flow is important. Underlying much of population genetics is the analysis of variation at selectively neutral marker loci, and microsatellites continue to be a popular choice of marker. In recent decades, software programs to estimate population genetics parameters have been developed at an increasing pace as computational science and theoretical knowledge advance. Numerous population genetics software programs are presently available to analyze microsatellite genotype data, but only a handful are commonly employed for calculating parameters such as genetic variation, genetic structure, patterns of spatial and temporal gene flow, population demography, individual population assignment, and genetic relationships within and between populations. In this chapter, we introduce statistical analyses and relevant population genetic software programs that are commonly employed in the field of population genetics and molecular ecology.

  19. Multivariate analysis of quantitative traits can effectively classify rapeseed germplasm

    Directory of Open Access Journals (Sweden)

    Jankulovska Mirjana

    2014-01-01

    Full Text Available In this study, the use of different multivariate approaches to classify rapeseed genotypes based on quantitative traits has been presented. Tree regression analysis, PCA analysis and two-way cluster analysis were applied in order todescribe and understand the extent of genetic variability in spring rapeseed genotype by trait data. The traits which highly influenced seed and oil yield in rapeseed were successfully identified by the tree regression analysis. Principal predictor for both response variables was number of pods per plant (NP. NP and 1000 seed weight could help in the selection of high yielding genotypes. High values for both traits and oil content could lead to high oil yielding genotypes. These traits may serve as indirect selection criteria and can lead to improvement of seed and oil yield in rapeseed. Quantitative traits that explained most of the variability in the studied germplasm were classified using principal component analysis. In this data set, five PCs were identified, out of which the first three PCs explained 63% of the total variance. It helped in facilitating the choice of variables based on which the genotypes’ clustering could be performed. The two-way cluster analysissimultaneously clustered genotypes and quantitative traits. The final number of clusters was determined using bootstrapping technique. This approach provided clear overview on the variability of the analyzed genotypes. The genotypes that have similar performance regarding the traits included in this study can be easily detected on the heatmap. Genotypes grouped in the clusters 1 and 8 had high values for seed and oil yield, and relatively short vegetative growth duration period and those in cluster 9, combined moderate to low values for vegetative growth duration and moderate to high seed and oil yield. These genotypes should be further exploited and implemented in the rapeseed breeding program. The combined application of these multivariate methods

  20. Quantitative Analysis in Nuclear Medicine Imaging

    CERN Document Server

    2006-01-01

    This book provides a review of image analysis techniques as they are applied in the field of diagnostic and therapeutic nuclear medicine. Driven in part by the remarkable increase in computing power and its ready and inexpensive availability, this is a relatively new yet rapidly expanding field. Likewise, although the use of radionuclides for diagnosis and therapy has origins dating back almost to the discovery of natural radioactivity itself, radionuclide therapy and, in particular, targeted radionuclide therapy has only recently emerged as a promising approach for therapy of cancer and, to a lesser extent, other diseases. As effort has, therefore, been made to place the reviews provided in this book in a broader context. The effort to do this is reflected by the inclusion of introductory chapters that address basic principles of nuclear medicine imaging, followed by overview of issues that are closely related to quantitative nuclear imaging and its potential role in diagnostic and therapeutic applications. ...

  1. Automatic quantitative morphological analysis of interacting galaxies

    CERN Document Server

    Shamir, Lior; Wallin, John

    2013-01-01

    The large number of galaxies imaged by digital sky surveys reinforces the need for computational methods for analyzing galaxy morphology. While the morphology of most galaxies can be associated with a stage on the Hubble sequence, morphology of galaxy mergers is far more complex due to the combination of two or more galaxies with different morphologies and the interaction between them. Here we propose a computational method based on unsupervised machine learning that can quantitatively analyze morphologies of galaxy mergers and associate galaxies by their morphology. The method works by first generating multiple synthetic galaxy models for each galaxy merger, and then extracting a large set of numerical image content descriptors for each galaxy model. These numbers are weighted using Fisher discriminant scores, and then the similarities between the galaxy mergers are deduced using a variation of Weighted Nearest Neighbor analysis such that the Fisher scores are used as weights. The similarities between the ga...

  2. QTL analysis for some quantitative traits in bread wheat

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Quantitative trait loci (QTL) analysis was conducted in bread wheat for 14 important traits utilizing data from four different mapping populations involving different approaches of QTL analysis. Analysis for grain protein content (GPC) suggested that the major part of genetic variation for this trait is due to environmental interactions. In contrast, pre-harvest sprouting tolerance (PHST) was controlled mainly by main effect QTL (M-QTL) with very little genetic variation due to environmental interactions; a major QTL for PHST was detected on chromosome arm 3AL. For grain weight, one QTL each was detected on chromosome arms 1AS, 2BS and 7AS. QTL for 4 growth related traits taken together detected by different methods ranged from 37 to 40; nine QTL that were detected by single-locus as well as two-locus analyses were all M-QTL. Similarly, single-locus and two-locus QTL analyses for seven yield and yield contributing traits in two populations respectively allowed detection of 25 and 50 QTL by composite interval mapping (CIM), 16 and 25 QTL by multiple-trait composite interval mapping (MCIM) and 38 and 37 QTL by two-locus analyses. These studies should prove useful in QTL cloning and wheat improvement through marker aided selection.

  3. QuASAR: quantitative allele-specific analysis of reads.

    Science.gov (United States)

    Harvey, Chris T; Moyerbrailean, Gregory A; Davis, Gordon O; Wen, Xiaoquan; Luca, Francesca; Pique-Regi, Roger

    2015-04-15

    Expression quantitative trait loci (eQTL) studies have discovered thousands of genetic variants that regulate gene expression, enabling a better understanding of the functional role of non-coding sequences. However, eQTL studies are costly, requiring large sample sizes and genome-wide genotyping of each sample. In contrast, analysis of allele-specific expression (ASE) is becoming a popular approach to detect the effect of genetic variation on gene expression, even within a single individual. This is typically achieved by counting the number of RNA-seq reads matching each allele at heterozygous sites and testing the null hypothesis of a 1:1 allelic ratio. In principle, when genotype information is not readily available, it could be inferred from the RNA-seq reads directly. However, there are currently no existing methods that jointly infer genotypes and conduct ASE inference, while considering uncertainty in the genotype calls. We present QuASAR, quantitative allele-specific analysis of reads, a novel statistical learning method for jointly detecting heterozygous genotypes and inferring ASE. The proposed ASE inference step takes into consideration the uncertainty in the genotype calls, while including parameters that model base-call errors in sequencing and allelic over-dispersion. We validated our method with experimental data for which high-quality genotypes are available. Results for an additional dataset with multiple replicates at different sequencing depths demonstrate that QuASAR is a powerful tool for ASE analysis when genotypes are not available. http://github.com/piquelab/QuASAR. fluca@wayne.edu or rpique@wayne.edu Supplementary Material is available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  4. Microsatellite data analysis for population genetics

    Science.gov (United States)

    Theories and analytical tools of population genetics have been widely applied for addressing various questions in the fields of ecological genetics, conservation biology, and any context where the role of dispersal or gene flow is important. Underlying much of population genetics is the analysis of ...

  5. Parent-offspring conflict and co-adaptation: behavioural ecology meets quantitative genetics.

    Science.gov (United States)

    Smiseth, Per T; Wright, Jonathan; Kölliker, Mathias

    2008-08-22

    The evolution of the complex and dynamic behavioural interactions between caring parents and their dependent offspring is a major area of research in behavioural ecology and quantitative genetics. While behavioural ecologists examine the evolution of interactions between parents and offspring in the light of parent-offspring conflict and its resolution, quantitative geneticists explore the evolution of such interactions in the light of parent-offspring co-adaptation due to combined effects of parental and offspring behaviours on fitness. To date, there is little interaction or integration between these two fields. Here, we first review the merits and limitations of each of these two approaches and show that they provide important complementary insights into the evolution of strategies for offspring begging and parental resource provisioning. We then outline how central ideas from behavioural ecology and quantitative genetics can be combined within a framework based on the concept of behavioural reaction norms, which provides a common basis for behavioural ecologists and quantitative geneticists to study the evolution of parent-offspring interactions. Finally, we discuss how the behavioural reaction norm approach can be used to advance our understanding of parent-offspring conflict by combining information about the genetic basis of traits from quantitative genetics with key insights regarding the adaptive function and dynamic nature of parental and offspring behaviours from behavioural ecology.

  6. Nonlinear dynamics and quantitative EEG analysis.

    Science.gov (United States)

    Jansen, B H

    1996-01-01

    Quantitative, computerized electroencephalogram (EEG) analysis appears to be based on a phenomenological approach to EEG interpretation, and is primarily rooted in linear systems theory. A fundamentally different approach to computerized EEG analysis, however, is making its way into the laboratories. The basic idea, inspired by recent advances in the area of nonlinear dynamics and chaos theory, is to view an EEG as the output of a deterministic system of relatively simple complexity, but containing nonlinearities. This suggests that studying the geometrical dynamics of EEGs, and the development of neurophysiologically realistic models of EEG generation may produce more successful automated EEG analysis techniques than the classical, stochastic methods. A review of the fundamentals of chaos theory is provided. Evidence supporting the nonlinear dynamics paradigm to EEG interpretation is presented, and the kind of new information that can be extracted from the EEG is discussed. A case is made that a nonlinear dynamic systems viewpoint to EEG generation will profoundly affect the way EEG interpretation is currently done.

  7. Analysis of Variance Components for Genetic Markers with Unphased Genotypes.

    Science.gov (United States)

    Wang, Tao

    2016-01-01

    An ANOVA type general multi-allele (GMA) model was proposed in Wang (2014) on analysis of variance components for quantitative trait loci or genetic markers with phased or unphased genotypes. In this study, by applying the GMA model, we further examine estimation of the genetic variance components for genetic markers with unphased genotypes based on a random sample from a study population. In one locus and two loci cases, we first derive the least square estimates (LSE) of model parameters in fitting the GMA model. Then we construct estimators of the genetic variance components for one marker locus in a Hardy-Weinberg disequilibrium population and two marker loci in an equilibrium population. Meanwhile, we explore the difference between the classical general linear model (GLM) and GMA based approaches in association analysis of genetic markers with quantitative traits. We show that the GMA model can retain the same partition on the genetic variance components as the traditional Fisher's ANOVA model, while the GLM cannot. We clarify that the standard F-statistics based on the partial reductions in sums of squares from GLM for testing the fixed allelic effects could be inadequate for testing the existence of the variance component when allelic interactions are present. We point out that the GMA model can reduce the confounding between the allelic effects and allelic interactions at least for independent alleles. As a result, the GMA model could be more beneficial than GLM for detecting allelic interactions.

  8. Genetic and Molecular Network Analysis of Behavior

    OpenAIRE

    Williams, Robert W.; Mulligan, Megan K.

    2012-01-01

    This chapter provides an introduction into the genetic control and analysis of behavioral variation using powerful online resources. We introduce you to the new field of systems genetics using "case studies" drawn from the world of behavioral genetics that exploit populations of genetically diverse lines of mice. These lines differ very widely in patterns of gene and protein expression in the brain and in patterns of behavior. In this chapter we address the following set of related questions:...

  9. Estimating quantitative genetic parameters in wild populations: a comparison of pedigree and genomic approaches.

    Science.gov (United States)

    Bérénos, Camillo; Ellis, Philip A; Pilkington, Jill G; Pemberton, Josephine M

    2014-07-01

    The estimation of quantitative genetic parameters in wild populations is generally limited by the accuracy and completeness of the available pedigree information. Using relatedness at genomewide markers can potentially remove this limitation and lead to less biased and more precise estimates. We estimated heritability, maternal genetic effects and genetic correlations for body size traits in an unmanaged long-term study population of Soay sheep on St Kilda using three increasingly complete and accurate estimates of relatedness: (i) Pedigree 1, using observation-derived maternal links and microsatellite-derived paternal links; (ii) Pedigree 2, using SNP-derived assignment of both maternity and paternity; and (iii) whole-genome relatedness at 37 037 autosomal SNPs. In initial analyses, heritability estimates were strikingly similar for all three methods, while standard errors were systematically lower in analyses based on Pedigree 2 and genomic relatedness. Genetic correlations were generally strong, differed little between the three estimates of relatedness and the standard errors declined only very slightly with improved relatedness information. When partitioning maternal effects into separate genetic and environmental components, maternal genetic effects found in juvenile traits increased substantially across the three relatedness estimates. Heritability declined compared to parallel models where only a maternal environment effect was fitted, suggesting that maternal genetic effects are confounded with direct genetic effects and that more accurate estimates of relatedness were better able to separate maternal genetic effects from direct genetic effects. We found that the heritability captured by SNP markers asymptoted at about half the SNPs available, suggesting that denser marker panels are not necessarily required for precise and unbiased heritability estimates. Finally, we present guidelines for the use of genomic relatedness in future quantitative genetics

  10. Quantitative risk analysis preoperational of gas pipeline

    Energy Technology Data Exchange (ETDEWEB)

    Manfredi, Carlos; Bispo, Gustavo G.; Esteves, Alvaro [Gie S.A., Buenos Aires (Argentina)

    2009-07-01

    The purpose of this analysis is to predict how it can be affected the individual risk and the public's general security due to the operation of a gas pipeline. In case that the single or social risks are considered intolerable, compared with the international standards, to be recommended measures of mitigation of the risk associated to the operation until levels that can be considered compatible with the best practices in the industry. The quantitative risk analysis calculates the probability of occurrence of an event based on the frequency of occurrence of the same one and it requires a complex mathematical treatment. The present work has as objective to develop a calculation methodology based on the previously mentioned publication. This calculation methodology is centered in defining the frequencies of occurrence of events, according to representative database of each case in study. Besides, it settles down the consequences particularly according to the considerations of each area and the different possibilities of interferences with the gas pipeline in study. For each one of the interferences a typical curve of ignition probabilities is developed in function from the distance to the pipe. (author)

  11. Quantitative analysis of protein turnover in plants.

    Science.gov (United States)

    Nelson, Clark J; Li, Lei; Millar, A Harvey

    2014-03-01

    Proteins are constantly being synthesised and degraded as plant cells age and as plants grow, develop and adapt the proteome. Given that plants develop through a series of events from germination to fruiting and even undertake whole organ senescence, an understanding of protein turnover as a fundamental part of this process in plants is essential. Both synthesis and degradation processes are spatially separated in a cell across its compartmented structure. The majority of protein synthesis occurs in the cytosol, while synthesis of specific components occurs inside plastids and mitochondria. Degradation of proteins occurs in both the cytosol, through the action of the plant proteasome, and in organelles and lytic structures through different protease classes. Tracking the specific synthesis and degradation rate of individual proteins can be undertaken using stable isotope feeding and the ability of peptide MS to track labelled peptide fractions over time. Mathematical modelling can be used to follow the isotope signature of newly synthesised protein as it accumulates and natural abundance proteins as they are lost through degradation. Different technical and biological constraints govern the potential for the use of (13)C, (15)N, (2)H and (18)O for these experiments in complete labelling and partial labelling strategies. Future development of quantitative protein turnover analysis will involve analysis of protein populations in complexes and subcellular compartments, assessing the effect of PTMs and integrating turnover studies into wider system biology study of plants.

  12. WOMBAT——A tool for mixed model analyses in quantitative genetics by restricted maximum likelihood (REML)

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    WOMBAT is a software package for quantitative genetic analyses of continuous traits, fitting a linear, mixed model;estimates of covariance components and the resulting genetic parameters are obtained by restricted maximum likelihood. A wide range of models, comprising numerous traits, multiple fixed and random effects, selected genetic covariance structures, random regression models and reduced rank estimation are accommodated. WOMBAT employs up-to-date numerical and computational methods. Together with the use of efficient compilers, this generates fast executable programs, suitable for large scale analyses.Use of WOMBAT is illustrated for a bivariate analysis. The package consists of the executable program, available for LINUX and WINDOWS environments, manual and a set of worked example, and can be downloaded free of charge from http://agbu.une.edu.au/~kmeyer/wombat.html

  13. The current and future use of ridge regression for prediction in quantitative genetics

    NARCIS (Netherlands)

    R. de Vlaming (Ronald); P.J.F. Groenen (Patrick)

    2015-01-01

    textabstractIn recent years, there has been a considerable amount of research on the use of regularization methods for inference and prediction in quantitative genetics. Such research mostly focuses on selection of markers and shrinkage of their effects. In this review paper, the use of ridge

  14. Quantitative PCR for Detection and Enumeration of Genetic Markers of Bovine Fecal Pollution

    Science.gov (United States)

    Accurate assessment of health risks associated with bovine (cattle) fecal pollution requires a reliable host-specific genetic marker and a rapid quantification method. We report the development of quantitative PCR assays for the detection of two recently described cow feces-spec...

  15. Multilevel selection 1: Quantitative genetics of inheritance and response to selection

    NARCIS (Netherlands)

    Bijma, P.; Muir, W.M.; Arendonk, van J.A.M.

    2007-01-01

    Interaction among individuals is universal, both in animals and in plants, and substantially affects evolution of natural populations and responses to artificial selection in agriculture. Although quantitative genetics has successfully been applied to many traits, it does not provide a general theor

  16. Multiparent intercross populations in analysis of quantitative traits

    Indian Academy of Sciences (India)

    Sujay Rakshit; Arunita Rakshit; J. V. Patil

    2011-04-01

    Most traits of interest to medical, agricultural and animal scientists show continuous variation and complex mode of inheritance. DNA-based markers are being deployed to analyse such complex traits, that are known as quantitative trait loci (QTL). In conventional QTL analysis, F2, backcross populations, recombinant inbred lines, backcross inbred lines and double haploids from biparental crosses are commonly used. Introgression lines and near isogenic lines are also being used for QTL analysis. However, such populations have major limitations like predominantly relying on the recombination events taking place in the F1 generation and mapping of only the allelic pairs present in the two parents. The second generation mapping resources like association mapping, nested association mapping and multiparent intercross populations potentially address the major limitations of available mapping resources. The potential of multiparent intercross populations in gene mapping has been discussed here. In such populations both linkage and association analysis can be conductted without encountering the limitations of structured populations. In such populations, larger genetic variation in the germplasm is accessed and various allelic and cytoplasmic interactions are assessed. For all practical purposes, across crop species, use of eight founders and a fixed population of 1000 individuals are most appropriate. Limitations with multiparent intercross populations are that they require longer time and more resource to be generated and they are likely to show extensive segregation for developmental traits, limiting their use in the analysis of complex traits. However, multiparent intercross population resources are likely to bring a paradigm shift towards QTL analysis in plant species.

  17. Quantitative analysis of bristle number in Drosophila mutants identifies genes involved in neural development

    Science.gov (United States)

    Norga, Koenraad K.; Gurganus, Marjorie C.; Dilda, Christy L.; Yamamoto, Akihiko; Lyman, Richard F.; Patel, Prajal H.; Rubin, Gerald M.; Hoskins, Roger A.; Mackay, Trudy F.; Bellen, Hugo J.

    2003-01-01

    BACKGROUND: The identification of the function of all genes that contribute to specific biological processes and complex traits is one of the major challenges in the postgenomic era. One approach is to employ forward genetic screens in genetically tractable model organisms. In Drosophila melanogaster, P element-mediated insertional mutagenesis is a versatile tool for the dissection of molecular pathways, and there is an ongoing effort to tag every gene with a P element insertion. However, the vast majority of P element insertion lines are viable and fertile as homozygotes and do not exhibit obvious phenotypic defects, perhaps because of the tendency for P elements to insert 5' of transcription units. Quantitative genetic analysis of subtle effects of P element mutations that have been induced in an isogenic background may be a highly efficient method for functional genome annotation. RESULTS: Here, we have tested the efficacy of this strategy by assessing the extent to which screening for quantitative effects of P elements on sensory bristle number can identify genes affecting neural development. We find that such quantitative screens uncover an unusually large number of genes that are known to function in neural development, as well as genes with yet uncharacterized effects on neural development, and novel loci. CONCLUSIONS: Our findings establish the use of quantitative trait analysis for functional genome annotation through forward genetics. Similar analyses of quantitative effects of P element insertions will facilitate our understanding of the genes affecting many other complex traits in Drosophila.

  18. Applying Knowledge of Quantitative Design and Analysis

    Science.gov (United States)

    Baskas, Richard S.

    2011-01-01

    This study compared and contrasted two quantitative scholarly articles in relation to their research designs. Their designs were analyzed by the comparison of research references and research specific vocabulary to describe how various research methods were used. When researching and analyzing quantitative scholarly articles, it is imperative to…

  19. Investigation of the genetic association between quantitative measures of psychosis and schizophrenia

    DEFF Research Database (Denmark)

    Derks, Eske M; Vorstman, Jacob A S; Ripke, Stephan

    2012-01-01

    The presence of subclinical levels of psychosis in the general population may imply that schizophrenia is the extreme expression of more or less continuously distributed traits in the population. In a previous study, we identified five quantitative measures of schizophrenia (positive, negative......, disorganisation, mania, and depression scores). The aim of this study is to examine the association between a direct measure of genetic risk of schizophrenia and the five quantitative measures of psychosis. Estimates of the log of the odds ratios of case/control allelic association tests were obtained from...... the Psychiatric GWAS Consortium (PGC) (minus our sample) which included genome-wide genotype data of 8,690 schizophrenia cases and 11,831 controls. These data were used to calculate genetic risk scores in 314 schizophrenia cases and 148 controls from the Netherlands for whom genotype data and quantitative symptom...

  20. Quantitative color analysis for capillaroscopy image segmentation.

    Science.gov (United States)

    Goffredo, Michela; Schmid, Maurizio; Conforto, Silvia; Amorosi, Beatrice; D'Alessio, Tommaso; Palma, Claudio

    2012-06-01

    This communication introduces a novel approach for quantitatively evaluating the role of color space decomposition in digital nailfold capillaroscopy analysis. It is clinically recognized that any alterations of the capillary pattern, at the periungual skin region, are directly related to dermatologic and rheumatic diseases. The proposed algorithm for the segmentation of digital capillaroscopy images is optimized with respect to the choice of the color space and the contrast variation. Since the color space is a critical factor for segmenting low-contrast images, an exhaustive comparison between different color channels is conducted and a novel color channel combination is presented. Results from images of 15 healthy subjects are compared with annotated data, i.e. selected images approved by clinicians. By comparison, a set of figures of merit, which highlights the algorithm capability to correctly segment capillaries, their shape and their number, is extracted. Experimental tests depict that the optimized procedure for capillaries segmentation, based on a novel color channel combination, presents values of average accuracy higher than 0.8, and extracts capillaries whose shape and granularity are acceptable. The obtained results are particularly encouraging for future developments on the classification of capillary patterns with respect to dermatologic and rheumatic diseases.

  1. Quantitative gold nanoparticle analysis methods: A review.

    Science.gov (United States)

    Yu, Lei; Andriola, Angelo

    2010-08-15

    Research and development in the area of gold nanoparticles' (AuNPs) preparation, characterization, and applications are burgeoning in recent years. Many of the techniques and protocols are very mature, but two major concerns are with the mass domestic production and the consumption of AuNP based products. First, how many AuNPs exist in a dispersion? Second, where are the AuNPs after digestion by the environment and how many are there? To answer these two questions, reliable and reproducible methods are needed to analyze the existence and the population of AuNP in samples. This review summarized the most recent chemical and particle quantitative analysis methods that have been used to characterize the concentration (in number of moles of gold per liter) or population (in number of particles per mL) of AuNPs. The methods summarized in this review include, mass spectroscopy, electroanalytical methods, spectroscopic methods, and particle counting methods. These methods may count the number of AuNP directly or analyze the total concentration of element gold in an AuNP dispersion.

  2. Spontaneous mutations and the origin and maintenance of quantitative genetic variation.

    Science.gov (United States)

    Huang, Wen; Lyman, Richard F; Lyman, Rachel A; Carbone, Mary Anna; Harbison, Susan T; Magwire, Michael M; Mackay, Trudy Fc

    2016-05-23

    Mutation and natural selection shape the genetic variation in natural populations. Here, we directly estimated the spontaneous mutation rate by sequencing new Drosophila mutation accumulation lines maintained with minimal natural selection. We inferred strong stabilizing natural selection on quantitative traits because genetic variation among wild-derived inbred lines was much lower than predicted from a neutral model and the mutational effects were much larger than allelic effects of standing polymorphisms. Stabilizing selection could act directly on the traits, or indirectly from pleiotropic effects on fitness. However, our data are not consistent with simple models of mutation-stabilizing selection balance; therefore, further empirical work is needed to assess the balance of evolutionary forces responsible for quantitative genetic variation.

  3. The quantitative basis of the Arabidopsis innate immune system to endemic pathogens depends on pathogen genetics

    DEFF Research Database (Denmark)

    Corwin, Jason A; Copeland, Daniel; Feusier, Julie

    2016-01-01

    the Arabidopsis-Botrytis pathosystem to explore the quantitative genetic architecture underlying host innate immune system in a population of Arabidopsis thaliana. By infecting a diverse panel of Arabidopsis accessions with four phenotypically and genotypically distinct isolates of the fungal necrotroph B...... of pathogen genetic variation in analyzing host quantitative resistance. While known resistance genes, such as receptor-like kinases (RLKs) and nucleotide-binding site leucine-rich repeat proteins (NLRs), were found to be enriched among associated genes, they only account for a small fraction of the total......, including defense hormone signaling and ROS production, as well as novel processes, such as leaf development. Validation of single gene T-DNA knockouts in a Col-0 background demonstrate a high success rate (60%) when accounting for differences in environmental and Botrytis genetic variation. This study...

  4. Quantitative Risk Analysis: Method And Process

    Directory of Open Access Journals (Sweden)

    Anass BAYAGA

    2010-03-01

    Full Text Available Recent and past studies (King III report, 2009: 73-75; Stoney 2007;Committee of Sponsoring Organisation-COSO, 2004, Bartell, 2003; Liebenberg and Hoyt, 2003; Reason, 2000; Markowitz 1957 lament that although, the introduction of quantifying risk to enhance degree of objectivity in finance for instance was quite parallel to its development in the manufacturing industry, it is not the same in Higher Education Institution (HEI. In this regard, the objective of the paper was to demonstrate the methods and process of Quantitative Risk Analysis (QRA through likelihood of occurrence of risk (phase I. This paper serves as first of a two-phased study, which sampled hundred (100 risk analysts in a University in the greater Eastern Cape Province of South Africa.The analysis of likelihood of occurrence of risk by logistic regression and percentages were conducted to investigate whether there were a significant difference or not between groups (analyst in respect of QRA.The Hosmer and Lemeshow test was non-significant with a chi-square(X2 =8.181; p = 0.300, which indicated that there was a good model fit, since the data did not significantly deviate from the model. The study concluded that to derive an overall likelihood rating that indicated the probability that a potential risk may be exercised within the construct of an associated threat environment, the following governing factors must be considered: (1 threat source motivation and capability (2 nature of the vulnerability (3 existence and effectiveness of current controls (methods and process.

  5. Quantitative risks analysis of maritime terminal petrochemical

    Energy Technology Data Exchange (ETDEWEB)

    Ferreira, Leandro Silveira; Leal, Cesar A. [Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS (Brazil). Programa de Pos-Graduacao em Engenharia Mecanica (PROMEC)]. E-mail: leandro19889900@yahoo.com.br

    2008-07-01

    This work consists of the application of a computer program (RISKAN) developed for studies of quantification of industrial risks and also a revision of the models used in the program. As part the evaluation made, a test was performed with the application of the computer program to estimate the risks for a marine terminal for storage of petrochemical products, in the city of Rio Grande, Brazil. Thus, as part of the work, it was performed a Quantitative Risk Analysis associated to the terminal, both for the workers and for the population nearby, with a verification of acceptability using the tolerability limits established by the State Licensing Agency (FEPAM-RS). In the risk analysis methodology used internationally, the most used way of presenting results of social risks is in the graphical form with the use of the FN curves and for the individual risk it is common the use of the iso-risk curves traced on the map of the area where is the plant. In the beginning of the study, both a historical analysis of accidents and use of the technique of Preliminary Analysis of Risks were made in order to aid in the process of identification of the possible scenarios of accidents related to the activities in the terminal. After identifying the initiating events, their frequencies or probabilities of occurrence were estimated and followed by the calculations of the physical effects and deaths, with the use, inside the computer program, of published models of Prins Mauritz Laboratory and of American Institute of Chemical Engineers. The average social risk obtained for the external populations was of 8.7x10{sup -7} fatality.year{sup -1} and for the internal population (people working inside the terminal), 3.2x10{sup -4} fatality.year-1. The accident scenario that most contributed to the social risk was death due to exposure to the thermal radiation caused by pool fire, with 84.3% of the total estimated for external populations and 82.9% for the people inside the terminal. The

  6. The quantitative genetic basis of polyandry in the parasitoid wasp, Nasonia vitripennis.

    Science.gov (United States)

    Shuker, D M; Phillimore, A J; Burton-Chellew, M N; Hodge, S E; West, S A

    2007-02-01

    Understanding the evolution of female multiple mating (polyandry) is crucial for understanding sexual selection and sexual conflict. Despite this interest, little is known about its genetic basis or whether genetics influences the evolutionary origin or maintenance of polyandry. Here, we explore the quantitative genetic basis of polyandry in the parasitoid wasp Nasonia vitripennis, a species in which female re-mating has been observed to evolve in the laboratory. We performed a quantitative genetic experiment on a recently collected population of wasps. We found low heritabilities of female polyandry (re-mating frequency after 18 h), low heritability of courtship duration and a slightly higher heritability of copulation duration. However, the coefficients of additive genetic variance for these traits were all reasonably large (CV(A)>7.0). We also found considerable dam effects for all traits after controlling for common environment, suggesting either dominance or maternal effects. Our work adds to the evidence that nonadditive genetic effects may influence the evolution of mating behaviour in Nasonia vitripennis, and the evolution of polyandry more generally.

  7. Quantitative Trait Locus Analysis of the Early Domestication of Sunflower

    OpenAIRE

    David M Wills; Burke, John M.

    2007-01-01

    Genetic analyses of the domestication syndrome have revealed that domestication-related traits typically have a very similar genetic architecture across most crops, being conditioned by a small number of quantitative trait loci (QTL), each with a relatively large effect on the phenotype. To date, the domestication of sunflower (Helianthus annuus L.) stands as the only counterexample to this pattern. In previous work involving a cross between wild sunflower (also H. annuus) and a highly improv...

  8. Gene set analysis for interpreting genetic studies

    DEFF Research Database (Denmark)

    Pers, Tune H

    2016-01-01

    Interpretation of genome-wide association study (GWAS) results is lacking behind the discovery of new genetic associations. Consequently, there is an urgent need for data-driven methods for interpreting genetic association studies. Gene set analysis (GSA) can identify aetiologic pathways and func......Interpretation of genome-wide association study (GWAS) results is lacking behind the discovery of new genetic associations. Consequently, there is an urgent need for data-driven methods for interpreting genetic association studies. Gene set analysis (GSA) can identify aetiologic pathways...

  9. Quantitative genetics of shape in cricket wings: developmental integration in a functional structure.

    Science.gov (United States)

    Klingenberg, Christian Peter; Debat, Vincent; Roff, Derek A

    2010-10-01

    The role of developmental and genetic integration for evolution is contentious. One hypothesis states that integration acts as a constraint on evolution, whereas an alternative is that developmental and genetic systems evolve to match the functional modularity of organisms. This study examined a morphological structure, the cricket wing, where developmental and functional modules are discordant, making it possible to distinguish the two alternatives. Wing shape was characterized with geometric morphometrics, quantitative genetic information was extracted using a full-sibling breeding design, and patterns of developmental integration were inferred from fluctuating asymmetry of wing shape. The patterns of genetic, phenotypic, and developmental integration were clearly similar, but not identical. Heritabilities for different shape variables varied widely, but no shape variables were devoid of genetic variation. Simulated selection for specific shape changes produced predicted responses with marked deflections due to the genetic covariance structure. Three hypotheses of modularity according to the wing structures involved in sound production were inconsistent with the genetic, phenotypic, or developmental covariance structure. Instead, there appears to be strong integration throughout the wing. The hypothesis that genetic and developmental integration evolve to match functional modularity can therefore be rejected for this example.

  10. The quantitative basis of the Arabidopsis innate immune system to endemic pathogens depends on pathogen genetics

    DEFF Research Database (Denmark)

    Corwin, Jason A; Copeland, Daniel; Feusier, Julie;

    2016-01-01

    The most established model of the eukaryotic innate immune system is derived from examples of large effect monogenic quantitative resistance to pathogens. However, many host-pathogen interactions involve many genes of small to medium effect and exhibit quantitative resistance. We used...... the Arabidopsis-Botrytis pathosystem to explore the quantitative genetic architecture underlying host innate immune system in a population of Arabidopsis thaliana. By infecting a diverse panel of Arabidopsis accessions with four phenotypically and genotypically distinct isolates of the fungal necrotroph B....... cinerea, we identified a total of 2,982 genes associated with quantitative resistance using lesion area and 3,354 genes associated with camalexin production as measures of the interaction. Most genes were associated with resistance to a specific Botrytis isolate, which demonstrates the influence...

  11. Are Genetically Informed Designs Genetically Informative?: Comment on McGue, Elkins, Walden, and Iacono (2005) and Quantitative Behavioral Genetics

    Science.gov (United States)

    Partridge, Ty

    2005-01-01

    M. McGue, I. Elkins, B. Walden, and W. G. Iacono (see record 2005-14938-011) presented the findings from a twin study examining the relative contributions of genetic and environmental factors to the developmental trajectories of parent-adolescent relationships. From a behavioral genetics perspective, this study is well conceptualized, is well…

  12. Quantitative Genetics Identifies Cryptic Genetic Variation Involved in the Paternal Regulation of Seed Development

    NARCIS (Netherlands)

    Pires, Nuno D.; Bemer, Marian; Müller, Lena M.; Baroux, Célia; Spillane, Charles; Grossniklaus, Ueli

    2016-01-01

    Embryonic development requires a correct balancing of maternal and paternal genetic information. This balance is mediated by genomic imprinting, an epigenetic mechanism that leads to parent-of-origin-dependent gene expression. The parental conflict (or kinship) theory proposes that imprinting can

  13. Quantitative Genetics Identifies Cryptic Genetic Variation Involved in the Paternal Regulation of Seed Development.

    Science.gov (United States)

    Pires, Nuno D; Bemer, Marian; Müller, Lena M; Baroux, Célia; Spillane, Charles; Grossniklaus, Ueli

    2016-01-01

    Embryonic development requires a correct balancing of maternal and paternal genetic information. This balance is mediated by genomic imprinting, an epigenetic mechanism that leads to parent-of-origin-dependent gene expression. The parental conflict (or kinship) theory proposes that imprinting can evolve due to a conflict between maternal and paternal alleles over resource allocation during seed development. One assumption of this theory is that paternal alleles can regulate seed growth; however, paternal effects on seed size are often very low or non-existent. We demonstrate that there is a pool of cryptic genetic variation in the paternal control of Arabidopsis thaliana seed development. Such cryptic variation can be exposed in seeds that maternally inherit a medea mutation, suggesting that MEA acts as a maternal buffer of paternal effects. Genetic mapping using recombinant inbred lines, and a novel method for the mapping of parent-of-origin effects using whole-genome sequencing of segregant bulks, indicate that there are at least six loci with small, paternal effects on seed development. Together, our analyses reveal the existence of a pool of hidden genetic variation on the paternal control of seed development that is likely shaped by parental conflict.

  14. Quantitative Genetics Identifies Cryptic Genetic Variation Involved in the Paternal Regulation of Seed Development.

    Directory of Open Access Journals (Sweden)

    Nuno D Pires

    2016-01-01

    Full Text Available Embryonic development requires a correct balancing of maternal and paternal genetic information. This balance is mediated by genomic imprinting, an epigenetic mechanism that leads to parent-of-origin-dependent gene expression. The parental conflict (or kinship theory proposes that imprinting can evolve due to a conflict between maternal and paternal alleles over resource allocation during seed development. One assumption of this theory is that paternal alleles can regulate seed growth; however, paternal effects on seed size are often very low or non-existent. We demonstrate that there is a pool of cryptic genetic variation in the paternal control of Arabidopsis thaliana seed development. Such cryptic variation can be exposed in seeds that maternally inherit a medea mutation, suggesting that MEA acts as a maternal buffer of paternal effects. Genetic mapping using recombinant inbred lines, and a novel method for the mapping of parent-of-origin effects using whole-genome sequencing of segregant bulks, indicate that there are at least six loci with small, paternal effects on seed development. Together, our analyses reveal the existence of a pool of hidden genetic variation on the paternal control of seed development that is likely shaped by parental conflict.

  15. Quantitative Genetics Identifies Cryptic Genetic Variation Involved in the Paternal Regulation of Seed Development.

    Directory of Open Access Journals (Sweden)

    Nuno D Pires

    2016-01-01

    Full Text Available Embryonic development requires a correct balancing of maternal and paternal genetic information. This balance is mediated by genomic imprinting, an epigenetic mechanism that leads to parent-of-origin-dependent gene expression. The parental conflict (or kinship theory proposes that imprinting can evolve due to a conflict between maternal and paternal alleles over resource allocation during seed development. One assumption of this theory is that paternal alleles can regulate seed growth; however, paternal effects on seed size are often very low or non-existent. We demonstrate that there is a pool of cryptic genetic variation in the paternal control of Arabidopsis thaliana seed development. Such cryptic variation can be exposed in seeds that maternally inherit a medea mutation, suggesting that MEA acts as a maternal buffer of paternal effects. Genetic mapping using recombinant inbred lines, and a novel method for the mapping of parent-of-origin effects using whole-genome sequencing of segregant bulks, indicate that there are at least six loci with small, paternal effects on seed development. Together, our analyses reveal the existence of a pool of hidden genetic variation on the paternal control of seed development that is likely shaped by parental conflict.

  16. The quantitative genetics of indirect genetic effects: a selective review of modelling issues : Review

    NARCIS (Netherlands)

    Bijma, P.

    2014-01-01

    Indirect genetic effects (IGE) occur when the genotype of an individual affects the phenotypic trait value of another conspecific individual. IGEs can have profound effects on both the magnitude and the direction of response to selection. Models of inheritance and response to selection in traits sub

  17. Quantitative Data Analysis--In the Graduate Curriculum

    Science.gov (United States)

    Albers, Michael J.

    2017-01-01

    A quantitative research study collects numerical data that must be analyzed to help draw the study's conclusions. Teaching quantitative data analysis is not teaching number crunching, but teaching a way of critical thinking for how to analyze the data. The goal of data analysis is to reveal the underlying patterns, trends, and relationships of a…

  18. The Curriculum in Quantitative Analysis: Results of a Survey.

    Science.gov (United States)

    Locke, David C.; Grossman, William E. L.

    1987-01-01

    Reports on the results of a survey of college level instructors of quantitative analysis courses. Discusses what topics are taught in such courses, how much weight is given to these topics, and which experiments are used in the laboratory. Poses some basic questions about the curriculum in quantitative analysis. (TW)

  19. The quantitative genetic architecture of the bold-shy continuum in zebrafish, Danio rerio.

    Directory of Open Access Journals (Sweden)

    Mary E Oswald

    Full Text Available In studies of consistent individual differences (personality along the bold-shy continuum, a pattern of behavioral correlations frequently emerges: individuals towards the bold end of the continuum are more likely to utilize risky habitat, approach potential predators, and feed under risky conditions. Here, we address the hypothesis that observed phenotypic correlations among component behaviors of the bold-shy continuum are a result of underlying genetic correlations (quantitative genetic architecture. We used a replicated three-generation pedigree of zebrafish (Danio rerio to study three putative components of the bold-shy continuum: horizontal position, swim level, and feeding latency. We detected significant narrow-sense heritabilities as well as significant genetic and phenotypic correlations among all three behaviors, such that fish selected for swimming at the front of the tank swam closer to the observer, swam higher in the water column, and fed more quickly than fish selected for swimming at the back of the tank. Further, the lines varied in their initial open field behavior (swim level and activity level. The quantitative genetic architecture of the bold-shy continuum indicates that the multivariate behavioral phenotype characteristic of a "bold" personality type may be a result of correlated evolution via underlying genetic correlations.

  20. Multivariate Survival Mixed Models for Genetic Analysis of Longevity Traits

    DEFF Research Database (Denmark)

    Pimentel Maia, Rafael; Madsen, Per; Labouriau, Rodrigo

    2013-01-01

    A class of multivariate mixed survival models for continuous and discrete time with a complex covariance structure is introduced in a context of quantitative genetic applications. The methods introduced can be used in many applications in quantitative genetics although the discussion presented...... concentrates on longevity studies. The framework presented allows to combine models based on continuous time with models based on discrete time in a joint analysis. The continuous time models are approximations of the frailty model in which the hazard function will be assumed to be piece-wise constant....... The discrete time models used are multivariate variants of the discrete relative risk models. These models allow for regular parametric likelihood-based inference by exploring a coincidence of their likelihood functions and the likelihood functions of suitably defined multivariate generalized linear mixed...

  1. Multivariate Survival Mixed Models for Genetic Analysis of Longevity Traits

    DEFF Research Database (Denmark)

    Pimentel Maia, Rafael; Madsen, Per; Labouriau, Rodrigo

    2014-01-01

    A class of multivariate mixed survival models for continuous and discrete time with a complex covariance structure is introduced in a context of quantitative genetic applications. The methods introduced can be used in many applications in quantitative genetics although the discussion presented...... concentrates on longevity studies. The framework presented allows to combine models based on continuous time with models based on discrete time in a joint analysis. The continuous time models are approximations of the frailty model in which the hazard function will be assumed to be piece-wise constant....... The discrete time models used are multivariate variants of the discrete relative risk models. These models allow for regular parametric likelihood-based inference by exploring a coincidence of their likelihood functions and the likelihood functions of suitably defined multivariate generalized linear mixed...

  2. Combination and Integration of Qualitative and Quantitative Analysis

    Directory of Open Access Journals (Sweden)

    Philipp Mayring

    2001-02-01

    Full Text Available In this paper, I am going to outline ways of combining qualitative and quantitative steps of analysis on five levels. On the technical level, programs for the computer-aided analysis of qualitative data offer various combinations. Where the data are concerned, the employment of categories (for instance by using qualitative content analysis allows for combining qualitative and quantitative forms of data analysis. On the individual level, the creation of types and the inductive generalisation of cases allow for proceeding from individual case material to quantitative generalisations. As for research design, different models can be distinguished (preliminary study, generalisation, elaboration, triangulation which combine qualitative and quantitative steps of analysis. Where the logic of research is concerned, it can be shown that an extended process model which combined qualitative and quantitative research can be appropriate and thus lead to an integration of the two approaches. URN: urn:nbn:de:0114-fqs010162

  3. Some Epistemological Considerations Concerning Quantitative Analysis

    Science.gov (United States)

    Dobrescu, Emilian

    2008-01-01

    This article presents the author's address at the 2007 "Journal of Applied Quantitative Methods" ("JAQM") prize awarding festivity. The festivity was included in the opening of the 4th International Conference on Applied Statistics, November 22, 2008, Bucharest, Romania. In the address, the author reflects on three theses that…

  4. Combined sequence-based and genetic mapping analysis of complex traits in outbred rats

    NARCIS (Netherlands)

    Baud, Amelie; Hermsen, Roel; Guryev, Victor; Stridh, Pernilla; Graham, Delyth; McBride, Martin W.; Foroud, Tatiana; Calderari, Sophie; Diez, Margarita; Ockinger, Johan; Beyeen, Amennai D.; Gillett, Alan; Abdelmagid, Nada; Guerreiro-Cacais, Andre Ortlieb; Jagodic, Maja; Tuncel, Jonatan; Norin, Ulrika; Beattie, Elisabeth; Huynh, Ngan; Miller, William H.; Koller, Daniel L.; Alam, Imranul; Falak, Samreen; Osborne-Pellegrin, Mary; Martinez-Membrives, Esther; Canete, Toni; Blazquez, Gloria; Vicens-Costa, Elia; Mont-Cardona, Carme; Diaz-Moran, Sira; Tobena, Adolf; Hummel, Oliver; Zelenika, Diana; Saar, Kathrin; Patone, Giannino; Bauerfeind, Anja; Bihoreau, Marie-Therese; Heinig, Matthias; Lee, Young-Ae; Rintisch, Carola; Schulz, Herbert; Wheeler, David A.; Worley, Kim C.; Muzny, Donna M.; Gibbs, Richard A.; Lathrop, Mark; Lansu, Nico; Toonen, Pim; Ruzius, Frans Paul; de Bruijn, Ewart; Hauser, Heidi; Adams, David J.; Keane, Thomas; Atanur, Santosh S.; Aitman, Tim J.; Flicek, Paul; Malinauskas, Tomas; Jones, E. Yvonne; Ekman, Diana; Lopez-Aumatell, Regina; Dominiczak, Anna F.; Johannesson, Martina; Holmdahl, Rikard; Olsson, Tomas; Gauguier, Dominique; Hubner, Norbert; Fernandez-Teruel, Alberto; Cuppen, Edwin; Mott, Richard; Flint, Jonathan

    2013-01-01

    Genetic mapping on fully sequenced individuals is transforming understanding of the relationship between molecular variation and variation in complex traits. Here we report a combined sequence and genetic mapping analysis in outbred rats that maps 355 quantitative trait loci for 122 phenotypes. We i

  5. A consensus map of rapeseed (Brassica napus L.) based on diversity array technology markers: applications in genetic dissection of qualitative and quantitative traits

    National Research Council Canada - National Science Library

    Raman, Harsh; Raman, Rosy; Kilian, Andrzej; Detering, Frank; Long, Yan; Edwards, David; Parkin, Isobel A P; Sharpe, Andrew G; Nelson, Matthew N; Larkan, Nick; Zou, Jun; Meng, Jinling; Aslam, M Naveed; Batley, Jacqueline; Cowling, Wallace A; Lydiate, Derek

    2013-01-01

    Dense consensus genetic maps based on high-throughput genotyping platforms are valuable for making genetic gains in Brassica napus through quantitative trait locus identification, efficient predictive...

  6. Quantitative Chemical-Genetic Interaction Map Connects Gene Alterations to Drug Responses | Office of Cancer Genomics

    Science.gov (United States)

    In a recent Cancer Discovery report, CTD2 researchers at the University of California in San Francisco developed a new quantitative chemical-genetic interaction mapping approach to evaluate drug sensitivity or resistance in isogenic cell lines. Performing a high-throughput screen with isogenic cell lines allowed the researchers to explore the impact of a panel of emerging and established drugs on cells overexpressing a single cancer-associated gene in isolation.

  7. Genetic analysis of rare disorders

    DEFF Research Database (Denmark)

    van den Berg, Stéphanie M; von Bornemann Hjelmborg, Jacob

    2012-01-01

    Twin concordance rates provide insight into the possibility of a genetic background for a disease. These concordance rates are usually estimated within a frequentistic framework. Here we take a Bayesian approach. For rare diseases, estimation methods based on asymptotic theory cannot be applied due...

  8. Quantitative genetics theory for genomic selection and efficiency of breeding value prediction in open-pollinated populations

    Directory of Open Access Journals (Sweden)

    José Marcelo Soriano Viana

    2016-06-01

    Full Text Available ABSTRACT To date, the quantitative genetics theory for genomic selection has focused mainly on the relationship between marker and additive variances assuming one marker and one quantitative trait locus (QTL. This study extends the quantitative genetics theory to genomic selection in order to prove that prediction of breeding values based on thousands of single nucleotide polymorphisms (SNPs depends on linkage disequilibrium (LD between markers and QTLs, assuming dominance. We also assessed the efficiency of genomic selection in relation to phenotypic selection, assuming mass selection in an open-pollinated population, all QTLs of lower effect, and reduced sample size, based on simulated data. We show that the average effect of a SNP substitution is proportional to LD measure and to average effect of a gene substitution for each QTL that is in LD with the marker. Weighted (by SNP frequencies and unweighted breeding value predictors have the same accuracy. Efficiency of genomic selection in relation to phenotypic selection is inversely proportional to heritability. Accuracy of breeding value prediction is not affected by the dominance degree and the method of analysis, however, it is influenced by LD extent and magnitude of additive variance. The increase in the number of markers asymptotically improved accuracy of breeding value prediction. The decrease in the sample size from 500 to 200 did not reduce considerably accuracy of breeding value prediction.

  9. Uncovering the genetic signature of quantitative trait evolution with replicated time series data.

    Science.gov (United States)

    Franssen, S U; Kofler, R; Schlötterer, C

    2017-01-01

    The genetic architecture of adaptation in natural populations has not yet been resolved: it is not clear to what extent the spread of beneficial mutations (selective sweeps) or the response of many quantitative trait loci drive adaptation to environmental changes. Although much attention has been given to the genomic footprint of selective sweeps, the importance of selection on quantitative traits is still not well studied, as the associated genomic signature is extremely difficult to detect. We propose 'Evolve and Resequence' as a promising tool, to study polygenic adaptation of quantitative traits in evolving populations. Simulating replicated time series data we show that adaptation to a new intermediate trait optimum has three characteristic phases that are reflected on the genomic level: (1) directional frequency changes towards the new trait optimum, (2) plateauing of allele frequencies when the new trait optimum has been reached and (3) subsequent divergence between replicated trajectories ultimately leading to the loss or fixation of alleles while the trait value does not change. We explore these 3 phase characteristics for relevant population genetic parameters to provide expectations for various experimental evolution designs. Remarkably, over a broad range of parameters the trajectories of selected alleles display a pattern across replicates, which differs both from neutrality and directional selection. We conclude that replicated time series data from experimental evolution studies provide a promising framework to study polygenic adaptation from whole-genome population genetics data.

  10. Multilevel selection 1: Quantitative genetics of inheritance and response to selection.

    Science.gov (United States)

    Bijma, Piter; Muir, William M; Van Arendonk, Johan A M

    2007-01-01

    Interaction among individuals is universal, both in animals and in plants, and substantially affects evolution of natural populations and responses to artificial selection in agriculture. Although quantitative genetics has successfully been applied to many traits, it does not provide a general theory accounting for interaction among individuals and selection acting on multiple levels. Consequently, current quantitative genetic theory fails to explain why some traits do not respond to selection among individuals, but respond greatly to selection among groups. Understanding the full impacts of heritable interactions on the outcomes of selection requires a quantitative genetic framework including all levels of selection and relatedness. Here we present such a framework and provide expressions for the response to selection. Results show that interaction among individuals may create substantial heritable variation, which is hidden to classical analyses. Selection acting on higher levels of organization captures this hidden variation and therefore always yields positive response, whereas individual selection may yield response in the opposite direction. Our work provides testable predictions of response to multilevel selection and reduces to classical theory in the absence of interaction. Statistical methodology provided elsewhere enables empirical application of our work to both natural and domestic populations.

  11. Detecting Genetic Interactions for Quantitative Traits Using m-Spacing Entropy Measure

    Directory of Open Access Journals (Sweden)

    Jaeyong Yee

    2015-01-01

    Full Text Available A number of statistical methods for detecting gene-gene interactions have been developed in genetic association studies with binary traits. However, many phenotype measures are intrinsically quantitative and categorizing continuous traits may not always be straightforward and meaningful. Association of gene-gene interactions with an observed distribution of such phenotypes needs to be investigated directly without categorization. Information gain based on entropy measure has previously been successful in identifying genetic associations with binary traits. We extend the usefulness of this information gain by proposing a nonparametric evaluation method of conditional entropy of a quantitative phenotype associated with a given genotype. Hence, the information gain can be obtained for any phenotype distribution. Because any functional form, such as Gaussian, is not assumed for the entire distribution of a trait or a given genotype, this method is expected to be robust enough to be applied to any phenotypic association data. Here, we show its use to successfully identify the main effect, as well as the genetic interactions, associated with a quantitative trait.

  12. Joint analysis of binary and quantitative traits with data sharing and outcome-dependent sampling.

    Science.gov (United States)

    Zheng, Gang; Wu, Colin O; Kwak, Minjung; Jiang, Wenhua; Joo, Jungnam; Lima, Joao A C

    2012-04-01

    We study the analysis of a joint association between a genetic marker with both binary (case-control) and quantitative (continuous) traits, where the quantitative trait values are only available for the cases due to data sharing and outcome-dependent sampling. Data sharing becomes common in genetic association studies, and the outcome-dependent sampling is the consequence of data sharing, under which a phenotype of interest is not measured for some subgroup. The trend test (or Pearson's test) and F-test are often, respectively, used to analyze the binary and quantitative traits. Because of the outcome-dependent sampling, the usual F-test can be applied using the subgroup with the observed quantitative traits. We propose a modified F-test by also incorporating the genotype frequencies of the subgroup whose traits are not observed. Further, a combination of this modified F-test and Pearson's test is proposed by Fisher's combination of their P-values as a joint analysis. Because of the correlation of the two analyses, we propose to use a Gamma (scaled chi-squared) distribution to fit the asymptotic null distribution for the joint analysis. The proposed modified F-test and the joint analysis can also be applied to test single trait association (either binary or quantitative trait). Through simulations, we identify the situations under which the proposed tests are more powerful than the existing ones. Application to a real dataset of rheumatoid arthritis is presented. © 2012 Wiley Periodicals, Inc.

  13. A bivariate quantitative genetic model for a linear Gaussian trait and a survival trait

    Directory of Open Access Journals (Sweden)

    Damgaard Lars

    2005-12-01

    Full Text Available Abstract With the increasing use of survival models in animal breeding to address the genetic aspects of mainly longevity of livestock but also disease traits, the need for methods to infer genetic correlations and to do multivariate evaluations of survival traits and other types of traits has become increasingly important. In this study we derived and implemented a bivariate quantitative genetic model for a linear Gaussian and a survival trait that are genetically and environmentally correlated. For the survival trait, we considered the Weibull log-normal animal frailty model. A Bayesian approach using Gibbs sampling was adopted. Model parameters were inferred from their marginal posterior distributions. The required fully conditional posterior distributions were derived and issues on implementation are discussed. The twoWeibull baseline parameters were updated jointly using a Metropolis-Hastingstep. The remaining model parameters with non-normalized fully conditional distributions were updated univariately using adaptive rejection sampling. Simulation results showed that the estimated marginal posterior distributions covered well and placed high density to the true parameter values used in the simulation of data. In conclusion, the proposed method allows inferring additive genetic and environmental correlations, and doing multivariate genetic evaluation of a linear Gaussian trait and a survival trait.

  14. A bivariate quantitative genetic model for a linear Gaussian trait and a survival trait.

    Science.gov (United States)

    Damgaard, Lars Holm; Korsgaard, Inge Riis

    2006-01-01

    With the increasing use of survival models in animal breeding to address the genetic aspects of mainly longevity of livestock but also disease traits, the need for methods to infer genetic correlations and to do multivariate evaluations of survival traits and other types of traits has become increasingly important. In this study we derived and implemented a bivariate quantitative genetic model for a linear Gaussian and a survival trait that are genetically and environmentally correlated. For the survival trait, we considered the Weibull log-normal animal frailty model. A Bayesian approach using Gibbs sampling was adopted. Model parameters were inferred from their marginal posterior distributions. The required fully conditional posterior distributions were derived and issues on implementation are discussed. The two Weibull baseline parameters were updated jointly using a Metropolis-Hasting step. The remaining model parameters with non-normalized fully conditional distributions were updated univariately using adaptive rejection sampling. Simulation results showed that the estimated marginal posterior distributions covered well and placed high density to the true parameter values used in the simulation of data. In conclusion, the proposed method allows inferring additive genetic and environmental correlations, and doing multivariate genetic evaluation of a linear Gaussian trait and a survival trait.

  15. Modeling development and quantitative trait mapping reveal independent genetic modules for leaf size and shape.

    Science.gov (United States)

    Baker, Robert L; Leong, Wen Fung; Brock, Marcus T; Markelz, R J Cody; Covington, Michael F; Devisetty, Upendra K; Edwards, Christine E; Maloof, Julin; Welch, Stephen; Weinig, Cynthia

    2015-10-01

    Improved predictions of fitness and yield may be obtained by characterizing the genetic controls and environmental dependencies of organismal ontogeny. Elucidating the shape of growth curves may reveal novel genetic controls that single-time-point (STP) analyses do not because, in theory, infinite numbers of growth curves can result in the same final measurement. We measured leaf lengths and widths in Brassica rapa recombinant inbred lines (RILs) throughout ontogeny. We modeled leaf growth and allometry as function valued traits (FVT), and examined genetic correlations between these traits and aspects of phenology, physiology, circadian rhythms and fitness. We used RNA-seq to construct a SNP linkage map and mapped trait quantitative trait loci (QTL). We found genetic trade-offs between leaf size and growth rate FVT and uncovered differences in genotypic and QTL correlations involving FVT vs STPs. We identified leaf shape (allometry) as a genetic module independent of length and width and identified selection on FVT parameters of development. Leaf shape is associated with venation features that affect desiccation resistance. The genetic independence of leaf shape from other leaf traits may therefore enable crop optimization in leaf shape without negative effects on traits such as size, growth rate, duration or gas exchange.

  16. Genetic algorithm based image binarization approach and its quantitative evaluation via pooling

    Science.gov (United States)

    Hu, Huijun; Liu, Ya; Liu, Maofu

    2015-12-01

    The binarized image is very critical to image visual feature extraction, especially shape feature, and the image binarization approaches have been attracted more attentions in the past decades. In this paper, the genetic algorithm is applied to optimizing the binarization threshold of the strip steel defect image. In order to evaluate our genetic algorithm based image binarization approach in terms of quantity, we propose the novel pooling based evaluation metric, motivated by information retrieval community, to avoid the lack of ground-truth binary image. Experimental results show that our genetic algorithm based binarization approach is effective and efficiency in the strip steel defect images and our quantitative evaluation metric on image binarization via pooling is also feasible and practical.

  17. Integrated analysis of genetic data with R

    Directory of Open Access Journals (Sweden)

    Zhao Jing

    2006-01-01

    Full Text Available Abstract Genetic data are now widely available. There is, however, an apparent lack of concerted effort to produce software systems for statistical analysis of genetic data compared with other fields of statistics. It is often a tremendous task for end-users to tailor them for particular data, especially when genetic data are analysed in conjunction with a large number of covariates. Here, R http://www.r-project.org, a free, flexible and platform-independent environment for statistical modelling and graphics is explored as an integrated system for genetic data analysis. An overview of some packages currently available for analysis of genetic data is given. This is followed by examples of package development and practical applications. With clear advantages in data management, graphics, statistical analysis, programming, internet capability and use of available codes, it is a feasible, although challenging, task to develop it into an integrated platform for genetic analysis; this will require the joint efforts of many researchers.

  18. Structural and quantitative analysis of Equisetum alkaloids.

    Science.gov (United States)

    Cramer, Luise; Ernst, Ludger; Lubienski, Marcus; Papke, Uli; Schiebel, Hans-Martin; Jerz, Gerold; Beuerle, Till

    2015-08-01

    Equisetum palustre L. is known for its toxicity for livestock. Several studies in the past addressed the isolation and identification of the responsible alkaloids. So far, palustrine (1) and N(5)-formylpalustrine (2) are known alkaloids of E. palustre. A HPLC-ESI-MS/MS method in combination with simple sample work-up was developed to identify and quantitate Equisetum alkaloids. Besides the two known alkaloids six related alkaloids were detected in different Equisetum samples. The structure of the alkaloid palustridiene (3) was derived by comprehensive 1D and 2D NMR experiments. N(5)-Acetylpalustrine (4) was also thoroughly characterized by NMR for the first time. The structure of N(5)-formylpalustridiene (5) is proposed based on mass spectrometry results. Twenty-two E. palustre samples were screened by a HPLC-ESI-MS/MS method after development of a simple sample work-up and in most cases the set of all eight alkaloids were detected in all parts of the plant. A high variability of the alkaloid content and distribution was found depending on plant organ, plant origin and season ranging from 88 to 597mg/kg dried weight. However, palustrine (1) and the alkaloid palustridiene (3) always represented the main alkaloids. For the first time, a comprehensive identification, quantitation and distribution of Equisetum alkaloids was achieved.

  19. Energy Dispersive Spectrometry and Quantitative Analysis Short Course. Introduction to X-ray Energy Dispersive Spectrometry and Quantitative Analysis

    Science.gov (United States)

    Carpenter, Paul; Curreri, Peter A. (Technical Monitor)

    2002-01-01

    This course will cover practical applications of the energy-dispersive spectrometer (EDS) to x-ray microanalysis. Topics covered will include detector technology, advances in pulse processing, resolution and performance monitoring, detector modeling, peak deconvolution and fitting, qualitative and quantitative analysis, compositional mapping, and standards. An emphasis will be placed on use of the EDS for quantitative analysis, with discussion of typical problems encountered in the analysis of a wide range of materials and sample geometries.

  20. Gene set analyses of genome-wide association studies on 49 quantitative traits measured in a single genetic epidemiology dataset.

    Science.gov (United States)

    Kim, Jihye; Kwon, Ji-Sun; Kim, Sangsoo

    2013-09-01

    Gene set analysis is a powerful tool for interpreting a genome-wide association study result and is gaining popularity these days. Comparison of the gene sets obtained for a variety of traits measured from a single genetic epidemiology dataset may give insights into the biological mechanisms underlying these traits. Based on the previously published single nucleotide polymorphism (SNP) genotype data on 8,842 individuals enrolled in the Korea Association Resource project, we performed a series of systematic genome-wide association analyses for 49 quantitative traits of basic epidemiological, anthropometric, or blood chemistry parameters. Each analysis result was subjected to subsequent gene set analyses based on Gene Ontology (GO) terms using gene set analysis software, GSA-SNP, identifying a set of GO terms significantly associated to each trait (pcorr neuronal or nerve systems.

  1. Gene Level Meta-Analysis of Quantitative Traits by Functional Linear Models.

    Science.gov (United States)

    Fan, Ruzong; Wang, Yifan; Boehnke, Michael; Chen, Wei; Li, Yun; Ren, Haobo; Lobach, Iryna; Xiong, Momiao

    2015-08-01

    Meta-analysis of genetic data must account for differences among studies including study designs, markers genotyped, and covariates. The effects of genetic variants may differ from population to population, i.e., heterogeneity. Thus, meta-analysis of combining data of multiple studies is difficult. Novel statistical methods for meta-analysis are needed. In this article, functional linear models are developed for meta-analyses that connect genetic data to quantitative traits, adjusting for covariates. The models can be used to analyze rare variants, common variants, or a combination of the two. Both likelihood-ratio test (LRT) and F-distributed statistics are introduced to test association between quantitative traits and multiple variants in one genetic region. Extensive simulations are performed to evaluate empirical type I error rates and power performance of the proposed tests. The proposed LRT and F-distributed statistics control the type I error very well and have higher power than the existing methods of the meta-analysis sequence kernel association test (MetaSKAT). We analyze four blood lipid levels in data from a meta-analysis of eight European studies. The proposed methods detect more significant associations than MetaSKAT and the P-values of the proposed LRT and F-distributed statistics are usually much smaller than those of MetaSKAT. The functional linear models and related test statistics can be useful in whole-genome and whole-exome association studies.

  2. China ASON Network Migration Scenarios and Their Quantitative Analysis

    Institute of Scientific and Technical Information of China (English)

    Soichiro; Araki; Itaru; Nishioka; Yoshihiko; Suemura

    2003-01-01

    This paper proposes two migration scenarios from China ring networks to ASON mesh networks. In our quantitative analysis with ASON/GMPLS simulator, a subnetwork protection scheme achieved best balanced performance in resource utilization and restoration time.

  3. China ASON Network Migration Scenarios and Their Quantitative Analysis

    Institute of Scientific and Technical Information of China (English)

    Guoying Zhang; Soichiro Araki; Itaru Nishioka; Yoshihiko Suemura

    2003-01-01

    This paper proposes two migration scenarios from China rin g networks to ASON mesh networks . In our quantitative analysis with ASON/GMPLS simulator, a subnetwork protection scheme achieved best balanced performance in resource utilization and restoration time.

  4. Quantitative and qualitative analysis of sterols/sterolins and ...

    African Journals Online (AJOL)

    STORAGESEVER

    2008-06-03

    Jun 3, 2008 ... Quantitative and qualitative analysis of sterols/sterolins ... method was developed to identify and quantify sterols (especially β-sitosterol) in chloroform extracts of ... Studies with phytosterols, especially β-sitosterol, have.

  5. Characteristic analysis and prevention on premature convergence in genetic algorithms

    Institute of Scientific and Technical Information of China (English)

    徐宗本; 高勇

    1997-01-01

    The identification and characteristics of premature convergence in genetic algorithms (GAs) are investigated Through a detailed quantitative analysis on the search capability and the degree of population diversity, the cause of premature convergence in GAs is recognized, and attributed to the maturation effect of the GAs: The minimum schema deduced from current population, which is the largest search space of a GA, converges to a homogeneous population in probability 1 ( so the search capability of the GA decreases and premature convergence occurs). It is shown that, as quantitative features of the maturation effect, the degree of population diversity converges to zero with probability 1, and the tendency for premature convergence is inversely proportional to the population size and directly proportional to the variance of the fitness ratio of zero allele at any gene position of the current population. Based on the theoretical analysis, several strategies for preventing premature convergence are suggest

  6. Rapid Genetic Analysis in Congenital Hyperinsulinism

    DEFF Research Database (Denmark)

    Christesen, Henrik Thybo; Brusgaard, Klaus; Alm, Jan

    2007-01-01

    . METHODS: In 4 patients, a rapid genetic analysis of the ABBC8 and KCNJ11 genes was performed within 2 weeks on request prior to the decision of pancreatic surgery. RESULTS: Two patients had no mutations, rendering the genetic analysis non-informative. Peroperative multiple biopsies showed diffuse disease....... One patient had a paternal KCNJ11 mutation and focal disease confirmed by positron emission tomography scan and biopsies. One patient had a de novo heterozygous ABBC8 mutation and unexplained diffuse disease confirmed by positron emission tomography scan and biopsies. CONCLUSION: A rapid analysis...

  7. Quantitative trait loci mapping and genetic dissection for lint percentage in upland cotton (Gossypium hirsutum)

    Indian Academy of Sciences (India)

    Min Wang; Chengqi Li; Qinglian Wang

    2014-08-01

    Lint percentage is an important character of cotton yield components and it is also correlated with cotton fibre development. In this study, we used a high lint percentage variety, Baimian1, and a low lint percentage, TM-1 genetic standard for Gossypium hirsutum, as parents to construct a mapping populations in upland cotton (G. hirsutum). A quantitative trait locus/loci (QTL) analysis of lint percentage was performed by using two mapping procedures; composite interval mapping (CIM), inclusive composite interval mapping (ICIM) and the F2:3 populations in 2 years. Six main-effect QTL (M-QTL) for lint percentage (four significant and two suggestive) were detected in both years by CIM, and were located on chr. 3, chr. 19, chr. 26 and chr. 5 /chr. 19. Of the six QTL, marker intervals and favourable gene sources of the significant M-QTL, qLP-3(2010) and qLP-3(2011) were consistent. These QTL were also detected by ICIM, and therefore, should preferentially be used for marker-assisted selection (MAS) of lint percentage. Another M-QTL, qLP-19(2010), was detected by two mapping procedures, and it could also be a candidate for MAS. We detected the interaction between two M-QTL and environment, and 11 epistatic QTL (E-QTL) and their interaction with environment by using ICIM. The study also found two EST-SSRs, NAU1187 and NAU1255, linked to M-QTL for lint percentage that could be candidate markers affecting cotton fibre development.

  8. Quantitative trait loci mapping and genetic dissection for lint percentage in upland cotton (Gossypium hirsutum).

    Science.gov (United States)

    Wang, Min; Li, Chengqi; Wang, Qinglian

    2014-08-01

    Lint percentage is an important character of cotton yield components and it is also correlated with cotton fibre development. In this study, we used a high lint percentage variety, Baimian1, and a low lint percentage, TM-1 genetic standard for Gossypium hirsutum, as parents to construct a mapping populations in upland cotton (G. hirsutum). A quantitative trait locus/loci (QTL) analysis of lint percentage was performed by using two mapping procedures; composite interval mapping (CIM), inclusive composite interval mapping (ICIM) and the F2:3 populations in 2 years. Six main-effect QTL (M-QTL) for lint percentage (four significant and two suggestive) were detected in both years by CIM, and were located on chr. 3, chr. 19, chr. 26 and chr. 5/chr. 19. Of the six QTL, marker intervals and favourable gene sources of the significant M-QTL, qLP-3(2010) and qLP-3(2011) were consistent. These QTL were also detected by ICIM, and therefore, should preferentially be used for markerassisted selection (MAS) of lint percentage. Another M-QTL, qLP-19(2010), was detected by two mapping procedures, and it could also be a candidate for MAS. We detected the interaction between two M-QTL and environment, and 11 epistatic QTL (E-QTL) and their interaction with environment by using ICIM. The study also found two EST-SSRs, NAU1187 and NAU1255, linked to M-QTL for lint percentage that could be candidate markers affecting cotton fibre development.

  9. A Novel Approach for Discovery Quantitative Fuzzy Multi-Level Association Rules Mining Using Genetic Algorithm

    Directory of Open Access Journals (Sweden)

    Saad M. Darwish

    2016-10-01

    Full Text Available Quantitative multilevel association rules mining is a central field to realize motivating associations among data components with multiple levels abstractions. The problem of expanding procedures to handle quantitative data has been attracting the attention of many researchers. The algorithms regularly discretize the attribute fields into sharp intervals, and then implement uncomplicated algorithms established for Boolean attributes. Fuzzy association rules mining approaches are intended to defeat such shortcomings based on the fuzzy set theory. Furthermore, most of the current algorithms in the direction of this topic are based on very tiring search methods to govern the ideal support and confidence thresholds that agonize from risky computational cost in searching association rules. To accelerate quantitative multilevel association rules searching and escape the extreme computation, in this paper, we propose a new genetic-based method with significant innovation to determine threshold values for frequent item sets. In this approach, a sophisticated coding method is settled, and the qualified confidence is employed as the fitness function. With the genetic algorithm, a comprehensive search can be achieved and system automation is applied, because our model does not need the user-specified threshold of minimum support. Experiment results indicate that the recommended algorithm can powerfully generate non-redundant fuzzy multilevel association rules.

  10. Quantitative Models and Analysis for Reactive Systems

    DEFF Research Database (Denmark)

    Thrane, Claus

    phones and websites. Acknowledging that now more than ever, systems come in contact with the physical world, we need to revise the way we construct models and verification algorithms, to take into account the behavior of systems in the presence of approximate, or quantitative information, provided...... by the environment in which they are embedded. This thesis studies the semantics and properties of a model-based framework for re- active systems, in which models and specifications are assumed to contain quantifiable information, such as references to time or energy. Our goal is to develop a theory of approximation......, by studying how small changes to our models affect the verification results. A key source of motivation for this work can be found in The Embedded Systems Design Challenge [HS06] posed by Thomas A. Henzinger and Joseph Sifakis. It contains a call for advances in the state-of-the-art of systems verification...

  11. Quantitative Models and Analysis for Reactive Systems

    DEFF Research Database (Denmark)

    Thrane, Claus

    phones and websites. Acknowledging that now more than ever, systems come in contact with the physical world, we need to revise the way we construct models and verification algorithms, to take into account the behavior of systems in the presence of approximate, or quantitative information, provided......, allowing verification procedures to quantify judgements, on how suitable a model is for a given specification — hence mitigating the usual harsh distinction between satisfactory and non-satisfactory system designs. This information, among other things, allows us to evaluate the robustness of our framework......, by studying how small changes to our models affect the verification results. A key source of motivation for this work can be found in The Embedded Systems Design Challenge [HS06] posed by Thomas A. Henzinger and Joseph Sifakis. It contains a call for advances in the state-of-the-art of systems verification...

  12. Towards a quantitative OCT image analysis.

    Directory of Open Access Journals (Sweden)

    Marina Garcia Garrido

    Full Text Available Optical coherence tomography (OCT is an invaluable diagnostic tool for the detection and follow-up of retinal pathology in patients and experimental disease models. However, as morphological structures and layering in health as well as their alterations in disease are complex, segmentation procedures have not yet reached a satisfactory level of performance. Therefore, raw images and qualitative data are commonly used in clinical and scientific reports. Here, we assess the value of OCT reflectivity profiles as a basis for a quantitative characterization of the retinal status in a cross-species comparative study.Spectral-Domain Optical Coherence Tomography (OCT, confocal Scanning-Laser Ophthalmoscopy (SLO, and Fluorescein Angiography (FA were performed in mice (Mus musculus, gerbils (Gerbillus perpadillus, and cynomolgus monkeys (Macaca fascicularis using the Heidelberg Engineering Spectralis system, and additional SLOs and FAs were obtained with the HRA I (same manufacturer. Reflectivity profiles were extracted from 8-bit greyscale OCT images using the ImageJ software package (http://rsb.info.nih.gov/ij/.Reflectivity profiles obtained from OCT scans of all three animal species correlated well with ex vivo histomorphometric data. Each of the retinal layers showed a typical pattern that varied in relative size and degree of reflectivity across species. In general, plexiform layers showed a higher level of reflectivity than nuclear layers. A comparison of reflectivity profiles from specialized retinal regions (e.g. visual streak in gerbils, fovea in non-human primates with respective regions of human retina revealed multiple similarities. In a model of Retinitis Pigmentosa (RP, the value of reflectivity profiles for the follow-up of therapeutic interventions was demonstrated.OCT reflectivity profiles provide a detailed, quantitative description of retinal layers and structures including specialized retinal regions. Our results highlight the

  13. The Current and Future Use of Ridge Regression for Prediction in Quantitative Genetics

    Directory of Open Access Journals (Sweden)

    Ronald de Vlaming

    2015-01-01

    Full Text Available In recent years, there has been a considerable amount of research on the use of regularization methods for inference and prediction in quantitative genetics. Such research mostly focuses on selection of markers and shrinkage of their effects. In this review paper, the use of ridge regression for prediction in quantitative genetics using single-nucleotide polymorphism data is discussed. In particular, we consider (i the theoretical foundations of ridge regression, (ii its link to commonly used methods in animal breeding, (iii the computational feasibility, and (iv the scope for constructing prediction models with nonlinear effects (e.g., dominance and epistasis. Based on a simulation study we gauge the current and future potential of ridge regression for prediction of human traits using genome-wide SNP data. We conclude that, for outcomes with a relatively simple genetic architecture, given current sample sizes in most cohorts (i.e., N<10,000 the predictive accuracy of ridge regression is slightly higher than the classical genome-wide association study approach of repeated simple regression (i.e., one regression per SNP. However, both capture only a small proportion of the heritability. Nevertheless, we find evidence that for large-scale initiatives, such as biobanks, sample sizes can be achieved where ridge regression compared to the classical approach improves predictive accuracy substantially.

  14. The Current and Future Use of Ridge Regression for Prediction in Quantitative Genetics.

    Science.gov (United States)

    de Vlaming, Ronald; Groenen, Patrick J F

    2015-01-01

    In recent years, there has been a considerable amount of research on the use of regularization methods for inference and prediction in quantitative genetics. Such research mostly focuses on selection of markers and shrinkage of their effects. In this review paper, the use of ridge regression for prediction in quantitative genetics using single-nucleotide polymorphism data is discussed. In particular, we consider (i) the theoretical foundations of ridge regression, (ii) its link to commonly used methods in animal breeding, (iii) the computational feasibility, and (iv) the scope for constructing prediction models with nonlinear effects (e.g., dominance and epistasis). Based on a simulation study we gauge the current and future potential of ridge regression for prediction of human traits using genome-wide SNP data. We conclude that, for outcomes with a relatively simple genetic architecture, given current sample sizes in most cohorts (i.e., N < 10,000) the predictive accuracy of ridge regression is slightly higher than the classical genome-wide association study approach of repeated simple regression (i.e., one regression per SNP). However, both capture only a small proportion of the heritability. Nevertheless, we find evidence that for large-scale initiatives, such as biobanks, sample sizes can be achieved where ridge regression compared to the classical approach improves predictive accuracy substantially.

  15. 59. Cold Spring Harbor symposium on quantitative biology: Molecular genetics of cancer

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1994-12-31

    Investigation of the mechanistic aspects of cancer has its roots in the studies on tumor viruses and their effects on cell proliferation, function, and growth. This outstanding progress was well documented in previous Cold Spring Harbor Symposia on Quantitative Biology. In the early to mid 1980s, progress on the development of chromosome mapping strategies and the accumulation of DNA probes that identified polymorphisms, encouraged by the international Human Genome Project, enabled the identification of other genes that contributed to familial inheritance of high susceptibility to specific cancers. This approach was very successful and led to a degree of optimism that one aspect of cancer, the multistep genetic process from early neoplasia to metastatic tumors, was beginning to be understood. It therefore seemed appropriate that the 59th Symposium on Quantitative Biology focus attention on the Molecular Genetics of Cancer. The concept was to combine the exciting progress on the identification of new genetic alterations in human tumor cells with studies on the function of the cancer gene products and how they go awry in tumor cells.

  16. The quantitative genetics of incipient speciation: heritability and genetic correlations of skeletal traits in populations of diverging Favia fragum ecomorphs.

    Science.gov (United States)

    Carlon, David B; Budd, Ann F; Lippé, Catherine; Andrew, Rose L

    2011-12-01

    Recent speciation events provide potential opportunities to understand the microevolution of reproductive isolation. We used a marker-based approach and a common garden to estimate the additive genetic variation in skeletal traits in a system of two ecomorphs within the coral species Favia fragum: a Tall ecomorph that is a seagrass specialist, and a Short ecomorph that is most abundant on coral reefs. Considering both ecomorphs, we found significant narrow-sense heritability (h(2) ) in a suite of measurements that define corallite architecture, and could partition additive and nonadditive variation for some traits. We found positive genetic correlations for homologous height and length measurements among different types of vertical plates (costosepta) within corallites, but negative correlations between height and length within, as well as between costosepta. Within ecomorphs, h(2) estimates were generally lower, compared to the combined ecomorph analysis. Marker-based estimates of h(2) were comparable to broad-sense heritability (H) obtained from parent-offspring regressions in a common garden for most traits, and similar genetic co-variance matrices for common garden and wild populations may indicate relatively small G × E interactions. The patterns of additive genetic variation in this system invite hypotheses of divergent selection or genetic drift as potential evolutionary drivers of reproductive isolation.

  17. Quantitative data analysis in education a critical introduction using SPSS

    CERN Document Server

    Connolly, Paul

    2007-01-01

    This book provides a refreshing and user-friendly guide to quantitative data analysis in education for students and researchers. It assumes absolutely no prior knowledge of quantitative methods or statistics. Beginning with the very basics, it provides the reader with the knowledge and skills necessary to be able to undertake routine quantitative data analysis to a level expected of published research. Rather than focusing on teaching statistics through mathematical formulae, the book places an emphasis on using SPSS to gain a real feel for the data and an intuitive grasp of t

  18. Genes and quantitative genetic variation involved with senescence in cells, organs and the whole plant

    Directory of Open Access Journals (Sweden)

    Benoit ePujol

    2015-02-01

    Full Text Available Senescence, the deterioration of morphological, physiological and reproductive functions with age that ends with the death of the organism, was widely studied in plants. Genes were identified that are linked to the deterioration of cells, organs and the whole plant. It is however unclear whether those genes are the source of age dependent deterioration or get activated to regulate such deterioration. Furthermore, it is also unclear whether such genes are active as a direct consequence of age or because they are specifically involved in some developmental stages. At the individual level, it is the relationship between quantitative genetic variation and age that can be used to detect the genetic signature of senescence. Surprisingly, the latter approach was only scarcely applied to plants. This may be the consequence of the demanding requirements for such approaches and/or the fact that most research interest was directed towards plants that avoid senescence. Here, I review those aspects in turn and call for an integrative genetic theory of senescence in plants. Such conceptual development would have implications for the management of plant genetic resources and generate progress on fundamental questions raised by ageing research.

  19. Applied quantitative analysis in the social sciences

    CERN Document Server

    Petscher, Yaacov; Compton, Donald L

    2013-01-01

    To say that complex data analyses are ubiquitous in the education and social sciences might be an understatement. Funding agencies and peer-review journals alike require that researchers use the most appropriate models and methods for explaining phenomena. Univariate and multivariate data structures often require the application of more rigorous methods than basic correlational or analysis of variance models. Additionally, though a vast set of resources may exist on how to run analysis, difficulties may be encountered when explicit direction is not provided as to how one should run a model

  20. Quantitative analysis of probabilistic BPMN workflows

    DEFF Research Database (Denmark)

    Herbert, Luke Thomas; Sharp, Robin

    2012-01-01

    We present a framework for modelling and analysis of realworld business workflows. We present a formalised core subset of the Business Process Modelling and Notation (BPMN) and then proceed to extend this language with probabilistic nondeterministic branching and general-purpose reward annotations...... of events, reward-based properties and best- and worst- case scenarios. We develop a simple example of medical workflow and demonstrate the utility of this analysis in accurate provisioning of drug stocks. Finally, we suggest a path to building upon these techniques to cover the entire BPMN language, allow...

  1. The quantitative failure of human reliability analysis

    Energy Technology Data Exchange (ETDEWEB)

    Bennett, C.T.

    1995-07-01

    This philosophical treatise argues the merits of Human Reliability Analysis (HRA) in the context of the nuclear power industry. Actually, the author attacks historic and current HRA as having failed in informing policy makers who make decisions based on risk that humans contribute to systems performance. He argues for an HRA based on Bayesian (fact-based) inferential statistics, which advocates a systems analysis process that employs cogent heuristics when using opinion, and tempers itself with a rational debate over the weight given subjective and empirical probabilities.

  2. Quantitative analysis of somatic mitochondrial DNA mutations by single-cell single-molecule PCR.

    Science.gov (United States)

    Kraytsberg, Yevgenya; Bodyak, Natalya; Myerow, Susan; Nicholas, Alexander; Ebralidze, Konstantin; Khrapko, Konstantin

    2009-01-01

    Mitochondrial genome integrity is an important issue in somatic mitochondrial genetics. Development of quantitative methods is indispensable to somatic mitochondrial genetics as quantitative studies are required to characterize heteroplasmy and mutation processes, as well as their effects on phenotypic developments. Quantitative studies include the identification and measurement of the load of pathogenic and non-pathogenic clonal mutations, screening mitochondrial genomes for mutations in order to determine the mutation spectra and characterize an ongoing mutation process. Single-molecule PCR (smPCR) has been shown to be an effective method that can be applied to all areas of quantitative studies. It has distinct advantages over conventional vector-based cloning techniques avoiding the well-known PCR-related artifacts such as the introduction of artificial mutations, preferential allelic amplifications, and "jumping" PCR. smPCR is a straightforward and robust method, which can be effectively used for molecule-by-molecule mutational analysis, even when mitochondrial whole genome (mtWG) analysis is involved. This chapter describes the key features of the smPCR method and provides three examples of its applications in single-cell analysis: di-plex smPCR for deletion quantification, smPCR cloning for clonal point mutation quantification, and smPCR cloning for whole genome sequencing (mtWGS).

  3. Effects of long-term averaging of quantitative blood pressure traits on the detection of genetic associations.

    Science.gov (United States)

    Ganesh, Santhi K; Chasman, Daniel I; Larson, Martin G; Guo, Xiuqing; Verwoert, Germain; Bis, Joshua C; Gu, Xiangjun; Smith, Albert V; Yang, Min-Lee; Zhang, Yan; Ehret, Georg; Rose, Lynda M; Hwang, Shih-Jen; Papanicolau, George J; Sijbrands, Eric J; Rice, Kenneth; Eiriksdottir, Gudny; Pihur, Vasyl; Ridker, Paul M; Vasan, Ramachandran S; Newton-Cheh, Christopher; Raffel, Leslie J; Amin, Najaf; Rotter, Jerome I; Liu, Kiang; Launer, Lenore J; Xu, Ming; Caulfield, Mark; Morrison, Alanna C; Johnson, Andrew D; Vaidya, Dhananjay; Dehghan, Abbas; Li, Guo; Bouchard, Claude; Harris, Tamara B; Zhang, He; Boerwinkle, Eric; Siscovick, David S; Gao, Wei; Uitterlinden, Andre G; Rivadeneira, Fernando; Hofman, Albert; Willer, Cristen J; Franco, Oscar H; Huo, Yong; Witteman, Jacqueline C M; Munroe, Patricia B; Gudnason, Vilmundur; Palmas, Walter; van Duijn, Cornelia; Fornage, Myriam; Levy, Daniel; Psaty, Bruce M; Chakravarti, Aravinda

    2014-07-03

    Blood pressure (BP) is a heritable, quantitative trait with intraindividual variability and susceptibility to measurement error. Genetic studies of BP generally use single-visit measurements and thus cannot remove variability occurring over months or years. We leveraged the idea that averaging BP measured across time would improve phenotypic accuracy and thereby increase statistical power to detect genetic associations. We studied systolic BP (SBP), diastolic BP (DBP), mean arterial pressure (MAP), and pulse pressure (PP) averaged over multiple years in 46,629 individuals of European ancestry. We identified 39 trait-variant associations across 19 independent loci (p < 5 × 10(-8)); five associations (in four loci) uniquely identified by our LTA analyses included those of SBP and MAP at 2p23 (rs1275988, near KCNK3), DBP at 2q11.2 (rs7599598, in FER1L5), and PP at 6p21 (rs10948071, near CRIP3) and 7p13 (rs2949837, near IGFBP3). Replication analyses conducted in cohorts with single-visit BP data showed positive replication of associations and a nominal association (p < 0.05). We estimated a 20% gain in statistical power with long-term average (LTA) as compared to single-visit BP association studies. Using LTA analysis, we identified genetic loci influencing BP. LTA might be one way of increasing the power of genetic associations for continuous traits in extant samples for other phenotypes that are measured serially over time. Copyright © 2014 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

  4. An integrated system for genetic analysis

    Directory of Open Access Journals (Sweden)

    Duan Xiao

    2006-04-01

    Full Text Available Abstract Background Large-scale genetic mapping projects require data management systems that can handle complex phenotypes and detect and correct high-throughput genotyping errors, yet are easy to use. Description We have developed an Integrated Genotyping System (IGS to meet this need. IGS securely stores, edits and analyses genotype and phenotype data. It stores information about DNA samples, plates, primers, markers and genotypes generated by a genotyping laboratory. Data are structured so that statistical genetic analysis of both case-control and pedigree data is straightforward. Conclusion IGS can model complex phenotypes and contain genotypes from whole genome association studies. The database makes it possible to integrate genetic analysis with data curation. The IGS web site http://bioinformatics.well.ox.ac.uk/project-igs.shtml contains further information.

  5. Quantitative analysis of cascade impactor samples - revisited

    Science.gov (United States)

    Orlić , I.; Chiam, S. Y.; Sanchez, J. L.; Tang, S. M.

    1999-04-01

    Concentrations of aerosols collected in Singapore during the three months long haze period that affected the whole South-East Asian region in 1997 are reported. Aerosol samples were continuously collected by using a fine aerosol sampler (PM2.5) and occasionally with a single orifice cascade impactor (CI) sampler. Our results show that in the fine fraction (<2.5 μm) the concentrations of two well-known biomass burning products, i.e. K and S were generally increased by a factor 2-3 compared to the non-hazy periods. However, a discrepancy was noticed, at least for elements with lower atomic number (Ti and below) between the results obtained by the fine aerosol sampler and the cascade impactor. Careful analysis by means of Nuclear Microscopy, in particular by the Scanning Transmission Ion Microscopy (STIM) technique, revealed that thicknesses of the lower CI stages exceeded thick target limits for 2 MeV protons. Detailed depth profiles of all CI stages were therefore measured using the STIM technique and concentrations corrected for absorption and proton energy loss. After correcting results for the actual sample thickness, concentrations of all major elements (S, Cl, K, Ca) agreed much better with the PM2.5 results. The importance of implementing thick target corrections in analysis of CI samples, especially those collected in the urban environments, is emphasized. Broad beam PIXE analysis approach is certainly not adequate in these cases.

  6. Quantitative analysis of Li by PIGE technique

    Science.gov (United States)

    Fonseca, M.; Mateus, R.; Santos, C.; Cruz, J.; Silva, H.; Luis, H.; Martins, L.; Jesus, A. P.

    2017-09-01

    In this work, the cross section of the reactions 7Li(p,pγ)7Li (γ - 478 keV) at the proton energy range 2.0-4.2 MeV was measured. The measurements were carried out at the 3 MV Tandem Accelerator at the CTN/IST Laboratory in Lisbon. To validate the obtained results, calculated gamma-ray yields were compared, at several proton energy values, with experimental yields for thick samples made of inorganic compounds containing lithium. In order to quantify the light elements present in the samples, we used a standard free method for PIGE in thick samples, based on a code - Emitted Radiation Yield Analysis (ERYA), which integrates the nuclear reaction excitation function along the depth of the sample. We also demonstrated the capacity of the technique for analysis of Li ores, as Spodumene, Lithium Muscovite and Holmquistite, and Li-alloys for plasma facing materials showing that this is a reliable and accurate method for PIGE analysis of Li in thick samples.

  7. Quantitative MRI analysis of dynamic enhancement of focal liver lesions

    Directory of Open Access Journals (Sweden)

    S. S. Bagnenko

    2012-01-01

    Full Text Available In our study 45 patients with different focal liver lesions (110 nodules were examined using high field MR-system (1,5 T. During this investigation quantitative MRI analysis of dynamic enhancement of various hepatic lesions and parenchymatous organs of abdomen were performed. It was shown that quantitative evaluation of enhanced MRI improves understanding of vascular transformation processes in pathologic hepatic focuses and in liver itself that is important for differential diagnoses of these diseases.

  8. Quantitative genome-wide genetic interaction screens reveal global epistatic relationships of protein complexes in Escherichia coli.

    Directory of Open Access Journals (Sweden)

    Mohan Babu

    2014-02-01

    Full Text Available Large-scale proteomic analyses in Escherichia coli have documented the composition and physical relationships of multiprotein complexes, but not their functional organization into biological pathways and processes. Conversely, genetic interaction (GI screens can provide insights into the biological role(s of individual gene and higher order associations. Combining the information from both approaches should elucidate how complexes and pathways intersect functionally at a systems level. However, such integrative analysis has been hindered due to the lack of relevant GI data. Here we present a systematic, unbiased, and quantitative synthetic genetic array screen in E. coli describing the genetic dependencies and functional cross-talk among over 600,000 digenic mutant combinations. Combining this epistasis information with putative functional modules derived from previous proteomic data and genomic context-based methods revealed unexpected associations, including new components required for the biogenesis of iron-sulphur and ribosome integrity, and the interplay between molecular chaperones and proteases. We find that functionally-linked genes co-conserved among γ-proteobacteria are far more likely to have correlated GI profiles than genes with divergent patterns of evolution. Overall, examining bacterial GIs in the context of protein complexes provides avenues for a deeper mechanistic understanding of core microbial systems.

  9. Genetic Analysis on Bent Characters of Cucumber Fruit

    Institute of Scientific and Technical Information of China (English)

    ZHANG Peng; QIN Zhiwei; WANG Lili; ZHOU Xiuyan

    2011-01-01

    Bent varieties and straight varieties were made as parents for the genetic analysis to investigate cucumber bending genetic mechanism. The results showed that the bent characters of the cucumber fruit (BCCF) were quantitative inheritance controlled by multiple genes and major genes. The additive effect played the main role and the dominance effect played the lesser role. Compared with the additive environmental variance, the dominant-environmental variance was more important and the cucumber fruit was more easily affected by the additive effect. The broad heritability and the narrow heritability of BCCF were both higher. The varieties of D0455 and D07299 could be used as parents which were benefit for improving the straight characters of the cucumber fruit

  10. Determination of Mycotoxin Production of Fusarium Species in Genetically Modified Maize Varieties by Quantitative Flow Immunocytometry

    Science.gov (United States)

    Bánáti, Hajnalka; Darvas, Béla; Fehér-Tóth, Szilvia; Czéh, Árpád; Székács, András

    2017-01-01

    Levels of mycotoxins produced by Fusarium species in genetically modified (GM) and near-isogenic maize, were determined using multi-analyte, microbead-based flow immunocytometry with fluorescence detection, for the parallel quantitative determination of fumonisin B1, deoxynivalenol, zearalenone, T-2, ochratoxin A, and aflatoxin B1. Maize varieties included the genetic events MON 810 and DAS-59122-7, and their isogenic counterparts. Cobs were artificially infested by F. verticillioides and F. proliferatum conidia, and contained F. graminearum and F. sporotrichoides natural infestation. The production of fumonisin B1 and deoxynivalenol was substantially affected in GM maize lines: F. verticillioides, with the addition of F. graminearum and F. sporotrichoides, produced significantly lower levels of fumonisin B1 (~300 mg·kg−1) in DAS-59122-7 than in its isogenic line (~580 mg·kg−1), while F. proliferatum, in addition to F. graminearum and F. sporotrichoides, produced significantly higher levels of deoxynivalenol (~18 mg·kg−1) in MON 810 than in its isogenic line (~5 mg·kg−1). Fusarium verticillioides, with F. graminearum and F. sporotrichoides, produced lower amounts of deoxynivalenol and zearalenone than F. proliferatum, with F. graminearum and F. sporotrichoides. T-2 toxin production remained unchanged when considering the maize variety. The results demonstrate the utility of the Fungi-Plex™ quantitative flow immunocytometry method, applied for the high throughput parallel determination of the target mycotoxins. PMID:28241411

  11. The genetic architecture of heterochronsy as a quantitative trait: lessons from a computational model.

    Science.gov (United States)

    Sun, Lidan; Sang, Mengmeng; Zheng, Chenfei; Wang, Dongyang; Shi, Hexin; Liu, Kaiyue; Guo, Yanfang; Cheng, Tangren; Zhang, Qixiang; Wu, Rongling

    2017-05-30

    Heterochrony is known as a developmental change in the timing or rate of ontogenetic events across phylogenetic lineages. It is a key concept synthesizing development into ecology and evolution to explore the mechanisms of how developmental processes impact on phenotypic novelties. A number of molecular experiments using contrasting organisms in developmental timing have identified specific genes involved in heterochronic variation. Beyond these classic approaches that can only identify single genes or pathways, quantitative models derived from current next-generation sequencing data serve as a more powerful tool to precisely capture heterochronic variation and systematically map a complete set of genes that contribute to heterochronic processes. In this opinion note, we discuss a computational framework of genetic mapping that can characterize heterochronic quantitative trait loci that determine the pattern and process of development. We propose a unifying model that charts the genetic architecture of heterochrony that perceives and responds to environmental perturbations and evolves over geologic time. The new model may potentially enhance our understanding of the adaptive value of heterochrony and its evolutionary origins, providing a useful context for designing new organisms that can best use future resources. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  12. FRET-based genetically-encoded sensors for quantitative monitoring of metabolites.

    Science.gov (United States)

    Mohsin, Mohd; Ahmad, Altaf; Iqbal, Muhammad

    2015-10-01

    Neighboring cells in the same tissue can exist in different states of dynamic activities. After genomics, proteomics and metabolomics, fluxomics is now equally important for generating accurate quantitative information on the cellular and sub-cellular dynamics of ions and metabolite, which is critical for functional understanding of organisms. Various spectrometry techniques are used for monitoring ions and metabolites, although their temporal and spatial resolutions are limited. Discovery of the fluorescent proteins and their variants has revolutionized cell biology. Therefore, novel tools and methods targeting sub-cellular compartments need to be deployed in specific cells and targeted to sub-cellular compartments in order to quantify the target-molecule dynamics directly. We require tools that can measure cellular activities and protein dynamics with sub-cellular resolution. Biosensors based on fluorescence resonance energy transfer (FRET) are genetically encoded and hence can specifically target sub-cellular organelles by fusion to proteins or targetted sequences. Since last decade, FRET-based genetically encoded sensors for molecules involved in energy production, reactive oxygen species and secondary messengers have helped to unravel key aspects of cellular physiology. This review, describing the design and principles of sensors, presents a database of sensors for different analytes/processes, and illustrate examples of application in quantitative live cell imaging.

  13. Financial indicators for municipalities: a quantitative analysis

    Directory of Open Access Journals (Sweden)

    Sreĉko Devjak

    2009-12-01

    Full Text Available From the characterization of Local Authority financing models and structures in Portugal and Slovenia, a set of financial and generic budget indicators has been established. These indicators may be used in a comparative analysis considering the Bragança District in Portugal, and municipalities of similar population size in Slovenia. The research identified significant differences, in terms of financing sources due to some discrepancies on financial models and competences of municipalities on each country. The results show that Portuguese and Slovenian municipalities, in 2003, for the economy indicator, had similar ranking behaviour, but in 2004, they changed this behaviour.

  14. QUANTITATIVE ANALYSIS OF DRAWING TUBES MICROSTRUCTURE

    Directory of Open Access Journals (Sweden)

    Maroš Martinkovič

    2009-05-01

    Full Text Available Final properties of forming pieces are affected by production, at first conditions of mechanical working. Application of stereology methods to statistic reconstruction of three-dimensional plastic deformed material structure by bulk forming led to detail analysis of material structure changes. The microstructure of cold drawing tubes from STN 411353 steel was analyzed. Grain boundaries orientation was measured on perpendicular and parallel section of tubes with different degree of deformation. Macroscopic deformation leads to grain boundaries deformation and these ones were compared.

  15. Chromatic Image Analysis For Quantitative Thermal Mapping

    Science.gov (United States)

    Buck, Gregory M.

    1995-01-01

    Chromatic image analysis system (CIAS) developed for use in noncontact measurements of temperatures on aerothermodynamic models in hypersonic wind tunnels. Based on concept of temperature coupled to shift in color spectrum for optical measurement. Video camera images fluorescence emitted by phosphor-coated model at two wavelengths. Temperature map of model then computed from relative brightnesses in video images of model at those wavelengths. Eliminates need for intrusive, time-consuming, contact temperature measurements by gauges, making it possible to map temperatures on complex surfaces in timely manner and at reduced cost.

  16. Segmentation and Quantitative Analysis of Epithelial Tissues.

    Science.gov (United States)

    Aigouy, Benoit; Umetsu, Daiki; Eaton, Suzanne

    2016-01-01

    Epithelia are tissues that regulate exchanges with the environment. They are very dynamic and can acquire virtually any shape; at the cellular level, they are composed of cells tightly connected by junctions. Most often epithelia are amenable to live imaging; however, the large number of cells composing an epithelium and the absence of informatics tools dedicated to epithelial analysis largely prevented tissue scale studies. Here we present Tissue Analyzer, a free tool that can be used to segment and analyze epithelial cells and monitor tissue dynamics.

  17. A Comparative Assessment of Greek Universities' Efficiency Using Quantitative Analysis

    Science.gov (United States)

    Katharaki, Maria; Katharakis, George

    2010-01-01

    In part due to the increased demand for higher education, typical evaluation frameworks for universities often address the key issue of available resource utilisation. This study seeks to estimate the efficiency of 20 public universities in Greece through quantitative analysis (including performance indicators, data envelopment analysis (DEA) and…

  18. A Comparative Assessment of Greek Universities' Efficiency Using Quantitative Analysis

    Science.gov (United States)

    Katharaki, Maria; Katharakis, George

    2010-01-01

    In part due to the increased demand for higher education, typical evaluation frameworks for universities often address the key issue of available resource utilisation. This study seeks to estimate the efficiency of 20 public universities in Greece through quantitative analysis (including performance indicators, data envelopment analysis (DEA) and…

  19. A Classifier Model based on the Features Quantitative Analysis for Facial Expression Recognition

    Directory of Open Access Journals (Sweden)

    Amir Jamshidnezhad

    2011-01-01

    Full Text Available In recent decades computer technology has considerable developed in use of intelligent systems for classification. The development of HCI systems is highly depended on accurate understanding of emotions. However, facial expressions are difficult to classify by a mathematical models because of natural quality. In this paper, quantitative analysis is used in order to find the most effective features movements between the selected facial feature points. Therefore, the features are extracted not only based on the psychological studies, but also based on the quantitative methods to arise the accuracy of recognitions. Also in this model, fuzzy logic and genetic algorithm are used to classify facial expressions. Genetic algorithm is an exclusive attribute of proposed model which is used for tuning membership functions and increasing the accuracy.

  20. Optimization of genetic analysis for single cell

    Directory of Open Access Journals (Sweden)

    hussein mouawia

    2012-12-01

    Full Text Available The molecular genetic analysis of microdissected cells by laser, a method for selecting a starting material of pure DNA or RNA uncontaminated. Our study focuses on technical pre-PCR (polymerase chain reaction for the amplification of DNA from a single cell (leukocyte isolated from human blood after laser microdissection and aims to optimize the yield of DNA extracted of this cell to be amplified without errors and provide reliable genetic analyzes. This study has allowed us to reduce the duration of cell lysis in order to perform the step of expanding genomic PEP (primer extension preamplification directly after lysis the same day and the quality of genomic amplification and eliminate purification step of the product PEP, step with a risk of contamination and risk of loss of genetic material related to manipulation. This approach has shown that the combination of at least 3 STR (short tandem repeat markers for genetic analysis of single cell improves the efficiency and accuracy of PCR and minimizes the loss of allele (allele drop out; ADO. This protocol can be applied to large scale and an effective means suitable for genetic testing for molecular diagnostic from isolated single cell (cancerous - fetal.

  1. Quantitative Analysis of Seismicity in Iran

    Science.gov (United States)

    Raeesi, Mohammad; Zarifi, Zoya; Nilfouroushan, Faramarz; Boroujeni, Samar Amini; Tiampo, Kristy

    2017-03-01

    We use historical and recent major earthquakes and GPS geodetic data to compute seismic strain rate, geodetic slip deficit, static stress drop, the parameters of the magnitude-frequency distribution and geodetic strain rate in the Iranian Plateau to identify seismically mature fault segments and regions. Our analysis suggests that 11 fault segments are in the mature stage of the earthquake cycle, with the possibility of generating major earthquakes. These faults primarily are located in the north and the east of Iran. Four seismically mature regions in southern Iran with the potential for damaging strong earthquakes are also identified. We also delineate four additional fault segments in Iran that can generate major earthquakes without robust clues to their maturity.The most important fault segment in this study is the strike-slip system near the capital city of Tehran, with the potential to cause more than one million fatalities.

  2. Quantitative Analysis of Seismicity in Iran

    Science.gov (United States)

    Raeesi, Mohammad; Zarifi, Zoya; Nilfouroushan, Faramarz; Boroujeni, Samar Amini; Tiampo, Kristy

    2016-12-01

    We use historical and recent major earthquakes and GPS geodetic data to compute seismic strain rate, geodetic slip deficit, static stress drop, the parameters of the magnitude-frequency distribution and geodetic strain rate in the Iranian Plateau to identify seismically mature fault segments and regions. Our analysis suggests that 11 fault segments are in the mature stage of the earthquake cycle, with the possibility of generating major earthquakes. These faults primarily are located in the north and the east of Iran. Four seismically mature regions in southern Iran with the potential for damaging strong earthquakes are also identified. We also delineate four additional fault segments in Iran that can generate major earthquakes without robust clues to their maturity.The most important fault segment in this study is the strike-slip system near the capital city of Tehran, with the potential to cause more than one million fatalities.

  3. Methods of sports genetics: dermatoglyphic analysis of human palmarprints (information 2

    Directory of Open Access Journals (Sweden)

    Serhiyenko L.P.

    2010-01-01

    Full Text Available Information is generalized about the dermatoglyphic analysis of hands of hands of man. The quantitative dermatoglyphic indexes of hands of hands are presented for youths and girls of the Podol region of Ukraine. The quantitative indexes of palm's dermatoglyphics are rotined for youths and girls of Ukrainian and Russian nationality in Kharkov. The most informing dermatoglyphic indexes of hands of hands which it is possible to use in sporting genetics are certain. Formed recommendation on technology of dermatoglyphic analysis of hands of hands of man in sporting genetics.

  4. Quantitative Assessment of Eye Phenotypes for Functional Genetic Studies Using Drosophila melanogaster

    Science.gov (United States)

    Iyer, Janani; Wang, Qingyu; Le, Thanh; Pizzo, Lucilla; Grönke, Sebastian; Ambegaokar, Surendra S.; Imai, Yuzuru; Srivastava, Ashutosh; Troisí, Beatriz Llamusí; Mardon, Graeme; Artero, Ruben; Jackson, George R.; Isaacs, Adrian M.; Partridge, Linda; Lu, Bingwei; Kumar, Justin P.; Girirajan, Santhosh

    2016-01-01

    About two-thirds of the vital genes in the Drosophila genome are involved in eye development, making the fly eye an excellent genetic system to study cellular function and development, neurodevelopment/degeneration, and complex diseases such as cancer and diabetes. We developed a novel computational method, implemented as Flynotyper software (http://flynotyper.sourceforge.net), to quantitatively assess the morphological defects in the Drosophila eye resulting from genetic alterations affecting basic cellular and developmental processes. Flynotyper utilizes a series of image processing operations to automatically detect the fly eye and the individual ommatidium, and calculates a phenotypic score as a measure of the disorderliness of ommatidial arrangement in the fly eye. As a proof of principle, we tested our method by analyzing the defects due to eye-specific knockdown of Drosophila orthologs of 12 neurodevelopmental genes to accurately document differential sensitivities of these genes to dosage alteration. We also evaluated eye images from six independent studies assessing the effect of overexpression of repeats, candidates from peptide library screens, and modifiers of neurotoxicity and developmental processes on eye morphology, and show strong concordance with the original assessment. We further demonstrate the utility of this method by analyzing 16 modifiers of sine oculis obtained from two genome-wide deficiency screens of Drosophila and accurately quantifying the effect of its enhancers and suppressors during eye development. Our method will complement existing assays for eye phenotypes, and increase the accuracy of studies that use fly eyes for functional evaluation of genes and genetic interactions. PMID:26994292

  5. Quantitative resistance against Bemisia tabaci in Solanum pennellii:Genetics and metabolomics

    Institute of Scientific and Technical Information of China (English)

    Alejandro F Lucatti; Sjaak van Heusden; Colette Broekgaarden; Roland Mumm; Marcel Dicke; Ben Vosman

    2016-01-01

    The whitefly Bemisia tabaci is a serious threat in tomato cultivation worldwide as all varieties grown today are highly susceptible to this devastating herbivorous insect. Many accessions of the tomato wild relative Solanum pennellii show a high resistance towards B. tabaci. A mapping approach was used to elucidate the genetic background of whitefly-resistance related traits and associated biochemical traits in this species. Minor quantitative trait loci (QTLs) for whitefly adult survival (AS) and oviposition rate (OR) were identified and some were confirmed in an F2BC1 population, where they showed increased percentages of explained variance (more than 30%). Bulked segregant analyses on pools of whitefly-resistant and-susceptible F2 plants enabled the identification of metabolites that correlate either with resistance or susceptibility. Genetic mapping of these metabolites showed that a large number of them co-localize with whitefly-resistance QTLs. Some of these whitefly-resistance QTLs are hotspots for metabolite QTLs. Although a large number of metabolite QTLs correlated to whitefly resistance or suscepti-bility, most of them are yet unknown compounds and further studies are needed to identify the metabolic pathways and genes involved. The results indicate a direct genetic correla-tion between biochemical-based resistance characteristics and reduced whitefly incidence in S. pennellii.

  6. Quantitative analysis of forest fire extinction efficiency

    Directory of Open Access Journals (Sweden)

    Miguel E. Castillo-Soto

    2015-08-01

    Full Text Available Aim of study: Evaluate the economic extinction efficiency of forest fires, based on the study of fire combat undertaken by aerial and terrestrial means. Area of study, materials and methods: Approximately 112,000 hectares in Chile. Records of 5,876 forest fires that occurred between 1998 and 2009 were analyzed. The area further provides a validation sector for results, by incorporating databases for the years 2010 and 2012. The criteria used for measuring extinction efficiency were economic value of forestry resources, Contraction Factor analysis and definition of the extinction costs function. Main results: It is possible to establish a relationship between burnt area, extinction costs and economic losses. The method proposed may be used and adapted to other fire situations, requiring unit costs for aerial and terrestrial operations, economic value of the property to be protected and speed attributes of fire spread in free advance. Research highlights: The determination of extinction efficiency in containment works of forest fires and potential projection of losses, different types of plant fuel and local conditions favoring the spread of fire broaden the admissible ranges of a, φ and Ce considerably.

  7. Uncertainty of quantitative microbiological methods of pharmaceutical analysis.

    Science.gov (United States)

    Gunar, O V; Sakhno, N G

    2015-12-30

    The total uncertainty of quantitative microbiological methods, used in pharmaceutical analysis, consists of several components. The analysis of the most important sources of the quantitative microbiological methods variability demonstrated no effect of culture media and plate-count techniques in the estimation of microbial count while the highly significant effect of other factors (type of microorganism, pharmaceutical product and individual reading and interpreting errors) was established. The most appropriate method of statistical analysis of such data was ANOVA which enabled not only the effect of individual factors to be estimated but also their interactions. Considering all the elements of uncertainty and combining them mathematically the combined relative uncertainty of the test results was estimated both for method of quantitative examination of non-sterile pharmaceuticals and microbial count technique without any product. These data did not exceed 35%, appropriated for a traditional plate count methods.

  8. Linkage analysis of quantitative trait loci in the presence of heterogeneity.

    Science.gov (United States)

    Ekstrøm, Claus Thorn; Dalgaard, Peter

    2003-01-01

    Variance component modeling for linkage analysis of quantitative traits is a powerful tool for detecting and locating genes affecting a trait of interest, but the presence of genetic heterogeneity will decrease the power of a linkage study and may even give biased estimates of the location of the quantitative trait loci. Many complex diseases are believed to be influenced by multiple genes and therefore genetic heterogeneity is likely to be present for many real applications of linkage analysis. We consider a mixture of multivariate normals to model locus heterogeneity by allowing only a proportion of the sampled pedigrees to segregate trait-influencing allele(s) at a specific locus. However, for mixtures of normals the classical asymptotic distribution theory of the maximum likelihood estimates does not hold, so tests of linkage and/or heterogeneity are evaluated using resampling methods. It is shown that allowing for genetic heterogeneity leads to an increase in power to detect linkage. This increase is more prominent when the genetic effect of the locus is small or when the percentage of pedigrees not segregating trait-influencing allele(s) at the locus is high.

  9. Pleiotropy analysis of quantitative traits at gene level by multivariate functional linear models.

    Science.gov (United States)

    Wang, Yifan; Liu, Aiyi; Mills, James L; Boehnke, Michael; Wilson, Alexander F; Bailey-Wilson, Joan E; Xiong, Momiao; Wu, Colin O; Fan, Ruzong

    2015-05-01

    In genetics, pleiotropy describes the genetic effect of a single gene on multiple phenotypic traits. A common approach is to analyze the phenotypic traits separately using univariate analyses and combine the test results through multiple comparisons. This approach may lead to low power. Multivariate functional linear models are developed to connect genetic variant data to multiple quantitative traits adjusting for covariates for a unified analysis. Three types of approximate F-distribution tests based on Pillai-Bartlett trace, Hotelling-Lawley trace, and Wilks's Lambda are introduced to test for association between multiple quantitative traits and multiple genetic variants in one genetic region. The approximate F-distribution tests provide much more significant results than those of F-tests of univariate analysis and optimal sequence kernel association test (SKAT-O). Extensive simulations were performed to evaluate the false positive rates and power performance of the proposed models and tests. We show that the approximate F-distribution tests control the type I error rates very well. Overall, simultaneous analysis of multiple traits can increase power performance compared to an individual test of each trait. The proposed methods were applied to analyze (1) four lipid traits in eight European cohorts, and (2) three biochemical traits in the Trinity Students Study. The approximate F-distribution tests provide much more significant results than those of F-tests of univariate analysis and SKAT-O for the three biochemical traits. The approximate F-distribution tests of the proposed functional linear models are more sensitive than those of the traditional multivariate linear models that in turn are more sensitive than SKAT-O in the univariate case. The analysis of the four lipid traits and the three biochemical traits detects more association than SKAT-O in the univariate case.

  10. Quantitative methods for the analysis of electron microscope images

    DEFF Research Database (Denmark)

    Skands, Peter Ulrik Vallø

    1996-01-01

    The topic of this thesis is an general introduction to quantitative methods for the analysis of digital microscope images. The images presented are primarily been acquired from Scanning Electron Microscopes (SEM) and interfermeter microscopes (IFM). The topic is approached though several examples...... foundation of the thesis fall in the areas of: 1) Mathematical Morphology; 2) Distance transforms and applications; and 3) Fractal geometry. Image analysis opens in general the possibility of a quantitative and statistical well founded measurement of digital microscope images. Herein lies also the conditions...

  11. Systems genetics of liver fibrosis: identification of fibrogenic and expression quantitative trait loci in the BXD murine reference population.

    Directory of Open Access Journals (Sweden)

    Rabea A Hall

    Full Text Available The progression of liver fibrosis in response to chronic injury varies considerably among individual patients. The underlying genetics is highly complex due to large numbers of potential genes, environmental factors and cell types involved. Here, we provide the first toxicogenomic analysis of liver fibrosis induced by carbon tetrachloride in the murine 'genetic reference panel' of recombinant inbred BXD lines. Our aim was to define the core of risk genes and gene interaction networks that control fibrosis progression. Liver fibrosis phenotypes and gene expression profiles were determined in 35 BXD lines. Quantitative trait locus (QTL analysis identified seven genomic loci influencing fibrosis phenotypes (pQTLs with genome-wide significance on chromosomes 4, 5, 7, 12, and 17. Stepwise refinement was based on expression QTL mapping with stringent selection criteria, reducing the number of 1,351 candidate genes located in the pQTLs to a final list of 11 cis-regulated genes. Our findings demonstrate that the BXD reference population represents a powerful experimental resource for shortlisting the genes within a regulatory network that determine the liver's vulnerability to chronic injury.

  12. Quantitative genetic analysis of methylxanthines and phenolic compounds in mate progenies Análise genética quantitativa de metilxantinas e compostos fenólicos em progênies de erva-mate

    Directory of Open Access Journals (Sweden)

    Euclides Lara Cardozo Junior

    2010-02-01

    Full Text Available The objective of this work was to determine the contents of methylxanthines, caffeine and theobromine, and phenolic compounds, chlorogenic and caffeic acids, in 51 mate progenies (half-sib families and estimate the heritability of genetic parameters. Mate progenies were from five Brazilian municipalities: Pinhão, Ivaí, Barão de Cotegipe, Quedas do Iguaçu, and Cascavel. The progenies were grown in the Ivaí locality. The contents of the compounds were obtained by high performance liquid chromatography (HPLC. The estimation of genetic parameters by the restricted maximum likelihood (REML and the prediction of genotypic values via best linear unbiased prediction (BLUP were obtained by the Selegen - REML/BLUP software. Caffeine (0.248-1.663% and theobromine (0.106-0.807% contents were significantly different (p0.5. The two different progeny groups determined for chlorogenic (1.365-2.281% and caffeic (0.027-0.037% acid contents were not significantly different (pO objetivo deste trabalho foi determinar o teor de metilxantinas, cafeína e teobromina, e de compostos fenólicos, ácido clorogênico e ácido cafeico, em 51 progênies de erva-mate e estimar componentes de variância e herdabilidade. As progênies de erva-mate eram oriundas de cinco municipios brasileiros: Pinhão, Ivaí, Barão do Cotegipe, Quedas do Iguaçu e Cascavel. Essas progênies foram cultivadas na localidade de Ivaí. O conteúdo dos compostos foi obtido por cromatografia líquida de alta eficiência (CLAE. Na estimativa dos componentes da variância e dos parâmetros genotípicos, utilizou-se a metodologia de modelos mistos para a obtenção da melhor predição linear não viciada (BLUP dos efeitos genotípicos e o processo da máxima verossimilhança restrita (REML, processados pelo programa Selegen - REML/BLUP. Os conteúdos de cafeína (0,248-1,663 % e teobromina (0,106-0.807% foram significativamente (p0,5. Foram determinados dois diferentes grupos de progênie para

  13. Impact of measurement error on testing genetic association with quantitative traits.

    Directory of Open Access Journals (Sweden)

    Jiemin Liao

    Full Text Available Measurement error of a phenotypic trait reduces the power to detect genetic associations. We examined the impact of sample size, allele frequency and effect size in presence of measurement error for quantitative traits. The statistical power to detect genetic association with phenotype mean and variability was investigated analytically. The non-centrality parameter for a non-central F distribution was derived and verified using computer simulations. We obtained equivalent formulas for the cost of phenotype measurement error. Effects of differences in measurements were examined in a genome-wide association study (GWAS of two grading scales for cataract and a replication study of genetic variants influencing blood pressure. The mean absolute difference between the analytic power and simulation power for comparison of phenotypic means and variances was less than 0.005, and the absolute difference did not exceed 0.02. To maintain the same power, a one standard deviation (SD in measurement error of a standard normal distributed trait required a one-fold increase in sample size for comparison of means, and a three-fold increase in sample size for comparison of variances. GWAS results revealed almost no overlap in the significant SNPs (p<10(-5 for the two cataract grading scales while replication results in genetic variants of blood pressure displayed no significant differences between averaged blood pressure measurements and single blood pressure measurements. We have developed a framework for researchers to quantify power in the presence of measurement error, which will be applicable to studies of phenotypes in which the measurement is highly variable.

  14. Boosting Principal Component Analysis by Genetic Algorithm

    Directory of Open Access Journals (Sweden)

    Divya Somvanshi

    2010-07-01

    Full Text Available This paper presents a new method of feature extraction by combining principal component analysis and genetic algorithm. Use of multiple pre-processors in combination with principal component analysis generates alternate feature spaces for data representation. The present method works out the fusion of these multiple spaces to create higher dimensionality feature vectors. The fused feature vectors are given chromosome representation by taking feature components to be genes. Then these feature vectors are allowed to undergo genetic evolution individually. For genetic algorithm, initial population is created by calculating probability distance matrix, and by applying a probability distance metric such that all the genes which lie farther than a defined threshold are tripped to zero. The genetic evolution of fused feature vector brings out most significant feature components (genes as survivours. A measure of significance is adapted on the basis of frequency of occurrence of the surviving genes in the current population. Finally, the feature vector is obtained by weighting the original feature components in proportion to their significance. The present algorithm is validated in combination with a neural network classifier based on error backpropagation algorithm, and by analysing a number of benchmark datasets available in the open sources.Defence Science Journal, 2010, 60(4, pp.392-398, DOI:http://dx.doi.org/10.14429/dsj.60.495

  15. Issues in Quantitative Analysis of Ultraviolet Imager (UV) Data: Airglow

    Science.gov (United States)

    Germany, G. A.; Richards, P. G.; Spann, J. F.; Brittnacher, M. J.; Parks, G. K.

    1999-01-01

    The GGS Ultraviolet Imager (UVI) has proven to be especially valuable in correlative substorm, auroral morphology, and extended statistical studies of the auroral regions. Such studies are based on knowledge of the location, spatial, and temporal behavior of auroral emissions. More quantitative studies, based on absolute radiometric intensities from UVI images, require a more intimate knowledge of the instrument behavior and data processing requirements and are inherently more difficult than studies based on relative knowledge of the oval location. In this study, UVI airglow observations are analyzed and compared with model predictions to illustrate issues that arise in quantitative analysis of UVI images. These issues include instrument calibration, long term changes in sensitivity, and imager flat field response as well as proper background correction. Airglow emissions are chosen for this study because of their relatively straightforward modeling requirements and because of their implications for thermospheric compositional studies. The analysis issues discussed here, however, are identical to those faced in quantitative auroral studies.

  16. Issues in Quantitative Analysis of Ultraviolet Imager (UV) Data: Airglow

    Science.gov (United States)

    Germany, G. A.; Richards, P. G.; Spann, J. F.; Brittnacher, M. J.; Parks, G. K.

    1999-01-01

    The GGS Ultraviolet Imager (UVI) has proven to be especially valuable in correlative substorm, auroral morphology, and extended statistical studies of the auroral regions. Such studies are based on knowledge of the location, spatial, and temporal behavior of auroral emissions. More quantitative studies, based on absolute radiometric intensities from UVI images, require a more intimate knowledge of the instrument behavior and data processing requirements and are inherently more difficult than studies based on relative knowledge of the oval location. In this study, UVI airglow observations are analyzed and compared with model predictions to illustrate issues that arise in quantitative analysis of UVI images. These issues include instrument calibration, long term changes in sensitivity, and imager flat field response as well as proper background correction. Airglow emissions are chosen for this study because of their relatively straightforward modeling requirements and because of their implications for thermospheric compositional studies. The analysis issues discussed here, however, are identical to those faced in quantitative auroral studies.

  17. Universal platform for quantitative analysis of DNA transposition

    Directory of Open Access Journals (Sweden)

    Pajunen Maria I

    2010-11-01

    Full Text Available Abstract Background Completed genome projects have revealed an astonishing diversity of transposable genetic elements, implying the existence of novel element families yet to be discovered from diverse life forms. Concurrently, several better understood transposon systems have been exploited as efficient tools in molecular biology and genomics applications. Characterization of new mobile elements and improvement of the existing transposition technology platforms warrant easy-to-use assays for the quantitative analysis of DNA transposition. Results Here we developed a universal in vivo platform for the analysis of transposition frequency with class II mobile elements, i.e., DNA transposons. For each particular transposon system, cloning of the transposon ends and the cognate transposase gene, in three consecutive steps, generates a multifunctional plasmid, which drives inducible expression of the transposase gene and includes a mobilisable lacZ-containing reporter transposon. The assay scores transposition events as blue microcolonies, papillae, growing within otherwise whitish Escherichia coli colonies on indicator plates. We developed the assay using phage Mu transposition as a test model and validated the platform using various MuA transposase mutants. For further validation and to illustrate universality, we introduced IS903 transposition system components into the assay. The developed assay is adjustable to a desired level of initial transposition via the control of a plasmid-borne E. coli arabinose promoter. In practice, the transposition frequency is modulated by varying the concentration of arabinose or glucose in the growth medium. We show that variable levels of transpositional activity can be analysed, thus enabling straightforward screens for hyper- or hypoactive transposase mutants, regardless of the original wild-type activity level. Conclusions The established universal papillation assay platform should be widely applicable to a

  18. Accuracy of Image Analysis in Quantitative Study of Cement Paste

    Directory of Open Access Journals (Sweden)

    Feng Shu-Xia

    2016-01-01

    Full Text Available Quantitative study on cement paste especially blended cement paste has been a hot and difficult issue over the years, and the technique of backscattered electron image analysis showed unique advantages in this field. This paper compared the test results of cement hydration degree, Ca(OH2 content and pore size distribution in pure pastes by image analysis and other methods. Then the accuracy of qualitative study by image analysis was analyzed. The results showed that image analysis technique had displayed higher accuracy in quantifying cement hydration degree and Ca(OH2 content than non-evaporable water test and thermal analysis respectively.

  19. Parameter estimation using the genetic algorithm and its impact on quantitative precipitation forecast

    Directory of Open Access Journals (Sweden)

    Y. H. Lee

    2006-12-01

    Full Text Available In this study, optimal parameter estimations are performed for both physical and computational parameters in a mesoscale meteorological model, and their impacts on the quantitative precipitation forecasting (QPF are assessed for a heavy rainfall case occurred at the Korean Peninsula in June 2005. Experiments are carried out using the PSU/NCAR MM5 model and the genetic algorithm (GA for two parameters: the reduction rate of the convective available potential energy in the Kain-Fritsch (KF scheme for cumulus parameterization, and the Asselin filter parameter for numerical stability. The fitness function is defined based on a QPF skill score. It turns out that each optimized parameter significantly improves the QPF skill. Such improvement is maximized when the two optimized parameters are used simultaneously. Our results indicate that optimizations of computational parameters as well as physical parameters and their adequate applications are essential in improving model performance.

  20. Developmental Patterning as a Quantitative Trait: Genetic Modulation of the Hoxb6 Mutant Skeletal Phenotype.

    Directory of Open Access Journals (Sweden)

    Claudia Kappen

    Full Text Available The process of patterning along the anterior-posterior axis in vertebrates is highly conserved. The function of Hox genes in the axis patterning process is particularly well documented for bone development in the vertebral column and the limbs. We here show that Hoxb6, in skeletal elements at the cervico-thoracic junction, controls multiple independent aspects of skeletal pattern, implicating discrete developmental pathways as substrates for this transcription factor. In addition, we demonstrate that Hoxb6 function is subject to modulation by genetic factors. These results establish Hox-controlled skeletal pattern as a quantitative trait modulated by gene-gene interactions, and provide evidence that distinct modifiers influence the function of conserved developmental genes in fundamental patterning processes.

  1. Estimation of genetic parameters and detection of quantitative trait loci for metabolites in Danish Holstein milk

    DEFF Research Database (Denmark)

    Buitenhuis, Albert Johannes; Sundekilde, Ulrik; Poulsen, Nina Aagaard;

    2013-01-01

    Small components and metabolites in milk are significant for the utilization of milk, not only in dairy food production but also as disease predictors in dairy cattle. This study focused on estimation of genetic parameters and detection of quantitative trait loci for metabolites in bovine milk....... For this purpose, milk samples were collected in mid lactation from 371 Danish Holstein cows in first to third parity. A total of 31 metabolites were detected and identified in bovine milk by using 1H nuclear magnetic resonance (NMR) spectroscopy. Cows were genotyped using a bovine high-density single nucleotide...... polymorphism (SNP) chip. Based on the SNP data, a genomic relationship matrix was calculated and used as a random factor in a model together with 2 fixed factors (herd and lactation stage) to estimate the heritability and breeding value for individual metabolites in the milk. Heritability was in the range of 0...

  2. Quantitative Recognizing Dissolved Hydrocarbons with Genetic Algorithm-Support Vector Regression

    Directory of Open Access Journals (Sweden)

    Qu Zhou

    2013-09-01

    Full Text Available Online monitoring of dissolved fault characteristic hydrocarbon gases, such as methane, ethane, ethylene and acetylene in power transformer oil has significant meaning for condition assessment of transformer. Recently, semiconductor tin oxide based gas sensor array has been widely applied in online monitoring apparatus, while cross sensitivity of the gas sensor array is inevitable due to same compositions and similar structures among the four hydrocarbon gases. Based on support vector regression (SVR with genetic algorithm (GA, a new pattern recognition method was proposed to reduce the cross sensitivity of the gas sensor array and further quantitatively recognize the concentration of dissolved hydrocarbon gases. The experimental data from a certain online monitoring device in China is used to illustrate the performance of the proposed GA-SVR model. Experimental results indicate that the GA-SVR method can effectively decrease the cross sensitivity and the regressed data is much more closed to the real values.

  3. Survival analysis with incomplete genetic data.

    Science.gov (United States)

    Lin, D Y

    2014-01-01

    Genetic data are now collected frequently in clinical studies and epidemiological cohort studies. For a large study, it may be prohibitively expensive to genotype all study subjects, especially with the next-generation sequencing technology. Two-phase sampling, such as case-cohort and nested case-control sampling, is cost-effective in such settings but entails considerable analysis challenges, especially if efficient estimators are desired. Another type of missing data arises when the investigators are interested in the haplotypes or the genetic markers that are not on the genotyping platform used for the current study. Valid and efficient analysis of such missing data is also interesting and challenging. This article provides an overview of these issues and outlines some directions for future research.

  4. Quantitative analysis of microtubule transport in growing nerve processes

    DEFF Research Database (Denmark)

    Ma*, Ytao; Shakiryanova*, Dinara; Vardya, Irina;

    2004-01-01

    the translocation of MT plus ends in the axonal shaft by expressing GFP-EB1 in Xenopus embryo neurons in culture. Formal quantitative analysis of MT assembly/disassembly indicated that none of the MTs in the axonal shaft were rapidly transported. Our results suggest that transport of axonal MTs is not required...

  5. Quantitative Analysis of Complex Tropical Forest Stands: A Review ...

    African Journals Online (AJOL)

    FIRST LADY

    The importance of data analysis in quantitative assessment of natural resources ... 350 km long extends from the eastern border of Sierra Leone all the way to. Ghana. .... consider whether data will likely fit the assumptions of a selected model. ... These tests are not alternatives to parametric tests, but rather are a means of.

  6. Analysis of Forecasting Sales By Using Quantitative And Qualitative Methods

    Directory of Open Access Journals (Sweden)

    B. Rama Sanjeeva Sresta,

    2016-09-01

    Full Text Available This paper focuses on analysis of forecasting sales using quantitative and qualitative methods. This forecast should be able to help create a model for measuring a successes and setting goals from financial and operational view points. The resulting model should tell if we have met our goals with respect to measures, targets, initiatives.

  7. Insights Into Quantitative Biology: analysis of cellular adaptation

    OpenAIRE

    Agoni, Valentina

    2013-01-01

    In the last years many powerful techniques have emerged to measure protein interactions as well as gene expression. Many progresses have been done since the introduction of these techniques but not toward quantitative analysis of data. In this paper we show how to study cellular adaptation and how to detect cellular subpopulations. Moreover we go deeper in analyzing signal transduction pathways dynamics.

  8. Genetic Analysis of Nitroaromatic Degradation by Clostridium

    Science.gov (United States)

    2013-07-30

    REPORT Final Report on Genetic Analysis of Nitroaromatic Degradation by Clostridium 14. ABSTRACT 16. SECURITY CLASSIFICATION OF: 2,4,6-trinitrotoluene...Among different microorganisms that act in TNT biodegradation, clostridium species were distinguished for their rapid degradation rate. Here we compared...TERMS clostridium , TNT, genes, electron carriers, metabolism George N. Bennett William Marsh Rice University Office of Sponsored Research 6100 Main St

  9. Quantitating the subtleties of microglial morphology with fractal analysis.

    Science.gov (United States)

    Karperien, Audrey; Ahammer, Helmut; Jelinek, Herbert F

    2013-01-01

    It is well established that microglial form and function are inextricably linked. In recent years, the traditional view that microglial form ranges between "ramified resting" and "activated amoeboid" has been emphasized through advancing imaging techniques that point to microglial form being highly dynamic even within the currently accepted morphological categories. Moreover, microglia adopt meaningful intermediate forms between categories, with considerable crossover in function and varying morphologies as they cycle, migrate, wave, phagocytose, and extend and retract fine and gross processes. From a quantitative perspective, it is problematic to measure such variability using traditional methods, but one way of quantitating such detail is through fractal analysis. The techniques of fractal analysis have been used for quantitating microglial morphology, to categorize gross differences but also to differentiate subtle differences (e.g., amongst ramified cells). Multifractal analysis in particular is one technique of fractal analysis that may be useful for identifying intermediate forms. Here we review current trends and methods of fractal analysis, focusing on box counting analysis, including lacunarity and multifractal analysis, as applied to microglial morphology.

  10. Quantitating the Subtleties of Microglial Morphology with Fractal Analysis

    Directory of Open Access Journals (Sweden)

    Audrey eKarperien

    2013-01-01

    Full Text Available It is well established that microglial form and function are inextricably linked. In recent years, the traditional view that microglial form ranges between "ramified resting" and "activated amoeboid" has been emphasized through advancing imaging techniques that point to microglial form being highly dynamic even within the currently accepted morphological categories. Moreover, microglia adopt meaningful intermediate forms between categories, with considerable crossover in function and varying morphologies as they cycle, migrate, wave, phagocytose, and extend and retract fine and gross processes. From a quantitative perspective, it is problematic to measure such variability using traditional methods, but one way of quantitating such detail is through fractal analysis. The techniques of fractal analysis have been used for quantitating microglial morphology, to categorize gross differences but also to differentiate subtle differences (e.g., amongst ramified cells. Multifractal analysis in particular is one technique of fractal analysis that may be useful for identifying intermediate forms. Here we review current trends and methods of fractal analysis, focusing on box counting analysis, including lacunarity and multifractal analysis, as applied to microglial morphology.

  11. A non-parametric mixture model for genome-enabled prediction of genetic value for a quantitative trait.

    Science.gov (United States)

    Gianola, Daniel; Wu, Xiao-Lin; Manfredi, Eduardo; Simianer, Henner

    2010-10-01

    A Bayesian nonparametric form of regression based on Dirichlet process priors is adapted to the analysis of quantitative traits possibly affected by cryptic forms of gene action, and to the context of SNP-assisted genomic selection, where the main objective is to predict a genomic signal on phenotype. The procedure clusters unknown genotypes into groups with distinct genetic values, but in a setting in which the number of clusters is unknown a priori, so that standard methods for finite mixture analysis do not work. The central assumption is that genetic effects follow an unknown distribution with some "baseline" family, which is a normal process in the cases considered here. A Bayesian analysis based on the Gibbs sampler produces estimates of the number of clusters, posterior means of genetic effects, a measure of credibility in the baseline distribution, as well as estimates of parameters of the latter. The procedure is illustrated with a simulation representing two populations. In the first one, there are 3 unknown QTL, with additive, dominance and epistatic effects; in the second, there are 10 QTL with additive, dominance and additive × additive epistatic effects. In the two populations, baseline parameters are inferred correctly. The Dirichlet process model infers the number of unique genetic values correctly in the first population, but it produces an understatement in the second one; here, the true number of clusters is over 900, and the model gives a posterior mean estimate of about 140, probably because more replication of genotypes is needed for correct inference. The impact on inferences of the prior distribution of a key parameter (M), and of the extent of replication, was examined via an analysis of mean body weight in 192 paternal half-sib families of broiler chickens, where each sire was genotyped for nearly 7,000 SNPs. In this small sample, it was found that inference about the number of clusters was affected by the prior distribution of M. For a

  12. Quantitative transverse flow assessment using OCT speckle decorrelation analysis

    Science.gov (United States)

    Liu, Xuan; Huang, Yong; Ramella-Roman, Jessica C.; Kang, Jin U.

    2013-03-01

    In this study, we demonstrate the use of inter-Ascan speckle decorrelation analysis of optical coherence tomography (OCT) to assess fluid flow. This method allows quantitative measurement of fluid flow in a plane normal to the scanning beam. To validate this method, OCT images were obtained from a micro fluid channel with bovine milk flowing at different speeds. We also imaged a blood vessel from in vivo animal models and performed speckle analysis to asses blood flow.

  13. Genetic heterogeneity, modifier genes, and quantitative phenotypes in psychiatric illness: searching for a framework.

    Science.gov (United States)

    Fanous, A H; Kendler, K S

    2005-01-01

    Schizophrenia has long been thought to be clinically heterogeneous. A range of studies suggests that this is due to genetic heterogeneity. Some clinical features, such as negative symptoms, are associated with a greater risk of illness in relatives. Affected sibling pairs are correlated for clinical and course features as well as subforms of illness, and twin studies suggest that this is due to genetic factors. This is further supported by findings that subjects from families linked to some chromosomal regions may differ clinically from those from unlinked families. Moreover, some genes may affect clinical features without altering susceptibility (ie are modifier genes). High-risk genotypes may have quantitative, rather than categorical effects, and may influence milder or subclinical phenotypes. Another recent finding is that nonpsychotic relatives may have personality features that resemble those of their affected relatives. These findings taken together suggest that there may be several classes of gene action in schizophrenia: some genes may influence susceptibility only, others may influence clinical features only, and still others may have a mixed effect. Furthermore, subsets of these classes may affect personality and other traits in nonpsychotic relatives. Understanding these classes of gene action may help guide the design of linkage and association studies that have increased power. We describe five classes of genes and their predictions of the outcomes of family, twin, and several types of linkage studies. We go on to explore how these predictions can in turn be used to aid in the design of linkage studies.

  14. The Evaluation Criteria of Some Botanical Quantitative Characters of Peach Genetic Resources

    Institute of Scientific and Technical Information of China (English)

    WANG Li-rong; ZHU Geng-rui; FANG Wei-chao

    2006-01-01

    There were two peach descriptors systems: one from IPRGI in 1980 and the other from China in 1990. The former had only reference cultivars without quantity grades; the latter had only a list of some characteristics. This makes it difficult sharing of genetic resource information for breeders. To describe the main quantitative characteristics, a new system was established. Ten characteristics of 346-476 peach cultivars were investigated from 1986 to 2002 in the National Peach Genetic Collection in Zhengzhou City, China. These characteristics and their coefficients of variation were as follows: flower diameter 19.55%, vertical diameter of fruit 14.24%, cheek diameter of fruit 10.36%, suture diameter of fruit 11.44%, stone length 19.04%, stone width 10.86%, stone thickness 11.19%, leaf length 7.9%, leaf width 10.55%, and leaf stalk length 19.03%, respectively. Grade index and reference cultivars were given by statistical data for peach description.These grade indexes were recorded on 1-5 grades, and the third grade as a middle one occupied 39% or more of the distribution. In general, two reference cultivars for each grade were chosen, one is USA cultivar and the other is Chinese cultivar. This paper tried to use them as the reference cultivars, which are planted or used widely by Chinese breeders.

  15. The quantitative genetic basis of adaptive divergence in the moor frog (Rana arvalis) and its implications for gene flow.

    Science.gov (United States)

    Hangartner, S; Laurila, A; Räsänen, K

    2012-08-01

    Knowledge on the relative contribution of direct genetic, maternal and environmental effects to adaptive divergence is important for understanding the drivers of biological diversification. The moor frog (Rana arvalis) shows adaptive divergence in embryonic and larval fitness traits along an acidification gradient in south-western Sweden. To understand the quantitative genetic basis of this divergence, we performed reciprocal crosses between three divergent population pairs and reared embryos and larvae at acid and neutral pH in the laboratory. Divergence in embryonic acid tolerance (survival) was mainly determined by maternal effects, whereas the relative contributions of maternal, additive and nonadditive genetic effects in larval life-history traits differed between traits, population pairs and rearing environments. These results emphasize the need to investigate the quantitative genetic basis of adaptive divergence in multiple populations and traits, as well as different environments. We discuss the implications of our findings for maintenance of local adaptation in the context of migrant and hybrid fitness.

  16. Quantitative numerical analysis of transient IR-experiments on buildings

    Science.gov (United States)

    Maierhofer, Ch.; Wiggenhauser, H.; Brink, A.; Röllig, M.

    2004-12-01

    Impulse-thermography has been established as a fast and reliable tool in many areas of non-destructive testing. In recent years several investigations have been done to apply active thermography to civil engineering. For quantitative investigations in this area of application, finite difference calculations have been performed for systematic studies on the influence of environmental conditions, heating power and time, defect depth and size and thermal properties of the bulk material (concrete). The comparison of simulated and experimental data enables the quantitative analysis of defects.

  17. Quantitative analysis of culture using millions of digitized books.

    Science.gov (United States)

    Michel, Jean-Baptiste; Shen, Yuan Kui; Aiden, Aviva Presser; Veres, Adrian; Gray, Matthew K; Pickett, Joseph P; Hoiberg, Dale; Clancy, Dan; Norvig, Peter; Orwant, Jon; Pinker, Steven; Nowak, Martin A; Aiden, Erez Lieberman

    2011-01-14

    We constructed a corpus of digitized texts containing about 4% of all books ever printed. Analysis of this corpus enables us to investigate cultural trends quantitatively. We survey the vast terrain of 'culturomics,' focusing on linguistic and cultural phenomena that were reflected in the English language between 1800 and 2000. We show how this approach can provide insights about fields as diverse as lexicography, the evolution of grammar, collective memory, the adoption of technology, the pursuit of fame, censorship, and historical epidemiology. Culturomics extends the boundaries of rigorous quantitative inquiry to a wide array of new phenomena spanning the social sciences and the humanities.

  18. Quantitative analysis of culture using millions of digitized books

    Science.gov (United States)

    Michel, Jean-Baptiste; Shen, Yuan Kui; Aiden, Aviva P.; Veres, Adrian; Gray, Matthew K.; Pickett, Joseph P.; Hoiberg, Dale; Clancy, Dan; Norvig, Peter; Orwant, Jon; Pinker, Steven; Nowak, Martin A.; Aiden, Erez Lieberman

    2011-01-01

    We constructed a corpus of digitized texts containing about 4% of all books ever printed. Analysis of this corpus enables us to investigate cultural trends quantitatively. We survey the vast terrain of ‘culturomics’, focusing on linguistic and cultural phenomena that were reflected in the English language between 1800 and 2000. We show how this approach can provide insights about fields as diverse as lexicography, the evolution of grammar, collective memory, the adoption of technology, the pursuit of fame, censorship, and historical epidemiology. ‘Culturomics’ extends the boundaries of rigorous quantitative inquiry to a wide array of new phenomena spanning the social sciences and the humanities. PMID:21163965

  19. Genetic parameters and mapping quantitative trait loci associated with tibia traits in broilers.

    Science.gov (United States)

    Ragognetti, B N N; Stafuzza, N B; Silva, T B R; Chud, T C S; Grupioni, N V; Cruz, V A R; Peixoto, J O; Nones, K; Ledur, M C; Munari, D P

    2015-12-21

    Selection among broilers for performance traits is resulting in locomotion problems and bone disorders, once skeletal structure is not strong enough to support body weight in broilers with high growth rates. In this study, genetic parameters were estimated for body weight at 42 days of age (BW42), and tibia traits (length, width, and weight) in a population of broiler chickens. Quantitative trait loci (QTL) were identified for tibia traits to expand our knowledge of the genetic architecture of the broiler population. Genetic correlations ranged from 0.56 ± 0.18 (between tibia length and BW42) to 0.89 ± 0.06 (between tibia width and weight), suggesting that these traits are either controlled by pleiotropic genes or by genes that are in linkage disequilibrium. For QTL mapping, the genome was scanned with 127 microsatellites, representing a coverage of 2630 cM. Eight QTL were mapped on Gallus gallus chromosomes (GGA): GGA1, GGA4, GGA6, GGA13, and GGA24. The QTL regions for tibia length and weight were mapped on GGA1, between LEI0079 and MCW145 markers. The gene DACH1 is located in this region; this gene acts to form the apical ectodermal ridge, responsible for limb development. Body weight at 42 days of age was included in the model as a covariate for selection effect of bone traits. Two QTL were found for tibia weight on GGA2 and GGA4, and one for tibia width on GGA3. Information originating from these QTL will assist in the search for candidate genes for these bone traits in future studies.

  20. Genetic Studies of Quantitative MCI and AD Phenotypes in ADNI: Progress, Opportunities, and Plans

    Science.gov (United States)

    Saykin, Andrew J.; Shen, Li; Yao, Xiaohui; Kim, Sungeun; Nho, Kwangsik; Risacher, Shannon L.; Ramanan, Vijay K.; Foroud, Tatiana M.; Faber, Kelly M.; Sarwar, Nadeem; Munsie, Leanne M.; Hu, Xiaolan; Soares, Holly D.; Potkin, Steven G.; Thompson, Paul M.; Kauwe, John S.K.; Kaddurah-Daouk, Rima; Green, Robert C.; Toga, Arthur W.; Weiner, Michael W.

    2015-01-01

    INTRODUCTION Genetic data from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) has been crucial in advancing the understanding of AD pathophysiology. Here we provide an update on sample collection, scientific progress and opportunities, conceptual issues, and future plans. METHODS Lymphoblastoid cell lines and DNA and RNA samples from blood have been collected and banked, and data and biosamples have been widely disseminated. To date, APOE genotyping, genome-wide association study (GWAS), and whole exome and whole genome sequencing (WES, WGS) data have been obtained and disseminated. RESULTS ADNI genetic data have been downloaded thousands of times and over 300 publications have resulted, including reports of large scale GWAS by consortia to which ADNI contributed. Many of the first applications of quantitative endophenotype association studies employed ADNI data, including some of the earliest GWAS and pathway-based studies of biospecimen and imaging biomarkers, as well as memory and other clinical/cognitive variables. Other contributions include some of the first WES and WGS data sets and reports in healthy controls, MCI, and AD. DISCUSSION Numerous genetic susceptibility and protective markers for AD and disease biomarkers have been identified and replicated using ADNI data, and have heavily implicated immune, mitochondrial, cell cycle/fate, and other biological processes. Early sequencing studies suggest that rare and structural variants are likely to account for significant additional phenotypic variation. Longitudinal analyses of transcriptomic, proteomic, metabolomic, and epigenomic changes will also further elucidate dynamic processes underlying preclinical and prodromal stages of disease. Integration of this unique collection of multi-omics data within a systems biology framework will help to separate truly informative markers of early disease mechanisms and potential novel therapeutic targets from the vast background of less relevant biological

  1. The effects of selection on linkage analysis for quantitative traits.

    Science.gov (United States)

    Mackinnon, M J; Georges, M A

    1992-12-01

    The effects of within-sample selection on the outcome of analyses detecting linkage between genetic markers and quantitative traits were studied. It was found that selection by truncation for the trait of interest significantly reduces the differences between marker genotype means thus reducing the power to detect linked quantitative trait loci (QTL). The size of this reduction is a function of proportion selected, the magnitude of the QTL effect, recombination rate between the marker locus and the QTL, and the allele frequency of the QTL. Proportion selected was the most influential of these factors on bias, e.g., for an allele substitution effect of one standard deviation unit, selecting the top 80%, 50% or 20% of the population required 2, 6 or 24 times the number of progeny, respectively, to offset the loss of power caused by this selection. The effect on power was approximately linear with respect to the size of gene effect, almost invariant to recombination rate, and a complex function of QTL allele frequency. It was concluded that experimental samples from animal populations which have been subjected to even minor amounts of selection will be inefficient in yielding information on linkage between markers and loci influencing the quantitative trait under selection.

  2. Arms race between selfishness and policing: two-trait quantitative genetic model for caste fate conflict in eusocial Hymenoptera.

    Science.gov (United States)

    Dobata, Shigeto

    2012-12-01

    Policing against selfishness is now regarded as the main force maintaining cooperation, by reducing costly conflict in complex social systems. Although policing has been studied extensively in social insect colonies, its coevolution against selfishness has not been fully captured by previous theories. In this study, I developed a two-trait quantitative genetic model of the conflict between selfish immature females (usually larvae) and policing workers in eusocial Hymenoptera over the immatures' propensity to develop into new queens. This model allows for the analysis of coevolution between genomes expressed in immatures and workers that collectively determine the immatures' queen caste fate. The main prediction of the model is that a higher level of polyandry leads to a smaller fraction of queens produced among new females through caste fate policing. The other main prediction of the present model is that, as a result of arms race, caste fate policing by workers coevolves with exaggerated selfishness of the immatures achieving maximum potential to develop into queens. Moreover, the model can incorporate genetic correlation between traits, which has been largely unexplored in social evolution theory. This study highlights the importance of understanding social traits as influenced by the coevolution of conflicting genomes. © 2012 The Author. Evolution© 2012 The Society for the Study of Evolution.

  3. Power analysis of artificial selection experiments using efficient whole genome simulation of quantitative traits.

    Science.gov (United States)

    Kessner, Darren; Novembre, John

    2015-04-01

    Evolve and resequence studies combine artificial selection experiments with massively parallel sequencing technology to study the genetic basis for complex traits. In these experiments, individuals are selected for extreme values of a trait, causing alleles at quantitative trait loci (QTL) to increase or decrease in frequency in the experimental population. We present a new analysis of the power of artificial selection experiments to detect and localize quantitative trait loci. This analysis uses a simulation framework that explicitly models whole genomes of individuals, quantitative traits, and selection based on individual trait values. We find that explicitly modeling QTL provides qualitatively different insights than considering independent loci with constant selection coefficients. Specifically, we observe how interference between QTL under selection affects the trajectories and lengthens the fixation times of selected alleles. We also show that a substantial portion of the genetic variance of the trait (50-100%) can be explained by detected QTL in as little as 20 generations of selection, depending on the trait architecture and experimental design. Furthermore, we show that power depends crucially on the opportunity for recombination during the experiment. Finally, we show that an increase in power is obtained by leveraging founder haplotype information to obtain allele frequency estimates.

  4. QTL analysis of the genetic architecture determining resistance to fire blight in an apple progeny

    NARCIS (Netherlands)

    Calenge, F.; Drouet, D.; Weg, van de W.E.; Brisset, M.N.; Paulin, J.P.; Durel, C.E.

    2004-01-01

    Fire blight, caused by the bacterial pathogen Erwinia amylovora, is one of the most destructive diseases of apple (Malus x domestica). In order to analyse the genetic determinism of resistance to fire blight in apple, a quantitative trait analysis (QTL) approach was used. A F1 progeny of 164

  5. Genetic Analysis of Health-Related Secondary Metabolites in a Brassica rapa Recombinant Inbred Line Population

    NARCIS (Netherlands)

    Bagheri, H.; Soda, El M.; Kim, H.K.; Fritsche, S.; Jung, C.; Aarts, M.G.M.

    2013-01-01

    The genetic basis of the wide variation for nutritional traits in Brassica rapa is largely unknown. A new Recombinant Inbred Line (RIL) population was profiled using High Performance Liquid Chromatography (HPLC) and Nuclear Magnetic Resonance (NMR) analysis to detect quantitative trait loci (QTLs) c

  6. QTL analysis of the genetic architecture determining resistance to fire blight in an apple progeny

    NARCIS (Netherlands)

    Calenge, F.; Drouet, D.; Weg, van de W.E.; Brisset, M.N.; Paulin, J.P.; Durel, C.E.

    2004-01-01

    Fire blight, caused by the bacterial pathogen Erwinia amylovora, is one of the most destructive diseases of apple (Malus x domestica). In order to analyse the genetic determinism of resistance to fire blight in apple, a quantitative trait analysis (QTL) approach was used. A F1 progeny of 164 individ

  7. Kernel Approach for Modeling Interaction Effects in Genetic Association Studies of Complex Quantitative Traits.

    Science.gov (United States)

    Broadaway, K Alaine; Duncan, Richard; Conneely, Karen N; Almli, Lynn M; Bradley, Bekh; Ressler, Kerry J; Epstein, Michael P

    2015-07-01

    The etiology of complex traits likely involves the effects of genetic and environmental factors, along with complicated interaction effects between them. Consequently, there has been interest in applying genetic association tests of complex traits that account for potential modification of the genetic effect in the presence of an environmental factor. One can perform such an analysis using a joint test of gene and gene-environment interaction. An optimal joint test would be one that remains powerful under a variety of models ranging from those of strong gene-environment interaction effect to those of little or no gene-environment interaction effect. To fill this demand, we have extended a kernel machine based approach for association mapping of multiple SNPs to consider joint tests of gene and gene-environment interaction. The kernel-based approach for joint testing is promising, because it incorporates linkage disequilibrium information from multiple SNPs simultaneously in analysis and permits flexible modeling of interaction effects. Using simulated data, we show that our kernel machine approach typically outperforms the traditional joint test under strong gene-environment interaction models and further outperforms the traditional main-effect association test under models of weak or no gene-environment interaction effects. We illustrate our test using genome-wide association data from the Grady Trauma Project, a cohort of highly traumatized, at-risk individuals, which has previously been investigated for interaction effects. © 2015 WILEY PERIODICALS, INC.

  8. Quantitative Genetics and Functional-Structural Plant Growth Models: Simulation of Quantitative Trait Loci Detection for Model Parameters and Application to Potential Yield Optimization

    CERN Document Server

    Letort, Veronique; Cournède, Paul-Henry; De Reffye, Philippe; Courtois, Brigitte; 10.1093/aob/mcm197

    2010-01-01

    Background and Aims: Prediction of phenotypic traits from new genotypes under untested environmental conditions is crucial to build simulations of breeding strategies to improve target traits. Although the plant response to environmental stresses is characterized by both architectural and functional plasticity, recent attempts to integrate biological knowledge into genetics models have mainly concerned specific physiological processes or crop models without architecture, and thus may prove limited when studying genotype x environment interactions. Consequently, this paper presents a simulation study introducing genetics into a functional-structural growth model, which gives access to more fundamental traits for quantitative trait loci (QTL) detection and thus to promising tools for yield optimization. Methods: The GreenLab model was selected as a reasonable choice to link growth model parameters to QTL. Virtual genes and virtual chromosomes were defined to build a simple genetic model that drove the settings ...

  9. Genetic diversity of upland rice germplasm in Malaysia based on quantitative traits.

    Science.gov (United States)

    Sohrabi, M; Rafii, M Y; Hanafi, M M; Siti Nor Akmar, A; Latif, M A

    2012-01-01

    Genetic diversity is prerequisite for any crop improvement program as it helps in the development of superior recombinants. Fifty Malaysian upland rice accessions were evaluated for 12 growth traits, yield and yield components. All of the traits were significant and highly significant among the accessions. The higher magnitudes of genotypic and phenotypic coefficients of variation were recorded for flag leaf length-to-width ratio, spikelet fertility, and days to flowering. High heritability along with high genetic advance was registered for yield of plant, days to flowering, and flag leaf length-to-width ratio suggesting preponderance of additive gene action in the gene expression of these characters. Plant height showed highly significant positive correlation with most of the traits. According to UPGMA cluster analysis all accessions were clustered into six groups. Twelve morphological traits provided around 77% of total variation among the accessions.

  10. Genetic Diversity of Upland Rice Germplasm in Malaysia Based on Quantitative Traits

    Directory of Open Access Journals (Sweden)

    M. Sohrabi

    2012-01-01

    Full Text Available Genetic diversity is prerequisite for any crop improvement program as it helps in the development of superior recombinants. Fifty Malaysian upland rice accessions were evaluated for 12 growth traits, yield and yield components. All of the traits were significant and highly significant among the accessions. The higher magnitudes of genotypic and phenotypic coefficients of variation were recorded for flag leaf length-to-width ratio, spikelet fertility, and days to flowering. High heritability along with high genetic advance was registered for yield of plant, days to flowering, and flag leaf length-to-width ratio suggesting preponderance of additive gene action in the gene expression of these characters. Plant height showed highly significant positive correlation with most of the traits. According to UPGMA cluster analysis all accessions were clustered into six groups. Twelve morphological traits provided around 77% of total variation among the accessions.

  11. Quantitative nanoscale analysis in 3D using electron tomography

    Energy Technology Data Exchange (ETDEWEB)

    Kuebel, Christian [Karlsruhe Institute of Technology, INT, 76344 Eggenstein-Leopoldshafen (Germany)

    2011-07-01

    State-of-the-art electron tomography has been established as a powerful tool to image complex structures with nanometer resolution in 3D. Especially STEM tomography is used extensively in materials science in such diverse areas as catalysis, semiconductor materials, and polymer composites mainly providing qualitative information on morphology, shape and distribution of materials. However, for an increasing number of studies quantitative information, e.g. surface area, fractal dimensions, particle distribution or porosity are needed. A quantitative analysis is typically performed after segmenting the tomographic data, which is one of the main sources of error for the quantification. In addition to noise, systematic errors due to the missing wedge and due to artifacts from the reconstruction algorithm itself are responsible for these segmentation errors and improved algorithms are needed. This presentation will provide an overview of the possibilities and limitations of quantitative nanoscale analysis by electron tomography. Using catalysts and nano composites as applications examples, intensities and intensity variations observed for the 3D volume reconstructed by WBP and SIRT will be quantitatively compared to alternative reconstruction algorithms; implications for quantification of electron (or X-ray) tomographic data will be discussed and illustrated for quantification of particle size distributions, particle correlations, surface area, and fractal dimensions in 3D.

  12. Combined sequence-based and genetic mapping analysis of complex traits in outbred rats

    Science.gov (United States)

    Baud, Amelie; Hermsen, Roel; Guryev, Victor; Stridh, Pernilla; Graham, Delyth; McBride, Martin W.; Foroud, Tatiana; Calderari, Sophie; Diez, Margarita; Ockinger, Johan; Beyeen, Amennai D.; Gillett, Alan; Abdelmagid, Nada; Guerreiro-Cacais, Andre Ortlieb; Jagodic, Maja; Tuncel, Jonatan; Norin, Ulrika; Beattie, Elisabeth; Huynh, Ngan; Miller, William H.; Koller, Daniel L.; Alam, Imranul; Falak, Samreen; Osborne-Pellegrin, Mary; Martinez-Membrives, Esther; Canete, Toni; Blazquez, Gloria; Vicens-Costa, Elia; Mont-Cardona, Carme; Diaz-Moran, Sira; Tobena, Adolf; Hummel, Oliver; Zelenika, Diana; Saar, Kathrin; Patone, Giannino; Bauerfeind, Anja; Bihoreau, Marie-Therese; Heinig, Matthias; Lee, Young-Ae; Rintisch, Carola; Schulz, Herbert; Wheeler, David A.; Worley, Kim C.; Muzny, Donna M.; Gibbs, Richard A.; Lathrop, Mark; Lansu, Nico; Toonen, Pim; Ruzius, Frans Paul; de Bruijn, Ewart; Hauser, Heidi; Adams, David J.; Keane, Thomas; Atanur, Santosh S.; Aitman, Tim J.; Flicek, Paul; Malinauskas, Tomas; Jones, E. Yvonne; Ekman, Diana; Lopez-Aumatell, Regina; Dominiczak, Anna F; Johannesson, Martina; Holmdahl, Rikard; Olsson, Tomas; Gauguier, Dominique; Hubner, Norbert; Fernandez-Teruel, Alberto; Cuppen, Edwin; Mott, Richard; Flint, Jonathan

    2013-01-01

    Genetic mapping on fully sequenced individuals is transforming our understanding of the relationship between molecular variation and variation in complex traits. Here we report a combined sequence and genetic mapping analysis in outbred rats that maps 355 quantitative trait loci for 122 phenotypes. We identify 35 causal genes involved in 31 phenotypes, implicating novel genes in models of anxiety, heart disease and multiple sclerosis. The relation between sequence and genetic variation is unexpectedly complex: at approximately 40% of quantitative trait loci a single sequence variant cannot account for the phenotypic effect. Using comparable sequence and mapping data from mice, we show the extent and spatial pattern of variation in inbred rats differ significantly from those of inbred mice, and that the genetic variants in orthologous genes rarely contribute to the same phenotype in both species. PMID:23708188

  13. Combined sequence-based and genetic mapping analysis of complex traits in outbred rats.

    Science.gov (United States)

    Baud, Amelie; Hermsen, Roel; Guryev, Victor; Stridh, Pernilla; Graham, Delyth; McBride, Martin W; Foroud, Tatiana; Calderari, Sophie; Diez, Margarita; Ockinger, Johan; Beyeen, Amennai D; Gillett, Alan; Abdelmagid, Nada; Guerreiro-Cacais, Andre Ortlieb; Jagodic, Maja; Tuncel, Jonatan; Norin, Ulrika; Beattie, Elisabeth; Huynh, Ngan; Miller, William H; Koller, Daniel L; Alam, Imranul; Falak, Samreen; Osborne-Pellegrin, Mary; Martinez-Membrives, Esther; Canete, Toni; Blazquez, Gloria; Vicens-Costa, Elia; Mont-Cardona, Carme; Diaz-Moran, Sira; Tobena, Adolf; Hummel, Oliver; Zelenika, Diana; Saar, Kathrin; Patone, Giannino; Bauerfeind, Anja; Bihoreau, Marie-Therese; Heinig, Matthias; Lee, Young-Ae; Rintisch, Carola; Schulz, Herbert; Wheeler, David A; Worley, Kim C; Muzny, Donna M; Gibbs, Richard A; Lathrop, Mark; Lansu, Nico; Toonen, Pim; Ruzius, Frans Paul; de Bruijn, Ewart; Hauser, Heidi; Adams, David J; Keane, Thomas; Atanur, Santosh S; Aitman, Tim J; Flicek, Paul; Malinauskas, Tomas; Jones, E Yvonne; Ekman, Diana; Lopez-Aumatell, Regina; Dominiczak, Anna F; Johannesson, Martina; Holmdahl, Rikard; Olsson, Tomas; Gauguier, Dominique; Hubner, Norbert; Fernandez-Teruel, Alberto; Cuppen, Edwin; Mott, Richard; Flint, Jonathan

    2013-07-01

    Genetic mapping on fully sequenced individuals is transforming understanding of the relationship between molecular variation and variation in complex traits. Here we report a combined sequence and genetic mapping analysis in outbred rats that maps 355 quantitative trait loci for 122 phenotypes. We identify 35 causal genes involved in 31 phenotypes, implicating new genes in models of anxiety, heart disease and multiple sclerosis. The relationship between sequence and genetic variation is unexpectedly complex: at approximately 40% of quantitative trait loci, a single sequence variant cannot account for the phenotypic effect. Using comparable sequence and mapping data from mice, we show that the extent and spatial pattern of variation in inbred rats differ substantially from those of inbred mice and that the genetic variants in orthologous genes rarely contribute to the same phenotype in both species.

  14. GENETIC ANALYSIS OF BLACK SLAVONIAN PIG

    Directory of Open Access Journals (Sweden)

    Vladimir Margeta

    2012-12-01

    Full Text Available Pairs (18 of microsatelite primers were used in this study to detect the genetic relationship within Black Slavonian Pig and between Turopolje Pig, Mangalitsa breed and Croatian Wild Pigs. The second goal of this study was to determine phylogenetic relationships among these breeds and some Asian and European pigs using the mtDNA D-loop sequence polymorphism. The third goal was to determine the MC1R genotype of Black Slavonian pigs and to find an efficient and simple PCR-RFLP method, based on differences in MC1R genotype, to distinguish between purebred Black Slavonian pigs and their crossings with commercial pig breeds and Wild Boars. Aiming to conduct microsatellite analysis each animal was genotyped for 18 microsatelite markers, chosen based on their quality, size, polymorphism and location on the porcine genome as proposed by the FAO. Two pairs of primers amplified a 511-bp fragment of control region between sites 15 390 and 15 900 (Mit1.F and Mit1.R and a 810-bp fragment between sites 15 825 and 16 634 (Mit2.F and Mi2.R were genotyped for mtDNA. Two primer pairs were used to amplify the majority of the single exon of MC1R gene aiming to determinate MC1R genotype of Black Slavonian pig. The first pair of primers, MERL1 and EPIG2, was used to amplify a 428-bp product from the 5’ half of the exon, whereas EPIG1 and EPIG3 amplified a 405-bp product from the 3’ half. Our results showed that the 18 microsatellites used in this study were useful markers to study genetic diversity among Croatian autochthonous pig breeds. This set of microsatellites may be used for identifying individuals and for genetic diversity studies for selection and conservation of the Black Slavonian pig, Turopolje pig and Mangalitsa breed. Genetic distances between populations made with Principal Component Analysis (PCA method noticed that studied populations are mostly clearly geneticaly defined. mtDNA analysis suggested that Black Slavonian and Turopolje pig showed

  15. Some selected quantitative methods of thermal image analysis in Matlab.

    Science.gov (United States)

    Koprowski, Robert

    2016-05-01

    The paper presents a new algorithm based on some selected automatic quantitative methods for analysing thermal images. It shows the practical implementation of these image analysis methods in Matlab. It enables to perform fully automated and reproducible measurements of selected parameters in thermal images. The paper also shows two examples of the use of the proposed image analysis methods for the area of ​​the skin of a human foot and face. The full source code of the developed application is also provided as an attachment. The main window of the program during dynamic analysis of the foot thermal image.

  16. Data from quantitative label free proteomics analysis of rat spleen

    Directory of Open Access Journals (Sweden)

    Khadar Dudekula

    2016-09-01

    Full Text Available The dataset presented in this work has been obtained using a label-free quantitative proteomic analysis of rat spleen. A robust method for extraction of proteins from rat spleen tissue and LC-MS-MS analysis was developed using a urea and SDS-based buffer. Different fractionation methods were compared. A total of 3484 different proteins were identified from the pool of all experiments run in this study (a total of 2460 proteins with at least two peptides. A total of 1822 proteins were identified from nine non-fractionated pulse gels, 2288 proteins and 2864 proteins were identified by SDS-PAGE fractionation into three and five fractions respectively. The proteomics data are deposited in ProteomeXchange Consortium via PRIDE PXD003520, Progenesis and Maxquant output are presented in the supported information. The generated list of proteins under different regimes of fractionation allow assessing the nature of the identified proteins; variability in the quantitative analysis associated with the different sampling strategy and allow defining a proper number of replicates for future quantitative analysis.

  17. Data from quantitative label free proteomics analysis of rat spleen.

    Science.gov (United States)

    Dudekula, Khadar; Le Bihan, Thierry

    2016-09-01

    The dataset presented in this work has been obtained using a label-free quantitative proteomic analysis of rat spleen. A robust method for extraction of proteins from rat spleen tissue and LC-MS-MS analysis was developed using a urea and SDS-based buffer. Different fractionation methods were compared. A total of 3484 different proteins were identified from the pool of all experiments run in this study (a total of 2460 proteins with at least two peptides). A total of 1822 proteins were identified from nine non-fractionated pulse gels, 2288 proteins and 2864 proteins were identified by SDS-PAGE fractionation into three and five fractions respectively. The proteomics data are deposited in ProteomeXchange Consortium via PRIDE PXD003520, Progenesis and Maxquant output are presented in the supported information. The generated list of proteins under different regimes of fractionation allow assessing the nature of the identified proteins; variability in the quantitative analysis associated with the different sampling strategy and allow defining a proper number of replicates for future quantitative analysis.

  18. An improved quantitative analysis method for plant cortical microtubules.

    Science.gov (United States)

    Lu, Yi; Huang, Chenyang; Wang, Jia; Shang, Peng

    2014-01-01

    The arrangement of plant cortical microtubules can reflect the physiological state of cells. However, little attention has been paid to the image quantitative analysis of plant cortical microtubules so far. In this paper, Bidimensional Empirical Mode Decomposition (BEMD) algorithm was applied in the image preprocessing of the original microtubule image. And then Intrinsic Mode Function 1 (IMF1) image obtained by decomposition was selected to do the texture analysis based on Grey-Level Cooccurrence Matrix (GLCM) algorithm. Meanwhile, in order to further verify its reliability, the proposed texture analysis method was utilized to distinguish different images of Arabidopsis microtubules. The results showed that the effect of BEMD algorithm on edge preserving accompanied with noise reduction was positive, and the geometrical characteristic of the texture was obvious. Four texture parameters extracted by GLCM perfectly reflected the different arrangements between the two images of cortical microtubules. In summary, the results indicate that this method is feasible and effective for the image quantitative analysis of plant cortical microtubules. It not only provides a new quantitative approach for the comprehensive study of the role played by microtubules in cell life activities but also supplies references for other similar studies.

  19. An Improved Quantitative Analysis Method for Plant Cortical Microtubules

    Directory of Open Access Journals (Sweden)

    Yi Lu

    2014-01-01

    Full Text Available The arrangement of plant cortical microtubules can reflect the physiological state of cells. However, little attention has been paid to the image quantitative analysis of plant cortical microtubules so far. In this paper, Bidimensional Empirical Mode Decomposition (BEMD algorithm was applied in the image preprocessing of the original microtubule image. And then Intrinsic Mode Function 1 (IMF1 image obtained by decomposition was selected to do the texture analysis based on Grey-Level Cooccurrence Matrix (GLCM algorithm. Meanwhile, in order to further verify its reliability, the proposed texture analysis method was utilized to distinguish different images of Arabidopsis microtubules. The results showed that the effect of BEMD algorithm on edge preserving accompanied with noise reduction was positive, and the geometrical characteristic of the texture was obvious. Four texture parameters extracted by GLCM perfectly reflected the different arrangements between the two images of cortical microtubules. In summary, the results indicate that this method is feasible and effective for the image quantitative analysis of plant cortical microtubules. It not only provides a new quantitative approach for the comprehensive study of the role played by microtubules in cell life activities but also supplies references for other similar studies.

  20. Quantitative risk analysis of oil storage facilities in seismic areas.

    Science.gov (United States)

    Fabbrocino, Giovanni; Iervolino, Iunio; Orlando, Francesca; Salzano, Ernesto

    2005-08-31

    Quantitative risk analysis (QRA) of industrial facilities has to take into account multiple hazards threatening critical equipment. Nevertheless, engineering procedures able to evaluate quantitatively the effect of seismic action are not well established. Indeed, relevant industrial accidents may be triggered by loss of containment following ground shaking or other relevant natural hazards, either directly or through cascade effects ('domino effects'). The issue of integrating structural seismic risk into quantitative probabilistic seismic risk analysis (QpsRA) is addressed in this paper by a representative study case regarding an oil storage plant with a number of atmospheric steel tanks containing flammable substances. Empirical seismic fragility curves and probit functions, properly defined both for building-like and non building-like industrial components, have been crossed with outcomes of probabilistic seismic hazard analysis (PSHA) for a test site located in south Italy. Once the seismic failure probabilities have been quantified, consequence analysis has been performed for those events which may be triggered by the loss of containment following seismic action. Results are combined by means of a specific developed code in terms of local risk contour plots, i.e. the contour line for the probability of fatal injures at any point (x, y) in the analysed area. Finally, a comparison with QRA obtained by considering only process-related top events is reported for reference.

  1. A quantitative genetic analysis of intermediate asthma phenotypes

    DEFF Research Database (Denmark)

    Thomsen, S F; Ferreira, M A R; Kyvik, K O;

    2009-01-01

    the Danish Twin Registry, a total of 575 subjects (256 intact pairs and 63 single twins) who either themselves and/or their co-twins reported a history of asthma at a nationwide questionnaire survey, were clinically examined. Traits were measured using standard techniques. Latent factor models were fitted...... responsiveness, rho(E) = 0.34. Conclusions: Asthma is a complex disease characterized by a set of etiologically heterogeneous biomarkers, which likely constitute diverse targets of intervention....

  2. Effects of long-term averaging of quantitative blood pressure traits on the detection of genetic associations

    NARCIS (Netherlands)

    S.K. Ganesh (Santhi); D.I. Chasman (Daniel); M.G. Larson (Martin); X. Guo (Xiuqing); G.C. Verwoert (Germaine); J.C. Bis (Joshua); X. Gu (Xiangjun); G.D. Smith; M.-L. Yang (Min-Lee); Y. Zhang (Yan); G.B. Ehret (Georg); L.M. Rose (Lynda); S.J. Hwang; G.J. Papanicolau (George); E.J.G. Sijbrands (Eric); K. Rice (Kenneth); G. Eiriksdottir (Gudny); V. Pihur (Vasyl); P.M. Ridker (Paul); R.S. Vasan (Ramachandran Srini); C. Newton-Cheh (Christopher); L.J. Raffel (Leslie); N. Amin (Najaf); J.I. Rotter (Jerome); K. Liu (Kiang); L.J. Launer (Lenore); M. Xu (Ming); M. Caulfield (Mark); A.C. Morrison (Alanna); A.D. Johnson (Andrew); D. Vaidya (Dhananjay); A. Dehghan (Abbas); G. Li (Guo); C. Bouchard (Claude); T.B. Harris (Tamara); H. Zhang (He); E.A. Boerwinkle (Eric); D.S. Siscovick (David); W. Gao (Wei); A.G. Uitterlinden (André); F. Rivadeneira Ramirez (Fernando); A. Hofman (Albert); E.M. Schmidt (Ellen); O.H. Franco (Oscar); Y. Huo (Yong); J.C.M. Witteman (Jacqueline); P. Munroe (Patricia); V. Gudnason (Vilmundur); W. Palmas (Walter); C.M. van Duijn (Cock); M. Fornage (Myriam); D. Levy (Daniel); B.M. Psaty (Bruce); A. Chakravarti (Aravinda)

    2014-01-01

    textabstractBlood pressure (BP) is a heritable, quantitative trait with intraindividual variability and susceptibility to measurement error. Genetic studies of BP generally use single-visit measurements and thus cannot remove variability occurring over months or years. We leveraged the idea that ave

  3. Study of quantitative genetics of gum arabic production complicated by variability in ploidy level of Acacia senegal (L.) Willd

    DEFF Research Database (Denmark)

    Diallo, Adja Madjiguene; Nielsen, Lene Rostgaard; Hansen, Jon Kehlet

    2015-01-01

    Gum arabic is an important international commodity produced by trees of Acacia senegal across Sahelian Africa, but documented results of breeding activities are limited. The objective of this study was to provide reliable estimates of quantitative genetic parameters in order to shed light...

  4. Qualitative and quantitative stability analysis of penta-rhythmic circuits

    Science.gov (United States)

    Schwabedal, Justus T. C.; Knapper, Drake E.; Shilnikov, Andrey L.

    2016-12-01

    Inhibitory circuits of relaxation oscillators are often-used models for dynamics of biological networks. We present a qualitative and quantitative stability analysis of such a circuit constituted by three generic oscillators (of a Fitzhugh-Nagumo type) as its nodes coupled reciprocally. Depending on inhibitory strengths, and parameters of individual oscillators, the circuit exhibits polyrhythmicity of up to five simultaneously stable rhythms. With methods of bifurcation analysis and phase reduction, we investigate qualitative changes in stability of these circuit rhythms for a wide range of parameters. Furthermore, we quantify robustness of the rhythms maintained under random perturbations by monitoring phase diffusion in the circuit. Our findings allow us to describe how circuit dynamics relate to dynamics of individual nodes. We also find that quantitative and qualitative stability properties of polyrhythmicity do not always align.

  5. Quantitative analysis of myocardial tissue with digital autofluorescence microscopy

    DEFF Research Database (Denmark)

    Jensen, Thomas; Holten-Rossing, Henrik; Svendsen, Ida M H;

    2016-01-01

    BACKGROUND: The opportunity offered by whole slide scanners of automated histological analysis implies an ever increasing importance of digital pathology. To go beyond the importance of conventional pathology, however, digital pathology may need a basic histological starting point similar...... to that of hematoxylin and eosin staining in conventional pathology. This study presents an automated fluorescence-based microscopy approach providing highly detailed morphological data from unstained microsections. This data may provide a basic histological starting point from which further digital analysis including...... staining may benefit. METHODS: This study explores the inherent tissue fluorescence, also known as autofluorescence, as a mean to quantitate cardiac tissue components in histological microsections. Data acquisition using a commercially available whole slide scanner and an image-based quantitation algorithm...

  6. Quantitative and qualitative analysis and interpretation of CT perfusion imaging.

    Science.gov (United States)

    Valdiviezo, Carolina; Ambrose, Marietta; Mehra, Vishal; Lardo, Albert C; Lima, Joao A C; George, Richard T

    2010-12-01

    Coronary artery disease (CAD) remains the leading cause of death in the United States. Rest and stress myocardial perfusion imaging has an important role in the non-invasive risk stratification of patients with CAD. However, diagnostic accuracies have been limited, which has led to the development of several myocardial perfusion imaging techniques. Among them, myocardial computed tomography perfusion imaging (CTP) is especially interesting as it has the unique capability of providing anatomic- as well as coronary stenosis-related functional data when combined with computed tomography angiography (CTA). The primary aim of this article is to review the qualitative, semi-quantitative, and quantitative analysis approaches to CTP imaging. In doing so, we will describe the image data required for each analysis and discuss the advantages and disadvantages of each approach.

  7. QuantUM: Quantitative Safety Analysis of UML Models

    Directory of Open Access Journals (Sweden)

    Florian Leitner-Fischer

    2011-07-01

    Full Text Available When developing a safety-critical system it is essential to obtain an assessment of different design alternatives. In particular, an early safety assessment of the architectural design of a system is desirable. In spite of the plethora of available formal quantitative analysis methods it is still difficult for software and system architects to integrate these techniques into their every day work. This is mainly due to the lack of methods that can be directly applied to architecture level models, for instance given as UML diagrams. Also, it is necessary that the description methods used do not require a profound knowledge of formal methods. Our approach bridges this gap and improves the integration of quantitative safety analysis methods into the development process. All inputs of the analysis are specified at the level of a UML model. This model is then automatically translated into the analysis model, and the results of the analysis are consequently represented on the level of the UML model. Thus the analysis model and the formal methods used during the analysis are hidden from the user. We illustrate the usefulness of our approach using an industrial strength case study.

  8. Genetic programming based quantitative structure-retention relationships for the prediction of Kovats retention indices.

    Science.gov (United States)

    Goel, Purva; Bapat, Sanket; Vyas, Renu; Tambe, Amruta; Tambe, Sanjeev S

    2015-11-13

    The development of quantitative structure-retention relationships (QSRR) aims at constructing an appropriate linear/nonlinear model for the prediction of the retention behavior (such as Kovats retention index) of a solute on a chromatographic column. Commonly, multi-linear regression and artificial neural networks are used in the QSRR development in the gas chromatography (GC). In this study, an artificial intelligence based data-driven modeling formalism, namely genetic programming (GP), has been introduced for the development of quantitative structure based models predicting Kovats retention indices (KRI). The novelty of the GP formalism is that given an example dataset, it searches and optimizes both the form (structure) and the parameters of an appropriate linear/nonlinear data-fitting model. Thus, it is not necessary to pre-specify the form of the data-fitting model in the GP-based modeling. These models are also less complex, simple to understand, and easy to deploy. The effectiveness of GP in constructing QSRRs has been demonstrated by developing models predicting KRIs of light hydrocarbons (case study-I) and adamantane derivatives (case study-II). In each case study, two-, three- and four-descriptor models have been developed using the KRI data available in the literature. The results of these studies clearly indicate that the GP-based models possess an excellent KRI prediction accuracy and generalization capability. Specifically, the best performing four-descriptor models in both the case studies have yielded high (>0.9) values of the coefficient of determination (R(2)) and low values of root mean squared error (RMSE) and mean absolute percent error (MAPE) for training, test and validation set data. The characteristic feature of this study is that it introduces a practical and an effective GP-based method for developing QSRRs in gas chromatography that can be gainfully utilized for developing other types of data-driven models in chromatography science.

  9. Country Risk Analysis: A Survey of the Quantitative Methods

    OpenAIRE

    Hiranya K Nath

    2008-01-01

    With globalization and financial integration, there has been rapid growth of international lending and foreign direct investment (FDI). In view of this emerging trend, country risk analysis has become extremely important for the international creditors and investors. This paper briefly discusses the concepts and definitions, and presents a survey of the quantitative methods that are used to address various issues related to country risk. It also gives a summary review of selected empirical st...

  10. Quantitative genetics approaches to study evolutionary processes in ecotoxicology; a perspective from research on the evolution of resistance.

    Science.gov (United States)

    Klerks, Paul L; Xie, Lingtian; Levinton, Jeffrey S

    2011-05-01

    Quantitative genetic approaches are often used to study evolutionary processes in ecotoxicology. This paper focuses on the evolution of resistance to environmental contaminants-an important evolutionary process in ecotoxicology. Three approaches are commonly employed to study the evolution of resistance: (1) Assessing whether a contaminant-exposed population has an increased resistance relative to a control population, using either spatial or temporal comparisons. (2) Estimating a population's heritability of resistance. (3) Investigating responses in a laboratory selection experiment. All three approaches provide valuable information on the potential for contaminants to affect a population's evolutionary trajectory via natural selection. However, all three approaches have inherent limitations, including difficulty in separating the various genetic and environmental variance components, responses being dependent on specific population and testing conditions, and inability to fully capture natural conditions in the laboratory. In order to maximize insights into the long-term consequences of adaptation, it is important to not just look at resistance itself, but also at the fitness consequences and at correlated responses in characteristics other than resistance. The rapid development of molecular genetics has yielded alternatives to the "black box" approach of quantitative genetics, but the presence of different limitations and strengths in the two fields means that they should be viewed as complementary rather than exchangeable. Quantitative genetics is benefiting from the incorporation of molecular tools and remains an important field for studying evolutionary toxicology.

  11. Quantitative clinical characteristics of 53 patients with MPS VII: a cross-sectional analysis.

    Science.gov (United States)

    Zielonka, Matthias; Garbade, Sven F; Kölker, Stefan; Hoffmann, Georg F; Ries, Markus

    2017-04-06

    The main purpose of the study was to provide quantitative data regarding survival and diagnostic delay. Mucopolysaccharidosis (MPS) type VII (OMIM 253220) is a progressive neurometabolic disorder caused by deficiency of the lysosomal enzyme β-glucuronidase (GUS). Hard clinical end points have not been quantitatedMethods:We quantitatively analyzed published cases with MPS VII (N = 53/88 with sufficient data). Main outcome measures were onset of disease and survival. The role of biomarkers such as GUS residual enzyme activity and levels of storage material assessed as urinary excretion of glucosaminoglycans (GAG) as potential predictors of clinical outcomes were investigated. The analysis was conducted according to STROBE criteria. Median survival of the postnatally diagnosed population was 42 months. Median age of disease onset was the first day of life; median age at diagnosis was 11 months. Hydrops fetalis was frequent. Patients with residual GUS activity in fibroblasts more than 1.4% or urinary GAG excretion less than 602% of normal survived longer than patients with GUS enzyme activity below or GAG excretion above these thresholds. MPS VII has its disease onset prenatally. In the absence of a prenatal diagnosis, most cases are clinically apparent at birth. Our data corroborate a phenotype-biomarker association in MPS VII. The survival data characterize the natural history with important implications for therapeutic studies.Genet Med advance online publication 06 April 2017Genetics in Medicine (2017); doi:10.1038/gim.2017.10.

  12. Quantitative Proteomic Approaches for Analysis of Protein S-Nitrosylation.

    Science.gov (United States)

    Qu, Zhe; Greenlief, C Michael; Gu, Zezong

    2016-01-01

    S-Nitrosylation is a redox-based post-translational modification of a protein in response to nitric oxide (NO) signaling, and it participates in a variety of processes in diverse biological systems. The significance of this type of protein modification in health and diseases is increasingly recognized. In the central nervous system, aberrant S-nitrosylation, due to excessive NO production, is known to cause protein misfolding, mitochondrial dysfunction, transcriptional dysregulation, and neuronal death. This leads to an altered physiological state and consequently contributes to pathogenesis of neurodegenerative disorders. To date, much effort has been made to understand the mechanisms underlying protein S-nitrosylation, and several approaches have been developed to unveil S-nitrosylated proteins from different organisms. Interest in determining the dynamic changes of protein S-nitrosylation under different physiological and pathophysiological conditions has underscored the need for the development of quantitative proteomic approaches. Currently, both gel-based and gel-free mass spectrometry-based quantitative methods are widely used, and they each have advantages and disadvantages but may also be used together to produce complementary data. This review evaluates current available quantitative proteomic techniques for the analysis of protein S-nitrosylation and highlights recent advances, with emphasis on applications in neurodegenerative diseases. An important goal is to provide a comprehensive guide of feasible quantitative proteomic methodologies for examining protein S-nitrosylation in research to yield insights into disease mechanisms, diagnostic biomarkers, and drug discovery.

  13. Comprehensive Quantitative Analysis of SQ Injection Using Multiple Chromatographic Technologies.

    Science.gov (United States)

    Chau, Siu-Leung; Huang, Zhi-Bing; Song, Yan-Gang; Yue, Rui-Qi; Ho, Alan; Lin, Chao-Zhan; Huang, Wen-Hua; Han, Quan-Bin

    2016-08-19

    Quality control of Chinese medicine injections remains a challenge due to our poor knowledge of their complex chemical profile. This study aims to investigate the chemical composition of one of the best-selling injections, Shenqi Fuzheng (SQ) injection (SQI), via a full component quantitative analysis. A total of 15 representative small molecular components of SQI were simultaneously determined using ultra-high performance liquid chromatography (UHPLC) coupled with quadrupole tandem time-of-flight mass spectrometry (Q-TOF-MS); saccharide composition of SQI was also quantitatively determined by high performance liquid chromatography (HPLC) with evaporative light scattering detector (ELSD) on an amino column before and after acid hydrolysis. The existence of polysaccharides was also examined on a gel permeation chromatography column. The method was well validated in terms of linearity, sensitivity, precision, accuracy and stability, and was successfully applied to analyze 13 SQI samples. The results demonstrate that up to 94.69% (w/w) of this injection product are quantitatively determined, in which small molecules and monosaccharide/sucrose account for 0.18%-0.21%, and 53.49%-58.2%, respectively. The quantitative information contributes to accumulating scientific evidence to better understand the therapy efficacy and safety of complex Chinese medicine injections.

  14. Comprehensive Quantitative Analysis of SQ Injection Using Multiple Chromatographic Technologies

    Directory of Open Access Journals (Sweden)

    Siu-Leung Chau

    2016-08-01

    Full Text Available Quality control of Chinese medicine injections remains a challenge due to our poor knowledge of their complex chemical profile. This study aims to investigate the chemical composition of one of the best-selling injections, Shenqi Fuzheng (SQ injection (SQI, via a full component quantitative analysis. A total of 15 representative small molecular components of SQI were simultaneously determined using ultra-high performance liquid chromatography (UHPLC coupled with quadrupole tandem time-of-flight mass spectrometry (Q-TOF-MS; saccharide composition of SQI was also quantitatively determined by high performance liquid chromatography (HPLC with evaporative light scattering detector (ELSD on an amino column before and after acid hydrolysis. The existence of polysaccharides was also examined on a gel permeation chromatography column. The method was well validated in terms of linearity, sensitivity, precision, accuracy and stability, and was successfully applied to analyze 13 SQI samples. The results demonstrate that up to 94.69% (w/w of this injection product are quantitatively determined, in which small molecules and monosaccharide/sucrose account for 0.18%–0.21%, and 53.49%–58.2%, respectively. The quantitative information contributes to accumulating scientific evidence to better understand the therapy efficacy and safety of complex Chinese medicine injections.

  15. Clarifying CLARITY: Quantitative Optimization of the Diffusion Based Delipidation Protocol for Genetically Labeled Tissue.

    Science.gov (United States)

    Magliaro, Chiara; Callara, Alejandro L; Mattei, Giorgio; Morcinelli, Marco; Viaggi, Cristina; Vaglini, Francesca; Ahluwalia, Arti

    2016-01-01

    Tissue clarification has been recently proposed to allow deep tissue imaging without light scattering. The clarification parameters are somewhat arbitrary and dependent on tissue type, source and dimension: every laboratory has its own protocol, but a quantitative approach to determine the optimum clearing time is still lacking. Since the use of transgenic mouse lines that express fluorescent proteins to visualize specific cell populations is widespread, a quantitative approach to determine the optimum clearing time for genetically labeled neurons from thick murine brain slices using CLARITY2 is described. In particular, as the main objective of the delipidation treatment is to clarify tissues, while limiting loss of fluorescent signal, the "goodness" of clarification was evaluated by considering the bulk tissue clarification index (BTCi) and the fraction of the fluorescent marker retained in the slice as easily quantifiable macroscale parameters. Here we describe the approach, illustrating an example of how it can be used to determine the optimum clearing time for 1 mm-thick cerebellar slice from transgenic L7GFP mice, in which Purkinje neurons express the GFP (green fluorescent protein) tag. To validate the method, we evaluated confocal stacks of our samples using standard image processing indices (i.e., the mean pixel intensity of neurons and the contrast-to-noise ratio) as figures of merit for image quality. The results show that detergent-based delipidation for more than 5 days does not increase tissue clarity but the fraction of GFP in the tissue continues to diminish. The optimum clearing time for 1 mm-thick slices was thus identified as 5 days, which is the best compromise between the increase in light penetration depth due to removal of lipids and a decrease in fluorescent signal as a consequence of protein loss: further clearing does not improve tissue transparency, but only leads to more protein removal or degradation. The rigorous quantitative approach

  16. QTL IciMapping:Integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations

    Institute of Scientific and Technical Information of China (English)

    Lei; Meng; Huihui; Li; Luyan; Zhang; Jiankang; Wang

    2015-01-01

    QTL Ici Mapping is freely available public software capable of building high-density linkage maps and mapping quantitative trait loci(QTL) in biparental populations. Eight functionalities are integrated in this software package:(1) BIN: binning of redundant markers;(2) MAP: construction of linkage maps in biparental populations;(3) CMP: consensus map construction from multiple linkage maps sharing common markers;(4) SDL: mapping of segregation distortion loci;(5) BIP: mapping of additive, dominant, and digenic epistasis genes;(6) MET: QTL-by-environment interaction analysis;(7) CSL: mapping of additive and digenic epistasis genes with chromosome segment substitution lines; and(8) NAM: QTL mapping in NAM populations. Input files can be arranged in plain text, MS Excel 2003, or MS Excel 2007 formats. Output files have the same prefix name as the input but with different extensions. As examples, there are two output files in BIN, one for summarizing the identified bin groups and deleted markers in each bin, and the other for using the MAP functionality. Eight output files are generated by MAP, including summary of the completed linkage maps, Mendelian ratio test of individual markers, estimates of recombination frequencies, LOD scores, and genetic distances, and the input files for using the BIP, SDL,and MET functionalities. More than 30 output files are generated by BIP, including results at all scanning positions, identified QTL, permutation tests, and detection powers for up to six mapping methods. Three supplementary tools have also been developed to display completed genetic linkage maps, to estimate recombination frequency between two loci,and to perform analysis of variance for multi-environmental trials.

  17. QTL IciMapping:Integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations

    Institute of Scientific and Technical Information of China (English)

    Lei Meng; Huihui Li; Luyan Zhang; Jiankang Wang

    2015-01-01

    QTL IciMapping is freely available public software capable of building high-density linkage maps and mapping quantitative trait loci (QTL) in biparental populations. Eight func-tionalities are integrated in this software package: (1) BIN:binning of redundant markers;(2) MAP: construction of linkage maps in biparental populations; (3) CMP: consensus map construction from multiple linkage maps sharing common markers; (4) SDL: mapping of segregation distortion loci;(5) BIP:mapping of additive, dominant, and digenic epistasis genes;(6) MET:QTL-by-environment interaction analysis;(7) CSL:mapping of additive and digenic epistasis genes with chromosome segment substitution lines; and (8) NAM: QTL mapping in NAM populations. Input files can be arranged in plain text, MS Excel 2003, or MS Excel 2007 formats. Output files have the same prefix name as the input but with different extensions. As examples, there are two output files in BIN, one for summarizing the identified bin groups and deleted markers in each bin, and the other for using the MAP functionality. Eight output files are generated by MAP, including summary of the completed linkage maps, Mendelian ratio test of individual markers, estimates of recombination frequencies, LOD scores, and genetic distances, and the input files for using the BIP, SDL, and MET functionalities. More than 30 output files are generated by BIP, including results at all scanning positions, identified QTL, permutation tests, and detection powers for up to six mapping methods. Three supplementary tools have also been developed to display completed genetic linkage maps, to estimate recombination frequency between two loci, and to perform analysis of variance for multi-environmental trials.

  18. QTL IciMapping: Integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations

    Directory of Open Access Journals (Sweden)

    Lei Meng

    2015-06-01

    Full Text Available QTL IciMapping is freely available public software capable of building high-density linkage maps and mapping quantitative trait loci (QTL in biparental populations. Eight functionalities are integrated in this software package: (1 BIN: binning of redundant markers; (2 MAP: construction of linkage maps in biparental populations; (3 CMP: consensus map construction from multiple linkage maps sharing common markers; (4 SDL: mapping of segregation distortion loci; (5 BIP: mapping of additive, dominant, and digenic epistasis genes; (6 MET: QTL-by-environment interaction analysis; (7 CSL: mapping of additive and digenic epistasis genes with chromosome segment substitution lines; and (8 NAM: QTL mapping in NAM populations. Input files can be arranged in plain text, MS Excel 2003, or MS Excel 2007 formats. Output files have the same prefix name as the input but with different extensions. As examples, there are two output files in BIN, one for summarizing the identified bin groups and deleted markers in each bin, and the other for using the MAP functionality. Eight output files are generated by MAP, including summary of the completed linkage maps, Mendelian ratio test of individual markers, estimates of recombination frequencies, LOD scores, and genetic distances, and the input files for using the BIP, SDL, and MET functionalities. More than 30 output files are generated by BIP, including results at all scanning positions, identified QTL, permutation tests, and detection powers for up to six mapping methods. Three supplementary tools have also been developed to display completed genetic linkage maps, to estimate recombination frequency between two loci, and to perform analysis of variance for multi-environmental trials.

  19. Genetic Analysis of Early Generation Stability in Rice

    Institute of Scientific and Technical Information of China (English)

    ZHOU Li-Jun; Ao Guang-Hui; XIAO Yi; WU Xian-Jun; LI Shi-Gui

    2005-01-01

    The mechanism of early generation stability (EGS) in rice was studied via genetic analysis. Three types of crosses were made, namely between EGS varieties, EGS and conventional rice variety, and conventional rice varieties. The genetic analysis was based on the stable lines in F2 population. The stable lines may appear from some combinations of EGS rice crossing with each other and EGS rice crossing with conventional varieties at different frequencies, but stable lines didn't appear in conventional varieties crossing with conventional varieties. Genetic analysis results indicated that the EGS phenomena should just exist in special rice materials, and the frequency of stable lines was closely related to the EGS traits of parents. The EGS traits were neither qualitative nor quantitative traits, and they were controlled by neither dominant genes nor recessive genes. The EGS traits might be inherited by F1 single plant, and the traits of F3 and F4 were corresponded to those of F2 population, i.e. F3 and F4 lines derived from non-segregating F2 showed uniform agronomic traits, and those from segregating F2.did not. The agronomic traits of EGS lines were consistent with those of F1 single plant. On the other hand, when EGS lines occurred, the segregating lines in Mendelian manner were also observed in all F2 population of the same combination. It was suggested that the reason why the stable strains occurred might be a special factor to control (open/close) gene at the beginning of cell division in zygote, resulting in closing mitosis and opening somatic reduction. The somatic reduction of zygote resulted in recombination and homozygosity forming in F1 single plant,and some lines with uniform agronomic traits were observed in some lines of F2 population.

  20. Genetic Parameters and Combining Ability Effects of Parents for Seed Yield and other Quantitative Traits in Black Gram [Vigna mungo (L. Hepper

    Directory of Open Access Journals (Sweden)

    Supriyo CHAKRABORTY

    2010-06-01

    Full Text Available Line x tester analysis was carried out in black gram [Vigna mungo (L. Hepper], an edible legume, to estimate the gca (general combining ability effects of parents (3 lines and 3 testers and the SCA (specific combining ability effects of 9 crosses for seed yield and other eleven quantitative traits. Though additive and nonadditive gene actions governed the expression of quantitative traits, the magnitude of nonadditive gene action was higher than that of additive gene action for each quantitative trait. Two parents viz. UG157 and DPU915 were good general combiners. Two crosses namely PDB 88-31/DPU 915 and PLU 277/KAU7 had high per se performance along with positive significant SCA effect for seed yield/plant. The degree of dominance revealed overdominance for all the traits except clusters/plant with partial dominance. The predictability ratio also revealed the predominant role of nonadditive gene action in the genetic control of quantitative traits. Narrow sense heritability was also low for each trait. Recurrent selection or biparental mating followed by selection which can exploit both additive and nonadditive gene actions would be of interest for yield improvement in black gram. Due to presence of high magnitude of nonadditive gene action, heterosis breeding could also be attempted to develop low cost hybrid variety using genetic male sterility system in black gram.

  1. Genetic Parameters and Combining Ability Effects of Parents for Seed Yield and other Quantitative Traits in Black Gram [Vigna mungo (L. Hepper

    Directory of Open Access Journals (Sweden)

    Supriyo CHAKRABORTY

    2010-06-01

    Full Text Available Line x tester analysis was carried out in black gram [Vigna mungo (L. Hepper], an edible legume, to estimate the gca (general combining ability effects of parents (3 lines and 3 testers and the SCA (specific combining ability effects of 9 crosses for seed yield and other eleven quantitative traits. Though additive and nonadditive gene actions governed the expression of quantitative traits, the magnitude of nonadditive gene action was higher than that of additive gene action for each quantitative trait. Two parents viz. �UG157� and �DPU915� were good general combiners. Two crosses namely �PDB 88-31�/�DPU 915� and �PLU 277�/�KAU7� had high per se performance along with positive significant SCA effect for seed yield/plant. The degree of dominance revealed overdominance for all the traits except clusters/plant with partial dominance. The predictability ratio also revealed the predominant role of nonadditive gene action in the genetic control of quantitative traits. Narrow sense heritability was also low for each trait. Recurrent selection or biparental mating followed by selection which can exploit both additive and nonadditive gene actions would be of interest for yield improvement in black gram. Due to presence of high magnitude of nonadditive gene action, heterosis breeding could also be attempted to develop low cost hybrid variety using genetic male sterility system in black gram.

  2. A genetic epidemiological mega analysis of smoking initiation in adolescents

    NARCIS (Netherlands)

    Maes, H.H.; Prom-Wormley, E.; Eaves, L.J.; Rhee, S.H.; Hewitt, J.K.; Young, S.; Corley, R.; McGue, M.K.; Iacono, W.G.; Legrand, L.; Samek, D.; Murrelle, E.L.; Silberg, J.L.; Miles, D.; Schieken, R.M.; Beunen, G.P.; Thomis, M.; Rose, R.J.; Dick, D.M.; Boomsma, D.I.; Bartels, M.; Vink, J.M.; Lichtenstein, P.; White, V.; Kaprio, J.; Neale, M.C.

    2017-01-01

    Introduction. Previous studies in adolescents were not adequately powered to accurately disentangle genetic and environmental influences on smoking initiation across adolescence. Methods. Mega-analysis of pooled genetically informative data on smoking initiation was performed, with structural

  3. Spectral Quantitative Analysis Model with Combining Wavelength Selection and Topology Structure Optimization

    Directory of Open Access Journals (Sweden)

    Qian Wang

    2016-01-01

    Full Text Available Spectroscopy is an efficient and widely used quantitative analysis method. In this paper, a spectral quantitative analysis model with combining wavelength selection and topology structure optimization is proposed. For the proposed method, backpropagation neural network is adopted for building the component prediction model, and the simultaneousness optimization of the wavelength selection and the topology structure of neural network is realized by nonlinear adaptive evolutionary programming (NAEP. The hybrid chromosome in binary scheme of NAEP has three parts. The first part represents the topology structure of neural network, the second part represents the selection of wavelengths in the spectral data, and the third part represents the parameters of mutation of NAEP. Two real flue gas datasets are used in the experiments. In order to present the effectiveness of the methods, the partial least squares with full spectrum, the partial least squares combined with genetic algorithm, the uninformative variable elimination method, the backpropagation neural network with full spectrum, the backpropagation neural network combined with genetic algorithm, and the proposed method are performed for building the component prediction model. Experimental results verify that the proposed method has the ability to predict more accurately and robustly as a practical spectral analysis tool.

  4. Quantitative analysis for nonlinear fluorescent spectra based on edges matching

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    A novel spectra-edge-matching approach is proposed for the quantitative analysis of the nonlinear fluorescence spectra of the air impurities excited by a femtosecond laser.The fluorescence spectra are first denoised and compressed,both by wavelet transform,and several peak groups are then picked from each spectrum according to a threshold of intensity and are used to extract the spectral features through principal component analysis.It is indicated that the first two principle components actually cover up to 98% of the total information and are sufficient for the final concentration analysis.The analysis reveals a monotone relationship between the spectra intensity and the concentration of the air impurities,suggesting that the femtosecond laser induced fluorescence spectroscopy along with the proposed spectra analysis method can become a powerful tool for monitoring environmental pollutants.

  5. Quantitative gait analysis following hemispherotomy for Rasmussen′s encephalitis

    Directory of Open Access Journals (Sweden)

    Santhosh George Thomas

    2007-01-01

    Full Text Available Peri-insular hemispherotomy is a form of disconnective hemispherectomy involving complete disconnection of all ascending / descending and commisural connections of one hemisphere. We report a case of a seven and a half year old child with intractable epilepsy due to Rasmussen′s encephalitis who underwent peri-insular hemispherotomy and achieved complete freedom from seizures. Quantitative gait analysis was used to describe the changes in the kinematic and kinetic parameters of gait with surface electromyographs 18 months after surgery. The focus of this paper is to highlight the utility of gait analysis following hemispherotomy with a view to directing postsurgical motor training and rehabilitation.

  6. Genetic mapping of quantitative trait loci for milk production in sheep.

    Science.gov (United States)

    Mateescu, R G; Thonney, M L

    2010-10-01

    A backcross pedigree using dairy East Friesian rams and non-dairy Dorset ewes was established specifically to map quantitative trait loci (QTL) affecting milk production in sheep. Ninety nine microsatellite markers of an initial set of 120 were successfully genotyped and informative on 188 animals of this backcross pedigree. Test-day milk records on individual ewes were used to estimate several milk yield related traits, including peak milk yield and cumulative milk yield to 50 (MY50), 100 (MY100) and 250 days (MY250). These traits, as well as estimated breeding value of backcross ewes extracted from the genetic evaluation file of the entire flock, were used in interval mapping. Ovine chromosomes 2, 12, 18, 20 and 24 were identified to harbour putative QTL for different measures of milk production. The QTL on Ovis aries chromosomes (OAR) 2 and 20 mapped to locations where similar trait QTL have already been mapped in other studies, whereas QTL on OAR 12, 18 and 24 were unique to our backcross pedigree and have not been reported previously. In addition, all identified QTL regions were syntenic with bovine chromosomal segments revealed to harbour QTL affecting milk production traits, providing supporting evidence for the QTL identified here.

  7. The first genetic map of the American cranberry: exploration of synteny conservation and quantitative trait loci.

    Science.gov (United States)

    Georgi, Laura; Johnson-Cicalese, Jennifer; Honig, Josh; Das, Sushma Parankush; Rajah, Veeran D; Bhattacharya, Debashish; Bassil, Nahla; Rowland, Lisa J; Polashock, James; Vorsa, Nicholi

    2013-03-01

    The first genetic map of cranberry (Vaccinium macrocarpon) has been constructed, comprising 14 linkage groups totaling 879.9 cM with an estimated coverage of 82.2 %. This map, based on four mapping populations segregating for field fruit-rot resistance, contains 136 distinct loci. Mapped markers include blueberry-derived simple sequence repeat (SSR) and cranberry-derived sequence-characterized amplified region markers previously used for fingerprinting cranberry cultivars. In addition, SSR markers were developed near cranberry sequences resembling genes involved in flavonoid biosynthesis or defense against necrotrophic pathogens, or conserved orthologous set (COS) sequences. The cranberry SSRs were developed from next-generation cranberry genomic sequence assemblies; thus, the positions of these SSRs on the genomic map provide information about the genomic location of the sequence scaffold from which they were derived. The use of SSR markers near COS and other functional sequences, plus 33 SSR markers from blueberry, facilitates comparisons of this map with maps of other plant species. Regions of the cranberry map were identified that showed conservation of synteny with Vitis vinifera and Arabidopsis thaliana. Positioned on this map are quantitative trait loci (QTL) for field fruit-rot resistance (FFRR), fruit weight, titratable acidity, and sound fruit yield (SFY). The SFY QTL is adjacent to one of the fruit weight QTL and may reflect pleiotropy. Two of the FFRR QTL are in regions of conserved synteny with grape and span defense gene markers, and the third FFRR QTL spans a flavonoid biosynthetic gene.

  8. Quantitative genetics model as the unifying model for defining genomic relationship and inbreeding coefficient.

    Science.gov (United States)

    Wang, Chunkao; Da, Yang

    2014-01-01

    The traditional quantitative genetics model was used as the unifying approach to derive six existing and new definitions of genomic additive and dominance relationships. The theoretical differences of these definitions were in the assumptions of equal SNP effects (equivalent to across-SNP standardization), equal SNP variances (equivalent to within-SNP standardization), and expected or sample SNP additive and dominance variances. The six definitions of genomic additive and dominance relationships on average were consistent with the pedigree relationships, but had individual genomic specificity and large variations not observed from pedigree relationships. These large variations may allow finding least related genomes even within the same family for minimizing genomic relatedness among breeding individuals. The six definitions of genomic relationships generally had similar numerical results in genomic best linear unbiased predictions of additive effects (GBLUP) and similar genomic REML (GREML) estimates of additive heritability. Predicted SNP dominance effects and GREML estimates of dominance heritability were similar within definitions assuming equal SNP effects or within definitions assuming equal SNP variance, but had differences between these two groups of definitions. We proposed a new measure of genomic inbreeding coefficient based on parental genomic co-ancestry coefficient and genomic additive correlation as a genomic approach for predicting offspring inbreeding level. This genomic inbreeding coefficient had the highest correlation with pedigree inbreeding coefficient among the four methods evaluated for calculating genomic inbreeding coefficient in a Holstein sample and a swine sample.

  9. A Quantitative Method for Microtubule Analysis in Fluorescence Images.

    Science.gov (United States)

    Lan, Xiaodong; Li, Lingfei; Hu, Jiongyu; Zhang, Qiong; Dang, Yongming; Huang, Yuesheng

    2015-12-01

    Microtubule analysis is of significant value for a better understanding of normal and pathological cellular processes. Although immunofluorescence microscopic techniques have proven useful in the study of microtubules, comparative results commonly rely on a descriptive and subjective visual analysis. We developed an objective and quantitative method based on image processing and analysis of fluorescently labeled microtubular patterns in cultured cells. We used a multi-parameter approach by analyzing four quantifiable characteristics to compose our quantitative feature set. Then we interpreted specific changes in the parameters and revealed the contribution of each feature set using principal component analysis. In addition, we verified that different treatment groups could be clearly discriminated using principal components of the multi-parameter model. High predictive accuracy of four commonly used multi-classification methods confirmed our method. These results demonstrated the effectiveness and efficiency of our method in the analysis of microtubules in fluorescence images. Application of the analytical methods presented here provides information concerning the organization and modification of microtubules, and could aid in the further understanding of structural and functional aspects of microtubules under normal and pathological conditions.

  10. Quantitative Phosphoproteomic Analysis of T-Cell Receptor Signaling.

    Science.gov (United States)

    Ahsan, Nagib; Salomon, Arthur R

    2017-01-01

    TCR signaling critically depends on protein phosphorylation across many proteins. Localization of each phosphorylation event relative to the T-cell receptor (TCR) and canonical T-cell signaling proteins will provide clues about the structure of TCR signaling networks. Quantitative phosphoproteomic analysis by mass spectrometry provides a wide-scale view of cellular phosphorylation networks. However, analysis of phosphorylation by mass spectrometry is still challenging due to the relative low abundance of phosphorylated proteins relative to all proteins and the extraordinary diversity of phosphorylation sites across the proteome. Highly selective enrichment of phosphorylated peptides is essential to provide the most comprehensive view of the phosphoproteome. Optimization of phosphopeptide enrichment methods coupled with highly sensitive mass spectrometry workflows significantly improves the sequencing depth of the phosphoproteome to over 10,000 unique phosphorylation sites from complex cell lysates. Here we describe a step-by-step method for phosphoproteomic analysis that has achieved widespread success for identification of serine, threonine, and tyrosine phosphorylation. Reproducible quantification of relative phosphopeptide abundance is provided by intensity-based label-free quantitation. An ideal set of mass spectrometry analysis parameters is also provided that optimize the yield of identified sites. We also provide guidelines for the bioinformatic analysis of this type of data to assess the quality of the data and to comply with proteomic data reporting requirements.

  11. What Really Happens in Quantitative Group Research? Results of a Content Analysis of Recent Quantitative Research in "JSGW"

    Science.gov (United States)

    Boyle, Lauren H.; Whittaker, Tiffany A.; Eyal, Maytal; McCarthy, Christopher J.

    2017-01-01

    The authors conducted a content analysis on quantitative studies published in "The Journal for Specialists in Group Work" ("JSGW") between 2012 and 2015. This brief report provides a general overview of the current practices of quantitative group research in counseling. The following study characteristics are reported and…

  12. Determinants of Neurotransmitters in Cerebrospinal Fluid and Plasma : from Seasonality to Quantitative Genetics

    NARCIS (Netherlands)

    Luykx, J.J.

    2013-01-01

    Most psychiatric conditions are complex genetic as the largest proportion of genetic variance is likely to derive from many genetic variants of small effect. Nonetheless, given the intricacies of the human brain and the heterogeneous nature of psychiatric disease entities, dissecting the genetic mec

  13. Quantitative multivariate analysis of dynamic multicellular morphogenic trajectories.

    Science.gov (United States)

    White, Douglas E; Sylvester, Jonathan B; Levario, Thomas J; Lu, Hang; Streelman, J Todd; McDevitt, Todd C; Kemp, Melissa L

    2015-07-01

    Interrogating fundamental cell biology principles that govern tissue morphogenesis is critical to better understanding of developmental biology and engineering novel multicellular systems. Recently, functional micro-tissues derived from pluripotent embryonic stem cell (ESC) aggregates have provided novel platforms for experimental investigation; however elucidating the factors directing emergent spatial phenotypic patterns remains a significant challenge. Computational modelling techniques offer a unique complementary approach to probe mechanisms regulating morphogenic processes and provide a wealth of spatio-temporal data, but quantitative analysis of simulations and comparison to experimental data is extremely difficult. Quantitative descriptions of spatial phenomena across multiple systems and scales would enable unprecedented comparisons of computational simulations with experimental systems, thereby leveraging the inherent power of computational methods to interrogate the mechanisms governing emergent properties of multicellular biology. To address these challenges, we developed a portable pattern recognition pipeline consisting of: the conversion of cellular images into networks, extraction of novel features via network analysis, and generation of morphogenic trajectories. This novel methodology enabled the quantitative description of morphogenic pattern trajectories that could be compared across diverse systems: computational modelling of multicellular structures, differentiation of stem cell aggregates, and gastrulation of cichlid fish. Moreover, this method identified novel spatio-temporal features associated with different stages of embryo gastrulation, and elucidated a complex paracrine mechanism capable of explaining spatiotemporal pattern kinetic differences in ESC aggregates of different sizes.

  14. Mini-Column Ion-Exchange Separation and Atomic Absorption Quantitation of Nickel, Cobalt, and Iron: An Undergraduate Quantitative Analysis Experiment.

    Science.gov (United States)

    Anderson, James L.; And Others

    1980-01-01

    Presents an undergraduate quantitative analysis experiment, describing an atomic absorption quantitation scheme that is fast, sensitive and comparatively simple relative to other titration experiments. (CS)

  15. Analysis of quantitative pore features based on mathematical morphology

    Institute of Scientific and Technical Information of China (English)

    QI Heng-nian; CHEN Feng-nong; WANG Hang-jun

    2008-01-01

    Wood identification is a basic technique of wood science and industry. Pore features are among the most important identification features for hardwoods. We have used a method based on an analysis of quantitative pore feature, which differs from traditional qualitative methods. We applies mathematical morphology methods such as dilation and erosion, open and close transformation of wood cross-sections, image repairing, noise filtering and edge detection to segment the pores from their background. Then the mean square errors (MSE) of pores were computed to describe the distribution of pores. Our experiment shows that it is easy to classift the pore features into three basic types, just as in traditional qualitative methods, but with the use of MSE of pores. This quantitative method improves wood identification considerably.

  16. A Generalized Genetic Random Field Method for the Genetic Association Analysis of Sequencing Data

    Science.gov (United States)

    Li, Ming; He, Zihuai; Zhang, Min; Zhan, Xiaowei; Wei, Changshuai; Elston, Robert C.; Lu, Qing

    2017-01-01

    With the advance of high-throughput sequencing technologies, it has become feasible to investigate the influence of the entire spectrum of sequencing variations on complex human diseases. Although association studies utilizing the new sequencing technologies hold great promise to unravel novel genetic variants, especially rare genetic variants that contribute to human diseases, the statistical analysis of high-dimensional sequencing data remains a challenge. Advanced analytical methods are in great need to facilitate high-dimensional sequencing data analyses. In this article, we propose a generalized genetic random field (GGRF) method for association analyses of sequencing data. Like other similarity-based methods (e.g., SIMreg and SKAT), the new method has the advantages of avoiding the need to specify thresholds for rare variants and allowing for testing multiple variants acting in different directions and magnitude of effects. The method is built on the generalized estimating equation framework and thus accommodates a variety of disease phenotypes (e.g., quantitative and binary phenotypes). Moreover, it has a nice asymptotic property, and can be applied to small-scale sequencing data without need for small-sample adjustment. Through simulations, we demonstrate that the proposed GGRF attains an improved or comparable power over a commonly used method, SKAT, under various disease scenarios, especially when rare variants play a significant role in disease etiology. We further illustrate GGRF with an application to a real dataset from the Dallas Heart Study. By using GGRF, we were able to detect the association of two candidate genes, ANGPTL3 and ANGPTL4, with serum triglyceride. PMID:24482034

  17. Quantitative risk analysis as a basis for emergency planning

    Energy Technology Data Exchange (ETDEWEB)

    Yogui, Regiane Tiemi Teruya [Bureau Veritas do Brasil, Rio de Janeiro, RJ (Brazil); Macedo, Eduardo Soares de [Instituto de Pesquisas Tecnologicas (IPT), Sao Paulo, SP (Brazil)

    2009-07-01

    Several environmental accidents happened in Brazil and in the world during the 70's and 80's. This strongly motivated the preparation for emergencies in the chemical and petrochemical industries. Environmental accidents affect the environment and the communities that are neighbor to the industrial facilities. The present study aims at subsidizing and providing orientation to develop Emergency Planning from the data obtained on Quantitative Risk Analysis, elaborated according to the Technical Standard P4.261/03 from CETESB (Sao Paulo Environmental Agency). It was observed, during the development of the research, that the data generated on these studies need a complementation and a deeper analysis, so that it is possible to use them on the Emergency Plans. The main issues that were analyzed and discussed on this study were the reevaluation of hazard identification for the emergency plans, the consequences and vulnerability analysis for the response planning, the risk communication, and the preparation to respond to the emergencies of the communities exposed to manageable risks. As a result, the study intends to improve the interpretation and use of the data deriving from the Quantitative Risk Analysis to develop the emergency plans. (author)

  18. Quantitative analysis of in vivo confocal microscopy images: a review.

    Science.gov (United States)

    Patel, Dipika V; McGhee, Charles N

    2013-01-01

    In vivo confocal microscopy (IVCM) is a non-invasive method of examining the living human cornea. The recent trend towards quantitative studies using IVCM has led to the development of a variety of methods for quantifying image parameters. When selecting IVCM images for quantitative analysis, it is important to be consistent regarding the location, depth, and quality of images. All images should be de-identified, randomized, and calibrated prior to analysis. Numerous image analysis software are available, each with their own advantages and disadvantages. Criteria for analyzing corneal epithelium, sub-basal nerves, keratocytes, endothelium, and immune/inflammatory cells have been developed, although there is inconsistency among research groups regarding parameter definition. The quantification of stromal nerve parameters, however, remains a challenge. Most studies report lower inter-observer repeatability compared with intra-observer repeatability, and observer experience is known to be an important factor. Standardization of IVCM image analysis through the use of a reading center would be crucial for any future large, multi-centre clinical trials using IVCM.

  19. Genetic analysis of haemophilia A in Bulgaria

    Directory of Open Access Journals (Sweden)

    Kremensky Ivo

    2004-03-01

    Full Text Available Abstract Background Haemophilias are the most common hereditary severe disorders of blood clotting. In families afflicted with heamophilia, genetic analysis provides opportunities to prevent recurrence of the disease. This study establishes a diagnostical strategy for carriership determination and prenatal diagnostics of haemophilia A in Bulgarian haemophilic population. Methods A diagnostical strategy consisting of screening for most common mutations in the factor VIII gene and analysis of a panel of eight linked to the factor VIII gene locus polymorphisms was established. Results Polymorphic analysis for carrier status determination of haemophilia A was successful in 30 families out of 32 (94%. Carrier status was determined in 25 of a total of 28 women at risk (89%. Fourteen prenatal diagnoses in women at high risk of having a haemophilia A – affected child were performed, resulting in 6 healthy boys and 5 girls. Conclusion The compound approach proves to be a highly informative and cost-effective strategy for prevention of recurrence of haemophilia A in Bulgaria. DNA analysis facilitates carriership determination and subsequent prenatal diagnosis in the majority of Bulgarian families affected by haemophilia A.

  20. Quantitative Selection Analysis of Bacteriophage φCbK Susceptibility in Caulobacter crescentus.

    Science.gov (United States)

    Christen, Matthias; Beusch, Christian; Bösch, Yvonne; Cerletti, Dario; Flores-Tinoco, Carlos Eduardo; Del Medico, Luca; Tschan, Flavia; Christen, Beat

    2016-01-29

    Classical molecular genetics uses stringent selective conditions to identify mutants with distinct phenotypic responses. Mutations giving rise to less pronounced phenotypes are often missed. However, to gain systems-level insights into complex genetic interaction networks requires genome-wide assignment of quantitative phenotypic traits. In this paper, we present a quantitative selection approach coupled with transposon sequencing (QS-TnSeq) to globally identify the cellular components that orchestrate susceptibility of the cell cycle model bacterium Caulobacter crescentus toward bacteriophage φCbK infection. We found that 135 genes representing 3.30% of the Caulobacter genome exhibit significant accumulation of transposon insertions upon φCbK selection. More than 85% thereof consist of new factors not previously associated with phage φCbK susceptibility. Using hierarchical clustering of dose-dependent TnSeq datasets, we grouped these genes into functional modules that correlate with different stages of the φCbK infection process. We assign φCbK susceptibility to eight new genes that represent novel components of the pilus secretion machinery. Further, we demonstrate that, from 86 motility genes, only seven genes encoding structural and regulatory components of the flagellar hook increase phage resistance when disrupted by transposons, suggesting a link between flagellar hook assembly and pili biogenesis. In addition, we observe high recovery of Tn5 insertions within regulatory sequences of the genes encoding the essential NADH:ubiquinone oxidoreductase complex indicating that intact proton motive force is crucial for effective phage propagation. In sum, QS-TnSeq is broadly applicable to perform quantitative and genome-wide systems-genetics analysis of complex phenotypic traits.

  1. Quantitative imaging of collective cell migration during Drosophila gastrulation: multiphoton microscopy and computational analysis.

    Science.gov (United States)

    Supatto, Willy; McMahon, Amy; Fraser, Scott E; Stathopoulos, Angelike

    2009-01-01

    This protocol describes imaging and computational tools to collect and analyze live imaging data of embryonic cell migration. Our five-step protocol requires a few weeks to move through embryo preparation and four-dimensional (4D) live imaging using multi-photon microscopy, to 3D cell tracking using image processing, registration of tracking data and their quantitative analysis using computational tools. It uses commercially available equipment and requires expertise in microscopy and programming that is appropriate for a biology laboratory. Custom-made scripts are provided, as well as sample datasets to permit readers without experimental data to carry out the analysis. The protocol has offered new insights into the genetic control of cell migration during Drosophila gastrulation. With simple modifications, this systematic analysis could be applied to any developing system to define cell positions in accordance with the body plan, to decompose complex 3D movements and to quantify the collective nature of cell migration.

  2. Quantitative phosphoproteomic analysis using iTRAQ method.

    Science.gov (United States)

    Asano, Tomoya; Nishiuchi, Takumi

    2014-01-01

    The MAPK (mitogen-activated kinase) cascade plays important roles in plant perception of and reaction to developmental and environmental cues. Phosphoproteomics are useful to identify target proteins regulated by MAPK-dependent signaling pathway. Here, we introduce the quantitative phosphoproteomic analysis using a chemical labeling method. The isobaric tag for relative and absolute quantitation (iTRAQ) method is a MS-based technique to quantify protein expression among up to eight different samples in one experiment. In this technique, peptides were labeled by some stable isotope-coded covalent tags. We perform quantitative phosphoproteomics comparing Arabidopsis wild type and a stress-responsive mapkk mutant after phytotoxin treatment. To comprehensively identify the downstream phosphoproteins of MAPKK, total proteins were extracted from phytotoxin-treated wild-type and mapkk mutant plants. The phosphoproteins were purified by Pro-Q(®) Diamond Phosphoprotein Enrichment Kit and were digested with trypsin. Resulting peptides were labeled with iTRAQ reagents and were quantified and identified by MALDI TOF/TOF analyzer. We identified many phosphoproteins that were decreased in the mapkk mutant compared with wild type.

  3. A quantitative analysis of IRAS maps of molecular clouds

    Science.gov (United States)

    Wiseman, Jennifer J.; Adams, Fred C.

    1994-01-01

    We present an analysis of IRAS maps of five molecular clouds: Orion, Ophiuchus, Perseus, Taurus, and Lupus. For the classification and description of these astrophysical maps, we use a newly developed technique which considers all maps of a given type to be elements of a pseudometric space. For each physical characteristic of interest, this formal system assigns a distance function (a pseudometric) to the space of all maps: this procedure allows us to measure quantitatively the difference between any two maps and to order the space of all maps. We thus obtain a quantitative classification scheme for molecular clouds. In this present study we use the IRAS continuum maps at 100 and 60 micrometer(s) to produce column density (or optical depth) maps for the five molecular cloud regions given above. For this sample of clouds, we compute the 'output' functions which measure the distribution of density, the distribution of topological components, the self-gravity, and the filamentary nature of the clouds. The results of this work provide a quantitative description of the structure in these molecular cloud regions. We then order the clouds according to the overall environmental 'complexity' of these star-forming regions. Finally, we compare our results with the observed populations of young stellar objects in these clouds and discuss the possible environmental effects on the star-formation process. Our results are consistent with the recently stated conjecture that more massive stars tend to form in more 'complex' environments.

  4. Simulating realistic predator signatures in quantitative fatty acid signature analysis

    Science.gov (United States)

    Bromaghin, Jeffrey F.

    2015-01-01

    Diet estimation is an important field within quantitative ecology, providing critical insights into many aspects of ecology and community dynamics. Quantitative fatty acid signature analysis (QFASA) is a prominent method of diet estimation, particularly for marine mammal and bird species. Investigators using QFASA commonly use computer simulation to evaluate statistical characteristics of diet estimators for the populations they study. Similar computer simulations have been used to explore and compare the performance of different variations of the original QFASA diet estimator. In both cases, computer simulations involve bootstrap sampling prey signature data to construct pseudo-predator signatures with known properties. However, bootstrap sample sizes have been selected arbitrarily and pseudo-predator signatures therefore may not have realistic properties. I develop an algorithm to objectively establish bootstrap sample sizes that generates pseudo-predator signatures with realistic properties, thereby enhancing the utility of computer simulation for assessing QFASA estimator performance. The algorithm also appears to be computationally efficient, resulting in bootstrap sample sizes that are smaller than those commonly used. I illustrate the algorithm with an example using data from Chukchi Sea polar bears (Ursus maritimus) and their marine mammal prey. The concepts underlying the approach may have value in other areas of quantitative ecology in which bootstrap samples are post-processed prior to their use.

  5. Chromatin immunoprecipitation: optimization, quantitative analysis and data normalization

    Directory of Open Access Journals (Sweden)

    Peterhansel Christoph

    2007-09-01

    Full Text Available Abstract Background Chromatin remodeling, histone modifications and other chromatin-related processes play a crucial role in gene regulation. A very useful technique to study these processes is chromatin immunoprecipitation (ChIP. ChIP is widely used for a few model systems, including Arabidopsis, but establishment of the technique for other organisms is still remarkably challenging. Furthermore, quantitative analysis of the precipitated material and normalization of the data is often underestimated, negatively affecting data quality. Results We developed a robust ChIP protocol, using maize (Zea mays as a model system, and present a general strategy to systematically optimize this protocol for any type of tissue. We propose endogenous controls for active and for repressed chromatin, and discuss various other controls that are essential for successful ChIP experiments. We experienced that the use of quantitative PCR (QPCR is crucial for obtaining high quality ChIP data and we explain why. The method of data normalization has a major impact on the quality of ChIP analyses. Therefore, we analyzed different normalization strategies, resulting in a thorough discussion of the advantages and drawbacks of the various approaches. Conclusion Here we provide a robust ChIP protocol and strategy to optimize the protocol for any type of tissue; we argue that quantitative real-time PCR (QPCR is the best method to analyze the precipitates, and present comprehensive insights into data normalization.

  6. Fluorescent foci quantitation for high-throughput analysis

    Science.gov (United States)

    Ledesma-Fernández, Elena; Thorpe, Peter H.

    2015-01-01

    A number of cellular proteins localize to discrete foci within cells, for example DNA repair proteins, microtubule organizing centers, P bodies or kinetochores. It is often possible to measure the fluorescence emission from tagged proteins within these foci as a surrogate for the concentration of that specific protein. We wished to develop tools that would allow quantitation of fluorescence foci intensities in high-throughput studies. As proof of principle we have examined the kinetochore, a large multi-subunit complex that is critical for the accurate segregation of chromosomes during cell division. Kinetochore perturbations lead to aneuploidy, which is a hallmark of cancer cells. Hence, understanding kinetochore homeostasis and regulation are important for a global understanding of cell division and genome integrity. The 16 budding yeast kinetochores colocalize within the nucleus to form a single focus. Here we have created a set of freely-available tools to allow high-throughput quantitation of kinetochore foci fluorescence. We use this ‘FociQuant’ tool to compare methods of kinetochore quantitation and we show proof of principle that FociQuant can be used to identify changes in kinetochore protein levels in a mutant that affects kinetochore function. This analysis can be applied to any protein that forms discrete foci in cells. PMID:26290880

  7. A quantitative genetic approach to assess the evolutionary potential of a coastal marine fish to ocean acidification

    Science.gov (United States)

    Malvezzi, Alex J; Murray, Christopher S; Feldheim, Kevin A; DiBattista, Joseph D; Garant, Dany; Gobler, Christopher J; Chapman, Demian D; Baumann, Hannes

    2015-01-01

    Assessing the potential of marine organisms to adapt genetically to increasing oceanic CO2 levels requires proxies such as heritability of fitness-related traits under ocean acidification (OA). We applied a quantitative genetic method to derive the first heritability estimate of survival under elevated CO2 conditions in a metazoan. Specifically, we reared offspring, selected from a wild coastal fish population (Atlantic silverside, Menidia menidia), at high CO2 conditions (∼2300 μatm) from fertilization to 15 days posthatch, which significantly reduced survival compared to controls. Perished and surviving offspring were quantitatively sampled and genotyped along with their parents, using eight polymorphic microsatellite loci, to reconstruct a parent–offspring pedigree and estimate variance components. Genetically related individuals were phenotypically more similar (i.e., survived similarly long at elevated CO2 conditions) than unrelated individuals, which translated into a significantly nonzero heritability (0.20 ± 0.07). The contribution of maternal effects was surprisingly small (0.05 ± 0.04) and nonsignificant. Survival among replicates was positively correlated with genetic diversity, particularly with observed heterozygosity. We conclude that early life survival of M. menidia under high CO2 levels has a significant additive genetic component that could elicit an evolutionary response to OA, depending on the strength and direction of future selection. PMID:25926880

  8. A quantitative genetic approach to assess the evolutionary potential of a coastal marine fish to ocean acidification.

    Science.gov (United States)

    Malvezzi, Alex J; Murray, Christopher S; Feldheim, Kevin A; DiBattista, Joseph D; Garant, Dany; Gobler, Christopher J; Chapman, Demian D; Baumann, Hannes

    2015-04-01

    Assessing the potential of marine organisms to adapt genetically to increasing oceanic CO2 levels requires proxies such as heritability of fitness-related traits under ocean acidification (OA). We applied a quantitative genetic method to derive the first heritability estimate of survival under elevated CO2 conditions in a metazoan. Specifically, we reared offspring, selected from a wild coastal fish population (Atlantic silverside, Menidia menidia), at high CO2 conditions (∼2300 μatm) from fertilization to 15 days posthatch, which significantly reduced survival compared to controls. Perished and surviving offspring were quantitatively sampled and genotyped along with their parents, using eight polymorphic microsatellite loci, to reconstruct a parent-offspring pedigree and estimate variance components. Genetically related individuals were phenotypically more similar (i.e., survived similarly long at elevated CO2 conditions) than unrelated individuals, which translated into a significantly nonzero heritability (0.20 ± 0.07). The contribution of maternal effects was surprisingly small (0.05 ± 0.04) and nonsignificant. Survival among replicates was positively correlated with genetic diversity, particularly with observed heterozygosity. We conclude that early life survival of M. menidia under high CO2 levels has a significant additive genetic component that could elicit an evolutionary response to OA, depending on the strength and direction of future selection.

  9. A quantitative genetic approach to assess the evolutionary potential of a coastal marine fish to ocean acidification

    KAUST Repository

    Malvezzi, Alex J.

    2015-02-01

    Assessing the potential of marine organisms to adapt genetically to increasing oceanic CO2 levels requires proxies such as heritability of fitness-related traits under ocean acidification (OA). We applied a quantitative genetic method to derive the first heritability estimate of survival under elevated CO2 conditions in a metazoan. Specifically, we reared offspring, selected from a wild coastal fish population (Atlantic silverside, Menidia menidia), at high CO2 conditions (~2300 μatm) from fertilization to 15 days posthatch, which significantly reduced survival compared to controls. Perished and surviving offspring were quantitatively sampled and genotyped along with their parents, using eight polymorphic microsatellite loci, to reconstruct a parent-offspring pedigree and estimate variance components. Genetically related individuals were phenotypically more similar (i.e., survived similarly long at elevated CO2 conditions) than unrelated individuals, which translated into a significantly nonzero heritability (0.20 ± 0.07). The contribution of maternal effects was surprisingly small (0.05 ± 0.04) and nonsignificant. Survival among replicates was positively correlated with genetic diversity, particularly with observed heterozygosity. We conclude that early life survival of M. menidia under high CO2 levels has a significant additive genetic component that could elicit an evolutionary response to OA, depending on the strength and direction of future selection.

  10. Quantitative multiphase analysis of archaeological bronzes by neutron diffraction

    CERN Document Server

    Siano, S; Celli, M; Pini, R; Salimbeni, R; Zoppi, M; Kockelmann, W A; Iozzo, M; Miccio, M; Moze, O

    2002-01-01

    In this paper, we report the first investigation on the potentials of neutron diffraction to characterize archaeological bronze artifacts. The preliminary feasibility of phase and structural analysis was demonstrated on standardised specimens with a typical bronze alloy composition. These were realised through different hardening and annealing cycles, simulating possible ancient working techniques. The Bragg peak widths that resulted were strictly dependent on the working treatment, thus providing an important analytical element to investigate ancient making techniques. The diagnostic criteria developed on the standardised specimens were then applied to study two Etruscan museum pieces. Quantitative multiphase analysis by Rietveld refinement of the diffraction patterns was successfully demonstrated. Furthermore, the analysis of patterns associated with different artifact elements also yielded evidence for some peculiar perspective of the neutron diffraction diagnostics in archeometric applications. (orig.)

  11. QUANTITATIVE METHODOLOGY FOR STABILITY ANALYSIS OF NONLINEAR ROTOR SYSTEMS

    Institute of Scientific and Technical Information of China (English)

    ZHENG Hui-ping; XUE Yu-sheng; CHEN Yu-shu

    2005-01-01

    Rotor-bearings systems applied widely in industry are nonlinear dynamic systems of multi-degree-of-freedom. Modem concepts on design and maintenance call for quantitative stability analysis. Using trajectory based stability-preserving and dimensional-reduction, a quanttative stability analysis method for rotor systems is presented. At first, an n-dimensional nonlinear non-autonomous rotor system is decoupled into n subsystems after numerical integration. Each of them has only onedegree-of-freedom and contains time-varying parameters to represent all other state variables. In this way, n-dimensional trajectory is mapped into a set of one-dimensional trajectories. Dynamic central point (DCP) of a subsystem is then defined on the extended phase plane, namely, force-position plane. Characteristics of curves on the extended phase plane and the DCP's kinetic energy difference sequence for general motion in rotor systems are studied. The corresponding stability margins of trajectory are evaluated quantitatively. By means of the margin and its sensitivity analysis, the critical parameters of the period doubling bifurcation and the Hopf bifurcation in a flexible rotor supported by two short journal beatings with nonlinear suspensionare are determined.

  12. Challenges and prospects in genome-wide quantitative trait loci mapping of standing genetic variation in natural populations.

    Science.gov (United States)

    Schielzeth, Holger; Husby, Arild

    2014-07-01

    A considerable challenge in evolutionary genetics is to understand the genetic mechanisms that facilitate or impede evolutionary adaptation in natural populations. For this, we must understand the genetic loci contributing to trait variation and the selective forces acting on them. The decreased costs and increased feasibility of obtaining genotypic data on a large number of individuals have greatly facilitated gene mapping in natural populations, particularly because organisms whose genetics have been historically difficult to study are now within reach. Here we review the methods available to evolutionary ecologists interested in dissecting the genetic basis of traits in natural populations. Our focus lies on standing genetic variation in outbred populations. We present an overview of the current state of research in the field, covering studies on both plants and animals. We also draw attention to particular challenges associated with the discovery of quantitative trait loci and discuss parallels to studies on crops, livestock, and humans. Finally, we point to some likely future developments in genetic mapping studies.

  13. Quantitative Analysis of Polarimetric Model-Based Decomposition Methods

    Directory of Open Access Journals (Sweden)

    Qinghua Xie

    2016-11-01

    Full Text Available In this paper, we analyze the robustness of the parameter inversion provided by general polarimetric model-based decomposition methods from the perspective of a quantitative application. The general model and algorithm we have studied is the method proposed recently by Chen et al., which makes use of the complete polarimetric information and outperforms traditional decomposition methods in terms of feature extraction from land covers. Nevertheless, a quantitative analysis on the retrieved parameters from that approach suggests that further investigations are required in order to fully confirm the links between a physically-based model (i.e., approaches derived from the Freeman–Durden concept and its outputs as intermediate products before any biophysical parameter retrieval is addressed. To this aim, we propose some modifications on the optimization algorithm employed for model inversion, including redefined boundary conditions, transformation of variables, and a different strategy for values initialization. A number of Monte Carlo simulation tests for typical scenarios are carried out and show that the parameter estimation accuracy of the proposed method is significantly increased with respect to the original implementation. Fully polarimetric airborne datasets at L-band acquired by German Aerospace Center’s (DLR’s experimental synthetic aperture radar (E-SAR system were also used for testing purposes. The results show different qualitative descriptions of the same cover from six different model-based methods. According to the Bragg coefficient ratio (i.e., β , they are prone to provide wrong numerical inversion results, which could prevent any subsequent quantitative characterization of specific areas in the scene. Besides the particular improvements proposed over an existing polarimetric inversion method, this paper is aimed at pointing out the necessity of checking quantitatively the accuracy of model-based PolSAR techniques for a

  14. European Identity in Russian Regions Bordering on Finland: Quantitative Analysis

    OpenAIRE

    A. O. Domanov

    2014-01-01

    Th e quantitative analysis of an opinion poll conducted in October 2013 in three Russian cities located near Finnish border (St-Petersburg, Kronstadt and Vyborg) explores European identity of their citizens. Th is area was chosen to illustrate the crucial importance of space interpretation in spatial identity formation by using critical geopolitical approach. Th e study shows how diff erent images of space on the same territory act as intermediate variables between objective territorial chara...

  15. Quantitative analysis of sideband coupling in photoinduced force microscopy

    Science.gov (United States)

    Jahng, Junghoon; Kim, Bongsu; Lee, Eun Seong; Potma, Eric Olaf

    2016-11-01

    We present a theoretical and experimental analysis of the cantilever motions detected in photoinduced force microscopy (PiFM) using the sideband coupling detection scheme. In sideband coupling, the cantilever dynamics are probed at a combination frequency of a fundamental mechanical eigenmode and the modulation frequency of the laser beam. Using this detection mode, we develop a method for reconstructing the modulated photoinduced force gradient from experimental parameters in a quantitative manner. We show evidence, both theoretically and experimentally, that the sideband coupling detection mode provides PiFM images with superior contrast compared to images obtained when detecting the cantilever motions directly at the laser modulation frequency.

  16. Quantitative and comparative analysis of hyperspectral data fusion performance

    Institute of Scientific and Technical Information of China (English)

    王强; 张晔; 李硕; 沈毅

    2002-01-01

    Hyperspectral data fusion technique is the key to hyperspectral data processing in recent years. Manyfusion methods have been proposed, but little research has been done to evaluate the performances of differentdata fusion methods. In order to meet the urgent need, quantitative correlation analysis (QCA) is proposed toanalyse and compare the performances of different fusion methods directly from data before and after fusion. Ex-periment results show that the new method is effective and the results of comparison are in agreement with theresults of application.

  17. Inbreeding and genetic diversity in dogs: results from DNA analysis.

    Science.gov (United States)

    Wade, Claire M

    2011-08-01

    This review assesses evidence from DNA analysis to determine whether there is sufficient genetic diversity within breeds to ensure that populations are sustainable in the absence of cross breeding and to determine whether genetic diversity is declining. On average, dog breeds currently retain approximately 87% of the available domestic canine genetic diversity. Requirements that breeding stock must be 'clear' for all genetic disorders may firstly place undue genetic pressure on animals tested as being 'clear' of known genetic disorders, secondly may contribute to loss of diversity and thirdly may result in the dissemination of new recessive disorders for which no genetic tests are available. Global exchange of genetic material may hasten the loss of alleles and this practice should be discussed in relation to the current effective population size of a breed and its expected future popularity. Genomic data do not always support the results from pedigree analysis and possible reasons for this are discussed.

  18. From beavis to beak color: a simulation study to examine how much qtl mapping can reveal about the genetic architecture of quantitative traits.

    Science.gov (United States)

    Slate, Jon

    2013-05-01

    Quantitative trait locus (QTL) mapping is frequently used in evolutionary studies to understand the genetic architecture of continuously varying traits. The majority of studies have been conducted in specially created crosses, in which genetic differences between parental lines are identified by linkage analysis. Detecting QTL segregating within populations is more problematic, especially in wild populations, because these populations typically have complicated and unbalanced multigenerational pedigrees. However, QTL mapping can still be conducted in such populations using a variance components mixed model approach, and the advent of appropriate statistical frameworks and better genotyping methods mean that the approach is gaining popularity. In this study it is shown that all studies described to date report evidence of QTL of major effect on trait variation, but that these findings are probably caused by inflated estimates of QTL effect sizes due to the Beavis effect. Using simulations I show that even the most powerful studies conducted to date are likely to give misleading descriptions of the genetic architecture of a trait. I show that an interpretation of a mapping study of beak color in the zebra finch (Taeniopygia guttata), that suggested genetic variation was determined by a small number of loci of large effect, which are possibly maintained by antagonistic pleiotropy, is likely to be incorrect. More generally, recommendations are made to how QTL mapping can be combined with other approaches to provide more accurate descriptions of a trait's genetic architecture.

  19. Automated, quantitative cognitive/behavioral screening of mice: for genetics, pharmacology, animal cognition and undergraduate instruction.

    Science.gov (United States)

    Gallistel, C R; Balci, Fuat; Freestone, David; Kheifets, Aaron; King, Adam

    2014-02-26

    We describe a high-throughput, high-volume, fully automated, live-in 24/7 behavioral testing system for assessing the effects of genetic and pharmacological manipulations on basic mechanisms of cognition and learning in mice. A standard polypropylene mouse housing tub is connected through an acrylic tube to a standard commercial mouse test box. The test box has 3 hoppers, 2 of which are connected to pellet feeders. All are internally illuminable with an LED and monitored for head entries by infrared (IR) beams. Mice live in the environment, which eliminates handling during screening. They obtain their food during two or more daily feeding periods by performing in operant (instrumental) and Pavlovian (classical) protocols, for which we have written protocol-control software and quasi-real-time data analysis and graphing software. The data analysis and graphing routines are written in a MATLAB-based language created to simplify greatly the analysis of large time-stamped behavioral and physiological event records and to preserve a full data trail from raw data through all intermediate analyses to the published graphs and statistics within a single data structure. The data-analysis code harvests the data several times a day and subjects it to statistical and graphical analyses, which are automatically stored in the "cloud" and on in-lab computers. Thus, the progress of individual mice is visualized and quantified daily. The data-analysis code talks to the protocol-control code, permitting the automated advance from protocol to protocol of individual subjects. The behavioral protocols implemented are matching, autoshaping, timed hopper-switching, risk assessment in timed hopper-switching, impulsivity measurement, and the circadian anticipation of food availability. Open-source protocol-control and data-analysis code makes the addition of new protocols simple. Eight test environments fit in a 48 in x 24 in x 78 in cabinet; two such cabinets (16 environments) may be

  20. Quantitative chemical analysis of ocular melanosomes in the TEM.

    Science.gov (United States)

    Eibl, O; Schultheiss, S; Blitgen-Heinecke, P; Schraermeyer, U

    2006-01-01

    Melanosomes in retinal tissues of a human, monkey and rat were analyzed by EDX in the TEM. Samples were prepared by ultramicrotomy at different thicknesses. The material was mounted on Al grids and samples were analyzed in a Zeiss 912 TEM equipped with an Omega filter and EDX detector with ultrathin window. Melanosomes consist of C and O as main components, mole fractions are about 90 and 3-10 at.%, respectively, and small mole fraction ratios, between 2 and 0.1 at.%, of Na, Mg, K, Si, P, S, Cl, Ca. All elements were measured quantitatively by standardless EDX with high precision. Mole fractions of transition metals Fe, Cu and Zn were also measured. For Fe a mole fraction ratio of less than 0.1at.% was found and gives the melanin its paramagnetic properties. Its mole fraction is however close to or below the minimum detectable mass fraction of the used equipment. Only in the human eye and only in the retinal pigment epitelium (rpe) the mole fractions of Zn (0.1 at.% or 5000 microg/g) and Cu were clearly beyond the minimum detectable mass fraction. In the rat and monkey eye the mole fraction of Zn was at or below the minimum detectable mass fraction and could not be measured quantitatively. The obtained results yielded the chemical composition of the melanosomes in the choroidal tissue and the retinal pigment epitelium (rpe) of the three different species. The results of the chemical analysis are discussed by mole fraction correlation diagrams. Similarities and differences between the different species are outlined. Correlation behavior was found to hold over species, e.g. the Ca-O correlation. It indicates that Ca is bound to oxygen rich sites in the melanin. These are the first quantitative analyses of melanosomes by EDX reported so far. The quantitative chemical analysis should open a deeper understanding of the metabolic processes in the eye that are of central importance for the understanding of a large number of eye-related diseases. The chemical analysis also

  1. Quantitative analysis of intermolecular interactions in orthorhombic rubrene

    Directory of Open Access Journals (Sweden)

    Venkatesha R. Hathwar

    2015-09-01

    Full Text Available Rubrene is one of the most studied organic semiconductors to date due to its high charge carrier mobility which makes it a potentially applicable compound in modern electronic devices. Previous electronic device characterizations and first principles theoretical calculations assigned the semiconducting properties of rubrene to the presence of a large overlap of the extended π-conjugated core between molecules. We present here the electron density distribution in rubrene at 20 K and at 100 K obtained using a combination of high-resolution X-ray and neutron diffraction data. The topology of the electron density and energies of intermolecular interactions are studied quantitatively. Specifically, the presence of Cπ...Cπ interactions between neighbouring tetracene backbones of the rubrene molecules is experimentally confirmed from a topological analysis of the electron density, Non-Covalent Interaction (NCI analysis and the calculated interaction energy of molecular dimers. A significant contribution to the lattice energy of the crystal is provided by H—H interactions. The electron density features of H—H bonding, and the interaction energy of molecular dimers connected by H—H interaction clearly demonstrate an importance of these weak interactions in the stabilization of the crystal structure. The quantitative nature of the intermolecular interactions is virtually unchanged between 20 K and 100 K suggesting that any changes in carrier transport at these low temperatures would have a different origin. The obtained experimental results are further supported by theoretical calculations.

  2. Quantitative analysis on electrooculography (EOG) for neurodegenerative disease

    Science.gov (United States)

    Liu, Chang-Chia; Chaovalitwongse, W. Art; Pardalos, Panos M.; Seref, Onur; Xanthopoulos, Petros; Sackellares, J. C.; Skidmore, Frank M.

    2007-11-01

    Many studies have documented abnormal horizontal and vertical eye movements in human neurodegenerative disease as well as during altered states of consciousness (including drowsiness and intoxication) in healthy adults. Eye movement measurement may play an important role measuring the progress of neurodegenerative diseases and state of alertness in healthy individuals. There are several techniques for measuring eye movement, Infrared detection technique (IR). Video-oculography (VOG), Scleral eye coil and EOG. Among those available recording techniques, EOG is a major source for monitoring the abnormal eye movement. In this real-time quantitative analysis study, the methods which can capture the characteristic of the eye movement were proposed to accurately categorize the state of neurodegenerative subjects. The EOG recordings were taken while 5 tested subjects were watching a short (>120 s) animation clip. In response to the animated clip the participants executed a number of eye movements, including vertical smooth pursued (SVP), horizontal smooth pursued (HVP) and random saccades (RS). Detection of abnormalities in ocular movement may improve our diagnosis and understanding a neurodegenerative disease and altered states of consciousness. A standard real-time quantitative analysis will improve detection and provide a better understanding of pathology in these disorders.

  3. Quantitative analysis in outcome assessment of instrumented lumbosacral arthrodesis.

    Science.gov (United States)

    Champain, Sabina; Mazel, Christian; Mitulescu, Anca; Skalli, Wafa

    2007-08-01

    The outcome assessment in instrumented lumbosacral fusion mostly focuses on clinical criteria, complications and scores, with a high variability of imaging means, methods of fusion grading and parameters describing degenerative changes, making comparisons between studies difficult. The aim of this retrospective evaluation was to evaluate the interest of quantified radiographic analysis of lumbar spine in global outcome assessment and to highlight the key biomechanical factors involved. Clinical data and Beaujon-Lassale scores were collected for 49 patients who underwent lumbosacral arthrodesis after prior lumbar discectomy (mean follow-up: 5 years). Sagittal standing and lumbar flexion-extension X-ray films allowed quantifying vertebral, lumbar, pelvic and kinematic parameters of the lumbar spine, which were compared to reference values. Statistics were performed to assess evolution for all variables. At long-term follow-up, 90% of patients presented satisfactory clinical outcomes, associated to normal sagittal alignment; vertebral parameters objectified adjacent level degeneration in four cases (8%). Clinical outcome was correlated (r = 0.8) with fusion that was confirmed in 80% of cases, doubtful in 16% and pseudarthrosis seemed to occur in 4% (2) of cases. In addition to clinical data (outcomes comparable to the literature), quantitative analysis accurately described lumbar spine geometry and kinematics, highlighting parameters related to adjacent level's degeneration and a significant correlation between clinical outcome and fusion. Furthermore, criteria proposed to quantitatively evaluate fusion from lumbar dynamic radiographs seem to be appropriate and in agreement with surgeon's qualitative grading in 87% of cases.

  4. Quantitative Analysis of the Interdisciplinarity of Applied Mathematics.

    Science.gov (United States)

    Xie, Zheng; Duan, Xiaojun; Ouyang, Zhenzheng; Zhang, Pengyuan

    2015-01-01

    The increasing use of mathematical techniques in scientific research leads to the interdisciplinarity of applied mathematics. This viewpoint is validated quantitatively here by statistical and network analysis on the corpus PNAS 1999-2013. A network describing the interdisciplinary relationships between disciplines in a panoramic view is built based on the corpus. Specific network indicators show the hub role of applied mathematics in interdisciplinary research. The statistical analysis on the corpus content finds that algorithms, a primary topic of applied mathematics, positively correlates, increasingly co-occurs, and has an equilibrium relationship in the long-run with certain typical research paradigms and methodologies. The finding can be understood as an intrinsic cause of the interdisciplinarity of applied mathematics.

  5. Fusing Quantitative Requirements Analysis with Model-based Systems Engineering

    Science.gov (United States)

    Cornford, Steven L.; Feather, Martin S.; Heron, Vance A.; Jenkins, J. Steven

    2006-01-01

    A vision is presented for fusing quantitative requirements analysis with model-based systems engineering. This vision draws upon and combines emergent themes in the engineering milieu. "Requirements engineering" provides means to explicitly represent requirements (both functional and non-functional) as constraints and preferences on acceptable solutions, and emphasizes early-lifecycle review, analysis and verification of design and development plans. "Design by shopping" emphasizes revealing the space of options available from which to choose (without presuming that all selection criteria have previously been elicited), and provides means to make understandable the range of choices and their ramifications. "Model-based engineering" emphasizes the goal of utilizing a formal representation of all aspects of system design, from development through operations, and provides powerful tool suites that support the practical application of these principles. A first step prototype towards this vision is described, embodying the key capabilities. Illustrations, implications, further challenges and opportunities are outlined.

  6. Quantitative Phase Analysis by the Rietveld Method for Forensic Science.

    Science.gov (United States)

    Deng, Fei; Lin, Xiaodong; He, Yonghong; Li, Shu; Zi, Run; Lai, Shijun

    2015-07-01

    Quantitative phase analysis (QPA) is helpful to determine the type attribute of the object because it could present the content of the constituents. QPA by Rietveld method requires neither measurement of calibration data nor the use of an internal standard; however, the approximate crystal structure of each phase in a mixture is necessary. In this study, 8 synthetic mixtures composed of potassium nitrate and sulfur were analyzed by Rietveld QPA method. The Rietveld refinement was accomplished with a material analysis using diffraction program and evaluated by three agreement indices. Results showed that Rietveld QPA yielded precise results, with errors generally less than 2.0% absolute. In addition, a criminal case which was broken successfully with the help of Rietveld QPA method was also introduced. This method will allow forensic investigators to acquire detailed information of the material evidence, which could point out the direction for case detection and court proceedings.

  7. [Quantitative analysis of butachlor, oxadiazon and simetryn by gas chromatography].

    Science.gov (United States)

    Liu, F; Mu, W; Wang, J

    1999-03-01

    The quantitative analysis of the ingredients in 26% B-O-S (butachlor, oxadiazon and simetryn) emulsion by gas chromatographic method was carried out with a 5% SE-30 on Chromosorb AW DMCS, 2 m x 3 mm i.d., glass column at column temperature of 210 degrees C and detector temperature of 230 degrees C. The internal standard is di-n-butyl sebacate. The retentions of simetryn, internal standard, butachlor and oxadiazon were 6.5, 8.3, 9.9 and 11.9 min respectively. This method has a recovery of 98.62%-100.77% and the coefficients of variation of this analysis of butachlor, oxadiazon and simetryn were 0.46%, 0.32% and 0.57% respectively. All coefficients of linear correlation were higher than 0.999.

  8. Fusing Quantitative Requirements Analysis with Model-based Systems Engineering

    Science.gov (United States)

    Cornford, Steven L.; Feather, Martin S.; Heron, Vance A.; Jenkins, J. Steven

    2006-01-01

    A vision is presented for fusing quantitative requirements analysis with model-based systems engineering. This vision draws upon and combines emergent themes in the engineering milieu. "Requirements engineering" provides means to explicitly represent requirements (both functional and non-functional) as constraints and preferences on acceptable solutions, and emphasizes early-lifecycle review, analysis and verification of design and development plans. "Design by shopping" emphasizes revealing the space of options available from which to choose (without presuming that all selection criteria have previously been elicited), and provides means to make understandable the range of choices and their ramifications. "Model-based engineering" emphasizes the goal of utilizing a formal representation of all aspects of system design, from development through operations, and provides powerful tool suites that support the practical application of these principles. A first step prototype towards this vision is described, embodying the key capabilities. Illustrations, implications, further challenges and opportunities are outlined.

  9. [Quantitative analysis of transformer oil dissolved gases using FTIR].

    Science.gov (United States)

    Zhao, An-xin; Tang, Xiao-jun; Wang, Er-zhen; Zhang, Zhong-hua; Liu, Jun-hua

    2013-09-01

    For the defects of requiring carrier gas and regular calibration, and low safety using chromatography to on line monitor transformer dissolved gases, it was attempted to establish a dissolved gas analysis system based on Fourier transform infrared spectroscopy. Taking into account the small amount of characteristic gases, many components, detection limit and safety requirements and the difficulty of degasser to put an end to the presence of interference gas, the quantitative analysis model was established based on sparse partial least squares, piecewise section correction and feature variable extraction algorithm using improvement TR regularization. With the characteristic gas of CH4, C2H6, C2H6, and CO2, the results show that using FTIR meets DGA requirements with the spectrum wave number resolution of 1 cm(-1) and optical path of 10 cm.

  10. Genetic dissection of milk yield traits and mastitis resistance quantitative trait loci on chromosome 20 in dairy cattle.

    Science.gov (United States)

    Kadri, Naveen K; Guldbrandtsen, Bernt; Lund, Mogens S; Sahana, Goutam

    2015-12-01

    Intense selection to increase milk yield has had negative consequences for mastitis incidence in dairy cattle. Due to low heritability of mastitis resistance and an unfavorable genetic correlation with milk yield, a reduction in mastitis through traditional breeding has been difficult to achieve. Here, we examined quantitative trait loci (QTL) that segregate for clinical mastitis and milk yield on Bos taurus autosome 20 (BTA20) to determine whether both traits are affected by a single polymorphism (pleiotropy) or by multiple closely linked polymorphisms. In the latter but not the former situation, undesirable genetic correlation could potentially be broken by selecting animals that have favorable variants for both traits. First, we performed a within-breed association study using a haplotype-based method in Danish Holstein cattle (HOL). Next, we analyzed Nordic Red dairy cattle (RDC) and Danish Jersey cattle (JER) with the goal of determining whether these QTL identified in Holsteins were segregating across breeds. Genotypes for 12,566 animals (5,966 HOL, 5,458 RDC, and 1,142 JER) were determined by using the Illumina Bovine SNP50 BeadChip (50K; Illumina, San Diego, CA), which identifies 1,568 single nucleotide polymorphisms on BTA20. Data were combined, phased, and clustered into haplotype states, followed by within- and across-breed haplotype-based association analyses using a linear mixed model. Association signals for both clinical mastitis and milk yield peaked in the 26- to 40-Mb region on BTA20 in HOL. Single-variant association analyses were carried out in the QTL region using whole sequence level variants imputed from references of 2,036 HD genotypes (BovineHD BeadChip; Illumina) and 242 whole-genome sequences. The milk QTL were also segregating in RDC and JER on the BTA20-targeted region; however, an indication of differences in the causal factor(s) was observed across breeds. A previously reported F279Y mutation (rs385640152) within the growth hormone

  11. Quantitative morphometric analysis for the tectonic characterisation of northern Tunisia.

    Science.gov (United States)

    Camafort, Miquel; Pérez-Peña, José Vicente; Booth-Rea, Guillermo; Ranero, César R.; Gràcia, Eulàlia; Azañón, José Miguel; Melki, Fetheddine; Ouadday, Mohamed

    2016-04-01

    Northern Tunisia is characterized by low deformation rates and low to moderate seismicity. Although instrumental seismicity reaches maximum magnitudes of Mw 5.5, some historical earthquakes have occurred with catastrophic consequences in this region. Aiming to improve our knowledge of active tectonics in Tunisia, we carried out both a quantitative morphometric analysis and field study in the north-western region. We applied different morphometric tools, like river profiles, knickpoint analysis, hypsometric curves and integrals and drainage pattern anomalies in order to differentiate between zones with high or low recent tectonic activity. This analysis helps identifying uplift and subsidence zones, which we relate to fault activity. Several active faults in a sparse distribution were identified. A selected sector was studied with a field campaign to test the results obtained with the quantitative analysis. During the fieldwork we identified geological evidence of recent activity and a considerable seismogenic potential along El Alia-Teboursouk (ETF) and Dkhila (DF) faults. The ETF fault could be responsible of one of the most devastating historical earthquakes in northern Tunisia that destroyed Utique in 412 A.D. Geological evidence include fluvial terraces folded by faults, striated and cracked pebbles, clastic dikes, sand volcanoes, coseismic cracks, etc. Although not reflected in the instrumental seismicity, our results support an important seismic hazard, evidenced by the several active tectonic structures identified and the two seismogenic faults described. After obtaining the current active tectonic framework of Tunisia we discuss our results within the western Mediterranean trying to contribute to the understanding of the western Mediterranean tectonic context. With our results, we suggest that the main reason explaining the sparse and scarce seismicity of the area in contrast with the adjacent parts of the Nubia-Eurasia boundary is due to its extended

  12. GENETIC ANALYSIS OF ABSCISIC ACID BIOSYNTHESIS

    Energy Technology Data Exchange (ETDEWEB)

    MCCARTY D R

    2012-01-10

    The carotenoid cleavage dioxygenases (CCD) catalyze synthesis of a variety of apo-carotenoid secondary metabolites in plants, animals and bacteria. In plants, the reaction catalyzed by the 11, 12, 9-cis-epoxy carotenoid dioxygenase (NCED) is the first committed and key regulated step in synthesis of the plant hormone, abscisic acid (ABA). ABA is a key regulator of plant stress responses and has critical functions in normal root and seed development. The molecular mechanisms responsible for developmental control of ABA synthesis in plant tissues are poorly understood. Five of the nine CCD genes present in the Arabidopsis genome encode NCED's involved in control of ABA synthesis in the plant. This project is focused on functional analysis of these five AtNCED genes as a key to understanding developmental regulation of ABA synthesis and dissecting the role of ABA in plant development. For this purpose, the project developed a comprehensive set of gene knockouts in the AtNCED genes that facilitate genetic dissection of ABA synthesis. These mutants were used in combination with key molecular tools to address the following specific objectives: (1) the role of ABA synthesis in root development; (2) developmental control of ABA synthesis in seeds; (3) analysis of ATNCED over-expressers; (4) preliminary crystallography of the maize VP14 protein.

  13. Methods for genetic linkage analysis using trisomies

    Energy Technology Data Exchange (ETDEWEB)

    Feingold, E. [Emory Univ. School of Public Health, Atlanta, GA (United States); Lamb, N.E.; Sherman, S.L. [Emory Univ., Atlanta, GA (United States)

    1995-02-01

    Certain genetic disorders are rare in the general population, but more common in individuals with specific trisomies. Examples of this include leukemia and duodenal atresia in trisomy 21. This paper presents a linkage analysis method for using trisomic individuals to map genes for such traits. It is based on a very general gene-specific dosage model that posits that the trait is caused by specific effects of different alleles at one or a few loci and that duplicate copies of {open_quotes}susceptibility{close_quotes} alleles inherited from the nondisjoining parent give increased likelihood of having the trait. Our mapping method is similar to identity-by-descent-based mapping methods using affected relative pairs and also to methods for mapping recessive traits using inbred individuals by looking for markers with greater than expected homozygosity by descent. In the trisomy case, one would take trisomic individuals and look for markers with greater than expected homozygosity in the chromosomes inherited from the nondisjoining parent. We present statistical methods for performing such a linkage analysis, including a test for linkage to a marker, a method for estimating the distance from the marker to the trait gene, a confidence interval for that distance, and methods for computing power and sample sizes. We also resolve some practical issues involved in implementing the methods, including how to use partially informative markers and how to test candidate genes. 20 refs., 5 figs., 1 tab.

  14. MATING DESIGNS: HELPFUL TOOL FOR QUANTITATIVE PLANT BREEDING ANALYSIS

    Directory of Open Access Journals (Sweden)

    Athanase Nduwumuremyi

    2013-12-01

    Full Text Available Selection of parental materials and good mating designs in conventional plant breeding are the keys to the successful plant breeding programme. However, there are several factors affecting the choices of mating designs. Mating design refers to the procedure of producing the progenies, in plant breeding, plant breeders and geneticists, theoretically and practically, they use different form of mating designs and arrangements for targeted purpose. The choice of a mating design for estimating genetic variances should be dictated by the objectives of the study, time, space, cost and other biological limitations. In all mating designs, the individuals are taken randomly and crossed to produce progenies which are related to each other as half-sibs or full-sibs. A form of multivariate analysis or the analysis of variance can be adopted to estimate the components of variances. Therefore, this review aimed at highlighting the most used mating design in plant breeding and genetics studies. It provides easy and quick insight of the different form of mating designs and some statistical components for successful plant breeding.

  15. Glioblastoma multiforme: exploratory radiogenomic analysis by using quantitative image features.

    Science.gov (United States)

    Gevaert, Olivier; Mitchell, Lex A; Achrol, Achal S; Xu, Jiajing; Echegaray, Sebastian; Steinberg, Gary K; Cheshier, Samuel H; Napel, Sandy; Zaharchuk, Greg; Plevritis, Sylvia K

    2014-10-01

    To derive quantitative image features from magnetic resonance (MR) images that characterize the radiographic phenotype of glioblastoma multiforme (GBM) lesions and to create radiogenomic maps associating these features with various molecular data. Clinical, molecular, and MR imaging data for GBMs in 55 patients were obtained from the Cancer Genome Atlas and the Cancer Imaging Archive after local ethics committee and institutional review board approval. Regions of interest (ROIs) corresponding to enhancing necrotic portions of tumor and peritumoral edema were drawn, and quantitative image features were derived from these ROIs. Robust quantitative image features were defined on the basis of an intraclass correlation coefficient of 0.6 for a digital algorithmic modification and a test-retest analysis. The robust features were visualized by using hierarchic clustering and were correlated with survival by using Cox proportional hazards modeling. Next, these robust image features were correlated with manual radiologist annotations from the Visually Accessible Rembrandt Images (VASARI) feature set and GBM molecular subgroups by using nonparametric statistical tests. A bioinformatic algorithm was used to create gene expression modules, defined as a set of coexpressed genes together with a multivariate model of cancer driver genes predictive of the module's expression pattern. Modules were correlated with robust image features by using the Spearman correlation test to create radiogenomic maps and to link robust image features with molecular pathways. Eighteen image features passed the robustness analysis and were further analyzed for the three types of ROIs, for a total of 54 image features. Three enhancement features were significantly correlated with survival, 77 significant correlations were found between robust quantitative features and the VASARI feature set, and seven image features were correlated with molecular subgroups (P < .05 for all). A radiogenomics map was

  16. Genetic Dissection and Molecular Dissection of Quantitative Traits%数量性状的遗传剖析和分子剖析

    Institute of Scientific and Technical Information of China (English)

    吴为人; 唐定中; 李维明

    2000-01-01

    生物的大多数重要性状都是数量性状,遗传基础复杂,遗传研究非常困难。近20年来,由于分子生物技术飞速发展,特别是分子标记技术和大片段DNA克隆和分析技术的出现,使遗传学开始向阐明人类和一些模式动植物整个基因组的宏伟目标进军,也使得数量性状的遗传剖析(即系统地对各个数量性状基因或QTL的遗传定位和效应分析)和分子剖析(即对QTL的克隆分离)成为可能,并在短短的10余年内取得了重大的进展。该领域的研究将使我们能精确地分析QTL的效应,可靠地对QTL进行标记辅助选择以及实现对数量性状的基因工程,从而使现代分子生物技术在动植物遗传改良和人类遗传病治疗方面发挥更大的作用。本文综述了近年来在数量性状遗传剖析和分子剖析的方法方面的研究进展。%Most of the important characters in living beings are quantitative traits,which have complicated genetic basis and are very difficult for genetic research.Due to the rapid progress of molecular biological technology in the last two decades,especially dne to the advent of molecularmarker techniques and the techniques for the analysis and clonning of large DNA fragments,genetics has begun to march towards the great goal of elncidating the whole genomes of human and some model animals and plants,and the genetic and molecular dissection of quantitative traits(mapping and cloning of individual quantitative trait loci orQTL)has therefore becomepossible,and great progress has been achieved since late 1980's.Studies in this will enable us to perfirm precise analysis of QTL's effects and reliable marker-assisted selection of QTL and to realize genetic engineering of quantitative traits so as to make modern molecular biotechnologyplay even greater role in the genetic improvement of animals and plants d in the terapy of human's genetic diseases.In this paper

  17. Quantitative trait analysis of yeast biodiversity yields novel gene tools for metabolic engineering

    NARCIS (Netherlands)

    Hubmann, Georg; Foulquié-Moreno, Maria R.; Nevoigt, Elke; Duitama, Jorge; Meurens, Nicolas; Pais, Thiago M.; Mathé, Lotte; Saerens, Sofie; Nguyen, Huyen Thi Thanh; Swinnen, Steve; Verstrepen, Kevin J.; Concilio, Luigi; de Troostembergh, Jean-Claude; Thevelein, Johan M.

    2013-01-01

    Engineering of metabolic pathways by genetic modification has been restricted largely to enzyme-encoding structural genes. The product yield of such pathways is a quantitative genetic trait. Out of 52 Saccharomyces cerevisiae strains phenotyped in small-scale fermentations, we identified strain CBS6

  18. Phenotypic analysis of Arabidopsis mutants: quantitative analysis of root growth.

    Science.gov (United States)

    Doerner, Peter

    2008-03-01

    INTRODUCTIONThe growth of plant roots is very easy to measure and is particularly straightforward in Arabidopsis thaliana, because the increase in organ size is essentially restricted to one dimension. The precise measurement of root apical growth can be used to accurately determine growth activity (the rate of growth at a given time) during development in mutants, transgenic backgrounds, or in response to experimental treatments. Root growth is measured in a number of ways, the simplest of which is to grow the seedlings in a Petri dish and record the position of the advancing root tip at appropriate time points. The increase in root length is measured with a ruler and the data are entered into Microsoft Excel for analysis. When dealing with large numbers of seedlings, however, this procedure can be tedious, as well as inaccurate. An alternative approach, described in this protocol, uses "snapshots" of the growing plants, which are taken using gel-documentation equipment (i.e., a video camera with a frame-grabber unit, now commonly used to capture images from ethidium-bromide-stained electrophoresis gels). The images are analyzed using publicly available software (NIH-Image), which allows the user simply to cut and paste data into Microsoft Excel.

  19. Quantitative ultrasound of the hand phalanges in a cohort of monozygotic twins: influence of genetic and environmental factors

    Energy Technology Data Exchange (ETDEWEB)

    Guglielmi, G. [Scientific Institute Hospital, Department of Radiology, San Giovanni Rotondo (Italy); Terlizzi, F. de [IGEA Biophysics Lab, Carpi (Italy); Torrente, I.; Mingarelli, R. [Mendel Institute, Rome (Italy); Dallapiccola, B. [Scientific Institute Hospital, Department of Radiology, San Giovanni Rotondo (Italy); Mendel Institute, Rome (Italy)

    2005-11-01

    Our objective was to evaluate the similarities and differences in bone mass and structure between pairs of monozygotic twins as measured by means of the quantitative ultrasound (QUS) technique. A cohort of monozygotic twins was measured by QUS of the hand phalanges using the DBM sonic bone profiler (IGEA, Carpi, Italy). The parameters studied were amplitude-dependent speed of sound (AD-SoS), ultrasound bone profile index (UBPI), signal dynamics (SDy) and bone transmission time (BTT). Linear correlation coefficients, multivariate linear analysis and the ANOVA test were used to assess intrapair associations between variables and to determine which factors influence the intrapair differences in QUS variables. One hundred and six pairs of monozygotic twins were enrolled in the study, 68 females and 38 males in the age range 5 to 71 years. Significant intrapair correlations were obtained in the whole population and separately for males and females, regarding height (r =0.98-0.99, p <0.0001), weight (r =0.95-0.96, p <0.0001), AD-SoS (r =0.90-0.92, p <0.0001), BTT (r =0.94-0.95, p <0.0001) and other QUS parameters (r >0.74, p <0.0001). Multivariate analysis revealed that intrapair differences between AD-SoS, SDy, UBPI and BTT are significantly influenced by age in the whole population and in the female population. Furthermore, the ANOVA test showed, for the female group, a significant increase in the intrapair differences in SDy and UBPI above 40 years. A relative contribution of genetic factors to skeletal status could be observed by phalangeal QUS measurement in monozygotic twins. A significant increase in the intrapair difference in QUS parameters with increasing age and onset of menopause also suggests the importance of environmental factors in the female twin population. (orig.)

  20. Epistasis analysis for quantitative traits by functional regression model.

    Science.gov (United States)

    Zhang, Futao; Boerwinkle, Eric; Xiong, Momiao

    2014-06-01

    The critical barrier in interaction analysis for rare variants is that most traditional statistical methods for testing interactions were originally designed for testing the interaction between common variants and are difficult to apply to rare variants because of their prohibitive computational time and poor ability. The great challenges for successful detection of interactions with next-generation sequencing (NGS) data are (1) lack of methods for interaction analysis with rare variants, (2) severe multiple testing, and (3) time-consuming computations. To meet these challenges, we shift the paradigm of interaction analysis between two loci to interaction analysis between two sets of loci or genomic regions and collectively test interactions between all possible pairs of SNPs within two genomic regions. In other words, we take a genome region as a basic unit of interaction analysis and use high-dimensional data reduction and functional data analysis techniques to develop a novel functional regression model to collectively test interactions between all possible pairs of single nucleotide polymorphisms (SNPs) within two genome regions. By intensive simulations, we demonstrate that the functional regression models for interaction analysis of the quantitative trait have the correct type 1 error rates and a much better ability to detect interactions than the current pairwise interaction analysis. The proposed method was applied to exome sequence data from the NHLBI's Exome Sequencing Project (ESP) and CHARGE-S study. We discovered 27 pairs of genes showing significant interactions after applying the Bonferroni correction (P-values < 4.58 × 10(-10)) in the ESP, and 11 were replicated in the CHARGE-S study.

  1. Toward genetics-based virus taxonomy: comparative analysis of a genetics-based classification and the taxonomy of picornaviruses.

    Science.gov (United States)

    Lauber, Chris; Gorbalenya, Alexander E

    2012-04-01

    Virus taxonomy has received little attention from the research community despite its broad relevance. In an accompanying paper (C. Lauber and A. E. Gorbalenya, J. Virol. 86:3890-3904, 2012), we have introduced a quantitative approach to hierarchically classify viruses of a family using pairwise evolutionary distances (PEDs) as a measure of genetic divergence. When applied to the six most conserved proteins of the Picornaviridae, it clustered 1,234 genome sequences in groups at three hierarchical levels (to which we refer as the "GENETIC classification"). In this study, we compare the GENETIC classification with the expert-based picornavirus taxonomy and outline differences in the underlying frameworks regarding the relation of virus groups and genetic diversity that represent, respectively, the structure and content of a classification. To facilitate the analysis, we introduce two novel diagrams. The first connects the genetic diversity of taxa to both the PED distribution and the phylogeny of picornaviruses. The second depicts a classification and the accommodated genetic diversity in a standardized manner. Generally, we found striking agreement between the two classifications on species and genus taxa. A few disagreements concern the species Human rhinovirus A and Human rhinovirus C and the genus Aphthovirus, which were split in the GENETIC classification. Furthermore, we propose a new supergenus level and universal, level-specific PED thresholds, not reached yet by many taxa. Since the species threshold is approached mostly by taxa with large sampling sizes and those infecting multiple hosts, it may represent an upper limit on divergence, beyond which homologous recombination in the six most conserved genes between two picornaviruses might not give viable progeny.

  2. Genetic analysis of captive proboscis monkeys.

    Science.gov (United States)

    Ogata, Mitsuaki; Seino, Satoru

    2015-01-01

    Information on the genetic relationships of captive founders is important for captive population management. In this study, we investigated DNA polymorphisms of four microsatellite loci and the mitochondrial control region sequence of five proboscis monkeys residing in a Japanese zoo as captive founders, to clarify their genetic relationship. We found that two of the five monkeys appeared to be genetically related. Furthermore, the haplotypes of the mitochondrial control region of the five monkeys were well differentiated from the haplotypes previously reported from wild populations from the northern area of Borneo, indicating a greater amount of genetic diversity in proboscis monkeys than previously reported. © 2014 Wiley Periodicals, Inc.

  3. WWW portal usage analysis using genetic algorithms

    Directory of Open Access Journals (Sweden)

    Ondřej Popelka

    2009-01-01

    Full Text Available The article proposes a new method suitable for advanced analysis of web portal visits. This is part of retrieving information and knowledge from web usage data (web usage mining. Such information is necessary in order to gain better insight into visitor’s needs and generally consumer behaviour. By le­ve­ra­ging this information a company can optimize the organization of its internet presentations and offer a better end-user experience. The proposed approach is using Grammatical evolution which is computational method based on genetic algorithms. Grammatical evolution is using a context-free grammar in order to generate the solution in arbitrary reusable form. This allows us to describe visitors’ behaviour in different manners depending on desired further processing. In this article we use description with a procedural programming language. Web server access log files are used as source data.The extraction of behaviour patterns can currently be solved using statistical analysis – specifically sequential analysis based methods. Our objective is to develop an alternative algorithm.The article further describes the basic algorithms of two-level grammatical evolution; this involves basic Grammatical Evolution and Differential Evolution, which forms the second phase of the computation. Grammatical evolution is used to generate the basic structure of the solution – in form of a part of application code. Differential evolution is used to find optimal parameters for this solution – the specific pages visited by a random visitor. The grammar used to conduct experiments is described along with explanations of the links to the actual implementation of the algorithm. Furthermore the fitness function is described and reasons which yield to its’ current shape. Finally the process of analyzing and filtering the raw input data is described as it is vital part in obtaining reasonable results.

  4. Quantitative CT analysis of small pulmonary vessels in lymphangioleiomyomatosis

    Energy Technology Data Exchange (ETDEWEB)

    Ando, Katsutoshi, E-mail: kando@juntendo.ac.jp [Department of Internal Medicine, Division of Respiratory Medicine, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-Ku, Tokyo 113-8421 (Japan); The Study Group of Pneumothorax and Cystic Lung Diseases, 4-8-1 Seta, Setagaya-Ku, Tokyo 158-0095 (Japan); Tobino, Kazunori [Department of Respiratory Medicine, Iizuka Hospital, 3-83 Yoshio-Machi, Iizuka-City, Fukuoka 820-8505 (Japan); The Study Group of Pneumothorax and Cystic Lung Diseases, 4-8-1 Seta, Setagaya-Ku, Tokyo 158-0095 (Japan); Kurihara, Masatoshi; Kataoka, Hideyuki [Pneumothorax Center, Nissan Tamagawa Hospital, 4-8-1 Seta, Setagaya-Ku, Tokyo 158-0095 (Japan); The Study Group of Pneumothorax and Cystic Lung Diseases, 4-8-1 Seta, Setagaya-Ku, Tokyo 158-0095 (Japan); Doi, Tokuhide [Fukuoka Clinic, 7-18-11 Umeda, Adachi-Ku, Tokyo 123-0851 (Japan); Hoshika, Yoshito [Department of Internal Medicine, Division of Respiratory Medicine, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-Ku, Tokyo 113-8421 (Japan); The Study Group of Pneumothorax and Cystic Lung Diseases, 4-8-1 Seta, Setagaya-Ku, Tokyo 158-0095 (Japan); Takahashi, Kazuhisa [Department of Internal Medicine, Division of Respiratory Medicine, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-Ku, Tokyo 113-8421 (Japan); Seyama, Kuniaki [Department of Internal Medicine, Division of Respiratory Medicine, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-Ku, Tokyo 113-8421 (Japan); The Study Group of Pneumothorax and Cystic Lung Diseases, 4-8-1 Seta, Setagaya-Ku, Tokyo 158-0095 (Japan)

    2012-12-15

    Backgrounds: Lymphangioleiomyomatosis (LAM) is a destructive lung disease that share clinical, physiologic, and radiologic features with chronic obstructive pulmonary disease (COPD). This study aims to identify those features that are unique to LAM by using quantitative CT analysis. Methods: We measured total cross-sectional areas of small pulmonary vessels (CSA) less than 5 mm{sup 2} and 5–10 mm{sup 2} and calculated percentages of those lung areas (%CSA), respectively, in 50 LAM and 42 COPD patients. The extent of cystic destruction (LAA%) and mean parenchymal CT value were also calculated and correlated with pulmonary function. Results: The diffusing capacity for carbon monoxide/alveolar volume (DL{sub CO}/VA %predicted) was similar for both groups (LAM, 44.4 ± 19.8% vs. COPD, 45.7 ± 16.0%, p = 0.763), but less tissue damage occurred in LAM than COPD (LAA% 21.7 ± 16.3% vs. 29.3 ± 17.0; p < 0.05). Pulmonary function correlated negatively with LAA% (p < 0.001) in both groups, yet the correlation with %CSA was significant only in COPD (p < 0.001). When the same analysis was conducted in two groups with equal levels of LAA% and DL{sub CO}/VA %predicted, %CSA and mean parenchymal CT value were still greater for LAM than COPD (p < 0.05). Conclusions: Quantitative CT analysis revealing a correlation between cystic destruction and CSA in COPD but not LAM indicates that this approach successfully reflects different mechanisms governing the two pathologic courses. Such determinations of small pulmonary vessel density may serve to differentiate LAM from COPD even in patients with severe lung destruction.

  5. The Quantitative Analysis of Chennai Automotive Industry Cluster

    Science.gov (United States)

    Bhaskaran, Ethirajan

    2016-07-01

    Chennai, also called as Detroit of India due to presence of Automotive Industry producing over 40 % of the India's vehicle and components. During 2001-2002, the Automotive Component Industries (ACI) in Ambattur, Thirumalizai and Thirumudivakkam Industrial Estate, Chennai has faced problems on infrastructure, technology, procurement, production and marketing. The objective is to study the Quantitative Performance of Chennai Automotive Industry Cluster before (2001-2002) and after the CDA (2008-2009). The methodology adopted is collection of primary data from 100 ACI using quantitative questionnaire and analyzing using Correlation Analysis (CA), Regression Analysis (RA), Friedman Test (FMT), and Kruskall Wallis Test (KWT).The CA computed for the different set of variables reveals that there is high degree of relationship between the variables studied. The RA models constructed establish the strong relationship between the dependent variable and a host of independent variables. The models proposed here reveal the approximate relationship in a closer form. KWT proves, there is no significant difference between three locations clusters with respect to: Net Profit, Production Cost, Marketing Costs, Procurement Costs and Gross Output. This supports that each location has contributed for development of automobile component cluster uniformly. The FMT proves, there is no significant difference between industrial units in respect of cost like Production, Infrastructure, Technology, Marketing and Net Profit. To conclude, the Automotive Industries have fully utilized the Physical Infrastructure and Centralised Facilities by adopting CDA and now exporting their products to North America, South America, Europe, Australia, Africa and Asia. The value chain analysis models have been implemented in all the cluster units. This Cluster Development Approach (CDA) model can be implemented in industries of under developed and developing countries for cost reduction and productivity

  6. Quantitative modeling and data analysis of SELEX experiments

    Science.gov (United States)

    Djordjevic, Marko; Sengupta, Anirvan M.

    2006-03-01

    SELEX (systematic evolution of ligands by exponential enrichment) is an experimental procedure that allows the extraction, from an initially random pool of DNA, of those oligomers with high affinity for a given DNA-binding protein. We address what is a suitable experimental and computational procedure to infer parameters of transcription factor-DNA interaction from SELEX experiments. To answer this, we use a biophysical model of transcription factor-DNA interactions to quantitatively model SELEX. We show that a standard procedure is unsuitable for obtaining accurate interaction parameters. However, we theoretically show that a modified experiment in which chemical potential is fixed through different rounds of the experiment allows robust generation of an appropriate dataset. Based on our quantitative model, we propose a novel bioinformatic method of data analysis for such a modified experiment and apply it to extract the interaction parameters for a mammalian transcription factor CTF/NFI. From a practical point of view, our method results in a significantly improved false positive/false negative trade-off, as compared to both the standard information theory based method and a widely used empirically formulated procedure.

  7. Quantitative analysis of multiple sclerosis: a feasibility study

    Science.gov (United States)

    Li, Lihong; Li, Xiang; Wei, Xinzhou; Sturm, Deborah; Lu, Hongbing; Liang, Zhengrong

    2006-03-01

    Multiple Sclerosis (MS) is an inflammatory and demyelinating disorder of the central nervous system with a presumed immune-mediated etiology. For treatment of MS, the measurements of white matter (WM), gray matter (GM), and cerebral spinal fluid (CSF) are often used in conjunction with clinical evaluation to provide a more objective measure of MS burden. In this paper, we apply a new unifying automatic mixture-based algorithm for segmentation of brain tissues to quantitatively analyze MS. The method takes into account the following effects that commonly appear in MR imaging: 1) The MR data is modeled as a stochastic process with an inherent inhomogeneity effect of smoothly varying intensity; 2) A new partial volume (PV) model is built in establishing the maximum a posterior (MAP) segmentation scheme; 3) Noise artifacts are minimized by a priori Markov random field (MRF) penalty indicating neighborhood correlation from tissue mixture. The volumes of brain tissues (WM, GM) and CSF are extracted from the mixture-based segmentation. Experimental results of feasibility studies on quantitative analysis of MS are presented.

  8. Quantitative colorimetric-imaging analysis of nickel in iron meteorites.

    Science.gov (United States)

    Zamora, L Lahuerta; López, P Alemán; Fos, G M Antón; Algarra, R Martín; Romero, A M Mellado; Calatayud, J Martínez

    2011-02-15

    A quantitative analytical imaging approach for determining the nickel content of metallic meteorites is proposed. The approach uses a digital image of a series of standard solutions of the nickel-dimethylglyoxime coloured chelate and a meteorite sample solution subjected to the same treatment as the nickel standards for quantitation. The image is processed with suitable software to assign a colour-dependent numerical value (analytical signal) to each standard. Such a value is directly proportional to the analyte concentration, which facilitates construction of a calibration graph where the value for the unknown sample can be interpolated to calculate the nickel content of the meteorite. The results thus obtained were validated by comparison with the official, ISO-endorsed spectrophotometric method for nickel. The proposed method is fairly simple and inexpensive; in fact, it uses a commercially available digital camera as measuring instrument and the images it provides are processed with highly user-friendly public domain software (specifically, ImageJ, developed by the National Institutes of Health and freely available for download on the Internet). In a scenario dominated by increasingly sophisticated and expensive equipment, the proposed method provides a cost-effective alternative based on simple, robust hardware that is affordable and can be readily accessed worldwide. This can be especially advantageous for countries were available resources for analytical equipment investments are scant. The proposed method is essentially an adaptation of classical chemical analysis to current, straightforward, robust, cost-effective instrumentation. Copyright © 2010 Elsevier B.V. All rights reserved.

  9. Quantitative analysis of tumor burden in mouse lung via MRI.

    Science.gov (United States)

    Tidwell, Vanessa K; Garbow, Joel R; Krupnick, Alexander S; Engelbach, John A; Nehorai, Arye

    2012-02-01

    Lung cancer is the leading cause of cancer death in the United States. Despite recent advances in screening protocols, the majority of patients still present with advanced or disseminated disease. Preclinical rodent models provide a unique opportunity to test novel therapeutic drugs for targeting lung cancer. Respiratory-gated MRI is a key tool for quantitatively measuring lung-tumor burden and monitoring the time-course progression of individual tumors in mouse models of primary and metastatic lung cancer. However, quantitative analysis of lung-tumor burden in mice by MRI presents significant challenges. Herein, a method for measuring tumor burden based upon average lung-image intensity is described and validated. The method requires accurate lung segmentation; its efficiency and throughput would be greatly aided by the ability to automatically segment the lungs. A technique for automated lung segmentation in the presence of varying tumor burden levels is presented. The method includes development of a new, two-dimensional parametric model of the mouse lungs and a multi-faceted cost function to optimally fit the model parameters to each image. Results demonstrate a strong correlation (0.93), comparable with that of fully manual expert segmentation, between the automated method's tumor-burden metric and the tumor burden measured by lung weight.

  10. Principal Component Analysis of Some Quantitative and Qualitative Traits in Iranian Spinach Landraces

    Directory of Open Access Journals (Sweden)

    Mohebodini Mehdi

    2017-08-01

    Full Text Available Landraces of spinach in Iran have not been sufficiently characterised for their morpho-agronomic traits. Such characterisation would be helpful in the development of new genetically improved cultivars. In this study 54 spinach accessions collected from the major spinach growing areas of Iran were evaluated to determine their phenotypic diversity profile of spinach genotypes on the basis of 10 quantitative and 9 qualitative morpho-agronomic traits. High coefficients of variation were recorded in some quantitative traits (dry yield and leaf area and all of the qualitative traits. Using principal component analysis, the first four principal components with eigen-values more than 1 contributed 87% of the variability among accessions for quantitative traits, whereas the first four principal components with eigen-values more than 0.8 contributed 79% of the variability among accessions for qualitative traits. The most important relations observed on the first two principal components were a strong positive association between leaf width and petiole length; between leaf length and leaf numbers in flowering; and among fresh yield, dry yield and petiole diameter; a near zero correlation between days to flowering with leaf width and petiole length. Prickly seeds, high percentage of female plants, smooth leaf texture, high numbers of leaves at flowering, greygreen leaves, erect petiole attitude and long petiole length are important characters for spinach breeding programmes.

  11. The Impact of Arithmetic Skills on Mastery of Quantitative Analysis

    Directory of Open Access Journals (Sweden)

    Bruce K. Blaylock

    2012-01-01

    Full Text Available Over the past several years math education has moved from a period where all math calculations were done by hand to an era where most calculations are done using a calculator or computer. There are certainly benefits to this approach, but when one concomitantly recognizes the declining scores on national standardized mathematics exams, it raises the question, “Could the lack of technology-assisted arithmetic manipulation skills have a carryover to understanding higher-level mathematical concepts or is it just a spurious correlation?” Eighty-seven students were tested for their ability to do simple arithmetic and algebra by hand. These scores were then regressed on three important areas of quantitative analysis: recognizing the appropriate tool to use in an analysis, creating a model to carry out the analysis, and interpreting the results of the analysis. The study revealed a significant relationship between the ability to accurately do arithmetic calculations and the ability to recognize the appropriate tool and creating a model. It found no significant relationship between results interpretation and arithmetic skills.

  12. Analysis of generalized interictal discharges using quantitative EEG.

    Science.gov (United States)

    da Silva Braga, Aline Marques; Fujisao, Elaine Keiko; Betting, Luiz Eduardo

    2014-12-01

    Experimental evidence from animal models of the absence seizures suggests a focal source for the initiation of generalized spike-and-wave (GSW) discharges. Furthermore, clinical studies indicate that patients diagnosed with idiopathic generalized epilepsy (IGE) exhibit focal electroencephalographic abnormalities, which involve the thalamo-cortical circuitry. This circuitry is a key network that has been implicated in the initiation of generalized discharges, and may contribute to the pathophysiology of GSW discharges. Quantitative electroencephalogram (qEEG) analysis may be able to detect abnormalities associated with the initiation of GSW discharges. The objective of this study was to determine whether interictal GSW discharges exhibit focal characteristics using qEEG analysis. In this study, 75 EEG recordings from 64 patients were analyzed. All EEG recordings analyzed contained at least one GSW discharge. EEG recordings were obtained by a 22-channel recorder with electrodes positioned according to the international 10-20 system of electrode placement. EEG activity was recorded for 20 min including photic stimulation and hyperventilation. The EEG recordings were visually inspected, and the first unequivocally confirmed generalized spike was marked for each discharge. Three methods of source imaging analysis were applied: dipole source imaging (DSI), classical LORETA analysis recursively applied (CLARA), and equivalent dipole of independent components with cluster analysis. A total of 753 GSW discharges were identified and spatiotemporally analyzed. Source evaluation analysis using all three techniques revealed that the frontal lobe was the principal source of GSW discharges (70%), followed by the parietal and occipital lobes (14%), and the basal ganglia (12%). The main anatomical sources of GSW discharges were the anterior cingulate cortex (36%) and the medial frontal gyrus (23%). Source analysis did not reveal a common focal source of GSW discharges. However

  13. Factor analysis models for structuring covariance matrices of additive genetic effects: a Bayesian implementation

    Directory of Open Access Journals (Sweden)

    Gianola Daniel

    2007-09-01

    Full Text Available Abstract Multivariate linear models are increasingly important in quantitative genetics. In high dimensional specifications, factor analysis (FA may provide an avenue for structuring (covariance matrices, thus reducing the number of parameters needed for describing (codispersion. We describe how FA can be used to model genetic effects in the context of a multivariate linear mixed model. An orthogonal common factor structure is used to model genetic effects under Gaussian assumption, so that the marginal likelihood is multivariate normal with a structured genetic (covariance matrix. Under standard prior assumptions, all fully conditional distributions have closed form, and samples from the joint posterior distribution can be obtained via Gibbs sampling. The model and the algorithm developed for its Bayesian implementation were used to describe five repeated records of milk yield in dairy cattle, and a one common FA model was compared with a standard multiple trait model. The Bayesian Information Criterion favored the FA model.

  14. COMPARITIVE GENETIC DIVERSITY ANALYSIS OF OAT (Avena ...

    African Journals Online (AJOL)

    knsccf

    Equivalence was appraised between phenotypic and molecular markers (ISSR) to analyze the genetic diversity of 20 ... Country of origin. Pedigree ... explain between and within geographical variation and granting ..... JM (2008). Development of PCR-based SCAR and ... Genetic. Resources and Crop Evolution, 56:465–480.

  15. Longitudinal Genetic Analysis of Anxiety Sensitivity

    Science.gov (United States)

    Zavos, Helena M. S.; Gregory, Alice M.; Eley, Thalia C.

    2012-01-01

    Anxiety sensitivity is associated with both anxiety and depression and has been shown to be heritable. Little, however, is known about the role of genetic influence on continuity and change of symptoms over time. The authors' aim was to examine the stability of anxiety sensitivity during adolescence. By using a genetically sensitive design, the…

  16. Genetic Identification of Quantitative Trait Loci for Contents of Mineral Nutrients in Rice Grain

    Institute of Scientific and Technical Information of China (English)

    Ana Luisa Garcia-Oliveira; Lubin Tan; Yongcai Fu; Chuanqing Sun

    2009-01-01

    In present study, Fe, Zn, Mn, Cu, Ca, Mg, P and K contents of 85 Introgression linee (ILs) derived from a cross between an elite indica cultivar Teqing and the wild rice (Oryza rufipogon) were measured by inductively coupled argon plasma (ICAP) spectrometry. Substantial variation was observed for all traits and most of the mineral elements were significantly positive correlated or independent except for Fe with Cu. A total of 31 putative quantitative trait loci (QTLs) were detected for these eight mineral elements by single point analysis. Wild rice (O. rufipogon) contributed favorable alleles for most of the QTLs (26 QTLs), and chromosomes 1, 9 and 12 exhibited 14 QTLs (45%) for these traits. One major effect of QTL for zinc content accounted for the largest proportion of phenotypic variation (11%-19%) was detected near the simple sequence repeats marker RM152 on chromosome 8. The co-locations of QTLs for some mineral elements observed in this mapping population suggested the relationship was at a molecular level among these traits and could be helpful for simultaneous improvement of these traits in rice grain by marker assisted selection.

  17. Methods for genetic linkage analysis using trisomies

    Energy Technology Data Exchange (ETDEWEB)

    Feingold, E.; Lamb, N.E.; Sherman, S.L. [Emory Univ., Atlanta, GA (United States)

    1994-09-01

    Certain genetic disorders (e.g. congenital cataracts, duodenal atresia) are rare in the general population, but more common in people with Down`s syndrome. We present a method for using individuals with trisomy 21 to map genes for such traits. Our methods are analogous to methods for mapping autosomal dominant traits using affected relative pairs by looking for markers with greater than expected identity-by-descent. In the trisomy case, one would take trisomic individuals and look for markers with greater than expected reduction to homozygosity in the chromosomes inherited form the non-disjoining parent. We present statistical methods for performing such a linkage analysis, including a test for linkage to a marker, a method for estimating the distance from the marker to the gene, a confidence interval for that distance, and methods for computing power and sample sizes. The methods are described in the context of gene-dosage model for the etiology of the disorder, but can be extended to other models. We also resolve some practical issues involved in implementing the methods, including how to use partially informative markers, how to test candidate genes, and how to handle the effect of reduced recombination associated with maternal meiosis I non-disjunction.

  18. Quantitative microstructure analysis of polymer-modified mortars.

    Science.gov (United States)

    Jenni, A; Herwegh, M; Zurbriggen, R; Aberle, T; Holzer, L

    2003-11-01

    Digital light, fluorescence and electron microscopy in combination with wavelength-dispersive spectroscopy were used to visualize individual polymers, air voids, cement phases and filler minerals in a polymer-modified cementitious tile adhesive. In order to investigate the evolution and processes involved in formation of the mortar microstructure, quantifications of the phase distribution in the mortar were performed including phase-specific imaging and digital image analysis. The required sample preparation techniques and imaging related topics are discussed. As a form of case study, the different techniques were applied to obtain a quantitative characterization of a specific mortar mixture. The results indicate that the mortar fractionates during different stages ranging from the early fresh mortar until the final hardened mortar stage. This induces process-dependent enrichments of the phases at specific locations in the mortar. The approach presented provides important information for a comprehensive understanding of the functionality of polymer-modified mortars.

  19. Ozone Determination: A Comparison of Quantitative Analysis Methods

    Directory of Open Access Journals (Sweden)

    Rachmat Triandi Tjahjanto

    2012-10-01

    Full Text Available A comparison of ozone quantitative analysis methods by using spectrophotometric and volumetric method has been studied. The aim of this research is to determine the better method by considering the effect of reagent concentration and volume on the measured ozone concentration. Ozone which was analyzed in this research was synthesized from air, then it is used to ozonize methyl orange and potassium iodide solutions at different concentration and volume. Ozonation was held for 20 minutes with 363 mL/minutes air flow rates. The concentrations of ozonized methyl orange and potassium iodide solutions was analyzed by spectrophotometric and volumetric method, respectively. The result of this research shows that concentration and volume of reagent having an effect on the measured ozone concentration. Based on the results of both methods, it can be concluded that volumetric method is better than spectrophotometric method.

  20. Quantitative analysis of gallstones using laser-induced breakdown spectroscopy.

    Science.gov (United States)

    Singh, Vivek K; Singh, Vinita; Rai, Awadhesh K; Thakur, Surya N; Rai, Pradeep K; Singh, Jagdish P

    2008-11-01

    The utility of laser-induced breakdown spectroscopy (LIBS) for categorizing different types of gallbladder stone has been demonstrated by analyzing their major and minor constituents. LIBS spectra of three types of gallstone have been recorded in the 200-900 nm spectral region. Calcium is found to be the major element in all types of gallbladder stone. The spectrophotometric method has been used to classify the stones. A calibration-free LIBS method has been used for the quantitative analysis of metal elements, and the results have been compared with those obtained from inductively coupled plasma atomic emission spectroscopy (ICP-AES) measurements. The single-shot LIBS spectra from different points on the cross section (in steps of 0.5 mm from one end to the other) of gallstones have also been recorded to study the variation of constituents from the center to the surface. The presence of different metal elements and their possible role in gallstone formation is discussed.

  1. Quantitative image analysis of WE43-T6 cracking behavior

    Science.gov (United States)

    Ahmad, A.; Yahya, Z.

    2013-06-01

    Environment-assisted cracking of WE43 cast magnesium (4.2 wt.% Yt, 2.3 wt.% Nd, 0.7% Zr, 0.8% HRE) in the T6 peak-aged condition was induced in ambient air in notched specimens. The mechanism of fracture was studied using electron backscatter diffraction, serial sectioning and in situ observations of crack propagation. The intermetallic (rare earthed-enriched divorced intermetallic retained at grain boundaries and predominantly at triple points) material was found to play a significant role in initiating cracks which leads to failure of this material. Quantitative measurements were required for this project. The populations of the intermetallic and clusters of intermetallic particles were analyzed using image analysis of metallographic images. This is part of the work to generate a theoretical model of the effect of notch geometry on the static fatigue strength of this material.

  2. qfasar: quantitative fatty acid signature analysis with R

    Science.gov (United States)

    Bromaghin, Jeffrey

    2017-01-01

    Knowledge of predator diets provides essential insights into their ecology, yet diet estimation is challenging and remains an active area of research.Quantitative fatty acid signature analysis (QFASA) is a popular method of estimating diet composition that continues to be investigated and extended. However, software to implement QFASA has only recently become publicly available.I summarize a new R package, qfasar, for diet estimation using QFASA methods. The package also provides functionality to evaluate and potentially improve the performance of a library of prey signature data, compute goodness-of-fit diagnostics, and support simulation-based research. Several procedures in the package have not previously been published.qfasar makes traditional and recently published QFASA diet estimation methods accessible to ecologists for the first time. Use of the package is illustrated with signature data from Chukchi Sea polar bears and potential prey species.

  3. Large-Scale Quantitative Analysis of Painting Arts

    Science.gov (United States)

    Kim, Daniel; Son, Seung-Woo; Jeong, Hawoong

    2014-12-01

    Scientists have made efforts to understand the beauty of painting art in their own languages. As digital image acquisition of painting arts has made rapid progress, researchers have come to a point where it is possible to perform statistical analysis of a large-scale database of artistic paints to make a bridge between art and science. Using digital image processing techniques, we investigate three quantitative measures of images - the usage of individual colors, the variety of colors, and the roughness of the brightness. We found a difference in color usage between classical paintings and photographs, and a significantly low color variety of the medieval period. Interestingly, moreover, the increment of roughness exponent as painting techniques such as chiaroscuro and sfumato have advanced is consistent with historical circumstances.

  4. Quantitative analysis of forest island pattern in selected Ohio landscapes

    Energy Technology Data Exchange (ETDEWEB)

    Bowen, G.W.; Burgess, R.L.

    1981-07-01

    The purpose of this study was to quantitatively describe the various aspects of regional distribution patterns of forest islands and relate those patterns to other landscape features. Several maps showing the forest cover of various counties in Ohio were selected as representative examples of forest patterns to be quantified. Ten thousand hectare study areas (landscapes) were delineated on each map. A total of 15 landscapes representing a wide variety of forest island patterns was chosen. Data were converted into a series of continuous variables which contained information pertinent to the sizes, shape, numbers, and spacing of woodlots within a landscape. The continuous variables were used in a factor analysis to describe the variation among landscapes in terms of forest island pattern. The results showed that forest island patterns are related to topography and other environmental features correlated with topography.

  5. Non-genetic variance in pigs: genetic analysis of reproduction and production traits

    NARCIS (Netherlands)

    Sell-Kubiak, E.B.

    2015-01-01

    Abstract Sell-Kubiak, E. (2015). Non-genetic variance in pigs: genetic analysis of reproduction and production traits. PhD thesis, Wageningen University, The Netherlands The main objective of this thesis was to study the origin of random variance in reproduction and production trait

  6. Quantitative analysis of secretome from adipocytes regulated by insulin

    Institute of Scientific and Technical Information of China (English)

    Hu Zhou; Yuanyuan Xiao; Rongxia Li; Shangyu Hong; Sujun Li; Lianshui Wang; Rong Zeng; Kan Liao

    2009-01-01

    Adipocyte is not only a central player involved in storage and release of energy, but also in regulation of energy metabolism in other organs via secretion of pep-tides and proteins. During the pathogenesis of insulin resistance and type 2 diabetes, adipocytes are subjected to the increased levels of insulin, which may have a major impact on the secretion of adipokines. We have undertaken cleavable isotope-coded affinity tag (clCAT) and label-free quantitation approaches to identify and quantify secretory factors that are differen-tially secreted by 3T3-LI adipocytes with or without insulin treatment. Combination of clCAT and label-free results, there are 317 proteins predicted or annotated as secretory proteins. Among these secretory proteins, 179 proteins and 53 proteins were significantly up-regulated and down-regulated, respectively. A total of 77 reported adipokines were quantified in our study, such as adiponectin, cathepsin D, cystatin C, resistin, and transferrin. Western blot analysis of these adipo-kines confirmed the quantitative results from mass spectrometry, and revealed individualized secreting pat-terns of these proteins by increasing insulin dose. In addition, 240 proteins were newly identified and quanti-fied as secreted proteins from 3T3-L1 adipocytes in our study, most of which were up-regulated upon insulin treatment. Further comprehensive bioinformatics analysis revealed that the secretory proteins in extra-cellular matrix-receptor interaction pathway and glycan structure degradation pathway were significantly up-regulated by insulin stimulation.

  7. The genetic variance for multiple linked quantitative trait loci conditional on marker information in a crossed population.

    Science.gov (United States)

    Matsuda, H; Iwaisaki, H

    2002-01-01

    In the prediction of genetic values and quantitative trait loci (QTLs) mapping via the mixed model method incorporating marker information in animal populations, it is important to model the genetic variance for individuals with an arbitrary pedigree structure. In this study, for a crossed population originated from different genetic groups such as breeds or outbred strains, the variance of additive genetic values for multiple linked QTLs that are contained in a chromosome segment, especially the segregation variance, is investigated assuming the use of marker data. The variance for a finite number of QTLs in one chromosomal segment is first examined for the crossed population with the general pedigree. Then, applying the concept of the expectation of identity-by-descent proportion, an approximation to the mean of the conditional probabilities for the linked QTLs over all loci is obtained, and using it an expression for the variance in the case of an infinite number of linked QTLs marked by flanking markers is derived. It appears that the approach presented can be useful in the segment mapping using, and in the genetic evaluation of, crosses with general pedigrees in the population of concern. The calculation of the segregation variance through the current approach is illustrated numerically, using a small data-set.

  8. PIQMIe: A web server for semi-quantitative proteomics data management and analysis

    NARCIS (Netherlands)

    A. Kuzniar (Arnold); R. Kanaar (Roland)

    2014-01-01

    textabstractWe present the Proteomics Identifications and Quantitations Data Management and Integration Service or PIQMIe that aids in reliable and scalable data management, analysis and visualization of semi-quantitative mass spectrometry based proteomics experiments. PIQMIe readily integrates pept

  9. Automatic quantitative analysis of cardiac MR perfusion images

    Science.gov (United States)

    Breeuwer, Marcel M.; Spreeuwers, Luuk J.; Quist, Marcel J.

    2001-07-01

    Magnetic Resonance Imaging (MRI) is a powerful technique for imaging cardiovascular diseases. The introduction of cardiovascular MRI into clinical practice is however hampered by the lack of efficient and accurate image analysis methods. This paper focuses on the evaluation of blood perfusion in the myocardium (the heart muscle) from MR images, using contrast-enhanced ECG-triggered MRI. We have developed an automatic quantitative analysis method, which works as follows. First, image registration is used to compensate for translation and rotation of the myocardium over time. Next, the boundaries of the myocardium are detected and for each position within the myocardium a time-intensity profile is constructed. The time interval during which the contrast agent passes for the first time through the left ventricle and the myocardium is detected and various parameters are measured from the time-intensity profiles in this interval. The measured parameters are visualized as color overlays on the original images. Analysis results are stored, so that they can later on be compared for different stress levels of the heart. The method is described in detail in this paper and preliminary validation results are presented.

  10. Quantitative polymerase chain reaction analysis by deconvolution of internal standard.

    Science.gov (United States)

    Hirakawa, Yasuko; Medh, Rheem D; Metzenberg, Stan

    2010-04-29

    Quantitative Polymerase Chain Reaction (qPCR) is a collection of methods for estimating the number of copies of a specific DNA template in a sample, but one that is not universally accepted because it can lead to highly inaccurate (albeit precise) results. The fundamental problem is that qPCR methods use mathematical models that explicitly or implicitly apply an estimate of amplification efficiency, the error of which is compounded in the analysis to unacceptable levels. We present a new method of qPCR analysis that is efficiency-independent and yields accurate and precise results in controlled experiments. The method depends on a computer-assisted deconvolution that finds the point of concordant amplification behavior between the "unknown" template and an admixed amplicon standard. We apply the method to demonstrate dexamethasone-induced changes in gene expression in lymphoblastic leukemia cell lines. This method of qPCR analysis does not use any explicit or implicit measure of efficiency, and may therefore be immune to problems inherent in other qPCR approaches. It yields an estimate of absolute initial copy number of template, and controlled tests show it generates accurate results.

  11. Quantitative polymerase chain reaction analysis by deconvolution of internal standard

    Directory of Open Access Journals (Sweden)

    Metzenberg Stan

    2010-04-01

    Full Text Available Abstract Background Quantitative Polymerase Chain Reaction (qPCR is a collection of methods for estimating the number of copies of a specific DNA template in a sample, but one that is not universally accepted because it can lead to highly inaccurate (albeit precise results. The fundamental problem is that qPCR methods use mathematical models that explicitly or implicitly apply an estimate of amplification efficiency, the error of which is compounded in the analysis to unacceptable levels. Results We present a new method of qPCR analysis that is efficiency-independent and yields accurate and precise results in controlled experiments. The method depends on a computer-assisted deconvolution that finds the point of concordant amplification behavior between the "unknown" template and an admixed amplicon standard. We apply the method to demonstrate dexamethasone-induced changes in gene expression in lymphoblastic leukemia cell lines. Conclusions This method of qPCR analysis does not use any explicit or implicit measure of efficiency, and may therefore be immune to problems inherent in other qPCR approaches. It yields an estimate of absolute initial copy number of template, and controlled tests show it generates accurate results.

  12. Variabilidad y genética en fríjol común (Phuseolus vulgaris L.: I. análisis de variables morfológicas y agronómicas cuantitativas. Genetic variability on shrab bean (Phaseolus vulgaris L.: 1. Morphological and quantitative agronomicals analysis

    Directory of Open Access Journals (Sweden)

    Ligarreto M. Gustavo A.

    2002-08-01

    Full Text Available Based in the evaluation of quantitative variables it was carried out the identification of the genetic variability of a shrub bean Colombian collection. The investigation was carried out with 30 accessions of which three are improved varieties and one is an elite line, the evaluations were carried out in seven environments, six of them in cold climate and one in template climate. The results were analyzed by univariated and multivariated methods by principal components analysis for the group of variables and cluster analysis among agreements. In the principal components analysis the first six
    components represented 87.31% of the total variation, which discriminated the cultivars of the colIection for Andean and Meso-American gene pool. The morphological and agronomical differences were bigger among the Andean accessions, because of its dispersion degree in the first three components, which is higher than in the Meso-American ones.
    The diversity among the gene pools is represented mainly by the growth habit, precocity, foliate area, yield per plant and the number of seeds by podoThe variables of high heredability represented by high repetibility coefficient r> 1 (Goodman and Paterniani, 1969 were: number of knots, pod length, pod apex length, the number of pods per plant, time to physiological maturity and the weight of 100 seeds which can be used for studies of morphological similarity and evolution.
    Con base en la evaluacón de variables cuantitativas, se llevó a cabo la identificación de la variabilidad genética de una colección colombiana de fríjol de crecimiento arbustivo. La investigación se realizó con 30 accesiones, de las cuales tres son variedades mejoradas y una línea élite; las evaluaciones se realizaron en siete ambientes, seis de ellos en clima frío y uno en clima medio. Los resultados se analizaron por métodos univariados y multivariados de componentes principales para el conjunto de variables y por an

  13. Genetic analysis of the Venezuelan Criollo horse.

    Science.gov (United States)

    Cothran, E G; Canelon, J L; Luis, C; Conant, E; Juras, R

    2011-10-07

    Various horse populations in the Americas have an origin in Spain; they are remnants of the first livestock introduced to the continent early in the colonial period (16th and 17th centuries). We evaluated genetic variability within the Venezuelan Criollo horse and its relationship with other horse breeds. We observed high levels of genetic diversity within the Criollo breed. Significant population differentiation was observed between all South American breeds. The Venezuelan Criollo horse showed high levels of genetic diversity, and from a conservation standpoint, there is no immediate danger of losing variation unless there is a large drop in population size.

  14. An approach for quantitative image quality analysis for CT

    Science.gov (United States)

    Rahimi, Amir; Cochran, Joe; Mooney, Doug; Regensburger, Joe

    2016-03-01

    An objective and standardized approach to assess image quality of Compute Tomography (CT) systems is required in a wide variety of imaging processes to identify CT systems appropriate for a given application. We present an overview of the framework we have developed to help standardize and to objectively assess CT image quality for different models of CT scanners used for security applications. Within this framework, we have developed methods to quantitatively measure metrics that should correlate with feature identification, detection accuracy and precision, and image registration capabilities of CT machines and to identify strengths and weaknesses in different CT imaging technologies in transportation security. To that end we have designed, developed and constructed phantoms that allow for systematic and repeatable measurements of roughly 88 image quality metrics, representing modulation transfer function, noise equivalent quanta, noise power spectra, slice sensitivity profiles, streak artifacts, CT number uniformity, CT number consistency, object length accuracy, CT number path length consistency, and object registration. Furthermore, we have developed a sophisticated MATLAB based image analysis tool kit to analyze CT generated images of phantoms and report these metrics in a format that is standardized across the considered models of CT scanners, allowing for comparative image quality analysis within a CT model or between different CT models. In addition, we have developed a modified sparse principal component analysis (SPCA) method to generate a modified set of PCA components as compared to the standard principal component analysis (PCA) with sparse loadings in conjunction with Hotelling T2 statistical analysis method to compare, qualify, and detect faults in the tested systems.

  15. A robust multiple-locus method for quantitative trait locus analysis of non-normally distributed multiple traits.

    Science.gov (United States)

    Li, Z; Möttönen, J; Sillanpää, M J

    2015-12-01

    Linear regression-based quantitative trait loci/association mapping methods such as least squares commonly assume normality of residuals. In genetics studies of plants or animals, some quantitative traits may not follow normal distribution because the data include outlying observations or data that are collected from multiple sources, and in such cases the normal regression methods may lose some statistical power to detect quantitative trait loci. In this work, we propose a robust multiple-locus regression approach for analyzing multiple quantitative traits without normality assumption. In our method, the objective function is least absolute deviation (LAD), which corresponds to the assumption of multivariate Laplace distributed residual errors. This distribution has heavier tails than the normal distribution. In addition, we adopt a group LASSO penalty to produce shrinkage estimation of the marker effects and to describe the genetic correlation among phenotypes. Our LAD-LASSO approach is less sensitive to the outliers and is more appropriate for the analysis of data with skewedly distributed phenotypes. Another application of our robust approach is on missing phenotype problem in multiple-trait analysis, where the missing phenotype items can simply be filled with some extreme values, and be treated as outliers. The efficiency of the LAD-LASSO approach is illustrated on both simulated and real data sets.

  16. Genetic Analysis of Micro-environmental Plasticity in Drosophila melanogaster

    DEFF Research Database (Denmark)

    Morgante, Fabio; Sorensen, Daniel A; Sørensen, Peter

    Quantitative genetic models recognize the potential for genotype by environment interaction, whereby different genotypes have different plastic responses to changes in macro-environmental conditions. Recently, it has been recognized that micro-environmental plasticity (‘residual’ variance) may also...... be genetically variable. This study utilized the Drosophila Genetic Reference Panel (DGRP) to accurately estimate the genetic variance of micro-environmental plasticity for chill coma recovery time and startle response. Estimates of broad sense heritabilities for both traits are substantial (from 0.51 to 0.......77), of the same order as the heritability at the level of the trait mean for startle response and even larger for chill coma recovery. Genome wide association analyses identified molecular variants (from 15 to 31 depending on the sex and the trait) associated with micro-environmental plasticity. These findings...

  17. Genetic Analysis of Micro-environmental Plasticity in Drosophila melanogaster

    DEFF Research Database (Denmark)

    Morgante, Fabio; Sorensen, Daniel A; Sørensen, Peter;

    Quantitative genetic models recognize the potential for genotype by environment interaction, whereby different genotypes have different plastic responses to changes in macro-environmental conditions. Recently, it has been recognized that micro-environmental plasticity (‘residual’ variance) may also...... be genetically variable. This study utilized the Drosophila Genetic Reference Panel (DGRP) to accurately estimate the genetic variance of micro-environmental plasticity for chill coma recovery time and startle response. Estimates of broad sense heritabilities for both traits are substantial (from 0.51 to 0.......77), of the same order as the heritability at the level of the trait mean for startle response and even larger for chill coma recovery. Genome wide association analyses identified molecular variants (from 15 to 31 depending on the sex and the trait) associated with micro-environmental plasticity. These findings...

  18. Quantitative analysis of food and feed samples with droplet digital PCR.

    Science.gov (United States)

    Morisset, Dany; Štebih, Dejan; Milavec, Mojca; Gruden, Kristina; Žel, Jana

    2013-01-01

    In this study, the applicability of droplet digital PCR (ddPCR) for routine analysis in food and feed samples was demonstrated with the quantification of genetically modified organisms (GMOs). Real-time quantitative polymerase chain reaction (qPCR) is currently used for quantitative molecular analysis of the presence of GMOs in products. However, its use is limited for detecting and quantifying very small numbers of DNA targets, as in some complex food and feed matrices. Using ddPCR duplex assay, we have measured the absolute numbers of MON810 transgene and hmg maize reference gene copies in DNA samples. Key performance parameters of the assay were determined. The ddPCR system is shown to offer precise absolute and relative quantification of targets, without the need for calibration curves. The sensitivity (five target DNA copies) of the ddPCR assay compares well with those of individual qPCR assays and of the chamber digital PCR (cdPCR) approach. It offers a dynamic range over four orders of magnitude, greater than that of cdPCR. Moreover, when compared to qPCR, the ddPCR assay showed better repeatability at low target concentrations and a greater tolerance to inhibitors. Finally, ddPCR throughput and cost are advantageous relative to those of qPCR for routine GMO quantification. It is thus concluded that ddPCR technology can be applied for routine quantification of GMOs, or any other domain where quantitative analysis of food and feed samples is needed.

  19. Quantitative analysis of food and feed samples with droplet digital PCR.

    Directory of Open Access Journals (Sweden)

    Dany Morisset

    Full Text Available In this study, the applicability of droplet digital PCR (ddPCR for routine analysis in food and feed samples was demonstrated with the quantification of genetically modified organisms (GMOs. Real-time quantitative polymerase chain reaction (qPCR is currently used for quantitative molecular analysis of the presence of GMOs in products. However, its use is limited for detecting and quantifying very small numbers of DNA targets, as in some complex food and feed matrices. Using ddPCR duplex assay, we have measured the absolute numbers of MON810 transgene and hmg maize reference gene copies in DNA samples. Key performance parameters of the assay were determined. The ddPCR system is shown to offer precise absolute and relative quantification of targets, without the need for calibration curves. The sensitivity (five target DNA copies of the ddPCR assay compares well with those of individual qPCR assays and of the chamber digital PCR (cdPCR approach. It offers a dynamic range over four orders of magnitude, greater than that of cdPCR. Moreover, when compared to qPCR, the ddPCR assay showed better repeatability at low target concentrations and a greater tolerance to inhibitors. Finally, ddPCR throughput and cost are advantageous relative to those of qPCR for routine GMO quantification. It is thus concluded that ddPCR technology can be applied for routine quantification of GMOs, or any other domain where quantitative analysis of food and feed samples is needed.

  20. Meta-analysis of quantitative pleiotropic traits for next-generation sequencing with multivariate functional linear models.

    Science.gov (United States)

    Chiu, Chi-Yang; Jung, Jeesun; Chen, Wei; Weeks, Daniel E; Ren, Haobo; Boehnke, Michael; Amos, Christopher I; Liu, Aiyi; Mills, James L; Ting Lee, Mei-Ling; Xiong, Momiao; Fan, Ruzong

    2017-02-01

    To analyze next-generation sequencing data, multivariate functional linear models are developed for a meta-analysis of multiple studies to connect genetic variant data to multiple quantitative traits adjusting for covariates. The goal is to take the advantage of both meta-analysis and pleiotropic analysis in order to improve power and to carry out a unified association analysis of multiple studies and multiple traits of complex disorders. Three types of approximate F -distributions based on Pillai-Bartlett trace, Hotelling-Lawley trace, and Wilks's Lambda are introduced to test for association between multiple quantitative traits and multiple genetic variants. Simulation analysis is performed to evaluate false-positive rates and power of the proposed tests. The proposed methods are applied to analyze lipid traits in eight European cohorts. It is shown that it is more advantageous to perform multivariate analysis than univariate analysis in general, and it is more advantageous to perform meta-analysis of multiple studies instead of analyzing the individual studies separately. The proposed models require individual observations. The value of the current paper can be seen at least for two reasons: (a) the proposed methods can be applied to studies that have individual genotype data; (b) the proposed methods can be used as a criterion for future work that uses summary statistics to build test statistics to meta-analyze the data.

  1. Integrative Lifecourse and Genetic Analysis of Military Working Dogs

    Science.gov (United States)

    2013-10-01

    1 Award Number: W81XWH-11-2-0226 TITLE: Integrative Lifecourse and Genetic Analysis of Military Working Dogs PRINCIPAL...insight into gene environment interactions. It leverages the simplified genetics and detailed records of the military working dog population. There are...regions associated with phenotypic variation between dog breeds using selection mapping. PLoS Genet . 7(10):e1002316. PubMed PMID: 22022279). In the

  2. Quantitative DNA methylation analysis of candidate genes in cervical cancer.

    Directory of Open Access Journals (Sweden)

    Erin M Siegel

    Full Text Available Aberrant DNA methylation has been observed in cervical cancer; however, most studies have used non-quantitative approaches to measure DNA methylation. The objective of this study was to quantify methylation within a select panel of genes previously identified as targets for epigenetic silencing in cervical cancer and to identify genes with elevated methylation that can distinguish cancer from normal cervical tissues. We identified 49 women with invasive squamous cell cancer of the cervix and 22 women with normal cytology specimens. Bisulfite-modified genomic DNA was amplified and quantitative pyrosequencing completed for 10 genes (APC, CCNA, CDH1, CDH13, WIF1, TIMP3, DAPK1, RARB, FHIT, and SLIT2. A Methylation Index was calculated as the mean percent methylation across all CpG sites analyzed per gene (~4-9 CpG site per sequence. A binary cut-point was defined at >15% methylation. Sensitivity, specificity and area under ROC curve (AUC of methylation in individual genes or a panel was examined. The median methylation index was significantly higher in cases compared to controls in 8 genes, whereas there was no difference in median methylation for 2 genes. Compared to HPV and age, the combination of DNA methylation level of DAPK1, SLIT2, WIF1 and RARB with HPV and age significantly improved the AUC from 0.79 to 0.99 (95% CI: 0.97-1.00, p-value = 0.003. Pyrosequencing analysis confirmed that several genes are common targets for aberrant methylation in cervical cancer and DNA methylation level of four genes appears to increase specificity to identify cancer compared to HPV detection alone. Alterations in DNA methylation of specific genes in cervical cancers, such as DAPK1, RARB, WIF1, and SLIT2, may also occur early in cervical carcinogenesis and should be evaluated.

  3. Quantitative analysis and parametric display of regional myocardial mechanics

    Science.gov (United States)

    Eusemann, Christian D.; Bellemann, Matthias E.; Robb, Richard A.

    2000-04-01

    Quantitative assessment of regional heart motion has significant potential for more accurate diagnosis of heart disease and/or cardiac irregularities. Local heart motion may be studied from medical imaging sequences. Using functional parametric mapping, regional myocardial motion during a cardiac cycle can be color mapped onto a deformable heart model to obtain better understanding of the structure- to-function relationships in the myocardium, including regional patterns of akinesis or diskinesis associated with ischemia or infarction. In this study, 3D reconstructions were obtained from the Dynamic Spatial Reconstructor at 15 time points throughout one cardiac cycle of pre-infarct and post-infarct hearts. Deformable models were created from the 3D images for each time point of the cardiac cycles. Form these polygonal models, regional excursions and velocities of each vertex representing a unit of myocardium were calculated for successive time-intervals. The calculated results were visualized through model animations and/or specially formatted static images. The time point of regional maximum velocity and excursion of myocardium through the cardiac cycle was displayed using color mapping. The absolute value of regional maximum velocity and maximum excursion were displayed in a similar manner. Using animations, the local myocardial velocity changes were visualized as color changes on the cardiac surface during the cardiac cycle. Moreover, the magnitude and direction of motion for individual segments of myocardium could be displayed. Comparison of these dynamic parametric displays suggest that the ability to encode quantitative functional information on dynamic cardiac anatomy enhances the diagnostic value of 4D images of the heart. Myocardial mechanics quantified this way adds a new dimension to the analysis of cardiac functional disease, including regional patterns of akinesis and diskinesis associated with ischemia and infarction. Similarly, disturbances in

  4. Quantitative analysis with the optoacoustic/ultrasound system OPUS

    Science.gov (United States)

    Haisch, Christoph; Zell, Karin; Sperl, Jonathan; Vogel, Mika W.; Niessner, Reinhard

    2009-02-01

    The OPUS (Optoacoustic plus Ultrasound) system is a combination of a medical ultrasound scanner with a highrepetition rate, wavelength-tunable laser system and a suitable triggering interface to synchronize the laser and the ultrasound system. The pulsed laser generates an optoacoustic (OA), or photoacoustic (PA), signal which is detected by the ultrasound system. Alternatively, imaging in conventional ultrasound mode can be performed. Both imaging modes can be superimposed. The laser light is coupled into the tissue laterally, parallel to the ultrasound transducer, which does not require for any major modification to the transducer or the ultrasound beam forming. This was a basic requirement on the instrument, as the intention of the project was to establish the optoacoustic imaging modality as add-on to a conventional standard ultrasound instrument. We believe that this approach may foster the introduction of OA imaging as routine tool in medical diagnosis. Another key aspect of the project was to exploit the capabilities of OA imaging for quantitative analysis. The intention of the presented work is to summarize all steps necessary to extract the significant information from the PA raw data, which are required for the quantification of local absorber distributions. We show results of spatially resolved absorption measurements in scattering samples and a comparison of four different image reconstruction algorithms, regarding their influence on lateral resolution as well as on the signal to noise ratio for different sample depths and absorption values. The reconstruction algorithms are based on Fourier transformation, on a generalized 2D Hough transformation, on circular back-projection and the classical delay-and-sum approach which is implemented in most ultrasound scanners. Furthermore, we discuss the influence of a newly developed laser source, combining diode and flash lamp pumping. Compared to all-flash-lamp pumped systems it features a significantly higher

  5. Quantitative DNA methylation analysis of candidate genes in cervical cancer.

    Science.gov (United States)

    Siegel, Erin M; Riggs, Bridget M; Delmas, Amber L; Koch, Abby; Hakam, Ardeshir; Brown, Kevin D

    2015-01-01

    Aberrant DNA methylation has been observed in cervical cancer; however, most studies have used non-quantitative approaches to measure DNA methylation. The objective of this study was to quantify methylation within a select panel of genes previously identified as targets for epigenetic silencing in cervical cancer and to identify genes with elevated methylation that can distinguish cancer from normal cervical tissues. We identified 49 women with invasive squamous cell cancer of the cervix and 22 women with normal cytology specimens. Bisulfite-modified genomic DNA was amplified and quantitative pyrosequencing completed for 10 genes (APC, CCNA, CDH1, CDH13, WIF1, TIMP3, DAPK1, RARB, FHIT, and SLIT2). A Methylation Index was calculated as the mean percent methylation across all CpG sites analyzed per gene (~4-9 CpG site) per sequence. A binary cut-point was defined at >15% methylation. Sensitivity, specificity and area under ROC curve (AUC) of methylation in individual genes or a panel was examined. The median methylation index was significantly higher in cases compared to controls in 8 genes, whereas there was no difference in median methylation for 2 genes. Compared to HPV and age, the combination of DNA methylation level of DAPK1, SLIT2, WIF1 and RARB with HPV and age significantly improved the AUC from 0.79 to 0.99 (95% CI: 0.97-1.00, p-value = 0.003). Pyrosequencing analysis confirmed that several genes are common targets for aberrant methylation in cervical cancer and DNA methylation level of four genes appears to increase specificity to identify cancer compared to HPV detection alone. Alterations in DNA methylation of specific genes in cervical cancers, such as DAPK1, RARB, WIF1, and SLIT2, may also occur early in cervical carcinogenesis and should be evaluated.

  6. Quantitative and qualitative proteome characteristics extracted from in-depth integrated genomics and proteomics analysis.

    Science.gov (United States)

    Low, Teck Yew; van Heesch, Sebastiaan; van den Toorn, Henk; Giansanti, Piero; Cristobal, Alba; Toonen, Pim; Schafer, Sebastian; Hübner, Norbert; van Breukelen, Bas; Mohammed, Shabaz; Cuppen, Edwin; Heck, Albert J R; Guryev, Victor

    2013-12-12

    Quantitative and qualitative protein characteristics are regulated at genomic, transcriptomic, and posttranscriptional levels. Here, we integrated in-depth transcriptome and proteome analyses of liver tissues from two rat strains to unravel the interactions within and between these layers. We obtained peptide evidence for 26,463 rat liver proteins. We validated 1,195 gene predictions, 83 splice events, 126 proteins with nonsynonymous variants, and 20 isoforms with nonsynonymous RNA editing. Quantitative RNA sequencing and proteomics data correlate highly between strains but poorly among each other, indicating extensive nongenetic regulation. Our multilevel analysis identified a genomic variant in the promoter of the most differentially expressed gene Cyp17a1, a previously reported top hit in genome-wide association studies for human hypertension, as a potential contributor to the hypertension phenotype in SHR rats. These results demonstrate the power of and need for integrative analysis for understanding genetic control of molecular dynamics and phenotypic diversity in a system-wide manner. Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.

  7. Quantitative and Qualitative Proteome Characteristics Extracted from In-Depth Integrated Genomics and Proteomics Analysis

    Directory of Open Access Journals (Sweden)

    Teck Yew Low

    2013-12-01

    Full Text Available Quantitative and qualitative protein characteristics are regulated at genomic, transcriptomic, and posttranscriptional levels. Here, we integrated in-depth transcriptome and proteome analyses of liver tissues from two rat strains to unravel the interactions within and between these layers. We obtained peptide evidence for 26,463 rat liver proteins. We validated 1,195 gene predictions, 83 splice events, 126 proteins with nonsynonymous variants, and 20 isoforms with nonsynonymous RNA editing. Quantitative RNA sequencing and proteomics data correlate highly between strains but poorly among each other, indicating extensive nongenetic regulation. Our multilevel analysis identified a genomic variant in the promoter of the most differentially expressed gene Cyp17a1, a previously reported top hit in genome-wide association studies for human hypertension, as a potential contributor to the hypertension phenotype in SHR rats. These results demonstrate the power of and need for integrative analysis for understanding genetic control of molecular dynamics and phenotypic diversity in a system-wide manner.

  8. Ascertainment correction for Markov chain Monte Carlo segregation and linkage analysis of a quantitative trait.

    Science.gov (United States)

    Ma, Jianzhong; Amos, Christopher I; Warwick Daw, E

    2007-09-01

    Although extended pedigrees are often sampled through probands with extreme levels of a quantitative trait, Markov chain Monte Carlo (MCMC) methods for segregation and linkage analysis have not been able to perform ascertainment corrections. Further, the extent to which ascertainment of pedigrees leads to biases in the estimation of segregation and linkage parameters has not been previously studied for MCMC procedures. In this paper, we studied these issues with a Bayesian MCMC approach for joint segregation and linkage analysis, as implemented in the package Loki. We first simulated pedigrees ascertained through individuals with extreme values of a quantitative trait in spirit of the sequential sampling theory of Cannings and Thompson [Cannings and Thompson [1977] Clin. Genet. 12:208-212]. Using our simulated data, we detected no bias in estimates of the trait locus location. However, in addition to allele frequencies, when the ascertainment threshold was higher than or close to the true value of the highest genotypic mean, bias was also found in the estimation of this parameter. When there were multiple trait loci, this bias destroyed the additivity of the effects of the trait loci, and caused biases in the estimation all genotypic means when a purely additive model was used for analyzing the data. To account for pedigree ascertainment with sequential sampling, we developed a Bayesian ascertainment approach and implemented Metropolis-Hastings updates in the MCMC samplers used in Loki. Ascertainment correction greatly reduced biases in parameter estimates. Our method is designed for multiple, but a fixed number of trait loci.

  9. Joint Analysis Method for Major Genes Controlling Multiple Correlated Quantitative Traits

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Based on the major gene and polygene mixed inheritance model for multiple correlated quantitative traits, the authors proposed a new joint segregation analysis method of major gene controlling multiple correlated quantitative traits, which include major gene detection and its effect and variation estimation. The effect and variation of major gene are estimated by the maximum likelihood method implemented via expectation-maximization (EM) algorithm. Major gene is tested with the likelihood ratio (LR) test statistic. Extensive simulation studies showed that joint analysis not only increases the statistical power of major gene detection but also improves the precision and accuracy of major gene effect estimates. An example of the plant height and the number of tiller of F2 population in rice cross Duonieai × Zhonghua 11 was used in the illustration. The results indicated that the genetic difference of these two traits in this cross refers to only one pleiotropic major gene. The additive effect and dominance effect of the major gene are estimated as -21.3 and 40.6 cm on plant height, and 22.7 and -25.3 on number of tiller, respectively. The major gene shows overdominance for plant height and close to complete dominance for number of tillers.

  10. Quantitative Phosphoproteomics Analysis of ERBB3/ERBB4 Signaling.

    Science.gov (United States)

    Wandinger, Sebastian K; Lahortiga, Idoya; Jacobs, Kris; Klammer, Martin; Jordan, Nicole; Elschenbroich, Sarah; Parade, Marc; Jacoby, Edgar; Linders, Joannes T M; Brehmer, Dirk; Cools, Jan; Daub, Henrik

    2016-01-01

    The four members of the epidermal growth factor receptor (EGFR/ERBB) family form homo- and heterodimers which mediate ligand-specific regulation of many key cellular processes in normal and cancer tissues. While signaling through the EGFR has been extensively studied on the molecular level, signal transduction through ERBB3/ERBB4 heterodimers is less well understood. Here, we generated isogenic mouse Ba/F3 cells that express full-length and functional membrane-integrated ERBB3 and ERBB4 or ERBB4 alone, to serve as a defined cellular model for biological and phosphoproteomics analysis of ERBB3/ERBB4 signaling. ERBB3 co-expression significantly enhanced Ba/F3 cell proliferation upon neuregulin-1 (NRG1) treatment. For comprehensive signaling studies we performed quantitative mass spectrometry (MS) experiments to compare the basal ERBB3/ERBB4 cell phosphoproteome to NRG1 treatment of ERBB3/ERBB4 and ERBB4 cells. We employed a workflow comprising differential isotope labeling with mTRAQ reagents followed by chromatographic peptide separation and final phosphopeptide enrichment prior to MS analysis. Overall, we identified 9686 phosphorylation sites which could be confidently localized to specific residues. Statistical analysis of three replicate experiments revealed 492 phosphorylation sites which were significantly changed in NRG1-treated ERBB3/ERBB4 cells. Bioinformatics data analysis recapitulated regulation of mitogen-activated protein kinase and Akt pathways, but also indicated signaling links to cytoskeletal functions and nuclear biology. Comparative assessment of NRG1-stimulated ERBB4 Ba/F3 cells revealed that ERBB3 did not trigger defined signaling pathways but more broadly enhanced phosphoproteome regulation in cells expressing both receptors. In conclusion, our data provide the first global picture of ERBB3/ERBB4 signaling and provide numerous potential starting points for further mechanistic studies.

  11. Quantitative Phosphoproteomics Analysis of ERBB3/ERBB4 Signaling.

    Directory of Open Access Journals (Sweden)

    Sebastian K Wandinger

    Full Text Available The four members of the epidermal growth factor receptor (EGFR/ERBB family form homo- and heterodimers which mediate ligand-specific regulation of many key cellular processes in normal and cancer tissues. While signaling through the EGFR has been extensively studied on the molecular level, signal transduction through ERBB3/ERBB4 heterodimers is less well understood. Here, we generated isogenic mouse Ba/F3 cells that express full-length and functional membrane-integrated ERBB3 and ERBB4 or ERBB4 alone, to serve as a defined cellular model for biological and phosphoproteomics analysis of ERBB3/ERBB4 signaling. ERBB3 co-expression significantly enhanced Ba/F3 cell proliferation upon neuregulin-1 (NRG1 treatment. For comprehensive signaling studies we performed quantitative mass spectrometry (MS experiments to compare the basal ERBB3/ERBB4 cell phosphoproteome to NRG1 treatment of ERBB3/ERBB4 and ERBB4 cells. We employed a workflow comprising differential isotope labeling with mTRAQ reagents followed by chromatographic peptide separation and final phosphopeptide enrichment prior to MS analysis. Overall, we identified 9686 phosphorylation sites which could be confidently localized to specific residues. Statistical analysis of three replicate experiments revealed 492 phosphorylation sites which were significantly changed in NRG1-treated ERBB3/ERBB4 cells. Bioinformatics data analysis recapitulated regulation of mitogen-activated protein kinase and Akt pathways, but also indicated signaling links to cytoskeletal functions and nuclear biology. Comparative assessment of NRG1-stimulated ERBB4 Ba/F3 cells revealed that ERBB3 did not trigger defined signaling pathways but more broadly enhanced phosphoproteome regulation in cells expressing both receptors. In conclusion, our data provide the first global picture of ERBB3/ERBB4 signaling and provide numerous potential starting points for further mechanistic studies.

  12. Quantitative analysis of cryptic splicing associated with TDP-43 depletion.

    Science.gov (United States)

    Humphrey, Jack; Emmett, Warren; Fratta, Pietro; Isaacs, Adrian M; Plagnol, Vincent

    2017-05-26

    Reliable exon recognition is key to the splicing of pre-mRNAs into mature mRNAs. TDP-43 is an RNA-binding protein whose nuclear loss and cytoplasmic aggregation are a hallmark pathology in amyotrophic lateral sclerosis and frontotemporal dementia (ALS/FTD). TDP-43 depletion causes the aberrant inclusion of cryptic exons into a range of transcripts, but their extent, relevance to disease pathogenesis and whether they are caused by other RNA-binding proteins implicated in ALS/FTD are unknown. We developed an analysis pipeline to discover and quantify cryptic exon inclusion and applied it to publicly available human and murine RNA-sequencing data. We detected widespread cryptic splicing in TDP-43 depletion datasets but almost none in another ALS/FTD-linked protein FUS. Sequence motif and iCLIP analysis of cryptic exons demonstrated that they are bound by TDP-43. Unlike the cryptic exons seen in hnRNP C depletion, those repressed by TDP-43 cannot be linked to transposable elements. Cryptic exons are poorly conserved and inclusion overwhelmingly leads to nonsense-mediated decay of the host transcript, with reduced transcript levels observed in differential expression analysis. RNA-protein interaction data on 73 different RNA-binding proteins showed that, in addition to TDP-43, 7 specifically bind TDP-43 linked cryptic exons. This suggests that TDP-43 competes with other splicing factors for binding to cryptic exons and can repress cryptic exon inclusion. Our quantitative analysis pipeline confirms the presence of cryptic exons during the depletion of TDP-43 but not FUS providing new insight into to RNA-processing dysfunction as a cause or consequence in ALS/FTD.

  13. A computational tool for quantitative analysis of vascular networks.

    Directory of Open Access Journals (Sweden)

    Enrique Zudaire

    Full Text Available Angiogenesis is the generation of mature vascular networks from pre-existing vessels. Angiogenesis is crucial during the organism' development, for wound healing and for the female reproductive cycle. Several murine experimental systems are well suited for studying developmental and pathological angiogenesis. They include the embryonic hindbrain, the post-natal retina and allantois explants. In these systems vascular networks are visualised by appropriate staining procedures followed by microscopical analysis. Nevertheless, quantitative assessment of angiogenesis is hampered by the lack of readily available, standardized metrics and software analysis tools. Non-automated protocols are being used widely and they are, in general, time--and labour intensive, prone to human error and do not permit computation of complex spatial metrics. We have developed a light-weight, user friendly software, AngioTool, which allows for quick, hands-off and reproducible quantification of vascular networks in microscopic images. AngioTool computes several morphological and spatial parameters including the area covered by a vascular network, the number of vessels, vessel length, vascular density and lacunarity. In addition, AngioTool calculates the so-called "branching index" (branch points/unit area, providing a measurement of the sprouting activity of a specimen of interest. We have validated AngioTool using images of embryonic murine hindbrains, post-natal retinas and allantois explants. AngioTool is open source and can be downloaded free of charge.

  14. Comprehensive Quantitative Analysis of Ovarian and Breast Cancer Tumor Peptidomes

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Zhe; Wu, Chaochao; Xie, Fang; Slysz, Gordon W.; Tolic, Nikola; Monroe, Matthew E.; Petyuk, Vladislav A.; Payne, Samuel H.; Fujimoto, Grant M.; Moore, Ronald J.; Fillmore, Thomas L.; Schepmoes, Athena A.; Levine, Douglas; Townsend, Reid; Davies, Sherri; Li, Shunqiang; Ellis, Matthew; Boja, Emily; Rivers, Robert; Rodriguez, Henry; Rodland, Karin D.; Liu, Tao; Smith, Richard D.

    2015-01-02

    Aberrant degradation of proteins is associated with many pathological states, including cancers. Mass spectrometric analysis of tumor peptidomes, the intracellular and intercellular products of protein degradation, has the potential to provide biological insights on proteolytic processing in cancer. However, attempts to use the information on these smaller protein degradation products from tumors for biomarker discovery and cancer biology studies have been fairly limited to date, largely due to the lack of effective approaches for robust peptidomics identification and quantification, and the prevalence of confounding factors and biases associated with sample handling and processing. Herein, we have developed an effective and robust analytical platform for comprehensive analyses of tissue peptidomes, which is suitable for high throughput quantitative studies. The reproducibility and coverage of the platform, as well as the suitability of clinical ovarian tumor and patient-derived breast tumor xenograft samples with post-excision delay of up to 60 min before freezing for peptidomics analysis, have been demonstrated. Moreover, our data also show that the peptidomics profiles can effectively separate breast cancer subtypes, reflecting tumor-associated protease activities. Peptidomics complements results obtainable from conventional bottom-up proteomics, and provides insights not readily obtainable from such approaches.

  15. Correlation between two methods of florbetapir PET quantitative analysis.

    Science.gov (United States)

    Breault, Christopher; Piper, Jonathan; Joshi, Abhinay D; Pirozzi, Sara D; Nelson, Aaron S; Lu, Ming; Pontecorvo, Michael J; Mintun, Mark A; Devous, Michael D

    2017-01-01

    This study evaluated performance of a commercially available standardized software program for calculation of florbetapir PET standard uptake value ratios (SUVr) in comparison with an established research method. Florbetapir PET images for 183 subjects clinically diagnosed as cognitively normal (CN), mild cognitive impairment (MCI) or probable Alzheimer's disease (AD) (45 AD, 60 MCI, and 78 CN) were evaluated using two software processing algorithms. The research method uses a single florbetapir PET template generated by averaging both amyloid positive and amyloid negative registered brains together. The commercial software simultaneously optimizes the registration between the florbetapir PET images and three templates: amyloid negative, amyloid positive, and an average. Cortical average SUVr values were calculated across six predefined anatomic regions with respect to the whole cerebellum reference region. SUVr values were well correlated between the two methods (r2 = 0.98). The relationship between the methods computed from the regression analysis is: Commercial method SUVr = (0.9757*Research SUVr) + 0.0299. A previously defined cutoff SUVr of 1.1 for distinguishing amyloid positivity by the research method corresponded to 1.1 (95% CI = 1.098, 1.11) for the commercial method. This study suggests that the commercial method is comparable to the published research method of SUVr analysis for florbetapir PET images, thus facilitating the potential use of standardized quantitative approaches to PET amyloid imaging.

  16. Quantitative evaluation of midpalatal suture maturation via fractal analysis

    Science.gov (United States)

    Kwak, Kyoung Ho; Kim, Yong-Il; Kim, Yong-Deok

    2016-01-01

    Objective The purpose of this study was to determine whether the results of fractal analysis can be used as criteria for midpalatal suture maturation evaluation. Methods The study included 131 subjects aged over 18 years of age (range 18.1–53.4 years) who underwent cone-beam computed tomography. Skeletonized images of the midpalatal suture were obtained via image processing software and used to calculate fractal dimensions. Correlations between maturation stage and fractal dimensions were calculated using Spearman's correlation coefficient. Optimal fractal dimension cut-off values were determined using a receiver operating characteristic curve. Results The distribution of maturation stages of the midpalatal suture according to the cervical vertebrae maturation index was highly variable, and there was a strong negative correlation between maturation stage and fractal dimension (−0.623, p Fractal dimension was a statistically significant indicator of dichotomous results with regard to maturation stage (area under curve = 0.794, p fractal dimension was used to predict the resulting variable that splits maturation stages into ABC and D or E yielded an optimal fractal dimension cut-off value of 1.0235. Conclusions There was a strong negative correlation between fractal dimension and midpalatal suture maturation. Fractal analysis is an objective quantitative method, and therefore we suggest that it may be useful for the evaluation of midpalatal suture maturation. PMID:27668195

  17. Therapeutic electrical stimulation for spasticity: quantitative gait analysis.

    Science.gov (United States)

    Pease, W S

    1998-01-01

    Improvement in motor function following electrical stimulation is related to strengthening of the stimulated spastic muscle and inhibition of the antagonist. A 26-year-old man with familial spastic paraparesis presented with gait dysfunction and bilateral lower limb spastic muscle tone. Clinically, muscle strength and sensation were normal. He was considered appropriate for a trial of therapeutic electrical stimulation following failed trials of physical therapy and baclofen. No other treatment was used concurrent with the electrical stimulation. Before treatment, quantitative gait analysis revealed 63% of normal velocity and a crouched gait pattern, associated with excessive electromyographic activity in the hamstrings and gastrocnemius muscles. Based on these findings, bilateral stimulation of the quadriceps and anterior compartment musculature was performed two to three times per week for three months. Repeat gait analysis was conducted three weeks after the cessation of stimulation treatment. A 27% increase in velocity was noted associated with an increase in both cadence and right step length. Right hip and bilateral knee stance motion returned to normal (rather than "crouched"). No change in the timing of dynamic electromyographic activity was seen. These findings suggest a role for the use of electrical stimulation for rehabilitation of spasticity. The specific mechanism of this improvement remains uncertain.

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

    Science.gov (United States)

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

    2014-01-20

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

  19. Quantitative Trait Locus Analysis of Mating Behavior and Male Sex Pheromones in Nasonia Wasps

    Directory of Open Access Journals (Sweden)

    Wenwen Diao

    2016-06-01

    Full Text Available A major focus in speciation genetics is to identify the chromosomal regions and genes that reduce hybridization and gene flow. We investigated the genetic architecture of mating behavior in the parasitoid wasp species pair Nasonia giraulti and Nasonia oneida that exhibit strong prezygotic isolation. Behavioral analysis showed that N. oneida females had consistently higher latency times, and broke off the mating sequence more often in the mounting stage when confronted with N. giraulti males compared with males of their own species. N. oneida males produce a lower quantity of the long-range male sex pheromone (4R,5S-5-hydroxy-4-decanolide (RS-HDL. Crosses between the two species yielded hybrid males with various pheromone quantities, and these males were used in mating trials with females of either species to measure female mate discrimination rates. A quantitative trait locus (QTL analysis involving 475 recombinant hybrid males (F2, 2148 reciprocally backcrossed females (F3, and a linkage map of 52 equally spaced neutral single nucleotide polymorphism (SNP markers plus SNPs in 40 candidate mating behavior genes revealed four QTL for male pheromone amount, depending on partner species. Our results demonstrate that the RS-HDL pheromone plays a role in the mating system of N. giraulti and N. oneida, but also that additional communication cues are involved in mate choice. No QTL were found for female mate discrimination, which points at a polygenic architecture of female choice with strong environmental influences.

  20. Linkage Map Construction and Quantitative Trait Locus Analysis of Agronomic and Fiber Quality Traits in Cotton

    Directory of Open Access Journals (Sweden)

    Michael A. Gore

    2014-03-01

    Full Text Available The superior fiber properties of L. serve as a source of novel variation for improving fiber quality in Upland cotton ( L., but introgression from has been largely unsuccessful due to hybrid breakdown and a lack of genetic and genomic resources. In an effort to overcome these limitations, we constructed a linkage map and conducted a quantitative trait locus (QTL analysis of 10 agronomic and fiber quality traits in a recombinant inbred mapping population derived from a cross between TM-1, an Upland cotton line, and NM24016, an elite line with stabilized introgression from . The linkage map consisted of 429 simple-sequence repeat (SSR and 412 genotyping-by-sequencing (GBS-based single-nucleotide polymorphism (SNP marker loci that covered half of the tetraploid cotton genome. Notably, the 841 marker loci were unevenly distributed among the 26 chromosomes of tetraploid cotton. The 10 traits evaluated on the TM-1 × NM24016 population in a multienvironment trial were highly heritable, and most of the fiber traits showed considerable transgressive variation. Through the QTL analysis, we identified a total of 28 QTLs associated with the 10 traits. Our study provides a novel resource that can be used by breeders and geneticists for the genetic improvement of agronomic and fiber quality traits in Upland cotton.

  1. Applying Qualitative Hazard Analysis to Support Quantitative Safety Analysis for Proposed Reduced Wake Separation Conops

    Science.gov (United States)

    Shortle, John F.; Allocco, Michael

    2005-01-01

    This paper describes a scenario-driven hazard analysis process to identify, eliminate, and control safety-related risks. Within this process, we develop selective criteria to determine the applicability of applying engineering modeling to hypothesized hazard scenarios. This provides a basis for evaluating and prioritizing the scenarios as candidates for further quantitative analysis. We have applied this methodology to proposed concepts of operations for reduced wake separation for closely spaced parallel runways. For arrivals, the process identified 43 core hazard scenarios. Of these, we classified 12 as appropriate for further quantitative modeling, 24 that should be mitigated through controls, recommendations, and / or procedures (that is, scenarios not appropriate for quantitative modeling), and 7 that have the lowest priority for further analysis.

  2. Genetic Analysis on Isoflavone Content in Soybean Seeds

    Institute of Scientific and Technical Information of China (English)

    SUN Jun-ming; DING An-lin; CHANG Ru-zhen

    2002-01-01

    Fifteen combinations with six soybean cultivars of different isoflavone content were formulated and planted in a randomized complete-block design model; genetic factors of isoflavone quantity were analyzed. Resuits indicated that genetic factors of isoflavone contents in F2 population inherited quantitatively. Isoflavone content of F1, F2 seeds normally trended. There were heterosis in F1, F2 of most combinations, and also heterobeltiosis in part of the crosses. The broad sense heritability of F2 was higher in parts of the crosses. It predicted the selection might be carried out preliminarily in F2 hybrids. There was significant positive correlation between hybrids and mid-parent.

  3. DNA microsatellite analysis for tomato genetic differentiation

    Directory of Open Access Journals (Sweden)

    Miskoska-Milevska Elizabeta

    2015-01-01

    Full Text Available Commonly used method for determination of the genetic diversity among the populations is the test for genetic differentiation. DNA microsatellite markers are usually used to investigate the genetic structure of natural populations. The aim of this study was to evaluate the applicability of eight DNA microsatellite loci (LECH13, LE21085, LEMDDNa, LEEF1Aa, LELEUZIP, LE20592, TMS9 and LE2A11 in genetic differentiation of six morphologically different tomato varieties (var. grandifolium from subsp. cultum; var. cerasiforme - red and yellow, var. pruniforme and var. pyriforme from subsp. subspontaneum; and var. racemigerum from subsp. spontaneum. The fragment analyses was performed using Applied Biosystems DNA analyzer (ABI 3130 and GeneMapper® Software program. The data were analysed using the specific program Power Marker Software. The average number of detected alleles was 3,625. Also, the average PIC value for all 8 DNA microsatellites loci was 0,3571. The genetic differentiation test in the researched tomato subspecies showed minor differentiation for locus LELEUZIP (- 0,0009, modest differentiation for locus LECH13 (0,0896, locus LEMDDNa (0,0896 and locus LE21085 (0,0551 and major differentiation for locus LE2A11 (0,7633, locus LEEF1Aa (0,6167, locus TMS9 (0.4967 and locus LE20592 (0,4263. On the other hand, in the estimated tomato varieties, locus LE21085 (0,0297, locus LECH13 (0,0256 and locus LELEUZIP (0,0005 showed minor differentiation, locus LEMDDNa (0,1333 showed modest differentiation, while locus TMS9 (0,5929, locus LEEF1Aa (0,5006, locus LE2A11 (0,4013 and locus LE20592 (0,2606 showed major differentiation. The eight DNA microsatellite loci can be applicable solution for tomato genetic differentiation. The overall results suggest that these microsatellite loci could be used in further population genetic studies of tomatoes.

  4. PCR-free quantitative detection of genetically modified organism from raw materials. An electrochemiluminescence-based bio bar code method.

    Science.gov (United States)

    Zhu, Debin; Tang, Yabing; Xing, Da; Chen, Wei R

    2008-05-15

    A bio bar code assay based on oligonucleotide-modified gold nanoparticles (Au-NPs) provides a PCR-free method for quantitative detection of nucleic acid targets. However, the current bio bar code assay requires lengthy experimental procedures including the preparation and release of bar code DNA probes from the target-nanoparticle complex and immobilization and hybridization of the probes for quantification. Herein, we report a novel PCR-free electrochemiluminescence (ECL)-based bio bar code assay for the quantitative detection of genetically modified organism (GMO) from raw materials. It consists of tris-(2,2'-bipyridyl) ruthenium (TBR)-labeled bar code DNA, nucleic acid hybridization using Au-NPs and biotin-labeled probes, and selective capture of the hybridization complex by streptavidin-coated paramagnetic beads. The detection of target DNA is realized by direct measurement of ECL emission of TBR. It can quantitatively detect target nucleic acids with high speed and sensitivity. This method can be used to quantitatively detect GMO fragments from real GMO products.

  5. Study of quantitative genetics of gum arabic production complicated by variability in ploidy level of Acacia senegal (L.) Willd

    DEFF Research Database (Denmark)

    Diallo, Adja Madjiguene; Nielsen, Lene Rostgaard; Hansen, Jon Kehlet;

    2015-01-01

    sibs, while the open-pollinated families of polyploids showed low variation within families. The difference in sibling relationship observed between ploidy levels complicated estimation of genetic parameters. However, based on the diploid trees, we conclude that heritability in gum arabic production......Gum arabic is an important international commodity produced by trees of Acacia senegal across Sahelian Africa, but documented results of breeding activities are limited. The objective of this study was to provide reliable estimates of quantitative genetic parameters in order to shed light...... on the breeding potential for improvement of gum yield and quality. For this purpose, we measured growth on 617 offspring from 60 open-pollinated trees after 18 years, and gum yield and quality based on two seasons, 18 and 19 years after establishment. Genotyping with eight microsatellite markers revealed...

  6. Quantitative Seq-LGS: Genome-Wide Identification of Genetic Drivers of Multiple Phenotypes in Malaria Parasites

    KAUST Repository

    Abkallo, Hussein M.

    2016-10-01

    Identifying the genetic determinants of phenotypes that impact on disease severity is of fundamental importance for the design of new interventions against malaria. Traditionally, such discovery has relied on labor-intensive approaches that require significant investments of time and resources. By combining Linkage Group Selection (LGS), quantitative whole genome population sequencing and a novel mathematical modeling approach (qSeq-LGS), we simultaneously identified multiple genes underlying two distinct phenotypes, identifying novel alleles for growth rate and strain specific immunity (SSI), while removing the need for traditionally required steps such as cloning, individual progeny phenotyping and marker generation. The detection of novel variants, verified by experimental phenotyping methods, demonstrates the remarkable potential of this approach for the identification of genes controlling selectable phenotypes in malaria and other apicomplexan parasites for which experimental genetic crosses are amenable.

  7. On the runtime analysis of the Simple Genetic Algorithm

    DEFF Research Database (Denmark)

    Oliveto, Pietro S.; Witt, Carsten

    2014-01-01

    For many years it has been a challenge to analyze the time complexity of Genetic Algorithms (GAs) using stochastic selection together with crossover and mutation. This paper presents a rigorous runtime analysis of the well-known Simple Genetic Algorithm (SGA) for OneMax. It is proved that the SGA...

  8. On the Analysis of the Simple Genetic Algorithm

    DEFF Research Database (Denmark)

    Oliveto, Pietro S.; Witt, Carsten

    2012-01-01

    For many years it has been a challenge to analyze the time complexity of Genetic Algorithms (GAs) using stochastic selection together with crossover and mutation. This paper presents a rigorous runtime analysis of the well-known Simple Genetic Algorithm (SGA) for OneMax. It is proved that the SGA...

  9. Genetic diversity analysis of pearl millet (Pennisetum glauccum [L ...

    African Journals Online (AJOL)

    PRECIOUS

    2009-11-16

    Nov 16, 2009 ... Random amplified polymorphic DNA (RAPD) analysis was applied ... ding reliable information for the calculation of genetic dis- tance and pedigree studies. Thus, for genetic diversity assessment, molecular markers offer considerable ad- .... morphism (%) = total number of bands - number of monomorphic.

  10. Evaluating the Quantitative Capabilities of Metagenomic Analysis Software.

    Science.gov (United States)

    Kerepesi, Csaba; Grolmusz, Vince

    2016-05-01

    DNA sequencing technologies are applied widely and frequently today to describe metagenomes, i.e., microbial communities in environmental or clinical samples, without the need for culturing them. These technologies usually return short (100-300 base-pairs long) DNA reads, and these reads are processed by metagenomic analysis software that assign phylogenetic composition-information to the dataset. Here we evaluate three metagenomic analysis software (AmphoraNet--a webserver implementation of AMPHORA2--, MG-RAST, and MEGAN5) for their capabilities of assigning quantitative phylogenetic information for the data, describing the frequency of appearance of the microorganisms of the same taxa in the sample. The difficulties of the task arise from the fact that longer genomes produce more reads from the same organism than shorter genomes, and some software assign higher frequencies to species with longer genomes than to those with shorter ones. This phenomenon is called the "genome length bias." Dozens of complex artificial metagenome benchmarks can be found in the literature. Because of the complexity of those benchmarks, it is usually difficult to judge the resistance of a metagenomic software to this "genome length bias." Therefore, we have made a simple benchmark for the evaluation of the "taxon-counting" in a metagenomic sample: we have taken the same number of copies of three full bacterial genomes of different lengths, break them up randomly to short reads of average length of 150 bp, and mixed the reads, creating our simple benchmark. Because of its simplicity, the benchmark is not supposed to serve as a mock metagenome, but if a software fails on that simple task, it will surely fail on most real metagenomes. We applied three software for the benchmark. The ideal quantitative solution would assign the same proportion to the three bacterial taxa. We have found that AMPHORA2/AmphoraNet gave the most accurate results and the other two software were under

  11. Quantitative analysis of left ventricular strain using cardiac computed tomography

    Energy Technology Data Exchange (ETDEWEB)

    Buss, Sebastian J., E-mail: sebastian.buss@med.uni-heidelberg.de [Department of Cardiology, University of Heidelberg, 69120 Heidelberg (Germany); Schulz, Felix; Mereles, Derliz [Department of Cardiology, University of Heidelberg, 69120 Heidelberg (Germany); Hosch, Waldemar [Department of Diagnostic and Interventional Radiology, University of Heidelberg, 69120 Heidelberg (Germany); Galuschky, Christian; Schummers, Georg; Stapf, Daniel [TomTec Imaging Systems GmbH, Munich (Germany); Hofmann, Nina; Giannitsis, Evangelos; Hardt, Stefan E. [Department of Cardiology, University of Heidelberg, 69120 Heidelberg (Germany); Kauczor, Hans-Ulrich [Department of Diagnostic and Interventional Radiology, University of Heidelberg, 69120 Heidelberg (Germany); Katus, Hugo A.; Korosoglou, Grigorios [Department of Cardiology, University of Heidelberg, 69120 Heidelberg (Germany)

    2014-03-15

    Objectives: To investigate whether cardiac computed tomography (CCT) can determine left ventricular (LV) radial, circumferential and longitudinal myocardial deformation in comparison to two-dimensional echocardiography in patients with congestive heart failure. Background: Echocardiography allows for accurate assessment of strain with high temporal resolution. A reduced strain is associated with a poor prognosis in cardiomyopathies. However, strain imaging is limited in patients with poor echogenic windows, so that, in selected cases, tomographic imaging techniques may be preferable for the evaluation of myocardial deformation. Methods: Consecutive patients (n = 27) with congestive heart failure who underwent a clinically indicated ECG-gated contrast-enhanced 64-slice dual-source CCT for the evaluation of the cardiac veins prior to cardiac resynchronization therapy (CRT) were included. All patients underwent additional echocardiography. LV radial, circumferential and longitudinal strain and strain rates were analyzed in identical midventricular short axis, 4-, 2- and 3-chamber views for both modalities using the same prototype software algorithm (feature tracking). Time for analysis was assessed for both modalities. Results: Close correlations were observed for both techniques regarding global strain (r = 0.93, r = 0.87 and r = 0.84 for radial, circumferential and longitudinal strain, respectively, p < 0.001 for all). Similar trends were observed for regional radial, longitudinal and circumferential strain (r = 0.88, r = 0.84 and r = 0.94, respectively, p < 0.001 for all). The number of non-diagnostic myocardial segments was significantly higher with echocardiography than with CCT (9.6% versus 1.9%, p < 0.001). In addition, the required time for complete quantitative strain analysis was significantly shorter for CCT compared to echocardiography (877 ± 119 s per patient versus 1105 ± 258 s per patient, p < 0.001). Conclusion: Quantitative assessment of LV strain

  12. High-Density Genetic Linkage Map Construction and Quantitative Trait Locus Mapping for Hawthorn (Crataegus pinnatifida Bunge).

    Science.gov (United States)

    Zhao, Yuhui; Su, Kai; Wang, Gang; Zhang, Liping; Zhang, Jijun; Li, Junpeng; Guo, Yinshan

    2017-07-14

    Genetic linkage maps are an important tool in genetic and genomic research. In this study, two hawthorn cultivars, Qiujinxing and Damianqiu, and 107 progenies from a cross between them were used for constructing a high-density genetic linkage map using the 2b-restriction site-associated DNA (2b-RAD) sequencing method, as well as for mapping quantitative trait loci (QTL) for flavonoid content. In total, 206,411,693 single-end reads were obtained, with an average sequencing depth of 57× in the parents and 23× in the progeny. After quality trimming, 117,896 high-quality 2b-RAD tags were retained, of which 42,279 were polymorphic; of these, 12,951 markers were used for constructing the genetic linkage map. The map contained 17 linkage groups and 3,894 markers, with a total map length of 1,551.97 cM and an average marker interval of 0.40 cM. QTL mapping identified 21 QTLs associated with flavonoid content in 10 linkage groups, which explained 16.30-59.00% of the variance. This is the first high-density linkage map for hawthorn, which will serve as a basis for fine-scale QTL mapping and marker-assisted selection of important traits in hawthorn germplasm and will facilitate chromosome assignment for hawthorn whole-genome assemblies in the future.

  13. Automated quantitative gait analysis in animal models of movement disorders

    Directory of Open Access Journals (Sweden)

    Vandeputte Caroline

    2010-08-01

    Full Text Available Abstract Background Accurate and reproducible behavioral tests in animal models are of major importance in the development and evaluation of new therapies for central nervous system disease. In this study we investigated for the first time gait parameters of rat models for Parkinson's disease (PD, Huntington's disease (HD and stroke using the Catwalk method, a novel automated gait analysis test. Static and dynamic gait parameters were measured in all animal models, and these data were compared to readouts of established behavioral tests, such as the cylinder test in the PD and stroke rats and the rotarod tests for the HD group. Results Hemiparkinsonian rats were generated by unilateral injection of the neurotoxin 6-hydroxydopamine in the striatum or in the medial forebrain bundle. For Huntington's disease, a transgenic rat model expressing a truncated huntingtin fragment with multiple CAG repeats was used. Thirdly, a stroke model was generated by a photothrombotic induced infarct in the right sensorimotor cortex. We found that multiple gait parameters were significantly altered in all three disease models compared to their respective controls. Behavioural deficits could be efficiently measured using the cylinder test in the PD and stroke animals, and in the case of the PD model, the deficits in gait essentially confirmed results obtained by the cylinder test. However, in the HD model and the stroke model the Catwalk analysis proved more sensitive than the rotarod test and also added new and more detailed information on specific gait parameters. Conclusion The automated quantitative gait analysis test may be a useful tool to study both motor impairment and recovery associated with various neurological motor disorders.

  14. Quantitative assessment of hip osteoarthritis based on image texture analysis.

    Science.gov (United States)

    Boniatis, I S; Costaridou, L I; Cavouras, D A; Panagiotopoulos, E C; Panayiotakis, G S

    2006-03-01

    A non-invasive method was developed to investigate the potential capacity of digital image texture analysis in evaluating the severity of hip osteoarthritis (OA) and in monitoring its progression. 19 textural features evaluating patterns of pixel intensity fluctuations were extracted from 64 images of radiographic hip joint spaces (HJS), corresponding to 32 patients with verified unilateral or bilateral OA. Images were enhanced employing custom developed software for the delineation of the articular margins on digitized pelvic radiographs. The severity of OA for each patient was assessed by expert orthopaedists employing the Kellgren and Lawrence (KL) scale. Additionally, an index expressing HJS-narrowing was computed considering patients from the unilateral OA-group. A textural feature that quantified pixel distribution non-uniformity (grey level non-uniformity, GLNU) demonstrated the strongest correlation with the HJS-narrowing index among all extracted features and utilized in further analysis. Classification rules employing GLNU feature were introduced to characterize a hip as normal or osteoarthritic and to assign it to one of three severity categories, formed in accordance with the KL scale. Application of the proposed rules resulted in relatively high classification accuracies in characterizing a hip as normal or osteoarthritic (90.6%) and in assigning it to the correct KL scale category (88.9%). Furthermore, the strong correlation between the HJS-narrowing index and the pathological GLNU (r = -0.9, p<0.001) was utilized to provide percentages quantifying hip OA-severity. Texture analysis may contribute in the quantitative assessment of OA-severity, in the monitoring of OA-progression and in the evaluation of a chondroprotective therapy.

  15. Nanotechnology patents in the automotive industry (a quantitative & qualitative analysis).

    Science.gov (United States)

    Prasad, Raghavendra; Bandyopadhyay, Tapas K

    2014-01-01

    The aim of the article is to present a trend in patent filings for application of nanotechnology to the automobile sector across the world, using the keyword-based patent search. Overviews of the patents related to nano technology in the automobile industry have been provided. The current work has started from the worldwide patent search to find the patents on nanotechnology in the automobile industry and classify the patents according to the various parts of an automobile to which they are related and the solutions which they are providing. In the next step various graphs have been produced to get an insight into various trends. In next step, analysis of patents in various classifications, have been performed. The trends shown in graphs provide the quantitative analysis whereas; the qualitative analysis has been done in another section. The classifications of patents based on the solution they provide have been performed by reading the claims, titles, abstract and full texts separately. Patentability of nano technology inventions have been discussed in a view to give an idea of requirements and statutory bars to the patentability of nanotechnology inventions. Another objective of the current work is to suggest appropriate framework for the companies regarding use of nano technology in the automobile industry and a suggestive strategy for patenting of the inventions related to the same. For example, US Patent, with patent number US2008-019426A1 discusses the invention related to Lubricant composition. This patent has been studied and classified to fall under classification of automobile parts. After studying this patent, it is deduced that, the problem of friction in engine is being solved by this patent. One classification is the "automobile part" based while other is the basis of "problem being solved". Hence, two classifications, namely reduction in friction and engine were created. Similarly, after studying all the patents, a similar matrix has been created.

  16. Beyond Punnett Squares: Student Word Association and Explanations of Phenotypic Variation through an Integrative Quantitative Genetics Unit Investigating Anthocyanin Inheritance and Expression in "Brassica rapa" Fast Plants

    Science.gov (United States)

    Batzli, Janet M.; Smith, Amber R.; Williams, Paul H.; McGee, Seth A.; Dosa, Katalin; Pfammatter, Jesse

    2014-01-01

    Genetics instruction in introductory biology is often confined to Mendelian genetics and avoids the complexities of variation in quantitative traits. Given the driving question "What determines variation in phenotype (Pv)? (Pv=Genotypic variation Gv + environmental variation Ev)," we developed a 4-wk unit for an inquiry-based laboratory…

  17. Beyond Punnett Squares: Student Word Association and Explanations of Phenotypic Variation through an Integrative Quantitative Genetics Unit Investigating Anthocyanin Inheritance and Expression in "Brassica rapa" Fast Plants

    Science.gov (United States)

    Batzli, Janet M.; Smith, Amber R.; Williams, Paul H.; McGee, Seth A.; Dosa, Katalin; Pfammatter, Jesse

    2014-01-01

    Genetics instruction in introductory biology is often confined to Mendelian genetics and avoids the complexities of variation in quantitative traits. Given the driving question "What determines variation in phenotype (Pv)? (Pv=Genotypic variation Gv + environmental variation Ev)," we developed a 4-wk unit for an inquiry-based laboratory…

  18. Quantitative determination of casein genetic variants in goat milk: Application in Girgentana dairy goat breed.

    Science.gov (United States)

    Montalbano, Maria; Segreto, Roberta; Di Gerlando, Rosalia; Mastrangelo, Salvatore; Sardina, Maria Teresa

    2016-02-01

    The study was conducted to develop a high-performance liquid chromatographic (HPLC) method to quantify casein genetic variants (αs2-, β-, and κ-casein) in milk of homozygous individuals of Girgentana goat breed. For calibration experiments, pure genetic variants were extracted from individual milk samples of animals with known genotypes. The described HPLC approach was precise, accurate and highly suitable for quantification of goat casein genetic variants of homozygous individuals. The amount of each casein per allele was: αs2-casein A = 2.9 ± 0.8 g/L and F = 1.8 ± 0.4 g/L; β-casein C = 3.0 ± 0.8 g/L and C1 = 2.0 ± 0.7 g/L and κ-casein A = 1.6 ± 0.3 g/L and B = 1.1 ± 0.2 g/L. A good correlation was found between the quantities of αs2-casein genetic variants A and F, and β-casein C and C1 with other previously described method. The main important result was obtained for κ-casein because, till now, no data were available on quantification of single genetic variants for this protein.

  19. Quantitative genetics of migration syndromes: a study of two barn swallow populations.

    Science.gov (United States)

    Teplitsky, C; Mouawad, N G; Balbontin, J; De Lope, F; Møller, A P

    2011-09-01

    Migration is a complex trait although little is known about genetic correlations between traits involved in such migration syndromes. To assess the migratory responses to climate change, we need information on genetic constraints on evolutionary potential of arrival dates in migratory birds. Using two long-term data sets on barn swallows Hirundo rustica (from Spain and Denmark), we show for the first time in wild populations that spring arrival dates are phenotypically and genetically correlated with morphological and life history traits. In the Danish population, length of outermost tail feathers and wing length were negatively genetically correlated with arrival date. In the Spanish population, we found a negative genetic correlation between arrival date and time elapsed between arrival date and laying date, constraining response to selection that favours both early arrival and shorter delays. This results in a decreased rate of adaptation, not because of constraints on arrival date, but constraints on delay before breeding, that is, a trait that can be equally important in the context of climate change.

  20. Quantitative analysis of polymorphic mixtures of ranitidine hydrochloride by Raman spectroscopy and principal components analysis.

    Science.gov (United States)

    Pratiwi, Destari; Fawcett, J Paul; Gordon, Keith C; Rades, Thomas

    2002-11-01

    Ranitidine hydrochloride exists as two polymorphs, forms I and II, both of which are used to manufacture commercial tablets. Raman spectroscopy can be used to differentiate the two forms but univariate methods of quantitative analysis of one polymorph as an impurity in the other lack sensitivity. We have applied principal components analysis (PCA) of Raman spectra to binary mixtures of the two polymorphs and to binary mixtures prepared by adding one polymorph to powdered tablets of the other. Based on absorption measurements of seven spectral regions, it was found that >97% of the spectral variation was accounted for by three principal components. Quantitative calibration models generated by multiple linear regression predicted a detection limit and quantitation limit for either forms I or II in mixtures of the two of 0.6 and 1.8%, respectively. This study demonstrates that PCA of Raman spectroscopic data provides a sensitive method for the quantitative analysis of polymorphic impurities of drugs in commercial tablets with a quantitation limit of less than 2%.

  1. Quantitative risk analysis of urban flooding in lowland areas

    NARCIS (Netherlands)

    Ten Veldhuis, J.A.E.

    2010-01-01

    Urban flood risk analyses suffer from a lack of quantitative historical data on flooding incidents. Data collection takes place on an ad hoc basis and is usually restricted to severe events. The resulting data deficiency renders quantitative assessment of urban flood risks uncertain. The study repor

  2. A Novel Quantitative Analysis Model for Information System Survivability Based on Conflict Analysis

    Institute of Scientific and Technical Information of China (English)

    WANG Jian; WANG Huiqiang; ZHAO Guosheng

    2007-01-01

    This paper describes a novel quantitative analysis model for system survivability based on conflict analysis, which provides a direct-viewing survivable situation. Based on the three-dimensional state space of conflict, each player's efficiency matrix on its credible motion set can be obtained. The player whose desire is the strongest in all initiates the moving and the overall state transition matrix of information system may be achieved. In addition, the process of modeling and stability analysis of conflict can be converted into a Markov analysis process, thus the obtained results with occurring probability of each feasible situation will help the players to quantitatively judge the probability of their pursuing situations in conflict. Compared with the existing methods which are limited to post-explanation of system's survivable situation, the proposed model is relatively suitable for quantitatively analyzing and forecasting the future development situation of system survivability. The experimental results show that the model may be effectively applied to quantitative analysis for survivability. Moreover, there will be a good application prospect in practice.

  3. APPLICATION OF NEOTAME IN CATCHUP: QUANTITATIVE DESCRIPTIVE AND PHYSICOCHEMICAL ANALYSIS

    Directory of Open Access Journals (Sweden)

    G. C. M. C. BANNWART

    2008-11-01

    Full Text Available

    In this study, fi ve prototypes of catchup were developed by replacing partially or totally the sucrose in the formulation by the sweetener Neotame (NTM. These prototypes were evaluated for their physicochemical characteristics and sensory profi le (Quantitative Descriptive Analysis. The main sensory differences observed among the prototypes were regarding to color, consistency, mouthfeel, sweet taste and tomato taste, for which lower means were obtained as the sugar level was decreased, and also in terms of salty taste, that had higher means with the decrease of sugar. In terms of bitter and sweetener aftertastes, the prototype 100% sweetened with NTM presented the higher mean score, but with no signifi cant difference when compared to other prototypes containing sucrose, for bitter taste, however, it had the highest mean score, statistically different from all the other prototypes. In terms of physicochemical characteristics, the differences were mainly in terms of consistency, solids and color. Despite the differences observed among the prototypes as the sugar level was reduced, it was concluded that NTM is a suitable sweetener for catchup, both for use in reduced calories and no sugar versions.

  4. Quantitative Analysis of AGV System in FMS Cell Layout

    Directory of Open Access Journals (Sweden)

    B. Ramana

    1997-01-01

    Full Text Available Material handling is a specialised activity for a modern manufacturing concern. Automated guided vehicles (AGVs are invariably used for material handling in flexible manufacturing Systems (FMSs due to their flexibility. The quantitative analysis of an AGV system is useful for determining the material flow rates, operation times, length of delivery, length of empty move of AGV and the number of AGVs required for a typical FMS cell layout. The efficiency of the material handling system, such as AGV can be improved by reducing the length of empty move. The length of empty move of AGV depends upon despatching and scheduling methods. If these methods of AGVs are not properly planned, the length of empty move of AGV is greater than the length of delivery .This results in increase in material handling time which in turn increases the number of AGVs required in FMS cell. This paper presents a method for optimising the length of empty travel of AGV in a typical FMS cell layout.

  5. Early child grammars: qualitative and quantitative analysis of morphosyntactic production.

    Science.gov (United States)

    Legendre, Géraldine

    2006-09-10

    This article reports on a series of 5 analyses of spontaneous production of verbal inflection (tense and person-number agreement) by 2-year-olds acquiring French as a native language. A formal analysis of the qualitative and quantitative results is developed using the unique resources of Optimality Theory (OT; Prince & Smolensky, 2004). It is argued that acquisition of morphosyntax proceeds via overlapping grammars (rather than through abrupt changes), which OT formalizes in terms of partial rather than total constraint rankings. Initially, economy of structure constraints take priority over faithfulness constraints that demand faithful expression of a speaker's intent, resulting in child production of tense that is comparable in level to that of child-directed speech. Using the independent Predominant Length of Utterance measure of syntactic development proposed in Vainikka, Legendre, and Todorova (1999), production of agreement is shown first to lag behind tense then to compete with tense at an intermediate stage of development. As the child's development progresses, faithfulness constraints become more dominant, and the overall production of tense and agreement becomes adult-like.

  6. Quantitative produced water analysis using mobile 1H NMR

    Science.gov (United States)

    Wagner, Lisabeth; Kalli, Chris; Fridjonsson, Einar O.; May, Eric F.; Stanwix, Paul L.; Graham, Brendan F.; Carroll, Matthew R. J.; Johns, Michael L.

    2016-10-01

    Measurement of oil contamination of produced water is required in the oil and gas industry to the (ppm) level prior to discharge in order to meet typical environmental legislative requirements. Here we present the use of compact, mobile 1H nuclear magnetic resonance (NMR) spectroscopy, in combination with solid phase extraction (SPE), to meet this metrology need. The NMR hardware employed featured a sufficiently homogeneous magnetic field, such that chemical shift differences could be used to unambiguously differentiate, and hence quantitatively detect, the required oil and solvent NMR signals. A solvent system consisting of 1% v/v chloroform in tetrachloroethylene was deployed, this provided a comparable 1H NMR signal intensity for the oil and the solvent (chloroform) and hence an internal reference 1H signal from the chloroform resulting in the measurement being effectively self-calibrating. The measurement process was applied to water contaminated with hexane or crude oil over the range 1-30 ppm. The results were validated against known solubility limits as well as infrared analysis and gas chromatography.

  7. Quantitative analysis of brain magnetic resonance imaging for hepatic encephalopathy

    Science.gov (United States)

    Syh, Hon-Wei; Chu, Wei-Kom; Ong, Chin-Sing

    1992-06-01

    High intensity lesions around ventricles have recently been observed in T1-weighted brain magnetic resonance images for patients suffering hepatic encephalopathy. The exact etiology that causes magnetic resonance imaging (MRI) gray scale changes has not been totally understood. The objective of our study was to investigate, through quantitative means, (1) the amount of changes to brain white matter due to the disease process, and (2) the extent and distribution of these high intensity lesions, since it is believed that the abnormality may not be entirely limited to the white matter only. Eleven patients with proven haptic encephalopathy and three normal persons without any evidence of liver abnormality constituted our current data base. Trans-axial, sagittal, and coronal brain MRI were obtained on a 1.5 Tesla scanner. All processing was carried out on a microcomputer-based image analysis system in an off-line manner. Histograms were decomposed into regular brain tissues and lesions. Gray scale ranges coded as lesion were then brought back to original images to identify distribution of abnormality. Our results indicated the disease process involved pallidus, mesencephalon, and subthalamic regions.

  8. European Identity in Russian Regions Bordering on Finland: Quantitative Analysis

    Directory of Open Access Journals (Sweden)

    A. O. Domanov

    2014-01-01

    Full Text Available Th e quantitative analysis of an opinion poll conducted in October 2013 in three Russian cities located near Finnish border (St-Petersburg, Kronstadt and Vyborg explores European identity of their citizens. Th is area was chosen to illustrate the crucial importance of space interpretation in spatial identity formation by using critical geopolitical approach. Th e study shows how diff erent images of space on the same territory act as intermediate variables between objective territorial characteristics and citizens’ identities. As the geographical position at the border of Russia provides the citizens with geopolitical alternatives to identify their location as a fortress defending the nation (as in the case of Kronstadt or a bridge between cultures, the given study allows us to compare reasons for these geopolitical choices of inhabitants. Furthermore, the research aims at bridging the gap in the studies of European and multiple identity in Russian regions and provides Northwest Russian perspective on the perpetual discussion about subjective Eastern border of Europe.

  9. Quantitative analysis of plasma interleiukin-6 by immunoassay on microchip

    Science.gov (United States)

    Abe, K.; Hashimoto, Y.; Yatsushiro, S.; Yamamura, S.; Tanaka, M.; Ooie, T.; Baba, Y.; Kataoka, M.

    2012-03-01

    Sandwich enzyme-linked immunoassay (ELISA) is one of the most frequently employed assays for clinical diagnosis, since this enables the investigator to identify specific protein biomarkers. However, the conventional assay using a 96-well microtitration plate is time- and sample-consuming, and therefore is not suitable for rapid diagnosis. To overcome these drawbacks, we performed a sandwich ELISA on a microchip. We employed the piezoelectric inkjet printing for deposition and fixation of 1st antibody on the microchannnel surface (300 μm width and 100 μm depth). Model analyte was interleukin-6 (IL-6) which was one of the inflammatory cytokine. After blocking the microchannel, antigen, biotin-labeled 2nd antibody, and avidin-labeled peroxidase were infused into the microchannel and incubated for 20 min, 10 min, and 5 min, respectively. This assay could detect 2 pg/ml and quantitatively measure the range of 0-32 pg/ml. Liner regression analysis of plasma IL-6 concentration obtained by microchip and conventional methods exhibited a significant relationship (R2 = 0.9964). This assay reduced the time for the antigen-antibody reaction to 1/6, and the consumption of samples and reagents to 1/50 compared with the conventional method. This assay enables us to determine plasma IL-6 with accuracy, high sensitivity, time saving ability, and low consumption of sample and reagents, and thus will be applicable to clinic diagnosis.

  10. Quantitative image analysis of HIV-1 infection in lymphoid tissue

    Energy Technology Data Exchange (ETDEWEB)

    Haase, A.T.; Zupancic, M.; Cavert, W. [Univ. of Minnesota Medical School, Minneapolis, MN (United States)] [and others

    1996-11-08

    Tracking human immunodeficiency virus-type 1 (HIV-1) infection at the cellular level in tissue reservoirs provides opportunities to better understand the pathogenesis of infection and to rationally design and monitor therapy. A quantitative technique was developed to determine viral burden in two important cellular compartments in lymphoid developed to determine viral burden in two important cellular compartments in lymphoid tissues. Image analysis and in situ hybridization were combined to show that in the presymptomatic stages of infection there is a large, relatively stable pool of virions on the surfaces of follicular dendritic cells and a smaller pool of productivity infected cells. Despite evidence of constraints on HIV-1 replication in the infected cell population in lymphoid tissues, estimates of the numbers of these cells and the virus they could produce are consistent with the quantities of virus that have been detected in the bloodstream. The cellular sources of virus production and storage in lymphoid tissues can now be studied with this approach over the course of infection and treatment. 22 refs., 2 figs., 2 tabs.

  11. Full-Range Public Health Leadership, Part 1: Quantitative Analysis

    Directory of Open Access Journals (Sweden)

    Erik L. Carlton

    2015-04-01

    Full Text Available Background. Workforce and leadership development are central to the future of public health. However, public health has been slow to translate and apply leadership models from other professions and to incorporate local perspectives in understanding public health leadership. Purpose. This study utilized the full-range leadership model in order to examine public health leadership. Specifically, it sought to measure leadership styles among local health department directors and to understand the context of leadership local health departments.Methods. Leadership styles among local health department directors (n=13 were examined using survey methodology. Quantitative analysis methods included descriptive statistics, boxplots, and Pearson bivariate correlations using SPSS v18.0. Findings. Self-reported leadership styles were highly correlated to leadership outcomes at the organizational level. However, they were not related to county health rankings. Results suggest the preeminence of leader behaviors and providing individual consideration to staff as compared to idealized attributes of leaders, intellectual stimulation, or inspirational motivation. Implications. Holistic leadership assessment instruments, such as the Multifactor Leadership Questionnaire (MLQ can be useful in assessing public health leaders approaches and outcomes. Comprehensive, 360-degree reviews may be especially helpful. Further research is needed to examine the effectiveness of public health leadership development models, as well as the extent that public health leadership impacts public health outcomes.

  12. Quantitative Analysis and Comparisons of EPON Protection Schemes

    Institute of Scientific and Technical Information of China (English)

    CHENHong; JINDepeng; ZENGLieguang; SULi

    2005-01-01

    This paper presents the relationship between the intensity of network damage and the network survivability. Then a method for quantitatively analyzing the survivability of tree network is studied. Based on the analysis, the survivability of Ethernet passive optical network (EPON) with three kinds of protection schemes (i.e., Trunk-fiber protection scheme, Node-fiber protection scheme, and Bus-fiber protection) is discussed. Following this, the comparisons of the survivability among these three kinds of protection schemes of F.PON are put forward. The simulation results show that, when the coverage area is the same, the survivability of EPON with Node-fiber protection scheme is better than that of EPON with Trunk-fiber protection scheme, and when the number and distribution of Optical network unit (ONU) are the same, the survivability of EPON with Bus-fiber protection scheme is better than that of EPON with Nodefiber protection scheme. Under the same constraints, the needed fiber of EPON with Bus-fiber protection scheme is the least when there are more than 12 ONU nodes. These results are useful not only for forecasting and evaluating the survivability of EPON access network, but also for its topology design.

  13. Quantitative analysis of regulatory flexibility under changing environmental conditions

    Science.gov (United States)

    Edwards, Kieron D; Akman, Ozgur E; Knox, Kirsten; Lumsden, Peter J; Thomson, Adrian W; Brown, Paul E; Pokhilko, Alexandra; Kozma-Bognar, Laszlo; Nagy, Ferenc; Rand, David A; Millar, Andrew J

    2010-01-01

    The circadian clock controls 24-h rhythms in many biological processes, allowing appropriate timing of biological rhythms relative to dawn and dusk. Known clock circuits include multiple, interlocked feedback loops. Theory suggested that multiple loops contribute the flexibility for molecular rhythms to track multiple phases of the external cycle. Clear dawn- and dusk-tracking rhythms illustrate the flexibility of timing in Ipomoea nil. Molecular clock components in Arabidopsis thaliana showed complex, photoperiod-dependent regulation, which was analysed by comparison with three contrasting models. A simple, quantitative measure, Dusk Sensitivity, was introduced to compare the behaviour of clock models with varying loop complexity. Evening-expressed clock genes showed photoperiod-dependent dusk sensitivity, as predicted by the three-loop model, whereas the one- and two-loop models tracked dawn and dusk, respectively. Output genes for starch degradation achieved dusk-tracking expression through light regulation, rather than a dusk-tracking rhythm. Model analysis predicted which biochemical processes could be manipulated to extend dusk tracking. Our results reveal how an operating principle of biological regulators applies specifically to the plant circadian clock. PMID:21045818

  14. Quantitative analysis of piperine in ayurvedic formulation by UV Spectrophotometry

    Directory of Open Access Journals (Sweden)

    Gupta Vishvnath

    2011-02-01

    Full Text Available A simple and reproducible UV- spectrophotometric method for the quantitative determination of piperine in Sitopaladi churna (STPLC were developed and validated in the present work. The parameters linearity, precision , accuracy, and standard error were studies according to indian herbal pharmacopiea. In this present study a new, simple, rapid, sensitive, precise and economic spectrophotometric method in ultraviolet region has been developed for the determination of piperine in market and laboratory herbal formulation of Sitopaladi churna. which were procured and purchased respectively from the local market and they were evaluated as per Indian herbal Pharmacopoeia and WHO guidelines. The concentration of piperine present in raw material of PSC was found to be 1.45±0.014 w/w in piper longum fruits. Piperine has the maximum wavelength at 342.5 nm and hence the UV spectrophotometric method was performed at 342.5 nm. The samples were prepared in methanol and methos obeys Beers law in concentration ranges employed for evaluation. The content of piperine in ayurvedic formulation was determined. The result of analysis have been validated statistically and recovery studies confirmed the accuracy of the proposed method. Hence the proposed method can be used for the reliable quantification of Piperine in crude drug and its herbal formulation.

  15. A Quantitative Analysis of Photovoltaic Modules Using Halved Cells

    Directory of Open Access Journals (Sweden)

    S. Guo

    2013-01-01

    Full Text Available In a silicon wafer-based photovoltaic (PV module, significant power is lost due to current transport through the ribbons interconnecting neighbour cells. Using halved cells in PV modules is an effective method to reduce the resistive power loss which has already been applied by some major PV manufacturers (Mitsubishi, BP Solar in their commercial available PV modules. As a consequence, quantitative analysis of PV modules using halved cells is needed. In this paper we investigate theoretically and experimentally the difference between modules made with halved and full-size solar cells. Theoretically, we find an improvement in fill factor of 1.8% absolute and output power of 90 mW for the halved cell minimodule. Experimentally, we find an improvement in fill factor of 1.3% absolute and output power of 60 mW for the halved cell module. Also, we investigate theoretically how this effect confers to the case of large-size modules. It is found that the performance increment of halved cell PV modules is even higher for high-efficiency solar cells. After that, the resistive loss of large-size modules with different interconnection schemes is analysed. Finally, factors influencing the performance and cost of industrial halved cell PV modules are discussed.

  16. Quantitative analysis of 3-OH oxylipins in fermentation yeast.

    Science.gov (United States)

    Potter, Greg; Xia, Wei; Budge, Suzanne M; Speers, R Alex

    2017-02-01

    Despite the ubiquitous distribution of oxylipins in plants, animals, and microbes, and the application of numerous analytical techniques to study these molecules, 3-OH oxylipins have never been quantitatively assayed in yeasts. The formation of heptafluorobutyrate methyl ester derivatives and subsequent analysis with gas chromatography - negative chemical ionization - mass spectrometry allowed for the first determination of yeast 3-OH oxylipins. The concentration of 3-OH 10:0 (0.68-4.82 ng/mg dry cell mass) in the SMA strain of Saccharomyces pastorianus grown in laboratory-scale beverage fermentations was elevated relative to oxylipin concentrations in plant tissues and macroalgae. In fermenting yeasts, the onset of 3-OH oxylipin formation has been related to fermentation progression and flocculation initiation. When the SMA strain was grown in laboratory-scale fermentations, the maximal sugar consumption rate preceded the lowest concentration of 3-OH 10:0 by ∼4.5 h and a distinct increase in 3-OH 10:0 concentration by ∼16.5 h.

  17. Genetic analysis of yield in peanut ( Arachis hypogaea L.) using ...

    African Journals Online (AJOL)

    Genetic analysis of yield in peanut ( Arachis hypogaea L.) using mixed model of ... parent) and a variety Yuhua No.4 (male parent) was used in this research. ... No.4 using the method of major gene plus polygene mixed inheritance model.

  18. 1 Hierarchical Approaches to the Analysis of Genetic Diversity in ...

    African Journals Online (AJOL)

    2015-04-14

    Apr 14, 2015 ... Keywords: Genetic diversity, Hierarchical approach, Plant, Clustering,. Descriptive ... utilization) or by clustering (based on a phonetic analysis of individual ...... Improvement of Food Crop Preservatives for the next Millennium.

  19. Analysis of genetic diversity and estimation of inbreeding coefficient ...

    African Journals Online (AJOL)

    Analysis of genetic diversity and estimation of inbreeding coefficient within ... The present work is a contribution to the knowledge of population structure and to the ... diversity that may be helpful to horse breeders in designing and managing ...

  20. Communication about vaccinations in Italian websites: a quantitative analysis.

    Science.gov (United States)

    Tafuri, Silvio; Gallone, Maria S; Gallone, Maria F; Zorico, Ivan; Aiello, Valeria; Germinario, Cinzia

    2014-01-01

    Babies' parents and people who look for information about vaccination often visit anti-vaccine movement's websites, blogs by naturopathic physicians or natural and alternative medicine practitioners. The aim of this work is to provide a quantitative analysis on the type of information available to Italian people regarding vaccination and a quality analysis of websites retrieved through our searches. A quality score was created to evaluate the technical level of websites. A research was performed through Yahoo, Google, and MSN using the keywords "vaccine" and "vaccination," with the function "OR" in order to identify the most frequently used websites. The 2 keywords were input in Italian, and the first 15 pages retrieved by each search engine were analyzed. 149 websites were selected through this methodology. Fifty-three per cent of the websites belonged to associations, groups, or scientific companies, 32.2% (n = 48) consisted of a personal blog and 14.8% (n = 22) belonged to some of the National Health System offices. Among all analyzed websites, 15.4% (n = 23) came from anti-vaccine movement groups. 37.6% reported webmaster name, 67.8% webmaster e-mail, 28.6% indicated the date of the last update and 46.6% the author's name. The quality score for government sites was higher on average than anti-vaccine websites; although, government sites don't use Web 2.0 functions, as the forums.: National Health System institutions who have to promote vaccination cannot avoid investing in web communication because it cannot be managed by private efforts but must be the result of Public Health, private and scientific association, and social movement synergy.