Arthritis Genetics Analysis Aids Drug Discovery

Science.gov (United States)

... NIH Research Matters January 13, 2014 Arthritis Genetics Analysis Aids Drug Discovery An international research team identified 42 new ... Edition Distracted Driving Raises Crash Risk Arthritis Genetics Analysis Aids Drug Discovery Oxytocin Affects Facial Recognition Connect with Us ...

Two-level mixed modeling of longitudinal pedigree data for genetic association analysis

DEFF Research Database (Denmark)

Tan, Q.

2013-01-01

of follow-up. Approaches have been proposed to integrate kinship correlation into the mixed effect models to explicitly model the genetic relationship which have been proven as an efficient way for dealing with sample clustering in pedigree data. Although useful for adjusting relatedness in the mixed...... assess the genetic associations with the mean level and the rate of change in a phenotype both with kinship correlation integrated in the mixed effect models. We apply our method to longitudinal pedigree data to estimate the genetic effects on systolic blood pressure measured over time in large pedigrees......Genetic association analysis on complex phenotypes under a longitudinal design involving pedigrees encounters the problem of correlation within pedigrees which could affect statistical assessment of the genetic effects on both the mean level of the phenotype and its rate of change over the time...

A hybrid correlation analysis with application to imaging genetics

Science.gov (United States)

Hu, Wenxing; Fang, Jian; Calhoun, Vince D.; Wang, Yu-Ping

2018-03-01

Investigating the association between brain regions and genes continues to be a challenging topic in imaging genetics. Current brain region of interest (ROI)-gene association studies normally reduce data dimension by averaging the value of voxels in each ROI. This averaging may lead to a loss of information due to the existence of functional sub-regions. Pearson correlation is widely used for association analysis. However, it only detects linear correlation whereas nonlinear correlation may exist among ROIs. In this work, we introduced distance correlation to ROI-gene association analysis, which can detect both linear and nonlinear correlations and overcome the limitation of averaging operations by taking advantage of the information at each voxel. Nevertheless, distance correlation usually has a much lower value than Pearson correlation. To address this problem, we proposed a hybrid correlation analysis approach, by applying canonical correlation analysis (CCA) to the distance covariance matrix instead of directly computing distance correlation. Incorporating CCA into distance correlation approach may be more suitable for complex disease study because it can detect highly associated pairs of ROI and gene groups, and may improve the distance correlation level and statistical power. In addition, we developed a novel nonlinear CCA, called distance kernel CCA, which seeks the optimal combination of features with the most significant dependence. This approach was applied to imaging genetic data from the Philadelphia Neurodevelopmental Cohort (PNC). Experiments showed that our hybrid approach produced more consistent results than conventional CCA across resampling and both the correlation and statistical significance were increased compared to distance correlation analysis. Further gene enrichment analysis and region of interest (ROI) analysis confirmed the associations of the identified genes with brain ROIs. Therefore, our approach provides a powerful tool for finding

Mouse genetic approaches applied to the normal tissue radiation response

International Nuclear Information System (INIS)

Haston, Christina K.

2012-01-01

The varying responses of inbred mouse models to radiation exposure present a unique opportunity to dissect the genetic basis of radiation sensitivity and tissue injury. Such studies are complementary to human association studies as they permit both the analysis of clinical features of disease, and of specific variants associated with its presentation, in a controlled environment. Herein I review how animal models are studied to identify specific genetic variants influencing predisposition to radiation-induced traits. Among these radiation-induced responses are documented strain differences in repair of DNA damage and in extent of tissue injury (in the lung, skin, and intestine) which form the base for genetic investigations. For example, radiation-induced DNA damage is consistently greater in tissues from BALB/cJ mice, than the levels in C57BL/6J mice, suggesting there may be an inherent DNA damage level per strain. Regarding tissue injury, strain specific inflammatory and fibrotic phenotypes have been documented for principally, C57BL/6 C3H and A/J mice but a correlation among responses such that knowledge of the radiation injury in one tissue informs of the response in another is not evident. Strategies to identify genetic differences contributing to a trait based on inbred strain differences, which include linkage analysis and the evaluation of recombinant congenic (RC) strains, are presented, with a focus on the lung response to irradiation which is the only radiation-induced tissue injury mapped to date. Such approaches are needed to reveal genetic differences in susceptibility to radiation injury, and also to provide a context for the effects of specific genetic variation uncovered in anticipated clinical association studies. In summary, mouse models can be studied to uncover heritable variation predisposing to specific radiation responses, and such variations may point to pathways of importance to phenotype development in the clinic.

The Analysis of Polyploid Genetic Data

NARCIS (Netherlands)

Meirmans, P.G.; Liu, S.; van Tienderen, P.H.

2018-01-01

Though polyploidy is an important aspect of the evolutionary genetics of both plants and animals, the development of population genetic theory of polyploids has seriously lagged behind that of diploids. This is unfortunate since the analysis of polyploid genetic data—and the interpretation of the

Genetic Diversity Analysis of Iranian Jujube Ecotypes (Ziziphus spp. Using RAPD Molecular Marker

Directory of Open Access Journals (Sweden)

S Abbasi

2012-12-01

Full Text Available Jujube (Ziziphus jujuba Mill. is a valuable medicinal plant which is important in Iranian traditional medicines. Although the regional plants such as jujube play an important role in our economy, but they are forgotten in research and technology. Considering the economic and medicinal importance of jujube, the first step in breeding programs is determination of the genetic diversity among the individuals. 34 ecotypes of jujube, which have been collected from eight provinces of Iran, were used in this study. The genetic relationships of Iranian jujube ecotypes were analyzed using Random Amplified Polymorphic DNA (RAPD marker. Six out of 15 random decamer primers applied for RAPD analysis, showed an informative polymorphism. According to clustering analysis using UPGMA's methods, the ecotypes were classified into two major groups at the 0.81 level of genetic similarity. The highest value of similarity coefficient (0.92 was detected between Mazandaran and Golestan ecotypes and the most genetic diversity was observed in ecotypes of Khorasan-Jonoubi. The affinity of Khorasan-Jonoubi and Esfahan ecotypes indicated a possible common origin for the variation in these areas. Results indicated that RAPD analysis could be successfully used for the estimation of genetic diversity among Ziziphus ecotypes and it can be useful for further investigations.

Genotyping-By-Sequencing for Plant Genetic Diversity Analysis: A Lab Guide for SNP Genotyping

Directory of Open Access Journals (Sweden)

Gregory W. Peterson

2014-10-01

Full Text Available Genotyping-by-sequencing (GBS has recently emerged as a promising genomic approach for exploring plant genetic diversity on a genome-wide scale. However, many uncertainties and challenges remain in the application of GBS, particularly in non-model species. Here, we present a GBS protocol we developed and use for plant genetic diversity analysis. It uses two restriction enzymes to reduce genome complexity, applies Illumina multiplexing indexes for barcoding and has a custom bioinformatics pipeline for genotyping. This genetic diversity-focused GBS (gd-GBS protocol can serve as an easy-to-follow lab guide to assist a researcher through every step of a GBS application with five main components: sample preparation, library assembly, sequencing, SNP calling and diversity analysis. Specifically, in this presentation, we provide a brief overview of the GBS approach, describe the gd-GBS procedures, illustrate it with an application to analyze genetic diversity in 20 flax (Linum usitatissimum L. accessions and discuss related issues in GBS application. Following these lab bench procedures and using the custom bioinformatics pipeline, one could generate genome-wide SNP genotype data for a conventional genetic diversity analysis of a non-model plant species.

An analysis of the genetic diversity and genetic structure of ...

African Journals Online (AJOL)

Scientific approaches to conservation of threatened species depend on a good understanding of the genetic information of wild and artificial population. The genetic diversity and structure analysis of 10 Eucommia ulmoides population was analyzed using inter-simple sequence repeat (ISSR) markers in this paper.

The Analysis of Polyploid Genetic Data.

Science.gov (United States)

Meirmans, Patrick G; Liu, Shenglin; van Tienderen, Peter H

2018-03-16

Though polyploidy is an important aspect of the evolutionary genetics of both plants and animals, the development of population genetic theory of polyploids has seriously lagged behind that of diploids. This is unfortunate since the analysis of polyploid genetic data-and the interpretation of the results-requires even more scrutiny than with diploid data. This is because of several polyploidy-specific complications in segregation and genotyping such as tetrasomy, double reduction, and missing dosage information. Here, we review the theoretical and statistical aspects of the population genetics of polyploids. We discuss several widely used types of inferences, including genetic diversity, Hardy-Weinberg equilibrium, population differentiation, genetic distance, and detecting population structure. For each, we point out how the statistical approach, expected result, and interpretation differ between different ploidy levels. We also discuss for each type of inference what biases may arise from the polyploid-specific complications and how these biases can be overcome. From our overview, it is clear that the statistical toolbox that is available for the analysis of genetic data is flexible and still expanding. Modern sequencing techniques will soon be able to overcome some of the current limitations to the analysis of polyploid data, though the techniques are lagging behind those available for diploids. Furthermore, the availability of more data may aggravate the biases that can arise, and increase the risk of false inferences. Therefore, simulations such as we used throughout this review are an important tool to verify the results of analyses of polyploid genetic data.

COMPUTER METHODS OF GENETIC ANALYSIS.

Directory of Open Access Journals (Sweden)

A. L. Osipov

2017-02-01

Full Text Available The basic statistical methods used in conducting the genetic analysis of human traits. We studied by segregation analysis, linkage analysis and allelic associations. Developed software for the implementation of these methods support.

Genetic analysis in Bartter syndrome from India.

Science.gov (United States)

Sharma, Pradeep Kumar; Saikia, Bhaskar; Sharma, Rachna; Ankur, Kumar; Khilnani, Praveen; Aggarwal, Vinay Kumar; Cheong, Hae

2014-10-01

Bartter syndrome is a group of inherited, salt-losing tubulopathies presenting as hypokalemic metabolic alkalosis with normotensive hyperreninemia and hyperaldosteronism. Around 150 cases have been reported in literature till now. Mutations leading to salt losing tubulopathies are not routinely tested in Indian population. The authors have done the genetic analysis for the first time in the Bartter syndrome on two cases from India. First case was antenatal Bartter syndrome presenting with massive polyuria and hyperkalemia. Mutational analysis revealed compound heterozygous mutations in KCNJ1(ROMK) gene [p(Leu220Phe), p(Thr191Pro)]. Second case had a phenotypic presentation of classical Bartter syndrome however, genetic analysis revealed only heterozygous novel mutation in SLC12A gene p(Ala232Thr). Bartter syndrome is a clinical diagnosis and genetic analysis is recommended for prognostication and genetic counseling.

The Information Content of Discrete Functions and Their Application in Genetic Data Analysis.

Science.gov (United States)

Sakhanenko, Nikita A; Kunert-Graf, James; Galas, David J

2017-12-01

The complex of central problems in data analysis consists of three components: (1) detecting the dependence of variables using quantitative measures, (2) defining the significance of these dependence measures, and (3) inferring the functional relationships among dependent variables. We have argued previously that an information theory approach allows separation of the detection problem from the inference of functional form problem. We approach here the third component of inferring functional forms based on information encoded in the functions. We present here a direct method for classifying the functional forms of discrete functions of three variables represented in data sets. Discrete variables are frequently encountered in data analysis, both as the result of inherently categorical variables and from the binning of continuous numerical variables into discrete alphabets of values. The fundamental question of how much information is contained in a given function is answered for these discrete functions, and their surprisingly complex relationships are illustrated. The all-important effect of noise on the inference of function classes is found to be highly heterogeneous and reveals some unexpected patterns. We apply this classification approach to an important area of biological data analysis-that of inference of genetic interactions. Genetic analysis provides a rich source of real and complex biological data analysis problems, and our general methods provide an analytical basis and tools for characterizing genetic problems and for analyzing genetic data. We illustrate the functional description and the classes of a number of common genetic interaction modes and also show how different modes vary widely in their sensitivity to noise.

Handbook of Applied Analysis

CERN Document Server

Papageorgiou, Nikolaos S

2009-01-01

Offers an examination of important theoretical methods and procedures in applied analysis. This book details the important theoretical trends in nonlinear analysis and applications to different fields. It is suitable for those working on nonlinear analysis.

Genetic algorithms and supernovae type Ia analysis

International Nuclear Information System (INIS)

Bogdanos, Charalampos; Nesseris, Savvas

2009-01-01

We introduce genetic algorithms as a means to analyze supernovae type Ia data and extract model-independent constraints on the evolution of the Dark Energy equation of state w(z) ≡ P DE /ρ DE . Specifically, we will give a brief introduction to the genetic algorithms along with some simple examples to illustrate their advantages and finally we will apply them to the supernovae type Ia data. We find that genetic algorithms can lead to results in line with already established parametric and non-parametric reconstruction methods and could be used as a complementary way of treating SNIa data. As a non-parametric method, genetic algorithms provide a model-independent way to analyze data and can minimize bias due to premature choice of a dark energy model

Applied longitudinal analysis

CERN Document Server

Fitzmaurice, Garrett M; Ware, James H

2012-01-01

Praise for the First Edition "". . . [this book] should be on the shelf of everyone interested in . . . longitudinal data analysis.""-Journal of the American Statistical Association   Features newly developed topics and applications of the analysis of longitudinal data Applied Longitudinal Analysis, Second Edition presents modern methods for analyzing data from longitudinal studies and now features the latest state-of-the-art techniques. The book emphasizes practical, rather than theoretical, aspects of methods for the analysis of diverse types of lo

Genetic and bioinformatic analysis of 41C and the 2R heterochromatin of Drosophila melanogaster: a window on the heterochromatin-euchromatin junction.

OpenAIRE

Myster, Steven H; Wang, Fei; Cavallo, Robert; Christian, Whitney; Bhotika, Seema; Anderson, Charles T; Peifer, Mark

2004-01-01

Genomic sequences provide powerful new tools in genetic analysis, making it possible to combine classical genetics with genomics to characterize the genes in a particular chromosome region. These approaches have been applied successfully to the euchromatin, but analysis of the heterochromatin has lagged somewhat behind. We describe a combined genetic and bioinformatics approach to the base of the right arm of the Drosophila melanogaster second chromosome, at the boundary between pericentric h...

Rapid Genetic Analysis in Congenital Hyperinsulinism

DEFF Research Database (Denmark)

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

2007-01-01

BACKGROUND: In severe, medically unresponsive congenital hyperinsulinism (CHI), the histological differentiation of focal versus diffuse disease is vital, since the surgical management is completely different. Genetic analysis may help in the differential diagnosis, as focal CHI is associated...... with a paternal germline ABCC8 or KCNJ11 mutation and a focal loss of maternal chromosome 11p15, whereas a maternal mutation, or homozygous/compound heterozygous ABCC8 and KCNJ11 mutations predict diffuse-type disease. However, genotyping usually takes too long to be helpful in the absence of a founder mutation....... 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...

Genetic algorithms and the analysis of SnIa data

International Nuclear Information System (INIS)

Nesseris, Savvas

2011-01-01

The Genetic Algorithm is a heuristic that can be used to produce model independent solutions to an optimization problem, thus making it ideal for use in cosmology and more specifically in the analysis of type Ia supernovae data. In this work we use the Genetic Algorithms (GA) in order to derive a null test on the spatially flat cosmological constant model ΛCDM. This is done in two steps: first, we apply the GA to the Constitution SNIa data in order to acquire a model independent reconstruction of the expansion history of the Universe H(z) and second, we use the reconstructed H(z) in conjunction with the Om statistic, which is constant only for the ΛCDM model, to derive our constraints. We find that while ΛCDM is consistent with the data at the 2σ level, some deviations from ΛCDM model at low redshifts can be accommodated.

Applying genetics in inflammatory disease drug discovery

DEFF Research Database (Denmark)

Folkersen, Lasse; Biswas, Shameek; Frederiksen, Klaus Stensgaard

2015-01-01

, with several notable exceptions, the journey from a small-effect genetic variant to a functional drug has proven arduous, and few examples of actual contributions to drug discovery exist. Here, we discuss novel approaches of overcoming this hurdle by using instead public genetics resources as a pragmatic guide...... alongside existing drug discovery methods. Our aim is to evaluate human genetic confidence as a rationale for drug target selection....

Bayesian analysis of genetic association across tree-structured routine healthcare data in the UK Biobank

DEFF Research Database (Denmark)

Cortes, Adrian; Dendrou, Calliope A; Motyer, Allan

2017-01-01

Genetic discovery from the multitude of phenotypes extractable from routine healthcare data can transform understanding of the human phenome and accelerate progress toward precision medicine. However, a critical question when analyzing high-dimensional and heterogeneous data is how best...... to interrogate increasingly specific subphenotypes while retaining statistical power to detect genetic associations. Here we develop and employ a new Bayesian analysis framework that exploits the hierarchical structure of diagnosis classifications to analyze genetic variants against UK Biobank disease phenotypes...... derived from self-reporting and hospital episode statistics. Our method displays a more than 20% increase in power to detect genetic effects over other approaches and identifies new associations between classical human leukocyte antigen (HLA) alleles and common immune-mediated diseases (IMDs). By applying...

A Review of Pathway-Based Analysis Tools That Visualize Genetic Variants

Directory of Open Access Journals (Sweden)

Elisa Cirillo

2017-11-01

Full Text Available Pathway analysis is a powerful method for data analysis in genomics, most often applied to gene expression analysis. It is also promising for single-nucleotide polymorphism (SNP data analysis, such as genome-wide association study data, because it allows the interpretation of variants with respect to the biological processes in which the affected genes and proteins are involved. Such analyses support an interactive evaluation of the possible effects of variations on function, regulation or interaction of gene products. Current pathway analysis software often does not support data visualization of variants in pathways as an alternate method to interpret genetic association results, and specific statistical methods for pathway analysis of SNP data are not combined with these visualization features. In this review, we first describe the visualization options of the tools that were identified by a literature review, in order to provide insight for improvements in this developing field. Tool evaluation was performed using a computational epistatic dataset of gene–gene interactions for obesity risk. Next, we report the necessity to include in these tools statistical methods designed for the pathway-based analysis with SNP data, expressly aiming to define features for more comprehensive pathway-based analysis tools. We conclude by recognizing that pathway analysis of genetic variations data requires a sophisticated combination of the most useful and informative visual aspects of the various tools evaluated.

Bayesian analysis of genetic association across tree-structured routine healthcare data in the UK Biobank.

Science.gov (United States)

Cortes, Adrian; Dendrou, Calliope A; Motyer, Allan; Jostins, Luke; Vukcevic, Damjan; Dilthey, Alexander; Donnelly, Peter; Leslie, Stephen; Fugger, Lars; McVean, Gil

2017-09-01

Genetic discovery from the multitude of phenotypes extractable from routine healthcare data can transform understanding of the human phenome and accelerate progress toward precision medicine. However, a critical question when analyzing high-dimensional and heterogeneous data is how best to interrogate increasingly specific subphenotypes while retaining statistical power to detect genetic associations. Here we develop and employ a new Bayesian analysis framework that exploits the hierarchical structure of diagnosis classifications to analyze genetic variants against UK Biobank disease phenotypes derived from self-reporting and hospital episode statistics. Our method displays a more than 20% increase in power to detect genetic effects over other approaches and identifies new associations between classical human leukocyte antigen (HLA) alleles and common immune-mediated diseases (IMDs). By applying the approach to genetic risk scores (GRSs), we show the extent of genetic sharing among IMDs and expose differences in disease perception or diagnosis with potential clinical implications.

Applied reproductive technologies and genetic resource banking for amphibian conservation.

Science.gov (United States)

Kouba, Andrew J; Vance, Carrie K

2009-01-01

As amphibian populations continue to decline, both government and non-government organisations are establishing captive assurance colonies to secure populations deemed at risk of extinction if left in the wild. For the most part, little is known about the nutritional ecology, reproductive biology or husbandry needs of the animals placed into captive breeding programs. Because of this lack of knowledge, conservation biologists are currently facing the difficult task of maintaining and reproducing these species. Academic and zoo scientists are beginning to examine different technologies for maintaining the genetic diversity of founder populations brought out of the wild before the animals become extinct from rapidly spreading epizootic diseases. One such technology is genetic resource banking and applied reproductive technologies for species that are difficult to reproduce reliably in captivity. Significant advances have been made in the last decade for amphibian assisted reproduction including the use of exogenous hormones for induction of spermiation and ovulation, in vitro fertilisation, short-term cold storage of gametes and long-term cryopreservation of spermatozoa. These scientific breakthroughs for a select few species will no doubt serve as models for future assisted breeding protocols and the increasing number of amphibians requiring conservation intervention. However, the development of specialised assisted breeding protocols that can be applied to many different families of amphibians will likely require species-specific modifications considering their wide range of reproductive modes. The purpose of this review is to summarise the current state of knowledge in the area of assisted reproduction technologies and gene banking for the conservation of amphibians.

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.

Smoking and caffeine consumption: a genetic analysis of their association.

Science.gov (United States)

Treur, Jorien L; Taylor, Amy E; Ware, Jennifer J; Nivard, Michel G; Neale, Michael C; McMahon, George; Hottenga, Jouke-Jan; Baselmans, Bart M L; Boomsma, Dorret I; Munafò, Marcus R; Vink, Jacqueline M

2017-07-01

Smoking and caffeine consumption show a strong positive correlation, but the mechanism underlying this association is unclear. Explanations include shared genetic/environmental factors or causal effects. This study employed three methods to investigate the association between smoking and caffeine. First, bivariate genetic models were applied to data of 10 368 twins from the Netherlands Twin Register in order to estimate genetic and environmental correlations between smoking and caffeine use. Second, from the summary statistics of meta-analyses of genome-wide association studies on smoking and caffeine, the genetic correlation was calculated by LD-score regression. Third, causal effects were tested using Mendelian randomization analysis in 6605 Netherlands Twin Register participants and 5714 women from the Avon Longitudinal Study of Parents and Children. Through twin modelling, a genetic correlation of r0.47 and an environmental correlation of r0.30 were estimated between current smoking (yes/no) and coffee use (high/low). Between current smoking and total caffeine use, this was r0.44 and r0.00, respectively. LD-score regression also indicated sizeable genetic correlations between smoking and coffee use (r0.44 between smoking heaviness and cups of coffee per day, r0.28 between smoking initiation and coffee use and r0.25 between smoking persistence and coffee use). Consistent with the relatively high genetic correlations and lower environmental correlations, Mendelian randomization provided no evidence for causal effects of smoking on caffeine or vice versa. Genetic factors thus explain most of the association between smoking and caffeine consumption. These findings suggest that quitting smoking may be more difficult for heavy caffeine consumers, given their genetic susceptibility. © 2016 The Authors.Addiction Biology published by John Wiley & Sons Ltd on behalf of Society for the Study of Addiction.

Analysis of genetic diversity inpigeonpeagermplasm using ...

Indian Academy of Sciences (India)

Navya

2016-11-25

Nov 25, 2016 ... accessions from Orissa (105) and AP (15) do not group with any Indian accessions. ... In the present work, comparison between SSAP and REMAP revealed ... (sequence-specific amplified polymorphism) for genetic analysis of sweet potato. ... Sharma,V.and Nandinemi, M.R. 2014 Assessment of genetic ...

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.

An efficient Bayesian meta-analysis approach for studying cross-phenotype genetic associations.

Directory of Open Access Journals (Sweden)

Arunabha Majumdar

2018-02-01

Full Text Available Simultaneous analysis of genetic associations with multiple phenotypes may reveal shared genetic susceptibility across traits (pleiotropy. For a locus exhibiting overall pleiotropy, it is important to identify which specific traits underlie this association. We propose a Bayesian meta-analysis approach (termed CPBayes that uses summary-level data across multiple phenotypes to simultaneously measure the evidence of aggregate-level pleiotropic association and estimate an optimal subset of traits associated with the risk locus. This method uses a unified Bayesian statistical framework based on a spike and slab prior. CPBayes performs a fully Bayesian analysis by employing the Markov Chain Monte Carlo (MCMC technique Gibbs sampling. It takes into account heterogeneity in the size and direction of the genetic effects across traits. It can be applied to both cohort data and separate studies of multiple traits having overlapping or non-overlapping subjects. Simulations show that CPBayes can produce higher accuracy in the selection of associated traits underlying a pleiotropic signal than the subset-based meta-analysis ASSET. We used CPBayes to undertake a genome-wide pleiotropic association study of 22 traits in the large Kaiser GERA cohort and detected six independent pleiotropic loci associated with at least two phenotypes. This includes a locus at chromosomal region 1q24.2 which exhibits an association simultaneously with the risk of five different diseases: Dermatophytosis, Hemorrhoids, Iron Deficiency, Osteoporosis and Peripheral Vascular Disease. We provide an R-package 'CPBayes' implementing the proposed method.

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...

Quantitative genetic analysis of total glucosinolate, oil and protein ...

African Journals Online (AJOL)

Quantitative genetic analysis of total glucosinolate, oil and protein contents in Ethiopian mustard ( Brassica carinata A. Braun) ... Seeds were analyzed using HPLC (glucosinolates), NMR (oil) and NIRS (protein). Analyses of variance, Hayman's method of diallel analysis and a mixed linear model of genetic analysis were ...

Pathway-based Analysis of the Hidden Genetic Heterogeneities in Cancers

Directory of Open Access Journals (Sweden)

Xiaolei Zhao

2014-02-01

Full Text Available Many cancers apparently showing similar phenotypes are actually distinct at the molecular level, leading to very different responses to the same treatment. It has been recently demonstrated that pathway-based approaches are robust and reliable for genetic analysis of cancers. Nevertheless, it remains unclear whether such function-based approaches are useful in deciphering molecular heterogeneities in cancers. Therefore, we aimed to test this possibility in the present study. First, we used a NCI60 dataset to validate the ability of pathways to correctly partition samples. Next, we applied the proposed method to identify the hidden subtypes in diffuse large B-cell lymphoma (DLBCL. Finally, the clinical significance of the identified subtypes was verified using survival analysis. For the NCI60 dataset, we achieved highly accurate partitions that best fit the clinical cancer phenotypes. Subsequently, for a DLBCL dataset, we identified three hidden subtypes that showed very different 10-year overall survival rates (90%, 46% and 20% and were highly significantly (P = 0.008 correlated with the clinical survival rate. This study demonstrated that the pathway-based approach is promising for unveiling genetic heterogeneities in complex human diseases.

Genetic variability of indigenous cowpea genotypes as determined ...

African Journals Online (AJOL)

Bayesian statistics coupled with the Markov chain Monte Carlo technique was applied to determine population structure, while the genetic variability was established by analysis of molecular variance. UPGMA analysis allowed the separation of the genotypes into three groups, but no relationship between the genetic and ...

A Multi-Marker Genetic Association Test Based on the Rasch Model Applied to Alzheimer's Disease.

Directory of Open Access Journals (Sweden)

Wenjia Wang

Full Text Available Results from Genome-Wide Association Studies (GWAS have shown that the genetic basis of complex traits often include many genetic variants with small to moderate effects whose identification remains a challenging problem. In this context multi-marker analysis at the gene and pathway level can complement traditional point-wise approaches that treat the genetic markers individually. In this paper we propose a novel statistical approach for multi-marker analysis based on the Rasch model. The method summarizes the categorical genotypes of SNPs by a generalized logistic function into a genetic score that can be used for association analysis. Through different sets of simulations, the false-positive rate and power of the proposed approach are compared to a set of existing methods, and shows good performances. The application of the Rasch model on Alzheimer's Disease (AD ADNI GWAS dataset also allows a coherent interpretation of the results. Our analysis supports the idea that APOE is a major susceptibility gene for AD. In the top genes selected by proposed method, several could be functionally linked to AD. In particular, a pathway analysis of these genes also highlights the metabolism of cholesterol, that is known to play a key role in AD pathogenesis. Interestingly, many of these top genes can be integrated in a hypothetic signalling network.

Genetic Analysis of Elevated Mastitis Risk Based on Mastitis Indicator Data

DEFF Research Database (Denmark)

Sørensen, Lars Peter; Løvendahl, Peter

Whole-genome sequences and multiple trait phenotypes from large numbers of individuals will soon be available. Well established statistical modeling approaches enable the genetic analyses of complex trait phenotypes while accounting for a variety of additive and non-additive genetic mechanisms....... These modeling approaches have proven to be highly useful to determine population genetic parameters as well as prediction of genetic risk or value. We present statistical modelling approaches that use prior biological information for evaluating the collective action of sets of genetic variants. We have applied...

Population genetic analysis and evidence of inter-specific introgression in Helichrysum armenium and H. rubicundum (Asteraceae

Directory of Open Access Journals (Sweden)

Taban Malahat

2015-01-01

Full Text Available Helichrysum armenium and H. rubicundum are two medicinally important plants of Iran that are distributed in various regions of the country. They are extensively used by locals as medicinal plants and a great negative selection pressure is applied on them. Therefore, due to importance of these plant species, we performed a population genetic study in both species. For this study, we used 66 randomly collected plants from 24 geographical populations of Helichrysum armenium and H. rubicundu. These species had areas of overlap and contact and we found some intermediate plants that were included in our study too. UPGMA and MDS analyses revealed morphological separation of these closely related species and placed intermediate plants in an intermediate position. ISSR analysis revealed inter-population genetic diversity and K-Means clustering and STRUCTURE analyses revealed populations. Genetic stratification in both species. Genetic difference of the studied populations was not correlated to geographical distance. Triangle plot of Bayesian analysis and NeighborNet plot showed inter-specific gene flow. The studied populations showed plants with 2n = 2x = 14 and 2n = 4x = 28 chromosomes and differed significantly in their meiotic behavior. Therefore, a combination of genetic stratification, and genetic admixture as well as polyploidy and chromosomes structural changes, have played rule in Helichrysum diversification.

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....... The Bayesian method is able to include prior information on both concordance rates and prevalence rates at the same time and is illustrated using twin data on cleft lip and rheumatoid arthritis....

Developments in statistical analysis in quantitative genetics

DEFF Research Database (Denmark)

Sorensen, Daniel

2009-01-01

of genetic means and variances, models for the analysis of categorical and count data, the statistical genetics of a model postulating that environmental variance is partly under genetic control, and a short discussion of models that incorporate massive genetic marker information. We provide an overview......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 by Markov chain Monte Carlo (McMC). In this overview a number of specific areas are chosen to illustrate the enormous flexibility that McMC has provided for fitting models and exploring features of data that were previously inaccessible. The selected areas are inferences of the trajectories over time...

Applied Behavior Analysis

Science.gov (United States)

Szapacs, Cindy

2006-01-01

Teaching strategies that work for typically developing children often do not work for those diagnosed with an autism spectrum disorder. However, teaching strategies that work for children with autism do work for typically developing children. In this article, the author explains how the principles and concepts of Applied Behavior Analysis can be…

[Using value of information analysis in decision making about applied research. The case of genetic screening for hemochromatosis in Germany].

Science.gov (United States)

Rogowski, W H; Grosse, S D; Meyer, E; John, J; Palmer, S

2012-05-01

Public decision makers face demands to invest in applied research in order to accelerate the adoption of new genetic tests. However, such an investment is profitable only if the results gained from further investigations have a significant impact on health care practice. An upper limit for the value of additional information aimed at improving the basis for reimbursement decisions is given by the expected value of perfect information (EVPI). This study illustrates the significance of the concept of EVPI on the basis of a probabilistic cost-effectiveness model of screening for hereditary hemochromatosis among German men. In the present example, population-based screening can barely be recommended at threshold values of 50,000 or 100,000 Euro per life year gained and also the value of additional research which might cause this decision to be overturned is small: At the mentioned threshold values, the EVPI in the German public health care system was ca. 500,000 and 2,200,000 Euro, respectively. An analysis of EVPI by individual parameters or groups of parameters shows that additional research about adherence to preventive phlebotomy could potentially provide the highest benefit. The potential value of further research also depends on methodological assumptions regarding the decision maker's time horizon as well as on scenarios with an impact on the number of affected patients and the cost-effectiveness of screening.

Applying ecological models to communities of genetic elements: the case of neutral theory.

Science.gov (United States)

Linquist, Stefan; Cottenie, Karl; Elliott, Tyler A; Saylor, Brent; Kremer, Stefan C; Gregory, T Ryan

2015-07-01

A promising recent development in molecular biology involves viewing the genome as a mini-ecosystem, where genetic elements are compared to organisms and the surrounding cellular and genomic structures are regarded as the local environment. Here, we critically evaluate the prospects of ecological neutral theory (ENT), a popular model in ecology, as it applies at the genomic level. This assessment requires an overview of the controversy surrounding neutral models in community ecology. In particular, we discuss the limitations of using ENT both as an explanation of community dynamics and as a null hypothesis. We then analyse a case study in which ENT has been applied to genomic data. Our central finding is that genetic elements do not conform to the requirements of ENT once its assumptions and limitations are made explicit. We further compare this genome-level application of ENT to two other, more familiar approaches in genomics that rely on neutral mechanisms: Kimura's molecular neutral theory and Lynch's mutational-hazard model. Interestingly, this comparison reveals that there are two distinct concepts of neutrality associated with these models, which we dub 'fitness neutrality' and 'competitive neutrality'. This distinction helps to clarify the various roles for neutral models in genomics, for example in explaining the evolution of genome size. © 2015 John Wiley & Sons Ltd.

Applied analysis and differential equations

CERN Document Server

Cârj, Ovidiu

2007-01-01

This volume contains refereed research articles written by experts in the field of applied analysis, differential equations and related topics. Well-known leading mathematicians worldwide and prominent young scientists cover a diverse range of topics, including the most exciting recent developments. A broad range of topics of recent interest are treated: existence, uniqueness, viability, asymptotic stability, viscosity solutions, controllability and numerical analysis for ODE, PDE and stochastic equations. The scope of the book is wide, ranging from pure mathematics to various applied fields such as classical mechanics, biomedicine, and population dynamics.

Social network analysis applied to team sports analysis

CERN Document Server

Clemente, Filipe Manuel; Mendes, Rui Sousa

2016-01-01

Explaining how graph theory and social network analysis can be applied to team sports analysis, This book presents useful approaches, models and methods that can be used to characterise the overall properties of team networks and identify the prominence of each team player. Exploring the different possible network metrics that can be utilised in sports analysis, their possible applications and variances from situation to situation, the respective chapters present an array of illustrative case studies. Identifying the general concepts of social network analysis and network centrality metrics, readers are shown how to generate a methodological protocol for data collection. As such, the book provides a valuable resource for students of the sport sciences, sports engineering, applied computation and the social sciences.

Dielectrophoretic capture and genetic analysis of single neuroblastoma tumor cells

Directory of Open Access Journals (Sweden)

Erica L Carpenter

2014-07-01

Full Text Available Our understanding of the diversity of cells that escape the primary tumor and seed micrometastases remains rudimentary, and approaches for studying circulating and disseminated tumor cells have been limited by low throughput and sensitivity, reliance on single parameter sorting, and a focus on enumeration rather than phenotypic and genetic characterization. Here we utilize a highly sensitive microfluidic and dielectrophoretic approach for the isolation and genetic analysis of individual tumor cells. We employed fluorescence labeling to isolate 208 single cells from spiking experiments conducted with 11 cell lines, including 8 neuroblastoma cell lines, and achieved a capture sensitivity of 1 tumor cell per 106 white blood cells. Sample fixation or freezing had no detectable effect on cell capture. Point mutations were accurately detected in the whole genome amplification product of captured single tumor cells but not in negative control white blood cells. We applied this approach to capture 144 single tumor cells from 10 bone marrow samples from patients suffering from neuroblastoma. In this pediatric malignancy, high-risk patients often exhibit wide-spread hematogenous metastasis, but access to primary tumor can be difficult or impossible. Here we used flow-based sorting to pre-enrich samples with tumor involvement below 0.02%. For all patients for whom a mutation in the Anaplastic Lymphoma Kinase gene had already been detected in their primary tumor, the same mutation was detected in single cells from their marrow. These findings demonstrate a novel, non-invasive, and adaptable method for the capture and genetic analysis of single tumor cells from cancer patients.

Genetic analysis of growth traits in Iranian Makuie sheep breed

Directory of Open Access Journals (Sweden)

Mohammad Farhadian

2012-01-01

Full Text Available The Makuie sheep is a fat-tailed sheep breed which can be found in the Azerbaijan province of Iran. In 1986, a Makuie sheep breeding station was established in the city of Maku in order to breed, protect and purify this breed. The genetic parameters for birth weight, weaning weight (3 months, 6-month, 9-month and yearling weight, and average daily gain from birth to weaning traits were estimated based on 25 years of data using DFREML software. Six different models were applied and a likelihood ratio test (LRT was used to select the appropriate model. Bivariate analysis was used to define the genetic correlation between studied traits. Based on the LRT, model II was selected as an appropriate model for all studied traits. Direct heritability estimates of birth, weaning, 6-month, 9-month and yearling weights and average daily gain from birth to weaning were 0.36, 0.41, 0.48, 0.42, 0.36 and 0.37, respectively. Estimates of direct genetic correlation between birth and weaning weights, birth and 6-month weights, birth and 9-month weights, as well as between birth and yearling weights were 0.57, 0.49, 0.46 and 0.32, respectively. The results suggest there is a substantial additive genetic variability for studied traits in the Makuie sheep breed population, and the direct additive effect and maternal permanent environment variance are the main source of phenotypic variance.

Analysis of genetic structure and relationship among nine ...

Indian Academy of Sciences (India)

These results indicated that the clustering analysis using the Structure program might provide an ..... of the current genetic relations among the breeds, and con- tribute to ... sis of the genetic structure of the Canary goat populations using.

A comparative analysis of three metaheuristic methods applied to fuzzy cognitive maps learning

Directory of Open Access Journals (Sweden)

Bruno A. Angélico

2013-12-01

Full Text Available This work analyses the performance of three different population-based metaheuristic approaches applied to Fuzzy cognitive maps (FCM learning in qualitative control of processes. Fuzzy cognitive maps permit to include the previous specialist knowledge in the control rule. Particularly, Particle Swarm Optimization (PSO, Genetic Algorithm (GA and an Ant Colony Optimization (ACO are considered for obtaining appropriate weight matrices for learning the FCM. A statistical convergence analysis within 10000 simulations of each algorithm is presented. In order to validate the proposed approach, two industrial control process problems previously described in the literature are considered in this work.

Genetic Algorithms for Agent-Based Infrastructure Interdependency Modeling and Analysis

Energy Technology Data Exchange (ETDEWEB)

May Permann

2007-03-01

Today’s society relies greatly upon an array of complex national and international infrastructure networks such as transportation, electric power, telecommunication, and financial networks. This paper describes initial research combining agent-based infrastructure modeling software and genetic algorithms (GAs) to help optimize infrastructure protection and restoration decisions. This research proposes to apply GAs to the problem of infrastructure modeling and analysis in order to determine the optimum assets to restore or protect from attack or other disaster. This research is just commencing and therefore the focus of this paper is the integration of a GA optimization method with a simulation through the simulation’s agents.

On the validity of within-nuclear-family genetic association analysis in samples of extended families.

Science.gov (United States)

Bureau, Alexandre; Duchesne, Thierry

2015-12-01

Splitting extended families into their component nuclear families to apply a genetic association method designed for nuclear families is a widespread practice in familial genetic studies. Dependence among genotypes and phenotypes of nuclear families from the same extended family arises because of genetic linkage of the tested marker with a risk variant or because of familial specificity of genetic effects due to gene-environment interaction. This raises concerns about the validity of inference conducted under the assumption of independence of the nuclear families. We indeed prove theoretically that, in a conditional logistic regression analysis applicable to disease cases and their genotyped parents, the naive model-based estimator of the variance of the coefficient estimates underestimates the true variance. However, simulations with realistic effect sizes of risk variants and variation of this effect from family to family reveal that the underestimation is negligible. The simulations also show the greater efficiency of the model-based variance estimator compared to a robust empirical estimator. Our recommendation is therefore, to use the model-based estimator of variance for inference on effects of genetic variants.

A methodology for the geometric design of heat recovery steam generators applying genetic algorithms

International Nuclear Information System (INIS)

Durán, M. Dolores; Valdés, Manuel; Rovira, Antonio; Rincón, E.

2013-01-01

This paper shows how the geometric design of heat recovery steam generators (HRSG) can be achieved. The method calculates the product of the overall heat transfer coefficient (U) by the area of the heat exchange surface (A) as a function of certain thermodynamic design parameters of the HRSG. A genetic algorithm is then applied to determine the best set of geometric parameters which comply with the desired UA product and, at the same time, result in a small heat exchange area and low pressure losses in the HRSG. In order to test this method, the design was applied to the HRSG of an existing plant and the results obtained were compared with the real exchange area of the steam generator. The findings show that the methodology is sound and offers reliable results even for complex HRSG designs. -- Highlights: ► The paper shows a methodology for the geometric design of heat recovery steam generators. ► Calculates product of the overall heat transfer coefficient by heat exchange area as a function of certain HRSG thermodynamic design parameters. ► It is a complement for the thermoeconomic optimization method. ► Genetic algorithms are used for solving the optimization problem

Going Forward with Genetics: Recent Technological Advances and Forward Genetics in Mice

OpenAIRE

Moresco, Eva Marie Y.; Li, Xiaohong; Beutler, Bruce

2013-01-01

Forward genetic analysis is an unbiased approach for identifying genes essential to defined biological phenomena. When applied to mice, it is one of the most powerful methods to facilitate understanding of the genetic basis of human biology and disease. The speed at which disease-causing mutations can be identified in mutagenized mice has been markedly increased by recent advances in DNA sequencing technology. Creating and analyzing mutant phenotypes may therefore become rate-limiting in forw...

Timing Analysis of Genetic Logic Circuits using D-VASim

DEFF Research Database (Denmark)

Baig, Hasan; Madsen, Jan

and propagation delay analysis of single as well as cascaded geneticlogic circuits can be performed. D-VASim allows user to change the circuit parameters during runtime simulation to observe its effectson circuit’s timing behavior. The results obtained from D-VASim can be used not only to characterize the timing...... delay analysis may play a very significant role in the designing of genetic logic circuits. In thisdemonstration, we present the capability of D-VASim (Dynamic Virtual Analyzer and Simulator) to perform the timing and propagationdelay analysis of genetic logic circuits. Using D-VASim, the timing...... behavior of geneticlogic circuits but also to analyze the timing constraints of cascaded genetic logic circuits....

Genetic analysis of Mexican Criollo cattle populations.

Science.gov (United States)

Ulloa-Arvizu, R; Gayosso-Vázquez, A; Ramos-Kuri, M; Estrada, F J; Montaño, M; Alonso, R A

2008-10-01

The objective of this study was to evaluate the genetic structure of Mexican Criollo cattle populations using microsatellite genetic markers. DNA samples were collected from 168 animals from four Mexican Criollo cattle populations, geographically isolated in remote areas of Sierra Madre Occidental (West Highlands). Also were included samples from two breeds with Iberian origin: the fighting bull (n = 24) and the milking central American Criollo (n = 24) and one Asiatic breed: Guzerat (n = 32). Genetic analysis consisted of the estimation of the genetic diversity in each population by the allele number and the average expected heterozygosity found in nine microsatellite loci. Furthermore, genetic relationships among the populations were defined by their genetic distances. Our data shows that Mexican cattle populations have a relatively high level of genetic diversity based either on the mean number of alleles (10.2-13.6) and on the expected heterozygosity (0.71-0.85). The degree of observed homozygosity within the Criollo populations was remarkable and probably caused by inbreeding (reduced effective population size) possibly due to reproductive structure within populations. Our data shows that considerable genetic differentiation has been occurred among the Criollo cattle populations in different regions of Mexico.

MEGA-CC: computing core of molecular evolutionary genetics analysis program for automated and iterative data analysis.

Science.gov (United States)

Kumar, Sudhir; Stecher, Glen; Peterson, Daniel; Tamura, Koichiro

2012-10-15

There is a growing need in the research community to apply the molecular evolutionary genetics analysis (MEGA) software tool for batch processing a large number of datasets and to integrate it into analysis workflows. Therefore, we now make available the computing core of the MEGA software as a stand-alone executable (MEGA-CC), along with an analysis prototyper (MEGA-Proto). MEGA-CC provides users with access to all the computational analyses available through MEGA's graphical user interface version. This includes methods for multiple sequence alignment, substitution model selection, evolutionary distance estimation, phylogeny inference, substitution rate and pattern estimation, tests of natural selection and ancestral sequence inference. Additionally, we have upgraded the source code for phylogenetic analysis using the maximum likelihood methods for parallel execution on multiple processors and cores. Here, we describe MEGA-CC and outline the steps for using MEGA-CC in tandem with MEGA-Proto for iterative and automated data analysis. http://www.megasoftware.net/.

Applied survival analysis using R

CERN Document Server

Moore, Dirk F

2016-01-01

Applied Survival Analysis Using R covers the main principles of survival analysis, gives examples of how it is applied, and teaches how to put those principles to use to analyze data using R as a vehicle. Survival data, where the primary outcome is time to a specific event, arise in many areas of biomedical research, including clinical trials, epidemiological studies, and studies of animals. Many survival methods are extensions of techniques used in linear regression and categorical data, while other aspects of this field are unique to survival data. This text employs numerous actual examples to illustrate survival curve estimation, comparison of survivals of different groups, proper accounting for censoring and truncation, model variable selection, and residual analysis. Because explaining survival analysis requires more advanced mathematics than many other statistical topics, this book is organized with basic concepts and most frequently used procedures covered in earlier chapters, with more advanced topics...

Extracting quantum dynamics from genetic learning algorithms through principal control analysis

International Nuclear Information System (INIS)

White, J L; Pearson, B J; Bucksbaum, P H

2004-01-01

Genetic learning algorithms are widely used to control ultrafast optical pulse shapes for photo-induced quantum control of atoms and molecules. An unresolved issue is how to use the solutions found by these algorithms to learn about the system's quantum dynamics. We propose a simple method based on covariance analysis of the control space, which can reveal the degrees of freedom in the effective control Hamiltonian. We have applied this technique to stimulated Raman scattering in liquid methanol. A simple model of two-mode stimulated Raman scattering is consistent with the results. (letter to the editor)

Applied regression analysis a research tool

CERN Document Server

Pantula, Sastry; Dickey, David

1998-01-01

Least squares estimation, when used appropriately, is a powerful research tool. A deeper understanding of the regression concepts is essential for achieving optimal benefits from a least squares analysis. This book builds on the fundamentals of statistical methods and provides appropriate concepts that will allow a scientist to use least squares as an effective research tool. Applied Regression Analysis is aimed at the scientist who wishes to gain a working knowledge of regression analysis. The basic purpose of this book is to develop an understanding of least squares and related statistical methods without becoming excessively mathematical. It is the outgrowth of more than 30 years of consulting experience with scientists and many years of teaching an applied regression course to graduate students. Applied Regression Analysis serves as an excellent text for a service course on regression for non-statisticians and as a reference for researchers. It also provides a bridge between a two-semester introduction to...

Applying theological developments to bioethical issues such as genetic screening.

Science.gov (United States)

Mallia, Pierre; ten Have, Henk

2005-01-01

Catholic movements within the centre of Roman Catholic doctrine recently have discussed Trinitarian theology as applied to sciences, arts, economics, health and other social areas. We explore the possibilities Trinitarian theology offers to bioethical debate, concentrating particularly on genetic screening and testing. It is important therefore to analyse the philosophical implications of this approach onto the bioethical world, where much disagreement occurs on fundamental issues. It is Catholic basic teaching to recognize and see God's hand in plurality, not merely as a cliche and then doing what we feel is right, but to recognize how to live in a pluralistic world. We recognize, in agreement with these theologians, that in order for a Trinitarian mode of understanding to be used by those doing bioethical debate, there is a need to depart from fundamentalism.

Genetic algorithms applied to nonlinear and complex domains

International Nuclear Information System (INIS)

Barash, D; Woodin, A E

1999-01-01

The dissertation, titled ''Genetic Algorithms Applied to Nonlinear and Complex Domains'', describes and then applies a new class of powerful search algorithms (GAS) to certain domains. GAS are capable of solving complex and nonlinear problems where many parameters interact to produce a ''final'' result such as the optimization of the laser pulse in the interaction of an atom with an intense laser field. GAS can very efficiently locate the global maximum by searching parameter space in problems which are unsuitable for a search using traditional methods. In particular, the dissertation contains new scientific findings in two areas. First, the dissertation examines the interaction of an ultra-intense short laser pulse with atoms. GAS are used to find the optimal frequency for stabilizing atoms in the ionization process. This leads to a new theoretical formulation, to explain what is happening during the ionization process and how the electron is responding to finite (real-life) laser pulse shapes. It is shown that the dynamics of the process can be very sensitive to the ramp of the pulse at high frequencies. The new theory which is formulated, also uses a novel concept (known as the (t,t') method) to numerically solve the time-dependent Schrodinger equation Second, the dissertation also examines the use of GAS in modeling decision making problems. It compares GAS with traditional techniques to solve a class of problems known as Markov Decision Processes. The conclusion of the dissertation should give a clear idea of where GAS are applicable, especially in the physical sciences, in problems which are nonlinear and complex, i.e. difficult to analyze by other means

Multivariate Methods for Meta-Analysis of Genetic Association Studies.

Science.gov (United States)

Dimou, Niki L; Pantavou, Katerina G; Braliou, Georgia G; Bagos, Pantelis G

2018-01-01

Multivariate meta-analysis of genetic association studies and genome-wide association studies has received a remarkable attention as it improves the precision of the analysis. Here, we review, summarize and present in a unified framework methods for multivariate meta-analysis of genetic association studies and genome-wide association studies. Starting with the statistical methods used for robust analysis and genetic model selection, we present in brief univariate methods for meta-analysis and we then scrutinize multivariate methodologies. Multivariate models of meta-analysis for a single gene-disease association studies, including models for haplotype association studies, multiple linked polymorphisms and multiple outcomes are discussed. The popular Mendelian randomization approach and special cases of meta-analysis addressing issues such as the assumption of the mode of inheritance, deviation from Hardy-Weinberg Equilibrium and gene-environment interactions are also presented. All available methods are enriched with practical applications and methodologies that could be developed in the future are discussed. Links for all available software implementing multivariate meta-analysis methods are also provided.

Conversation Analysis in Applied Linguistics

DEFF Research Database (Denmark)

Kasper, Gabriele; Wagner, Johannes

2014-01-01

on applied CA, the application of basic CA's principles, methods, and findings to the study of social domains and practices that are interactionally constituted. We consider three strands—foundational, social problem oriented, and institutional applied CA—before turning to recent developments in CA research...... on learning and development. In conclusion, we address some emerging themes in the relationship of CA and applied linguistics, including the role of multilingualism, standard social science methods as research objects, CA's potential for direct social intervention, and increasing efforts to complement CA......For the last decade, conversation analysis (CA) has increasingly contributed to several established fields in applied linguistics. In this article, we will discuss its methodological contributions. The article distinguishes between basic and applied CA. Basic CA is a sociological endeavor concerned...

RAPD-SCAR marker and genetic relationship analysis of three Demodex species (Acari: Demodicidae).

Science.gov (United States)

Zhao, Ya-E; Wu, Li-Ping

2012-06-01

For a long time, classification of Demodex mites has been mainly based on their hosts and phenotype characteristics. The study was the first to conduct molecular identification and genetic relationship analysis for six isolates of three Demodex species by random amplified polymorphic DNA (RAPD) and sequence-characterized amplified region (SCAR) marker. Totally, 239 DNA fragments were amplified from six Demodex isolates with 10 random primers in RAPD, of which 165 were polymorphic. Using a single primer, at least five fragments and at most 40 in the six isolates were amplified, whereas within a single isolate, a range of 35-49 fragments were amplified. DNA fingerprints of primers CZ 1-9 revealed intra- and interspecies difference in six Demodex isolates, whereas primer CZ 10 only revealed interspecies difference. The genetic distance and dendrogram showed the intraspecific genetic distances were closer than the interspecific genetic distances. The interspecific genetic distances of Demodex folliculorum and Demodex canis (0.7931-0.8140) were shorter than that of Demodex brevis and D. canis (0.8182-0.8987). The RAPD-SCAR marker displayed primer CZ 10 could be applied to identify the three Demodex species. The 479-bp fragment was specific for D. brevis, and the 261-bp fragment was specific for D. canis. The conclusion was that the RAPD-SCAR multi-marker was effective in molecular identification of three Demodex species. The genetic relationship between D. folliculorum and D. canis was nearer than that between D. folliculorum and D. brevis.

Analysis of genetic relationships of mulberry (Morus L.) germplasm ...

African Journals Online (AJOL)

STORAGESEVER

2009-06-03

Jun 3, 2009 ... Full Length Research Paper. Analysis of genetic ... Key words: Mulberry, molecular marker, genetic diversity, SRAP. ... Europe, North and South America, and Africa, and it is cultivated ... Xingjiang autonomous region, China.

A landscape genetic analysis of important agricultural pest species in Tunisia: The whitefly Bemisia tabaci.

Directory of Open Access Journals (Sweden)

Ahmed Ben Abdelkrim

Full Text Available Combining landscape ecology and genetics provides an excellent framework to appreciate pest population dynamics and dispersal. The genetic architectures of many species are always shaped by environmental constraints. Because little is known about the ecological and genetic traits of Tunisian whitefly populations, the main objective of this work is to highlight patterns of biodiversity, genetic structure and migration routes of this pest. We used nuclear microsatellite loci to analyze B. tabaci populations collected from various agricultural areas across the country and we determine their biotype status. Molecular data were subsequently interpreted in an ecological context supplied from a species distribution model to infer habitat suitability and hereafter the potential connection paths between sampling localities. An analysis of landscape resistance to B. tabaci genetic flow was thus applied to take into account habitat suitability, genetic relatedness and functional connectivity of habitats within a varied landscape matrix. We shed light on the occurrence of three geographically delineated genetic groups with high levels of genetic differentiation within each of them. Potential migration corridors of this pest were then established providing significant advances toward the understanding of genetic features and the dynamic dispersal of this pest. This study supports the hypothesis of a long-distance dispersal of B. tabaci followed by infrequent long-term isolations. The Inference of population sources and colonization routes is critical for the design and implementation of accurate management strategies against this pest.

A landscape genetic analysis of important agricultural pest species in Tunisia: The whitefly Bemisia tabaci.

Science.gov (United States)

Ben Abdelkrim, Ahmed; Hattab, Tarek; Fakhfakh, Hatem; Belkadhi, Mohamed Sadok; Gorsane, Faten

2017-01-01

Combining landscape ecology and genetics provides an excellent framework to appreciate pest population dynamics and dispersal. The genetic architectures of many species are always shaped by environmental constraints. Because little is known about the ecological and genetic traits of Tunisian whitefly populations, the main objective of this work is to highlight patterns of biodiversity, genetic structure and migration routes of this pest. We used nuclear microsatellite loci to analyze B. tabaci populations collected from various agricultural areas across the country and we determine their biotype status. Molecular data were subsequently interpreted in an ecological context supplied from a species distribution model to infer habitat suitability and hereafter the potential connection paths between sampling localities. An analysis of landscape resistance to B. tabaci genetic flow was thus applied to take into account habitat suitability, genetic relatedness and functional connectivity of habitats within a varied landscape matrix. We shed light on the occurrence of three geographically delineated genetic groups with high levels of genetic differentiation within each of them. Potential migration corridors of this pest were then established providing significant advances toward the understanding of genetic features and the dynamic dispersal of this pest. This study supports the hypothesis of a long-distance dispersal of B. tabaci followed by infrequent long-term isolations. The Inference of population sources and colonization routes is critical for the design and implementation of accurate management strategies against this pest.

Going forward with genetics: recent technological advances and forward genetics in mice.

Science.gov (United States)

Moresco, Eva Marie Y; Li, Xiaohong; Beutler, Bruce

2013-05-01

Forward genetic analysis is an unbiased approach for identifying genes essential to defined biological phenomena. When applied to mice, it is one of the most powerful methods to facilitate understanding of the genetic basis of human biology and disease. The speed at which disease-causing mutations can be identified in mutagenized mice has been markedly increased by recent advances in DNA sequencing technology. Creating and analyzing mutant phenotypes may therefore become rate-limiting in forward genetic experimentation. We review the forward genetic approach and its future in the context of recent technological advances, in particular massively parallel DNA sequencing, induced pluripotent stem cells, and haploid embryonic stem cells. Copyright © 2013 American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.

Genetic analysis of repeated, biparental, diploid, hydatidiform moles

DEFF Research Database (Denmark)

Sunde, Lone; Vejerslev, Lars O.; Jensen, Mie Poulsen

1993-01-01

for the abnormal development can be envisaged, environmental as well as genetic. To conform to current ideas of molar pathogenesis, it is suggested that the present conceptuses might have arisen from imbalances in imprinted genomic regions. This could be a consequence of uniparental disomy in critical regions......A woman presented with five consecutive pregnancies displaying molar morphology. In the fifth pregnancy, a non-malformed, liveborn infant was delivered. Genetic analyses (RFLP analysis, cytogenetics, flow cytometry) were performed in pregnancies II-V. It was demonstrated that these pregnancies...... originated in separate conceptions, all conceptuses were diploid, and all had maternally as well as paternally derived genetic markers. By cytogenetic analysis, aberrant heteromorphisms were noted; no other abnormalities were observed in chromosome structure or in DNA sequence. Many different causes...

Genetic diversity of popcorn genotypes using molecular analysis.

Science.gov (United States)

Resh, F S; Scapim, C A; Mangolin, C A; Machado, M F P S; do Amaral, A T; Ramos, H C C; Vivas, M

2015-08-19

In this study, we analyzed dominant molecular markers to estimate the genetic divergence of 26 popcorn genotypes and evaluate whether using various dissimilarity coefficients with these dominant markers influences the results of cluster analysis. Fifteen random amplification of polymorphic DNA primers produced 157 amplified fragments, of which 65 were monomorphic and 92 were polymorphic. To calculate the genetic distances among the 26 genotypes, the complements of the Jaccard, Dice, and Rogers and Tanimoto similarity coefficients were used. A matrix of Dij values (dissimilarity matrix) was constructed, from which the genetic distances among genotypes were represented in a more simplified manner as a dendrogram generated using the unweighted pair-group method with arithmetic average. Clusters determined by molecular analysis generally did not group material from the same parental origin together. The largest genetic distance was between varieties 17 (UNB-2) and 18 (PA-091). In the identification of genotypes with the smallest genetic distance, the 3 coefficients showed no agreement. The 3 dissimilarity coefficients showed no major differences among their grouping patterns because agreement in determining the genotypes with large, medium, and small genetic distances was high. The largest genetic distances were observed for the Rogers and Tanimoto dissimilarity coefficient (0.74), followed by the Jaccard coefficient (0.65) and the Dice coefficient (0.48). The 3 coefficients showed similar estimations for the cophenetic correlation coefficient. Correlations among the matrices generated using the 3 coefficients were positive and had high magnitudes, reflecting strong agreement among the results obtained using the 3 evaluated dissimilarity coefficients.

Concept analysis of culture applied to nursing.

Science.gov (United States)

Marzilli, Colleen

2014-01-01

Culture is an important concept, especially when applied to nursing. A concept analysis of culture is essential to understanding the meaning of the word. This article applies Rodgers' (2000) concept analysis template and provides a definition of the word culture as it applies to nursing practice. This article supplies examples of the concept of culture to aid the reader in understanding its application to nursing and includes a case study demonstrating components of culture that must be respected and included when providing health care.

Crossover versus Mutation: A Comparative Analysis of the Evolutionary Strategy of Genetic Algorithms Applied to Combinatorial Optimization Problems

Directory of Open Access Journals (Sweden)

E. Osaba

2014-01-01

Full Text Available Since their first formulation, genetic algorithms (GAs have been one of the most widely used techniques to solve combinatorial optimization problems. The basic structure of the GAs is known by the scientific community, and thanks to their easy application and good performance, GAs are the focus of a lot of research works annually. Although throughout history there have been many studies analyzing various concepts of GAs, in the literature there are few studies that analyze objectively the influence of using blind crossover operators for combinatorial optimization problems. For this reason, in this paper a deep study on the influence of using them is conducted. The study is based on a comparison of nine techniques applied to four well-known combinatorial optimization problems. Six of the techniques are GAs with different configurations, and the remaining three are evolutionary algorithms that focus exclusively on the mutation process. Finally, to perform a reliable comparison of these results, a statistical study of them is made, performing the normal distribution z-test.

Crossover versus Mutation: A Comparative Analysis of the Evolutionary Strategy of Genetic Algorithms Applied to Combinatorial Optimization Problems

Science.gov (United States)

Osaba, E.; Carballedo, R.; Diaz, F.; Onieva, E.; de la Iglesia, I.; Perallos, A.

2014-01-01

Since their first formulation, genetic algorithms (GAs) have been one of the most widely used techniques to solve combinatorial optimization problems. The basic structure of the GAs is known by the scientific community, and thanks to their easy application and good performance, GAs are the focus of a lot of research works annually. Although throughout history there have been many studies analyzing various concepts of GAs, in the literature there are few studies that analyze objectively the influence of using blind crossover operators for combinatorial optimization problems. For this reason, in this paper a deep study on the influence of using them is conducted. The study is based on a comparison of nine techniques applied to four well-known combinatorial optimization problems. Six of the techniques are GAs with different configurations, and the remaining three are evolutionary algorithms that focus exclusively on the mutation process. Finally, to perform a reliable comparison of these results, a statistical study of them is made, performing the normal distribution z-test. PMID:25165731

Methodology for single-cell genetic analysis of planktonic foraminifera for studies of protist diversity and evolution

Directory of Open Access Journals (Sweden)

Agnes Katharina Maria Weiner

2016-12-01

Full Text Available Single-cell genetic analysis is an essential method to investigate the biodiversity and evolutionary ecology of marine protists. In protist groups that do not reproduce under laboratory conditions, this approach provides the only means to directly associate molecular sequences with cell morphology. The resulting unambiguous taxonomic identification of the DNA sequences is a prerequisite for barcoding and analyses of environmental metagenomic data. Extensive single-cell genetic studies have been carried out on planktonic foraminifera over the past 20 years to elucidate their phylogeny, cryptic diversity, biogeography and the relationship between genetic and morphological variability. In the course of these investigations, it has become evident that genetic analysis at the individual specimen level is confronted by innumerable challenges ranging from the negligible amount of DNA present in the single cell to the substantial amount of DNA contamination introduced by endosymbionts or food particles. Consequently, a range of methods has been developed and applied throughout the years for the genetic analysis of planktonic foraminifera in order to enhance DNA amplification success rates. Yet, the description of these methods in the literature rarely occurred with equivalent levels of detail and the different approaches have never been compared in terms of their efficiency and reproducibility. Here, aiming at a standardization of methods, we provide a comprehensive review of all methods that have been employed for the single-cell genetic analysis of planktonic foraminifera. We compile data on success rates of DNA amplification and use these to evaluate the effects of key parameters associated with the methods of sample collection, storage and extraction of single-cell DNA. We show that the chosen methods influence the success rates of single-cell genetic studies, but the differences between them are not sufficient to hinder comparisons between studies

Gregor Mendel's Genetic Experiments: A Statistical Analysis after 150 Years

Czech Academy of Sciences Publication Activity Database

Kalina, Jan

2016-01-01

Roč. 12, č. 2 (2016), s. 20-26 ISSN 1801-5603 Institutional support: RVO:67985807 Keywords : genetics * history of science * biostatistics * design of experiments Subject RIV: BB - Applied Statistics, Operational Research

RESEARCH NOTE Molecular genetic analysis of consanguineous ...

Indian Academy of Sciences (India)

Navya

Molecular genetic analysis of consanguineous families with primary microcephaly ... Translational Research Institute, Academic Health System, Hamad Medical ..... bridging the gap between homozygosity mapping and deep sequencing.

A genetic analysis of Trichuris trichiura and Trichuris suis from Ecuador

DEFF Research Database (Denmark)

Meekums, Hayley; Hawash, Mohamed B F; Sparks, Alexandra M

2015-01-01

BACKGROUND: Since the nematodes Trichuris trichiura and T. suis are morphologically indistinguishable, genetic analysis is required to assess epidemiological cross-over between people and pigs. This study aimed to clarify the transmission biology of trichuriasis in Ecuador. FINDINGS: Adult...... Trichuris worms were collected during a parasitological survey of 132 people and 46 pigs in Esmeraldas Province, Ecuador. Morphometric analysis of 49 pig worms and 64 human worms revealed significant variation. In discriminant analysis morphometric characteristics correctly classified male worms according...... to genetically analyse Trichuris parasites. Although T. trichiura does not appear to be zoonotic in Ecuador, there is evidence of genetic exchange between T. trichiura and T. suis warranting more detailed genetic sampling....

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.

Moving Forward: Positive Behavior Support and Applied Behavior Analysis

Science.gov (United States)

Tincani, Matt

2007-01-01

A controversy has emerged about the relationship between positive behavior support and applied behavior analysis. Some behavior analysts suggest that positive behavior support and applied behavior analysis are the same (e.g., Carr & Sidener, 2002). Others argue that positive behavior support is harmful to applied behavior analysis (e.g., Johnston,…

Genetic Diversity and Phylogenetic Analysis of the Iranian Leishmania Parasites Based on HSP70 Gene PCR-RFLP and Sequence Analysis.

Science.gov (United States)

Nemati, Sara; Fazaeli, Asghar; Hajjaran, Homa; Khamesipour, Ali; Anbaran, Mohsen Falahati; Bozorgomid, Arezoo; Zarei, Fatah

2017-08-01

Despite the broad distribution of leishmaniasis among Iranians and animals across the country, little is known about the genetic characteristics of the causative agents. Applying both HSP70 PCR-RFLP and sequence analyses, this study aimed to evaluate the genetic diversity and phylogenetic relationships among Leishmania spp. isolated from Iranian endemic foci and available reference strains. A total of 36 Leishmania isolates from almost all districts across the country were genetically analyzed for the HSP70 gene using both PCR-RFLP and sequence analysis. The original HSP70 gene sequences were aligned along with homologous Leishmania sequences retrieved from NCBI, and subjected to the phylogenetic analysis. Basic parameters of genetic diversity were also estimated. The HSP70 PCR-RFLP presented 3 different electrophoretic patterns, with no further intraspecific variation, corresponding to 3 Leishmania species available in the country, L. tropica, L. major, and L. infantum. Phylogenetic analyses presented 5 major clades, corresponding to 5 species complexes. Iranian lineages, including L. major, L. tropica, and L. infantum, were distributed among 3 complexes L. major, L. tropica, and L. donovani. However, within the L. major and L. donovani species complexes, the HSP70 phylogeny was not able to distinguish clearly between the L. major and L. turanica isolates, and between the L. infantum, L. donovani, and L. chagasi isolates, respectively. Our results indicated that both HSP70 PCR-RFLP and sequence analyses are medically applicable tools for identification of Leishmania species in Iranian patients. However, the reduced genetic diversity of the target gene makes it inevitable that its phylogeny only resolves the major groups, namely, the species complexes.

System Response Analysis and Model Order Reduction, Using Conventional Method, Bond Graph Technique and Genetic Programming

Directory of Open Access Journals (Sweden)

Lubna Moin

2009-04-01

Full Text Available This research paper basically explores and compares the different modeling and analysis techniques and than it also explores the model order reduction approach and significance. The traditional modeling and simulation techniques for dynamic systems are generally adequate for single-domain systems only, but the Bond Graph technique provides new strategies for reliable solutions of multi-domain system. They are also used for analyzing linear and non linear dynamic production system, artificial intelligence, image processing, robotics and industrial automation. This paper describes a unique technique of generating the Genetic design from the tree structured transfer function obtained from Bond Graph. This research work combines bond graphs for model representation with Genetic programming for exploring different ideas on design space tree structured transfer function result from replacing typical bond graph element with their impedance equivalent specifying impedance lows for Bond Graph multiport. This tree structured form thus obtained from Bond Graph is applied for generating the Genetic Tree. Application studies will identify key issues and importance for advancing this approach towards becoming on effective and efficient design tool for synthesizing design for Electrical system. In the first phase, the system is modeled using Bond Graph technique. Its system response and transfer function with conventional and Bond Graph method is analyzed and then a approach towards model order reduction is observed. The suggested algorithm and other known modern model order reduction techniques are applied to a 11th order high pass filter [1], with different approach. The model order reduction technique developed in this paper has least reduction errors and secondly the final model retains structural information. The system response and the stability analysis of the system transfer function taken by conventional and by Bond Graph method is compared and

Analysis of genetic structure in Melia volkensii (Gurke.) populations ...

African Journals Online (AJOL)

Administrator

2Farm Forestry Programme, Kenya Forestry Research Institute, P. O. Box 20412, Nairobi, Kenya. Accepted 5 ... were used to estimate genetic distances between populations and for construction of neighbour-joining phenograms. Analysis of Molecular Variance (AMOVA) indicated significant genetic differentiation between ...

Capturing the spectrum of interaction effects in genetic association studies by simulated evaporative cooling network analysis.

Directory of Open Access Journals (Sweden)

Brett A McKinney

2009-03-01

Full Text Available Evidence from human genetic studies of several disorders suggests that interactions between alleles at multiple genes play an important role in influencing phenotypic expression. Analytical methods for identifying Mendelian disease genes are not appropriate when applied to common multigenic diseases, because such methods investigate association with the phenotype only one genetic locus at a time. New strategies are needed that can capture the spectrum of genetic effects, from Mendelian to multifactorial epistasis. Random Forests (RF and Relief-F are two powerful machine-learning methods that have been studied as filters for genetic case-control data due to their ability to account for the context of alleles at multiple genes when scoring the relevance of individual genetic variants to the phenotype. However, when variants interact strongly, the independence assumption of RF in the tree node-splitting criterion leads to diminished importance scores for relevant variants. Relief-F, on the other hand, was designed to detect strong interactions but is sensitive to large backgrounds of variants that are irrelevant to classification of the phenotype, which is an acute problem in genome-wide association studies. To overcome the weaknesses of these data mining approaches, we develop Evaporative Cooling (EC feature selection, a flexible machine learning method that can integrate multiple importance scores while removing irrelevant genetic variants. To characterize detailed interactions, we construct a genetic-association interaction network (GAIN, whose edges quantify the synergy between variants with respect to the phenotype. We use simulation analysis to show that EC is able to identify a wide range of interaction effects in genetic association data. We apply the EC filter to a smallpox vaccine cohort study of single nucleotide polymorphisms (SNPs and infer a GAIN for a collection of SNPs associated with adverse events. Our results suggest an important

MetaGenyo: a web tool for meta-analysis of genetic association studies.

Science.gov (United States)

Martorell-Marugan, Jordi; Toro-Dominguez, Daniel; Alarcon-Riquelme, Marta E; Carmona-Saez, Pedro

2017-12-16

Genetic association studies (GAS) aims to evaluate the association between genetic variants and phenotypes. In the last few years, the number of this type of study has increased exponentially, but the results are not always reproducible due to experimental designs, low sample sizes and other methodological errors. In this field, meta-analysis techniques are becoming very popular tools to combine results across studies to increase statistical power and to resolve discrepancies in genetic association studies. A meta-analysis summarizes research findings, increases statistical power and enables the identification of genuine associations between genotypes and phenotypes. Meta-analysis techniques are increasingly used in GAS, but it is also increasing the amount of published meta-analysis containing different errors. Although there are several software packages that implement meta-analysis, none of them are specifically designed for genetic association studies and in most cases their use requires advanced programming or scripting expertise. We have developed MetaGenyo, a web tool for meta-analysis in GAS. MetaGenyo implements a complete and comprehensive workflow that can be executed in an easy-to-use environment without programming knowledge. MetaGenyo has been developed to guide users through the main steps of a GAS meta-analysis, covering Hardy-Weinberg test, statistical association for different genetic models, analysis of heterogeneity, testing for publication bias, subgroup analysis and robustness testing of the results. MetaGenyo is a useful tool to conduct comprehensive genetic association meta-analysis. The application is freely available at http://bioinfo.genyo.es/metagenyo/ .

Applying personal genetic data to injury risk assessment in athletes.

Directory of Open Access Journals (Sweden)

Gabrielle T Goodlin

Full Text Available Recent studies have identified genetic markers associated with risk for certain sports-related injuries and performance-related conditions, with the hope that these markers could be used by individual athletes to personalize their training and diet regimens. We found that we could greatly expand the knowledge base of sports genetic information by using published data originally found in health and disease studies. For example, the results from large genome-wide association studies for low bone mineral density in elderly women can be re-purposed for low bone mineral density in young endurance athletes. In total, we found 124 single-nucleotide polymorphisms associated with: anterior cruciate ligament tear, Achilles tendon injury, low bone mineral density and stress fracture, osteoarthritis, vitamin/mineral deficiencies, and sickle cell trait. Of these single nucleotide polymorphisms, 91% have not previously been used in sports genetics. We conducted a pilot program on fourteen triathletes using this expanded knowledge base of genetic variants associated with sports injury. These athletes were genotyped and educated about how their individual genetic make-up affected their personal risk profile during an hour-long personal consultation. Overall, participants were favorable of the program, found it informative, and most acted upon their genetic results. This pilot program shows that recent genetic research provides valuable information to help reduce sports injuries and to optimize nutrition. There are many genetic studies for health and disease that can be mined to provide useful information to athletes about their individual risk for relevant injuries.

[Public health, genetics and ethics].

Science.gov (United States)

Kottow, Miguel H

2002-10-01

Genetics research has shown enormous developments in recent decades, although as yet with only limited clinical application. Bioethical analysis has been unable to deal with the vast problems of genetics because emphasis has been put on the principlism applied to both clinical and research bioethics. Genetics nevertheless poses its most complex moral dilemmas at the public level, where a social brand of ethics ought to supersede the essentially interpersonal perspective of principlism. A more social understanding of ethics in genetics is required to unravel issues such as research and clinical explorations, ownership and patents, genetic manipulation, and allocation of resources. All these issues require reflection based on the requirements of citizenry, consideration of common assets, and definition of public policies in regulating genetic endeavors and protecting the society as a whole Bioethics has privileged the approach to individual ethical issues derived from genetic intervention, thereby neglecting the more salient aspects of genetics and social ethics.

Genetic algorithms applied to nonlinear and complex domains; TOPICAL

International Nuclear Information System (INIS)

Barash, D; Woodin, A E

1999-01-01

The dissertation, titled ''Genetic Algorithms Applied to Nonlinear and Complex Domains'', describes and then applies a new class of powerful search algorithms (GAS) to certain domains. GAS are capable of solving complex and nonlinear problems where many parameters interact to produce a ''final'' result such as the optimization of the laser pulse in the interaction of an atom with an intense laser field. GAS can very efficiently locate the global maximum by searching parameter space in problems which are unsuitable for a search using traditional methods. In particular, the dissertation contains new scientific findings in two areas. First, the dissertation examines the interaction of an ultra-intense short laser pulse with atoms. GAS are used to find the optimal frequency for stabilizing atoms in the ionization process. This leads to a new theoretical formulation, to explain what is happening during the ionization process and how the electron is responding to finite (real-life) laser pulse shapes. It is shown that the dynamics of the process can be very sensitive to the ramp of the pulse at high frequencies. The new theory which is formulated, also uses a novel concept (known as the (t,t') method) to numerically solve the time-dependent Schrodinger equation Second, the dissertation also examines the use of GAS in modeling decision making problems. It compares GAS with traditional techniques to solve a class of problems known as Markov Decision Processes. The conclusion of the dissertation should give a clear idea of where GAS are applicable, especially in the physical sciences, in problems which are nonlinear and complex, i.e. difficult to analyze by other means

Applying genetic algorithms for programming manufactoring cell tasks

Directory of Open Access Journals (Sweden)

Efredy Delgado

2005-05-01

Full Text Available This work was aimed for developing computational intelligence for scheduling a manufacturing cell's tasks, based manily on genetic algorithms. The manufacturing cell was modelled as beign a production-line; the makespan was calculated by using heuristics adapted from several libraries for genetic algorithms computed in C++ builder. Several problems dealing with small, medium and large list of jobs and machinery were resolved. The results were compared with other heuristics. The approach developed here would seem to be promising for future research concerning scheduling manufacturing cell tasks involving mixed batches.

Genetic structure of populations and differentiation in forest trees

Science.gov (United States)

Raymond P. Guries; F. Thomas Ledig

1981-01-01

Electrophoretic techniques permit population biologists to analyze genetic structure of natural populations by using large numbers of allozyme loci. Several methods of analysis have been applied to allozyme data, including chi-square contingency tests, F-statistics, and genetic distance. This paper compares such statistics for pitch pine (Pinus rigida...

Comparative linkage meta-analysis reveals regionally-distinct, disparate genetic architectures: application to bipolar disorder and schizophrenia.

Directory of Open Access Journals (Sweden)

Brady Tang

2011-04-01

Full Text Available New high-throughput, population-based methods and next-generation sequencing capabilities hold great promise in the quest for common and rare variant discovery and in the search for "missing heritability." However, the optimal analytic strategies for approaching such data are still actively debated, representing the latest rate-limiting step in genetic progress. Since it is likely a majority of common variants of modest effect have been identified through the application of tagSNP-based microarray platforms (i.e., GWAS, alternative approaches robust to detection of low-frequency (1-5% MAF and rare (<1% variants are of great importance. Of direct relevance, we have available an accumulated wealth of linkage data collected through traditional genetic methods over several decades, the full value of which has not been exhausted. To that end, we compare results from two different linkage meta-analysis methods--GSMA and MSP--applied to the same set of 13 bipolar disorder and 16 schizophrenia GWLS datasets. Interestingly, we find that the two methods implicate distinct, largely non-overlapping, genomic regions. Furthermore, based on the statistical methods themselves and our contextualization of these results within the larger genetic literatures, our findings suggest, for each disorder, distinct genetic architectures may reside within disparate genomic regions. Thus, comparative linkage meta-analysis (CLMA may be used to optimize low-frequency and rare variant discovery in the modern genomic era.

Genetic association of telomere length with hepatocellular carcinoma risk: A Mendelian randomization analysis.

Science.gov (United States)

Cheng, Yue; Yu, Chengxiao; Huang, Mingtao; Du, Fangzhi; Song, Ci; Ma, Zijian; Zhai, Xiangjun; Yang, Yuan; Liu, Jibin; Bei, Jin-Xin; Jia, Weihua; Jin, Guangfu; Li, Shengping; Zhou, Weiping; Liu, Jianjun; Dai, Juncheng; Hu, Zhibin

2017-10-01

Observational studies show an association between telomere length and Hepatocellular carcinoma (HCC) risk, but the relationship is controversial. Particularly, it remains unclear whether the association is due to confounding or biases inherent in conventional epidemiological studies. Here, we applied Mendelian randomization approach to evaluate whether telomere length is causally associated with HCC risk. Individual-level data were from HBV-related HCC Genome-wide association studies (1,538 HBV positive HCC patients and 1,465 HBV positive controls). Genetic risk score, as proxy for actual measured telomere length, derived from nine telomere length-associated genetic variants was used to evaluate the effect of telomere length on HCC risk. We observed a significant risk signal between genetically increased telomere length and HBV-related HCC risk (OR=2.09, 95% CI 1.32-3.31, P=0.002). Furthermore, a U-shaped curve was fitted by the restricted cubic spline curve, which indicated that either short or long telomere length would increase HCC risk (P=0.0022 for non-linearity test). Subgroup analysis did not reveal significant heterogeneity between different age, gender, smoking status and drinking status groups. Our results indicated that a genetic background that favors longer or shorter telomere length may increase HBV-related HCC risk-a U-shaped association. Copyright © 2017 Elsevier Ltd. All rights reserved.

Applying Multivariate Discrete Distributions to Genetically Informative Count Data.

Science.gov (United States)

Kirkpatrick, Robert M; Neale, Michael C

2016-03-01

We present a novel method of conducting biometric analysis of twin data when the phenotypes are integer-valued counts, which often show an L-shaped distribution. Monte Carlo simulation is used to compare five likelihood-based approaches to modeling: our multivariate discrete method, when its distributional assumptions are correct, when they are incorrect, and three other methods in common use. With data simulated from a skewed discrete distribution, recovery of twin correlations and proportions of additive genetic and common environment variance was generally poor for the Normal, Lognormal and Ordinal models, but good for the two discrete models. Sex-separate applications to substance-use data from twins in the Minnesota Twin Family Study showed superior performance of two discrete models. The new methods are implemented using R and OpenMx and are freely available.

Genetic high throughput screening in Retinitis Pigmentosa based on high resolution melting (HRM) analysis.

Science.gov (United States)

Anasagasti, Ander; Barandika, Olatz; Irigoyen, Cristina; Benitez, Bruno A; Cooper, Breanna; Cruchaga, Carlos; López de Munain, Adolfo; Ruiz-Ederra, Javier

2013-11-01

Retinitis Pigmentosa (RP) involves a group of genetically determined retinal diseases caused by a large number of mutations that result in rod photoreceptor cell death followed by gradual death of cone cells. Most cases of RP are monogenic, with more than 80 associated genes identified so far. The high number of genes and variants involved in RP, among other factors, is making the molecular characterization of RP a real challenge for many patients. Although HRM has been used for the analysis of isolated variants or single RP genes, as far as we are concerned, this is the first study that uses HRM analysis for a high-throughput screening of several RP genes. Our main goal was to test the suitability of HRM analysis as a genetic screening technique in RP, and to compare its performance with two of the most widely used NGS platforms, Illumina and PGM-Ion Torrent technologies. RP patients (n = 96) were clinically diagnosed at the Ophthalmology Department of Donostia University Hospital, Spain. We analyzed a total of 16 RP genes that meet the following inclusion criteria: 1) size: genes with transcripts of less than 4 kb; 2) number of exons: genes with up to 22 exons; and 3) prevalence: genes reported to account for, at least, 0.4% of total RP cases worldwide. For comparison purposes, RHO gene was also sequenced with Illumina (GAII; Illumina), Ion semiconductor technologies (PGM; Life Technologies) and Sanger sequencing (ABI 3130xl platform; Applied Biosystems). Detected variants were confirmed in all cases by Sanger sequencing and tested for co-segregation in the family of affected probands. We identified a total of 65 genetic variants, 15 of which (23%) were novel, in 49 out of 96 patients. Among them, 14 (4 novel) are probable disease-causing genetic variants in 7 RP genes, affecting 15 patients. Our HRM analysis-based study, proved to be a cost-effective and rapid method that provides an accurate identification of genetic RP variants. This approach is effective for

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...

SimHap GUI: an intuitive graphical user interface for genetic association analysis.

Science.gov (United States)

Carter, Kim W; McCaskie, Pamela A; Palmer, Lyle J

2008-12-25

Researchers wishing to conduct genetic association analysis involving single nucleotide polymorphisms (SNPs) or haplotypes are often confronted with the lack of user-friendly graphical analysis tools, requiring sophisticated statistical and informatics expertise to perform relatively straightforward tasks. Tools, such as the SimHap package for the R statistics language, provide the necessary statistical operations to conduct sophisticated genetic analysis, but lacks a graphical user interface that allows anyone but a professional statistician to effectively utilise the tool. We have developed SimHap GUI, a cross-platform integrated graphical analysis tool for conducting epidemiological, single SNP and haplotype-based association analysis. SimHap GUI features a novel workflow interface that guides the user through each logical step of the analysis process, making it accessible to both novice and advanced users. This tool provides a seamless interface to the SimHap R package, while providing enhanced functionality such as sophisticated data checking, automated data conversion, and real-time estimations of haplotype simulation progress. SimHap GUI provides a novel, easy-to-use, cross-platform solution for conducting a range of genetic and non-genetic association analyses. This provides a free alternative to commercial statistics packages that is specifically designed for genetic association analysis.

Examining applying high performance genetic data feature selection and classification algorithms for colon cancer diagnosis.

Science.gov (United States)

Al-Rajab, Murad; Lu, Joan; Xu, Qiang

2017-07-01

This paper examines the accuracy and efficiency (time complexity) of high performance genetic data feature selection and classification algorithms for colon cancer diagnosis. The need for this research derives from the urgent and increasing need for accurate and efficient algorithms. Colon cancer is a leading cause of death worldwide, hence it is vitally important for the cancer tissues to be expertly identified and classified in a rapid and timely manner, to assure both a fast detection of the disease and to expedite the drug discovery process. In this research, a three-phase approach was proposed and implemented: Phases One and Two examined the feature selection algorithms and classification algorithms employed separately, and Phase Three examined the performance of the combination of these. It was found from Phase One that the Particle Swarm Optimization (PSO) algorithm performed best with the colon dataset as a feature selection (29 genes selected) and from Phase Two that the Support Vector Machine (SVM) algorithm outperformed other classifications, with an accuracy of almost 86%. It was also found from Phase Three that the combined use of PSO and SVM surpassed other algorithms in accuracy and performance, and was faster in terms of time analysis (94%). It is concluded that applying feature selection algorithms prior to classification algorithms results in better accuracy than when the latter are applied alone. This conclusion is important and significant to industry and society. Copyright © 2017 Elsevier B.V. All rights reserved.

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

RAPD analysis for genetic diversity of two populations of Mystus ...

African Journals Online (AJOL)

) was applied to analyze the genetic variation of the 2 populations of Mystus vittatus (Bloch) of Madhya Pradesh, India. 10 random 10-mer primers were primarily scored in 3 individuals from each of the 2 locations. Five primers, which gave ...

Parameter determination for quantitative PIXE analysis using genetic algorithms

International Nuclear Information System (INIS)

Aspiazu, J.; Belmont-Moreno, E.

1996-01-01

For biological and environmental samples, PIXE technique is in particular advantage for elemental analysis, but the quantitative analysis implies accomplishing complex calculations that require the knowledge of more than a dozen parameters. Using a genetic algorithm, the authors give here an account of the procedure to obtain the best values for the parameters necessary to fit the efficiency for a X-ray detector. The values for some variables involved in quantitative PIXE analysis, were manipulated in a similar way as the genetic information is treated in a biological process. The authors carried out the algorithm until they reproduce, within the confidence interval, the elemental concentrations corresponding to a reference material

Building an applied activation analysis centre

International Nuclear Information System (INIS)

Bartosek, J.; Kasparec, I.; Masek, J.

1972-01-01

Requirements are defined and all available background material is reported and discussed for the building up of a centre of applied activation analysis in Czechoslovakia. A detailed analysis of potential users and the centre's envisaged availability is also presented as part of the submitted study. A brief economic analysis is annexed. The study covers the situation up to the end of 1972. (J.K.)

Genetic analysis of Myanmar Vigna species in responses to salt ...

African Journals Online (AJOL)

Genetic analysis of Myanmar Vigna species in responses to salt stress at the ... of reduction was highly dependent on different genotypes and salinity levels. ... the mechanism of salt tolerance and for the provision of genetic resources for ...

Genetic engineering applied to agriculture has a long row to hoe.

Science.gov (United States)

Miller, Henry I

2018-01-02

In spite of the lack of scientific justification for skepticism about crops modified with molecular techniques of genetic engineering, they have been the most scrutinized agricultural products in human history. The assumption that "genetically engineered" or "genetically modified" is a meaningful - and dangerous - classification has led to excessive and dilatory regulation. The modern molecular techniques are an extension, or refinement, of older, less precise, less predictable methods of genetic modification, but as long as today's activists and regulators remain convinced that so called "GMOs" represent a distinct and dangerous category of research and products, genetic engineering will fall short of its potential.

Genetic analysis for grain quality traits in pakistani wheat varieties

International Nuclear Information System (INIS)

Minhas, N.M.; Ajmal, S.U.; Iqbal, Z.; Munir, M.

2014-01-01

A set of eight parental diallel involving seven commercial wheat cultivars and one breeding line was made to investigate the nature of gene action determining inheritance pattern of grain quality characters. Highly significant differences were observed among the genotypes for 1000 grain weight, protein content, wet gluten and lysine content. Adequacy tests were employed to estimate the fitness of data sets to additive dominance model. Both the tests i.e. analysis of uniformity of Wr, Vr and joint regression analysis validated the data of these traits for genetic analysis. Gene actions for grain quality traits were ascertained following Hayman's analysis of variance. Results of the genetic analysis revealed that both additive and dominance genetic components were involved in the manifestation of characters under study. However, additive gene effects were more pronounced in the genetic control of these traits. Non significance of b1, b2 and b3 values revealed the absence of directional dominance, symmetrical distribution of genes among the parental lines and absence of specific genes action respectively in all the traits. Maternal effects were also noted in 1000 grain weight, protein content and wet gluten percentage. It is concluded that additive effects are crucial in the expression of grain quality characters of wheat in germplasm under study and single plant selection may be recommended in segregating generations for effective improvement in these characters. (author)

Genetic algorithms applied to the nuclear power plant operation

International Nuclear Information System (INIS)

Schirru, R.; Martinez, A.S.; Pereira, C.M.N.A.

2000-01-01

Nuclear power plant operation often involves very important human decisions, such as actions to be taken after a nuclear accident/transient, or finding the best core reload pattern, a complex combinatorial optimization problem which requires expert knowledge. Due to the complexity involved in the decisions to be taken, computerized systems have been intensely explored in order to aid the operator. Following hardware advances, soft computing has been improved and, nowadays, intelligent technologies, such as genetic algorithms, neural networks and fuzzy systems, are being used to support operator decisions. In this chapter two main problems are explored: transient diagnosis and nuclear core refueling. Here, solutions to such kind of problems, based on genetic algorithms, are described. A genetic algorithm was designed to optimize the nuclear fuel reload of Angra-1 nuclear power plant. Results compared to those obtained by an expert reveal a gain in the burn-up cycle. Two other genetic algorithm approaches were used to optimize real time diagnosis systems. The first one learns partitions in the time series that represents the transients, generating a set of classification centroids. The other one involves the optimization of an adaptive vector quantization neural network. Results are shown and commented. (orig.)

Caldwell University's Department of Applied Behavior Analysis.

Science.gov (United States)

Reeve, Kenneth F; Reeve, Sharon A

2016-05-01

Since 2004, faculty members at Caldwell University have developed three successful graduate programs in Applied Behavior Analysis (i.e., PhD, MA, non-degree programs), increased program faculty from two to six members, developed and operated an on-campus autism center, and begun a stand-alone Applied Behavior Analysis Department. This paper outlines a number of strategies used to advance these initiatives, including those associated with an extensive public relations campaign. We also outline challenges that have limited our programs' growth. These strategies, along with a consideration of potential challenges, might prove useful in guiding academicians who are interested in starting their own programs in behavior analysis.

Genetic data analysis for plant and animal breeding

Science.gov (United States)

This book is an advanced textbook covering the application of quantitative genetics theory to analysis of actual data (both trait and DNA marker information) for breeding populations of crops, trees, and animals. Chapter 1 is an introduction to basic software used for trait data analysis. Chapter 2 ...

Variable-number-of-tandem-repeats analysis of genetic diversity in Pasteuria ramosa.

Science.gov (United States)

Mouton, L; Ebert, D

2008-05-01

Variable-number-of-tandem-repeats (VNTR) markers are increasingly being used in population genetic studies of bacteria. They were recently developed for Pasteuria ramosa, an endobacterium that infects Daphnia species. In the present study, we genotyped P. ramosa in 18 infected hosts from the United Kingdom, Belgium, and two lakes in the United States using seven VNTR markers. Two Daphnia species were collected: D. magna and D. dentifera. Six loci showed length polymorphism, with as many as five alleles identified for a single locus. Similarity coefficient calculations showed that the extent of genetic variation between pairs of isolates within populations differed according to the population, but it was always less than the genetic distances among populations. Analysis of the genetic distances performed using principal component analysis revealed strong clustering by location of origin, but not by host Daphnia species. Our study demonstrated that the VNTR markers available for P. ramosa are informative in revealing genetic differences within and among populations and may therefore become an important tool for providing detailed analysis of population genetics and epidemiology.

A roadmap for the genetic analysis of renal aging.

Science.gov (United States)

Noordmans, Gerda A; Hillebrands, Jan-Luuk; van Goor, Harry; Korstanje, Ron

2015-10-01

Several studies show evidence for the genetic basis of renal disease, which renders some individuals more prone than others to accelerated renal aging. Studying the genetics of renal aging can help us to identify genes involved in this process and to unravel the underlying pathways. First, this opinion article will give an overview of the phenotypes that can be observed in age-related kidney disease. Accurate phenotyping is essential in performing genetic analysis. For kidney aging, this could include both functional and structural changes. Subsequently, this article reviews the studies that report on candidate genes associated with renal aging in humans and mice. Several loci or candidate genes have been found associated with kidney disease, but identification of the specific genetic variants involved has proven to be difficult. CUBN, UMOD, and SHROOM3 were identified by human GWAS as being associated with albuminuria, kidney function, and chronic kidney disease (CKD). These are promising examples of genes that could be involved in renal aging, and were further mechanistically evaluated in animal models. Eventually, we will provide approaches for performing genetic analysis. We should leverage the power of mouse models, as testing in humans is limited. Mouse and other animal models can be used to explain the underlying biological mechanisms of genes and loci identified by human GWAS. Furthermore, mouse models can be used to identify genetic variants associated with age-associated histological changes, of which Far2, Wisp2, and Esrrg are examples. A new outbred mouse population with high genetic diversity will facilitate the identification of genes associated with renal aging by enabling high-resolution genetic mapping while also allowing the control of environmental factors, and by enabling access to renal tissues at specific time points for histology, proteomics, and gene expression. © 2015 The Authors. Aging Cell published by the Anatomical Society and John

A roadmap for the genetic analysis of renal aging

Science.gov (United States)

Noordmans, Gerda A; Hillebrands, Jan-Luuk; van Goor, Harry; Korstanje, Ron

2015-01-01

Several studies show evidence for the genetic basis of renal disease, which renders some individuals more prone than others to accelerated renal aging. Studying the genetics of renal aging can help us to identify genes involved in this process and to unravel the underlying pathways. First, this opinion article will give an overview of the phenotypes that can be observed in age-related kidney disease. Accurate phenotyping is essential in performing genetic analysis. For kidney aging, this could include both functional and structural changes. Subsequently, this article reviews the studies that report on candidate genes associated with renal aging in humans and mice. Several loci or candidate genes have been found associated with kidney disease, but identification of the specific genetic variants involved has proven to be difficult. CUBN, UMOD, and SHROOM3 were identified by human GWAS as being associated with albuminuria, kidney function, and chronic kidney disease (CKD). These are promising examples of genes that could be involved in renal aging, and were further mechanistically evaluated in animal models. Eventually, we will provide approaches for performing genetic analysis. We should leverage the power of mouse models, as testing in humans is limited. Mouse and other animal models can be used to explain the underlying biological mechanisms of genes and loci identified by human GWAS. Furthermore, mouse models can be used to identify genetic variants associated with age-associated histological changes, of which Far2, Wisp2, and Esrrg are examples. A new outbred mouse population with high genetic diversity will facilitate the identification of genes associated with renal aging by enabling high-resolution genetic mapping while also allowing the control of environmental factors, and by enabling access to renal tissues at specific time points for histology, proteomics, and gene expression. PMID:26219736

Multilayer perceptron for robust nonlinear interval regression analysis using genetic algorithms.

Science.gov (United States)

Hu, Yi-Chung

2014-01-01

On the basis of fuzzy regression, computational models in intelligence such as neural networks have the capability to be applied to nonlinear interval regression analysis for dealing with uncertain and imprecise data. When training data are not contaminated by outliers, computational models perform well by including almost all given training data in the data interval. Nevertheless, since training data are often corrupted by outliers, robust learning algorithms employed to resist outliers for interval regression analysis have been an interesting area of research. Several approaches involving computational intelligence are effective for resisting outliers, but the required parameters for these approaches are related to whether the collected data contain outliers or not. Since it seems difficult to prespecify the degree of contamination beforehand, this paper uses multilayer perceptron to construct the robust nonlinear interval regression model using the genetic algorithm. Outliers beyond or beneath the data interval will impose slight effect on the determination of data interval. Simulation results demonstrate that the proposed method performs well for contaminated datasets.

Polyglot programming in applications used for genetic data analysis.

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Nowak, Robert M

2014-01-01

Applications used for the analysis of genetic data process large volumes of data with complex algorithms. High performance, flexibility, and a user interface with a web browser are required by these solutions, which can be achieved by using multiple programming languages. In this study, I developed a freely available framework for building software to analyze genetic data, which uses C++, Python, JavaScript, and several libraries. This system was used to build a number of genetic data processing applications and it reduced the time and costs of development.

The Double Helix: Applying an Ethic of Care to the Duty to Warn Genetic Relatives of Genetic Information.

Science.gov (United States)

Weaver, Meaghann

2016-03-01

Genetic testing reveals information about a patient's health status and predictions about the patient's future wellness, while also potentially disclosing health information relevant to other family members. With the increasing availability and affordability of genetic testing and the integration of genetics into mainstream medicine, the importance of clarifying the scope of confidentiality and the rules regarding disclosure of genetic findings to genetic relatives is prime. The United Nations International Declaration on Human Genetic Data urges an appreciation for principles of equality, justice, solidarity and responsibility in the context of genetic testing, including a commitment to honoring the privacy and security of the person tested. Considering this global mandate and recent professional statements in the context of a legal amendment to patient privacy policies in Australia, a fresh scrutiny of the legal history of a physician's duty to warn is warranted. This article inquiries whether there may be anything ethically or socially amiss with a potential future recommendation for health professionals or patients to universally disclose particular cancer predisposition genetic diagnosis to genetic family members. While much of the discussion remains applicable to all genetic diagnosis, the article focuses on the practice of disclosure within the context of BRCA1/2 diagnosis. An 'ethic of care' interpretation of legal tradition and current practice will serve to reconcile law and medical policy on the issue of physician disclosure of genetic results to family members without patient consent. © 2015 John Wiley & Sons Ltd.

GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research--an update.

Science.gov (United States)

Peakall, Rod; Smouse, Peter E

2012-10-01

GenAlEx: Genetic Analysis in Excel is a cross-platform package for population genetic analyses that runs within Microsoft Excel. GenAlEx offers analysis of diploid codominant, haploid and binary genetic loci and DNA sequences. Both frequency-based (F-statistics, heterozygosity, HWE, population assignment, relatedness) and distance-based (AMOVA, PCoA, Mantel tests, multivariate spatial autocorrelation) analyses are provided. New features include calculation of new estimators of population structure: G'(ST), G''(ST), Jost's D(est) and F'(ST) through AMOVA, Shannon Information analysis, linkage disequilibrium analysis for biallelic data and novel heterogeneity tests for spatial autocorrelation analysis. Export to more than 30 other data formats is provided. Teaching tutorials and expanded step-by-step output options are included. The comprehensive guide has been fully revised. GenAlEx is written in VBA and provided as a Microsoft Excel Add-in (compatible with Excel 2003, 2007, 2010 on PC; Excel 2004, 2011 on Macintosh). GenAlEx, and supporting documentation and tutorials are freely available at: http://biology.anu.edu.au/GenAlEx. rod.peakall@anu.edu.au.

Pushing the envelope in genetic analysis of species invasion

Science.gov (United States)

Samuel A. Cushman

2015-01-01

How a species spreads once introduced into a new environment is a major question in landscape genetics. When the species in question is a potential disease vector, the findings are important not only for fundamental science, but can impact applied science and public health as well. In this issue of Molecular Ecology Medley et al. (2014) study, the invasion...

Analysis of the interaction between experimental and applied behavior analysis.

Science.gov (United States)

Virues-Ortega, Javier; Hurtado-Parrado, Camilo; Cox, Alison D; Pear, Joseph J

2014-01-01

To study the influences between basic and applied research in behavior analysis, we analyzed the coauthorship interactions of authors who published in JABA and JEAB from 1980 to 2010. We paid particular attention to authors who published in both JABA and JEAB (dual authors) as potential agents of cross-field interactions. We present a comprehensive analysis of dual authors' coauthorship interactions using social networks methodology and key word analysis. The number of dual authors more than doubled (26 to 67) and their productivity tripled (7% to 26% of JABA and JEAB articles) between 1980 and 2010. Dual authors stood out in terms of number of collaborators, number of publications, and ability to interact with multiple groups within the field. The steady increase in JEAB and JABA interactions through coauthors and the increasing range of topics covered by dual authors provide a basis for optimism regarding the progressive integration of basic and applied behavior analysis. © Society for the Experimental Analysis of Behavior.

Systems Genetics Analysis to Identify the Genetic Modulation of a Glaucoma-Associated Gene.

Science.gov (United States)

Chintalapudi, Sumana R; Jablonski, Monica M

2017-01-01

Loss of retinal ganglion cells (RGCs) is one of the hallmarks of retinal neurodegenerative diseases, glaucoma being one of the most common. Recently, γ-synuclein (SNCG) was shown to be highly expressed in the somas and axons of RGCs. In various mouse models of glaucoma, downregulation of Sncg gene expression correlates with RGC loss. To investigate the regulation of Sncg in RGCs, we used a systems genetics approach to identify a gene that modulates the expression of Sncg, followed by confirmatory studies in both healthy and diseased retinas. We found that chromosome 1 harbors an eQTL that modulates the expression of Sncg in the mouse retina and identified Pfdn2 as the candidate upstream modulator of Sncg expression. Downregulation of Pfdn2 in enriched RGCs causes a concomitant reduction in Sncg. In this chapter, we describe our strategy and methods for identifying and confirming a genetic modulation of a glaucoma-associated gene. A similar method can be applied to other genes expressed in other tissues.

Pitfalls in genetic analysis of pheochromocytomas/paragangliomas-case report.

Science.gov (United States)

Canu, Letizia; Rapizzi, Elena; Zampetti, Benedetta; Fucci, Rossella; Nesi, Gabriella; Richter, Susan; Qin, Nan; Giachè, Valentino; Bergamini, Carlo; Parenti, Gabriele; Valeri, Andrea; Ercolino, Tonino; Eisenhofer, Graeme; Mannelli, Massimo

2014-07-01

About 35% of patients with pheochromocytoma/paraganglioma carry a germline mutation in one of the 10 main susceptibility genes. The recent introduction of next-generation sequencing will allow the analysis of all these genes in one run. When positive, the analysis is generally unequivocal due to the association between a germline mutation and a concordant clinical presentation or positive family history. When genetic analysis reveals a novel mutation with no clinical correlates, particularly in the presence of a missense variant, the question arises whether the mutation is pathogenic or a rare polymorphism. We report the case of a 35-year-old patient operated for a pheochromocytoma who turned out to be a carrier of a novel SDHD (succinate dehydrogenase subunit D) missense mutation. With no positive family history or clinical correlates, we decided to perform additional analyses to test the clinical significance of the mutation. We performed in silico analysis, tissue loss of heterozygosity analysis, immunohistochemistry, Western blot analysis, SDH enzymatic assay, and measurement of the succinate/fumarate concentration ratio in the tumor tissue by tandem mass spectrometry. Although the in silico analysis gave contradictory results according to the different methods, all the other tests demonstrated that the SDH complex was conserved and normally active. We therefore came to the conclusion that the variant was a nonpathogenic polymorphism. Advancements in technology facilitate genetic analysis of patients with pheochromocytoma but also offer new challenges to the clinician who, in some cases, needs clinical correlates and/or functional tests to give significance to the results of the genetic assay.

The fuzzy clearing approach for a niching genetic algorithm applied to a nuclear reactor core design optimization problem

International Nuclear Information System (INIS)

Sacco, Wagner F.; Machado, Marcelo D.; Pereira, Claudio M.N.A.; Schirru, Roberto

2004-01-01

This article extends previous efforts on genetic algorithms (GAs) applied to a core design optimization problem. We introduce the application of a new Niching Genetic Algorithm (NGA) to this problem and compare its performance to these previous works. The optimization problem consists in adjusting several reactor cell parameters, such as dimensions, enrichment and materials, in order to minimize the average peak-factor in a three-enrichment zone reactor, considering restrictions on the average thermal flux, criticality and sub-moderation. After exhaustive experiments we observed that our new niching method performs better than the conventional GA due to a greater exploration of the search space

Genetic diversity analysis of common beans based on molecular markers

Directory of Open Access Journals (Sweden)

Homar R. Gill-Langarica

2011-01-01

Full Text Available A core collection of the common bean (Phaseolus vulgaris L., representing genetic diversity in the entire Mexican holding, is kept at the INIFAP (Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias, Mexico Germplasm Bank. After evaluation, the genetic structure of this collection (200 accessions was compared with that of landraces from the states of Oaxaca, Chiapas and Veracruz (10 genotypes from each, as well as a further 10 cultivars, by means of four amplified fragment length polymorphisms (AFLP +3/+3 primer combinations and seven simple sequence repeats (SSR loci, in order to define genetic diversity, variability and mutual relationships. Data underwent cluster (UPGMA and molecular variance (AMOVA analyses. AFLP analysis produced 530 bands (88.5% polymorphic while SSR primers amplified 174 alleles, all polymorphic (8.2 alleles per locus. AFLP indicated that the highest genetic diversity was to be found in ten commercial-seed classes from two major groups of accessions from Central Mexico and Chiapas, which seems to be an important center of diversity in the south. A third group included genotypes from Nueva Granada, Mesoamerica, Jalisco and Durango races. Here, SSR analysis indicated a reduced number of shared haplotypes among accessions, whereas the highest genetic components of AMOVA variation were found within accessions. Genetic diversity observed in the common-bean core collection represents an important sample of the total Phaseolus genetic variability at the main Germplasm Bank of INIFAP. Molecular marker strategies could contribute to a better understanding of the genetic structure of the core collection as well as to its improvement and validation.

Genetic diversity analysis of common beans based on molecular markers

Directory of Open Access Journals (Sweden)

Homar R. Gill-Langarica

Full Text Available A core collection of the common bean (Phaseolus vulgaris L., representing genetic diversity in the entire Mexican holding, is kept at the INIFAP (Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias, Mexico Germplasm Bank. After evaluation, the genetic structure of this collection (200 accessions was compared with that of landraces from the states of Oaxaca, Chiapas and Veracruz (10 genotypes from each, as well as a further 10 cultivars, by means of four amplified fragment length polymorphisms (AFLP +3/+3 primer combinations and seven simple sequence repeats (SSR loci, in order to define genetic diversity, variability and mutual relationships. Data underwent cluster (UPGMA and molecular variance (AMOVA analyses. AFLP analysis produced 530 bands (88.5% polymorphic while SSR primers amplified 174 alleles, all polymorphic (8.2 alleles per locus. AFLP indicated that the highest genetic diversity was to be found in ten commercial-seed classes from two major groups of accessions from Central Mexico and Chiapas, which seems to be an important center of diversity in the south. A third group included genotypes from Nueva Granada, Mesoamerica, Jalisco and Durango races. Here, SSR analysis indicated a reduced number of shared haplotypes among accessions, whereas the highest genetic components of AMOVA variation were found within accessions. Genetic diversity observed in the common-bean core collection represents an important sample of the total Phaseolus genetic variability at the main Germplasm Bank of INIFAP. Molecular marker strategies could contribute to a better understanding of the genetic structure of the core collection as well as to its improvement and validation.

Genetic diversity analysis of common beans based on molecular markers.

Science.gov (United States)

Gill-Langarica, Homar R; Muruaga-Martínez, José S; Vargas-Vázquez, M L Patricia; Rosales-Serna, Rigoberto; Mayek-Pérez, Netzahualcoyotl

2011-10-01

A core collection of the common bean (Phaseolus vulgaris L.), representing genetic diversity in the entire Mexican holding, is kept at the INIFAP (Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias, Mexico) Germplasm Bank. After evaluation, the genetic structure of this collection (200 accessions) was compared with that of landraces from the states of Oaxaca, Chiapas and Veracruz (10 genotypes from each), as well as a further 10 cultivars, by means of four amplified fragment length polymorphisms (AFLP) +3/+3 primer combinations and seven simple sequence repeats (SSR) loci, in order to define genetic diversity, variability and mutual relationships. Data underwent cluster (UPGMA) and molecular variance (AMOVA) analyses. AFLP analysis produced 530 bands (88.5% polymorphic) while SSR primers amplified 174 alleles, all polymorphic (8.2 alleles per locus). AFLP indicated that the highest genetic diversity was to be found in ten commercial-seed classes from two major groups of accessions from Central Mexico and Chiapas, which seems to be an important center of diversity in the south. A third group included genotypes from Nueva Granada, Mesoamerica, Jalisco and Durango races. Here, SSR analysis indicated a reduced number of shared haplotypes among accessions, whereas the highest genetic components of AMOVA variation were found within accessions. Genetic diversity observed in the common-bean core collection represents an important sample of the total Phaseolus genetic variability at the main Germplasm Bank of INIFAP. Molecular marker strategies could contribute to a better understanding of the genetic structure of the core collection as well as to its improvement and validation.

Applied Behavior Analysis and Statistical Process Control?

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Hopkins, B. L.

1995-01-01

Incorporating statistical process control (SPC) methods into applied behavior analysis is discussed. It is claimed that SPC methods would likely reduce applied behavior analysts' intimate contacts with problems and would likely yield poor treatment and research decisions. Cases and data presented by Pfadt and Wheeler (1995) are cited as examples.…

Study on the Method of Association Rules Mining Based on Genetic Algorithm and Application in Analysis of Seawater Samples

Directory of Open Access Journals (Sweden)

Qiuhong Sun

2014-04-01

Full Text Available Based on the data mining research, the data mining based on genetic algorithm method, the genetic algorithm is briefly introduced, while the genetic algorithm based on two important theories and theoretical templates principle implicit parallelism is also discussed. Focuses on the application of genetic algorithms for association rule mining method based on association rule mining, this paper proposes a genetic algorithm fitness function structure, data encoding, such as the title of the improvement program, in particular through the early issues study, proposed the improved adaptive Pc, Pm algorithm is applied to the genetic algorithm, thereby improving efficiency of the algorithm. Finally, a genetic algorithm based association rule mining algorithm, and be applied in sea water samples database in data mining and prove its effective.

A genetic analysis of Trichuris trichiura and Trichuris suis from Ecuador.

Science.gov (United States)

Meekums, Hayley; Hawash, Mohamed B F; Sparks, Alexandra M; Oviedo, Yisela; Sandoval, Carlos; Chico, Martha E; Stothard, J Russell; Cooper, Philip J; Nejsum, Peter; Betson, Martha

2015-03-19

Since the nematodes Trichuris trichiura and T. suis are morphologically indistinguishable, genetic analysis is required to assess epidemiological cross-over between people and pigs. This study aimed to clarify the transmission biology of trichuriasis in Ecuador. Adult Trichuris worms were collected during a parasitological survey of 132 people and 46 pigs in Esmeraldas Province, Ecuador. Morphometric analysis of 49 pig worms and 64 human worms revealed significant variation. In discriminant analysis morphometric characteristics correctly classified male worms according to host species. In PCR-RFLP analysis of the ribosomal Internal Transcribed Spacer (ITS-2) and 18S DNA (59 pig worms and 82 human worms), nearly all Trichuris exhibited expected restriction patterns. However, two pig-derived worms showed a "heterozygous-type" ITS-2 pattern, with one also having a "heterozygous-type" 18S pattern. Phylogenetic analysis of the mitochondrial large ribosomal subunit partitioned worms by host species. Notably, some Ecuadorian T. suis clustered with porcine Trichuris from USA and Denmark and some with Chinese T. suis. This is the first study in Latin America to genetically analyse Trichuris parasites. Although T. trichiura does not appear to be zoonotic in Ecuador, there is evidence of genetic exchange between T. trichiura and T. suis warranting more detailed genetic sampling.

Applied multivariate statistical analysis

CERN Document Server

Härdle, Wolfgang Karl

2015-01-01

Focusing on high-dimensional applications, this 4th edition presents the tools and concepts used in multivariate data analysis in a style that is also accessible for non-mathematicians and practitioners.  It surveys the basic principles and emphasizes both exploratory and inferential statistics; a new chapter on Variable Selection (Lasso, SCAD and Elastic Net) has also been added.  All chapters include practical exercises that highlight applications in different multivariate data analysis fields: in quantitative financial studies, where the joint dynamics of assets are observed; in medicine, where recorded observations of subjects in different locations form the basis for reliable diagnoses and medication; and in quantitative marketing, where consumers’ preferences are collected in order to construct models of consumer behavior.  All of these examples involve high to ultra-high dimensions and represent a number of major fields in big data analysis. The fourth edition of this book on Applied Multivariate ...

A markerless protocol for genetic analysis of Aggregatibacter actinomycetemcomitans

Science.gov (United States)

Cheng, Ya-An; Jee, Jason; Hsu, Genie; Huang, Yanyan; Chen, Casey; Lin, Chun-Pin

2015-01-01

Background/Purpose The genomes of different Aggregatibacter actinomycetemcomitans strains contain many strain-specific genes and genomic islands (defined as DNA found in some but not all strains) of unknown functions. Genetic analysis for the functions of these islands will be constrained by the limited availability of genetic markers and vectors for A. actinomycetemcomitans. In this study we tested a novel genetic approach of gene deletion and restoration in a naturally competent A. actinomycetemcomitans strain D7S-1. Methods Specific genes’ deletion mutants and mutants restored with the deleted genes were constructed by a markerless loxP/Cre system. In mutants with sequential deletion of multiple genes loxP with different spacer regions were used to avoid unwanted recombinations between loxP sites. Results Eight single-gene deletion mutants, four multiple-gene deletion mutants, and two mutants with restored genes were constructed. No unintended non-specific deletion mutants were generated by this protocol. The protocol did not negatively affect the growth and biofilm formation of A. actinomycetemcomitans. Conclusion The protocol described in this study is efficient and specific for genetic manipulation of A. actinomycetemcomitans, and will be amenable for functional analysis of multiple genes in A. actinomycetemcomitans. PMID:24530245

Problems of applied geochemistry

Energy Technology Data Exchange (ETDEWEB)

Ovchinnikov, L N

1983-01-01

The concept of applied geochemistry was introduced for the first time by A. Ye. Fersman. He linked the branched and complicated questions of geochemistry with specific problems of developing the mineral and raw material base of our country. Geochemical prospecting and geochemistry of mineral raw materials are the most important sections of applied geochemistry. This now allows us the right to view applied geochemistry as a sector of science which applies geochemical methodology, set of geochemical methods of analysis, synthesis, geological interpretation of data based on laws governing theoretical geochemistry to the solution of different tasks of geology, petrology, tectonics, stratigraphy, science of minerals and other geological sciences, and also the technology of mineral raw materials, interrelationships of man and nature (ecogeochemistry, technogeochemistry, agrogeochemistry). The main problem of applied geochemistry, geochemistry of ore fields is the prehistory of ore formation. This is especially important for metallogenic and forecasting constructions, for an understanding of the reasons for the development of fields and the detection of laws governing their distribution, their genetic links with the general geological processes and the products of these processes.

Genetic Engineering and the Amelioration of Genetic Defect

Science.gov (United States)

Lederberg, Joshua

1970-01-01

Discusses the claims for a brave new world of genetic manipulation" and concludes that if we could agree upon applying genetic (or any other effective) remedies to global problems we probably would need no rescourse to them. Suggests that effective methods of preventing genetic disease are prevention of mutations and detection and…

Genetic analysis of PAX3 for diagnosis of Waardenburg syndrome type I.

Science.gov (United States)

Matsunaga, Tatsuo; Mutai, Hideki; Namba, Kazunori; Morita, Noriko; Masuda, Sawako

2013-04-01

PAX3 genetic analysis increased the diagnostic accuracy for Waardenburg syndrome type I (WS1). Analysis of the three-dimensional (3D) structure of PAX3 helped verify the pathogenicity of a missense mutation, and multiple ligation-dependent probe amplification (MLPA) analysis of PAX3 increased the sensitivity of genetic diagnosis in patients with WS1. Clinical diagnosis of WS1 is often difficult in individual patients with isolated, mild, or non-specific symptoms. The objective of the present study was to facilitate the accurate diagnosis of WS1 through genetic analysis of PAX3 and to expand the spectrum of known PAX3 mutations. In two Japanese families with WS1, we conducted a clinical evaluation of symptoms and genetic analysis, which involved direct sequencing, MLPA analysis, quantitative PCR of PAX3, and analysis of the predicted 3D structure of PAX3. The normal-hearing control group comprised 92 subjects who had normal hearing according to pure tone audiometry. In one family, direct sequencing of PAX3 identified a heterozygous mutation, p.I59F. Analysis of PAX3 3D structures indicated that this mutation distorted the DNA-binding site of PAX3. In the other family, MLPA analysis and subsequent quantitative PCR detected a large, heterozygous deletion spanning 1759-2554 kb that eliminated 12-18 genes including a whole PAX3 gene.

Artificial intelligence applied to the automatic analysis of absorption spectra. Objective measurement of the fine structure constant

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Bainbridge, Matthew B.; Webb, John K.

2017-06-01

A new and automated method is presented for the analysis of high-resolution absorption spectra. Three established numerical methods are unified into one `artificial intelligence' process: a genetic algorithm (Genetic Voigt Profile FIT, gvpfit); non-linear least-squares with parameter constraints (vpfit); and Bayesian model averaging (BMA). The method has broad application but here we apply it specifically to the problem of measuring the fine structure constant at high redshift. For this we need objectivity and reproducibility. gvpfit is also motivated by the importance of obtaining a large statistical sample of measurements of Δα/α. Interactive analyses are both time consuming and complex and automation makes obtaining a large sample feasible. In contrast to previous methodologies, we use BMA to derive results using a large set of models and show that this procedure is more robust than a human picking a single preferred model since BMA avoids the systematic uncertainties associated with model choice. Numerical simulations provide stringent tests of the whole process and we show using both real and simulated spectra that the unified automated fitting procedure out-performs a human interactive analysis. The method should be invaluable in the context of future instrumentation like ESPRESSO on the VLT and indeed future ELTs. We apply the method to the zabs = 1.8389 absorber towards the zem = 2.145 quasar J110325-264515. The derived constraint of Δα/α = 3.3 ± 2.9 × 10-6 is consistent with no variation and also consistent with the tentative spatial variation reported in Webb et al. and King et al.

DMPD: The Toll-like receptors: analysis by forward genetic methods. [Dynamic Macrophage Pathway CSML Database

Lifescience Database Archive (English)

Full Text Available 16001129 The Toll-like receptors: analysis by forward genetic methods. Beutler B. I...mmunogenetics. 2005 Jul;57(6):385-92. (.png) (.svg) (.html) (.csml) Show The Toll-like receptors: analysis by forwar...d genetic methods. PubmedID 16001129 Title The Toll-like receptors: analysis by forward genetic meth

Analysis of genetic effects of nuclear-cytoplasmic interaction on quantitative traits: genetic model for diploid plants.

Science.gov (United States)

Han, Lide; Yang, Jian; Zhu, Jun

2007-06-01

A genetic model was proposed for simultaneously analyzing genetic effects of nuclear, cytoplasm, and nuclear-cytoplasmic interaction (NCI) as well as their genotype by environment (GE) interaction for quantitative traits of diploid plants. In the model, the NCI effects were further partitioned into additive and dominance nuclear-cytoplasmic interaction components. Mixed linear model approaches were used for statistical analysis. On the basis of diallel cross designs, Monte Carlo simulations showed that the genetic model was robust for estimating variance components under several situations without specific effects. Random genetic effects were predicted by an adjusted unbiased prediction (AUP) method. Data on four quantitative traits (boll number, lint percentage, fiber length, and micronaire) in Upland cotton (Gossypium hirsutum L.) were analyzed as a worked example to show the effectiveness of the model.

GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research—an update

Science.gov (United States)

Peakall, Rod; Smouse, Peter E.

2012-01-01

Summary: GenAlEx: Genetic Analysis in Excel is a cross-platform package for population genetic analyses that runs within Microsoft Excel. GenAlEx offers analysis of diploid codominant, haploid and binary genetic loci and DNA sequences. Both frequency-based (F-statistics, heterozygosity, HWE, population assignment, relatedness) and distance-based (AMOVA, PCoA, Mantel tests, multivariate spatial autocorrelation) analyses are provided. New features include calculation of new estimators of population structure: G′ST, G′′ST, Jost’s Dest and F′ST through AMOVA, Shannon Information analysis, linkage disequilibrium analysis for biallelic data and novel heterogeneity tests for spatial autocorrelation analysis. Export to more than 30 other data formats is provided. Teaching tutorials and expanded step-by-step output options are included. The comprehensive guide has been fully revised. Availability and implementation: GenAlEx is written in VBA and provided as a Microsoft Excel Add-in (compatible with Excel 2003, 2007, 2010 on PC; Excel 2004, 2011 on Macintosh). GenAlEx, and supporting documentation and tutorials are freely available at: http://biology.anu.edu.au/GenAlEx. Contact: rod.peakall@anu.edu.au PMID:22820204

Parallel island genetic algorithm applied to a nuclear power plant auxiliary feedwater system surveillance tests policy optimization

International Nuclear Information System (INIS)

Pereira, Claudio M.N.A.; Lapa, Celso M.F.

2003-01-01

In this work, we focus the application of an Island Genetic Algorithm (IGA), a coarse-grained parallel genetic algorithm (PGA) model, to a Nuclear Power Plant (NPP) Auxiliary Feedwater System (AFWS) surveillance tests policy optimization. Here, the main objective is to outline, by means of comparisons, the advantages of the IGA over the simple (non-parallel) genetic algorithm (GA), which has been successfully applied in the solution of such kind of problem. The goal of the optimization is to maximize the system's average availability for a given period of time, considering realistic features such as: i) aging effects on standby components during the tests; ii) revealing failures in the tests implies on corrective maintenance, increasing outage times; iii) components have distinct test parameters (outage time, aging factors, etc.) and iv) tests are not necessarily periodic. In our experiments, which were made in a cluster comprised by 8 1-GHz personal computers, we could clearly observe gains not only in the computational time, which reduced linearly with the number of computers, but in the optimization outcome

EMBO Course “Formal Analysis of Genetic Regulation”

CERN Document Server

1979-01-01

The E M B 0 course on "Formal Analysis of Genetic Regulation" A course entitled "Formal analysis of Genetic Regulation" was held at the University of Brussels from 6 to 16 September 1977 under the auspices of EMBO (European Molecular Biology Organization). As indicated by the title of the book (but not explicitly enough by the title of the course), the main emphasis was put on a dynamic analysis of systems using logical methods, that is, methods in which functions and variables take only a limited number of values - typically two. In this respect, this course was complementary to an EMBO course using continuous methods which was held some months later in Israel by Prof. Segel. People from four very different laboratories took an active part in teaching our course in Brussels : Drs Anne LEUSSLER and Philippe VAN HAM, from the Laboratory of Prof. Jean FLORINE (Laboratoire des Systemes logiques et numeriques, Faculte des Sciences appliquees, Universite Libre de Bruxelles). Dr Stuart KAUFFMAN (Dept. of Biochemist...

Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data.

Science.gov (United States)

Fan, Jean; Lee, Hae-Ock; Lee, Soohyun; Ryu, Da-Eun; Lee, Semin; Xue, Catherine; Kim, Seok Jin; Kim, Kihyun; Barkas, Nikolas; Park, Peter J; Park, Woong-Yang; Kharchenko, Peter V

2018-06-13

Characterization of intratumoral heterogeneity is critical to cancer therapy, as presence of phenotypically diverse cell populations commonly fuels relapse and resistance to treatment. Although genetic variation is a well-studied source of intratumoral heterogeneity, the functional impact of most genetic alterations remains unclear. Even less understood is the relative importance of other factors influencing heterogeneity, such as epigenetic state or tumor microenvironment. To investigate the relationship between genetic and transcriptional heterogeneity in a context of cancer progression, we devised a computational approach called HoneyBADGER to identify copy number variation and loss-of-heterozygosity in individual cells from single-cell RNA-sequencing data. By integrating allele and normalized expression information, HoneyBADGER is able to identify and infer the presence of subclone-specific alterations in individual cells and reconstruct underlying subclonal architecture. Examining several tumor types, we show that HoneyBADGER is effective at identifying deletion, amplifications, and copy-neutral loss-of-heterozygosity events, and is capable of robustly identifying subclonal focal alterations as small as 10 megabases. We further apply HoneyBADGER to analyze single cells from a progressive multiple myeloma patient to identify major genetic subclones that exhibit distinct transcriptional signatures relevant to cancer progression. Surprisingly, other prominent transcriptional subpopulations within these tumors did not line up with the genetic subclonal structure, and were likely driven by alternative, non-clonal mechanisms. These results highlight the need for integrative analysis to understand the molecular and phenotypic heterogeneity in cancer. Published by Cold Spring Harbor Laboratory Press.

Comparative genomic analysis of Lactobacillus plantarum ZJ316 reveals its genetic adaptation and potential probiotic profiles.

Science.gov (United States)

Li, Ping; Li, Xuan; Gu, Qing; Lou, Xiu-Yu; Zhang, Xiao-Mei; Song, Da-Feng; Zhang, Chen

2016-08-01

In previous studies, Lactobacillus plantarum ZJ316 showed probiotic properties, such as antimicrobial activity against various pathogens and the capacity to significantly improve pig growth and pork quality. The purpose of this study was to reveal the genes potentially related to its genetic adaptation and probiotic profiles based on comparative genomic analysis. The genome sequence of L. plantarum ZJ316 was compared with those of eight L. plantarum strains deposited in GenBank. BLASTN, Mauve, and MUMmer programs were used for genome alignment and comparison. CRISPRFinder was applied for searching the clustered regularly interspaced short palindromic repeats (CRISPRs). We identified genes that encode proteins related to genetic adaptation and probiotic profiles, including carbohydrate transport and metabolism, proteolytic enzyme systems and amino acid biosynthesis, CRISPR adaptive immunity, stress responses, bile salt resistance, ability to adhere to the host intestinal wall, exopolysaccharide (EPS) biosynthesis, and bacteriocin biosynthesis. Comparative characterization of the L. plantarum ZJ316 genome provided the genetic basis for further elucidating the functional mechanisms of its probiotic properties. ZJ316 could be considered a potential probiotic candidate.

Comparative genomic analysis of Lactobacillus plantarum ZJ316 reveals its genetic adaptation and potential probiotic profiles* #

Science.gov (United States)

Li, Ping; Li, Xuan; Gu, Qing; Lou, Xiu-yu; Zhang, Xiao-mei; Song, Da-feng; Zhang, Chen

2016-01-01

Objective: In previous studies, Lactobacillus plantarum ZJ316 showed probiotic properties, such as antimicrobial activity against various pathogens and the capacity to significantly improve pig growth and pork quality. The purpose of this study was to reveal the genes potentially related to its genetic adaptation and probiotic profiles based on comparative genomic analysis. Methods: The genome sequence of L. plantarum ZJ316 was compared with those of eight L. plantarum strains deposited in GenBank. BLASTN, Mauve, and MUMmer programs were used for genome alignment and comparison. CRISPRFinder was applied for searching the clustered regularly interspaced short palindromic repeats (CRISPRs). Results: We identified genes that encode proteins related to genetic adaptation and probiotic profiles, including carbohydrate transport and metabolism, proteolytic enzyme systems and amino acid biosynthesis, CRISPR adaptive immunity, stress responses, bile salt resistance, ability to adhere to the host intestinal wall, exopolysaccharide (EPS) biosynthesis, and bacteriocin biosynthesis. Conclusions: Comparative characterization of the L. plantarum ZJ316 genome provided the genetic basis for further elucidating the functional mechanisms of its probiotic properties. ZJ316 could be considered a potential probiotic candidate. PMID:27487802

Phenotypic and molecular genetic analysis of Pyruvate Kinase ...

African Journals Online (AJOL)

Phenotypic and molecular genetic analysis of Pyruvate Kinase deficiency in a Tunisian family. Jaouani Mouna, Hamdi Nadia, Chaouch Leila, Kalai Miniar, Mellouli Fethi, Darragi Imen, Boudriga Imen, Chaouachi Dorra, Bejaoui Mohamed, Abbes Salem ...

Adaptive divergence despite strong genetic drift: genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (Urocyon littoralis)

Science.gov (United States)

FUNK, W. CHRIS; LOVICH, ROBERT E.; HOHENLOHE, PAUL A.; HOFMAN, COURTNEY A.; MORRISON, SCOTT A.; SILLETT, T. SCOTT; GHALAMBOR, CAMERON K.; MALDONADO, JESUS E.; RICK, TORBEN C.; DAY, MITCH D.; POLATO, NICHOLAS R.; FITZPATRICK, SARAH W.; COONAN, TIMOTHY J.; CROOKS, KEVIN R.; DILLON, ADAM; GARCELON, DAVID K.; KING, JULIE L.; BOSER, CHRISTINA L.; GOULD, NICHOLAS; ANDELT, WILLIAM F.

2016-01-01

The evolutionary mechanisms generating the tremendous biodiversity of islands have long fascinated evolutionary biologists. Genetic drift and divergent selection are predicted to be strong on islands and both could drive population divergence and speciation. Alternatively, strong genetic drift may preclude adaptation. We conducted a genomic analysis to test the roles of genetic drift and divergent selection in causing genetic differentiation among populations of the island fox (Urocyon littoralis). This species consists of 6 subspecies, each of which occupies a different California Channel Island. Analysis of 5293 SNP loci generated using Restriction-site Associated DNA (RAD) sequencing found support for genetic drift as the dominant evolutionary mechanism driving population divergence among island fox populations. In particular, populations had exceptionally low genetic variation, small Ne (range = 2.1–89.7; median = 19.4), and significant genetic signatures of bottlenecks. Moreover, islands with the lowest genetic variation (and, by inference, the strongest historical genetic drift) were most genetically differentiated from mainland gray foxes, and vice versa, indicating genetic drift drives genome-wide divergence. Nonetheless, outlier tests identified 3.6–6.6% of loci as high FST outliers, suggesting that despite strong genetic drift, divergent selection contributes to population divergence. Patterns of similarity among populations based on high FST outliers mirrored patterns based on morphology, providing additional evidence that outliers reflect adaptive divergence. Extremely low genetic variation and small Ne in some island fox populations, particularly on San Nicolas Island, suggest that they may be vulnerable to fixation of deleterious alleles, decreased fitness, and reduced adaptive potential. PMID:26992010

Adaptive divergence despite strong genetic drift: genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (Urocyon littoralis).

Science.gov (United States)

Funk, W Chris; Lovich, Robert E; Hohenlohe, Paul A; Hofman, Courtney A; Morrison, Scott A; Sillett, T Scott; Ghalambor, Cameron K; Maldonado, Jesus E; Rick, Torben C; Day, Mitch D; Polato, Nicholas R; Fitzpatrick, Sarah W; Coonan, Timothy J; Crooks, Kevin R; Dillon, Adam; Garcelon, David K; King, Julie L; Boser, Christina L; Gould, Nicholas; Andelt, William F

2016-05-01

The evolutionary mechanisms generating the tremendous biodiversity of islands have long fascinated evolutionary biologists. Genetic drift and divergent selection are predicted to be strong on islands and both could drive population divergence and speciation. Alternatively, strong genetic drift may preclude adaptation. We conducted a genomic analysis to test the roles of genetic drift and divergent selection in causing genetic differentiation among populations of the island fox (Urocyon littoralis). This species consists of six subspecies, each of which occupies a different California Channel Island. Analysis of 5293 SNP loci generated using Restriction-site Associated DNA (RAD) sequencing found support for genetic drift as the dominant evolutionary mechanism driving population divergence among island fox populations. In particular, populations had exceptionally low genetic variation, small Ne (range = 2.1-89.7; median = 19.4), and significant genetic signatures of bottlenecks. Moreover, islands with the lowest genetic variation (and, by inference, the strongest historical genetic drift) were most genetically differentiated from mainland grey foxes, and vice versa, indicating genetic drift drives genome-wide divergence. Nonetheless, outlier tests identified 3.6-6.6% of loci as high FST outliers, suggesting that despite strong genetic drift, divergent selection contributes to population divergence. Patterns of similarity among populations based on high FST outliers mirrored patterns based on morphology, providing additional evidence that outliers reflect adaptive divergence. Extremely low genetic variation and small Ne in some island fox populations, particularly on San Nicolas Island, suggest that they may be vulnerable to fixation of deleterious alleles, decreased fitness and reduced adaptive potential. © 2016 John Wiley & Sons Ltd.

Development of a multiplex PCR for the genetic analysis of paddlefish (Polyodon spathula Walbaum,1792 populations

Directory of Open Access Journals (Sweden)

K. Kurta

2017-12-01

Full Text Available Purpose. Paddlefish is commercially important species owing to its biological features and consumer characteristics, namely it produces valuable and delicious fish products, such as high quality meat and black caviar. Consequently, its cultivation under Ukrainian fish farm conditions and further realization in domestic and foreign markets are economically efficient. However, the paddlefish broodstock in Ukraine requires the efficient solution of increasing its productivity, identification and assessment of its genetic variation. Thus, the aim of our study was to develop and implement a multiplex PCR-analysis of paddlefish (Polyodon spathula for population-genetic monitoring of its artificial broodstocks in Ukraine. Methodology. A multiplex PCR was used for the study. The multiplex PCR development was performed for four microsatellite DNA markers: Psp12, Psp21, Psp26 and Psp28. Each investigated DNA loci, for which the multiplex PCR was optimized, was selected in such a way that the colored PCR products labeled with fluorescent dye did not overlap the length of the amplified fragments. Evaluation of the multiplex PCR effectiveness and processing of the data were performed by fragment analysis of DNA on the genetic analyzer ABI Prism 3130 (Applied Biosystem, USA. The size of the identified alleles was determined using the "Gene Mapper 3.7" program (Applied Biosystems, USA and LIZ-500 size standard (Applied Biosystems, USA. Results. Based on the results of capillary electrophoresis of multiplex PCR products, it was found that the amplified fragments for each of the four studied loci: Psp12, Psp21, Psp26 and Psp28 in one PCR reaction were within the expected size range. Data analysis on the electrophoregram demonstrated that Psp21 had the highest peak intensity at 611 fluorescent units (FU and the lowest peak intensity at 105 FU was observed for Psp26 locus. In the multiplex PCR after proper interpretation of the data we identified heterozygous

Analytical Plug-In Method for Kernel Density Estimator Applied to Genetic Neutrality Study

Directory of Open Access Journals (Sweden)

Samir Saoudi

2008-07-01

Full Text Available The plug-in method enables optimization of the bandwidth of the kernel density estimator in order to estimate probability density functions (pdfs. Here, a faster procedure than that of the common plug-in method is proposed. The mean integrated square error (MISE depends directly upon J(f which is linked to the second-order derivative of the pdf. As we intend to introduce an analytical approximation of J(f, the pdf is estimated only once, at the end of iterations. These two kinds of algorithm are tested on different random variables having distributions known for their difficult estimation. Finally, they are applied to genetic data in order to provide a better characterisation in the mean of neutrality of Tunisian Berber populations.

A genetic algorithm applied to a PWR turbine extraction optimization to increase cycle efficiency

International Nuclear Information System (INIS)

Sacco, Wagner F.; Schirru, Roberto

2002-01-01

In nuclear power plants feedwater heaters are used to heat feedwater from its temperature leaving the condenser to final feedwater temperature using steam extracted from various stages of the turbines. The purpose of this process is to increase cycle efficiency. The determination of the optimal fraction of mass flow rate to be extracted from each stage of the turbines is a complex optimization problem. This kind of problem has been efficiently solved by means of evolutionary computation techniques, such as Genetic Algorithms (GAs). GAs, which are systems based upon principles from biological genetics, have been successfully applied to several combinatorial optimization problems in nuclear engineering, as the nuclear fuel reload optimization problem. We introduce the use of GAs in cycle efficiency optimization by finding an optimal combination of turbine extractions. In order to demonstrate the effectiveness of our approach, we have chosen a typical PWR as case study. The secondary side of the PWR was simulated using PEPSE, which is a modeling tool used to perform integrated heat balances for power plants. The results indicate that the GA is a quite promising tool for cycle efficiency optimization. (author)

Genetic analysis of rare disorders: Bayesian estimation of twin concordance rates

NARCIS (Netherlands)

van den Berg, Stéphanie Martine; Hjelmborg, J.

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

A novel genetic tool for clonal analysis of fourth chromosome mutations

OpenAIRE

Sousa-Neves, Rui; Schinaman, Joseph M.

2012-01-01

The fourth chromosome of Drosophila remains one of the most intractable regions of the fly genome to genetic analysis. The main difficulty posed to the genetic analyses of mutations on this chromosome arises from the fact that it does not undergo meiotic recombination, which makes recombination mapping impossible, and also prevents clonal analysis of mutations, a technique which relies on recombination to introduce the prerequisite recessive markers and FLP-recombinase recognition targets (FR...

Analysis of genetic polymorphism of nine short tandem repeat loci in ...

African Journals Online (AJOL)

Yomi

2012-03-15

Mar 15, 2012 ... Key words: short tandem repeat, repeat motif, genetic polymorphism, Han population, forensic genetics. INTRODUCTION. Short tandem repeat (STR) is widely .... Data analysis. The exact test of Hardy-Weinberg equilibrium was conducted with. Arlequin version 3.5 software (Computational and Molecular.

Lessons learned in applying function analysis

International Nuclear Information System (INIS)

Mitchel, G.R.; Davey, E.; Basso, R.

2001-01-01

This paper summarizes the lessons learned in undertaking and applying function analysis based on the recent experience of utility, AECL and international design and assessment projects. Function analysis is an analytical technique that can be used to characterize and asses the functions of a system and is widely recognized as an essential component of a 'systematic' approach to design, on that integrated operational and user requirements into the standard design process. (author)

Applying homotopy analysis method for solving differential-difference equation

International Nuclear Information System (INIS)

Wang Zhen; Zou Li; Zhang Hongqing

2007-01-01

In this Letter, we apply the homotopy analysis method to solving the differential-difference equations. A simple but typical example is applied to illustrate the validity and the great potential of the generalized homotopy analysis method in solving differential-difference equation. Comparisons are made between the results of the proposed method and exact solutions. The results show that the homotopy analysis method is an attractive method in solving the differential-difference equations

Microchip capillary gel electrophoresis using programmed field strength gradients for the ultra-fast analysis of genetically modified organisms in soybeans.

Science.gov (United States)

Kim, Yun-Jeong; Chae, Joon-Seok; Chang, Jun Keun; Kang, Seong Ho

2005-08-12

We have developed a novel method for the ultra-fast analysis of genetically modified organisms (GMOs) in soybeans by microchip capillary gel electrophoresis (MCGE) using programmed field strength gradients (PFSG) in a conventional glass double-T microchip. Under the programmed electric field strength and 0.3% poly(ethylene oxide) sieving matrix, the GMO in soybeans was analyzed within only 11 s of the microchip. The MCGE-PFSG method was a program that changes the electric field strength during GMO analysis, and was also applied to the ultra-fast analysis of PCR products. Compared to MCGE using a conventional and constantly applied electric field, the MCGE-PFSG analysis generated faster results without the loss of resolving power and reproducibility for specific DNA fragments (100- and 250-bp DNA) of GM-soybeans. The MCGE-PFSG technique may prove to be a new tool in the GMO analysis due to its speed, simplicity, and high efficiency.

Genetic Code Analysis Toolkit: A novel tool to explore the coding properties of the genetic code and DNA sequences

Science.gov (United States)

Kraljić, K.; Strüngmann, L.; Fimmel, E.; Gumbel, M.

2018-01-01

The genetic code is degenerated and it is assumed that redundancy provides error detection and correction mechanisms in the translation process. However, the biological meaning of the code's structure is still under current research. This paper presents a Genetic Code Analysis Toolkit (GCAT) which provides workflows and algorithms for the analysis of the structure of nucleotide sequences. In particular, sets or sequences of codons can be transformed and tested for circularity, comma-freeness, dichotomic partitions and others. GCAT comes with a fertile editor custom-built to work with the genetic code and a batch mode for multi-sequence processing. With the ability to read FASTA files or load sequences from GenBank, the tool can be used for the mathematical and statistical analysis of existing sequence data. GCAT is Java-based and provides a plug-in concept for extensibility. Availability: Open source Homepage:http://www.gcat.bio/

Different approaches in Partial Least Squares and Artificial Neural Network models applied for the analysis of a ternary mixture of Amlodipine, Valsartan and Hydrochlorothiazide

Science.gov (United States)

Darwish, Hany W.; Hassan, Said A.; Salem, Maissa Y.; El-Zeany, Badr A.

2014-03-01

Different chemometric models were applied for the quantitative analysis of Amlodipine (AML), Valsartan (VAL) and Hydrochlorothiazide (HCT) in ternary mixture, namely, Partial Least Squares (PLS) as traditional chemometric model and Artificial Neural Networks (ANN) as advanced model. PLS and ANN were applied with and without variable selection procedure (Genetic Algorithm GA) and data compression procedure (Principal Component Analysis PCA). The chemometric methods applied are PLS-1, GA-PLS, ANN, GA-ANN and PCA-ANN. The methods were used for the quantitative analysis of the drugs in raw materials and pharmaceutical dosage form via handling the UV spectral data. A 3-factor 5-level experimental design was established resulting in 25 mixtures containing different ratios of the drugs. Fifteen mixtures were used as a calibration set and the other ten mixtures were used as validation set to validate the prediction ability of the suggested methods. The validity of the proposed methods was assessed using the standard addition technique.

Genetic association analysis of vitamin D receptor gene polymorphisms and obesity-related phenotypes.

Science.gov (United States)

Correa-Rodríguez, M; Carrillo-Ávila, J A; Schmidt-RioValle, J; González-Jiménez, E; Vargas, S; Martín, J; Rueda-Medina, B

2018-01-15

Vitamin D has been established as a key factor in the development of obesity through the vitamin D receptor (VDR). The aim of this study was to investigate the contribution of the VDR gene to obesity-related phenotypes in a population of Caucasian young adults. The study population consisted of 701 healthy Spanish young adults (mean age 20.41±2.48). Three single-nucleotide polymorphisms (SNPs) of VDR (TaqI, BsmI and FokI) were selected as genetic markers. Body composition measurements including weight, body mass index (BMI), fat mass (FM), percentage of fat mass (PFM), fat-free mass (FFM) and visceral fat level (VFL) were analysed. Differences in obesity traits across the genotypes were determined using analysis of covariance (ANCOVA). The FokI polymorphism showed a significant association with PFM across the whole population after adjusting for age and sex (p=0.022). Age-adjusted analysis revealed an association between body weight and the TaqI and BsmI SNPs in males (p=0.033 and p=0.028, respectively). However, these positive findings did not remain significant after applying the Bonferroni correction for multiple testing. Our findings suggest that VDR genetic variants are unlikely to play a major role in obesity-related phenotypes in a population of Caucasian young adults. Copyright © 2017 Elsevier B.V. All rights reserved.

Logic analysis and verification of n-input genetic logic circuits

DEFF Research Database (Denmark)

Baig, Hasan; Madsen, Jan

2017-01-01

. In this paper, we present an approach to analyze and verify the Boolean logic of a genetic circuit from the data obtained through stochastic analog circuit simulations. The usefulness of this analysis is demonstrated through different case studies illustrating how our approach can be used to verify the expected......Nature is using genetic logic circuits to regulate the fundamental processes of life. These genetic logic circuits are triggered by a combination of external signals, such as chemicals, proteins, light and temperature, to emit signals to control other gene expressions or metabolic pathways...... accordingly. As compared to electronic circuits, genetic circuits exhibit stochastic behavior and do not always behave as intended. Therefore, there is a growing interest in being able to analyze and verify the logical behavior of a genetic circuit model, prior to its physical implementation in a laboratory...

Population genetic analysis and trichothecene profiling of Fusarium graminearum from wheat in Uruguay.

Science.gov (United States)

Pan, D; Mionetto, A; Calero, N; Reynoso, M M; Torres, A; Bettucci, L

2016-03-11

Fusarium graminearum sensu stricto (F. graminearum s.s.) is the major causal agent of Fusarium head blight of wheat worldwide, and contaminates grains with trichothecene mycotoxins that cause serious threats to food safety and animal health. An important aspect of managing this pathogen and reducing mycotoxin contamination of wheat is knowledge regarding its population genetics. Therefore, isolates of F. graminearum s.s. from the major wheat-growing region of Uruguay were analyzed by amplified fragment length polymorphism assays, PCR genotyping, and chemical analysis of trichothecene production. Of the 102 isolates identified as having the 15-ADON genotype via PCR genotyping, all were DON producers, but only 41 strains were also 15-ADON producers, as determined by chemical analysis. The populations were genotypically diverse but genetically similar, with significant genetic exchange occurring between them. Analysis of molecular variance indicated that most of the genetic variability resulted from differences between isolates within populations. Multilocus linkage disequilibrium analysis suggested that the isolates had a panmictic population genetic structure and that there is significant recombination occurs in F. graminearum s.s. In conclusion, tour findings provide the first detailed description of the genetic structure and trichothecene production of populations of F. graminearum s.s. from Uruguay, and expands our understanding of the agroecology of F. graminearum and of the correlation between genotypes and trichothecene chemotypes.

Genetic Diversity of Rose germplasm based on RAPD analysis

African Journals Online (AJOL)

AHSAN IQBAL

2012-06-12

Jun 12, 2012 ... identification and analysis of genetic variation within a collection of 4 species and 30 accessions of rose using RAPD analysis technique. The results showed the molecular distinctions among the ... that range in colour from white and yellow to many shades of pink and red have been developed. Since.

Analytical Plug-In Method for Kernel Density Estimator Applied to Genetic Neutrality Study

Science.gov (United States)

Troudi, Molka; Alimi, Adel M.; Saoudi, Samir

2008-12-01

The plug-in method enables optimization of the bandwidth of the kernel density estimator in order to estimate probability density functions (pdfs). Here, a faster procedure than that of the common plug-in method is proposed. The mean integrated square error (MISE) depends directly upon [InlineEquation not available: see fulltext.] which is linked to the second-order derivative of the pdf. As we intend to introduce an analytical approximation of [InlineEquation not available: see fulltext.], the pdf is estimated only once, at the end of iterations. These two kinds of algorithm are tested on different random variables having distributions known for their difficult estimation. Finally, they are applied to genetic data in order to provide a better characterisation in the mean of neutrality of Tunisian Berber populations.

Applying data envelopment analysis to preventive medicine: a novel method for constructing a personalized risk model of obesity.

Directory of Open Access Journals (Sweden)

Hiroto Narimatsu

Full Text Available Data envelopment analysis (DEA is a method of operations research that has not yet been applied in the field of obesity research. However, DEA might be used to evaluate individuals' susceptibility to obesity, which could help establish effective risk models for the onset of obesity. Therefore, we conducted this study to evaluate the feasibility of applying DEA to predict obesity, by calculating efficiency scores and evaluating the usefulness of risk models. In this study, we evaluated data from the Takahata study, which was a population-based cohort study (with a follow-up study of Japanese people who are >40 years old. For our analysis, we used the input-oriented Charnes-Cooper-Rhodes model of DEA, and defined the decision-making units (DMUs as individual subjects. The inputs were defined as (1 exercise (measured as calories expended and (2 the inverse of food intake (measured as calories ingested. The output was defined as the inverse of body mass index (BMI. Using the β coefficients for the participants' single nucleotide polymorphisms, we then calculated their genetic predisposition score (GPS. Both efficiency scores and GPS were available for 1,620 participants from the baseline survey, and for 708 participants from the follow-up survey. To compare the strengths of the associations, we used models of multiple linear regressions. To evaluate the effects of genetic factors and efficiency score on body mass index (BMI, we used multiple linear regression analysis, with BMI as the dependent variable, GPS and efficiency scores as the explanatory variables, and several demographic controls, including age and sex. Our results indicated that all factors were statistically significant (p < 0.05, with an adjusted R2 value of 0.66. Therefore, it is possible to use DEA to predict environmentally driven obesity, and thus to establish a well-fitted model for risk of obesity.

DATE analysis: A general theory of biological change applied to microarray data.

Science.gov (United States)

Rasnick, David

2009-01-01

In contrast to conventional data mining, which searches for specific subsets of genes (extensive variables) to correlate with specific phenotypes, DATE analysis correlates intensive state variables calculated from the same datasets. At the heart of DATE analysis are two biological equations of state not dependent on genetic pathways. This result distinguishes DATE analysis from other bioinformatics approaches. The dimensionless state variable F quantifies the relative overall cellular activity of test cells compared to well-chosen reference cells. The variable pi(i) is the fold-change in the expression of the ith gene of test cells relative to reference. It is the fraction phi of the genome undergoing differential expression-not the magnitude pi-that controls biological change. The state variable phi is equivalent to the control strength of metabolic control analysis. For tractability, DATE analysis assumes a linear system of enzyme-connected networks and exploits the small average contribution of each cellular component. This approach was validated by reproducible values of the state variables F, RNA index, and phi calculated from random subsets of transcript microarray data. Using published microarray data, F, RNA index, and phi were correlated with: (1) the blood-feeding cycle of the malaria parasite, (2) embryonic development of the fruit fly, (3) temperature adaptation of Killifish, (4) exponential growth of cultured S. pneumoniae, and (5) human cancers. DATE analysis was applied to aCGH data from the great apes. A good example of the power of DATE analysis is its application to genomically unstable cancers, which have been refractory to data mining strategies. 2009 American Institute of Chemical Engineers Biotechnol.

Assessing the impact of a combined analysis of four common low-risk genetic variants on autism risk

Directory of Open Access Journals (Sweden)

Carayol Jerome

2010-02-01

Full Text Available Abstract Background Autism is a complex disorder characterized by deficits involving communication, social interaction, and repetitive and restrictive patterns of behavior. Twin studies have shown that autism is strongly heritable, suggesting a strong genetic component. In other disease states with a complex etiology, such as type 2 diabetes, cancer and cardiovascular disease, combined analysis of multiple genetic variants in a genetic score has helped to identify individuals at high risk of disease. Genetic scores are designed to test for association of genetic markers with disease. Method The accumulation of multiple risk alleles markedly increases the risk of being affected, and compared with studying polymorphisms individually, it improves the identification of subgroups of individuals at greater risk. In the present study, we show that this approach can be applied to autism by specifically looking at a high-risk population of children who have siblings with autism. A two-sample study design and the generation of a genetic score using multiple independent genes were used to assess the risk of autism in a high-risk population. Results In both samples, odds ratios (ORs increased significantly as a function of the number of risk alleles, with a genetic score of 8 being associated with an OR of 5.54 (95% confidence interval [CI] 2.45 to 12.49. The sensitivities and specificities for each genetic score were similar in both analyses, and the resultant area under the receiver operating characteristic curves were identical (0.59. Conclusions These results suggest that the accumulation of multiple risk alleles in a genetic score is a useful strategy for assessing the risk of autism in siblings of affected individuals, and may be better than studying single polymorphisms for identifying subgroups of individuals with significantly greater risk.

Analysis of intra-host genetic diversity of Prunus necrotic ringspot virus (PNRSV) using amplicon next generation sequencing.

Science.gov (United States)

Kinoti, Wycliff M; Constable, Fiona E; Nancarrow, Narelle; Plummer, Kim M; Rodoni, Brendan

2017-01-01

PCR amplicon next generation sequencing (NGS) analysis offers a broadly applicable and targeted approach to detect populations of both high- or low-frequency virus variants in one or more plant samples. In this study, amplicon NGS was used to explore the diversity of the tripartite genome virus, Prunus necrotic ringspot virus (PNRSV) from 53 PNRSV-infected trees using amplicons from conserved gene regions of each of PNRSV RNA1, RNA2 and RNA3. Sequencing of the amplicons from 53 PNRSV-infected trees revealed differing levels of polymorphism across the three different components of the PNRSV genome with a total number of 5040, 2083 and 5486 sequence variants observed for RNA1, RNA2 and RNA3 respectively. The RNA2 had the lowest diversity of sequences compared to RNA1 and RNA3, reflecting the lack of flexibility tolerated by the replicase gene that is encoded by this RNA component. Distinct PNRSV phylo-groups, consisting of closely related clusters of sequence variants, were observed in each of PNRSV RNA1, RNA2 and RNA3. Most plant samples had a single phylo-group for each RNA component. Haplotype network analysis showed that smaller clusters of PNRSV sequence variants were genetically connected to the largest sequence variant cluster within a phylo-group of each RNA component. Some plant samples had sequence variants occurring in multiple PNRSV phylo-groups in at least one of each RNA and these phylo-groups formed distinct clades that represent PNRSV genetic strains. Variants within the same phylo-group of each Prunus plant sample had ≥97% similarity and phylo-groups within a Prunus plant sample and between samples had less ≤97% similarity. Based on the analysis of diversity, a definition of a PNRSV genetic strain was proposed. The proposed definition was applied to determine the number of PNRSV genetic strains in each of the plant samples and the complexity in defining genetic strains in multipartite genome viruses was explored.

Analysis of intra-host genetic diversity of Prunus necrotic ringspot virus (PNRSV using amplicon next generation sequencing.

Directory of Open Access Journals (Sweden)

Wycliff M Kinoti

Full Text Available PCR amplicon next generation sequencing (NGS analysis offers a broadly applicable and targeted approach to detect populations of both high- or low-frequency virus variants in one or more plant samples. In this study, amplicon NGS was used to explore the diversity of the tripartite genome virus, Prunus necrotic ringspot virus (PNRSV from 53 PNRSV-infected trees using amplicons from conserved gene regions of each of PNRSV RNA1, RNA2 and RNA3. Sequencing of the amplicons from 53 PNRSV-infected trees revealed differing levels of polymorphism across the three different components of the PNRSV genome with a total number of 5040, 2083 and 5486 sequence variants observed for RNA1, RNA2 and RNA3 respectively. The RNA2 had the lowest diversity of sequences compared to RNA1 and RNA3, reflecting the lack of flexibility tolerated by the replicase gene that is encoded by this RNA component. Distinct PNRSV phylo-groups, consisting of closely related clusters of sequence variants, were observed in each of PNRSV RNA1, RNA2 and RNA3. Most plant samples had a single phylo-group for each RNA component. Haplotype network analysis showed that smaller clusters of PNRSV sequence variants were genetically connected to the largest sequence variant cluster within a phylo-group of each RNA component. Some plant samples had sequence variants occurring in multiple PNRSV phylo-groups in at least one of each RNA and these phylo-groups formed distinct clades that represent PNRSV genetic strains. Variants within the same phylo-group of each Prunus plant sample had ≥97% similarity and phylo-groups within a Prunus plant sample and between samples had less ≤97% similarity. Based on the analysis of diversity, a definition of a PNRSV genetic strain was proposed. The proposed definition was applied to determine the number of PNRSV genetic strains in each of the plant samples and the complexity in defining genetic strains in multipartite genome viruses was explored.

Analysis of the human diseasome using phenotype similarity between common, genetic, and infectious diseases

KAUST Repository

Hoehndorf, Robert

2015-06-08

Phenotypes are the observable characteristics of an organism arising from its response to the environment. Phenotypes associated with engineered and natural genetic variation are widely recorded using phenotype ontologies in model organisms, as are signs and symptoms of human Mendelian diseases in databases such as OMIM and Orphanet. Exploiting these resources, several computational methods have been developed for integration and analysis of phenotype data to identify the genetic etiology of diseases or suggest plausible interventions. A similar resource would be highly useful not only for rare and Mendelian diseases, but also for common, complex and infectious diseases. We apply a semantic text-mining approach to identify the phenotypes (signs and symptoms) associated with over 6,000 diseases. We evaluate our text-mined phenotypes by demonstrating that they can correctly identify known disease-associated genes in mice and humans with high accuracy. Using a phenotypic similarity measure, we generate a human disease network in which diseases that have similar signs and symptoms cluster together, and we use this network to identify closely related diseases based on common etiological, anatomical as well as physiological underpinnings.

Analysis of the human diseasome using phenotype similarity between common, genetic, and infectious diseases

Science.gov (United States)

Hoehndorf, Robert; Schofield, Paul N.; Gkoutos, Georgios V.

2015-06-01

Phenotypes are the observable characteristics of an organism arising from its response to the environment. Phenotypes associated with engineered and natural genetic variation are widely recorded using phenotype ontologies in model organisms, as are signs and symptoms of human Mendelian diseases in databases such as OMIM and Orphanet. Exploiting these resources, several computational methods have been developed for integration and analysis of phenotype data to identify the genetic etiology of diseases or suggest plausible interventions. A similar resource would be highly useful not only for rare and Mendelian diseases, but also for common, complex and infectious diseases. We apply a semantic text-mining approach to identify the phenotypes (signs and symptoms) associated with over 6,000 diseases. We evaluate our text-mined phenotypes by demonstrating that they can correctly identify known disease-associated genes in mice and humans with high accuracy. Using a phenotypic similarity measure, we generate a human disease network in which diseases that have similar signs and symptoms cluster together, and we use this network to identify closely related diseases based on common etiological, anatomical as well as physiological underpinnings.

Hierarchical linear modeling of longitudinal pedigree data for genetic association analysis

DEFF Research Database (Denmark)

Tan, Qihua; B Hjelmborg, Jacob V; Thomassen, Mads

2014-01-01

-effect models to explicitly model the genetic relationship. These have proved to be an efficient way of dealing with sample clustering in pedigree data. Although current algorithms implemented in popular statistical packages are useful for adjusting relatedness in the mixed modeling of genetic effects...... associated with blood pressure with estimated inflation factors of 0.99, suggesting that our modeling of random effects efficiently handles the genetic relatedness in pedigrees. Application to simulated data captures important variants specified in the simulation. Our results show that the method is useful......Genetic association analysis on complex phenotypes under a longitudinal design involving pedigrees encounters the problem of correlation within pedigrees, which could affect statistical assessment of the genetic effects. Approaches have been proposed to integrate kinship correlation into the mixed...

Raps markers for genetic diversity analysis in rice (Oryza sativa L)

Energy Technology Data Exchange (ETDEWEB)

Alvarez, A; Fuentes, Jorge L [Centro de Estudios Aplicados al Desarrollo Nuclear, La Habana (Cuba); Deus, Juan E [Instituto de Investigaciones del Arroz, Habana (Cuba); Duque, Maria C [Centro Internacional de la Agricultura Tropical. Proyecto de Arroz , Cali (Colombia)

1999-07-01

The establishment of relationships between genotypes existing in gene banks that may be used in new crosses, and about genetic diversity in available germplasm, is very useful for plant breeders. In this work, a genetic diversity analysis among 20 varieties of the Cuban rice germplasm bank was performed by using RAPD markers. Twenty four decamer primers were screened which produced 61 polymorphic bands out of 105 consistent and reproducible amplified fragments (58.1 %). The proportion of polymorphic bands varied for each primer, with an average of 3 polymorphic bands per primer, these results agreed with previous reports on RAPD polymorphism in rice germplasm. Depending on the primer, 1 to 7 distinct patterns were obtained among the screened genotypes. Pair-wise genetic distances between genotypes were computed based on Dice's coefficient. Three major, statistically robust groups were obtained in the UPGMA dendrogram (A, B and C) which clearly corresponded to different genetic pools. Additionally, more insight could be gained according to the sub-grouping pattern within group A, which included the principal semi-dwarf commercial varieties. The present study allowed to prove the efficiency of RAPD markers for genetic diversity analysis in closely related germplasm, particularly for the semi-dwarf Cuban commercial rice cultivars. Also, the existence of a narrow genetic base among these varieties has been confirmed, pointing at the urgent necessity of widen it.

Raps markers for genetic diversity analysis in rice (Oryza sativa L)

International Nuclear Information System (INIS)

Alvarez, A.; Fuentes, Jorge L.; Deus, Juan E.; Duque, Maria C.

1999-01-01

The establishment of relationships between genotypes existing in gene banks that may be used in new crosses, and about genetic diversity in available germplasm, is very useful for plant breeders. In this work, a genetic diversity analysis among 20 varieties of the Cuban rice germplasm bank was performed by using RAPD markers. Twenty four decamer primers were screened which produced 61 polymorphic bands out of 105 consistent and reproducible amplified fragments (58.1 %). The proportion of polymorphic bands varied for each primer, with an average of 3 polymorphic bands per primer, these results agreed with previous reports on RAPD polymorphism in rice germplasm. Depending on the primer, 1 to 7 distinct patterns were obtained among the screened genotypes. Pair-wise genetic distances between genotypes were computed based on Dice's coefficient. Three major, statistically robust groups were obtained in the UPGMA dendrogram (A, B and C) which clearly corresponded to different genetic pools. Additionally, more insight could be gained according to the sub-grouping pattern within group A, which included the principal semi-dwarf commercial varieties. The present study allowed to prove the efficiency of RAPD markers for genetic diversity analysis in closely related germplasm, particularly for the semi-dwarf Cuban commercial rice cultivars. Also, the existence of a narrow genetic base among these varieties has been confirmed, pointing at the urgent necessity of widen it

Genetic structure and variability within and among populations of the ...

African Journals Online (AJOL)

Lalouta

2014-01-01

Jan 1, 2014 ... The clustering analysis performed with 'structure' detected the absence of .... tance of molecular information in the establishment of genetic improvement ... applied using a Markov Chain Monte Carlo simulation (100 batches,.

Microsatellite DNA analysis of northern pike ( Esox lucius L.) populations: insights into the genetic structure and demographic history of a genetically depauperate species

DEFF Research Database (Denmark)

Jacobsen, B. H.; Hansen, Michael Møller; Loeschcke, V.

2005-01-01

The northern pike Esox lucius L. is a freshwater fish exhibiting pronounced population subdivision and low genetic variability. However, there is limited knowledge on phylogeographical patterns within the species, and it is not known whether the low genetic variability reflects primarily current...... low effective population sizes or historical bottlenecks. We analysed six microsatellite loci in ten populations from Europe and North America. Genetic variation was low, with the average number of alleles within populations ranging from 2.3 to 4.0 per locus. Genetic differentiation among populations...... was high (overall theta(ST) = 0.51; overall rho(ST) = 0.50). Multidimensional scaling analysis of genetic distances between populations and spatial analysis of molecular variance suggested a single phylogeographical race within the sampled populations from northern Europe, whereas North American...

A finding in genetic polymorphism analysis study: A case of non-mosaic 47, XXX without manifestations.

Science.gov (United States)

Yang, Xingyi; Ye, Zilan; Zhang, Xiaofang; Wang, Huijun; Liu, Chao

2017-07-01

Trisomy X (47, XXX) is a sex chromosome aneuploidy condition in which females have an extra X chromosome, compared to the 46, XX karyotype in typical females. There is considerable variation in the phenotype, with some individuals very mildly affected and others with more significant physical and psychological features. However, the trisomy X in this case, without any of these phenotype, is rarely reported. Here, we report a case found during DNA sample collection in a study of genetic polymorphism analysis of loci in Chinese ethnic group, of a female with neither laboratory or clinical signs of Triple X syndrome. She was born at her mother's 60years old and her father's 62years old. Advanced maternal age was found acting as a significant risk factor of Triplo-X. Moreover, her child are also born without manifestations of 47, XXX syndrome. Pedigree study demonstrated the normal karyotype of the children. A diagnosis of 47XXX was made on the basis of a chromosomal study. Therefore, laboratory investigations (including PCR amplification, more than two kinds of X-STR genotyping, G-banding karyotyping analysis and Pedigree study) are applied to rule out the possibility of Mosaicism (45, X0/47, XXX) and ascertain her 47XXX karyotype without mosaic. The objective of this study was to report a case of trisomy X, diagnostic investigation and management of the case, and to analysis the genetically possible reasons behind the case. To our knowledge, this case is a rare one, found in DNA sample collection for the estimation of gene frequency in the process of genetic polymorphism study, of non-mosaic 47, XXX without signs of physical syndrome and born healthy children. In this study, it revealed that the proportion of trisomy X would be more than official statistics and risk of systemic disabilities is lower than estimated. Moreover, we found out that sample mixture and mosaicism act as the interference factors in forensic test. Therefore, we draw the conclusion that

Analysis of conditional genetic effects and variance components in developmental genetics.

Science.gov (United States)

Zhu, J

1995-12-01

A genetic model with additive-dominance effects and genotype x environment interactions is presented for quantitative traits with time-dependent measures. The genetic model for phenotypic means at time t conditional on phenotypic means measured at previous time (t-1) is defined. Statistical methods are proposed for analyzing conditional genetic effects and conditional genetic variance components. Conditional variances can be estimated by minimum norm quadratic unbiased estimation (MINQUE) method. An adjusted unbiased prediction (AUP) procedure is suggested for predicting conditional genetic effects. A worked example from cotton fruiting data is given for comparison of unconditional and conditional genetic variances and additive effects.

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 co...... applications. The methods presented are implemented in such a way that large and complex quantitative genetic data can be analyzed......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...

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 co...... applications. The methods presented are implemented in such a way that large and complex quantitative genetic data can be analyzed......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...

A niching genetic algorithm applied to a nuclear power plant auxiliary feedwater system surveillance tests policy optimization

International Nuclear Information System (INIS)

Sacco, W.F.; Lapa, Celso M.F.; Pereira, C.M.N.A.; Oliveira, C.R.E. de

2006-01-01

This article extends previous efforts on genetic algorithms (GAs) applied to a nuclear power plant (NPP) auxiliary feedwater system (AFWS) surveillance tests policy optimization. We introduce the application of a niching genetic algorithm (NGA) to this problem and compare its performance to previous results. The NGA maintains a populational diversity during the search process, thus promoting a greater exploration of the search space. The optimization problem consists in maximizing the system's average availability for a given period of time, considering realistic features such as: (i) aging effects on standby components during the tests; (ii) revealing failures in the tests implies on corrective maintenance, increasing outage times; (iii) components have distinct test parameters (outage time, aging factors, etc.) and (iv) tests are not necessarily periodic. We find that the NGA performs better than the conventional GA and the island GA due to a greater exploration of the search space

Multivariate Meta-Analysis of Genetic Association Studies: A Simulation Study.

Directory of Open Access Journals (Sweden)

Binod Neupane

Full Text Available In a meta-analysis with multiple end points of interests that are correlated between or within studies, multivariate approach to meta-analysis has a potential to produce more precise estimates of effects by exploiting the correlation structure between end points. However, under random-effects assumption the multivariate estimation is more complex (as it involves estimation of more parameters simultaneously than univariate estimation, and sometimes can produce unrealistic parameter estimates. Usefulness of multivariate approach to meta-analysis of the effects of a genetic variant on two or more correlated traits is not well understood in the area of genetic association studies. In such studies, genetic variants are expected to roughly maintain Hardy-Weinberg equilibrium within studies, and also their effects on complex traits are generally very small to modest and could be heterogeneous across studies for genuine reasons. We carried out extensive simulation to explore the comparative performance of multivariate approach with most commonly used univariate inverse-variance weighted approach under random-effects assumption in various realistic meta-analytic scenarios of genetic association studies of correlated end points. We evaluated the performance with respect to relative mean bias percentage, and root mean square error (RMSE of the estimate and coverage probability of corresponding 95% confidence interval of the effect for each end point. Our simulation results suggest that multivariate approach performs similarly or better than univariate method when correlations between end points within or between studies are at least moderate and between-study variation is similar or larger than average within-study variation for meta-analyses of 10 or more genetic studies. Multivariate approach produces estimates with smaller bias and RMSE especially for the end point that has randomly or informatively missing summary data in some individual studies, when

Conservation and Use of Genetic Resources of Underutilized Crops in the Americas—A Continental Analysis

Directory of Open Access Journals (Sweden)

Gea Galluzzi

2014-02-01

Full Text Available Latin America is home to dramatically diverse agroecological regions which harbor a high concentration of underutilized plant species, whose genetic resources hold the potential to address challenges such as sustainable agricultural development, food security and sovereignty, and climate change. This paper examines the status of an expert-informed list of underutilized crops in Latin America and analyses how the most common features of underuse apply to these. The analysis pays special attention to if and how existing international policy and legal frameworks on biodiversity and plant genetic resources effectively support or not the conservation and sustainable use of underutilized crops. Results show that not all minor crops are affected by the same degree of neglect, and that the aspects under which any crop is underutilized vary greatly, calling for specific analyses and interventions. We also show that current international policy and legal instruments have so far provided limited stimulus and funding for the conservation and sustainable use of the genetic resources of these crops. Finally, the paper proposes an analytical framework for identifying and evaluating a crop’s underutilization, in order to define the most appropriate type and levels of intervention (international, national, local for improving its status.

Isolation and characterization of microsatellite markers and analysis of genetic variability in Curculigo latifolia Dryand.

Science.gov (United States)

Babaei, Nahid; Abdullah, Nur Ashikin Psyquay; Saleh, Ghizan; Abdullah, Thohirah Lee

2012-11-01

Curculin, a sweet protein found in Curculigo latifolia fruit has great potential for the pharmaceutical industry. This protein interestingly has been found to have both sweet taste and taste-modifying capacities comparable with other natural sweeteners. According to our knowledge this is the first reported case on the isolation of microsatellite loci in this genus. Hence, the current development of microsatellite markers for C. latifolia will facilitate future population genetic studies and breeding programs for this valuable plant. In this study 11 microsatellite markers were developed using 3' and 5' ISSR markers. The primers were tested on 27 accessions from all states of Peninsular Malaysia. The number of alleles per locus ranged from three to seven, with allele size ranging from 141 to 306 bp. The observed and expected heterozygosity ranged between 0.00-0.65 and 0.38-0.79, respectively. The polymorphic information content ranged from 0.35 to 0.74 and the Shannon's information index ranged from 0.82 to 1.57. These developed polymorphic microsatellites were used for constructing a dendrogram by unweighted pair group method with arithmetic mean cluster analysis using the Dice's similarity coefficient. Accessions association according to their geographical origin was observed. Based on characteristics of isolated microsatellites for C. latifolia accessions all genotype can be distinguished using these 11 microsatellite markers. These polymorphic markers could also be applied to studies on uniformity determination and somaclonal variation of tissue culture plantlets, varieties identification, genetic diversity, analysis of phylogenetic relationship, genetic linkage maps and quantitative trait loci in C. latifolia.

Evaluation of schistosome promoter expression for transgenesis and genetic analysis.

Directory of Open Access Journals (Sweden)

Shuang Liang

Full Text Available Schistosome worms of the genus Schistosoma are the causative agents of schistosomiasis, a devastating parasitic disease affecting more than 240 million people worldwide. Schistosomes have complex life cycles, and have been challenging to manipulate genetically due to the dearth of molecular tools. Although the use of gene overexpression, gene knockouts or knockdowns are straight-forward genetic tools applied in many model systems, gene misexpression and genetic manipulation of schistosome genes in vivo has been exceptionally challenging, and plasmid based transfection inducing gene expression is limited. We recently reported the use of polyethyleneimine (PEI as a simple and effective method for schistosome transfection and gene expression. Here, we use PEI-mediated schistosome plasmid transgenesis to define and compare gene expression profiles from endogenous and nonendogenous promoters in the schistosomula stage of schistosomes that are potentially useful to misexpress (underexpress or overexpress gene product levels. In addition, we overexpress schistosome genes in vivo using a strong promoter and show plasmid-based misregulation of genes in schistosomes, producing a clear and distinct phenotype--death. These data focus on the schistosomula stage, but they foreshadow strong potential for genetic characterization of schistosome molecular pathways, and potential for use in overexpression screens and drug resistance studies in schistosomes using plasmid-based gene expression.

Analysis of genetic diversity in Bolivian llama populations using microsatellites.

Science.gov (United States)

Barreta, J; Gutiérrez-Gil, B; Iñiguez, V; Romero, F; Saavedra, V; Chiri, R; Rodríguez, T; Arranz, J J

2013-08-01

South American camelids (SACs) have a major role in the maintenance and potential future of rural Andean human populations. More than 60% of the 3.7 million llamas living worldwide are found in Bolivia. Due to the lack of studies focusing on genetic diversity in Bolivian llamas, this analysis investigates both the genetic diversity and structure of 12 regional groups of llamas that span the greater part of the range of distribution for this species in Bolivia. The analysis of 42 microsatellite markers in the considered regional groups showed that, in general, there were high levels of polymorphism (a total of 506 detected alleles; average PIC across per marker: 0.66), which are comparable with those reported for other populations of domestic SACs. The estimated diversity parameters indicated that there was high intrapopulational genetic variation (average number of alleles and average expected heterozygosity per marker: 12.04 and 0.68, respectively) and weak genetic differentiation among populations (FST range: 0.003-0.052). In agreement with these estimates, Bolivian llamas showed a weak genetic structure and an intense gene flow between all the studied regional groups, which is due to the exchange of reproductive males between the different flocks. Interestingly, the groups for which the largest pairwise FST estimates were observed, Sud Lípez and Nor Lípez, showed a certain level of genetic differentiation that is probably due to the pattern of geographic isolation and limited communication infrastructures of these southern localities. Overall, the population parameters reported here may serve as a reference when establishing conservation policies that address Bolivian llama populations. © 2012 Blackwell Verlag GmbH.

A genetic analysis of segregation distortion revealed by molecular ...

Indian Academy of Sciences (India)

Journal of Genetics, Vol. 90, No. ... Segregation analysis was based on 64 molecular markers, including 26 .... FHB of RIL populations was controlled by quantitative trait ... The authors acknowledge financial support by the National Basic.

Analysis of genetic diversity of certain species of Piper using RAPD-based molecular markers.

Science.gov (United States)

Chowdhury, Utpal; Tanti, Bhaben; Rethy, Parakkal; Gajurel, Padma Raj

2014-09-01

The utility of RAPD markers in assessing genetic diversity and phenetic relationships of six different species of Piper from Northeast India was investigated. Polymerase chain reaction (PCR) with four arbitrary 10-mer oligonucleotide primers applied to the six species produced a total of 195 marker bands, of which, 159 were polymorphic. On average, six RAPD fragments were amplified per reaction. In the UPGMA phenetic dendrogram based on Jaccard's coefficient, the different accessions of Piper showed a high level of genetic variation. This study may be useful in identifying diverse genetic stocks of Piper, which may then be conserved on a priority basis.

New trends in applied harmonic analysis sparse representations, compressed sensing, and multifractal analysis

CERN Document Server

Cabrelli, Carlos; Jaffard, Stephane; Molter, Ursula

2016-01-01

This volume is a selection of written notes corresponding to courses taught at the CIMPA School: "New Trends in Applied Harmonic Analysis: Sparse Representations, Compressed Sensing and Multifractal Analysis". New interactions between harmonic analysis and signal and image processing have seen striking development in the last 10 years, and several technological deadlocks have been solved through the resolution of deep theoretical problems in harmonic analysis. New Trends in Applied Harmonic Analysis focuses on two particularly active areas that are representative of such advances: multifractal analysis, and sparse representation and compressed sensing. The contributions are written by leaders in these areas, and covers both theoretical aspects and applications. This work should prove useful not only to PhD students and postdocs in mathematics and signal and image processing, but also to researchers working in related topics.

Genetic Analysis of Oncorhynchus Nerka : Life History and Genetic Analysis of Redfish Lake Oncorhynchus Nerka, 1993-1994 Completion Report.

Energy Technology Data Exchange (ETDEWEB)

Brannon, E.L.; Thorgaard, G.H.; Cummings, S.A.

1994-10-01

The study has shown through life history examination and DNA analysis that three forms of O. nerka are present in Redfish Lake. The three forms are closely related, but may be sufficiently different to be considered three separate stocks. Fishhook Creek kokanee are temporally isolated from the beach spawners, and may represent the gene pool most similar to the historic sockeye population that once spawned there. Fishhook Creek offers the best spawning area available in the lake system, and should be considered for use in reestablishing an anadromous Fishhook Creek sockeye swain. The resident beach spawning strain of O. nerka is likewise the most similar genetic form of the companion anadromous beach spawning O. nerka, and needs to be considered the most appropriate genetic source to help minimize reduced fitness of the sockeye from inbreeding.

Analysis of genetic diversity of Piper spp. in Hainan Island (China ...

African Journals Online (AJOL)

Inter-simple sequence repeat (ISSR) analysis was used to evaluate the genetic variation of Piper spp. from Hainan, China. 247 polymorphic bands out of a total of 248 (99.60%) were generated from 74 individual plants of Piper spp. The overall level of genetic diversity among Piper spp. in Hainan was high, with the mean ...

Genetic analysis of a consanguineous Pakistani family with Leber ...

Indian Academy of Sciences (India)

2014-08-01

Aug 1, 2014 ... RESEARCH NOTE. Genetic analysis of a consanguineous Pakistani family with Leber .... representation of the deleterious mutation at genomic and protein level. ... In the last couple of years, numerous mutations in. GUCY2D ...

A theoretical analysis of population genetics of plants on restored habitats

Energy Technology Data Exchange (ETDEWEB)

Bogoliubov, A.G. [Botanical Institute, Russian Academy of Science, St. Petersburg (Russian Federation); Loehle, C. [Argonne National Lab., IL (United States)

1995-02-01

Seed and propagules used for habitat restoration are not likely to be closely adapted to local site conditions. Rapid changes of genotypes frequencies on local microsites and/or microevolution would allow plants to become better adapted to a site. These same factors would help to maintain genetic diversity and ensure the survival of small endangered populations. We used population genetics models to examine the selection of genotypes during establishment on restored sites. Vegetative spread was shown to affect selection and significantly reduce genetic diversity. To study general microevolution, we linked a model of resource usage with a genetics model and analyzed competition between genotypes. A complex suite of feasible ecogenetic states was shown to result. The state actually resulting would depend strongly on initial conditions. This analysis indicated that genetic structure can vary locally and can produce overall genetic variability that is not simply the result of microsite adaptations. For restoration activities, the implication is that small differences in seed source could lead to large differences in local genetic structure after selection.

A theoretical analysis of population genetics of plants on restored habitats

Energy Technology Data Exchange (ETDEWEB)

Bogoliubov, A.G. [Russian Academy of Science, St. Petersburg (Russian Federation). Botanical Inst.; Loehle, C. [Argonne National Lab., IL (United States). Environmental Research Div.

1997-07-01

Seed and propagules used for habitat restoration are not likely to be closely adapted to local site conditions. Rapid changes of genotypes frequencies on local microsites and/or microevolution would allow plants to become better adapted to a site. These same factors would help to maintain genetic diversity and ensure the survival of small endangered populations. The authors used population genetics models to examine the selection of genotypes during establishment on restored sites. Vegetative spread was shown to affect selection and significantly reduce genetic diversity. To study general microevolution, the authors linked a model of resource usage with a genetics model and analyzed competition between genotypes. A complex suite of feasible ecogenetic states was shown to result. The state actually resulting would depend strongly on initial conditions. This analysis indicated that genetic structure can vary locally and can produce overall genetic variability that is not simply the result of microsite adaptations. For restoration activities, the implication is that small differences in seed source could lead to large differences in local genetic structure after selection.

Application of medical cases in general genetics teaching in universities.

Science.gov (United States)

He, Zhumei; Bie, Linsai; Li, Wei

2018-01-20

General genetics is a core course in life sciences, medicine, agriculture and other related fields. As one of the most fast-developing disciplines of life sciences in the 21th century, the influence of the genetics knowledge on daily life is expanding, especially on human health and reproduction. In order to make it easier for students to understand the profound principles of genetics and to better apply the theories to daily life, we have introduced appropriate medical cases in general genetics teaching and further extended them combined with theoretical basis of genetics. This approach will be beneficial to enhance students' abilities of genetic analysis and promote their enthusiasm to learn and master practical skills. In this paper, we enumerate medical cases related to the modern genetics teaching system to provide a reference for genetics teaching in general and normal universities.

A Tri-Part Model for Genetics Literacy: Exploring Undergraduate Student Reasoning about Authentic Genetics Dilemmas

Science.gov (United States)

Shea, Nicole A.; Duncan, Ravit Golan; Stephenson, Celeste

2015-01-01

Genetics literacy is becoming increasingly important as advancements in our application of genetic technologies such as stem cell research, cloning, and genetic screening become more prevalent. Very few studies examine how genetics literacy is applied when reasoning about authentic genetic dilemmas. However, there is evidence that situational…

Genet-specific DNA methylation probabilities detected in a spatial epigenetic analysis of a clonal plant population.

Directory of Open Access Journals (Sweden)

Kiwako S Araki

Full Text Available In sessile organisms such as plants, spatial genetic structures of populations show long-lasting patterns. These structures have been analyzed across diverse taxa to understand the processes that determine the genetic makeup of organismal populations. For many sessile organisms that mainly propagate via clonal spread, epigenetic status can vary between clonal individuals in the absence of genetic changes. However, fewer previous studies have explored the epigenetic properties in comparison to the genetic properties of natural plant populations. Here, we report the simultaneous evaluation of the spatial structure of genetic and epigenetic variation in a natural population of the clonal plant Cardamine leucantha. We applied a hierarchical Bayesian model to evaluate the effects of membership of a genet (a group of individuals clonally derived from a single seed and vegetation cover on the epigenetic variation between ramets (clonal plants that are physiologically independent individuals. We sampled 332 ramets in a 20 m × 20 m study plot that contained 137 genets (identified using eight SSR markers. We detected epigenetic variation in DNA methylation at 24 methylation-sensitive amplified fragment length polymorphism (MS-AFLP loci. There were significant genet effects at all 24 MS-AFLP loci in the distribution of subepiloci. Vegetation cover had no statistically significant effect on variation in the majority of MS-AFLP loci. The spatial aggregation of epigenetic variation is therefore largely explained by the aggregation of ramets that belong to the same genets. By applying hierarchical Bayesian analyses, we successfully identified a number of genet-specific changes in epigenetic status within a natural plant population in a complex context, where genotypes and environmental factors are unevenly distributed. This finding suggests that it requires further studies on the spatial epigenetic structure of natural populations of diverse organisms

Genet-specific DNA methylation probabilities detected in a spatial epigenetic analysis of a clonal plant population.

Science.gov (United States)

Araki, Kiwako S; Kubo, Takuya; Kudoh, Hiroshi

2017-01-01

In sessile organisms such as plants, spatial genetic structures of populations show long-lasting patterns. These structures have been analyzed across diverse taxa to understand the processes that determine the genetic makeup of organismal populations. For many sessile organisms that mainly propagate via clonal spread, epigenetic status can vary between clonal individuals in the absence of genetic changes. However, fewer previous studies have explored the epigenetic properties in comparison to the genetic properties of natural plant populations. Here, we report the simultaneous evaluation of the spatial structure of genetic and epigenetic variation in a natural population of the clonal plant Cardamine leucantha. We applied a hierarchical Bayesian model to evaluate the effects of membership of a genet (a group of individuals clonally derived from a single seed) and vegetation cover on the epigenetic variation between ramets (clonal plants that are physiologically independent individuals). We sampled 332 ramets in a 20 m × 20 m study plot that contained 137 genets (identified using eight SSR markers). We detected epigenetic variation in DNA methylation at 24 methylation-sensitive amplified fragment length polymorphism (MS-AFLP) loci. There were significant genet effects at all 24 MS-AFLP loci in the distribution of subepiloci. Vegetation cover had no statistically significant effect on variation in the majority of MS-AFLP loci. The spatial aggregation of epigenetic variation is therefore largely explained by the aggregation of ramets that belong to the same genets. By applying hierarchical Bayesian analyses, we successfully identified a number of genet-specific changes in epigenetic status within a natural plant population in a complex context, where genotypes and environmental factors are unevenly distributed. This finding suggests that it requires further studies on the spatial epigenetic structure of natural populations of diverse organisms, particularly for

A Genetic Analysis of Mortality in Pigs

DEFF Research Database (Denmark)

Varona, Luis; Sorensen, Daniel

2010-01-01

to investigate whether there is support for genetic variation for mortality and to study the quality of fit and predictive properties of the various models. In both breeds, the model that provided the best fit to the data was the standard binomial hierarchical model. The model that performed best in terms......An analysis of mortality is undertaken in two breeds of pigs: Danish Landrace and Yorkshire. Zero-inflated and standard versions of hierarchical Poisson, binomial, and negative binomial Bayesian models were fitted using Markov chain Monte Carlo (MCMC). The objectives of the study were...... of the ability to predict the distribution of stillbirths was the hierarchical zero-inflated negative binomial model. The best fit of the binomial hierarchical model and of the zero-inflated hierarchical negative binomial model was obtained when genetic variation was included as a parameter. For the hierarchical...

Radiation mutagenesis in development of genetic fundamentals of cotton selection

International Nuclear Information System (INIS)

Musaev, D.A.; Almatov, A.S.

1987-01-01

Some results of investigations on preparation and genetic analysis of mutants in inbreeding lines of genetic collections of cotton plants, as well as problems on mutant application in practical selection are covered. The results show that the scientific authenticity and efficiency of fundamental and applied investigations in the field of experimental mutagenesis of cotton plants,being a facultative self-polinator, depend on keeping necessary methodical requirements. Application of inbreeding lines of genetic collection with marker features as the initial material, isolation of plants usinng self-polination of flowers on all stages of investigation are related to these requirements. Several methodical recommendations on genetic-selective investigations are developed

Molecular genetic analysis of activation-tagged transcription factors thought to be involved in photomorphogenesis

Energy Technology Data Exchange (ETDEWEB)

Neff, Michael M.

2011-06-23

This is a final report for Department of Energy Grant No. DE-FG02-08ER15927 entitled “Molecular Genetic Analysis of Activation-Tagged Transcription Factors Thought to be Involved in Photomorphogenesis”. Based on our preliminary photobiological and genetic analysis of the sob1-D mutant, we hypothesized that OBP3 is a transcription factor involved in both phytochrome and cryptochrome-mediated signal transduction. In addition, we hypothesized that OBP3 is involved in auxin signaling and root development. Based on our preliminary photobiological and genetic analysis of the sob2-D mutant, we also hypothesized that a related gene, LEP, is involved in hormone signaling and seedling development.

Influence of genetic variants on toxicity to anti-tubercular agents: a systematic review and meta-analysis (protocol).

Science.gov (United States)

Richardson, Marty; Kirkham, Jamie; Dwan, Kerry; Sloan, Derek; Davies, Geraint; Jorgensen, Andrea

2017-07-13

Tuberculosis patients receiving anti-tuberculosis treatment may experience serious adverse drug reactions, such as hepatotoxicity. Genetic risk factors, such as polymorphisms of the NAT2, CYP2E1 and GSTM1 genes, may increase the risk of experiencing such toxicity events. Many pharmacogenetic studies have investigated the association between genetic variants and anti-tuberculosis drug-related toxicity events, and several meta-analyses have synthesised data from these studies, although conclusions from these meta-analyses are conflicting. Many meta-analyses also have serious methodological limitations, such as applying restrictive inclusion criteria, or not assessing the quality of included studies. Most also only consider hepatotoxicity outcomes and specific genetic variants. The purpose of this systematic review and meta-analysis is to give a comprehensive evaluation of the evidence base for associations between any genetic variant and anti-tuberculosis drug-related toxicity. We will search for studies in MEDLINE, EMBASE, BIOSIS and Web of Science. We will also hand search reference lists from relevant studies and contact experts in the field. We will include cohort studies, case-control studies and randomised controlled trials that recruited patients with tuberculosis who were either already established on anti-tuberculosis treatment or were commencing treatment and who were genotyped to investigate the effect of genetic variants on any anti-tuberculosis drug-related toxicity outcome. One author will screen abstracts to identify potentially relevant studies and will then obtain the full text for each potentially relevant study in order to assess eligibility. At each of these stages, a second author will independently screen/assess 10% of studies. Two authors will independently extract data and assess the quality of studies using a pre-piloted data extraction form. If appropriate, we will pool estimates of effect for each genotype on each outcome using meta

Analysis of the Threat of Genetically Modified Organisms for Biological Warfare

Science.gov (United States)

2011-05-01

biological warfare. The primary focus of the framework are those aspects of the technology directly affecting humans by inducing virulent infectious disease...applications. Simple organisms such as fruit flies have been used to study the effects of genetic changes across generations. Transgenic mice are...Analysis * Multi-cell pathogens * Toxins (Chemical products of living cells.) * Fungi (Robust organism; no genetic manipulation needed

The genetic component of human longevity

DEFF Research Database (Denmark)

Dato, Serena; Thinggaard, Mette Sørensen; De Rango, Francesco

2018-01-01

In human longevity studies, single nucleotide polymorphism (SNP) analysis identified a large number of genetic variants with small effects, yet not easily replicable in different populations. New insights may come from the combined analysis of different SNPs, especially when grouped by metabolic...... pathway. We applied this approach to study the joint effect on longevity of SNPs belonging to three candidate pathways, the insulin/insulin-like growth factor signalling (IIS), DNA repair and pro/antioxidant. We analysed data from 1,058 tagging SNPs in 140 genes, collected in 1825 subjects (1......, was further found influencing longitudinal survival in nonagenarian females (p = .026). Results here presented highlight the validity of SNP-SNP interactions analyses for investigating the genetics of human longevity, confirming previously identified markers but also pointing to novel genes as central nodes...

Applied research of environmental monitoring using instrumental neutron activation analysis

Energy Technology Data Exchange (ETDEWEB)

Chung, Young Sam; Moon, Jong Hwa; Chung, Young Ju

1997-08-01

This technical report is written as a guide book for applied research of environmental monitoring using Instrumental Neutron Activation Analysis. The contents are as followings; sampling and sample preparation as a airborne particulate matter, analytical methodologies, data evaluation and interpretation, basic statistical methods of data analysis applied in environmental pollution studies. (author). 23 refs., 7 tabs., 9 figs.

SecureMA: protecting participant privacy in genetic association meta-analysis.

Science.gov (United States)

Xie, Wei; Kantarcioglu, Murat; Bush, William S; Crawford, Dana; Denny, Joshua C; Heatherly, Raymond; Malin, Bradley A

2014-12-01

Sharing genomic data is crucial to support scientific investigation such as genome-wide association studies. However, recent investigations suggest the privacy of the individual participants in these studies can be compromised, leading to serious concerns and consequences, such as overly restricted access to data. We introduce a novel cryptographic strategy to securely perform meta-analysis for genetic association studies in large consortia. Our methodology is useful for supporting joint studies among disparate data sites, where privacy or confidentiality is of concern. We validate our method using three multisite association studies. Our research shows that genetic associations can be analyzed efficiently and accurately across substudy sites, without leaking information on individual participants and site-level association summaries. Our software for secure meta-analysis of genetic association studies, SecureMA, is publicly available at http://github.com/XieConnect/SecureMA. Our customized secure computation framework is also publicly available at http://github.com/XieConnect/CircuitService. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Analysis of genetic polymorphism and genetic distance among four ...

African Journals Online (AJOL)

use

2011-11-21

Nov 21, 2011 ... The genomes of 4 sheep populations {Yuanqu white Tan sheep (YWT), Baozhongchang white Tan sheep. (BWT), black Tan sheep (BT) and small-tailed Han sheep (Han)} were screened using 10 microsatellite. DNA markers to estimate the genetic diversities and genetic distances among these ...

Analysis of the genetic basis of disease in the context of worldwide human relationships and migration.

Directory of Open Access Journals (Sweden)

Erik Corona

2013-05-01

Full Text Available Genetic diversity across different human populations can enhance understanding of the genetic basis of disease. We calculated the genetic risk of 102 diseases in 1,043 unrelated individuals across 51 populations of the Human Genome Diversity Panel. We found that genetic risk for type 2 diabetes and pancreatic cancer decreased as humans migrated toward East Asia. In addition, biliary liver cirrhosis, alopecia areata, bladder cancer, inflammatory bowel disease, membranous nephropathy, systemic lupus erythematosus, systemic sclerosis, ulcerative colitis, and vitiligo have undergone genetic risk differentiation. This analysis represents a large-scale attempt to characterize genetic risk differentiation in the context of migration. We anticipate that our findings will enable detailed analysis pertaining to the driving forces behind genetic risk differentiation.

Genetic Alterations in Pesticide Exposed Bolivian Farmers

DEFF Research Database (Denmark)

Jørs, Erik; González, Ana Rosa; Ascarrunz, Maria Eugenia

2007-01-01

: Questionnaires were applied and blood tests taken from 81 volunteers from La Paz County, of whom 48 were pesticide exposed farmers and 33 non-exposed controls. Sixty males and 21 females participated with a mean age of 37.3 years (range 17-76). Data of exposure and possible genetic damage were collected...... and evaluated by well known statistical methods, controlling for relevant confounders. To measure genetic damage chromosomal aberrations and the comet assay analysis were performed. Results: Pesticide exposed farmers had a higher degree of genetic damage compared to the control group. The number of chromosomal......, probably related to exposure to pesticides. Due to the potentially negative long term health effects of genetic damage on reproduction and the development of cancer, preventive measures are recommended. Effective control with imports and sales, banning of the most toxic pesticides, education...

Genetic Variance in Processing Speed Drives Variation in Aging of Spatial and Memory Abilities

Science.gov (United States)

Finkel, Deborah; Reynolds, Chandra A.; McArdle, John J.; Hamagami, Fumiaki; Pedersen, Nancy L.

2009-01-01

Previous analyses have identified a genetic contribution to the correlation between declines with age in processing speed and higher cognitive abilities. The goal of the current analysis was to apply the biometric dual change score model to consider the possibility of temporal dynamics underlying the genetic covariance between aging trajectories…

Potential uses of genetic geological modelling to identify new uranium provinces

International Nuclear Information System (INIS)

Finch, W.I.

1982-01-01

Genetic-geological modelling is the placing of the various processes of the development of a uranium province into distinct stages that are ordered chronologically and made part of a matrix with corresponding geologic evidence. The models can be applied to a given region by using one of several methods to determine a numerical favorability rating. Two of the possible methods, geologic decision analysis and an oil-and-gas type of play analysis, are briefly described. Simplified genetic models are given for environments of the quartz-pebble conglomerate, unconformity-related vein, and sandstone types of deposits. Comparison of the genetic models of these three sedimentary-related environments reveals several common attributes that may define a general uranium province environment

A hybrid niched-island genetic algorithm applied to a nuclear core optimization problem

International Nuclear Information System (INIS)

Pereira, Claudio M.N.A.

2005-01-01

Diversity maintenance is a key-feature in most genetic-based optimization processes. The quest for such characteristic, has been motivating improvements in the original genetic algorithm (GA). The use of multiple populations (called islands) has demonstrating to increase diversity, delaying the genetic drift. Island Genetic Algorithms (IGA) lead to better results, however, the drift is only delayed, but not avoided. An important advantage of this approach is the simplicity and efficiency for parallel processing. Diversity can also be improved by the use of niching techniques. Niched Genetic Algorithms (NGA) are able to avoid the genetic drift, by containing evolution in niches of a single-population GA, however computational cost is increased. In this work it is investigated the use of a hybrid Niched-Island Genetic Algorithm (NIGA) in a nuclear core optimization problem found in literature. Computational experiments demonstrate that it is possible to take advantage of both, performance enhancement due to the parallelism and drift avoidance due to the use of niches. Comparative results shown that the proposed NIGA demonstrated to be more efficient and robust than an IGA and a NGA for solving the proposed optimization problem. (author)

Genetic analysis for two italian siblings with usher syndrome and schizophrenia.

Science.gov (United States)

Domanico, Daniela; Fragiotta, Serena; Trabucco, Paolo; Nebbioso, Marcella; Vingolo, Enzo Maria

2012-01-01

Usher syndrome is a group of autosomal recessive genetic disorders characterized by deafness, retinitis pigmentosa, and sometimes vestibular areflexia. The relationship between Usher syndrome and mental disorders, most commonly a "schizophrenia-like" psychosis, is sometimes described in the literature. The etiology of psychiatric expression of Usher syndrome is still unclear. We reported a case of two natural siblings with congenital hypoacusis, retinitis pigmentosa, and psychiatric symptoms. Clinical features and genetic analysis were also reported. We analyzed possible causes to explain the high prevalence of psychiatric manifestations in Usher syndrome: genetic factors, brain damage, and "stress-related" hypothesis.

Genetic Analysis for Two Italian Siblings with Usher Syndrome and Schizophrenia

Directory of Open Access Journals (Sweden)

Daniela Domanico

2012-01-01

Full Text Available Usher syndrome is a group of autosomal recessive genetic disorders characterized by deafness, retinitis pigmentosa, and sometimes vestibular areflexia. The relationship between Usher syndrome and mental disorders, most commonly a “schizophrenia-like” psychosis, is sometimes described in the literature. The etiology of psychiatric expression of Usher syndrome is still unclear. We reported a case of two natural siblings with congenital hypoacusis, retinitis pigmentosa, and psychiatric symptoms. Clinical features and genetic analysis were also reported. We analyzed possible causes to explain the high prevalence of psychiatric manifestations in Usher syndrome: genetic factors, brain damage, and “stress-related” hypothesis.

Population and genomic lessons from genetic analysis of two Indian populations.

Science.gov (United States)

Juyal, Garima; Mondal, Mayukh; Luisi, Pierre; Laayouni, Hafid; Sood, Ajit; Midha, Vandana; Heutink, Peter; Bertranpetit, Jaume; Thelma, B K; Casals, Ferran

2014-10-01

Indian demographic history includes special features such as founder effects, interpopulation segregation, complex social structure with a caste system and elevated frequency of consanguineous marriages. It also presents a higher frequency for some rare mendelian disorders and in the last two decades increased prevalence of some complex disorders. Despite the fact that India represents about one-sixth of the human population, deep genetic studies from this terrain have been scarce. In this study, we analyzed high-density genotyping and whole-exome sequencing data of a North and a South Indian population. Indian populations show higher differentiation levels than those reported between populations of other continents. In this work, we have analyzed its consequences, by specifically assessing the transferability of genetic markers from or to Indian populations. We show that there is limited genetic marker portability from available genetic resources such as HapMap or the 1,000 Genomes Project to Indian populations, which also present an excess of private rare variants. Conversely, tagSNPs show a high level of portability between the two Indian populations, in contrast to the common belief that North and South Indian populations are genetically very different. By estimating kinship from mates and consanguinity in our data from trios, we also describe different patterns of assortative mating and inbreeding in the two populations, in agreement with distinct mating preferences and social structures. In addition, this analysis has allowed us to describe genomic regions under recent adaptive selection, indicating differential adaptive histories for North and South Indian populations. Our findings highlight the importance of considering demography for design and analysis of genetic studies, as well as the need for extending human genetic variation catalogs to new populations and particularly to those with particular demographic histories.

The Significance of Regional Analysis in Applied Geography.

Science.gov (United States)

Sommers, Lawrence M.

Regional analysis is central to applied geographic research, contributing to better planning and policy development for a variety of societal problems facing the United States. The development of energy policy serves as an illustration of the capabilities of this type of analysis. The United States has had little success in formulating a national…

SSR Analysis of Genetic Diversity Among 192 Diploid Potato Cultivars

Directory of Open Access Journals (Sweden)

Xiaoyan Song

2016-05-01

Full Text Available In potato breeding, it is difficult to improve the traits of interest at the tetraploid level due to the tetrasomic inheritance. A promising alternative is diploid breeding. Thus it is necessary to assess the genetic diversity of diploid potato germplasm for efficient exploration and deployment of desirable traits. In this study, we used SSR markers to evaluate the genetic diversity of diploid potato cultivars. To screen polymorphic SSR markers, 55 pairs of SSR primers were employed to amplify 39 cultivars with relatively distant genetic relationships. Among them, 12 SSR markers with high polymorphism located at 12 chromosomes were chosen to evaluate the genetic diversity of 192 diploid potato cultivars. The primers produced 6 to 18 bands with an average of 8.2 bands per primer. In total, 98 bands were amplified from 192 cultivars, and 97 of them were polymorphic. Cluster analysis using UPGMA showed the genetic relationships of all accessions tested: 186 of the 192 accessions could be distinguished by only 12 pairs of SSR primers, and the 192 diploid cultivars were divided into 11 groups, and 83.3% constituted the first group. Clustering results showed relatively low genetic diversity among 192 diploid cultivars, with closer relationship at the molecular level. The results can provide molecular basis for diploid potato breeding.

Diagnostic and therapeutic implications of genetic heterogeneity in myeloid neoplasms uncovered by comprehensive mutational analysis

Directory of Open Access Journals (Sweden)

Sarah M. Choi

2017-01-01

Full Text Available While growing use of comprehensive mutational analysis has led to the discovery of innumerable genetic alterations associated with various myeloid neoplasms, the under-recognized phenomenon of genetic heterogeneity within such neoplasms creates a potential for diagnostic confusion. Here, we describe two cases where expanded mutational testing led to amendment of an initial diagnosis of chronic myelogenous leukemia with subsequent altered treatment of each patient. We demonstrate the power of comprehensive testing in ensuring appropriate classification of genetically heterogeneous neoplasms, and emphasize thoughtful analysis of molecular and genetic data as an essential component of diagnosis and management.

Genetic relatedness and recombination analysis of Allorhizobium vitis strains associated with grapevine crown gall outbreaks in Europe.

Science.gov (United States)

Kuzmanović, N; Biondi, E; Bertaccini, A; Obradović, A

2015-09-01

To analyse genetic diversity and epidemiological relationships among 54 strains of Allorhizobium vitis isolated in Europe during an 8-year period and to assess the relative contribution of mutation and recombination in shaping their diversity. By using random amplified polymorphic DNA (RAPD) PCR, strains studied were distributed into 12 genetic groups. Sequence analysis of dnaK, gyrB and recA housekeeping genes was employed to characterize a representative subcollection of 28 strains. A total of 15 different haplotypes were found. Nucleotide sequence analysis suggested the presence of recombination events in A. vitis, particularly affecting dnaK locus. Although prevalence of mutation over recombination was found, impact of recombination was about two times greater than mutation in the evolution of the housekeeping genes analysed. The RAPD analysis indicated high degree of genetic diversity among the strains. However, the most abundant RAPD group was composed of 35 strains, which could lead to the conclusion that they share a common origin and were distributed by the movement of infected grapevine planting material as a most common way of crossing long distances. Furthermore, it seems that recombination is acting as an important driving force in the evolution of A. vitis. As no substantial evidence of recombination was detected within recA gene fragment, this phylogenetic marker could be reliable to characterize phylogenetic relationships among A. vitis strains. We demonstrated clear epidemiological relationship between majority of strains studied, suggesting a need for more stringent phytosanitary measures in international trade. Moreover, this is the first study to report recombination in A. vitis. © 2015 The Society for Applied Microbiology.

[Advance in the methods of preimplantation genetic diagnosis for single gene diseases].

Science.gov (United States)

Ren, Yixin; Qiao, Jie; Yan, Liying

2017-06-10

More than 7000 single gene diseases have been identified and most of them lack effective treatment. As an early form of prenatal diagnosis, preimplantation genetic diagnosis (PGD) is a combination of in vitro fertilization and genetic diagnosis. PGD has been applied in clinics for more than 20 years to avoid the transmission of genetic defects through analysis of embryos at early stages of development. In this paper, a review for the recent advances in PGD for single gene diseases is provided.

Genetic and environmental contributions to body mass index: comparative analysis of monozygotic twins, dizygotic twins and same-age unrelated siblings.

Science.gov (United States)

Segal, N L; Feng, R; McGuire, S A; Allison, D B; Miller, S

2009-01-01

Earlier studies have established that a substantial percentage of variance in obesity-related phenotypes is explained by genetic components. However, only one study has used both virtual twins (VTs) and biological twins and was able to simultaneously estimate additive genetic, non-additive genetic, shared environmental and unshared environmental components in body mass index (BMI). Our current goal was to re-estimate four components of variance in BMI, applying a more rigorous model to biological and virtual multiples with additional data. Virtual multiples share the same family environment, offering unique opportunities to estimate common environmental influence on phenotypes that cannot be separated from the non-additive genetic component using only biological multiples. Data included 929 individuals from 164 monozygotic twin pairs, 156 dizygotic twin pairs, five triplet sets, one quadruplet set, 128 VT pairs, two virtual triplet sets and two virtual quadruplet sets. Virtual multiples consist of one biological child (or twins or triplets) plus one same-aged adoptee who are all raised together since infancy. We estimated the additive genetic, non-additive genetic, shared environmental and unshared random components in BMI using a linear mixed model. The analysis was adjusted for age, age(2), age(3), height, height(2), height(3), gender and race. Both non-additive genetic and common environmental contributions were significant in our model (P-valuesrole in BMI and that common environmental factors such as diet or exercise also affect BMI. This conclusion is consistent with our earlier study using a smaller sample and shows the utility of virtual multiples for separating non-additive genetic variance from common environmental variance.

Applied decision analysis and risk evaluation

International Nuclear Information System (INIS)

Ferse, W.; Kruber, S.

1995-01-01

During 1994 the workgroup 'Applied Decision Analysis and Risk Evaluation; continued the work on the knowledge based decision support system XUMA-GEFA for the evaluation of the hazard potential of contaminated sites. Additionally a new research direction was started which aims at the support of a later stage of the treatment of contaminated sites: The clean-up decision. For the support of decisions arising at this stage, the methods of decision analysis will be used. Computational aids for evaluation and decision support were implemented and a case study at a waste disposal site in Saxony which turns out to be a danger for the surrounding groundwater ressource was initiated. (orig.)

[The importance of genealogy applied to genetic research in Costa Rica].

Science.gov (United States)

Meléndez Obando, Mauricio O

2004-09-01

The extensive development of genealogical studies based on archival documents has provided powerful support for genetic research in Costa Rica over the past quarter century. As a result, several questions of population history have been answered, such as those involving hereditary illnesses, suggesting additional avenues and questions as well. Similarly, the preservation of massive amounts of historical documentation highlights the major advantages that the Costa Rican population offers to genetic research.

Genetic diversity analysis of Jatropha curcas L. (Euphorbiaceae) based on methylation-sensitive amplification polymorphism.

Science.gov (United States)

Kanchanaketu, T; Sangduen, N; Toojinda, T; Hongtrakul, V

2012-04-13

Genetic analysis of 56 samples of Jatropha curcas L. collected from Thailand and other countries was performed using the methylation-sensitive amplification polymorphism (MSAP) technique. Nine primer combinations were used to generate MSAP fingerprints. When the data were interpreted as amplified fragment length polymorphism (AFLP) markers, 471 markers were scored. All 56 samples were classified into three major groups: γ-irradiated, non-toxic and toxic accessions. Genetic similarity among the samples was extremely high, ranging from 0.95 to 1.00, which indicated very low genetic diversity in this species. The MSAP fingerprint was further analyzed for DNA methylation polymorphisms. The results revealed differences in the DNA methylation level among the samples. However, the samples collected from saline areas and some species hybrids showed specific DNA methylation patterns. AFLP data were used, together with methylation-sensitive AFLP (MS-AFLP) data, to construct a phylogenetic tree, resulting in higher efficiency to distinguish the samples. This combined analysis separated samples previously grouped in the AFLP analysis. This analysis also distinguished some hybrids. Principal component analysis was also performed; the results confirmed the separation in the phylogenetic tree. Some polymorphic bands, involving both nucleotide and DNA methylation polymorphism, that differed between toxic and non-toxic samples were identified, cloned and sequenced. BLAST analysis of these fragments revealed differences in DNA methylation in some known genes and nucleotide polymorphism in chloroplast DNA. We conclude that MSAP is a powerful technique for the study of genetic diversity for organisms that have a narrow genetic base.

Genetic analysis on three South Indian sympatric hipposiderid bats (Chiroptera, Hipposideridae

Directory of Open Access Journals (Sweden)

Kanagaraj, C

2010-12-01

Full Text Available In mitochondrial DNA, variations in the sequence of 16S rRNA region were analyzed to infer the genetic relationship and population history of three sympatric hipposiderid bats, Hipposideros speoris, H. fulvus and H. ater. Based on the DNA sequence data, we observed relatively lower haplotype and higher nucleotide diversity in H. speoris than in the other two species. The pairwise comparisons of the genetic divergence inferred a genetic relationship between the three hipposiderid bats. We used haplotype sequences to construct a phylogenetic tree. Maximum parsimony and Bayesian inference analysis generated a tree with similar topology. H. fulvus and H. ater formed one cluster and H. speoris formed another cluster. Analysis of the demographic history of populations using Jajima’s D test revealed past changes in populations. Comparison of the observed distribution of pairwise differences in the nucleotides with expected sudden expansion model accepts for H. fulvus and H. ater but not for H. speoris populations.

Genetic diversity and structure analysis in wild and landraces of barley from Jordan by using ISJ markers

International Nuclear Information System (INIS)

Baloch, A. W.; Balogh, M. J.; Baloch, M.; Baloch, I. A.

2016-01-01

The present experiment was carried out to estimate genetic diversity and genetic structure in cultivated and wild barley populations collected from Jordan which is considered as primary gene pool of barley. In a total, 94 cultivated barley accessions composed of 4 populations and 52 wild barley accessions consisted of 3 populations were used for genetic analysis using 7 Intron Splice Junction (ISJ) markers. The genetic diversity index (He) of cultivated barley ranged between 0.049 and 0.060; whereas that of wild barley populations ranged between 0.084 and 0.146, suggesting that wild resources of barley harbored greater genetic diversity than its domesticated counterpart, reflecting that barley domestication occurred with genetic bottleneck. Analysis of molecular variance showed high genetic variations among rather than within populations, referring that high genetic differentiation of barley populations caused by genetic and geographical separation of the populations in the harsh growing conditions of Fertile Crescent. Principal coordinate, clustering and structure analysis not only separated cultivated and wild barley, but also each single population, showing their genetic basis and original sample site. The obtained Results also revealed that there is lesser genetic communication between cultivated and wild barley under natural environments. The current findings can better be exploited for collection and utilization of plant germplasms. (author)

Differential network analysis reveals genetic effects on catalepsy modules.

Directory of Open Access Journals (Sweden)

Ovidiu D Iancu

Full Text Available We performed short-term bi-directional selective breeding for haloperidol-induced catalepsy, starting from three mouse populations of increasingly complex genetic structure: an F2 intercross, a heterogeneous stock (HS formed by crossing four inbred strains (HS4 and a heterogeneous stock (HS-CC formed from the inbred strain founders of the Collaborative Cross (CC. All three selections were successful, with large differences in haloperidol response emerging within three generations. Using a custom differential network analysis procedure, we found that gene coexpression patterns changed significantly; importantly, a number of these changes were concordant across genetic backgrounds. In contrast, absolute gene-expression changes were modest and not concordant across genetic backgrounds, in spite of the large and similar phenotypic differences. By inferring strain contributions from the parental lines, we are able to identify significant differences in allelic content between the selected lines concurrent with large changes in transcript connectivity. Importantly, this observation implies that genetic polymorphisms can affect transcript and module connectivity without large changes in absolute expression levels. We conclude that, in this case, selective breeding acts at the subnetwork level, with the same modules but not the same transcripts affected across the three selections.

Analysis of genetic variation and potential applications in genome-scale metabolic modeling

DEFF Research Database (Denmark)

Cardoso, Joao; Andersen, Mikael Rørdam; Herrgard, Markus

2015-01-01

scale and resolution by re-sequencing thousands of strains systematically. In this article, we review challenges in the integration and analysis of large-scale re-sequencing data, present an extensive overview of bioinformatics methods for predicting the effects of genetic variants on protein function......Genetic variation is the motor of evolution and allows organisms to overcome the environmental challenges they encounter. It can be both beneficial and harmful in the process of engineering cell factories for the production of proteins and chemicals. Throughout the history of biotechnology......, there have been efforts to exploit genetic variation in our favor to create strains with favorable phenotypes. Genetic variation can either be present in natural populations or it can be artificially created by mutagenesis and selection or adaptive laboratory evolution. On the other hand, unintended genetic...

Animal Research in the "Journal of Applied Behavior Analysis"

Science.gov (United States)

Edwards, Timothy L.; Poling, Alan

2011-01-01

This review summarizes the 6 studies with nonhuman animal subjects that have appeared in the "Journal of Applied Behavior Analysis" and offers suggestions for future research in this area. Two of the reviewed articles described translational research in which pigeons were used to illustrate and examine behavioral phenomena of applied significance…

Preimplantation genetic diagnosis of X-linked diseases examined by indirect linkage analysis.

Science.gov (United States)

Borgulova, I; Putzova, M; Soldatova, I; Krautova, L; Pecnova, L; Mika, J; Kren, R; Potuznikova, P; Stejskal, D

2015-01-01

Many centers of assisted reproduction in the Czech Republic offer preimplantation genetic diagnosis with fluorescent in situ hybridization (FISH) to couples requiring preimplantation genetic diagnosis (PGD) of X-linked diseases. However, this process results in discarding all male embryos and is not able to distinguish a carrier or healthy female embryo in X-linked recessive disorders. The main aim of this study was to summarize a six-year period of PGD of X-linked monogenic diseases using indirect linkage analysis. We wanted to accentuate the advantage indirect analysis of PGD using multiple displacement amplification (MDA) followed by short tandem repeat (STR) analysis. We present forty-six PGD cycles, including pre-case haplotyping (PGH) panel, for fifteen X-linked diseases. Embryo transfer was made thirty-eight times and gravidity was confirmed in thirteen female probands with a success rate of pregnancy calculated at 42 %. PGD procedure using MDA amplification followed by STR analysis provides help in identifying genetic defects within embryos prior to implantation. The reliability of the method was also supported by high pregnancy rate compared to other publications, which commonly achieved a 30-35 % success rate (Tab. 2, Fig. 1, Ref. 33).

Modern problems in applied analysis

CERN Document Server

Rogosin, Sergei

2018-01-01

This book features a collection of recent findings in Applied Real and Complex Analysis that were presented at the 3rd International Conference “Boundary Value Problems, Functional Equations and Applications” (BAF-3), held in Rzeszow, Poland on 20-23 April 2016. The contributions presented here develop a technique related to the scope of the workshop and touching on the fields of differential and functional equations, complex and real analysis, with a special emphasis on topics related to boundary value problems. Further, the papers discuss various applications of the technique, mainly in solid mechanics (crack propagation, conductivity of composite materials), biomechanics (viscoelastic behavior of the periodontal ligament, modeling of swarms) and fluid dynamics (Stokes and Brinkman type flows, Hele-Shaw type flows). The book is addressed to all readers who are interested in the development and application of innovative research results that can help solve theoretical and real-world problems.

Genetic analysis of human parainfluenza virus type 3 obtained in Croatia, 2011-2015.

Science.gov (United States)

Košutić-Gulija, Tanja; Slovic, Anamarija; Ljubin-Sternak, Sunčanica; Mlinarić-Galinović, Gordana; Forčić, Dubravko

2017-04-01

This study investigated the HPIV3 circulating strains in Croatia and whether the other parts of HPIV3 genome (F gene and HN 582 nucleotides fragment) could be equally suitable for genetic and phylogenetic analysis. Clinical materials were collected in period 2011-2015 from children suffering from respiratory illnesses. In positive HPIV3 samples viral genome was partially amplified and sequenced for HN and F genes. Obtained sequences were analysed by phylogenetic analysis and genetic characterization was performed. All samples from this study belonged to subcluster C and over a short period of time, genetic lineage C3a gained prevalence over the other C genetic lineages, from 39 % in 2011 to more than 90 % in 2013 and 2014. Phylogenetic classifications of HPIV3 based on the entire HN gene, HN 582 nt fragment and entire fusion (F) gene showed identical classification results for Croatian strains and the reference strains. Molecular analysis of the F and HN glycoproteins, showed their similar nucleotide diversity (Fcds P=0.0244 and HNcds P=0.0231) and similar Ka/Ks ratios (F Ka/Ks=0.0553 and HN Ka/Ks=0.0428). Potential N-glycosylation sites, cysteine residues and antigenic sites are generally strongly conserved in HPIV3 glycoproteins from both our and the reference samples. The HPIV3 subclaster C3 (genetic lineage C3a) became the most detected circulating HPIV3 strain in Croatia. The results indicated that the HN 582 nt and the entire F gene sequences were as good for phylogenetic analysis as the entire HN gene sequence.

Analysis of genetic diversity in mango ( Mangifera indica L.) using ...

African Journals Online (AJOL)

Analysis of genetic diversity in mango ( Mangifera indica L.) using isozymetic polymorphism. ... All the isozymes, used in the present study showed polymorphism for mango. A total of 25 different electrophoretic ... HOW TO USE AJOL.

Fourier convergence analysis applied to neutron diffusion Eigenvalue problem

International Nuclear Information System (INIS)

Lee, Hyun Chul; Noh, Jae Man; Joo, Hyung Kook

2004-01-01

Fourier error analysis has been a standard technique for the stability and convergence analysis of linear and nonlinear iterative methods. Though the methods can be applied to Eigenvalue problems too, all the Fourier convergence analyses have been performed only for fixed source problems and a Fourier convergence analysis for Eigenvalue problem has never been reported. Lee et al proposed new 2-D/1-D coupling methods and they showed that the new ones are unconditionally stable while one of the two existing ones is unstable at a small mesh size and that the new ones are better than the existing ones in terms of the convergence rate. In this paper the convergence of method A in reference 4 for the diffusion Eigenvalue problem was analyzed by the Fourier analysis. The Fourier convergence analysis presented in this paper is the first one applied to a neutronics eigenvalue problem to the best of our knowledge

Evaluation of PCR-based preimplantation genetic diagnosis applied to monogenic diseases: a collaborative ESHRE PGD consortium study

Science.gov (United States)

Dreesen, Jos; Destouni, Aspasia; Kourlaba, Georgia; Degn, Birte; Mette, Wulf Christensen; Carvalho, Filipa; Moutou, Celine; Sengupta, Sioban; Dhanjal, Seema; Renwick, Pamela; Davies, Steven; Kanavakis, Emmanouel; Harton, Gary; Traeger-Synodinos, Joanne

2014-01-01

Preimplantation genetic diagnosis (PGD) for monogenic disorders currently involves polymerase chain reaction (PCR)-based methods, which must be robust, sensitive and highly accurate, precluding misdiagnosis. Twelve adverse misdiagnoses reported to the ESHRE PGD-Consortium are likely an underestimate. This retrospective study, involving six PGD centres, assessed the validity of PCR-based PGD through reanalysis of untransferred embryos from monogenic-PGD cycles. Data were collected on the genotype concordance at PGD and follow-up from 940 untransferred embryos, including details on the parameters of PGD cycles: category of monogenic disease, embryo morphology, embryo biopsy and genotype assay strategy. To determine the validity of PCR-based PGD, the sensitivity (Se), specificity (Sp) and diagnostic accuracy were calculated. Stratified analyses were also conducted to assess the influence of the parameters above on the validity of PCR-based PGD. The analysis of overall data showed that 93.7% of embryos had been correctly classified at the time of PGD, with Se of 99.2% and Sp of 80.9%. The stratified analyses found that diagnostic accuracy is statistically significantly higher when PGD is performed on two cells versus one cell (P=0.001). Se was significantly higher when multiplex protocols versus singleplex protocols were applied (P=0.005), as well as for PGD applied on cells from good compared with poor morphology embryos (P=0.032). Morphology, however, did not affect diagnostic accuracy. Multiplex PCR-based methods on one cell, are as robust as those on two cells regarding false negative rate, which is the most important criteria for clinical PGD applications. Overall, this study demonstrates the validity, robustness and high diagnostic value of PCR-based PGD. PMID:24301057

Analysis of the genetic diversity of selected East African sweet potato

African Journals Online (AJOL)

The genetic relationship of the germplasm was evaluated using the Jaccard's coefficient for dissimilarity analysis, unweighted pair group method with arithmetic means (UPGMA) tree and principal component analysis (PCoA) on DARwin software, while summary statistics was done using PowerMarker and Popgene ...

Genetic analysis of Schizosaccharomyces pombe

DEFF Research Database (Denmark)

Ekwall, Karl; Thon, Genevieve

2017-01-01

In this introduction we discuss some basic genetic tools and techniques that are used with the fission yeast Schizosaccharomyces pombe. Genes commonly used for selection or as reporters are discussed, with an emphasis on genes that permit counterselection, intragenic complementation, or colony......-color assays. S. pombe is most stable as a haploid organism. We describe its mating-type system, how to perform genetic crosses and methods for selecting and propagating diploids. We discuss the relative merits of tetrad dissection and random spore preparation in strain construction and genetic analyses...

The genetic analysis of repeated measures I: Simplex models

NARCIS (Netherlands)

Molenaar, P.C.M.; Boomsma, D.I.

1987-01-01

Extends the simplex model to a model that may be used for the genetic and environmental analysis of covariance (ANCOVA) structures. This "double" simplex structure can be specified as a linear structural relationships model. It is shown that data that give rise to a simplex correlation structure,

A new method for studying population genetics of cyst nematodes based on Pool-Seq and genomewide allele frequency analysis.

Science.gov (United States)

Mimee, Benjamin; Duceppe, Marc-Olivier; Véronneau, Pierre-Yves; Lafond-Lapalme, Joël; Jean, Martine; Belzile, François; Bélair, Guy

2015-11-01

Cyst nematodes are important agricultural pests responsible for billions of dollars of losses each year. Plant resistance is the most effective management tool, but it requires a close monitoring of population genetics. Current technologies for pathotyping and genotyping cyst nematodes are time-consuming, expensive and imprecise. In this study, we capitalized on the reproduction mode of cyst nematodes to develop a simple population genetic analysis pipeline based on genotyping-by-sequencing and Pool-Seq. This method yielded thousands of SNPs and allowed us to study the relationships between populations of different origins or pathotypes. Validation of the method on well-characterized populations also demonstrated that it was a powerful and accurate tool for population genetics. The genomewide allele frequencies of 23 populations of golden nematode, from nine countries and representing the five known pathotypes, were compared. A clear separation of the pathotypes and fine genetic relationships between and among global populations were obtained using this method. In addition to being powerful, this tool has proven to be very time- and cost-efficient and could be applied to other cyst nematode species. © 2015 Her Majesty the Queen in Right of Canada Molecular Ecology Resources © 2015 John Wiley & Sons Ltd Reproduced with the permission of the Minister of Agriculture and Agri-food.

Feature selection using genetic algorithms for fetal heart rate analysis

International Nuclear Information System (INIS)

Xu, Liang; Redman, Christopher W G; Georgieva, Antoniya; Payne, Stephen J

2014-01-01

The fetal heart rate (FHR) is monitored on a paper strip (cardiotocogram) during labour to assess fetal health. If necessary, clinicians can intervene and assist with a prompt delivery of the baby. Data-driven computerized FHR analysis could help clinicians in the decision-making process. However, selecting the best computerized FHR features that relate to labour outcome is a pressing research problem. The objective of this study is to apply genetic algorithms (GA) as a feature selection method to select the best feature subset from 64 FHR features and to integrate these best features to recognize unfavourable FHR patterns. The GA was trained on 404 cases and tested on 106 cases (both balanced datasets) using three classifiers, respectively. Regularization methods and backward selection were used to optimize the GA. Reasonable classification performance is shown on the testing set for the best feature subset (Cohen's kappa values of 0.45 to 0.49 using different classifiers). This is, to our knowledge, the first time that a feature selection method for FHR analysis has been developed on a database of this size. This study indicates that different FHR features, when integrated, can show good performance in predicting labour outcome. It also gives the importance of each feature, which will be a valuable reference point for further studies. (paper)

Genetic algorithm using independent component analysis in x-ray reflectivity curve fitting of periodic layer structures

International Nuclear Information System (INIS)

Tiilikainen, J; Bosund, V; Tilli, J-M; Sormunen, J; Mattila, M; Hakkarainen, T; Lipsanen, H

2007-01-01

A novel genetic algorithm (GA) utilizing independent component analysis (ICA) was developed for x-ray reflectivity (XRR) curve fitting. EFICA was used to reduce mutual information, or interparameter dependences, during the combinatorial phase. The performance of the new algorithm was studied by fitting trial XRR curves to target curves which were computed using realistic multilayer models. The median convergence properties of conventional GA, GA using principal component analysis and the novel GA were compared. GA using ICA was found to outperform the other methods with problems having 41 parameters or more to be fitted without additional XRR curve calculations. The computational complexity of the conventional methods was linear but the novel method had a quadratic computational complexity due to the applied ICA method which sets a practical limit for the dimensionality of the problem to be solved. However, the novel algorithm had the best capability to extend the fitting analysis based on Parratt's formalism to multiperiodic layer structures

Using cytogenetic analysis RAPD in determination of genetic variations among four species of ornamental fishes of family: Poecilidae (Order: Cyprinodontiform

Directory of Open Access Journals (Sweden)

Abu-Almaaty A.H.

2015-01-01

Full Text Available The karyological and molecular analysis of four fresh water fish species of Family: Poecilidae and their genetic relationships have been studied. Xiphophorus maculates and Xiphophorus hellerii have the same diploid chromosome number 2n=48, but they were different in their karyotypes. Poecilia sphenops and Poecilia reticulata have the same diploid chromosome number 2n=46 and the same fundamental number FN=46, also the same karyotype one group of acrocentric chromosomes. Nine RAPD primers, showed monomorphic bands, were used for the construction of the dendrogram and a similarity matrix. A total of 65 bands were obtained; 39 of them were monomorphic bands. Similarity values among the studied samples ranged from 21% to 38%. High similarity value was obtained between Xiphophorus maculates and Xiphophorus hellerii. (38% and the low similarity values were obtained between Xiphophorus hellerii and Poecilia reticulata (21%. The cluster analysis clearly differentiated Xiphophorus maculates and Xiphophorus hellerii from Poecilia sphenops and Poecilia reticulata. RAPD analysis confirmed that the four species under study are genetically different from each other. These cytogenetic data obtained can be applied for further studies in cytotaxonomy and evolutionary relationships of fishes.

Analysis of the genetic diversity of four rabbit genotypes using ...

African Journals Online (AJOL)

Dr.Ola

2013-05-15

May 15, 2013 ... consumption and low cost, it has been widely utilized in genetics analysis in ... isozyme variation among the selected individuals within each rabbit genotype. ... with different embryo survival (Bolet and Theau-Clement, 1994).

Genetic Counseling, Professional Values, and Habitus: An Analysis of Disability Narratives in Textbooks.

Science.gov (United States)

Reed, Amy R

2016-10-19

This article analyzes narrative illustrations in genetic counseling textbooks as a way of understanding professional habitus--the dispositions that motivate professional behavior. In particular, this analysis shows that there are significant differences in how the textbooks' expository and narrative portions represent Down syndrome, genetic counseling practice, and patient behaviors. While the narrative portions of the text position the genetic counseling profession as working in service to the values of genetic medicine, the expository portions represent genetic counselors as neutral parties. Ultimately, this article argues that this ambiguity is harmful to the production of a professional habitus that is consistent with espoused professional values concerning respect for persons with disabilities and the promotion of psychosocial counseling.

Pathway analysis of GWAS provides new insights into genetic susceptibility to 3 inflammatory diseases.

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Hariklia Eleftherohorinou

2009-11-01

Full Text Available Although the introduction of genome-wide association studies (GWAS have greatly increased the number of genes associated with common diseases, only a small proportion of the predicted genetic contribution has so far been elucidated. Studying the cumulative variation of polymorphisms in multiple genes acting in functional pathways may provide a complementary approach to the more common single SNP association approach in understanding genetic determinants of common disease. We developed a novel pathway-based method to assess the combined contribution of multiple genetic variants acting within canonical biological pathways and applied it to data from 14,000 UK individuals with 7 common diseases. We tested inflammatory pathways for association with Crohn's disease (CD, rheumatoid arthritis (RA and type 1 diabetes (T1D with 4 non-inflammatory diseases as controls. Using a variable selection algorithm, we identified variants responsible for the pathway association and evaluated their use for disease prediction using a 10 fold cross-validation framework in order to calculate out-of-sample area under the Receiver Operating Curve (AUC. The generalisability of these predictive models was tested on an independent birth cohort from Northern Finland. Multiple canonical inflammatory pathways showed highly significant associations (p 10(-3-10(-20 with CD, T1D and RA. Variable selection identified on average a set of 205 SNPs (149 genes for T1D, 350 SNPs (189 genes for RA and 493 SNPs (277 genes for CD. The pattern of polymorphisms at these SNPS were found to be highly predictive of T1D (91% AUC and RA (85% AUC, and weakly predictive of CD (60% AUC. The predictive ability of the T1D model (without any parameter refitting had good predictive ability (79% AUC in the Finnish cohort. Our analysis suggests that genetic contribution to common inflammatory diseases operates through multiple genes interacting in functional pathways.

Genetic analysis of fibre quality traits in upland cotton

International Nuclear Information System (INIS)

Khan, I.A.; Shakeel, A.; Azhar, F.M.

2001-01-01

Five-parent diallel cross data were analysed following Hayman-Jinks genetic model in order to study pattern of inheritance of staple length, fibre strength, fibre fineness and fibre uniformity of upland cotton. The regression analysis of the F/sub 1/ data revealed that the simple additive dominance model was adequate for genetic analysis. Graphic analysis showed the presence of over-dominance type of gene action in the inheritance e of all the traits. The comparison of array means indicated that varieties Co-2-1 and B-682 had good general combining ability for staple length and fibre strength respectively, whilst CIM-443 showed better general combining ability for fibre fineness and fibre uniformity than the other varieties. The cross combination of Co-2-1 and CIM-443 with B-682 expressed best specific combining ability for staple length and fibre uniformity respectively. Similarly variety B-682 nickel well with DPL 7740-424 for the fibre strength, and coker-307 with CO-2-1 for fibre fineness. The type of gene action controlling inheritance of these characters, and better performance of some of the hybrids suggest that improvement may be possible by developing on appropriate breeding programme. (author)

Animal research in the Journal of Applied Behavior Analysis.

Science.gov (United States)

Edwards, Timothy L; Poling, Alan

2011-01-01

This review summarizes the 6 studies with nonhuman animal subjects that have appeared in the Journal of Applied Behavior Analysis and offers suggestions for future research in this area. Two of the reviewed articles described translational research in which pigeons were used to illustrate and examine behavioral phenomena of applied significance (say-do correspondence and fluency), 3 described interventions that changed animals' behavior (self-injury by a baboon, feces throwing and spitting by a chimpanzee, and unsafe trailer entry by horses) in ways that benefited the animals and the people in charge of them, and 1 described the use of trained rats that performed a service to humans (land-mine detection). We suggest that each of these general research areas merits further attention and that the Journal of Applied Behavior Analysis is an appropriate outlet for some of these publications.

Cost-Effectiveness Analysis of Different Genetic Testing Strategies for Lynch Syndrome in Taiwan.

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Ying-Erh Chen

Full Text Available Patients with Lynch syndrome (LS have a significantly increased risk of developing colorectal cancer (CRC and other cancers. Genetic screening for LS among patients with newly diagnosed CRC aims to identify mutations in the disease-causing genes (i.e., the DNA mismatch repair genes in the patients, to offer genetic testing for relatives of the patients with the mutations, and then to provide early prevention for the relatives with the mutations. Several genetic tests are available for LS, such as DNA sequencing for MMR genes and tumor testing using microsatellite instability and immunohistochemical analyses. Cost-effectiveness analyses of different genetic testing strategies for LS have been performed in several studies from different countries such as the US and Germany. However, a cost-effectiveness analysis for the testing has not yet been performed in Taiwan. In this study, we evaluated the cost-effectiveness of four genetic testing strategies for LS described in previous studies, while population-specific parameters, such as the mutation rates of the DNA mismatch repair genes and treatment costs for CRC in Taiwan, were used. The incremental cost-effectiveness ratios based on discounted life years gained due to genetic screening were calculated for the strategies relative to no screening and to the previous strategy. Using the World Health Organization standard, which was defined based on Taiwan's Gross Domestic Product per capita, the strategy based on immunohistochemistry as a genetic test followed by BRAF mutation testing was considered to be highly cost-effective relative to no screening. Our probabilistic sensitivity analysis results also suggest that the strategy has a probability of 0.939 of being cost-effective relative to no screening based on the commonly used threshold of $50,000 to determine cost-effectiveness. To the best of our knowledge, this is the first cost-effectiveness analysis for evaluating different genetic testing

Assessment of Genetic Diversity and Population Genetic Structure of Corylus mandshurica in China Using SSR Markers.

Science.gov (United States)

Zong, Jian-Wei; Zhao, Tian-Tian; Ma, Qing-Hua; Liang, Li-Song; Wang, Gui-Xi

2015-01-01

Corylus mandshurica, also known as pilose hazelnut, is an economically and ecologically important species in China. In this study, ten polymorphic simple sequence repeat (SSR) markers were applied to evaluate the genetic diversity and population structure of 348 C. mandshurica individuals among 12 populations in China. The SSR markers expressed a relatively high level of genetic diversity (Na = 15.3, Ne = 5.6604, I = 1.8853, Ho = 0.6668, and He = 0.7777). According to the coefficient of genetic differentiation (Fst = 0.1215), genetic variation within the populations (87.85%) were remarkably higher than among populations (12.15%). The average gene flow (Nm = 1.8080) significantly impacts the genetic structure of C. mandshurica populations. The relatively high gene flow (Nm = 1.8080) among wild C. mandshurica may be caused by wind-pollinated flowers, highly nutritious seeds and self-incompatible mating system. The UPGMA (unweighted pair group method of arithmetic averages) dendrogram was divided into two main clusters. Moreover, the results of STRUCTURE analysis suggested that C. mandshurica populations fell into two main clusters. Comparison of the UPGMA dendrogram and the Bayesian STRUCTURE analysis showed general agreement between the population subdivisions and the genetic relationships among populations of C. mandshurica. Group I accessions were located in Northeast China, while Group II accessions were in North China. It is worth noting that a number of genetically similar populations were located in the same geographic region. The results further showed that there was obvious genetic differentiation among populations from Northeast China to North China. Results from the Mantel test showed a weak but still significant positive correlation between Nei's genetic distance and geographic distance (km) among populations (r = 0.419, P = 0.005), suggesting that genetic differentiation in the 12 C. mandshurica populations might be related to geographic distance. These

Assessment of Genetic Diversity and Population Genetic Structure of Corylus mandshurica in China Using SSR Markers.

Directory of Open Access Journals (Sweden)

Jian-Wei Zong

Full Text Available Corylus mandshurica, also known as pilose hazelnut, is an economically and ecologically important species in China. In this study, ten polymorphic simple sequence repeat (SSR markers were applied to evaluate the genetic diversity and population structure of 348 C. mandshurica individuals among 12 populations in China. The SSR markers expressed a relatively high level of genetic diversity (Na = 15.3, Ne = 5.6604, I = 1.8853, Ho = 0.6668, and He = 0.7777. According to the coefficient of genetic differentiation (Fst = 0.1215, genetic variation within the populations (87.85% were remarkably higher than among populations (12.15%. The average gene flow (Nm = 1.8080 significantly impacts the genetic structure of C. mandshurica populations. The relatively high gene flow (Nm = 1.8080 among wild C. mandshurica may be caused by wind-pollinated flowers, highly nutritious seeds and self-incompatible mating system. The UPGMA (unweighted pair group method of arithmetic averages dendrogram was divided into two main clusters. Moreover, the results of STRUCTURE analysis suggested that C. mandshurica populations fell into two main clusters. Comparison of the UPGMA dendrogram and the Bayesian STRUCTURE analysis showed general agreement between the population subdivisions and the genetic relationships among populations of C. mandshurica. Group I accessions were located in Northeast China, while Group II accessions were in North China. It is worth noting that a number of genetically similar populations were located in the same geographic region. The results further showed that there was obvious genetic differentiation among populations from Northeast China to North China. Results from the Mantel test showed a weak but still significant positive correlation between Nei's genetic distance and geographic distance (km among populations (r = 0.419, P = 0.005, suggesting that genetic differentiation in the 12 C. mandshurica populations might be related to geographic

GENETIC DIVERSITY ANALYSIS OF MANGABA (Hancornia speciosa Gomes, AN EXOTIC BRAZILIAN TROPICAL SPECIES

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Ana Veruska Cruz da Silva

2012-05-01

Full Text Available Twenty genotypes from natural population of mangaba located in Itaporanga D’Ajuda (Sergipe state - Brazil were subjected to analysis using RAPD markers. Polymorphism, genetic diversity and structure parameters were determined to characterize the differences between plants. 60 DNA fragments were generated by 10 primers, 85% of which were polymorphic. Results show a quantitative genetic diversity value of 0.35 and a Shannon index of 0.46 in the population. The similarity among the specimens according to Jaccard’s coefficient ranged from 0.36 to 0.87. Using cluster analysis it was possible to indentify five groups. Three individuals also stand out since they presented significant divergence from the groups. The PCoA formed four groups, with three of the groups isolated from the others. This investigation showed that genetic diversity was relatively large among these individuals. In addition, the results demonstrated that RAPD markers are a useful tool for evaluating the genetic diversity and relationships among mangaba.

Genetic Diversity and Relationships of Neolamarckia cadamba (Roxb. Bosser progenies through cluster analysis

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M. Preethi Shree

2018-04-01

Full Text Available Genetic diversity analysis was conducted for biometric attributes in 20 progenies of Neolamarckia cadamba. The application of D2 clustering technique in Neolamarckia cadamba genetic resources resolved the 20 progenies into five clusters. The maximum intra cluster distance was shown by the cluster II. The maximum inter cluster distance was recorded between cluster III and V which indicated the presence of wider genetic distance between Neolamarckia cadamba progenies. Among the growth attributes, volume (36.84 % contributed maximum towards genetic divergence followed by bole height, basal diameter, tree height, number of branches in Neolamarckia cadamba progenies.

Clinical application of antenatal genetic diagnosis of osteogenesis imperfecta type IV.

Science.gov (United States)

Yuan, Jing; Li, Song; Xu, YeYe; Cong, Lin

2015-04-02

Clinical analysis and genetic testing of a family with osteogenesis imperfecta type IV were conducted, aiming to discuss antenatal genetic diagnosis of osteogenesis imperfecta type IV. Preliminary genotyping was performed based on clinical characteristics of the family members and then high-throughput sequencing was applied to rapidly and accurately detect the changes in candidate genes. Genetic testing of the III5 fetus and other family members revealed missense mutation in c.2746G>A, pGly916Arg in COL1A2 gene coding region and missense and synonymous mutation in COL1A1 gene coding region. Application of antenatal genetic diagnosis provides fast and accurate genetic counseling and eugenics suggestions for patients with osteogenesis imperfecta type IV and their families.

PeachVar-DB: A Curated Collection of Genetic Variations for the Interactive Analysis of Peach Genome Data.

Science.gov (United States)

Cirilli, Marco; Flati, Tiziano; Gioiosa, Silvia; Tagliaferri, Ilario; Ciacciulli, Angelo; Gao, Zhongshan; Gattolin, Stefano; Geuna, Filippo; Maggi, Francesco; Bottoni, Paolo; Rossini, Laura; Bassi, Daniele; Castrignanò, Tiziana; Chillemi, Giovanni

2018-01-01

Applying next-generation sequencing (NGS) technologies to species of agricultural interest has the potential to accelerate the understanding and exploration of genetic resources. The storage, availability and maintenance of huge quantities of NGS-generated data remains a major challenge. The PeachVar-DB portal, available at http://hpc-bioinformatics.cineca.it/peach, is an open-source catalog of genetic variants present in peach (Prunus persica L. Batsch) and wild-related species of Prunus genera, annotated from 146 samples publicly released on the Sequence Read Archive (SRA). We designed a user-friendly web-based interface of the database, providing search tools to retrieve single nucleotide polymorphism (SNP) and InDel variants, along with useful statistics and information. PeachVar-DB results are linked to the Genome Database for Rosaceae (GDR) and the Phytozome database to allow easy access to other external useful plant-oriented resources. In order to extend the genetic diversity covered by the PeachVar-DB further, and to allow increasingly powerful comparative analysis, we will progressively integrate newly released data. © The Author 2017. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Methods for genetic linkage analysis using trisomies.

OpenAIRE

Feingold, E; Lamb, N E; Sherman, S L

1995-01-01

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 "susceptibility" ...

Analysis of genetic diversity in pigeon pea germplasm using ...

Indian Academy of Sciences (India)

MANEESHA

2017-08-16

Aug 16, 2017 ... Th, Thailand; It, Italy; B, Barbados; Ta, Taiwan; J, Jamaica; V, Venezuela; UK, United Kingdom; My, Myanmar; U, Uganda; G,. Germany. .... from Orissa (105) and AP (15) do not group with any .... In the present work, comparison between SSAP and ... fied polymorphism) for genetic analysis of sweet potato.

Genetic diversity analysis of pearl millet ( Pennisetum glauccum [L ...

African Journals Online (AJOL)

between genotype PT 2835/1 and PT 5552 and lowest similarity index was observed between PT 5554 and PT 2835/1. Analysis of RAPD data appears to be helpful in determining the genetic relationship among 20 pearl millet genotypes. The associations among the 20 genotypes were also examined with Principle ...

Symptom Cluster Research With Biomarkers and Genetics Using Latent Class Analysis.

Science.gov (United States)

Conley, Samantha

2017-12-01

The purpose of this article is to provide an overview of latent class analysis (LCA) and examples from symptom cluster research that includes biomarkers and genetics. A review of LCA with genetics and biomarkers was conducted using Medline, Embase, PubMed, and Google Scholar. LCA is a robust latent variable model used to cluster categorical data and allows for the determination of empirically determined symptom clusters. Researchers should consider using LCA to link empirically determined symptom clusters to biomarkers and genetics to better understand the underlying etiology of symptom clusters. The full potential of LCA in symptom cluster research has not yet been realized because it has been used in limited populations, and researchers have explored limited biologic pathways.

Applied Behavior Analysis: Beyond Discrete Trial Teaching

Science.gov (United States)

Steege, Mark W.; Mace, F. Charles; Perry, Lora; Longenecker, Harold

2007-01-01

We discuss the problem of autism-specific special education programs representing themselves as Applied Behavior Analysis (ABA) programs when the only ABA intervention employed is Discrete Trial Teaching (DTT), and often for limited portions of the school day. Although DTT has many advantages to recommend its use, it is not well suited to teach…

Comparative analysis of phenotypes features in two common genetic variants of limb-girdle muscular dystrophy

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I. V. Sharkova

2015-01-01

Full Text Available The algorithm of differential diagnosis of the two most common genetic variants the limb-girdle muscular dystrophy (LGMD2A and DMD, developed on the basis of a comprehensive survey of 85 patients with a diagnosis specification using techniques of DNA analysis. It is shown that the accurate diagnosis of LGMD genetic types should be based on the results of the clinical and genealogical, biochemical and molecular genetic analysis. The proposed algorithm will significantly reduces the economic and time costs with expensive DNA testing.

Genetic interaction analysis of point mutations enables interrogation of gene function at a residue-level resolution

Science.gov (United States)

Braberg, Hannes; Moehle, Erica A.; Shales, Michael; Guthrie, Christine; Krogan, Nevan J.

2014-01-01

We have achieved a residue-level resolution of genetic interaction mapping – a technique that measures how the function of one gene is affected by the alteration of a second gene – by analyzing point mutations. Here, we describe how to interpret point mutant genetic interactions, and outline key applications for the approach, including interrogation of protein interaction interfaces and active sites, and examination of post-translational modifications. Genetic interaction analysis has proven effective for characterizing cellular processes; however, to date, systematic high-throughput genetic interaction screens have relied on gene deletions or knockdowns, which limits the resolution of gene function analysis and poses problems for multifunctional genes. Our point mutant approach addresses these issues, and further provides a tool for in vivo structure-function analysis that complements traditional biophysical methods. We also discuss the potential for genetic interaction mapping of point mutations in human cells and its application to personalized medicine. PMID:24842270

Genetic analysis of radiation-induced mouse thymic lymphomas

International Nuclear Information System (INIS)

Kominami, R.; Wakabayashi, Y.; Niwa, O.

2003-01-01

Mouse thymic lymphomas are one of the classic models of radiation-induced malignancies, and the model has been used for the study of genes involved in carcinogenesis. ras oncogenes are the first isolate which undergoes mutations in 10 to 30 % of lymphomas, and p16INK4a and p19ARF in the INK4a-ARF locus are also frequently inactivated. In our previous study, the inactivation of Ikaros, a key regurator of lymphoid system, was found in those lymphomas, and it was suggested that there are other responsible genes yet to be discovered. On the other hand, genetic predisposition to radiation-induced lymphoma often differs in different strains, and this reflects the presence of low penetrance genes that can modify the impact of a given mutation. Little study of such modifiers or susceptibility genes has been performed, either. Recent availability of databases on mouse genome information and the power of mouse genetic system underline usefulness of the lymphoma model in search for novel genes involved, which may provide clues to molecular mechanisms of development of the radiogenic lymphoma and also genes involved in human lymphomas and other malignancies. Accordingly, we have carried out positional cloning for the two different types of tumor-related genes. In this symposium, our current progress is presented that includes genetic mapping of susceptibility/ resistance loci on mouse chromosomes 4, 5 and 19, and also functional analysis of a novel tumor suppressor gene, Rit1/Bcl11b, that has been isolated from allelic loss (LOH) mapping and sequence analysis for γ -ray induced mouse thymic lymphomas

Study on characteristic points of boiling curve by using wavelet analysis and genetic algorithm

International Nuclear Information System (INIS)

Wei Huiming; Su Guanghui; Qiu Suizheng; Yang Xingbo

2009-01-01

Based on the wavelet analysis theory of signal singularity detection,the critical heat flux (CHF) and minimum film boiling starting point (q min ) of boiling curves can be detected and analyzed by using the wavelet multi-resolution analysis. To predict the CHF in engineering, empirical relations were obtained based on genetic algorithm. The results of wavelet detection and genetic algorithm prediction are consistent with experimental data very well. (authors)

Identification of the genetic and clinical characteristics of neuroblastomas using genome-wide analysis.

Science.gov (United States)

Uryu, Kumiko; Nishimura, Riki; Kataoka, Keisuke; Sato, Yusuke; Nakazawa, Atsuko; Suzuki, Hiromichi; Yoshida, Kenichi; Seki, Masafumi; Hiwatari, Mitsuteru; Isobe, Tomoya; Shiraishi, Yuichi; Chiba, Kenichi; Tanaka, Hiroko; Miyano, Satoru; Koh, Katsuyoshi; Hanada, Ryoji; Oka, Akira; Hayashi, Yasuhide; Ohira, Miki; Kamijo, Takehiko; Nagase, Hiroki; Takimoto, Tetsuya; Tajiri, Tatsuro; Nakagawara, Akira; Ogawa, Seishi; Takita, Junko

2017-12-08

To provide better insight into the genetic signatures of neuroblastomas, we analyzed 500 neuroblastomas (included specimens from JNBSG) using targeted-deep sequencing for 10 neuroblastoma-related genes and SNP arrays analysis. ALK expression was evaluated using immunohistochemical analysis in 259 samples. Based on genetic alterations, the following 6 subgroups were identified: groups A ( ALK abnormalities), B (other gene mutations), C ( MYCN amplification), D (11q loss of heterozygosity [LOH]), E (at least 1 copy number variants), and F (no genetic changes). Groups A to D showed advanced disease and poor prognosis, whereas groups E and F showed excellent prognosis. Intriguingly, in group A, MYCN amplification was not a significant prognostic marker, while high ALK expression was a relevant indicator for prognosis ( P = 0.033). Notably, the co-existence of MYCN amplification and 1p LOH, and the co-deletion of 3p and 11q were significant predictors of relapse ( P = 0.043 and P = 0.040). Additionally, 6q/8p LOH and 17q gain were promising indicators of survival in patients older than 5 years, and 1p, 4p, and 11q LOH potentially contributed to outcome prediction in the intermediate-risk group. Our genetic overview clarifies the clinical impact of genetic signatures and aids in the better understanding of genetic basis of neuroblastoma.

Keloid Scarring: Understanding the Genetic Basis, Advances, and Prospects

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Ahmad Sukari Halim

2012-05-01

Full Text Available Keloid disease is a fibroproliferative dermal tumor with an unknown etiology that occurs after a skin injury in genetically susceptible individuals. Increased familial aggregation, a higher prevalence in certain races, parallelism in identical twins, and alteration in gene expression all favor a remarkable genetic contribution to keloid pathology. It seems that the environment triggers the disease in genetically susceptible individuals. Several genes have been implicated in the etiology of keloid disease, but no single gene mutation has thus far been found to be responsible. Therefore, a combination of methods such as association, gene-gene interaction, epigenetics, linkage, gene expression, and protein analysis should be applied to determine keloid etiology.

Positive Behavior Support and Applied Behavior Analysis

Science.gov (United States)

Johnston, J. M.; Foxx, R. M.; Jacobson, J. W.; Green, G.; Mulick, J. A.

2006-01-01

This article reviews the origins and characteristics of the positive behavior support (PBS) movement and examines those features in the context of the field of applied behavior analysis (ABA). We raise a number of concerns about PBS as an approach to delivery of behavioral services and its impact on how ABA is viewed by those in human services. We…

Progressive-Ratio Schedules and Applied Behavior Analysis

Science.gov (United States)

Poling, Alan

2010-01-01

Establishing appropriate relations between the basic and applied areas of behavior analysis has been of long and persistent interest to the author. In this article, the author illustrates that there is a direct relation between how hard an organism will work for access to an object or activity, as indexed by the largest ratio completed under a…

Genetic analysis on the competitive ability of barley ( Hordeum ...

African Journals Online (AJOL)

Genetic analysis on the competitive ability of barley ( Hordeum vulgare L.) recombinant inbred lines intercropped with oat ( Avena sativa L.) weeds. ... Furthermore, the commonly used herbicide price is soaring from time to time and out of the reach of the poor farmers in the developing countries. Therefore, this method is an ...

Sparse redundancy analysis of high-dimensional genetic and genomic data

NARCIS (Netherlands)

Csala, Attila; Voorbraak, Frans P. J. M.; Zwinderman, Aeilko H.; Hof, Michel H.

2017-01-01

Motivation: Recent technological developments have enabled the possibility of genetic and genomic integrated data analysis approaches, where multiple omics datasets from various biological levels are combined and used to describe (disease) phenotypic variations. The main goal is to explain and

Hardware Genetic Algorithm Optimization by Critical Path Analysis using a Custom VLSI Architecture

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Farouk Smith

2015-07-01

Full Text Available This paper propose a Virtual-Field Programmable Gate Array (V-FPGA architecture that allows direct access to its configuration bits to facilitate hardware evolution, thereby allowing any combinational or sequential digital circuit to be realized. By using the V-FPGA, this paper investigates two possible ways of making evolutionary hardware systems more scalable: by optimizing the system’s genetic algorithm (GA; and by decomposing the solution circuit into smaller, evolvable sub-circuits. GA optimization is done by: omitting a canonical GA’s crossover operator (i.e. by using a 1+λ algorithm; applying evolution constraints; and optimizing the fitness function. A noteworthy contribution this research has made is the in-depth analysis of the phenotypes’ CPs. Through analyzing the CPs, it has been shown that a great amount of insight can be gained into a phenotype’s fitness. We found that as the number of columns in the Cartesian Genetic Programming array increases, so the likelihood of an external output being placed in the column decreases. Furthermore, the number of used LEs per column also substantially decreases per added column. Finally, we demonstrated the evolution of a state-decomposed control circuit. It was shown that the evolution of each state’s sub-circuit was possible, and suggest that modular evolution can be a successful tool when dealing with scalability.

Application of soybean shoot-cutting in SMV-resistance genetic analysis

Institute of Scientific and Technical Information of China (English)

Haifeng Chen; Zhihui Shan; Xin'an zhou; Zhonglu Yang; Qiao Wan; Yanyan Yang; Shuilian Chen; Chanjuan Zhang; Limiao Chen; Songli Yuan; Dezhen Qiu

2016-01-01

Soybean mosaic virus (SMV) is one of the most serious diseases affecting soy-bean yield. Recombination inbred lines (RILs) are common materials for resistance genetic research. However, the population construction always takes quite a long time which pro-long the breading process. Shoot-cutting is a well-established technique for plant multipli-cation. It has high successful ratio in soybean. In this study, we use shoot-cutting to multiply two F2 populations from the crosses of susceptible and resistant varieties. Soybean plants can be multiplied from 1 into 3 homogenous ones within 30 days, bringing on well-grown plants with normal seeds. The SMV resistance from cutting-shoot plants was consistent with that from original plants. When shoot-cutting is applied in a F2 population, the pheno-typic and genotypic data can be simultaneously collected and corresponding saved during population development. The genetic research and resistant breeding can be effectively promoted by this technology.

Genetic analysis of calf and heifer losses in Danish Holstein

DEFF Research Database (Denmark)

Fuerst-Walti, B; Sørensen, Morten Kargo

2010-01-01

Mortality in dairy cattle is not only relevant with regard to economic losses but also to animal health and welfare. Thus, the aim of this investigation was to explore the genetic background of postnatal mortality in calves and replacement heifers in different age groups until first calving...... periods, whereas their records were kept for preceding periods. After further data editing, more than 840,000 calves and heifers born in the years 1998 to 2007 were investigated. Mortality rates were 3.23, 2.66, 0.97, 1.92, and 9.36% for the defined periods P1 to P5, respectively. For the estimation...... of genetic parameters, linear and threshold sire models were applied. Effects accounted for were the random effects herd × year × season and sire as well as the fixed effects year × month, number of dam's parity (parities >5 were set to 5), calf size, and calving ease. In total, the pedigree consisted of 4...

A strategy analysis for genetic association studies with known inbreeding

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del Giacco Stefano

2011-07-01

Full Text Available Abstract Background Association studies consist in identifying the genetic variants which are related to a specific disease through the use of statistical multiple hypothesis testing or segregation analysis in pedigrees. This type of studies has been very successful in the case of Mendelian monogenic disorders while it has been less successful in identifying genetic variants related to complex diseases where the insurgence depends on the interactions between different genes and the environment. The current technology allows to genotype more than a million of markers and this number has been rapidly increasing in the last years with the imputation based on templates sets and whole genome sequencing. This type of data introduces a great amount of noise in the statistical analysis and usually requires a great number of samples. Current methods seldom take into account gene-gene and gene-environment interactions which are fundamental especially in complex diseases. In this paper we propose to use a non-parametric additive model to detect the genetic variants related to diseases which accounts for interactions of unknown order. Although this is not new to the current literature, we show that in an isolated population, where the most related subjects share also most of their genetic code, the use of additive models may be improved if the available genealogical tree is taken into account. Specifically, we form a sample of cases and controls with the highest inbreeding by means of the Hungarian method, and estimate the set of genes/environmental variables, associated with the disease, by means of Random Forest. Results We have evidence, from statistical theory, simulations and two applications, that we build a suitable procedure to eliminate stratification between cases and controls and that it also has enough precision in identifying genetic variants responsible for a disease. This procedure has been successfully used for the beta-thalassemia, which is

Strategic decision analysis applied to borehole seismology

International Nuclear Information System (INIS)

Menke, M.M.; Paulsson, B.N.P.

1994-01-01

Strategic Decision Analysis (SDA) is the evolving body of knowledge on how to achieve high quality in the decision that shapes an organization's future. SDA comprises philosophy, process concepts, methodology, and tools for making good decisions. It specifically incorporates many concepts and tools from economic evaluation and risk analysis. Chevron Petroleum Technology Company (CPTC) has applied SDA to evaluate and prioritize a number of its most important and most uncertain R and D projects, including borehole seismology. Before SDA, there were significant issues and concerns about the value to CPTC of continuing to work on borehole seismology. The SDA process created a cross-functional team of experts to structure and evaluate this project. A credible economic model was developed, discrete risks and continuous uncertainties were assessed, and an extensive sensitivity analysis was performed. The results, even applied to a very restricted drilling program for a few years, were good enough to demonstrate the value of continuing the project. This paper explains the SDA philosophy concepts, and process and demonstrates the methodology and tools using the borehole seismology project example. SDA is useful in the upstream industry not just in the R and D/technology decisions, but also in major exploration and production decisions. Since a major challenge for upstream companies today is to create and realize value, the SDA approach should have a very broad applicability

Conservation genetics of Iberian raptors

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Martinez–Cruz, B.

2011-12-01

Full Text Available In this paper I provide an overview of conservation genetics and describe the management actions in the wild that can benefit from conservation genetic studies. I describe the genetic factors of risk for the survival of wild species, the consequences of loss of genetic diversity, inbreeding and outbreeding depression, and the use of genetic tools to delimitate units of conservation. Then I introduce the most common applications of conservation genetics in the management of wild populations. In a second part of the paper I review the conservation genetic studies carried on the Iberian raptors. I introduce several studies on the Spanish imperial eagle, the bearded vulture, the black vulture and the red kite that were carried out using autosomal microsatellite markers and mitochondrial DNA (mtDNA sequencing. I describe studies on the lesser kestrel and Egyptian vulture that additionally applied major histocompatibility complex (MHC markers, with the purpose of incorporating the study of non–neutral variation. For every species I explain how these studies can be and/or are applied in the strategy of conservation in the wild.

Examining the role of unmeasured confounding in mediation analysis with genetic and genomic applications.

Science.gov (United States)

Lutz, Sharon M; Thwing, Annie; Schmiege, Sarah; Kroehl, Miranda; Baker, Christopher D; Starling, Anne P; Hokanson, John E; Ghosh, Debashis

2017-07-19

In mediation analysis if unmeasured confounding is present, the estimates for the direct and mediated effects may be over or under estimated. Most methods for the sensitivity analysis of unmeasured confounding in mediation have focused on the mediator-outcome relationship. The Umediation R package enables the user to simulate unmeasured confounding of the exposure-mediator, exposure-outcome, and mediator-outcome relationships in order to see how the results of the mediation analysis would change in the presence of unmeasured confounding. We apply the Umediation package to the Genetic Epidemiology of Chronic Obstructive Pulmonary Disease (COPDGene) study to examine the role of unmeasured confounding due to population stratification on the effect of a single nucleotide polymorphism (SNP) in the CHRNA5/3/B4 locus on pulmonary function decline as mediated by cigarette smoking. Umediation is a flexible R package that examines the role of unmeasured confounding in mediation analysis allowing for normally distributed or Bernoulli distributed exposures, outcomes, mediators, measured confounders, and unmeasured confounders. Umediation also accommodates multiple measured confounders, multiple unmeasured confounders, and allows for a mediator-exposure interaction on the outcome. Umediation is available as an R package at https://github.com/SharonLutz/Umediation A tutorial on how to install and use the Umediation package is available in the Additional file 1.

A weighted U statistic for association analyses considering genetic heterogeneity.

Science.gov (United States)

Wei, Changshuai; Elston, Robert C; Lu, Qing

2016-07-20

Converging evidence suggests that common complex diseases with the same or similar clinical manifestations could have different underlying genetic etiologies. While current research interests have shifted toward uncovering rare variants and structural variations predisposing to human diseases, the impact of heterogeneity in genetic studies of complex diseases has been largely overlooked. Most of the existing statistical methods assume the disease under investigation has a homogeneous genetic effect and could, therefore, have low power if the disease undergoes heterogeneous pathophysiological and etiological processes. In this paper, we propose a heterogeneity-weighted U (HWU) method for association analyses considering genetic heterogeneity. HWU can be applied to various types of phenotypes (e.g., binary and continuous) and is computationally efficient for high-dimensional genetic data. Through simulations, we showed the advantage of HWU when the underlying genetic etiology of a disease was heterogeneous, as well as the robustness of HWU against different model assumptions (e.g., phenotype distributions). Using HWU, we conducted a genome-wide analysis of nicotine dependence from the Study of Addiction: Genetics and Environments dataset. The genome-wide analysis of nearly one million genetic markers took 7h, identifying heterogeneous effects of two new genes (i.e., CYP3A5 and IKBKB) on nicotine dependence. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Integrating Genetic and Gene Co-expression Analysis Identifies Gene Networks Involved in Alcohol and Stress Responses.

Science.gov (United States)

Luo, Jie; Xu, Pei; Cao, Peijian; Wan, Hongjian; Lv, Xiaonan; Xu, Shengchun; Wang, Gangjun; Cook, Melloni N; Jones, Byron C; Lu, Lu; Wang, Xusheng

2018-01-01

Although the link between stress and alcohol is well recognized, the underlying mechanisms of how they interplay at the molecular level remain unclear. The purpose of this study is to identify molecular networks underlying the effects of alcohol and stress responses, as well as their interaction on anxiety behaviors in the hippocampus of mice using a systems genetics approach. Here, we applied a gene co-expression network approach to transcriptomes of 41 BXD mouse strains under four conditions: stress, alcohol, stress-induced alcohol and control. The co-expression analysis identified 14 modules and characterized four expression patterns across the four conditions. The four expression patterns include up-regulation in no restraint stress and given an ethanol injection (NOE) but restoration in restraint stress followed by an ethanol injection (RSE; pattern 1), down-regulation in NOE but rescue in RSE (pattern 2), up-regulation in both restraint stress followed by a saline injection (RSS) and NOE, and further amplification in RSE (pattern 3), and up-regulation in RSS but reduction in both NOE and RSE (pattern 4). We further identified four functional subnetworks by superimposing protein-protein interactions (PPIs) to the 14 co-expression modules, including γ-aminobutyric acid receptor (GABA) signaling, glutamate signaling, neuropeptide signaling, cAMP-dependent signaling. We further performed module specificity analysis to identify modules that are specific to stress, alcohol, or stress-induced alcohol responses. Finally, we conducted causality analysis to link genetic variation to these identified modules, and anxiety behaviors after stress and alcohol treatments. This study underscores the importance of integrative analysis and offers new insights into the molecular networks underlying stress and alcohol responses.

Integrating Genetic and Gene Co-expression Analysis Identifies Gene Networks Involved in Alcohol and Stress Responses

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Jie Luo

2018-04-01

Full Text Available Although the link between stress and alcohol is well recognized, the underlying mechanisms of how they interplay at the molecular level remain unclear. The purpose of this study is to identify molecular networks underlying the effects of alcohol and stress responses, as well as their interaction on anxiety behaviors in the hippocampus of mice using a systems genetics approach. Here, we applied a gene co-expression network approach to transcriptomes of 41 BXD mouse strains under four conditions: stress, alcohol, stress-induced alcohol and control. The co-expression analysis identified 14 modules and characterized four expression patterns across the four conditions. The four expression patterns include up-regulation in no restraint stress and given an ethanol injection (NOE but restoration in restraint stress followed by an ethanol injection (RSE; pattern 1, down-regulation in NOE but rescue in RSE (pattern 2, up-regulation in both restraint stress followed by a saline injection (RSS and NOE, and further amplification in RSE (pattern 3, and up-regulation in RSS but reduction in both NOE and RSE (pattern 4. We further identified four functional subnetworks by superimposing protein-protein interactions (PPIs to the 14 co-expression modules, including γ-aminobutyric acid receptor (GABA signaling, glutamate signaling, neuropeptide signaling, cAMP-dependent signaling. We further performed module specificity analysis to identify modules that are specific to stress, alcohol, or stress-induced alcohol responses. Finally, we conducted causality analysis to link genetic variation to these identified modules, and anxiety behaviors after stress and alcohol treatments. This study underscores the importance of integrative analysis and offers new insights into the molecular networks underlying stress and alcohol responses.

Population genetic analysis of Enterocytozoon bieneusi in humans.

Science.gov (United States)

Li, Wei; Cama, Vitaliano; Feng, Yaoyu; Gilman, Robert H; Bern, Caryn; Zhang, Xichen; Xiao, Lihua

2012-01-01

Genotyping based on sequence analysis of the ribosomal internal transcribed spacer has revealed significant genetic diversity in Enterocytozoonbieneusi. Thus far, the population genetics of E. bieneusi and its significance in the epidemiology of microsporidiosis have not been examined. In this study, a multilocus sequence typing of E. bieneusi in AIDS patients in Lima, Peru was conducted, using 72 specimens previously genotyped as A, D, IV, EbpC, WL11, Peru7, Peru8, Peru10 and Peru11 at the internal transcribed spacer locus. Altogether, 39 multilocus genotypes were identified among the 72 specimens. The observation of strong intragenic linkage disequilibria and limited genetic recombination among markers were indicative of an overall clonal population structure of E. bieneusi. Measures of pair-wise intergenic linkage disequilibria and a standardised index of association (IAS) based on allelic profile data further supported this conclusion. Both sequence-based and allelic profile-based phylogenetic analyses showed the presence of two genetically isolated groups in the study population, one (group 1) containing isolates of the anthroponotic internal transcribed spacer genotype A, and the other (group 2) containing isolates of multiple internal transcribed spacer genotypes (mainly genotypes D and IV) with zoonotic potential. The measurement of linkage disequilibria and recombination indicated group 2 had a clonal population structure, whereas group 1 had an epidemic population structure. The formation of the two sub-populations was confirmed by STRUCTURE and Wright's fixation index (FST) analyses. The data highlight the power of MLST in understanding the epidemiology of E. bieneusi. Published by Elsevier Ltd.

Genetic analysis of feather pecking behavior in laying hens

NARCIS (Netherlands)

Buitenhuis, A.J.

2003-01-01

This thesis describes the genetic analysis of feather pecking behavior in laying hens. Feather pecking (FP) is a major welfare problem in laying hens.In the European

AFLP analysis of Genetic Diversity Among Different Jatropha curcas L. Genotypes from Africa and Ecuador

Directory of Open Access Journals (Sweden)

Konan, NO.

2018-01-01

Full Text Available Six populations amounting to a total number of seventy genotypes of Jatropha curcas L. originating from Africa (Senegal, Mali, Burkina Faso and Madagascar and Ecuador were investigated for genetic diversity using two AFLP primer combinations. The results revealed a high genetic diversity in the populations studied. The population with greatest genetic diversity was Madagascar (He = 0.2638 and I = 0.4066 and the least diverse was Senegal-Tamba (He = 0.1962 and I = 0.3079. AMOVA (analysis of molecular variance detected the highest proportion of variation within populations (81% of the total molecular variation. This may be attributed to the high level of allogamy observed in this species. The Nei's standard unbiased genetic distance (D between the populations ranged from 0.010 (Senegal-Tamba and Burkina Faso to 0.131 (Mali and Ecuador; the average was 0.063. Analysis of the genetic relationships among the 6 populations using both neighbor-joining cluster analysis and principal component analysis (PCoA showed five clusters with globally, groupings of i most of Burkina Faso and Senegal-Tamba genotypes, ii most of Mali and Senegal-Diobass genotypes , iii most of Madagascar and Ecuador genotypes, and iv some mixings of genotypes with different origins. Considering the distance existing between the different origins there are prospects to develop F1 hybrids. The greatest heterosis might be expected from crossing involving genotypes of cluster I and cluster V which group the more distant genotypes. Such crossing schemes might produce greater success in the production of genetic variability and might maximize the exploitation of heterosis and segregation.

A practical guide to propensity score analysis for applied clinical research.

Science.gov (United States)

Lee, Jaehoon; Little, Todd D

2017-11-01

Observational studies are often the only viable options in many clinical settings, especially when it is unethical or infeasible to randomly assign participants to different treatment régimes. In such case propensity score (PS) analysis can be applied to accounting for possible selection bias and thereby addressing questions of causal inference. Many PS methods exist, yet few guidelines are available to aid applied researchers in their conduct and evaluation of a PS analysis. In this article we give an overview of available techniques for PS estimation and application, balance diagnostic, treatment effect estimation, and sensitivity assessment, as well as recent advances. We also offer a tutorial that can be used to emulate the steps of PS analysis. Our goal is to provide information that will bring PS analysis within the reach of applied clinical researchers and practitioners. Copyright © 2017 Elsevier Ltd. All rights reserved.

Inference and Analysis of Population Structure Using Genetic Data and Network Theory.

Science.gov (United States)

Greenbaum, Gili; Templeton, Alan R; Bar-David, Shirli

2016-04-01

Clustering individuals to subpopulations based on genetic data has become commonplace in many genetic studies. Inference about population structure is most often done by applying model-based approaches, aided by visualization using distance-based approaches such as multidimensional scaling. While existing distance-based approaches suffer from a lack of statistical rigor, model-based approaches entail assumptions of prior conditions such as that the subpopulations are at Hardy-Weinberg equilibria. Here we present a distance-based approach for inference about population structure using genetic data by defining population structure using network theory terminology and methods. A network is constructed from a pairwise genetic-similarity matrix of all sampled individuals. The community partition, a partition of a network to dense subgraphs, is equated with population structure, a partition of the population to genetically related groups. Community-detection algorithms are used to partition the network into communities, interpreted as a partition of the population to subpopulations. The statistical significance of the structure can be estimated by using permutation tests to evaluate the significance of the partition's modularity, a network theory measure indicating the quality of community partitions. To further characterize population structure, a new measure of the strength of association (SA) for an individual to its assigned community is presented. The strength of association distribution (SAD) of the communities is analyzed to provide additional population structure characteristics, such as the relative amount of gene flow experienced by the different subpopulations and identification of hybrid individuals. Human genetic data and simulations are used to demonstrate the applicability of the analyses. The approach presented here provides a novel, computationally efficient model-free method for inference about population structure that does not entail assumption of

Unifying diseases from a genetic point of view: the example of the genetic theory of infectious diseases.

Science.gov (United States)

Darrason, Marie

2013-08-01

In the contemporary biomedical literature, every disease is considered genetic. This extension of the concept of genetic disease is usually interpreted either in a trivial or genocentrist sense, but it is never taken seriously as the expression of a genetic theory of disease. However, a group of French researchers defend the idea of a genetic theory of infectious diseases. By identifying four common genetic mechanisms (Mendelian predisposition to multiple infections, Mendelian predisposition to one infection, and major gene and polygenic predispositions), they attempt to unify infectious diseases from a genetic point of view. In this article, I analyze this explicit example of a genetic theory, which relies on mechanisms and is applied only to a specific category of diseases, what we call "a regional genetic theory." I have three aims: to prove that a genetic theory of disease can be devoid of genocentrism, to consider the possibility of a genetic theory applied to every disease, and to introduce two hypotheses about the form that such a genetic theory could take by distinguishing between a genetic theory of diseases and a genetic theory of Disease. Finally, I suggest that network medicine could be an interesting framework for a genetic theory of Disease.

A simple ssr analysis for genetic diversity estimation of maize landraces

Directory of Open Access Journals (Sweden)

Ignjatovic-Micic Dragana

2015-01-01

Full Text Available collection of 2217 landraces from western Balkan (former Yugoslavia is maintained at Maize Research Institute Zemun Polje gene bank. Nine flint and nine dent accessions from six agro-ecological groups (races, chosen on the basis of diverse pedigrees, were analyzed for genetic relatedness using phenotypic and simple sequence repeat (SSR markers. One of the aims was to establish a reliable set of SSR markers for a rapid diversity analysis using polyacrilamide gels and ethidium bromide staining. In the principal component analysis (PCA the first three principal components accounted for 80.86% of total variation and separated most of the flint from dent landraces. Ten SSR primers revealed a total of 56 and 63 alleles in flint and dent landraces, respectively, with low stuttering and good allele resolution on the gels. High average PIC value (0.822 also supports informativeness and utility of the markers used in this study. Higher genetic variation was observed among flint genotypes, as genetic distances between flint landraces covered a larger range of values (0.11- 0.38 than between dent (0.22 - 0.33 genotypes. Both phenotypic and SSR analyses distinguished flint and dent landraces, but neither of them could abstract agro-ecological groups. The SSR method used gave clear, easy to read band patterns that could be used for reliable allele frequency determination. Genetic diversity revealed for both markers indicated that the landraces were highly adapted to specific environmental conditions and purposes and could be valuable sources of genetic variability. [Projekat Ministarstva nauke Republike Srbije, br. TR31028: Exploitation of maize diversity to improve grain quality and drought tolerance

Genetics of Obesity Traits: A Bivariate Genome-Wide Association Analysis

DEFF Research Database (Denmark)

Wu, Yili; Duan, Haiping; Tian, Xiaocao

2018-01-01

Previous genome-wide association studies on anthropometric measurements have identified more than 100 related loci, but only a small portion of heritability in obesity was explained. Here we present a bivariate twin study to look for the genetic variants associated with body mass index and waist......-hip ratio, and to explore the obesity-related pathways in Northern Han Chinese. Cholesky decompositionmodel for 242monozygotic and 140 dizygotic twin pairs indicated a moderate genetic correlation (r = 0.53, 95%CI: 0.42–0.64) between body mass index and waist-hip ratio. Bivariate genome-wide association.......05. Expression quantitative trait loci analysis identified rs2242044 as a significant cis-eQTL in both the normal adipose-subcutaneous (P = 1.7 × 10−9) and adipose-visceral (P = 4.4 × 10−15) tissue. These findings may provide an important entry point to unravel genetic pleiotropy in obesity traits....

Ancestry inference using principal component analysis and spatial analysis: a distance-based analysis to account for population substructure.

Science.gov (United States)

Byun, Jinyoung; Han, Younghun; Gorlov, Ivan P; Busam, Jonathan A; Seldin, Michael F; Amos, Christopher I

2017-10-16

Accurate inference of genetic ancestry is of fundamental interest to many biomedical, forensic, and anthropological research areas. Genetic ancestry memberships may relate to genetic disease risks. In a genome association study, failing to account for differences in genetic ancestry between cases and controls may also lead to false-positive results. Although a number of strategies for inferring and taking into account the confounding effects of genetic ancestry are available, applying them to large studies (tens thousands samples) is challenging. The goal of this study is to develop an approach for inferring genetic ancestry of samples with unknown ancestry among closely related populations and to provide accurate estimates of ancestry for application to large-scale studies. In this study we developed a novel distance-based approach, Ancestry Inference using Principal component analysis and Spatial analysis (AIPS) that incorporates an Inverse Distance Weighted (IDW) interpolation method from spatial analysis to assign individuals to population memberships. We demonstrate the benefits of AIPS in analyzing population substructure, specifically related to the four most commonly used tools EIGENSTRAT, STRUCTURE, fastSTRUCTURE, and ADMIXTURE using genotype data from various intra-European panels and European-Americans. While the aforementioned commonly used tools performed poorly in inferring ancestry from a large number of subpopulations, AIPS accurately distinguished variations between and within subpopulations. Our results show that AIPS can be applied to large-scale data sets to discriminate the modest variability among intra-continental populations as well as for characterizing inter-continental variation. The method we developed will protect against spurious associations when mapping the genetic basis of a disease. Our approach is more accurate and computationally efficient method for inferring genetic ancestry in the large-scale genetic studies.

Genetic Diversity Analysis of South and East Asian Duck Populations Using Highly Polymorphic Microsatellite Markers

Directory of Open Access Journals (Sweden)

Dongwon Seo

2016-04-01

Full Text Available Native duck populations have lower productivity, and have not been developed as much as commercials duck breeds. However, native ducks have more importance in terms of genetic diversity and potentially valuable economic traits. For this reason, population discriminable genetic markers are needed for conservation and development of native ducks. In this study, 24 highly polymorphic microsatellite (MS markers were investigated using commercial ducks and native East and South Asian ducks. The average polymorphic information content (PIC value for all MS markers was 0.584, indicating high discrimination power. All populations were discriminated using 14 highly polymorphic MS markers by genetic distance and phylogenetic analysis. The results indicated that there were close genetic relationships among populations. In the structure analysis, East Asian ducks shared more haplotypes with commercial ducks than South Asian ducks, and they had more independent haplotypes than others did. These results will provide useful information for genetic diversity studies in ducks and for the development of duck traceability systems in the market.

An Inverse Kinematic Approach Using Groebner Basis Theory Applied to Gait Cycle Analysis

Science.gov (United States)

2013-03-01

AN INVERSE KINEMATIC APPROACH USING GROEBNER BASIS THEORY APPLIED TO GAIT CYCLE ANALYSIS THESIS Anum Barki AFIT-ENP-13-M-02 DEPARTMENT OF THE AIR...copyright protection in the United States. AFIT-ENP-13-M-02 AN INVERSE KINEMATIC APPROACH USING GROEBNER BASIS THEORY APPLIED TO GAIT CYCLE ANALYSIS THESIS...APPROACH USING GROEBNER BASIS THEORY APPLIED TO GAIT CYCLE ANALYSIS Anum Barki, BS Approved: Dr. Ronald F. Tuttle (Chairman) Date Dr. Kimberly Kendricks

Genetic Segregation Analysis of a Rapeseed Dwarf Mutant

International Nuclear Information System (INIS)

Xiang, G.; Yu, S.; Zhang, T.; Zhao, J.; Lei, S.; Du, C.

2016-01-01

Dwarf resources in Brassica napus are very important for developing high-yield cultivars through dwarf-type and lodging-resistant breeding. However, few dwarf varieties have been available for this species. Here, we reported a new rapeseed dwarf mutant GRC1157, which exhibits obvious phenotypic variations on dwarf. Six generations (P /sub 1/, P/sub 1/, F/sub 1/, F/sub 1/, B/sub 1/, and B/sub 1/) were produced from a cross between dwarf mutant GRC1157 and an elite tall-type line XR16 to analyze genetic inheritances of plant height (PH), numbers of the 1st valid branch (VBN), main inflorescence length (MIL), pod numbers per main inflorescence (MPN), pod length (PL) and seed numbers per pod (PSN) using the mixed major gene plus polygene inheritance model. The genetic analysis shows different traits were controlled by different inheritance models: PH and PL by two pairs of additive-dominant-epistatic major genes plus additive-dominant-epistatic polygenes, MPN and PSN by two-pair additive-dominant-epistatic major genes plus additive-dominant polygenes, MIL by two-pair additive-dominant-epistatic major genes and VBN by one-pair additive-dominant major genes plus additive-dominant-epistatic polygenes. Furthermore, positive correlations between PH and some other traits were observed, suggesting that some traits may be co-regulated by several linkage or same loci/genes. In addition, high heritability (40.35-93.7 percent) were found for five traits (except VBN) in different segregating generations, indicating these traits were mainly affected by hereditary factors and suitable for early artificial selection. In sum, the dwarf mutant GRC1157 can serve as a valuable resource for rapeseed dwarf breeding and the genetic analysis in this study provided a foundation for further mapping and cloning dwarf genes in mutant GRC1157. (author)

Genome wide characterization of simple sequence repeats in watermelon genome and their application in comparative mapping and genetic diversity analysis.

Science.gov (United States)

Zhu, Huayu; Song, Pengyao; Koo, Dal-Hoe; Guo, Luqin; Li, Yanman; Sun, Shouru; Weng, Yiqun; Yang, Luming

2016-08-05

Microsatellite markers are one of the most informative and versatile DNA-based markers used in plant genetic research, but their development has traditionally been difficult and costly. The whole genome sequencing with next-generation sequencing (NGS) technologies provides large amounts of sequence data to develop numerous microsatellite markers at whole genome scale. SSR markers have great advantage in cross-species comparisons and allow investigation of karyotype and genome evolution through highly efficient computation approaches such as in silico PCR. Here we described genome wide development and characterization of SSR markers in the watermelon (Citrullus lanatus) genome, which were then use in comparative analysis with two other important crop species in the Cucurbitaceae family: cucumber (Cucumis sativus L.) and melon (Cucumis melo L.). We further applied these markers in evaluating the genetic diversity and population structure in watermelon germplasm collections. A total of 39,523 microsatellite loci were identified from the watermelon draft genome with an overall density of 111 SSRs/Mbp, and 32,869 SSR primers were designed with suitable flanking sequences. The dinucleotide SSRs were the most common type representing 34.09 % of the total SSR loci and the AT-rich motifs were the most abundant in all nucleotide repeat types. In silico PCR analysis identified 832 and 925 SSR markers with each having a single amplicon in the cucumber and melon draft genome, respectively. Comparative analysis with these cross-species SSR markers revealed complicated mosaic patterns of syntenic blocks among the genomes of three species. In addition, genetic diversity analysis of 134 watermelon accessions with 32 highly informative SSR loci placed these lines into two groups with all accessions of C.lanatus var. citorides and three accessions of C. colocynthis clustered in one group and all accessions of C. lanatus var. lanatus and the remaining accessions of C. colocynthis

Ensemble Genetic Fuzzy Neuro Model Applied for the Emergency Medical Service via Unbalanced Data Evaluation

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Muammar Sadrawi

2018-03-01

Full Text Available Equally partitioned data are essential for prediction. However, in some important cases, the data distribution is severely unbalanced. In this study, several algorithms are utilized to maximize the learning accuracy when dealing with a highly unbalanced dataset. A linguistic algorithm is applied to evaluate the input and output relationship, namely Fuzzy c-Means (FCM, which is applied as a clustering algorithm for the majority class to balance the minority class data from about 3 million cases. Each cluster is used to train several artificial neural network (ANN models. Different techniques are applied to generate an ensemble genetic fuzzy neuro model (EGFNM in order to select the models. The first ensemble technique, the intra-cluster EGFNM, works by evaluating the best combination from all the models generated by each cluster. Another ensemble technique is the inter-cluster model EGFNM, which is based on selecting the best model from each cluster. The accuracy of these techniques is evaluated using the receiver operating characteristic (ROC via its area under the curve (AUC. Results show that the AUC of the unbalanced data is 0.67974. The random cluster and best ANN single model have AUCs of 0.7177 and 0.72806, respectively. For the ensemble evaluations, the intra-cluster and the inter-cluster EGFNMs produce 0.7293 and 0.73038, respectively. In conclusion, this study achieved improved results by performing the EGFNM method compared with the unbalanced training. This study concludes that selecting several best models will produce a better result compared with all models combined.

Applied spectrophotometry: analysis of a biochemical mixture.

Science.gov (United States)

Trumbo, Toni A; Schultz, Emeric; Borland, Michael G; Pugh, Michael Eugene

2013-01-01

Spectrophotometric analysis is essential for determining biomolecule concentration of a solution and is employed ubiquitously in biochemistry and molecular biology. The application of the Beer-Lambert-Bouguer Lawis routinely used to determine the concentration of DNA, RNA or protein. There is however a significant difference in determining the concentration of a given species (RNA, DNA, protein) in isolation (a contrived circumstance) as opposed to determining that concentration in the presence of other species (a more realistic situation). To present the student with a more realistic laboratory experience and also to fill a hole that we believe exists in student experience prior to reaching a biochemistry course, we have devised a three week laboratory experience designed so that students learn to: connect laboratory practice with theory, apply the Beer-Lambert-Bougert Law to biochemical analyses, demonstrate the utility and limitations of example quantitative colorimetric assays, demonstrate the utility and limitations of UV analyses for biomolecules, develop strategies for analysis of a solution of unknown biomolecular composition, use digital micropipettors to make accurate and precise measurements, and apply graphing software. Copyright © 2013 Wiley Periodicals, Inc.

Applied Drama and the Higher Education Learning Spaces: A Reflective Analysis

Science.gov (United States)

Moyo, Cletus

2015-01-01

This paper explores Applied Drama as a teaching approach in Higher Education learning spaces. The exploration takes a reflective analysis approach by first examining the impact that Applied Drama has had on my career as a Lecturer/Educator/Teacher working in Higher Education environments. My engagement with Applied Drama practice and theory is…

Contribution of genetics to ecological restoration.

Science.gov (United States)

Mijangos, Jose Luis; Pacioni, Carlo; Spencer, Peter B S; Craig, Michael D

2015-01-01

Ecological restoration of degraded ecosystems has emerged as a critical tool in the fight to reverse and ameliorate the current loss of biodiversity and ecosystem services. Approaches derived from different genetic disciplines are extending the theoretical and applied frameworks on which ecological restoration is based. We performed a search of scientific articles and identified 160 articles that employed a genetic approach within a restoration context to shed light on the links between genetics and restoration. These articles were then classified on whether they examined association between genetics and fitness or the application of genetics in demographic studies, and on the way the studies informed restoration practice. Although genetic research in restoration is rapidly growing, we found that studies could make better use of the extensive toolbox developed by applied fields in genetics. Overall, 41% of reviewed studies used genetic information to evaluate or monitor restoration, and 59% provided genetic information to guide prerestoration decision-making processes. Reviewed studies suggest that restoration practitioners often overlook the importance of including genetic aspects within their restoration goals. Even though there is a genetic basis influencing the provision of ecosystem services, few studies explored this relationship. We provide a view of research gaps, future directions and challenges in the genetics of restoration. © 2014 John Wiley & Sons Ltd.

Optimisation of shock absorber process parameters using failure mode and effect analysis and genetic algorithm

Science.gov (United States)

Mariajayaprakash, Arokiasamy; Senthilvelan, Thiyagarajan; Vivekananthan, Krishnapillai Ponnambal

2013-07-01

The various process parameters affecting the quality characteristics of the shock absorber during the process were identified using the Ishikawa diagram and by failure mode and effect analysis. The identified process parameters are welding process parameters (squeeze, heat control, wheel speed, and air pressure), damper sealing process parameters (load, hydraulic pressure, air pressure, and fixture height), washing process parameters (total alkalinity, temperature, pH value of rinsing water, and timing), and painting process parameters (flowability, coating thickness, pointage, and temperature). In this paper, the process parameters, namely, painting and washing process parameters, are optimized by Taguchi method. Though the defects are reasonably minimized by Taguchi method, in order to achieve zero defects during the processes, genetic algorithm technique is applied on the optimized parameters obtained by Taguchi method.

Genetic analysis of 430 Chinese Cynodon dactylon accessions using sequence-related amplified polymorphism markers.

Science.gov (United States)

Huang, Chunqiong; Liu, Guodao; Bai, Changjun; Wang, Wenqiang

2014-10-21

Although Cynodon dactylon (C. dactylon) is widely distributed in China, information on its genetic diversity within the germplasm pool is limited. The objective of this study was to reveal the genetic variation and relationships of 430 C. dactylon accessions collected from 22 Chinese provinces using sequence-related amplified polymorphism (SRAP) markers. Fifteen primer pairs were used to amplify specific C. dactylon genomic sequences. A total of 481 SRAP fragments were generated, with fragment sizes ranging from 260-1800 base pairs (bp). Genetic similarity coefficients (GSC) among the 430 accessions averaged 0.72 and ranged from 0.53-0.96. Cluster analysis conducted by two methods, namely the unweighted pair-group method with arithmetic averages (UPGMA) and principle coordinate analysis (PCoA), separated the accessions into eight distinct groups. Our findings verify that Chinese C. dactylon germplasms have rich genetic diversity, which is an excellent basis for C. dactylon breeding for new cultivars.

DNA degradation and genetic analysis of empty puparia: genetic identification limits in forensic entomology.

Science.gov (United States)

Mazzanti, Morena; Alessandrini, Federica; Tagliabracci, Adriano; Wells, Jeffrey D; Campobasso, Carlo P

2010-02-25

Puparial cases are common remnants of necrophagous flies in crime investigations. They usually represent the longest developmental time and, therefore, they can be very useful for the estimation of the post-mortem interval (PMI). However, before any PMI estimate, it is crucial to identify the species of fly eclosed from each puparium associated with the corpse. Morphological characteristics of the puparium are often distinctive enough to permit a species identification. But, even an accurate morphological analysis of empty puparia cannot discriminate among different species of closely related flies. Furthermore, morphological identification may be impossible if the fly puparia are poorly preserved or in fragments. This study explores the applicability of biomolecular techniques on empty puparia and their fragments for identification purposes. A total of 63 empty puparia of necrophagous Diptera resulting from forensic casework were examined. Samples were divided into three groups according to size, type and time of eclosion in order to verify whether the physical characteristics and puparia weathering can influence the amount of DNA extraction. The results suggest that a reliable genetic identification of forensically important flies may also be performed from empty puparia and/or their fragments. However, DNA degradation can deeply compromise the genetic analysis since the older the fly puparia, the smaller are the amplified fragments. 2009 Elsevier Ireland Ltd. All rights reserved.

Genetic diversity analysis of Chrysopidae family (Insecta, Neuroptera) via molecular markers.

Science.gov (United States)

Yari, Kheirollah; Mirmoayedi, Alinaghi; Marami, Marzieh; Kazemi, Elham; Kahrizi, Danial

2014-09-01

In entomology, improvement of molecular methods would be beneficial tools for accurate identification and detecting the genetic diversity of insect species to discover a corroborative evidence for the traditional classification based on morphology. The aim of this study was focused on RAPD-PCR method for distinguishing the genetic diversity between eight species of Chrysopidae family. In current research, many specimens were collected in different locations of Tehran province (Iran), between them 24 specimens were identified. The wing venation, male genitalia and other morphological characters were used for identification and also the sexing of species was recognized with study of external genitalia. Then, the DNA was extracted with CTAB method. The RAPD-PCR method was carried out with twenty random primers. The agarose gel electrophoresis was used for separation of the PCR products. Based on electrophoresis results, 133 bands were amplified and between them, 126 bands were poly-morph and others were mono-morph. Also, among the applied primers, the primers OPA02 with 19 bands and OPA03 with 8 bands were amplified the maximum and minimum of bands, respectively. The results showed that 80.35 and 73.21 % of genetic similarity existed between Chrysopa pallens-Chrysopa dubitans, and between the Chrysoperla kolthoffi and Chrysoperla carnea, respectively. The minimum (45.53 %) of genetic similarity was observed between C. kolthoffi and C. dubitans, and the maximum (0.80 %) was seen between C. pallens and C. dubitans.

Genetic analysis reveals diversity and genetic relationship among Trichoderma isolates from potting media, cultivated soil and uncultivated soil.

Science.gov (United States)

Al-Sadi, Abdullah M; Al-Oweisi, Fatma A; Edwards, Simon G; Al-Nadabi, Hamed; Al-Fahdi, Ahmed M

2015-07-28

Trichoderma is one of the most common fungi in soil. However, little information is available concerning the diversity of Trichoderma in soil with no previous history of cultivation. This study was conducted to investigate the most common species and the level of genetic relatedness of Trichoderma species from uncultivated soil in relation to cultivated soil and potting media. A total of 24, 15 and 13 Trichoderma isolates were recovered from 84 potting media samples, 45 cultivated soil samples and 65 uncultivated soil samples, respectively. Analysis based on the internal transcribed spacer region of the ribosomal RNA (rRNA) and the translation elongation factor gene (EF1) indicated the presence of 9 Trichoderma species: T. harzianum (16 isolates), T. asperellum (13), T. citrinoviride (9), T. orientalis (3), T. ghanense (3), T. hamatum (3), T. longibrachiatum (2), T. atroviride (2), and T. viride (1). All species were found to occur in potting media samples, while five Trichoderma species were recovered from the cultivated soils and four from the uncultivated soils. AFLP analysis of the 52 Trichoderma isolates produced 52 genotypes and 993 polymorphic loci. Low to moderate levels of genetic diversity were found within populations of Trichoderma species (H = 0.0780 to 0.2208). Analysis of Molecular Variance indicated the presence of very low levels of genetic differentiation (Fst = 0.0002 to 0.0139) among populations of the same Trichoderma species obtained from the potting media, cultivated soil and uncultivated soil. The study provides evidence for occurrence of Trichoderma isolates in soil with no previous history of cultivation. The lack of genetic differentiation among Trichoderma populations from potting media, cultivated soil and uncultivated soil suggests that some factors could have been responsible for moving Trichoderma propagules among the three substrates. The study reports for the first time the presence of 4 Trichoderma species in Oman: T

Biotecnologia aplicada ao melhoramento genético do cafeeiro Biotechnology applied to the genetic improvement of coffee plant

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Tâmara Prado de Morais

2011-05-01

Full Text Available O melhoramento genético do cafeeiro mediante técnicas convencionais é trabalhoso e demorado. A biotecnologia oferece estratégias alternativas para auxiliar na multiplicação e no desenvolvimento de novas variedades com resistência a estresses bióticos e abióticos, melhor qualidade de bebida e maturação mais uniforme dos frutos. As técnicas de cultura de tecidos têm possibilitado a obtenção de grande número de plantas e a garantia da uniformidade genética do material. O emprego de marcadores moleculares, principalmente através da seleção assistida, facilitou o rápido progresso do melhoramento genético da cultura, assim como a transformação genética, via cultura e fusão de protoplastos, biobalística ou mediada por Agrobacterium sp. Esta revisão objetiva sumarizar o histórico, situação atual e perspectivas da biotecnologia no melhoramento genético do cafeeiro.Genetic improvement of coffee through classical breeding is laborious and time consuming. Biotechnology offers alternative strategies to assist multiplication and development of new and improved coffee varieties, including those resistant to biotic and abiotic stresses, with better cup quality, and with uniform fruit maturation. Tissue culture techniques have enabled the production of a large number of plants with genetic uniformity. The use of molecular markers, especially through assisted selection, led to rapid progress of coffee plant breeding, as well as the use of genetic transformation by protoplasts culture and fusion, biobalistics, or Agrobacterium-mediated. This review provides a summary of biotechnology history, current situation and directions applied to the genetic improvement of coffee plant.

Analysis of genetic code ambiguity arising from nematode-specific misacylated tRNAs.

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Kiyofumi Hamashima

Full Text Available The faithful translation of the genetic code requires the highly accurate aminoacylation of transfer RNAs (tRNAs. However, it has been shown that nematode-specific V-arm-containing tRNAs (nev-tRNAs are misacylated with leucine in vitro in a manner that transgresses the genetic code. nev-tRNA(Gly (CCC and nev-tRNA(Ile (UAU, which are the major nev-tRNA isotypes, could theoretically decode the glycine (GGG codon and isoleucine (AUA codon as leucine, causing GGG and AUA codon ambiguity in nematode cells. To test this hypothesis, we investigated the functionality of nev-tRNAs and their impact on the proteome of Caenorhabditis elegans. Analysis of the nucleotide sequences in the 3' end regions of the nev-tRNAs showed that they had matured correctly, with the addition of CCA, which is a crucial posttranscriptional modification required for tRNA aminoacylation. The nuclear export of nev-tRNAs was confirmed with an analysis of their subcellular localization. These results show that nev-tRNAs are processed to their mature forms like common tRNAs and are available for translation. However, a whole-cell proteome analysis found no detectable level of nev-tRNA-induced mistranslation in C. elegans cells, suggesting that the genetic code is not ambiguous, at least under normal growth conditions. Our findings indicate that the translational fidelity of the nematode genetic code is strictly maintained, contrary to our expectations, although deviant tRNAs with misacylation properties are highly conserved in the nematode genome.

Fusion genetic analysis of jasmonate-signalling mutants in Arabidopsis

DEFF Research Database (Denmark)

Jensen, Anders Bøgh; Raventos, D.; Mundy, John Williams

2002-01-01

as two recessive mutants, designated joe1 and 2, that overexpress the reporter. Genetic analysis indicated that reporter overexpression in the joe mutants requires COI. joe1 responded to MeJA with increased anthocyanin accumulation, while joe2 responded with decreased root growth inhibition. In addition...... activity was also induced by the protein kinase inhibitor staurosporine and antagonized by the protein phosphatase inhibitor okadaic acid. FLUC bio-imaging, RNA gel-blot analysis and progeny analyses identified three recessive mutants that underexpress the FLUC reporter, designated jue1, 2 and 3, as well...

Functional Data Analysis Applied in Chemometrics

DEFF Research Database (Denmark)

Muller, Martha

nutritional status and metabolic phenotype. We want to understand how metabolomic spectra can be analysed using functional data analysis to detect the in uence of dierent factors on specic metabolites. These factors can include, for example, gender, diet culture or dietary intervention. In Paper I we apply...... representation of each spectrum. Subset selection of wavelet coecients generates the input to mixed models. Mixed-model methodology enables us to take the study design into account while modelling covariates. Bootstrap-based inference preserves the correlation structure between curves and enables the estimation...

Irradiation influence on the detection of genetic-modified soybeans

International Nuclear Information System (INIS)

Villavicencio, A.L.C.H.; Araujo, M.M.; Baldasso, J.G.; Aquino, S.; Konietzny, U.; Greiner, R.

2004-01-01

Three soybean varieties were analyzed to evaluate the irradiation influence on the detection of genetic modification. Samples were treated in a 60 Co facility at dose levels of 0, 500, 800, and 1000 Gy. The seeds were at first analyzed by Comet Assay as a rapid screening irradiation detection method. Secondly, germination test was performed to detect the viability of irradiated soybeans. Finally, because of its high sensitivity, its specificity and rapidity the polimerase chain reaction was the method applied for genetic modified organism detection. The analysis of DNA by the single technique of microgel electrophoresis of single cells (DNA Comet Assay) showed that DNA damage increased with increasing radiation doses. No negative influence of irradiation on the genetic modification detection was found

Genetic diversity of different accessions of Thymus kotschyanus using RAPD marker

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Ahmad Ismaili

2014-11-01

Full Text Available Analysis of genetic diversity is a major step for understanding evolution and breeding applications. Recent advances in the application of the polymerase chain reaction make it possible to score individuals at a large number of loci. The RAPD technique has been successfully used in a variety of taxonomic and genetic diversity studies. The genetic diversity of 18 accessions of Thymus kotschyanus collected from different districts of Iran has been reported in this study, using 30 random amplified polymorphic DNA primers. Multivariate statistical analyses including principal coordinate analysis (PCOA and cluster analysis were used to group the accessions. From 29 primers, 385 bands were scored corresponding to an average of 13.27 bands per primer with 298 bands showing polymorphism (77.40%. A dendrogram constructed based on the UPGMA clustering method revealed three major clusters. The obtained results from grouping 18 accessions of T. kotschyanus with two studied methods indicated that in the most cases the applied methods produced similar grouping results. This study revealed nearly rich genetic diversity among T. kotschyanus accessions from different regions of Iran. The results showed RAPD marker was a useful marker for genetic diversity studies of T. kotschyanus and it was indicative of geographica variations.

Estimating the actual subject-specific genetic correlations in behavior genetics.

Science.gov (United States)

Molenaar, Peter C M

2012-10-01

Generalization of the standard behavior longitudinal genetic factor model for the analysis of interindividual phenotypic variation to a genetic state space model for the analysis of intraindividual variation enables the possibility to estimate subject-specific heritabilities.

Evolutionary genetics

National Research Council Canada - National Science Library

Maynard Smith, John

1989-01-01

.... It differs from other textbooks of population genetics in applying the basic theory to topics, such as social behaviour, molecular evolution, reiterated DNA, and sex, which are the main subjects...

Genetics in the art and art in genetics.

Science.gov (United States)

Bukvic, Nenad; Elling, John W

2015-01-15

"Healing is best accomplished when art and science are conjoined, when body and spirit are probed together", says Bernard Lown, in his book "The Lost Art of Healing". Art has long been a witness to disease either through diseases which affected artists or diseases afflicting objects of their art. In particular, artists have often portrayed genetic disorders and malformations in their work. Sometimes genetic disorders have mystical significance; other times simply have intrinsic interest. Recognizing genetic disorders is also an art form. From the very beginning of my work as a Medical Geneticist I have composed personal "algorithms" to piece together evidence of genetics syndromes and diseases from the observable signs and symptoms. In this paper we apply some 'gestalt' Genetic Syndrome Diagnostic algorithms to virtual patients found in some art masterpieces. In some the diagnosis is clear and in others the artists' depiction only supports a speculative differential diagnosis. Copyright © 2014 Elsevier B.V. All rights reserved.

Applications of genetic programming in cancer research.

Science.gov (United States)

Worzel, William P; Yu, Jianjun; Almal, Arpit A; Chinnaiyan, Arul M

2009-02-01

The theory of Darwinian evolution is the fundamental keystones of modern biology. Late in the last century, computer scientists began adapting its principles, in particular natural selection, to complex computational challenges, leading to the emergence of evolutionary algorithms. The conceptual model of selective pressure and recombination in evolutionary algorithms allow scientists to efficiently search high dimensional space for solutions to complex problems. In the last decade, genetic programming has been developed and extensively applied for analysis of molecular data to classify cancer subtypes and characterize the mechanisms of cancer pathogenesis and development. This article reviews current successes using genetic programming and discusses its potential impact in cancer research and treatment in the near future.

Genetic and phylogenetic analysis of ten Gobiidae species in China ...

African Journals Online (AJOL)

To study the genetic and phylogenetic relationship of gobioid fishes in China, the representatives of 10 gobioid fishes from 2 subfamilies in China were examined by amplified fragment length polymorphism (AFLP) analysis. We established 220 AFLP bands for 45 individuals from the 10 species, and the percentage of ...

Genetic analysis of yield in peanut ( Arachis hypogaea L.) using ...

African Journals Online (AJOL)

The yield had significant major gene effect and the results implied that not only should the two major genes' effects be considered but also the polygene's effect should be considered in breeding to increase peanut yield. Key words: Peanut, yield, major gene plus polygene inheritance model, genetic analysis.

New application of intelligent agents in sporadic amyotrophic lateral sclerosis identifies unexpected specific genetic background

Directory of Open Access Journals (Sweden)

Marocchi Alessandro

2008-05-01

Full Text Available Abstract Background Few genetic factors predisposing to the sporadic form of amyotrophic lateral sclerosis (ALS have been identified, but the pathology itself seems to be a true multifactorial disease in which complex interactions between environmental and genetic susceptibility factors take place. The purpose of this study was to approach genetic data with an innovative statistical method such as artificial neural networks to identify a possible genetic background predisposing to the disease. A DNA multiarray panel was applied to genotype more than 60 polymorphisms within 35 genes selected from pathways of lipid and homocysteine metabolism, regulation of blood pressure, coagulation, inflammation, cellular adhesion and matrix integrity, in 54 sporadic ALS patients and 208 controls. Advanced intelligent systems based on novel coupling of artificial neural networks and evolutionary algorithms have been applied. The results obtained have been compared with those derived from the use of standard neural networks and classical statistical analysis Results Advanced intelligent systems based on novel coupling of artificial neural networks and evolutionary algorithms have been applied. The results obtained have been compared with those derived from the use of standard neural networks and classical statistical analysis. An unexpected discovery of a strong genetic background in sporadic ALS using a DNA multiarray panel and analytical processing of the data with advanced artificial neural networks was found. The predictive accuracy obtained with Linear Discriminant Analysis and Standard Artificial Neural Networks ranged from 70% to 79% (average 75.31% and from 69.1 to 86.2% (average 76.6% respectively. The corresponding value obtained with Advanced Intelligent Systems reached an average of 96.0% (range 94.4 to 97.6%. This latter approach allowed the identification of seven genetic variants essential to differentiate cases from controls: apolipoprotein E arg

New application of intelligent agents in sporadic amyotrophic lateral sclerosis identifies unexpected specific genetic background.

Science.gov (United States)

Penco, Silvana; Buscema, Massimo; Patrosso, Maria Cristina; Marocchi, Alessandro; Grossi, Enzo

2008-05-30

Few genetic factors predisposing to the sporadic form of amyotrophic lateral sclerosis (ALS) have been identified, but the pathology itself seems to be a true multifactorial disease in which complex interactions between environmental and genetic susceptibility factors take place. The purpose of this study was to approach genetic data with an innovative statistical method such as artificial neural networks to identify a possible genetic background predisposing to the disease. A DNA multiarray panel was applied to genotype more than 60 polymorphisms within 35 genes selected from pathways of lipid and homocysteine metabolism, regulation of blood pressure, coagulation, inflammation, cellular adhesion and matrix integrity, in 54 sporadic ALS patients and 208 controls. Advanced intelligent systems based on novel coupling of artificial neural networks and evolutionary algorithms have been applied. The results obtained have been compared with those derived from the use of standard neural networks and classical statistical analysis Advanced intelligent systems based on novel coupling of artificial neural networks and evolutionary algorithms have been applied. The results obtained have been compared with those derived from the use of standard neural networks and classical statistical analysis. An unexpected discovery of a strong genetic background in sporadic ALS using a DNA multiarray panel and analytical processing of the data with advanced artificial neural networks was found. The predictive accuracy obtained with Linear Discriminant Analysis and Standard Artificial Neural Networks ranged from 70% to 79% (average 75.31%) and from 69.1 to 86.2% (average 76.6%) respectively. The corresponding value obtained with Advanced Intelligent Systems reached an average of 96.0% (range 94.4 to 97.6%). This latter approach allowed the identification of seven genetic variants essential to differentiate cases from controls: apolipoprotein E arg158cys; hepatic lipase -480 C/T; endothelial

Applied Behavior Analysis: Current Myths in Public Education

Science.gov (United States)

Fielding, Cheryl; Lowdermilk, John; Lanier, Lauren L.; Fannin, Abigail G.; Schkade, Jennifer L.; Rose, Chad A.; Simpson, Cynthia G.

2013-01-01

The effective use of behavior management strategies and related policies continues to be a debated issue in public education. Despite overwhelming evidence espousing the benefits of the implementation of procedures derived from principles based on the science of applied behavior analysis (ABA), educators often indicate many common misconceptions…

Shedding subspecies: The influence of genetics on reptile subspecies taxonomy.

Science.gov (United States)

Torstrom, Shannon M; Pangle, Kevin L; Swanson, Bradley J

2014-07-01

The subspecies concept influences multiple aspects of biology and management. The 'molecular revolution' altered traditional methods (morphological traits) of subspecies classification by applying genetic analyses resulting in alternative or contradictory classifications. We evaluated recent reptile literature for bias in the recommendations regarding subspecies status when genetic data were included. Reviewing characteristics of the study, genetic variables, genetic distance values and noting the species concepts, we found that subspecies were more likely elevated to species when using genetic analysis. However, there was no predictive relationship between variables used and taxonomic recommendation. There was a significant difference between the median genetic distance values when researchers elevated or collapsed a subspecies. Our review found nine different concepts of species used when recommending taxonomic change, and studies incorporating multiple species concepts were more likely to recommend a taxonomic change. Since using genetic techniques significantly alter reptile taxonomy there is a need to establish a standard method to determine the species-subspecies boundary in order to effectively use the subspecies classification for research and conservation purposes. Copyright © 2014 Elsevier Inc. All rights reserved.

Genetic parameters and path analysis in cowpea genotypes grown in the Cerrado/Pantanal ecotone.

Science.gov (United States)

Lopes, K V; Teodoro, P E; Silva, F A; Silva, M T; Fernandes, R L; Rodrigues, T C; Faria, T C; Corrêa, A M

2017-05-18

Estimating genetic parameters in plant breeding allows us to know the population potential for selecting and designing strategies that can maximize the achievement of superior genotypes. The objective of this study was to evaluate the genetic potential of a population of 20 cowpea genotypes by estimating genetic parameters and path analysis among the traits to guide the selection strategies. The trial was conducted in randomized block design with four replications. Its morphophysiological components, components of green grain production and dry grain yield were estimated from genetic use and correlations between the traits. Phenotypic correlations were deployed through path analysis into direct and indirect effects of morphophysiological traits and yield components on dry grain yield. There were significant differences (P < 0.01) between the genotypes for most the traits, indicating the presence of genetic variability in the population and the possibility of practicing selection. The population presents the potential for future genetic breeding studies and is highly promising for the selection of traits dry grain yield, the number of grains per pod, and hundred grains mass. A number of grains per green pod is the main determinant trait of dry grain yield that is also influenced by the cultivar cycle and that the selection for the dry grain yield can be made indirectly by selecting the green pod mass and green pod length.

Cause and effect analysis by fuzzy relational equations and a genetic algorithm

International Nuclear Information System (INIS)

Rotshtein, Alexander P.; Posner, Morton; Rakytyanska, Hanna B.

2006-01-01

This paper proposes using a genetic algorithm as a tool to solve the fault diagnosis problem. The fault diagnosis problem is based on a cause and effect analysis which is formally described by fuzzy relations. Fuzzy relations are formed on the basis of expert assessments. Application of expert fuzzy relations to restore and identify the causes through the observed effects requires the solution to a system of fuzzy relational equations. In this study this search for a solution amounts to solving a corresponding optimization problem. An optimization algorithm is based on the application of genetic operations of crossover, mutation and selection. The genetic algorithm suggested here represents an application in expert systems of fault diagnosis and quality control

Oligonucleotide arrays vs. metaphase-comparative genomic hybridisation and BAC arrays for single-cell analysis: first applications to preimplantation genetic diagnosis for Robertsonian translocation carriers.

Science.gov (United States)

Ramos, Laia; del Rey, Javier; Daina, Gemma; García-Aragonés, Manel; Armengol, Lluís; Fernandez-Encinas, Alba; Parriego, Mònica; Boada, Montserrat; Martinez-Passarell, Olga; Martorell, Maria Rosa; Casagran, Oriol; Benet, Jordi; Navarro, Joaquima

2014-01-01

Comprehensive chromosome analysis techniques such as metaphase-Comparative Genomic Hybridisation (CGH) and array-CGH are available for single-cell analysis. However, while metaphase-CGH and BAC array-CGH have been widely used for Preimplantation Genetic Diagnosis, oligonucleotide array-CGH has not been used in an extensive way. A comparison between oligonucleotide array-CGH and metaphase-CGH has been performed analysing 15 single fibroblasts from aneuploid cell-lines and 18 single blastomeres from human cleavage-stage embryos. Afterwards, oligonucleotide array-CGH and BAC array-CGH were also compared analysing 16 single blastomeres from human cleavage-stage embryos. All three comprehensive analysis techniques provided broadly similar cytogenetic profiles; however, non-identical profiles appeared when extensive aneuploidies were present in a cell. Both array techniques provided an optimised analysis procedure and a higher resolution than metaphase-CGH. Moreover, oligonucleotide array-CGH was able to define extra segmental imbalances in 14.7% of the blastomeres and it better determined the specific unbalanced chromosome regions due to a higher resolution of the technique (≈ 20 kb). Applicability of oligonucleotide array-CGH for Preimplantation Genetic Diagnosis has been demonstrated in two cases of Robertsonian translocation carriers 45,XY,der(13;14)(q10;q10). Transfer of euploid embryos was performed in both cases and pregnancy was achieved by one of the couples. This is the first time that an oligonucleotide array-CGH approach has been successfully applied to Preimplantation Genetic Diagnosis for balanced chromosome rearrangement carriers.

Oligonucleotide arrays vs. metaphase-comparative genomic hybridisation and BAC arrays for single-cell analysis: first applications to preimplantation genetic diagnosis for Robertsonian translocation carriers.

Directory of Open Access Journals (Sweden)

Laia Ramos

Full Text Available Comprehensive chromosome analysis techniques such as metaphase-Comparative Genomic Hybridisation (CGH and array-CGH are available for single-cell analysis. However, while metaphase-CGH and BAC array-CGH have been widely used for Preimplantation Genetic Diagnosis, oligonucleotide array-CGH has not been used in an extensive way. A comparison between oligonucleotide array-CGH and metaphase-CGH has been performed analysing 15 single fibroblasts from aneuploid cell-lines and 18 single blastomeres from human cleavage-stage embryos. Afterwards, oligonucleotide array-CGH and BAC array-CGH were also compared analysing 16 single blastomeres from human cleavage-stage embryos. All three comprehensive analysis techniques provided broadly similar cytogenetic profiles; however, non-identical profiles appeared when extensive aneuploidies were present in a cell. Both array techniques provided an optimised analysis procedure and a higher resolution than metaphase-CGH. Moreover, oligonucleotide array-CGH was able to define extra segmental imbalances in 14.7% of the blastomeres and it better determined the specific unbalanced chromosome regions due to a higher resolution of the technique (≈ 20 kb. Applicability of oligonucleotide array-CGH for Preimplantation Genetic Diagnosis has been demonstrated in two cases of Robertsonian translocation carriers 45,XY,der(13;14(q10;q10. Transfer of euploid embryos was performed in both cases and pregnancy was achieved by one of the couples. This is the first time that an oligonucleotide array-CGH approach has been successfully applied to Preimplantation Genetic Diagnosis for balanced chromosome rearrangement carriers.

Oligonucleotide Arrays vs. Metaphase-Comparative Genomic Hybridisation and BAC Arrays for Single-Cell Analysis: First Applications to Preimplantation Genetic Diagnosis for Robertsonian Translocation Carriers

Science.gov (United States)

Ramos, Laia; del Rey, Javier; Daina, Gemma; García-Aragonés, Manel; Armengol, Lluís; Fernandez-Encinas, Alba; Parriego, Mònica; Boada, Montserrat; Martinez-Passarell, Olga; Martorell, Maria Rosa; Casagran, Oriol; Benet, Jordi; Navarro, Joaquima

2014-01-01

Comprehensive chromosome analysis techniques such as metaphase-Comparative Genomic Hybridisation (CGH) and array-CGH are available for single-cell analysis. However, while metaphase-CGH and BAC array-CGH have been widely used for Preimplantation Genetic Diagnosis, oligonucleotide array-CGH has not been used in an extensive way. A comparison between oligonucleotide array-CGH and metaphase-CGH has been performed analysing 15 single fibroblasts from aneuploid cell-lines and 18 single blastomeres from human cleavage-stage embryos. Afterwards, oligonucleotide array-CGH and BAC array-CGH were also compared analysing 16 single blastomeres from human cleavage-stage embryos. All three comprehensive analysis techniques provided broadly similar cytogenetic profiles; however, non-identical profiles appeared when extensive aneuploidies were present in a cell. Both array techniques provided an optimised analysis procedure and a higher resolution than metaphase-CGH. Moreover, oligonucleotide array-CGH was able to define extra segmental imbalances in 14.7% of the blastomeres and it better determined the specific unbalanced chromosome regions due to a higher resolution of the technique (≈20 kb). Applicability of oligonucleotide array-CGH for Preimplantation Genetic Diagnosis has been demonstrated in two cases of Robertsonian translocation carriers 45,XY,der(13;14)(q10;q10). Transfer of euploid embryos was performed in both cases and pregnancy was achieved by one of the couples. This is the first time that an oligonucleotide array-CGH approach has been successfully applied to Preimplantation Genetic Diagnosis for balanced chromosome rearrangement carriers. PMID:25415307

Genetic diversity in cultivated carioca common beans based on molecular marker analysis

Directory of Open Access Journals (Sweden)

Juliana Morini Küpper Cardoso Perseguini

2011-01-01

Full Text Available A wide array of molecular markers has been used to investigate the genetic diversity among common bean species. However, the best combination of markers for studying such diversity among common bean cultivars has yet to be determined. Few reports have examined the genetic diversity of the carioca bean, commercially one of the most important common beans in Brazil. In this study, we examined the usefulness of two molecular marker systems (simple sequence repeats - SSRs and amplified fragment length polymorphisms - AFLPs for assessing the genetic diversity of carioca beans. The amount of information provided by Roger's modified genetic distance was used to analyze SSR data and Jaccards similarity coefficient was used for AFLP data. Seventy SSRs were polymorphic and 20 AFLP primer combinations produced 635 polymorphic bands. Molecular analysis showed that carioca genotypes were quite diverse. AFLPs revealed greater genetic differentiation and variation within the carioca genotypes (Gst = 98% and Fst = 0.83, respectively than SSRs and provided better resolution for clustering the carioca genotypes. SSRs and AFLPs were both suitable for assessing the genetic diversity of Brazilian carioca genotypes since the number of markers used in each system provided a low coefficient of variation. However, fingerprint profiles were generated faster with AFLPs, making them a better choice for assessing genetic diversity in the carioca germplasm.

Inclusion Criteria for NCI Cancer Genetics Services Directory

Science.gov (United States)

Professionals who provide services related to cancer genetics (cancer risk assessment, genetic counseling, genetic susceptibility testing, and others) must meet these criteria before applying to be listed in the National Cancer Institute's Cancer Genetics Services Directory.

Personality and divorce: a genetic analysis.

Science.gov (United States)

Jocklin, V; McGue, M; Lykken, D T

1996-08-01

M. McGue and D.T. Lykken (1992) found that divorce risk was, to a substantial degree, genetically mediated; prior research has identified numerous social and psychological factors that affect divorce risk (G.C. Kitson, K.B. Barbi, & M.J. Roach, 1985). The present study attempted to link these domains by examining the extent to which genetic influences on one such psychological factor, personality, explain divorce risk heritability. A sample of adult twins from the Minnesota Twin Registry completed a marital history questionnaire and the Multidimensional Personality Questionnaire (A. Tellegen, 1982). Positive Emotionality and Negative Emotionality factors were positively related to divorce risk, whereas Constraint was negatively related. In women and men, respectively, 30% and 42% of the heritability of divorce risk consisted of genetic factors affecting personality and divorce risk correlated largely as a result of these common genetic influences.

A methodological overview on molecular preimplantation genetic diagnosis and screening: a genomic future?

Science.gov (United States)

Vendrell, Xavier; Bautista-Llácer, Rosa

2012-12-01

The genetic diagnosis and screening of preimplantation embryos generated by assisted reproduction technology has been consolidated in the prenatal care framework. The rapid evolution of DNA technologies is tending to molecular approaches. Our intention is to present a detailed methodological view, showing different diagnostic strategies based on molecular techniques that are currently applied in preimplantation genetic diagnosis. The amount of DNA from one single, or a few cells, obtained by embryo biopsy is a limiting factor for the molecular analysis. In this sense, genetic laboratories have developed molecular protocols considering this restrictive condition. Nevertheless, the development of whole-genome amplification methods has allowed preimplantation genetic diagnosis for two or more indications simultaneously, like the selection of histocompatible embryos plus detection of monogenic diseases or aneuploidies. Moreover, molecular techniques have permitted preimplantation genetic screening to progress, by implementing microarray-based comparative genome hybridization. Finally, a future view of the embryo-genetics field based on molecular advances is proposed. The normalization, cost-effectiveness analysis, and new technological tools are the next topics for preimplantation genetic diagnosis and screening. Concomitantly, these additions to assisted reproduction technologies could have a positive effect on the schedules of preimplantation studies.

Genetic analysis of yield in peanut (Arachis hypogaea L.) using ...

African Journals Online (AJOL)

Jane

2011-07-20

Jul 20, 2011 ... only should the two major genes' effects be considered but also the polygene's effect should be considered in breeding to increase peanut yield. Key words: Peanut, yield, major gene plus polygene inheritance model, genetic analysis. INTRODUCTION. Peanut consists of diploid (2n = 2x = 20), tetraploid ...

A Genetic-Algorithms-Based Approach for Programming Linear and Quadratic Optimization Problems with Uncertainty

Directory of Open Access Journals (Sweden)

Weihua Jin

2013-01-01

Full Text Available This paper proposes a genetic-algorithms-based approach as an all-purpose problem-solving method for operation programming problems under uncertainty. The proposed method was applied for management of a municipal solid waste treatment system. Compared to the traditional interactive binary analysis, this approach has fewer limitations and is able to reduce the complexity in solving the inexact linear programming problems and inexact quadratic programming problems. The implementation of this approach was performed using the Genetic Algorithm Solver of MATLAB (trademark of MathWorks. The paper explains the genetic-algorithms-based method and presents details on the computation procedures for each type of inexact operation programming problems. A comparison of the results generated by the proposed method based on genetic algorithms with those produced by the traditional interactive binary analysis method is also presented.

Population genetic analysis of ascertained SNP data

Directory of Open Access Journals (Sweden)

Nielsen Rasmus

2004-03-01

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

AFLP analysis of Cynodon dactylon (L.) Pers. var. dactylon genetic variation.

Science.gov (United States)

Wu, Y Q; Taliaferro, C M; Bai, G H; Anderson, M P

2004-08-01

Cynodon dactylon (L.) Pers. var. dactylon (common bermudagrass) is geographically widely distributed between about lat 45 degrees N and lat 45 degrees S, penetrating to about lat 53 degrees N in Europe. The extensive variation of morphological and adaptive characteristics of the taxon is substantially documented, but information is lacking on DNA molecular variation in geographically disparate forms. Accordingly, this study was conducted to assess molecular genetic variation and genetic relatedness among 28 C. dactylon var. dactylon accessions originating from 11 countries on 4 continents (Africa, Asia, Australia, and Europe). A fluorescence-labeled amplified fragment length polymorphism (AFLP) DNA profiling method was used to detect the genetic diversity and relatedness. On the basis of 443 polymorphic AFLP fragments from 8 primer combinations, the accessions were grouped into clusters and subclusters associating with their geographic origins. Genetic similarity coefficients (SC) for the 28 accessions ranged from 0.53 to 0.98. Accessions originating from Africa, Australia, Asia, and Europe formed major groupings as indicated by cluster and principal coordinate analysis. Accessions from Australia and Asia, though separately clustered, were relatively closely related and most distantly related to accessions of European origin. African accessions formed two distant clusters and had the greatest variation in genetic relatedness relative to accessions from other geographic regions. Sampling the full extent of genetic variation in C. dactylon var. dactylon would require extensive germplasm collection in the major geographic regions of its distributional range.

Spectral analysis and filter theory in applied geophysics

CERN Document Server

Buttkus, Burkhard

2000-01-01

This book is intended to be an introduction to the fundamentals and methods of spectral analysis and filter theory and their appli­ cations in geophysics. The principles and theoretical basis of the various methods are described, their efficiency and effectiveness eval­ uated, and instructions provided for their practical application. Be­ sides the conventional methods, newer methods arediscussed, such as the spectral analysis ofrandom processes by fitting models to the ob­ served data, maximum-entropy spectral analysis and maximum-like­ lihood spectral analysis, the Wiener and Kalman filtering methods, homomorphic deconvolution, and adaptive methods for nonstation­ ary processes. Multidimensional spectral analysis and filtering, as well as multichannel filters, are given extensive treatment. The book provides a survey of the state-of-the-art of spectral analysis and fil­ ter theory. The importance and possibilities ofspectral analysis and filter theory in geophysics for data acquisition, processing an...

Analysis of genetic diversity among rapeseed cultivars and breeding lines by srap and ssr molecular markers

International Nuclear Information System (INIS)

Channa, S.A.; Tian, H.

2016-01-01

The knowledge of genetic diversity is very important for developing new rapeseed (Brassica napus L.) cultivars. The genetic diversity among 77 rapeseed accessions, including 22 varieties and 55 advanced breeding lines were analyzed by 47 sequence-related amplified polymorphism (SRAP) and 56 simple sequence repeat (SSR) primers. A total of 270 SRAP and 194 SSR polymorphic fragments were detected with an average of 5.74 and 3.46 for SRAP and SSR primer, respectively. The cluster analysis grouped the 77 accessions into five major clusters. Cluster I contained spring and winter type varieties from Czech Republic and semi-winter varieties and their respective breeding lines from China. The 16 elite breeding lines discovered in Cluster II, III, IV and V indicated higher genetic distance than accessions in Cluster I. The principal component analysis and structure analysis exhibited similar results to the cluster analysis. Analysis of molecular variance revealed that genetic diversity of the selected breeding lines was comparable to the rapeseed varieties, and variation among varieties and lines was significant. The diverse and unique group of 16 elite breeding lines detected in this study can be utilized in the future breeding program as a source for development of commercial varieties with more desirable characters. (author)

Genetics researchers’ and iRB professionals’ attitudes toward genetic research review: a comparative analysis

Science.gov (United States)

Edwards, Karen L.; Lemke, Amy A.; Trinidad, Susan B.; Lewis, Susan M.; Starks, Helene; Snapinn, Katherine W.; Griffin, Mary Quinn; Wiesner, Georgia L.; Burke, Wylie

2012-01-01

Purpose Genetic research involving human participants can pose challenging questions related to ethical and regulatory standards for research oversight. However, few empirical studies describe how genetic researchers and institutional review board (IRB) professionals conceptualize ethical issues in genetic research or where common ground might exist. Methods Parallel online surveys collected information from human genetic researchers (n = 351) and IRB professionals (n = 208) regarding their views about human participant oversight for genetic protocols. Results A range of opinions were observed within groups on most issues. In both groups, a minority thought it likely that people would be harmed by participation in genetic research or identified from coded genetic data. A majority of both groups agreed that reconsent should be required for four of the six scenarios presented. Statistically significant differences were observed between groups on some issues, with more genetic researcher respondents trusting the confidentiality of coded data, fewer expecting harms from reidentification, and fewer considering reconsent necessary in certain scenarios. Conclusions The range of views observed within and between IRB and genetic researcher groups highlights the complexity and unsettled nature of many ethical issues in genome research. Our findings also identify areas where researcher and IRB views diverge and areas of common ground. PMID:22241102

Genetic origin and dispersal of the invasive soybean aphid inferred from population genetic analysis and approximate Bayesian computation.

Science.gov (United States)

Fang, Fang; Chen, Jing; Jiang, Li-Yun; Qu, Yan-Hua; Qiao, Ge-Xia

2018-01-09

Biological invasion is considered one of the most important global environmental problems. Knowledge of the source and dispersal routes of invasion could facilitate the eradication and control of invasive species. Soybean aphid, Aphis glycines Matsumura, is one of the most destructive soybean pests. For effective management of this pest, we conducted genetic analyses and approximate Bayesian computation (ABC) analysis to determine the origins and dispersal of the aphid species, as well as the source of its invasion in the USA, using eight microsatellite loci and the mitochondrial cytochrome c oxidase subunit I (COI) gene. We were able to identify a significant isolation by distance (IBD) pattern and three genetic lineages in the microsatellite data but not in the mtDNA dataset. The genetic structure showed that the USA population has the closest relationship with those from Korea and Japan, indicating that the two latter populations might be the sources of the invasion to the USA. Both population genetic analyses and ABC showed that the northeastern populations in China were the possible sources of the further spread of A. glycines to Indonesia. The dispersal history of this aphid can provide useful information for pest management strategies and can further help predict areas at risk of invasion. This article is protected by copyright. All rights reserved.

Molecular analysis for genetic diversity and distance of introduced Grus antigone sharpii L. to Thailand.

Science.gov (United States)

Tanee, T; Chaveerach, A; Anuniwat, A; Tanomtong, A; Pinthong, K; Sudmoon, R; Mokkamul, P

2009-01-15

The genetic relationship was examined in a population of Grus antigone sharpii L. using DNA markers from the ISSR technique for applying towards breeding purposes for conservation of species. Since their extinction from Thailand, sixteen eastern sarus cranes: Grus antigone sharpii L. provided from Cambodia were fed and bred to sixty individuals at Nakhonratchasima Zoo, Northeastern Thailand to re-exist in Thai natural sites. Their genetic diversity and distance were examined to test their possibility to adapt to environmental variation. Blood samples from 27 individuals of Grus antigone sharpii L. were collected and DNA was extracted. These DNA samples were amplified using the successful fifteen from twenty four primers inter simple sequences repeat markers. A dendrogram was constructed and shows distance values of the species between 12.1 and 53.5. The samples produced 63.96% polymorphic banding profiles. The genetic diversity (H') in this population was estimated using Shannon's index. The high H' value of 0.501 reflected the somewhat wide range of distribution sites, which would adapt to environmental variations. Genetic evenness is 0.152. This value supports that all the studied samples have a small equal genetic abundance.

Research in applied mathematics, numerical analysis, and computer science

Science.gov (United States)

1984-01-01

Research conducted at the Institute for Computer Applications in Science and Engineering (ICASE) in applied mathematics, numerical analysis, and computer science is summarized and abstracts of published reports are presented. The major categories of the ICASE research program are: (1) numerical methods, with particular emphasis on the development and analysis of basic numerical algorithms; (2) control and parameter identification; (3) computational problems in engineering and the physical sciences, particularly fluid dynamics, acoustics, and structural analysis; and (4) computer systems and software, especially vector and parallel computers.

Applied behavior analysis: understanding and changing behavior in the community-a representative review.

Science.gov (United States)

Luyben, Paul D

2009-01-01

Applied behavior analysis, a psychological discipline, has been characterized as the science of behavior change (Chance, 2006). Research in applied behavior analysis has been published for approximately 40 years since the initial publication of the Journal of Applied Behavior Analysis in 1968. The field now encompasses a wide range of human behavior. Although much of the published research centers on problem behaviors that occur in schools and among people with disabilities, a substantial body of knowledge has emerged in community settings. This article provides a review of the behavioral community research published in the Journal of Applied Behavior Analysis as representative of this work, including research in the areas of home and family, health, safety, community involvement and the environment, recreation and sports, crime and delinquency, and organizations. In the interest of space, research in schools and with people with disabilities has been excluded from this review.

B. F. Skinner's Contributions to Applied Behavior Analysis

Science.gov (United States)

Morris, Edward K.; Smith, Nathaniel G.; Altus, Deborah E.

2005-01-01

Our paper reviews and analyzes B. F. Skinner's contributions to applied behavior analysis in order to assess his role as the field's originator and founder. We found, first, that his contributions fall into five categorizes: the style and content of his science, his interpretations of typical and atypical human behavior, the implications he drew…

Applied research in uncertainty modeling and analysis

CERN Document Server

Ayyub, Bilal

2005-01-01

Uncertainty has been a concern to engineers, managers, and scientists for many years. For a long time uncertainty has been considered synonymous with random, stochastic, statistic, or probabilistic. Since the early sixties views on uncertainty have become more heterogeneous. In the past forty years numerous tools that model uncertainty, above and beyond statistics, have been proposed by several engineers and scientists. The tool/method to model uncertainty in a specific context should really be chosen by considering the features of the phenomenon under consideration, not independent of what is known about the system and what causes uncertainty. In this fascinating overview of the field, the authors provide broad coverage of uncertainty analysis/modeling and its application. Applied Research in Uncertainty Modeling and Analysis presents the perspectives of various researchers and practitioners on uncertainty analysis and modeling outside their own fields and domain expertise. Rather than focusing explicitly on...

Neural networks for genetic epidemiology: past, present, and future

Directory of Open Access Journals (Sweden)

Motsinger-Reif Alison A

2008-07-01

Full Text Available Abstract During the past two decades, the field of human genetics has experienced an information explosion. The completion of the human genome project and the development of high throughput SNP technologies have created a wealth of data; however, the analysis and interpretation of these data have created a research bottleneck. While technology facilitates the measurement of hundreds or thousands of genes, statistical and computational methodologies are lacking for the analysis of these data. New statistical methods and variable selection strategies must be explored for identifying disease susceptibility genes for common, complex diseases. Neural networks (NN are a class of pattern recognition methods that have been successfully implemented for data mining and prediction in a variety of fields. The application of NN for statistical genetics studies is an active area of research. Neural networks have been applied in both linkage and association analysis for the identification of disease susceptibility genes. In the current review, we consider how NN have been used for both linkage and association analyses in genetic epidemiology. We discuss both the successes of these initial NN applications, and the questions that arose during the previous studies. Finally, we introduce evolutionary computing strategies, Genetic Programming Neural Networks (GPNN and Grammatical Evolution Neural Networks (GENN, for using NN in association studies of complex human diseases that address some of the caveats illuminated by previous work.

Genetic diversity and geographic differentiation analysis of duckweed using inter-simple sequence repeat markers.

Science.gov (United States)

Xue, Huiling; Xiao, Yao; Jin, Yanling; Li, Xinbo; Fang, Yang; Zhao, Hai; Zhao, Yun; Guan, Jiafa

2012-01-01

Duckweed, with rapid growth rate and high starch content, is a new alternate feedstock for bioethanol production. The genetic diversity among 27 duckweed populations of seven species in genus Lemna and Spirodela from China and Vietnam was analyzed by ISSR-PCR. Eight ISSR primers generating a reproducible amplification banding pattern had been screened. 89 polymorphic bands were scored out of the 92 banding patterns of 16 Lemna populations, accounting for 96.74% of the polymorphism. 98 polymorphic bands of 11 Spirodela populations were scored out of 99 banding patterns, and the polymorphism was 98.43%. The genetic distance of Lemna varied from 0.127 to 0.784, and from 0.138 to 0.902 for Spirodela, which indicated a high level of genetic variation among the populations studied. The unweighted pair group method with arithmetic average (UPGMA) cluster analysis corresponded well with the genetic distance. Populations from Sichuan China grouped together and so did the populations from Vietnam, which illuminated populations collected from the same region clustered into one group. Especially, the only one population from Tibet was included in subgroup A2 alone. Clustering analysis indicated that the geographic differentiation of collected sites correlated closely with the genetic differentiation of duckweeds. The results suggested that geographic differentiation had great influence on genetic diversity of duckweed in China and Vietnam at the regional scale. This study provided primary guidelines for collection, conservation, characterization of duckweed resources for bioethanol production etc.

Polytene chromosome analysis in relation to genetic sex separation in the Mediterranean fruit fly, Ceratitis capitata (Wied.)

International Nuclear Information System (INIS)

Kerremans, P.; Busch-Petersen, E.

1990-01-01

The development of stable genetic sexing strains in the Mediterranean fruit fly (medfly), Ceratitis capitata (Wiedemann), is hampered by the presence of low levels of male recombination. Such recombination may be reduced by minimizing the distance between the translocation breakpoint and the translocated 'sexing' allele. Cytogenetic analysis of mitotic/meiotic and polytene chromosomes could provide information on the selection of such potentially stable genetic sexing strains. Translocation breakpoints in two genetic sexing strains in the medfly, based on a white female/brown male pupal colour dimorphism, have been determined. Preliminary results are described and the advantages and limitations of polytene chromosome analysis for the isolation of stable genetic sexing strains of the medfly are discussed. (author). 31 refs

Market organization and animal genetic resource management: a revealed preference analysis of sheep pricing.

Science.gov (United States)

Tindano, K; Moula, N; Leroy, P; Traoré, A; Antoine-Moussiaux, N

2017-10-01

Farm animal genetic resources are threatened worldwide. Participation in markets, while representing a crucial way out of poverty for many smallholders, affects genetic management choices with associated sustainability concerns. This paper proposes a contextualized study of the interactions between markets and animal genetic resources management, in the case of sheep markets in Ouagadougou, Burkina Faso. It focusses on the organization of marketing chains and the valuation of genetic characteristics by value chain actors. Marketing chain characterization was tackled through semi-structured interviews with 25 exporters and 15 butchers, both specialized in sheep. Moreover, revealed preference methods were applied to analyse the impact of animals' attributes on market pricing. Data were collected from 338 transactions during three different periods: Eid al-Adha, Christmas and New Year period, and a neutral period. The neutral period is understood as a period not close to any event likely to influence the demand for sheep. The results show that physical characteristics such as live weight, height at withers and coat colour have a strong influence on the animals' prices. Live weight has also had an increasing marginal impact on price. The different markets (local butcher, feasts, export market, sacrifices) represent distinct demands for genetic characteristics, entailing interesting consequences for animal genetic resource management. Any breeding programme should therefore take this diversity into account to allow this sector to contribute better to a sustainable development of the country.

A Genetic Epidemiological Mega Analysis of Smoking Initiation in Adolescents.

Science.gov (United States)

Maes, Hermine H; Prom-Wormley, Elizabeth; Eaves, Lindon J; Rhee, Soo Hyun; Hewitt, John K; Young, Susan; Corley, Robin; McGue, Matt; Iacono, William G; Legrand, Lisa; Samek, Diana R; Murrelle, E Lenn; Silberg, Judy L; Miles, Donna R; Schieken, Richard M; Beunen, Gaston P; Thomis, Martine; Rose, Richard J; Dick, Danielle M; Boomsma, Dorret I; Bartels, Meike; Vink, Jacqueline M; Lichtenstein, Paul; White, Victoria; Kaprio, Jaakko; Neale, Michael C

2017-04-01

Previous studies in adolescents were not adequately powered to accurately disentangle genetic and environmental influences on smoking initiation (SI) across adolescence. Mega-analysis of pooled genetically informative data on SI was performed, with structural equation modeling, to test equality of prevalence and correlations across cultural backgrounds, and to estimate the significance and effect size of genetic and environmental effects according to the classical twin study, in adolescent male and female twins from same-sex and opposite-sex twin pairs (N = 19 313 pairs) between ages 10 and 19, with 76 358 longitudinal assessments between 1983 and 2007, from 11 population-based twin samples from the United States, Europe, and Australia. Although prevalences differed between samples, twin correlations did not, suggesting similar etiology of SI across developed countries. The estimate of additive genetic contributions to liability of SI increased from approximately 15% to 45% from ages 13 to 19. Correspondingly, shared environmental factors accounted for a substantial proportion of variance in liability to SI at age 13 (70%) and gradually less by age 19 (40%). Both additive genetic and shared environmental factors significantly contribute to variance in SI throughout adolescence. The present study, the largest genetic epidemiological study on SI to date, found consistent results across 11 studies for the etiology of SI. Environmental factors, especially those shared by siblings in a family, primarily influence SI variance in early adolescence, while an increasing role of genetic factors is seen at later ages, which has important implications for prevention strategies. This is the first study to find evidence of genetic factors in liability to SI at ages as young as 12. It also shows the strongest evidence to date for decay of effects of the shared environment from early adolescence to young adulthood. We found remarkable consistency of twin correlations across

Translation and genetic criticism : genetic and editorial approaches to the 'untranslatable' in Joyce and Beckett

OpenAIRE

Hulle, Van, Dirk

2015-01-01

Abstract: Genetics of translation may suggest a unidirectional link between two fields of research (genetic criticism applied to translation), but there are many ways in which translation and genetic criticism interact. This article's research hypothesis is that an exchange of ideas between translation studies and genetic criticism can be mutually beneficial in more than one way. The main function of this exchange is to enhance a form of textual awareness, and to realize this enhanced textual...

Genetic analysis of relative traits for a drought-sensitive mutant

International Nuclear Information System (INIS)

Gao Kangning; Wang Huaqi

2009-01-01

A drought-sensitive mutant (M616), selected from Handao 616 (HD616) by 60 Co γ-irradiation at 200Gy, was used. Some morphological and yield related traits of M166 and HD616 related to drought resistance were investigated. We further developed F 1 and F 2 reciprocal hybrid combinations derived from the crosses between M616 and HD616, between M616 and IRAT109, respectively, and genetic analysis of 3 traits including plant height, culm width of main stem and seed setting rate on main panicle were camed out. The results showed that M616 showed obviously sensitive to drought stress. Analysis of variance for three traits in upland and paddy between F 1 reciprocal hybrid combinations showed that each trait had no significant difference, and indicated that there were no differences of cytoplasmic hereditary effect. In addition, 3 traits of F 2 populations, were found that the frequency distributions of culm width showed normal distribution, indicating that culm width was polygenic trait, and the frequency distribution of plant height and seed setting rate did not show normal distribution, indicating that the two traits were qualitative-quantitative traits. Genetic analysis of relative traits for a drought-sensitive mutant of upland rice was a basic work for the gene location and cloning. (authors)

A cluster analysis on road traffic accidents using genetic algorithms

Science.gov (United States)

Saharan, Sabariah; Baragona, Roberto

2017-04-01

The analysis of traffic road accidents is increasingly important because of the accidents cost and public road safety. The availability or large data sets makes the study of factors that affect the frequency and severity accidents are viable. However, the data are often highly unbalanced and overlapped. We deal with the data set of the road traffic accidents recorded in Christchurch, New Zealand, from 2000-2009 with a total of 26440 accidents. The data is in a binary set and there are 50 factors road traffic accidents with four level of severity. We used genetic algorithm for the analysis because we are in the presence of a large unbalanced data set and standard clustering like k-means algorithm may not be suitable for the task. The genetic algorithm based on clustering for unknown K, (GCUK) has been used to identify the factors associated with accidents of different levels of severity. The results provided us with an interesting insight into the relationship between factors and accidents severity level and suggest that the two main factors that contributes to fatal accidents are "Speed greater than 60 km h" and "Did not see other people until it was too late". A comparison with the k-means algorithm and the independent component analysis is performed to validate the results.

X-ray fluorescence spectrometry applied to soil analysis

International Nuclear Information System (INIS)

Salvador, Vera Lucia Ribeiro; Sato, Ivone Mulako; Scapin Junior, Wilson Santo; Scapin, Marcos Antonio; Imakima, Kengo

1997-01-01

This paper studies the X-ray fluorescence spectrometry applied to the soil analysis. A comparative study of the WD-XRFS and ED-XRFS techniques was carried out by using the following soil samples: SL-1, SOIL-7 and marine sediment SD-M-2/TM, from IAEA, and clay, JG-1a from Geological Survey of Japan (GSJ)

Neutron activation analysis applied to energy and environment

International Nuclear Information System (INIS)

Lyon, W.S.

1975-01-01

Neutron activation analysis was applied to a number of problems concerned with energy production and the environment. Burning of fossil fuel, the search for new sources of uranium, possible presence of toxic elements in food and water, and the relationship of trace elements to cardiovascular disease are some of the problems in which neutron activation was used. (auth)

Research in progress in applied mathematics, numerical analysis, and computer science

Science.gov (United States)

1990-01-01

Research conducted at the Institute in Science and Engineering in applied mathematics, numerical analysis, and computer science is summarized. The Institute conducts unclassified basic research in applied mathematics in order to extend and improve problem solving capabilities in science and engineering, particularly in aeronautics and space.

Applied data analysis and modeling for energy engineers and scientists

CERN Document Server

Reddy, T Agami

2011-01-01

""Applied Data Analysis and Modeling for Energy Engineers and Scientists"" discusses mathematical models, data analysis, and decision analysis in modeling. The approach taken in this volume focuses on the modeling and analysis of thermal systems in an engineering environment, while also covering a number of other critical areas. Other material covered includes the tools that researchers and engineering professionals will need in order to explore different analysis methods, use critical assessment skills and reach sound engineering conclusions. The book also covers process and system design and

Using recurrence plot for determinism analysis of EEG recordings in genetic absence epilepsy rats.

Science.gov (United States)

Ouyang, Gaoxiang; Li, Xiaoli; Dang, Chuangyin; Richards, Douglas A

2008-08-01

Understanding the transition of brain activity towards an absence seizure is a challenging task. In this paper, we use recurrence quantification analysis to indicate the deterministic dynamics of EEG series at the seizure-free, pre-seizure and seizure states in genetic absence epilepsy rats. The determinism measure, DET, based on recurrence plot, was applied to analyse these three EEG datasets, each dataset containing 300 single-channel EEG epochs of 5-s duration. Then, statistical analysis of the DET values in each dataset was carried out to determine whether their distributions over the three groups were significantly different. Furthermore, a surrogate technique was applied to calculate the significance level of determinism measures in EEG recordings. The mean (+/-SD) DET of EEG was 0.177+/-0.045 in pre-seizure intervals. The DET values of pre-seizure EEG data are significantly higher than those of seizure-free intervals, 0.123+/-0.023, (Pdeterminism in EEG epochs was present in 25 of 300 (8.3%), 181 of 300 (60.3%) and 289 of 300 (96.3%) in seizure-free, pre-seizure and seizure intervals, respectively. Results provide some first indications that EEG epochs during pre-seizure intervals exhibit a higher degree of determinism than seizure-free EEG epochs, but lower than those in seizure EEG epochs in absence epilepsy. The proposed methods have the potential of detecting the transition between normal brain activity and the absence seizure state, thus opening up the possibility of intervention, whether electrical or pharmacological, to prevent the oncoming seizure.

MS-based analytical methodologies to characterize genetically modified crops.

Science.gov (United States)

García-Cañas, Virginia; Simó, Carolina; León, Carlos; Ibáñez, Elena; Cifuentes, Alejandro

2011-01-01

The development of genetically modified crops has had a great impact on the agriculture and food industries. However, the development of any genetically modified organism (GMO) requires the application of analytical procedures to confirm the equivalence of the GMO compared to its isogenic non-transgenic counterpart. Moreover, the use of GMOs in foods and agriculture faces numerous criticisms from consumers and ecological organizations that have led some countries to regulate their production, growth, and commercialization. These regulations have brought about the need of new and more powerful analytical methods to face the complexity of this topic. In this regard, MS-based technologies are increasingly used for GMOs analysis to provide very useful information on GMO composition (e.g., metabolites, proteins). This review focuses on the MS-based analytical methodologies used to characterize genetically modified crops (also called transgenic crops). First, an overview on genetically modified crops development is provided, together with the main difficulties of their analysis. Next, the different MS-based analytical approaches applied to characterize GM crops are critically discussed, and include "-omics" approaches and target-based approaches. These methodologies allow the study of intended and unintended effects that result from the genetic transformation. This information is considered to be essential to corroborate (or not) the equivalence of the GM crop with its isogenic non-transgenic counterpart. Copyright © 2010 Wiley Periodicals, Inc.

Genetic Diversity and Population Structure of Theileria annulata in Oman.

Science.gov (United States)

Al-Hamidhi, Salama; H Tageldin, Mohammed; Weir, William; Al-Fahdi, Amira; Johnson, Eugene H; Bobade, Patrick; Alqamashoui, Badar; Beja-Pereira, Albano; Thompson, Joanne; Kinnaird, Jane; Shiels, Brian; Tait, Andy; Babiker, Hamza

2015-01-01

Theileriosis, caused by a number of species within the genus Theileria, is a common disease of livestock in Oman. It is a major constraint to the development of the livestock industry due to a high rate of morbidity and mortality in both cattle and sheep. Since little is currently known about the genetic diversity of the parasites causing theileriosis in Oman, the present study was designed to address this issue with specific regard to T. annulata in cattle. Blood samples were collected from cattle from four geographically distinct regions in Oman for genetic analysis of the Theileria annulata population. Ten genetic markers (micro- and mini-satellites) representing all four chromosomes of T. annulata were applied to these samples using a combination of PCR amplification and fragment analysis. The resultant genetic data was analysed to provide a first insight into the structure of the T. annulata population in Oman. We applied ten micro- and mini-satellite markers to a total of 310 samples obtained from different regions (174 [56%] from Dhofar, 68 [22%] from Dhira, 44 [14.5%] from Batinah and 24 [8%] from Sharqia). A high degree of allelic diversity was observed among the four parasite populations. Expected heterozygosity for each site ranged from 0.816 to 0.854. A high multiplicity of infection was observed in individual hosts, with an average of 3.3 to 3.4 alleles per locus, in samples derived from Batinah, Dhofar and Sharqia regions. In samples from Dhira region, an average of 2.9 alleles per locus was observed. Mild but statistically significant linkage disequilibrium between pairs of markers was observed in populations from three of the four regions. In contrast, when the analysis was performed at farm level, no significant linkage disequilibrium was observed. Finally, no significant genetic differentiation was seen between the four populations, with most pair-wise FST values being less than 0.03. Slightly higher FST values (GST' = 0.075, θ = 0.07) were

Genetic Diversity and Population Structure of Theileria annulata in Oman.

Directory of Open Access Journals (Sweden)

Salama Al-Hamidhi

Full Text Available Theileriosis, caused by a number of species within the genus Theileria, is a common disease of livestock in Oman. It is a major constraint to the development of the livestock industry due to a high rate of morbidity and mortality in both cattle and sheep. Since little is currently known about the genetic diversity of the parasites causing theileriosis in Oman, the present study was designed to address this issue with specific regard to T. annulata in cattle.Blood samples were collected from cattle from four geographically distinct regions in Oman for genetic analysis of the Theileria annulata population. Ten genetic markers (micro- and mini-satellites representing all four chromosomes of T. annulata were applied to these samples using a combination of PCR amplification and fragment analysis. The resultant genetic data was analysed to provide a first insight into the structure of the T. annulata population in Oman.We applied ten micro- and mini-satellite markers to a total of 310 samples obtained from different regions (174 [56%] from Dhofar, 68 [22%] from Dhira, 44 [14.5%] from Batinah and 24 [8%] from Sharqia. A high degree of allelic diversity was observed among the four parasite populations. Expected heterozygosity for each site ranged from 0.816 to 0.854. A high multiplicity of infection was observed in individual hosts, with an average of 3.3 to 3.4 alleles per locus, in samples derived from Batinah, Dhofar and Sharqia regions. In samples from Dhira region, an average of 2.9 alleles per locus was observed. Mild but statistically significant linkage disequilibrium between pairs of markers was observed in populations from three of the four regions. In contrast, when the analysis was performed at farm level, no significant linkage disequilibrium was observed. Finally, no significant genetic differentiation was seen between the four populations, with most pair-wise FST values being less than 0.03. Slightly higher FST values (GST' = 0.075, �

Molecular analysis of genetic diversity in elite II synthetic hexaploid ...

African Journals Online (AJOL)

The present study was conducted to assess the genetic diversity of Elite-II synthetic hexaploid (SH) wheat by genome DNA fingerprinting as revealed by random amplified polymorphic DNA (RAPD) analysis. Ten decamer RAPD primers (OPG-1, OPG-2, OPG-3, OPG-4, OPG-5, OPA-3, OPA-4, OPA-5, OPA-8, and OPA-15) ...

Multiobjective Genetic Algorithm applied to dengue control.

Science.gov (United States)

Florentino, Helenice O; Cantane, Daniela R; Santos, Fernando L P; Bannwart, Bettina F

2014-12-01

Dengue fever is an infectious disease caused by a virus of the Flaviridae family and transmitted to the person by a mosquito of the genus Aedes aegypti. This disease has been a global public health problem because a single mosquito can infect up to 300 people and between 50 and 100 million people are infected annually on all continents. Thus, dengue fever is currently a subject of research, whether in the search for vaccines and treatments for the disease or efficient and economical forms of mosquito control. The current study aims to study techniques of multiobjective optimization to assist in solving problems involving the control of the mosquito that transmits dengue fever. The population dynamics of the mosquito is studied in order to understand the epidemic phenomenon and suggest strategies of multiobjective programming for mosquito control. A Multiobjective Genetic Algorithm (MGA_DENGUE) is proposed to solve the optimization model treated here and we discuss the computational results obtained from the application of this technique. Copyright © 2014 Elsevier Inc. All rights reserved.

High-throughput genetic analysis in a cohort of patients with Ocular Developmental Anomalies

Directory of Open Access Journals (Sweden)

Suganya Kandeeban

2017-10-01

Full Text Available Anophthalmia and microphthalmia (A/M are developmental ocular malformations in which the eye fails to form or is smaller than normal with both genetic and environmental etiology. Microphthalmia is often associated with additional ocular anomalies, most commonly coloboma or cataract [1, 2]. A/M has a combined incidence between 1-3.2 cases per 10,000 live births in Caucasians [3, 4]. The spectrum of genetic abnormalities (chromosomal and molecular associated with these ocular developmental defects are being investigated in the current study. A detailed pedigree analysis and ophthalmic examination have been documented for the enrolled patients followed by blood collection and DNA extraction. The strategies for genetic analysis included chromosomal analysis by conventional and array based (affymetrix cytoscan HD array methods, targeted re-sequencing of the candidate genes and whole exome sequencing (WES in Illumina HiSEQ 2500. WES was done in families excluded for mutations in candidate genes. Twenty four samples (Microphthalmia (M-5, Anophthalmia (A-7,Coloboma-2, M&A-1, microphthalmia and coloboma / other ocular features-9 were initially analyzed using conventional Geimsa Trypsin Geimsa banding of which 4 samples revealed gross chromosomal aberrations (deletions in 3q26.3-28, 11p13 (N=2 and 11q23 regions. Targeted re sequencing of candidate genes showed mutations in CHX10, PAX6, FOXE3, ABCB6 and SHH genes in 6 samples. High throughput array based chromosomal analysis revealed aberrations in 4 samples (17q21dup (n=2, 8p11del (n=2. Overall, genetic alterations in known candidate genes are seen in 50% of the study subjects. Whole exome sequencing was performed in samples that were excluded for mutations in candidate genes and the results are discussed.

Comparative Proteomic Analysis of Two Varieties of Genetically Modified (GM) Embrapa 5.1 Common Bean (Phaseolus vulgaris L.) and Their Non-GM Counterparts.

Science.gov (United States)

Balsamo, Geisi M; Valentim-Neto, Pedro A; Mello, Carla S; Arisi, Ana C M

2015-12-09

The genetically modified (GM) common bean event Embrapa 5.1 was commercially approved in Brazil in 2011; it is resistant to golden mosaic virus infection. In the present work grain proteome profiles of two Embrapa 5.1 common bean varieties, Pérola and Pontal, and their non-GM counterparts were compared by two-dimensional gel electrophoresis (2-DE) followed by mass spectrometry (MS). Analyses detected 23 spots differentially accumulated between GM Pérola and non-GM Pérola and 21 spots between GM Pontal and non-GM Pontal, although they were not the same proteins in Pérola and Pontal varieties, indicating that the variability observed may not be due to the genetic transformation. Among them, eight proteins were identified in Pérola varieties, and four proteins were identified in Pontal. Moreover, we applied principal component analysis (PCA) on 2-DE data, and variation between varieties was explained in the first two principal components. This work provides a first 2-DE-MS/MS-based analysis of Embrapa 5.1 common bean grains.

Design and rationale for examining neuroimaging genetics in ischemic stroke

Science.gov (United States)

Giese, Anne-Katrin; Schirmer, Markus D.; Donahue, Kathleen L.; Cloonan, Lisa; Irie, Robert; Winzeck, Stefan; Bouts, Mark J.R.J.; McIntosh, Elissa C.; Mocking, Steven J.; Dalca, Adrian V.; Sridharan, Ramesh; Xu, Huichun; Frid, Petrea; Giralt-Steinhauer, Eva; Holmegaard, Lukas; Roquer, Jaume; Wasselius, Johan; Cole, John W.; McArdle, Patrick F.; Broderick, Joseph P.; Jimenez-Conde, Jordi; Jern, Christina; Kissela, Brett M.; Kleindorfer, Dawn O.; Lemmens, Robin; Lindgren, Arne; Meschia, James F.; Rundek, Tatjana; Sacco, Ralph L.; Schmidt, Reinhold; Sharma, Pankaj; Slowik, Agnieszka; Thijs, Vincent; Woo, Daniel; Worrall, Bradford B.; Kittner, Steven J.; Mitchell, Braxton D.; Rosand, Jonathan; Golland, Polina; Wu, Ona

2017-01-01

Objective: To describe the design and rationale for the genetic analysis of acute and chronic cerebrovascular neuroimaging phenotypes detected on clinical MRI in patients with acute ischemic stroke (AIS) within the scope of the MRI–GENetics Interface Exploration (MRI-GENIE) study. Methods: MRI-GENIE capitalizes on the existing infrastructure of the Stroke Genetics Network (SiGN). In total, 12 international SiGN sites contributed MRIs of 3,301 patients with AIS. Detailed clinical phenotyping with the web-based Causative Classification of Stroke (CCS) system and genome-wide genotyping data were available for all participants. Neuroimaging analyses include the manual and automated assessments of established MRI markers. A high-throughput MRI analysis pipeline for the automated assessment of cerebrovascular lesions on clinical scans will be developed in a subset of scans for both acute and chronic lesions, validated against gold standard, and applied to all available scans. The extracted neuroimaging phenotypes will improve characterization of acute and chronic cerebrovascular lesions in ischemic stroke, including CCS subtypes, and their effect on functional outcomes after stroke. Moreover, genetic testing will uncover variants associated with acute and chronic MRI manifestations of cerebrovascular disease. Conclusions: The MRI-GENIE study aims to develop, validate, and distribute the MRI analysis platform for scans acquired as part of clinical care for patients with AIS, which will lead to (1) novel genetic discoveries in ischemic stroke, (2) strategies for personalized stroke risk assessment, and (3) personalized stroke outcome assessment. PMID:28852707

Diagnosing ARVC in Pediatric Patients Applying the Revised Task Force Criteria: Importance of Imaging, 12-Lead ECG, and Genetics.

Science.gov (United States)

Steinmetz, Michael; Krause, Ulrich; Lauerer, Peter; Konietschke, Frank; Aguayo, Randolph; Ritter, Christian Oliver; Schuster, Andreas; Lotz, Joachim; Paul, Thomas; Staab, Wieland

2018-05-12

Arrhythmogenic right ventricular cardiomyopathy (ARVC) is a potentially lethal disease that is well described in adults. In pediatric patients, however, identification of patients at risk of adverse events of ARVC remains a challenge. We aimed to determine which criteria of the revised Task Force Criteria (rTFC), alone or combined, have an impact on diagnosis of ARVC when compared to disease-specific genetic mutations in pediatric patients ≤ 18 years. Between September 2010 and December 2013, 48 consecutive young patients ≤ 18 years of age (mean 14, range of 12.9-15.1 years) underwent contrast-enhanced magnetic resonance imaging (CMR), genetic testing, and comprehensive clinical work-up for ARVC criteria to test for clinically suspected ARVC. As specified by the rTFC, patients were grouped into four categories: "definite," "borderline," "possible," and "none" ARVC. Of the 48 patients, 12 were found to have gene mutations of either the desmoplakin (9/12) or plakophilin (3/12) locus. According to rTFC 12/48 patients were considered as "definite" ARVC (25%), while 10/12 (83.3%) had an ARVC-specific gene mutation. Of the remaining 36 patients, 6 (12.5%) were grouped as "borderline" ARVC, 7 (14.6%) as "possible" ARVC (including the remaining two genetic mutations), and 22 (45.8%) as "none" ARVC, respectively. Statistical analysis of ARVC criteria in patients diagnosed with "definite" ARVC revealed high prevalence of positive findings by imaging (CMR and echocardiography) and positive genetics. The positive predictive value to detect "definite" ARVC by genotyping was 83.3%, while the negative predictive value was 94%. Logistic regression analyses for different criteria combinations revealed that imaging modalities (echo and CMR combined) and abnormalities of 12-lead ECG were significant markers (p < 0.01). Positive results of endomyocardial biopsies or arrhythmia on ECG or Holter as defined by the rTFC were not significant in this analysis. The rTFC for

Whole-genome sequencing and genetic variant analysis of a Quarter Horse mare.

KAUST Repository

Doan, Ryan; Cohen, Noah D; Sawyer, Jason; Ghaffari, Noushin; Johnson, Charlie D; Dindot, Scott V

2012-01-01

BACKGROUND: The catalog of genetic variants in the horse genome originates from a few select animals, the majority originating from the Thoroughbred mare used for the equine genome sequencing project. The purpose of this study was to identify genetic variants, including single nucleotide polymorphisms (SNPs), insertion/deletion polymorphisms (INDELs), and copy number variants (CNVs) in the genome of an individual Quarter Horse mare sequenced by next-generation sequencing. RESULTS: Using massively parallel paired-end sequencing, we generated 59.6 Gb of DNA sequence from a Quarter Horse mare resulting in an average of 24.7X sequence coverage. Reads were mapped to approximately 97% of the reference Thoroughbred genome. Unmapped reads were de novo assembled resulting in 19.1 Mb of new genomic sequence in the horse. Using a stringent filtering method, we identified 3.1 million SNPs, 193 thousand INDELs, and 282 CNVs. Genetic variants were annotated to determine their impact on gene structure and function. Additionally, we genotyped this Quarter Horse for mutations of known diseases and for variants associated with particular traits. Functional clustering analysis of genetic variants revealed that most of the genetic variation in the horse's genome was enriched in sensory perception, signal transduction, and immunity and defense pathways. CONCLUSIONS: This is the first sequencing of a horse genome by next-generation sequencing and the first genomic sequence of an individual Quarter Horse mare. We have increased the catalog of genetic variants for use in equine genomics by the addition of novel SNPs, INDELs, and CNVs. The genetic variants described here will be a useful resource for future studies of genetic variation regulating performance traits and diseases in equids.

Whole-genome sequencing and genetic variant analysis of a Quarter Horse mare.

KAUST Repository

Doan, Ryan

2012-02-17

BACKGROUND: The catalog of genetic variants in the horse genome originates from a few select animals, the majority originating from the Thoroughbred mare used for the equine genome sequencing project. The purpose of this study was to identify genetic variants, including single nucleotide polymorphisms (SNPs), insertion/deletion polymorphisms (INDELs), and copy number variants (CNVs) in the genome of an individual Quarter Horse mare sequenced by next-generation sequencing. RESULTS: Using massively parallel paired-end sequencing, we generated 59.6 Gb of DNA sequence from a Quarter Horse mare resulting in an average of 24.7X sequence coverage. Reads were mapped to approximately 97% of the reference Thoroughbred genome. Unmapped reads were de novo assembled resulting in 19.1 Mb of new genomic sequence in the horse. Using a stringent filtering method, we identified 3.1 million SNPs, 193 thousand INDELs, and 282 CNVs. Genetic variants were annotated to determine their impact on gene structure and function. Additionally, we genotyped this Quarter Horse for mutations of known diseases and for variants associated with particular traits. Functional clustering analysis of genetic variants revealed that most of the genetic variation in the horse\\'s genome was enriched in sensory perception, signal transduction, and immunity and defense pathways. CONCLUSIONS: This is the first sequencing of a horse genome by next-generation sequencing and the first genomic sequence of an individual Quarter Horse mare. We have increased the catalog of genetic variants for use in equine genomics by the addition of novel SNPs, INDELs, and CNVs. The genetic variants described here will be a useful resource for future studies of genetic variation regulating performance traits and diseases in equids.

Genetic evidence for monogamy in the dwarf seahorse, Hippocampus zosterae.

Science.gov (United States)

Rose, Emily; Small, Clayton M; Saucedo, Hector A; Harper, Cristin; Jones, Adam G

2014-01-01

Syngnathid fishes (pipefishes, seahorses, and seadragons) exhibit a wide array of mating systems ranging from monogamy with long-term pair bonds to more promiscuous mating systems, such as polyandry and polygynandry. Some seahorses, including the dwarf seahorse Hippocampus zosterae, have been found to be socially monogamous. Although several seahorse species have also been shown to be genetically monogamous, parentage analysis has not yet been applied to the dwarf seahorse. We developed 8 novel microsatellites for the dwarf seahorse to conduct genetic parentage analysis to confirm that this species is indeed monogamous. Using 4 selected loci and a total of 16 pregnant male seahorses, with 8 collected in Florida and 8 sampled in Texas, we genotyped all of the offspring within each male's brood to determine the maternal contributions to each brood. We found a maximum of 4 alleles per locus segregating within each pregnant male's brood, a pattern consistent with each brood having exactly 1 mother and 1 father. These results support previous laboratory-based behavioral studies and indicate that the dwarf seahorse, H. zosterae, is genetically monogamous. © The American Genetic Association 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Field release of genetically modified Pseudomonas putida WCS358r : molecular analysis of effects on microbial communities in the rhizosphere of wheat

NARCIS (Netherlands)

Viebahn, Mareike

2005-01-01

Genetically modified microorganisms (GMMs) with enhanced biocontrol activity are attractive to apply in agriculture. To investigate potential ecological risks of field introduction of GMMs, effects of P. putida strain WCS358r and two genetically modified derivatives of this strain on the indigenous

Analysis of concrete beams using applied element method

Science.gov (United States)

Lincy Christy, D.; Madhavan Pillai, T. M.; Nagarajan, Praveen

2018-03-01

The Applied Element Method (AEM) is a displacement based method of structural analysis. Some of its features are similar to that of Finite Element Method (FEM). In AEM, the structure is analysed by dividing it into several elements similar to FEM. But, in AEM, elements are connected by springs instead of nodes as in the case of FEM. In this paper, background to AEM is discussed and necessary equations are derived. For illustrating the application of AEM, it has been used to analyse plain concrete beam of fixed support condition. The analysis is limited to the analysis of 2-dimensional structures. It was found that the number of springs has no much influence on the results. AEM could predict deflection and reactions with reasonable degree of accuracy.

Analysis of genetic diversity in female, male and half sibs willow ...

African Journals Online (AJOL)

hp

Seberg O, Kremer A, Boursot P, Arctander P, Tautz D, Hewitt GM. (1997) Newer molecular technologies for biodiversity evaluation: Opportunities and challenges. Nat. Biotechnol. 15:625-628. Loarce Y, Gallego R, Ferrer EA, (1996). Comparative analysis of genetic relationships between rye cultivars using RFLP and RAPD.

Decomposition of multivariate phenotypic means in multigroup genetic covarinace structure analysis

NARCIS (Netherlands)

Dolan, C.V.; Molenaar, P.C.M.; Boomsma, D.I.

1992-01-01

Uses D. Sorbom's (1974) method to study differences in latent means in multivariate twin data. By restricting the analysis to a comparison between groups, the results pertain only to the additive contributions of common genetic and environmental factors to the deviation of the group means from what

The genetic analysis of repeated measures II: The Karhunen-Loeve expansion.

NARCIS (Netherlands)

Molenaar, P.C.M.; Boomsma, D.I.

1987-01-01

Outlines the Karhunen-Loeve (N. Ahmed and K. R. Rao, 1975) approach to the genetic analysis of time series of arbitrary length and with arbitrary covariance function. This approach is based on the simultaneous eigenvalue decomposition of the covariance matrices of the original time series obtained

Genome-wide linkage meta-analysis identifies susceptibility loci at 2q34 and 13q31.3 for genetic generalized epilepsies.

Science.gov (United States)

Leu, Costin; de Kovel, Carolien G F; Zara, Federico; Striano, Pasquale; Pezzella, Marianna; Robbiano, Angela; Bianchi, Amedeo; Bisulli, Francesca; Coppola, Antonietta; Giallonardo, Anna Teresa; Beccaria, Francesca; Trenité, Dorothée Kasteleijn-Nolst; Lindhout, Dick; Gaus, Verena; Schmitz, Bettina; Janz, Dieter; Weber, Yvonne G; Becker, Felicitas; Lerche, Holger; Kleefuss-Lie, Ailing A; Hallman, Kerstin; Kunz, Wolfram S; Elger, Christian E; Muhle, Hiltrud; Stephani, Ulrich; Møller, Rikke S; Hjalgrim, Helle; Mullen, Saul; Scheffer, Ingrid E; Berkovic, Samuel F; Everett, Kate V; Gardiner, Mark R; Marini, Carla; Guerrini, Renzo; Lehesjoki, Anna-Elina; Siren, Auli; Nabbout, Rima; Baulac, Stephanie; Leguern, Eric; Serratosa, Jose M; Rosenow, Felix; Feucht, Martha; Unterberger, Iris; Covanis, Athanasios; Suls, Arvid; Weckhuysen, Sarah; Kaneva, Radka; Caglayan, Hande; Turkdogan, Dilsad; Baykan, Betul; Bebek, Nerses; Ozbek, Ugur; Hempelmann, Anne; Schulz, Herbert; Rüschendorf, Franz; Trucks, Holger; Nürnberg, Peter; Avanzini, Giuliano; Koeleman, Bobby P C; Sander, Thomas

2012-02-01

Genetic generalized epilepsies (GGEs) have a lifetime prevalence of 0.3% with heritability estimates of 80%. A considerable proportion of families with siblings affected by GGEs presumably display an oligogenic inheritance. The present genome-wide linkage meta-analysis aimed to map: (1) susceptibility loci shared by a broad spectrum of GGEs, and (2) seizure type-related genetic factors preferentially predisposing to either typical absence or myoclonic seizures, respectively. Meta-analysis of three genome-wide linkage datasets was carried out in 379 GGE-multiplex families of European ancestry including 982 relatives with GGEs. To dissect out seizure type-related susceptibility genes, two family subgroups were stratified comprising 235 families with predominantly genetic absence epilepsies (GAEs) and 118 families with an aggregation of juvenile myoclonic epilepsy (JME). To map shared and seizure type-related susceptibility loci, both nonparametric loci (NPL) and parametric linkage analyses were performed for a broad trait model (GGEs) in the entire set of GGE-multiplex families and a narrow trait model (typical absence or myoclonic seizures) in the subgroups of JME and GAE families. For the entire set of 379 GGE-multiplex families, linkage analysis revealed six loci achieving suggestive evidence for linkage at 1p36.22, 3p14.2, 5q34, 13q12.12, 13q31.3, and 19q13.42. The linkage finding at 5q34 was consistently supported by both NPL and parametric linkage results across all three family groups. A genome-wide significant nonparametric logarithm of odds score of 3.43 was obtained at 2q34 in 118 JME families. Significant parametric linkage to 13q31.3 was found in 235 GAE families assuming recessive inheritance (heterogeneity logarithm of odds = 5.02). Our linkage results support an oligogenic predisposition of familial GGE syndromes. The genetic risk factor at 5q34 confers risk to a broad spectrum of familial GGE syndromes, whereas susceptibility loci at 2q34 and 13q31

Simulated evolution applied to study the genetic code optimality using a model of codon reassignments.

Science.gov (United States)

Santos, José; Monteagudo, Angel

2011-02-21

As the canonical code is not universal, different theories about its origin and organization have appeared. The optimization or level of adaptation of the canonical genetic code was measured taking into account the harmful consequences resulting from point mutations leading to the replacement of one amino acid for another. There are two basic theories to measure the level of optimization: the statistical approach, which compares the canonical genetic code with many randomly generated alternative ones, and the engineering approach, which compares the canonical code with the best possible alternative. Here we used a genetic algorithm to search for better adapted hypothetical codes and as a method to guess the difficulty in finding such alternative codes, allowing to clearly situate the canonical code in the fitness landscape. This novel proposal of the use of evolutionary computing provides a new perspective in the open debate between the use of the statistical approach, which postulates that the genetic code conserves amino acid properties far better than expected from a random code, and the engineering approach, which tends to indicate that the canonical genetic code is still far from optimal. We used two models of hypothetical codes: one that reflects the known examples of codon reassignment and the model most used in the two approaches which reflects the current genetic code translation table. Although the standard code is far from a possible optimum considering both models, when the more realistic model of the codon reassignments was used, the evolutionary algorithm had more difficulty to overcome the efficiency of the canonical genetic code. Simulated evolution clearly reveals that the canonical genetic code is far from optimal regarding its optimization. Nevertheless, the efficiency of the canonical code increases when mistranslations are taken into account with the two models, as indicated by the fact that the best possible codes show the patterns of the

Simulated evolution applied to study the genetic code optimality using a model of codon reassignments

Directory of Open Access Journals (Sweden)

Monteagudo Ángel

2011-02-01

Full Text Available Abstract Background As the canonical code is not universal, different theories about its origin and organization have appeared. The optimization or level of adaptation of the canonical genetic code was measured taking into account the harmful consequences resulting from point mutations leading to the replacement of one amino acid for another. There are two basic theories to measure the level of optimization: the statistical approach, which compares the canonical genetic code with many randomly generated alternative ones, and the engineering approach, which compares the canonical code with the best possible alternative. Results Here we used a genetic algorithm to search for better adapted hypothetical codes and as a method to guess the difficulty in finding such alternative codes, allowing to clearly situate the canonical code in the fitness landscape. This novel proposal of the use of evolutionary computing provides a new perspective in the open debate between the use of the statistical approach, which postulates that the genetic code conserves amino acid properties far better than expected from a random code, and the engineering approach, which tends to indicate that the canonical genetic code is still far from optimal. We used two models of hypothetical codes: one that reflects the known examples of codon reassignment and the model most used in the two approaches which reflects the current genetic code translation table. Although the standard code is far from a possible optimum considering both models, when the more realistic model of the codon reassignments was used, the evolutionary algorithm had more difficulty to overcome the efficiency of the canonical genetic code. Conclusions Simulated evolution clearly reveals that the canonical genetic code is far from optimal regarding its optimization. Nevertheless, the efficiency of the canonical code increases when mistranslations are taken into account with the two models, as indicated by the

Multidisciplinary Design, Analysis, and Optimization Tool Development Using a Genetic Algorithm

Science.gov (United States)

Pak, Chan-gi; Li, Wesley

2009-01-01

Multidisciplinary design, analysis, and optimization using a genetic algorithm is being developed at the National Aeronautics and Space Administration Dryden Flight Research Center (Edwards, California) to automate analysis and design process by leveraging existing tools to enable true multidisciplinary optimization in the preliminary design stage of subsonic, transonic, supersonic, and hypersonic aircraft. This is a promising technology, but faces many challenges in large-scale, real-world application. This report describes current approaches, recent results, and challenges for multidisciplinary design, analysis, and optimization as demonstrated by experience with the Ikhana fire pod design.!

Cross-Disorder Genetic Analysis of Tic Disorders, Obsessive-Compulsive, and Hoarding Symptoms.

Science.gov (United States)

Zilhão, Nuno R; Smit, Dirk J; Boomsma, Dorret I; Cath, Danielle C

2016-01-01

Hoarding, obsessive-compulsive disorder (OCD), and Tourette's disorder (TD) are psychiatric disorders that share symptom overlap, which might partly be the result of shared genetic variation. Population-based twin studies have found significant genetic correlations between hoarding and OCD symptoms, with genetic correlations varying between 0.1 and 0.45. For tic disorders, studies examining these correlations are lacking. Other lines of research, including clinical samples and GWAS or CNV data to explore genetic relationships between tic disorders and OCD, have only found very modest if any shared genetic variation. Our aim was to extend current knowledge on the genetic structure underlying hoarding, OC symptoms (OCS), and lifetime tic symptoms and, in a trivariate analysis, assess the degree of common and unique genetic factors contributing to the etiology of these disorders. Data have been gathered from participants in the Netherlands Twin Register comprising a total of 5293 individuals from a sample of adult monozygotic (n = 2460) and dizygotic (n = 2833) twin pairs (mean age 33.61 years). The data on Hoarding, OCS, and tic symptoms were simultaneously analyzed in Mplus. A liability threshold model was fitted to the twin data, analyzing heritability of phenotypes and of their comorbidity. Following the criteria for a probable clinical diagnosis in all phenotypes, 6.8% of participants had a diagnosis of probable hoarding disorder (HD), 6.3% of OCS, and 12.8% of any probable lifetime tic disorder. Genetic factors explained 50.4, 70.1, and 61.1% of the phenotypic covariance between hoarding-OCS, hoarding-tics, and OCS-tics, respectively. Substantial genetic correlations were observed between hoarding and OCS (0.41), hoarding and tics (0.35), and between OCS and tics (0.37). These results support the contribution of genetic factors in the development of these disorders and their comorbidity. Furthermore, tics were mostly influenced by specific

Cross-Disorder Genetic Analysis of Tic Disorders, Obsessive–Compulsive, and Hoarding Symptoms

Science.gov (United States)

Zilhão, Nuno R.; Smit, Dirk J.; Boomsma, Dorret I.; Cath, Danielle C.

2016-01-01

Hoarding, obsessive–compulsive disorder (OCD), and Tourette’s disorder (TD) are psychiatric disorders that share symptom overlap, which might partly be the result of shared genetic variation. Population-based twin studies have found significant genetic correlations between hoarding and OCD symptoms, with genetic correlations varying between 0.1 and 0.45. For tic disorders, studies examining these correlations are lacking. Other lines of research, including clinical samples and GWAS or CNV data to explore genetic relationships between tic disorders and OCD, have only found very modest if any shared genetic variation. Our aim was to extend current knowledge on the genetic structure underlying hoarding, OC symptoms (OCS), and lifetime tic symptoms and, in a trivariate analysis, assess the degree of common and unique genetic factors contributing to the etiology of these disorders. Data have been gathered from participants in the Netherlands Twin Register comprising a total of 5293 individuals from a sample of adult monozygotic (n = 2460) and dizygotic (n = 2833) twin pairs (mean age 33.61 years). The data on Hoarding, OCS, and tic symptoms were simultaneously analyzed in Mplus. A liability threshold model was fitted to the twin data, analyzing heritability of phenotypes and of their comorbidity. Following the criteria for a probable clinical diagnosis in all phenotypes, 6.8% of participants had a diagnosis of probable hoarding disorder (HD), 6.3% of OCS, and 12.8% of any probable lifetime tic disorder. Genetic factors explained 50.4, 70.1, and 61.1% of the phenotypic covariance between hoarding-OCS, hoarding-tics, and OCS-tics, respectively. Substantial genetic correlations were observed between hoarding and OCS (0.41), hoarding and tics (0.35), and between OCS and tics (0.37). These results support the contribution of genetic factors in the development of these disorders and their comorbidity. Furthermore, tics were mostly influenced by specific

International publication trends in the Journal of Applied Behavior Analysis: 2000-2014.

Science.gov (United States)

Martin, Neil T; Nosik, Melissa R; Carr, James E

2016-06-01

Dymond, Clarke, Dunlap, and Steiner's (2000) analysis of international publication trends in the Journal of Applied Behavior Analysis (JABA) from 1970 to 1999 revealed low numbers of publications from outside North America, leading the authors to express concern about the lack of international involvement in applied behavior analysis. They suggested that a future review would be necessary to evaluate any changes in international authorship in the journal. As a follow-up, we analyzed non-U.S. publication trends in the most recent 15 years of JABA and found similar results. We discuss potential reasons for the relative paucity of international authors and suggest potential strategies for increasing non-U.S. contributions to the advancement of behavior analysis. © 2015 Society for the Experimental Analysis of Behavior.

Deep Learning for Population Genetic Inference.

Science.gov (United States)

Sheehan, Sara; Song, Yun S

2016-03-01

Given genomic variation data from multiple individuals, computing the likelihood of complex population genetic models is often infeasible. To circumvent this problem, we introduce a novel likelihood-free inference framework by applying deep learning, a powerful modern technique in machine learning. Deep learning makes use of multilayer neural networks to learn a feature-based function from the input (e.g., hundreds of correlated summary statistics of data) to the output (e.g., population genetic parameters of interest). We demonstrate that deep learning can be effectively employed for population genetic inference and learning informative features of data. As a concrete application, we focus on the challenging problem of jointly inferring natural selection and demography (in the form of a population size change history). Our method is able to separate the global nature of demography from the local nature of selection, without sequential steps for these two factors. Studying demography and selection jointly is motivated by Drosophila, where pervasive selection confounds demographic analysis. We apply our method to 197 African Drosophila melanogaster genomes from Zambia to infer both their overall demography, and regions of their genome under selection. We find many regions of the genome that have experienced hard sweeps, and fewer under selection on standing variation (soft sweep) or balancing selection. Interestingly, we find that soft sweeps and balancing selection occur more frequently closer to the centromere of each chromosome. In addition, our demographic inference suggests that previously estimated bottlenecks for African Drosophila melanogaster are too extreme.

Molecular genetic analysis of phosphomannomutase genes in Triticum monococcum

Institute of Scientific and Technical Information of China (English)

Chunmei; Yu; Xinyan; Liu; Qian; Zhang; Xinyu; He; Wan; Huai; Baohua; Wang; Yunying; Cao; Rong; Zhou

2015-01-01

In higher plants, phosphomannomutase(PMM) is essential for synthesizing the antioxidant ascorbic acid through the Smirnoff–Wheeler pathway. Previously, we characterized six PMM genes(Ta PMM-A1, A2, B1, B2, D1 and D2) in common wheat(Triticum aestivum, AABBDD).Here, we report a molecular genetic analysis of PMM genes in Triticum monococcum(AmAm), a diploid wheat species whose Amgenome is closely related to the A genome of common wheat. Two distinct PMM genes, Tm PMM-1 and Tm PMM-2, were found in T. monococcum. The coding region of Tm PMM-1 was intact and highly conserved. In contrast, two main Tm PMM-2 alleles were identified, with Tm PMM-2a possessing an intact coding sequence and Tm PMM-2b being a pseudogene. The transcript level of Tm PMM-2a was much higher than that of Tm PMM-2b, and a bacterially expressed Tm PMM-2a recombinant protein displayed relatively high PMM activity. In general, the total transcript level of PMM was substantially higher in accessions carrying Tm PMM-1 and Tm PMM-2a than those harboring Tm PMM-1 and Tm PMM-2b. However, total PMM protein and activity levels did not differ drastically between the two genotypes. This work provides new information on PMM genes in T. monococcum and expands our understanding on Triticeae PMM genes, which may aid further functional and applied studies of PMM in crop plants.

Genetic Diversity Analysis of Medicinally Important Horticultural Crop Aegle marmelos by ISSR Markers.

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Mujeeb, Farina; Bajpai, Preeti; Pathak, Neelam; Verma, Smita Rastogi

2017-01-01

Inter simple sequence repeat (ISSR) markers help in identifying and determining the extent of genetic diversity in cultivars. Here, we describe their application in determining the genetic diversity of bael (Aegle marmelos Corr.). Universal ISSR primers are selected and their marker characteristics such as polymorphism information content, effective multiplex ratio and marker index have been evaluated. ISSR-PCR is then performed using universal ISSR primers to generate polymorphic bands. This information is used to determine the degree of genetic similarity among the bael varieties/accessions by cluster analysis using unweighted pair-group method with arithmetic averages (UPGMA). This technology is valuable for biodiversity conservation and for making an efficient choice of parents in breeding programs.

Recruitment and Participation of Recreational Runners in a Large Epidemiological and Genetic Research Study: Retrospective Data Analysis.

Science.gov (United States)

Manzanero, Silvia; Kozlovskaia, Maria; Vlahovich, Nicole; Hughes, David C

2018-05-23

With the increasing capacity for remote collection of both data and samples for medical research, a thorough assessment is needed to determine the association of population characteristics and recruitment methodologies with response rates. The aim of this research was to assess population representativeness in a two-stage study of health and injury in recreational runners, which consisted of an epidemiological arm and genetic analysis. The cost and success of various classical and internet-based methods were analyzed, and demographic representativeness was assessed for recruitment to the epidemiological survey, reported willingness to participate in the genetic arm of the study, actual participation, sample return, and approval for biobank storage. A total of 4965 valid responses were received, of which 1664 were deemed eligible for genetic analysis. Younger age showed a negative association with initial recruitment rate, expressed willingness to participate in genetic analysis, and actual participation. Additionally, female sex was associated with higher initial recruitment rates, and ethnic origin impacted willingness to participate in the genetic analysis (all P<.001). The sharp decline in retention through the different stages of the study in young respondents suggests the necessity to develop specific recruitment and retention strategies when investigating a young, physically active population. ©Silvia Manzanero, Maria Kozlovskaia, Nicole Vlahovich, David C Hughes. Originally published in JMIR Research Protocols (http://www.researchprotocols.org), 23.05.2018.

Fault Diagnosis of Power System Based on Improved Genetic Optimized BP-NN

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Yuan Pu

2015-01-01

Full Text Available BP neural network (Back-Propagation Neural Network, BP-NN is one of the most widely neural network models and is applied to fault diagnosis of power system currently. BP neural network has good self-learning and adaptive ability and generalization ability, but the operation process is easy to fall into local minima. Genetic algorithm has global optimization features, and crossover is the most important operation of the Genetic Algorithm. In this paper, we can modify the crossover of traditional Genetic Algorithm, using improved genetic algorithm optimized BP neural network training initial weights and thresholds, to avoid the problem of BP neural network fall into local minima. The results of analysis by an example, the method can efficiently diagnose network fault location, and improve fault-tolerance and grid fault diagnosis effect.

Genetically-directed, cell type-specific sparse labeling for the analysis of neuronal morphology.

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Thomas Rotolo

Full Text Available In mammals, genetically-directed cell labeling technologies have not yet been applied to the morphologic analysis of neurons with very large and complex arbors, an application that requires extremely sparse labeling and that is only rendered practical by limiting the labeled population to one or a few predetermined neuronal subtypes.In the present study we have addressed this application by using CreER technology to non-invasively label very small numbers of neurons so that their morphologies can be fully visualized. Four lines of IRES-CreER knock-in mice were constructed to permit labeling selectively in cholinergic or catecholaminergic neurons [choline acetyltransferase (ChAT-IRES-CreER or tyrosine hydroxylase (TH-IRES-CreER], predominantly in projection neurons [neurofilament light chain (NFL-IRES-CreER], or broadly in neurons and some glia [vesicle-associated membrane protein2 (VAMP2-IRES-CreER]. When crossed to the Z/AP reporter and exposed to 4-hydroxytamoxifen in the early postnatal period, the number of neurons expressing the human placental alkaline phosphatase reporter can be reproducibly lowered to fewer than 50 per brain. Sparse Cre-mediated recombination in ChAT-IRES-CreER;Z/AP mice shows the full axonal and dendritic arbors of individual forebrain cholinergic neurons, the first time that the complete morphologies of these very large neurons have been revealed in any species.Sparse genetically-directed, cell type-specific neuronal labeling with IRES-creER lines should prove useful for studying a wide variety of questions in neuronal development and disease.

Defining asthma in genetic studies

NARCIS (Netherlands)

Koppelman, GH; Postma, DS; Meijer, G.

1999-01-01

Genetic studies have been hampered by the lack of a gold standard to diagnose asthma. The complex nature of asthma makes it more difficult to identify asthma genes. Therefore, approaches to define phenotypes, which have been successful in other genetically complex diseases, may be applied to define

Model Proposition for the Fiscal Policies Analysis Applied in Economic Field

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Larisa Preda

2007-05-01

Full Text Available This paper presents a study about fiscal policy applied in economic development. Correlations between macroeconomics and fiscal indicators signify the first steep in our analysis. Next step is a new model proposal for the fiscal and budgetary choices. This model is applied on the date of the Romanian case.

A Genetically Informed Cross-lagged Analysis of Autistic-Like Traits and Affective Problems in Early Childhood

Science.gov (United States)

Micalizzi, Lauren; Ronald, Angelica; Saudino, Kimberly J.

2015-01-01

A genetically informed cross-lagged model was applied to twin data to explore etiological links between autistic-like traits and affective problems in early childhood. The sample comprised 310 same-sex twin pairs (143 monozygotic and 167 dizygotic; 53% male). Autistic-like traits and affective problems were assessed at ages 2 and 3 using parent ratings. Both constructs were related within and across age (r = .30−.53) and showed moderate stability (r = .45−.54). Autistic-like traits and affective problems showed genetic and environmental influences at both ages. Whereas at age 2, the covariance between autistic-like traits and affective problems was entirely due to environmental influences (shared and nonshared), at age 3, genetic factors also contributed to the covariance between constructs. The stability paths, but not the cross-lagged paths, were significant, indicating that there is stability in both autistic-like traits and affective problems but they do not mutually influence each other across age. Stability effects were due to genetic, shared, and nonshared environmental influences. Substantial novel genetic and nonshared environmental influences emerge at age 3 and suggest change in the etiology of these constructs over time. During early childhood, autistic-like traits tend to occur alongside affective problems and partly overlapping genetic and environmental influences explain this association. PMID:26456961

Application of computational methods in genetic study of inflammatory bowel disease.

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Li, Jin; Wei, Zhi; Hakonarson, Hakon

2016-01-21

Genetic factors play an important role in the etiology of inflammatory bowel disease (IBD). The launch of genome-wide association study (GWAS) represents a landmark in the genetic study of human complex disease. Concurrently, computational methods have undergone rapid development during the past a few years, which led to the identification of numerous disease susceptibility loci. IBD is one of the successful examples of GWAS and related analyses. A total of 163 genetic loci and multiple signaling pathways have been identified to be associated with IBD. Pleiotropic effects were found for many of these loci; and risk prediction models were built based on a broad spectrum of genetic variants. Important gene-gene, gene-environment interactions and key contributions of gut microbiome are being discovered. Here we will review the different types of analyses that have been applied to IBD genetic study, discuss the computational methods for each type of analysis, and summarize the discoveries made in IBD research with the application of these methods.

Pantoea ananatis Genetic Diversity Analysis Reveals Limited Genomic Diversity as Well as Accessory Genes Correlated with Onion Pathogenicity

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Shaun P. Stice

2018-02-01

Full Text Available Pantoea ananatis is a member of the family Enterobacteriaceae and an enigmatic plant pathogen with a broad host range. Although P. ananatis strains can be aggressive on onion causing foliar necrosis and onion center rot, previous genomic analysis has shown that P. ananatis lacks the primary virulence secretion systems associated with other plant pathogens. We assessed a collection of fifty P. ananatis strains collected from Georgia over three decades to determine genetic factors that correlated with onion pathogenic potential. Previous genetic analysis studies have compared strains isolated from different hosts with varying diseases potential and isolation sources. Strains varied greatly in their pathogenic potential and aggressiveness on different cultivated Allium species like onion, leek, shallot, and chive. Using multi-locus sequence analysis (MLSA and repetitive extragenic palindrome repeat (rep-PCR techniques, we did not observe any correlation between onion pathogenic potential and genetic diversity among strains. Whole genome sequencing and pan-genomic analysis of a sub-set of 10 strains aided in the identification of a novel series of genetic regions, likely plasmid borne, and correlating with onion pathogenicity observed on single contigs of the genetic assemblies. We named these loci Onion Virulence Regions (OVR A-D. The OVR loci contain genes involved in redox regulation as well as pectate lyase and rhamnogalacturonase genes. Previous studies have not identified distinct genetic loci or plasmids correlating with onion foliar pathogenicity or pathogenicity on a single host pathosystem. The lack of focus on a single host system for this phytopathgenic disease necessitates the pan-genomic analysis performed in this study.

Microsatellite marker-based genetic analysis of relatedness between commercial and heritage turkeys (Meleagris gallopavo).

Science.gov (United States)

Kamara, D; Gyenai, K B; Geng, T; Hammade, H; Smith, E J

2007-01-01

The turkey is second only to the chicken in importance as an agriculturally important poultry species. Unlike the chicken, however, genetic studies of the turkey continue to be limited. For example, to date, many genomic investigations have been conducted to characterize genetic relationships between commercial (CO) and non-CO chicken breeds, whereas the nature of the genetic relatedness between CO and heritage turkeys remains unknown. The objective of the current research was to use microsatellites to analyze the genetic relatedness between CO and heritage domestic turkeys including Narragansett, Bourbon Red, Blue Slate, Spanish Black, and Royal Palm. Primer pairs specific for 10 previously described turkey microsatellite markers were used. The phylogenetic analysis showed that the Blue Slate, Bourbon Red, and Narragansett were genetically closely related to the CO strain, with a Nei distance of 0.30, and the Royal Palm and Spanish Black were the least related to the CO strain, with Nei distances of 0.41 and 0.40, respectively. The present work provides a foundation for the basis of using heritage turkeys to genetically improve CO populations by introgression.

A Value-Based Medicine cost-utility analysis of genetic testing for neovascular macular degeneration.

Science.gov (United States)

Brown, Gary C; Brown, Melissa M; Lieske, Heidi B; Lieske, Philip A; Brown, Kathryn S

2015-01-01

There is a dearth of patient, preference-based cost-effectiveness analyses evaluating genetic testing for neovascular age-related macular degeneration (NVAMD). A Value-Based Medicine, 12-year, combined-eye model, cost-utility analysis evaluated genetic testing of Category 3 AMD patients at age 65 for progression to NVAMD. The benefit of genetic testing was predicated upon the fact that early-treatment ranibizumab therapy (baseline vision 20/40-20/80) for NVAMD confers greater patient value than late-treatment (baseline vision ≤20/160). Published genetic data and MARINA Study ranibizumab therapy data were utilized in the analysis. Patient value (quality-of-life gain) and financial value (2012 US real dollar) outcomes were discounted at 3 % annually. Genetic testing-enabled, early-treatment ranibizumab therapy per patient conferred mean 20/40 -1 vision, a 0.845 QALY gain and 14.1 % quality-of-life gain over sham therapy. Late-treatment ranibizumab therapy conferred mean 20/160 +2 vision, a 0.250 QALY gain and 4.2 % quality-of-life gain over sham therapy. The gain from early-treatment over late-treatment was 0.595 QALY (10.0 % quality-of-life gain). The per-patient cost for genetic testing/closer monitoring was $2205 per screened person, $2.082 billion for the 944,000 estimated new Category 3 AMD patients annually. Genetic testing/monitoring costs per early-treatment patient totaled $66,180. Costs per early-treatment patient included: genetic testing costs: $66,180 + direct non-ophthalmic medical costs: -$40,914 + caregiver costs: -$172,443 + employment costs: -$14,098 = a net societal cost saving of $160,582 per early treatment patient. When genetic screening facilitated an incremental 12,965 (8.0 %) of the 161,754, new annual NVAMD patients aged ≥65 in the US to undergo early-treatment ranibizumab therapy, each additional patient treated accrued an overall, net financial gain for society of $160,582. Genetic screening was cost-effective, using World

Genetic Analysis of Pinus sylvestris L. and Pinus sylvestris forma turfosa L. Using RAPD Markers

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Beáta ÁBRAHÁM

2010-03-01

Full Text Available The purpose of the present study was to determine the level of genetic diversity within and among Ciuc basin, Romania (populations from Mohos and Luci raised bogs in Harghita Mountain and Sumuleu in Ciuc Mountain Pinus sylvestris populations using molecular markers. Two of populations (Mohos and Luci seems to be the descendants that survived the continental glaciation. Genetic diversity was analyzed by RAPD (Random Amplified Polymorphic DNA. Nine primers were selected for analysis, which generated reproducible bands. On base of presence or absence of homologues bands Nei’s gene diversity, the percentage of polymorphic loci and Nei’s unbiased genetic distance were calculated. The level of genetic variation among populations was found to be low. For both populations the variation values among populations were higher than within populations. The fossil records and geological historical data explain the extremely low genetic diversity of this species. Pinus sylvestris experienced strong bottlenecks during its evolutionary history, which caused the loss of genetic variation. Genetic drift and breeding in post-bottlenecked small populations may be the major forces that contribute to low genetic diversity and genetic differentiation of populations. Human activities may have accelerated the loss of genetic diversity in Pinus sylvestris.

Network-assisted crop systems genetics: network inference and integrative analysis.

Science.gov (United States)

Lee, Tak; Kim, Hyojin; Lee, Insuk

2015-04-01

Although next-generation sequencing (NGS) technology has enabled the decoding of many crop species genomes, most of the underlying genetic components for economically important crop traits remain to be determined. Network approaches have proven useful for the study of the reference plant, Arabidopsis thaliana, and the success of network-based crop genetics will also require the availability of a genome-scale functional networks for crop species. In this review, we discuss how to construct functional networks and elucidate the holistic view of a crop system. The crop gene network then can be used for gene prioritization and the analysis of resequencing-based genome-wide association study (GWAS) data, the amount of which will rapidly grow in the field of crop science in the coming years. Copyright © 2015 Elsevier Ltd. All rights reserved.

Assessment of genetically modified soybean crops and different cultivars by Fourier transform infrared spectroscopy and chemometric analysis

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Glaucia Braz Alcantara

2010-06-01

Full Text Available This paper describes the potentiality of Fourier transform infrared (FT-IR spectroscopy associated to chemometric analysis for assessment of conventional and genetically modified soybean crops. Recently, genetically modified organisms have been queried about their influence on the environment and their safety as food/feed. In this regard, chemical investigations are ever more required. Thus three different soybean cultivars distributed in transgenic Roundup ReadyTM soybean and theirs conventional counterparts were directly investigated by FT-IR spectroscopy and chemometric analysis. The application of PCA and KNN methods permitted the discrimination and classification of the genetically modified samples from conventional ones when they were separately analysed. The analyses showed the chemical variation according to genetic modification. Furthermore, this methodology was efficient for cultivar grouping and highlights cultivar dependence for discrimination between transgenic and non-transgenic samples. According to this study, FT-IR and chemometrics could be used as a quick, easy and low cost tool to assess the chemical composition variation in genetically modified organisms.

Optimal support arrangement of piping systems using genetic algorithm

International Nuclear Information System (INIS)

Chiba, T.; Okado, S.; Fujii, I.; Itami, K.

1996-01-01

The support arrangement is one of the important factors in the design of piping systems. Much time is required to decide the arrangement of the supports. The authors applied a genetic algorithm to find the optimum support arrangement for piping systems. Examples are provided to illustrate the effectiveness of the genetic algorithm. Good results are obtained when applying the genetic algorithm to the actual designing of the piping system

Genetic Contributions to Clinical Pain and Analgesia: Avoiding Pitfalls in Genetic Research

Science.gov (United States)

Kim, Hyungsuk; Clark, David; Dionne, Raymond A.

2010-01-01

Understanding the genetic basis of human variations in pain is critical to elucidating the molecular basis of pain sensitivity, variable responses to analgesic drugs, and, ultimately, to individualized treatment of pain and improved public health. With the help of recently accumulated knowledge and advanced technologies, pain researchers hope to gain insight into genetic mechanisms of pain and eventually apply this knowledge to pain treatment. Perspective We critically reviewed the published literature to examine the strength of evidence supporting genetic influences on clinical and human experimental pain. Based on this evidence and the experience of false associations that have occurred in other related disciplines, we provide recommendations for avoiding pitfalls in pain genetic research. PMID:19559388

Genetics in the courts

Energy Technology Data Exchange (ETDEWEB)

Coyle, Heather; Drell, Dan

2000-12-01

Various: (1)TriState 2000 Genetics in the Courts (2) Growing impact of the new genetics on the courts (3)Human testing (4) Legal analysis - in re G.C. (5) Legal analysis - GM ''peanots'', and (6) Legal analysis for State vs Miller

Partial Results Regarding the Genetic Analysis of Thoroughbred Horse from Cislău Studfarm: Reproductive Isolation and Age Structure

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Marius Maftei

2011-05-01

Full Text Available This study is a part of an ample research concerning the genetic analysis (history of Thoroughbred horses from Cislău studfarm. The genetic analysis studies are a part of Animal Genetic Resources Management because just start of them we elaborate the strategies for inbreeding management. This study has as purpose to present two important aspects of genetic analysis: reproductive isolation level and age structure.This parameters has a capital importance in animal breeding because there has a directly influence in animal population evolution. The reproductive isolation situation was quantified using the relation elaborated by S. Wright in 1921. The age structure situation is based on the age distribution histogram. The analysis showed that the Nonius horse from Izvin stud is a reproductively isolated population and have its own evolutionary path. Age structure is not balanced with negative repercurssions on generation interval.

Applied Genetics and Genomics in Alfalfa Breeding

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E. Charles Brummer

2012-03-01

Full Text Available Alfalfa (Medicago sativa L., a perennial and outcrossing species, is a widely planted forage legume for hay, pasture and silage throughout the world. Currently, alfalfa breeding relies on recurrent phenotypic selection, but alternatives incorporating molecular marker assisted breeding could enhance genetic gain per unit time and per unit cost, and accelerate alfalfa improvement. Many major quantitative trait loci (QTL related to agronomic traits have been identified by family-based QTL mapping, but in relatively large genomic regions. Candidate genes elucidated from model species have helped to identify some potential causal loci in alfalfa mapping and breeding population for specific traits. Recently, high throughput sequencing technologies, coupled with advanced bioinformatics tools, have been used to identify large numbers of single nucleotide polymorphisms (SNP in alfalfa, which are being developed into markers. These markers will facilitate fine mapping of quantitative traits and genome wide association mapping of agronomic traits and further advanced breeding strategies for alfalfa, such as marker-assisted selection and genomic selection. Based on ideas from the literature, we suggest several ways to improve selection in alfalfa including (1 diversity selection and paternity testing, (2 introgression of QTL and (3 genomic selection.

Genetics applied to the constitution new varieties of plants

International Nuclear Information System (INIS)

Stamigna, Carla; Chiaretti, Emiliano; Chiaretti, Domenico

2015-01-01

The genetic improvement of plants intended to create new varieties, as well as the study of principles and techniques to get them to answer for the real needs of farmers. This process requires advanced agricultural techniques to obtain a continuous and progressive increase crop productivity and higher profitability the processes employed in agriculture. Enea continues to recognize new plant varieties in collaboration with the company ISEAAGROSERVICE seed, which in the past it has been the one that has more commercialized the Croesus wheat, a variety of durum wheat obtained at the laboratories of the Center Casaccia Research in the early 70s. [it

Rapid identification of Enterobacter hormaechei and Enterobacter cloacae genetic cluster III.

Science.gov (United States)

Ohad, S; Block, C; Kravitz, V; Farber, A; Pilo, S; Breuer, R; Rorman, E

2014-05-01

Enterobacter cloacae complex bacteria are of both clinical and environmental importance. Phenotypic methods are unable to distinguish between some of the species in this complex, which often renders their identification incomplete. The goal of this study was to develop molecular assays to identify Enterobacter hormaechei and Ent. cloacae genetic cluster III which are relatively frequently encountered in clinical material. The molecular assays developed in this study are qPCR technology based and served to identify both Ent. hormaechei and Ent. cloacae genetic cluster III. qPCR results were compared to hsp60 sequence analysis. Most clinical isolates were assigned to Ent. hormaechei subsp. steigerwaltii and Ent. cloacae genetic cluster III. The latter was proportionately more frequently isolated from bloodstream infections than from other material (P < 0·05). The qPCR assays detecting Ent. hormaechei and Ent. cloacae genetic cluster III demonstrated high sensitivity and specificity. The presented qPCR assays allow accurate and rapid identification of clinical isolates of the Ent. cloacae complex. The improved identifications obtained can specifically assist analysis of Ent. hormaechei and Ent. cloacae genetic cluster III in nosocomial outbreaks and can promote rapid environmental monitoring. An association was observed between Ent. cloacae cluster III and systemic infection that deserves further attention. © 2014 The Society for Applied Microbiology.

Introduction to applied statistical signal analysis guide to biomedical and electrical engineering applications

CERN Document Server

Shiavi, Richard

2007-01-01

Introduction to Applied Statistical Signal Analysis is designed for the experienced individual with a basic background in mathematics, science, and computer. With this predisposed knowledge, the reader will coast through the practical introduction and move on to signal analysis techniques, commonly used in a broad range of engineering areas such as biomedical engineering, communications, geophysics, and speech.Introduction to Applied Statistical Signal Analysis intertwines theory and implementation with practical examples and exercises. Topics presented in detail include: mathematical

Applied Behavior Analysis Is a Science And, Therefore, Progressive

Science.gov (United States)

Leaf, Justin B.; Leaf, Ronald; McEachin, John; Taubman, Mitchell; Ala'i-Rosales, Shahla; Ross, Robert K.; Smith, Tristram; Weiss, Mary Jane

2016-01-01

Applied behavior analysis (ABA) is a science and, therefore, involves progressive approaches and outcomes. In this commentary we argue that the spirit and the method of science should be maintained in order to avoid reductionist procedures, stifled innovation, and rote, unresponsive protocols that become increasingly removed from meaningful…

Emerging Global Initiatives in Neurogenetics: The Enhancing Neuroimaging Genetics through Meta-analysis (ENIGMA) Consortium.

Science.gov (United States)

Bearden, Carrie E; Thompson, Paul M

2017-04-19

The Enhancing Neuroimaging Genetics through Meta-analysis (ENIGMA) Consortium is a global team science effort, now including over 800 scientists spread across 340 institutions in 35 countries, with the shared goal of understanding disease and genetic influences on the brain. This "crowdsourcing" approach to team neuroscience has unprecedented power for advancing our understanding of both typical and atypical human brain development. Copyright © 2017 Elsevier Inc. All rights reserved.

Genetic diversity and relationship analysis of Gossypium arboreum accessions.

Science.gov (United States)

Liu, F; Zhou, Z L; Wang, C Y; Wang, Y H; Cai, X Y; Wang, X X; Zhang, Z S; Wang, K B

2015-11-19

Simple sequence repeat techniques were used to identify the genetic diversity of 101 Gossypium arboreum accessions collected from India, Vietnam, and the southwest of China (Guizhou, Guangxi, and Yunnan provinces). Twenty-six pairs of SSR primers produced a total of 103 polymorphic loci with an average of 3.96 polymorphic loci per primer. The average of the effective number of alleles, Nei's gene diversity, and Shannon's information index were 0.59, 0.2835, and 0.4361, respectively. The diversity varied among different geographic regions. The result of principal component analysis was consistent with that of unweighted pair group method with arithmetic mean clustering analysis. The 101 G. arboreum accessions were clustered into 2 groups.

Genetic diversity analysis of Cuban traditional rice (Oryza sativa L. varieties based on microsatellite markers

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Alba Alvarez

2007-01-01

Full Text Available Microsatellite polymorphism was studied in a sample of 39 traditional rice (Oryza sativa L. varieties and 11 improved varieties widely planted in Cuba. The study was aimed at assessing the extent of genetic variation in traditional and improved varieties and to establish their genetic relationship for breeding purposes. Heterozygosity was analyzed at each microsatellite loci and for each genotype using 10 microsatellite primer pairs. Between varieties genetic relationship was estimated. The number of alleles per microsatellite loci was 4 to 8, averaging 6.6 alleles per locus. Higher heterozygosity (H was found in traditional varieties (H TV = 0.72 than in improved varieties (H IV = 0.42, and 68% of the total microsatellite alleles were found exclusively in the traditional varieties. Genetic diversity, represented by cluster analysis, indicated three different genetic groups based on their origin. Genetic relationship estimates based on the proportion of microsatellite loci with shared alleles indicated that the majority of traditional varieties were poorly related to the improved varieties. We also discuss the more efficient use of the available genetic diversity in future programs involving genetic crosses.

Genetic diversity assessed by microsatellite markers in sweet corn cultivars

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Ana Daniela Lopes

2015-12-01

Full Text Available Information on genetic diversity is essential to the characterization and utilization of germplasm. The genetic diversity of twenty-two sweet corn cultivars (seventeen open-pollinated varieties, OPV, and five hybrids, H was investigated by applying simple sequence repeat markers. A total of 257 primers were tested, of which 160 were found to be usable in terms of high reproducibility for all the samples tested; 45 were polymorphic loci, of which 30 were used to assess the genetic diversity of sweet corn cultivars. We detected a total of 86 alleles using 30 microsatellite primers. The mean polymorphism was 82 %. The highest heterozygosity values (Ho = 0.20 were found in the PR030-Doce Flor da Serra and BR427 III OPVs, whereas the lowest values (0.14 were recorded in the MG161-Branco Doce and Doce Cubano OPVs. The polymorphism information content ranged from 0.19 (Umc2319 to 0.71 (Umc2205. The analysis of molecular variance revealed that most of the genetic variability was concentrated within the cultivars of sweet corn (75 %, with less variability between them (25 %. The consensus tree derived from the neighbor-joining (NJ algorithm using 1,000 bootstrapping replicates revealed seven genetically different groups. Nei’s diversity values varied between 0.103 (Doce do Hawai × CNPH-1 cultivars and 0.645 (Amarelo Doce × Lili cultivars, indicating a narrow genetic basis. The Lili hybrid was the most distant cultivar, as revealed by Principal Coordinates Analysis and the NJ tree. This study on genetic diversity will be useful for planning future studies on sweet corn genetic resources and can complement the breeding programs for this crop.

Host traits explain the genetic structure of parasites: a meta-analysis

Czech Academy of Sciences Publication Activity Database

Blasco-Costa, Maria Isabel; Poulin, R.

2013-01-01

Roč. 140, č. 10 (2013), s. 1316-1322 ISSN 0031-1820 EU Projects: European Commission(XE) 252124 - PARAPOPGENE Institutional support: RVO:60077344 Keywords : meta-analysis * host traits * parasite traits * F-statistics * population genetic structure * dispersal * autogenic life cycle * allogenic life cycle Subject RIV: EH - Ecology, Behaviour Impact factor: 2.350, year: 2013

The genetic algorithm for a signal enhancement

International Nuclear Information System (INIS)

Karimova, L.; Kuadykov, E.; Makarenko, N.

2004-01-01

The paper is devoted to the problem of time series enhancement, which is based on the analysis of local regularity. The model construction using this analysis does not require any a priori assumption on the structure of the noise and the functional relationship between original signal and noise. The signal itself may be nowhere differentiable with rapidly varying local regularity, what is overcome with the help of the new technique of increasing the local Hoelder regularity of the signal under research. A new signal with prescribed regularity is constructed using the genetic algorithm. This approach is applied to enhancement of time series in the paleoclimatology, solar physics, dendrochronology, meteorology and hydrology

The genetic algorithm for a signal enhancement

Energy Technology Data Exchange (ETDEWEB)

Karimova, L. [Laboratory of Computer Modelling, Institute of Mathematics, Pushkin Street 125, 480100 Almaty (Kazakhstan)]. E-mail: karimova@math.kz; Kuadykov, E. [Laboratory of Computer Modelling, Institute of Mathematics, Pushkin Street 125, 480100 Almaty (Kazakhstan); Makarenko, N. [Laboratory of Computer Modelling, Institute of Mathematics, Pushkin Street 125, 480100 Almaty (Kazakhstan)

2004-11-21

The paper is devoted to the problem of time series enhancement, which is based on the analysis of local regularity. The model construction using this analysis does not require any a priori assumption on the structure of the noise and the functional relationship between original signal and noise. The signal itself may be nowhere differentiable with rapidly varying local regularity, what is overcome with the help of the new technique of increasing the local Hoelder regularity of the signal under research. A new signal with prescribed regularity is constructed using the genetic algorithm. This approach is applied to enhancement of time series in the paleoclimatology, solar physics, dendrochronology, meteorology and hydrology.

Genetic diversity and structure analysis based on hordein protein polymorphism in barley landrace populations from jordan

International Nuclear Information System (INIS)

Baloch, A.W.; Ali, M.; Baloch, A.M.; Mangan, B.U.N.; Song, W

2014-01-01

Jordan is unanimously considered to be one of the centers of genetic diversity for barley, where wild and landraces of barley has been grown under different climatic conditions. The genetic diversity and genetic structure based on hordein polymorphism was assessed in 90 different accessions collected from four different sites of Jordan. A-PAGE was used to reveal hordein polymorphism among the genotypes. A total of 29 distinct bands were identified, out of them 9 bands were distinguished for D, 11 for C, and 9 for the B hordein regions. The observed genetic similarity was an exceptionally high between the populations than expected, which is probably due to high gene flow estimated between them. The genetic diversity parameters were not differ largely among the populations, indicating that local selection of a particular site did not play a key role in shaping genetic diversity. Analysis of molecular variance (AMOVA) revealed significant population structure when accessions were structured according to population site. There was 94% of hordein variation resided within the populations and only 8% present among the populations. Both Bayesian and Principale Coordinate Analysis (PCoA) concordantly demonstrated admixture genotypes of the landraces barley populations. Consequently, none of the population found to be clustered separately according to its population site. It is concluded that this approach can be useful to explore the germplasm for genetic diversity but perhaps is not suitable for determining phylogenic relations in barley. (author)

Applying new genetic approaches to improve quality of population assessment of green and loggerhead turtles

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — As the NOAA-Fisheries? National Sea Turtle Genetics Lab, the SWFSC Marine Turtle Genetics Program has the lead responsibility for generating, analyzing and...

A rapid, simple method for the genetic discrimination of intact Arabidopsis thaliana mutant seeds using metabolic profiling by direct analysis in real-time mass spectrometry

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Jang Young

2011-06-01

Full Text Available Abstract Background Efficient high throughput screening systems of useful mutants are prerequisite for study of plant functional genomics and lots of application fields. Advance in such screening tools, thanks to the development of analytic instruments. Direct analysis in real-time (DART-mass spectrometry (MS by ionization of complex materials at atmospheric pressure is a rapid, simple, high-resolution analytical technique. Here we describe a rapid, simple method for the genetic discrimination of intact Arabidopsis thaliana mutant seeds using metabolic profiling by DART-MS. Results To determine whether this DART-MS combined by multivariate analysis can perform genetic discrimination based on global metabolic profiling, intact Arabidopsis thaliana mutant seeds were subjected to DART-MS without any sample preparation. Partial least squares-discriminant analysis (PLS-DA of DART-MS spectral data from intact seeds classified 14 different lines of seeds into two distinct groups: Columbia (Col-0 and Landsberg erecta (Ler ecotype backgrounds. A hierarchical dendrogram based on partial least squares-discriminant analysis (PLS-DA subdivided the Col-0 ecotype into two groups: mutant lines harboring defects in the phenylpropanoid biosynthetic pathway and mutants without these defects. These results indicated that metabolic profiling with DART-MS could discriminate intact Arabidopsis seeds at least ecotype level and metabolic pathway level within same ecotype. Conclusion The described DART-MS combined by multivariate analysis allows for rapid screening and metabolic characterization of lots of Arabidopsis mutant seeds without complex metabolic preparation steps. Moreover, potential novel metabolic markers can be detected and used to clarify the genetic relationship between Arabidopsis cultivars. Furthermore this technique can be applied to predict the novel gene function of metabolic mutants regardless of morphological phenotypes.

The genetic diversity of the mangrove kandelia obovata in China revealed by ISSR analysis

International Nuclear Information System (INIS)

Chen, Shao-Bo; Ding, When-Young; Qiu, Jia-Biao; Wang, Guang-Yin; Zhou, Zhi-Min; Chen- Jiao-Fei; Ai, Wewi-ming; Wang, Cheng-Yi; Xie, Qi-Lang

2010-01-01

The genetic diversity of 7 populations of Kandelia obovata in China was characterized using inter simple sequence repeats (ISSR) technique. A total of 50 primers were screened, of which 9 polymorphic and informative patterns were selected to determine genetic relationships. ISSR amplification was conducted on 140 individuals from 7 populations, and 88 polymorphic loci were detected from 106 total loci. The total percentage of polymorphic loci (PPL) was 83.02%. The percentage of PPL at the population level ranged from 32.08% to 47.17%, with an average of 39.89%. Nei's gene diversity (H) and Shannon's information index (I) of K. obovata at the species level were 0.3631 and 0.5203, respectively. The genetic differentiation coefficient (Gst) among populations was 0.5548. Among populations component accounted for 55.48% of the total variation, whereas the within populations component accounted for 44.52%, suggesting that genetic differentiation among K. obovata populations was relatively high. The gene flow among populations was 0.4012, indicating that gene flow was low among geographically diverse populations of K. obovata. The results of the genetic diversity and cluster analysis suggest that geographical isolation of K. obovata populations mainly results in low gene flow and random genetic drift, leading to genetic differentiation. (author)