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Sample records for genetic variability detected

  1. [Detection of genetic variability in Cercospora kikuchii isolates from a single soybean field].

    Science.gov (United States)

    Lurá, M C; Di Conza, J A; González, A M; Latorre Rapela, M G; Turino, L; Ibáñez, M M; Iacona, V

    2007-01-01

    Detection of genetic variability in Cercospora kikuchii isolates from a single soybean field. Current knowledge about epidemiology and population structure of Cercospora kikuchii is little developed and no studies regarding this subject have been reported in Argentina. The aim of this work was to select primers to study genetic variability in C. kikuchii isolated from the same soybean field using RAPD (Random Amplified Polymorphism DNA). RAPD was applied to the DNA of 5 C. kikuchii, isolated from diseased tissue of the soybean in the same field, another isolate, from a strain collection. Out of seven primers, five of them proved to be useful to study the population of C. kikuchii isolates.

  2. SSR-based detection of genetic variability in the charcoal root rot pathogen Macrophomina phaseolina.

    Science.gov (United States)

    Jana, Tarakanta; Sharma, Tilak R; Singh, Nagendra K

    2005-01-01

    Macrophomina phaseolina, the causal agent of charcoal root or collar rot, is an important plant pathogen especially in soybean and cotton. Single primers of simple sequence repeats (SSR) or microsatellite markers have been used for the characterization of genetic variability of different populations of M. phaseolina obtained from soybean and cotton grown in India and the USA. Genetic similarity between isolates was calculated, and cluster analysis was used to generate a dendrogram showing relationships between isolates collected from the two hosts. Forty isolates could be clustered into three major groups corresponding to their hosts and geographical region. The wide distribution of microsatellites in M. phaseolina genome was assessed by agarose gel electrophoresis of the PCR products generated by direct amplification of inter SSR regions DNA. This is the first report of the use of microsatellite markers to characterize the charcoal root rot pathogen. The SSR fingerprints (0.25-3.5 kb) generated using DNA from different populations of M. phaseolina of two hosts indicated that these repeats are interspersed within the genome of this pathogen. The variability found within closely related isolates of M. phaseolina indicated that such microsatellites are useful in population studies and represents a step towards identification of potential isolate diagnostic markers specific to soybean and cotton.

  3. Genetic fusion of single-chain variable fragments to partial spider silk improves target detection in micro- and nanoarrays.

    Science.gov (United States)

    Thatikonda, Naresh; Delfani, Payam; Jansson, Ronnie; Petersson, Linn; Lindberg, Diana; Wingren, Christer; Hedhammar, My

    2016-03-01

    Immobilizing biomolecules with retained functionality and stability on solid supports is crucial for generation of sensitive immunoassays. However, upon use of conventional immobilization strategies, a major portion of the biomolecules (e.g. antibodies) frequently tends to lose their bioactivity. In this study, we describe a procedure to immobilize human single-chain variable fragment (scFv) via genetic fusion to partial spider silk, which have a high tendency to adhere to solid supports. Two scFvs, directed towards serum proteins, were genetically fused to partial spider silk proteins and expressed as silk fusion proteins in E. coli. Antigen binding ability of scFvs attached to a partial silk protein denoted RC was investigated using microarray analysis, whereas scFvs fused to the NC silk variant were examined using nanoarrays. Results from micro- and nanoarrays confirmed the functionality of scFvs attached to both RC and NC silk, and also for binding of targets in crude serum. Furthermore, the same amount of added scFv gives higher signal intensity when immobilized via partial spider silk compared to when immobilized alone. Together, the results suggest that usage of scFv-silk fusion proteins in immunoassays could improve target detection, in the long run enabling novel biomarkers to be detected in crude serum proteomes. Copyright © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Depauperate genetic variability detected in the American and European bison using genomic techniques

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    Wilson Gregory A

    2009-12-01

    Full Text Available Abstract A total of 929 polymorphic SNPs in EB (out of 54, 000 SNPs screened using a BovineSNP50 Illumina Genotyping BeadChip, and 1, 524 and 1, 403 polymorphic SNPs in WB and PB, respectively, were analysed. EB, WB and PB have all undergone recent drastic reductions in population size. Accordingly, they exhibited extremely depauperate genomes, deviations from genetic equilibrium and a genome organization consisting of a mosaic of haplotype blocks: regions with low haplotype diversity and high levels of linkage disequilibrium. No evidence for positive or stabilizing selection was found in EB, WB and PB, likely reflecting drift overwhelming selection. We suggest that utilization of genome-wide screening technologies, followed by utilization of less expensive techniques (e.g. VeraCode and Fluidigm EP1, holds large potential for genetic monitoring of populations. Additionally, these techniques will allow radical improvements of breeding practices in captive or managed populations, otherwise hampered by the limited availability of polymorphic markers. This result in improved possibilities for 1 estimating genetic relationships among individuals and 2 designing breeding strategies which attempt to preserve or reduce polymorphism in ecologically relevant genes and/or entire blocks. Reviewers This article was reviewed by: Fyodor Kondrashov and Shamil Sunyaev

  5. Depauperate genetic variability detected in the American and European bison using genomic techniques

    DEFF Research Database (Denmark)

    Pertoldi, Cino; Tokarska, Magorzata; Wójcik, Jan M;

    2009-01-01

    A total of 929 polymorphic SNPs in EB (out of 54, 000 SNPs screened using a BovineSNP50 Illumina Genotyping BeadChip), and 1, 524 and 1, 403 polymorphic SNPs in WB and PB, respectively, were analysed. EB, WB and PB have all undergone recent drastic reductions in population size. Accordingly......, likely reflecting drift overwhelming selection. We suggest that utilization of genome-wide screening technologies, followed by utilization of less expensive techniques (e.g. VeraCode and Fluidigm EP1), holds large potential for genetic monitoring of populations. Additionally, these techniques will allow...

  6. Genetic variability in the natural populations of Lasioderma serricorne (F.) (Coleoptera: Anobiidae), detected by RAPD markers and by esterase isozymes.

    Science.gov (United States)

    Coelho-Bortolo, T; Mangolin, C A; Lapenta, A S

    2016-02-01

    Lasioderma serricorne (F.) is a small cosmopolitan beetle regarded as a destructive pest of several stored products such as grains, flour, spices, dried fruit and tobacco. Chemical insecticides are one of the measures used against the pest. However, intensive insecticide use has resulted in the appearance of resistant insect populations. Therefore, for the elaboration of more effective control programs, it is necessary to know the biological aspects of L. serricorne. Among these aspects, the genetic variability knowledge is very important and may help in the development of new control methods. The objective of this study was to evaluate the genetic variability of 11 natural populations of L. serricorne collected respectively in three and four towns in the states of Paraná and São Paulo, Brazil, using 20 primers random amplified polymorphic DNA (RAPD) and polymorphisms of esterases. These primers produced 352 polymorphic bands. Electrophoretic analysis of esterases allowed the identification of four polymorphic loci (Est-2, Est-4, Est-5 and Est-6) and 18 alleles. Results show that populations are genetically differentiated and there is a high level of genetic variability within populations. The high degree of genetic differentiation is not directly correlated to geographical distance. Thus, our data indicate that movement of infested commodities may contribute to the dissemination of L. serricorne, facilitating gene flow.

  7. Genetic variation in variability

    NARCIS (Netherlands)

    Mulder, Herman; Gienapp, Phillip; Visser, Marcel E.

    2016-01-01

    Variation in traits is essential for natural selection to operate and genetic and environmental effects can contribute to this phenotypic variation. From domesticated populations, we know that families can differ in their level of within-family variance, which leads to the intriguing situation th

  8. Genetic Variability Under the Seedbank Coalescent.

    Science.gov (United States)

    Blath, Jochen; González Casanova, Adrián; Eldon, Bjarki; Kurt, Noemi; Wilke-Berenguer, Maite

    2015-07-01

    We analyze patterns of genetic variability of populations in the presence of a large seedbank with the help of a new coalescent structure called the seedbank coalescent. This ancestral process appears naturally as a scaling limit of the genealogy of large populations that sustain seedbanks, if the seedbank size and individual dormancy times are of the same order as those of the active population. Mutations appear as Poisson processes on the active lineages and potentially at reduced rate also on the dormant lineages. The presence of "dormant" lineages leads to qualitatively altered times to the most recent common ancestor and nonclassical patterns of genetic diversity. To illustrate this we provide a Wright-Fisher model with a seedbank component and mutation, motivated from recent models of microbial dormancy, whose genealogy can be described by the seedbank coalescent. Based on our coalescent model, we derive recursions for the expectation and variance of the time to most recent common ancestor, number of segregating sites, pairwise differences, and singletons. Estimates (obtained by simulations) of the distributions of commonly employed distance statistics, in the presence and absence of a seedbank, are compared. The effect of a seedbank on the expected site-frequency spectrum is also investigated using simulations. Our results indicate that the presence of a large seedbank considerably alters the distribution of some distance statistics, as well as the site-frequency spectrum. Thus, one should be able to detect from genetic data the presence of a large seedbank in natural populations.

  9. Genetic variability of marine shrimp in the Brazilian industry

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    Rodrigo Maggioni

    2013-08-01

    Full Text Available The objective of this work was to estimate the genetic variability level and distribution in Brazilian broodstocks of marine shrimp (Litopenaeus vannamei. Nine of the country's largest hatcheries were evaluated using codominant and highly polymorphic microsatellite markers. The results obtained from genotyping of ten microsatellite loci are indicative of genetic variability that is compatible with that found in wild populations of L. vannamei in Mexico and Central America. A possible explanation is the highly diversified and relatively recent origin of the available broodstocks. Bayesian analysis detected a signal for five founding populations. The distribution of genetic distances partially reflects geographical location, and this information will be useful for the creation of new broodstocks. Therefore, L. vannamei genetic variability among nine of the largest national hatcheries can be considered high.

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

    African Journals Online (AJOL)

    ONOS

    2010-05-10

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

  11. Detecting lateral genetic material transfer

    CERN Document Server

    Calderón, C; Mireles, V; Miramontes, P

    2012-01-01

    The bioinformatical methods to detect lateral gene transfer events are mainly based on functional coding DNA characteristics. In this paper, we propose the use of DNA traits not depending on protein coding requirements. We introduce several semilocal variables that depend on DNA primary sequence and that reflect thermodynamic as well as physico-chemical magnitudes that are able to tell apart the genome of different organisms. After combining these variables in a neural classificator, we obtain results whose power of resolution go as far as to detect the exchange of genomic material between bacteria that are phylogenetically close.

  12. Induction of genetic variability in oat

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    Jefferson Luis Meirelles Coimbra

    2007-01-01

    Full Text Available Genetic variability in plants can be maximized through techniques of induction to make selection of genotypeswith improved adaptation to cultivation conditions possible. For oat, these techniques are important for a sustainabledevelopment through plant breeding programs in southern Brazil. The effects of mutagens (one physical: 60Co gamma raysand two chemical agents: ethyl - methanesulfonate and methyl-methanesulfonate were compared in the segregating M2 andM3 generations derived from artificial hybridization and induced mutation to compare mechanisms of widening the geneticvariability of oat. The methodologies increased the genetic variability in the trait vegetative cycle effectively, by either increasingor reducing the number of days from emergence to full heading; both can be applied in oat breeding programs.

  13. Genetic variability of Italian Heavy Draught Horse

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    Fabio Maretto

    2010-01-01

    Full Text Available This study aimed to analyze the genetic variability of the Italian Heavy Draught Horse (IHDH breed using a panel of 23 microsatellite markers. We also compared the population structure of the IHDH to other two unrelated breeds (Italian Haflinger, IH and Quarter Horse, QH. The IHDH showed a genetic variability comparable with other European heavy draught horse breeds and with the IH and QH breeds analyzed. Clustering analyses using a posterior Bayesian approach clearly differentiated the three breeds; it also showed a fragmentation of the IHDH in three subpopulations that need to be further investigated. These findings are an indicator of the present situation of the IHDH and will contribute to the conservation and implementation of the selection programme for this breed.

  14. Genetic basis of pain variability: recent advances.

    Science.gov (United States)

    Young, Erin E; Lariviere, William R; Belfer, Inna

    2012-01-01

    An estimated 15-50% of the population experiences pain at any given time, at great personal and societal cost. Pain is the most common reason patients seek medical attention, and there is a high degree of individual variability in reporting the incidence and severity of symptoms. Research suggests that pain sensitivity and risk for chronic pain are complex heritable traits of polygenic origin. Animal studies and candidate gene testing in humans have provided some progress in understanding the heritability of pain, but the application of the genome-wide association methodology offers a new tool for further elucidating the genetic contributions to normal pain responding and pain in clinical populations. Although the determination of the genetics of pain is still in its infancy, it is clear that a number of genes play a critical role in determining pain sensitivity or susceptibility to chronic pain. This review presents an update of the most recent findings that associate genetic variation with variability in pain and an overview of the candidate genes with the highest translational potential.

  15. Genetic variability in three Amazon parrot species

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    IF. Lopes

    Full Text Available Parrots of the genus Amazona are among the most threatened species of the Order Pscittaciformes. This work describes allozyme polymorphisms in three Amazon parrot species - the Blue-fronted Amazon (Amazona aestiva, the Orange-winged Amazon (Amazona amazonica, and the Festive Amazon (Amazona festiva -, and provides useful data for the evaluation of their genetic variability. We electrophoretically analyzed blood samples from 68 wild-caught individuals, maintained in captivity in three Brazilian zoos. Eight of the ten studied enzyme loci exhibited polymorphism. Glucosephosphate isomerase (Gpi proved to be a diagnostic locus for the identification of these Amazon species. The expected average heterozygosity of the Blue-fronted Amazon (0.060 differed significantly from the expected heterozygosities of the Orange-winged Amazon and the Festive Amazon (0.040 and 0.039, respectively. This result was discussed as a consequence of hybridization between two geographic A. aestiva subspecies, and alternatively as a particular trait of this species. Genetic variability of the Blue-fronted Amazon compared to birds in general is not low on a species-wide level, despite the fact that this parrot is one of the most illegally traded species. Allozyme analysis proved to be an useful tool in monitoring the genetic variation within the genus Amazona and can be applied in the management program of other threatened species of this genus.

  16. Milk metabolites and their genetic variability.

    Science.gov (United States)

    Wittenburg, D; Melzer, N; Willmitzer, L; Lisec, J; Kesting, U; Reinsch, N; Repsilber, D

    2013-04-01

    The composition of milk is crucial to evaluate milk performance and quality measures. Milk components partly contribute to breeding scores, and they can be assessed to judge metabolic and energy status of the cow as well as to serve as predictive markers for diseases. In addition to the milk composition measures (e.g., fat, protein, lactose) traditionally recorded during milk performance test via infrared spectroscopy, novel techniques, such as gas chromatography-mass spectrometry, allow for a further analysis of milk into its metabolic components. Gas chromatography-mass spectrometry is suitable for measuring several hundred metabolites with high throughput, and thus it is applicable to study sources of genetic and nongenetic variation of milk metabolites in dairy cows. Heritability and mode of inheritance of metabolite measurements were studied in a linear mixed model approach including expected (pedigree) and realized (genomic) relationship between animals. The genetic variability of 190 milk metabolite intensities was analyzed from 1,295 cows held on 18 farms in Mecklenburg-Western Pomerania, Germany. Besides extensive pedigree information, genotypic data comprising 37,180 single nucleotide polymorphism markers were available. Goodness of fit and significance of genetic variance components based on likelihood ratio tests were investigated with a full model, including marker- and pedigree-based genetic effects. Broad-sense heritability varied from zero to 0.699, with a median of 0.125. Significant additive genetic variance was observed for highly heritable metabolites, but dominance variance was not significantly present. As some metabolites are particularly favorable for human nutrition, for instance, future research should address the identification of locus-specific genetic effects and investigate metabolites as the molecular basis of traditional milk performance test traits.

  17. Genetic variability of sorghum landraces from lower Eastern Kenya ...

    African Journals Online (AJOL)

    Reuben M. Muasya

    2016-02-24

    Feb 24, 2016 ... Key words: Genetic variability, landraces, simple sequence repeats, sorghum. ... determining the fate of new genetic combinations from ..... Systematics and evolution of Sorghum Sect. ... Farm Management Handbook of Kenya, ... environment for genetic marker analysis. ... Introduction to population biology.

  18. Genetic variability of Euglena agilis (Euglenophyceae

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    Bożena Zakryś

    2011-01-01

    Full Text Available The results of the internal transcribed spacer (ITS2 of extrachromosomal rDNA and the chloroplast SSU rDNA sequence analysis presented here confirmed elevated genetic polymorphism revealed earlier by RFLP and RAPD for seven clones of the cosmopolitan species - Euglena agilis Carter. High diversity among these clonal strains was not reflected by morphological criteria, with the exception of the only one character - the ability of the cell in its non-motile dividing states (palmella to produce mucus and form a slimy envelope. Evolutionary adaptation as formation of slimy envelope may be attributed to different survival strategy of the species by which it adapts to life in a highly variable environment.

  19. Genetic variability of broodstocks of restocking programs in Brazil

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    Nelson Lopera-Barrero

    2015-09-01

    Full Text Available Objective. The aim of this study was evaluate the genetic diversity of the following broodstocks: piapara (Leporinus elongatus, dourado (Salminus brasiliensis, jundiá (Rhamdia quelen and cachara (Pseudoplatystoma fasciatum already useful for restocking programs in the Paranapanema, Iguaçu and Paraná Brazilian Rivers. Materials and methods. Samples from the caudal fin of 122 fish were analyzed. DNA was extracted by NaCl protocol. PCR products were separated by a horizontal agarose gel electrophoresis. The fragments were visualized by staining with ethidium bromide. Results. The amplification of 25 primers generated different fragments in studied species that allowed characterizing 440 fragments of 100-2900 bp. High percentage of polymorphic fragments (66.67 to 86.29, Shannon index (0.365 to 0.486 and genetic diversity of Nei (0.248 to 0.331 were detected. Conclusions. The level of genetic variability in the broodstocks was adequate for allowing their use in restocking programs in the studied Rivers. However, periodical monitoring studies of genetic variability in these stocks, the mating system, reproductive system and general management must be made to guarantee the preservation of wild populations.

  20. TMTI Task 1.6 Genetic Engineering Methods and Detection

    Energy Technology Data Exchange (ETDEWEB)

    Slezak, T; Lenhoff, R; Allen, J; Borucki, M; Vitalis, E; Gardner, S

    2009-12-04

    A large number of GE techniques can be adapted from other microorganisms to biothreat bacteria and viruses. Detection of GE in a microorganism increases in difficulty as the size of the genetic change decreases. In addition to the size of the engineered change, the consensus genomic sequence of the microorganism can impact the difficulty of detecting an engineered change in genomes that are highly variable from strain to strain. This problem will require comprehensive databases of whole genome sequences for more genetically variable biothreat bacteria and viruses. Preliminary work with microarrays for detecting synthetic elements or virulence genes and analytic bioinformatic approaches for whole genome sequence comparison to detect genetic engineering show promise for attacking this difficult problem but a large amount of future work remains.

  1. Next-generation genomic shotgun sequencing indicates greater genetic variability in the mitochondria of Hypophthalmichthys molitrix relative to H. nobilis from the Mississippi River, USA and provides tools for research and detection

    Science.gov (United States)

    Miller, John J; Eackles, Michael S.; Stauffer, Jay R; King, Timothy L.

    2015-01-01

    We characterized variation within the mitochondrial genomes of the invasive silver carp (Hypophthalmichthys molitrix) and bighead carp (H. nobilis) from the Mississippi River drainage by mapping our Next-Generation sequences to their publicly available genomes. Variant detection resulted in 338 single-nucleotide polymorphisms for H. molitrix and 39 for H. nobilis. The much greater genetic variation in H. molitrix mitochondria relative to H. nobilis may be indicative of a greater North American female effective population size of the former. When variation was quantified by gene, many tRNA loci appear to have little or no variability based on our results whereas protein-coding regions were more frequently polymorphic. These results provide biologists with additional regions of DNA to be used as markers to study the invasion dynamics of these species.

  2. [Phenotypic variability of the 1q21.1 microdeletion syndrome in members of the same family: relevance of detection of neuropsychiatric disorders for diagnosis of genetic syndromes].

    Science.gov (United States)

    Natera-De Benito, Daniel; Vidal-Esteban, Arantxa; Sanchez-Del Pozo, Jaime; Moreno-Garcia, Marta; Suela-Rubio, Javier; Cruz-Rojo, Jaime; Rivero-Martin, María José

    2015-12-16

    Introduccion. El sindrome de microdelecion 1q21.1 esta causado por una delecion recurrente de aproximadamente 800 kb que incluye al menos siete genes y se asocia a un fenotipo variable. Esta variacion en el numero de copias patogenica puede aparecer de novo o ser heredada de uno de los progenitores. La presencia de trastornos psiquiatricos se ha descrito en muchos de los casos publicados, pero se desconoce su prevalencia exacta. Objetivo. Exponer la variabilidad fenotipica de los individuos que presentan una microdelecion 1q21.1. Casos clinicos. Se incluyen cuatro individuos portadores de una delecion de 1,74 Mb en 1q21.1, todos miembros de la misma familia. El estudio genetico del caso indice se llevo a cabo mediante array de hibridacion genomica comparada, y el del resto de familiares mediante hibridacion in situ fluorescente, con una sonda especifica para la region delecionada. Los individuos presentan un fenotipo heterogeneo, y es comun a todos ellos la presencia de alteraciones psiquiatricas o del comportamiento, con un claro predominio de la presencia de trastornos relacionados con las dificultades para el control de impulsos en sus diferentes subtipos. Conclusiones. El sindrome de microdelecion 1q21.1 es fenotipicamente heterogeneo, incluso entre los miembros de una misma familia. Destaca la presencia de alteraciones psiquiatricas o del comportamiento como rasgo comun en todos los pacientes que presentamos. Existen formas paucisintomaticas en las que el individuo portador de la delecion presenta exclusivamente alteraciones psiquiatricas.

  3. Molecular analysis of RAPD DNA based markers: their potential use for the detection of genetic variability in jojoba (Simmondsia chinensis L Schneider).

    Science.gov (United States)

    Amarger, V; Mercier, L

    1995-01-01

    We have applied the recently developed technique of random amplified polymorphic DNA (RAPD) for the discrimination between two jojoba clones at the genomic level. Among a set of 30 primers tested, a simple reproducible pattern with three distinct fragments for clone D and two distinct fragments for clone E was obtained with primer OPB08. Since RAPD products are the results of arbitrarily priming events and because a given primer can amplify a number of non-homologous sequences, we wondered whether or not RAPD bands, even those of similar size, were derived from different loci in the two clones. To answer this question, two complementary approaches were used: i) cloning and sequencing of the amplification products from clone E; and ii) complementary Southern analysis of RAPD gels using cloned or amplified fragments (directly recovered from agarose gels) as RFLP probes. The data reported here show that the RAPD reaction generates multiple amplified fragments. Some fragments, although resolved as a single band on agarose gels, contain different DNA species of the same size. Furthermore, it appears that the cloned RAPD products of known sequence that do not target repetitive DNA can be used as hybridization probes in RFLP to detect a polymorphism among individuals.

  4. Genetic variability among Andrographis paniculata in Chhattisgarh ...

    African Journals Online (AJOL)

    Preeti minz

    2013-09-25

    Sep 25, 2013 ... 2 Department of Bio and Nano Technology, Guru Jambheshwar University of Science &Technology, Hisar ... Genetic tools that use hybridization, polymerase chain ... based molecular markers have been found to be useful in.

  5. Variable selection based cotton bollworm odor spectroscopic detection

    Science.gov (United States)

    Lü, Chengxu; Gai, Shasha; Luo, Min; Zhao, Bo

    2016-10-01

    Aiming at rapid automatic pest detection based efficient and targeting pesticide application and shooting the trouble of reflectance spectral signal covered and attenuated by the solid plant, the possibility of near infrared spectroscopy (NIRS) detection on cotton bollworm odor is studied. Three cotton bollworm odor samples and 3 blank air gas samples were prepared. Different concentrations of cotton bollworm odor were prepared by mixing the above gas samples, resulting a calibration group of 62 samples and a validation group of 31 samples. Spectral collection system includes light source, optical fiber, sample chamber, spectrometer. Spectra were pretreated by baseline correction, modeled with partial least squares (PLS), and optimized by genetic algorithm (GA) and competitive adaptive reweighted sampling (CARS). Minor counts differences are found among spectra of different cotton bollworm odor concentrations. PLS model of all the variables was built presenting RMSEV of 14 and RV2 of 0.89, its theory basis is insect volatilizes specific odor, including pheromone and allelochemics, which are used for intra-specific and inter-specific communication and could be detected by NIR spectroscopy. 28 sensitive variables are selected by GA, presenting the model performance of RMSEV of 14 and RV2 of 0.90. Comparably, 8 sensitive variables are selected by CARS, presenting the model performance of RMSEV of 13 and RV2 of 0.92. CARS model employs only 1.5% variables presenting smaller error than that of all variable. Odor gas based NIR technique shows the potential for cotton bollworm detection.

  6. STUDY OF GENETIC VARIABILITY OF TRITICALE VARIETIES BY SSR MARKERS

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    Jana Ondroušková

    2013-04-01

    Full Text Available For the detection of genetic variability ten genotypes of winter triticale (×Triticosecale Wittmack, 2n = 6x = 42; BBAARR were selected: nine varieties and one breeding line with good bread-making quality KM 4-09 with the chromosome translocation 1R.1D 5+10-2. 25 microsatellites markers located in the genome A, B, D and R were chosen for analysis. Eighty-four alleles were detected with an average of 3.36 alleles per locus were detected. For each microsatellite statistical values were calculated diversity index (DI, probabilities of identity (PI and polymorphic information content (PIC were calculated and averages statistical values are: DI 0.55, PI 0.27 and 0.5 PIC. Overall dendrogram based on the UPGMA method (Jaccards similarity coefficient significantly distinguished two groups of genotypes and these groups were divided into sub-clusters. A set of 5 SSR markers (Xwms0752, Xbarc128, Xrems1237, Xwms0861 and Xbrac170 which have the calculated PIC value higher than 0.68 that are sufficient for the identification of the analyzed genotypes was described.

  7. Genetics Home Reference: common variable immune deficiency

    Science.gov (United States)

    ... or Free article on PubMed Central Park JH, Resnick ES, Cunningham-Rundles C. Perspectives on common variable ... on PubMed or Free article on PubMed Central Resnick ES, Cunningham-Rundles C. The many faces of ...

  8. Adaptive Genetic Algorithm Model for Intrusion Detection

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    K. S. Anil Kumar

    2012-09-01

    Full Text Available Intrusion detection systems are intelligent systems designed to identify and prevent the misuse of computer networks and systems. Various approaches to Intrusion Detection are currently being used, but they are relatively ineffective. Thus the emerging network security systems need be part of the life system and this ispossible only by embedding knowledge into the network. The Adaptive Genetic Algorithm Model - IDS comprising of K-Means clustering Algorithm, Genetic Algorithm and Neural Network techniques. Thetechnique is tested using multitude of background knowledge sets in DARPA network traffic datasets.

  9. Using genetic programming to discover nonlinear variable interactions.

    Science.gov (United States)

    Westbury, Chris; Buchanan, Lori; Sanderson, Michael; Rhemtulla, Mijke; Phillips, Leah

    2003-05-01

    Psychology has to deal with many interacting variables. The analyses usually used to uncover such relationships have many constraints that limit their utility. We briefly discuss these and describe recent work that uses genetic programming to evolve equations to combine variables in nonlinear ways in a number of different domains. We focus on four studies of interactions from lexical access experiments and psychometric problems. In all cases, genetic programming described nonlinear combinations of items in a manner that was subsequently independently verified. We discuss the general implications of genetic programming and related computational methods for multivariate problems in psychology.

  10. Genetic fidelity and variability of micropropagated cassava plants (Manihot esculenta Crantz) evaluated using ISSR markers.

    Science.gov (United States)

    Vidal, Á M; Vieira, L J; Ferreira, C F; Souza, F V D; Souza, A S; Ledo, C A S

    2015-07-14

    Molecular markers are efficient for assessing the genetic fidelity of various species of plants after in vitro culture. In this study, we evaluated the genetic fidelity and variability of micropropagated cassava plants (Manihot esculenta Crantz) using inter-simple sequence repeat markers. Twenty-two cassava accessions from the Embrapa Cassava & Fruits Germplasm Bank were used. For each accession, DNA was extracted from a plant maintained in the field and from 3 plants grown in vitro. For DNA amplification, 27 inter-simple sequence repeat primers were used, of which 24 generated 175 bands; 100 of those bands were polymorphic and were used to study genetic variability among accessions of cassava plants maintained in the field. Based on the genetic distance matrix calculated using the arithmetic complement of the Jaccard's index, genotypes were clustered using the unweighted pair group method using arithmetic averages. The number of bands per primer was 2-13, with an average of 7.3. For most micropropagated accessions, the fidelity study showed no genetic variation between plants of the same accessions maintained in the field and those maintained in vitro, confirming the high genetic fidelity of the micropropagated plants. However, genetic variability was observed among different accessions grown in the field, and clustering based on the dissimilarity matrix revealed 7 groups. Inter-simple sequence repeat markers were efficient for detecting the genetic homogeneity of cassava plants derived from meristem culture, demonstrating the reliability of this propagation system.

  11. Drowsiness detection using heart rate variability.

    Science.gov (United States)

    Vicente, José; Laguna, Pablo; Bartra, Ariadna; Bailón, Raquel

    2016-06-01

    It is estimated that 10-30 % of road fatalities are related to drowsy driving. Driver's drowsiness detection based on biological and vehicle signals is being studied in preventive car safety. Autonomous nervous system activity, which can be measured noninvasively from the heart rate variability (HRV) signal obtained from surface electrocardiogram, presents alterations during stress, extreme fatigue and drowsiness episodes. We hypothesized that these alterations manifest on HRV and thus could be used to detect driver's drowsiness. We analyzed three driving databases in which drivers presented different sleep-deprivation levels, and in which each driving minute was annotated as drowsy or awake. We developed two different drowsiness detectors based on HRV. While the drowsiness episodes detector assessed each minute of driving as "awake" or "drowsy" with seven HRV derived features (positive predictive value 0.96, sensitivity 0.59, specificity 0.98 on 3475 min of driving), the sleep-deprivation detector discerned if a driver was suitable for driving or not, at driving onset, as function of his sleep-deprivation state. Sleep-deprivation state was estimated from the first three minutes of driving using only one HRV feature (positive predictive value 0.80, sensitivity 0.62, specificity 0.88 on 30 drivers). Incorporating drowsiness assessment based on HRV signal may add significant improvements to existing car safety systems.

  12. Genetic variability for tuber yield, quality, and virus disease complex ...

    African Journals Online (AJOL)

    Genetic variability for tuber yield, quality, and virus disease complex traits in Uganda ... Silk and Sowola which showed high flowering ability failed to fertilise and set ... Up to five genes may be involved in â-carotene synthesis and probably in ...

  13. Genetic variability assessment in the genus Passiflora by SSR markers

    Directory of Open Access Journals (Sweden)

    Claudia Lougon Paiva

    2014-09-01

    Full Text Available The genus Passiflora encompasses many species that are endemic to the Brazilian territory, including some with economic value. Studies on genetic diversity in this genus are fundamental because they allow understanding genetic variability and distance. The present study aimed to determine the genetic variability and distances among 10 species of the genus Passiflora by using microsatellite markers (Simple Sequence Repeat, SSR. Twenty-eight heterologous microsatellite markers were tested, but only 12 were used in the diversity analysis because they amplified in at least 80% of the species. A clear separation was observed among the subgenuses studied, as well as wide variation among the accessions of Passiflora. This knowledge enables breeders to explore diversity and transfer favorable alleles found in wild species.

  14. Loss of genetic variability at the transferrin locus in five hatchery stocks of tambaqui (Colossoma macropomum

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    Calcagnotto Daniela

    2000-01-01

    Full Text Available Knowledge and conservation of the genetic variability in stocks maintained as live gene banks have become a high priority task for Brazilian fish culture. The aim of the present survey was to assess the transferrin allelic diversity of five hatchery stocks of tambaqui (Colossoma macropomum. The tambaqui stock from Pentecoste, the oldest maintained in Brazilian hatchery stations, retained three of the six alleles detected in wild populations of tambaqui from the Amazon River. Other hatchery stocks, directly or indirectly derived from the Pentecoste stock, did not show transferrin allelic variability. Insufficient number of founders and genetic drift due to sampling errors seem to be the main causes leading to loss of genetic diversity in tambaqui hatchery stocks. Appropriate management strategies are required in order to improve the genetic potential of tambaqui stocks in Brazil.

  15. Constraints on the Genetic and Antigenic Variability of Measles Virus.

    Science.gov (United States)

    Beaty, Shannon M; Lee, Benhur

    2016-04-21

    Antigenic drift and genetic variation are significantly constrained in measles virus (MeV). Genetic stability of MeV is exceptionally high, both in the lab and in the field, and few regions of the genome allow for rapid genetic change. The regions of the genome that are more tolerant of mutations (i.e., the untranslated regions and certain domains within the N, C, V, P, and M proteins) indicate genetic plasticity or structural flexibility in the encoded proteins. Our analysis reveals that strong constraints in the envelope proteins (F and H) allow for a single serotype despite known antigenic differences among its 24 genotypes. This review describes some of the many variables that limit the evolutionary rate of MeV. The high genomic stability of MeV appears to be a shared property of the Paramyxovirinae, suggesting a common mechanism that biologically restricts the rate of mutation.

  16. Genetic influence on inflammation variables in the elderly

    DEFF Research Database (Denmark)

    de Maat, Moniek P M; Bladbjerg, Else Marie; Hjelmborg, Jacob v. B.

    2004-01-01

    BACKGROUND: Inflammation variables (C-reactive protein [CRP], fibrinogen, and soluble intercellular adhesion molecule-1 [sICAM-1]) have been identified as risk factors for cardiovascular disease. It is still not known how much the regulation of inflammatory risk factors is determined by genetic...... factors, and the aim of this study was to determine the heritability of these inflammation variables and of the acute phase regulating cytokines interleukin-6 (IL-6) and tumor necrosis factor-alpha (TNF-alpha) at older ages. METHODS AND RESULTS: The heritability of CRP, fibrinogen, sICAM-1, IL-6, and TNF...... factors accounted for 20% to 55% of the variation in plasma levels of the inflammation variables. The highest heritability was found for sICAM-1. The genetic polymorphisms we studied explained only a small, insignificant part of the heritability. CONCLUSIONS: This study in elderly twins provides evidence...

  17. Genetic variability of grey snow mould (Typhula incarnata).

    Science.gov (United States)

    Vergara, Georgina V; Bughrara, Suleiman S; Jung, Geunhwa

    2004-11-01

    Randomly amplified polymorphic DNA (RAPD) markers were used to assess the genetic diversity of isolates of grey snow mould ('gray snow mold'), Typhula incarnata, taken from infected turfgrasses from 40 different locations in the northern USA. Data from 115 markers using 37 RAPD primers showed 48 % polymorphism. The distance coefficients between isolates indicate the wide genetic diversity of T. incarnata across the sample area. Dendrograms generated using neighbour-joining (NJ) bootstrap analyses showed three clades and suggest possible recent colonization from common founder groups. Partitioning of the genetic variance using analysis of molecular variance (AMOVA) of four groups based on geographic locations (Michigan, lower and upper peninsula; Minnesota; Wisconsin) showed that genetic variation attributable among groups and within groups was 12.67 and 87.33 %, respectively. No correlation was found between geographic distance and pairwise genetic distance of the groups. High outcrossing and sexual recombination of T. incarnata may well be key factors explaining the genetic variability as shown with the low Fixation index (FST) and high average of genetic diversity per locus within groups.

  18. Transfer of intracolonial genetic variability through gametes in Acropora hyacinthus corals

    Science.gov (United States)

    Schweinsberg, M.; González Pech, R. A.; Tollrian, R.; Lampert, K. P.

    2014-03-01

    In recent years, the new phenomenon of intracolonial genetic variability within a single coral colony has been described. This connotes that coral colonies do not necessarily consist of only a single genotype, but may contain several distinct genotypes. Harboring more than one genotype could improve survival under stressful environmental conditions, e.g., climate change. However, so far it remained unclear whether the intracolonial genetic variability of the adult coral is also present in the gametes. We investigated the occurrence of intracolonial genetic variability in 14 mature colonies of the coral Acropora hyacinthus using eight microsatellite loci. A grid was placed over each colony before spawning, and the emerging egg/sperm bundles were collected separately in each grid. The underlying tissues as well as the egg/sperm bundles were genotyped to determine whether different genotypes were present. Within the 14 mature colonies, we detected 10 colonies with more than one genotype (intracolonial genetic variability). Four out of these 10 mature colonies showed a transfer of different genotypes via the eggs to the next generation. In two out of these four cases, we found additional alleles, and in the two other cases, we found only a subset of alleles in the unfertilized eggs. Our results suggest that during reproduction of A. hyacinthus, more than one genotype per colony is able to reproduce. We discuss the occurrence of different genotypes within a single coral colony and the ability for those to release eggs which are genetically distinct.

  19. Genetic variability in five species of Anostomidae (Ostariophysi - Characiformes

    Directory of Open Access Journals (Sweden)

    Chiari Lucimara

    1999-01-01

    Full Text Available Genetic variability was studied in five fish species (Anostomidae: Schizodon intermedius and S. nasutus and Leporinus friderici, L. elongatus and L. obtusidens, collected at one location on the Tibagi River (Paraná, Brazil. The protein data from seven systems coded collectively for 19 loci in the liver, muscle and heart. Nine of these loci were polymorphic. The estimated proportion of polymorphism loci ( varied from 16.7% in S. intermedius to 36.9% in L. friderici; the mean heterozygosity observed (o was 0.027 ± 0.015 and 0.109 ± 0.042, respectively. The estimated value of the genetic identity among L. friderici and S. intermedius (0.749 and S. nasutus (0.787 suggested that these are "congeneric" species. Morphological characteristics indicate that these species belong to distinct genera, while isoenzymatic data show that they are very similar at the genetic/biochemical level.

  20. Genetic variations involved in interindividual variability in carotenoid status.

    OpenAIRE

    Borel, Patrick

    2012-01-01

    International audience; As shown in most clinical studies dedicated to carotenoids, there is a huge interindividual variability in absorption, and blood and tissue responses, of dietary carotenoids. The recent discovery that several proteins are involved in carotenoid metabolism in humans has prompted a possible explanation for this phenomenon: genetic variants in genes encoding for these proteins may affect their expression or activity, and in turn carotenoid metabolism and carotenoid status...

  1. Assessment of genetic and chemical variability in Thymus caramanicus.

    Science.gov (United States)

    Hadian, Javad; Bigdeloo, Mahdi; Nazeri, Vahideh; Khadivi-Khub, Abdollah

    2014-05-01

    Thymus caramanicus is an endemic species grown in Iran with interesting pharmacological and biological properties. In the present work, essential oil compositions and inter-simple sequences repeat (ISSR) markers were used to estimate the relationships among and within seven populations of T. caramanicus, belonging to three provinces in Iran. The studied individuals were distinguished on the basis of ISSR markers and constituents of essential oil. A total of 127 band positions were produced by 12 ISSR primers, of which 105 were found polymorphic with 82.68% polymorphism. Genetic similarity values among individuals ranged between 0.15 and 0.82 which was indicative of a high level of genetic variation. On the basis of their genetic similarities, ISSR analysis allowed to group the samples into two main clusters. One of these included populations originated from Kerman and Isfahan provinces, and the other cluster consists of populations from Semnan province. Chemical compounds of essential oils were found variable in the various individuals and all samples were principally composed of phenolic constituents (carvacrol and/or thymol). As a consequence, the plants were classified into two major chemotypes including carvacrol and thymol/carvacrol. A relationship between genetic and chemical variability and geographic distribution has been observed in studied populations of T. caramanicus.

  2. FUS and TDP43 genetic variability in FTD and CBS.

    Science.gov (United States)

    Huey, Edward D; Ferrari, Raffaele; Moreno, Jorge H; Jensen, Christopher; Morris, Christopher M; Potocnik, Felix; Kalaria, Rajesh N; Tierney, Michael; Wassermann, Eric M; Hardy, John; Grafman, Jordan; Momeni, Parastoo

    2012-05-01

    This study aimed to evaluate genetic variability in the FUS and TDP-43 genes, known to be mainly associated with amyotrophic lateral sclerosis (ALS), in patients with the diagnoses of frontotemporal lobar degeneration (FTLD) and corticobasal syndrome (CBS). We screened the DNA of 228 patients for all the exons and flanking introns of FUS and TDP-43 genes. We identified 2 novel heterozygous missense mutations in FUS: P106L (g.22508384C>T) in a patient with behavioral variant frontotemporal dementia (bvFTD) and Q179H in several members of a family with behavioral variant FTD. We also identified the N267S mutation in TDP-43 in a CBS patient, previously only reported in 1 ALS family and 1 FTD patient. Additionally, we identified 2 previously reported heterozygous insertion and deletion mutations in Exon 5 of FUS; Gly174-Gly175 del GG (g. 4180-4185 delGAGGTG) in an FTD patient and Gly175-Gly176 ins GG (g. 4185-4186 insGAGGTG) in a patient with diagnosis of CBS. Not least, we have found a series of variants in FUS also in neurologically normal controls. In summary, we report that genetic variability in FUS and TDP-43 encompasses a wide range of phenotypes (including ALS, FTD, and CBS) and that there is substantial genetic variability in FUS gene in neurologically normal controls. Copyright © 2012 Elsevier Inc. All rights reserved.

  3. Detection methods and performance criteria for genetically modified organisms.

    Science.gov (United States)

    Bertheau, Yves; Diolez, Annick; Kobilinsky, André; Magin, Kimberly

    2002-01-01

    Detection methods for genetically modified organisms (GMOs) are necessary for many applications, from seed purity assessment to compliance of food labeling in several countries. Numerous analytical methods are currently used or under development to support these needs. The currently used methods are bioassays and protein- and DNA-based detection protocols. To avoid discrepancy of results between such largely different methods and, for instance, the potential resulting legal actions, compatibility of the methods is urgently needed. Performance criteria of methods allow evaluation against a common standard. The more-common performance criteria for detection methods are precision, accuracy, sensitivity, and specificity, which together specifically address other terms used to describe the performance of a method, such as applicability, selectivity, calibration, trueness, precision, recovery, operating range, limit of quantitation, limit of detection, and ruggedness. Performance criteria should provide objective tools to accept or reject specific methods, to validate them, to ensure compatibility between validated methods, and be used on a routine basis to reject data outside an acceptable range of variability. When selecting a method of detection, it is also important to consider its applicability, its field of applications, and its limitations, by including factors such as its ability to detect the target analyte in a given matrix, the duration of the analyses, its cost effectiveness, and the necessary sample sizes for testing. Thus, the current GMO detection methods should be evaluated against a common set of performance criteria.

  4. Variabilidade genética da raça Brahman no Brasil detectada por meio de análise de pedigree Genetic variability detection in Brahman cattle in Brazil trough pedigree analysis

    Directory of Open Access Journals (Sweden)

    Lydio Cosac de Faria

    2010-10-01

    Full Text Available O objetivo deste trabalho foi analisar a variabilidade genética da raça Brahman no Brasil, por meio da análise de 15.851 pedigrees. O arquivo de dados foi dividido em dois períodos: 1998-2001 e 2002-2005. A variabilidade genética foi avaliada por parâmetros baseados na probabilidade de origem do gene: número efetivo de ancestrais, número efetivo de fundadores, número efetivo de genomas remanescentes e coeficientes de parentesco e de endogamia. Os valores encontrados quanto ao número de fundadores mostraram que a população está em expansão, embora o número efetivo de fundadores tenha diminuído de um período para outro. Os resultados foram diferentes em relação ao número de ancestrais e genomas remanescentes, que apresentaram crescimento de 23% nos períodos avaliados. O coeficiente de endogamia diminuiu nos períodos estudados, porém o coeficiente de parentesco "inter se" cresceu. Poucos ancestrais apresentaram grande contribuição genética para a população, o que evidencia a utilização de poucos indivíduos na reprodução. A raça Brahman, no Brasil, encontra-se em expansão, caracterizada pela diminuição do coeficiente de endogamia e aumento nos números efetivos de fundadores e de genótipos remanescentes. Entretanto, a variabilidade genética da raça mostra aumento do parentesco "inter se" e grande concentração do patrimônio genético de poucos indivíduos na população.This work aimed to analyse the genetic variability of Brahman breed in Brazil, through the analysis of 15,851 pedigrees. The data file was divided into two periods: 1998-2001 and 2002-2005. The genetic variability was evaluated by the following parameters, based on the probability of gene origin: number of ancestors, effective number of founders, effective number of remaining genomes, and the relationship and inbreeding coefficients. The values for the number of founders showed that the population is expanding, although the effective number

  5. VARIABILITY AND GENETIC STRUCTURE IN A COMMERCIAL FIELD OF TEQUILA PLANTS, Agave tequilana WEBER (AGAVACEAE

    Directory of Open Access Journals (Sweden)

    Martha Isabel Torres-Moran

    2013-01-01

    Full Text Available Crops of the tequila plant (Agave tequilana are produced mainly from offshoots of mother plants in established commercial fields. This propagation method is significant, as it is believed that it facilitates the spread of disease because of the crop’s low genetic variability and is also necessary because it is regulate the use of just that variety in tequila industry. Different levels of genetic variability have been reported for A. tequilana and so we tested individuals from representative cultivation zones to determine the actual variability in fields and to assess the genetic structure of populations in commercial plantations. Four additional Agave spp. were used as a control group while Fourcrea spp. individuals were used as an external group. Morphological traits and molecular markers were analyzed. The differences between A. tequilana individuals collected from southern Jalisco state and those collected in the principal Denomination of Origin zone confirmed the existence of different genotypes, which were conserved in different regions by asexual propagation. Leaf length, plant height and number of leaves were the most significant variables that explained the variability within the A. tequilana group. At the molecular level, we found genetic differentiation with a minimum similarity of 0.253 (Jaccard’s coefficient and genetic structure analysis indicated five groups with significant genotypic differences. Genetic structure analysis, grouped accessions according to the dispersion of plant material from the initial sites of cultivation. These results might facilitate the correlation of different groups with crop yield or tequila quality and the establishment of elite lines for breeding programs. It is recommendable in a future, to determinate the different levels of inulines produced by each detected group.

  6. Does beekeeping reduce genetic variability in Melipona scutellaris (Apidae, Meliponini)?

    Science.gov (United States)

    Carvalho-Zilse, G A; Costa-Pinto, M F F; Nunes-Silva, C G; Kerr, W E

    2009-06-30

    Many factors have contributed to reductions in wild populations of stingless bees, such as: deforestation, displacement and destruction of nests by honey gatherers, as well as use of insecticides and other agrochemicals. All of these can potentially affect the populational structure of native species. We analyzed genetic variability and populational structure of Melipona scutellaris, based on five microsatellite loci, using heterologous primers of M. bicolor. Samples were taken from 43 meliponaries distributed among 30 sites of four northeastern states of Brazil (Pernambuco, Alagoas, Sergipe, and Bahia). Thirty-one alleles were found to be well distributed among the populations, with sizes ranging from 85 to 146 bp. In general, there was a variable distribution and frequency of alleles among populations, with either exclusive and/or fixed alleles at some sites. The population of Pernambuco was the most polymorphic, followed by Bahia, Alagoas and Sergipe. The heterozygosity was Ho = 0.36 on average, much lower than what has been reported for M. bicolor (Ho = 0.65). Most populations were not under Hardy-Weinberg equilibrium. We found a higher variation within rather than among populations, indicating no genetic structuring in those bees maintained in meliponaries. This apparent homogenization may be due to intense beekeeping activity, including exchange of genetic material among beekeepers. Based on our findings, we recommend more studies of meliponaries and of wild populations in order to help orient management and conservation of these native pollinators.

  7. Genetic variability of six French meat sheep breeds in relation to their genetic management

    Directory of Open Access Journals (Sweden)

    Coralie Danchin-Burge

    2003-11-01

    Full Text Available Abstract Some demographic parameters, the genetic structure and the evolution of the genetic variability of six French meat sheep breeds were analysed in relation with their management. Four of these breeds are submitted to more or less intense selection: the Berrichon du Cher (BCH, Blanc du Massif Central (BMC, Charollais (CHA and Limousin (LIM; the other two breeds are under conservation: the Roussin de La Hague (RLH and Solognot (SOL. Genealogical data of the recorded animals born from 1970 to 2000 and of their known ancestors were used. The most balanced contributions of the different flocks to the sire-daughter path was found in the SOL. In the BCH, a single flock provided 43% of the sire-AI sire path, whereas the contributions of the flocks were more balanced in the BMC and LIM (the only other breeds where AI is used to a substantial amount. The distribution of the expected genetic contribution of the founder animals was found to be unbalanced, especially in the BCH and LIM. The effective numbers of ancestors (founders or not for the ewes born from 1996 to 2000 were equal to 35 (BCH, 144 (BMC, 112 (CHA, 69 (LIM, 40 (RLH and 49 (SOL. Inbreeding was not analysed in the BMC, due to incomplete pedigree information. From 1980 on, the rates of inbreeding, in percentage points per year, were +0.112 (BCH, +0.045 (CHA, +0.036 (LIM, +0.098 (RLH and +0.062 (SOL. The implications of the observed trends on genetic variability are discussed in relation to the genetic management of each breed. The need for a larger selection basis in the BCH, the efficiency of the rules applied in the SOL to preserve the genetic variability and the need for a more collective organisation in the CHA and RLH are outlined.

  8. Genetic Variability in Susceptibility to Occupational Respiratory Sensitization

    Directory of Open Access Journals (Sweden)

    Berran Yucesoy

    2011-01-01

    Full Text Available Respiratory sensitization can be caused by a variety of substances at workplaces, and the health and economic burden linked to allergic respiratory diseases continues to increase. Although the main factors that affect the onset of the symptoms are the types and intensity of allergen exposure, there is a wide range of interindividual variation in susceptibility to occupational/environmental sensitizers. A number of gene variants have been reported to be associated with various occupational allergic respiratory diseases. Examples of genes include, but are not limited to, genes involved in immune/inflammatory regulation, antioxidant defenses, and fibrotic processes. Most of these variants act in combination with other genes and environmental factors to modify disease progression, severity, or resolution after exposure to allergens. Therefore, understanding the role of genetic variability and the interaction between genetic and environmental/occupational factors provides new insights into disease etiology and may lead to the development of novel preventive and therapeutic strategies. This paper will focus on the current state of knowledge regarding genetic influences on allergic respiratory diseases, with specific emphasis on diisocyanate-induced asthma and chronic beryllium disease.

  9. Multi-taxa integrated landscape genetics for zoonotic infectious diseases: deciphering variables influencing disease emergence.

    Science.gov (United States)

    Leo, Sarah S T; Gonzalez, Andrew; Millien, Virginie

    2016-05-01

    Zoonotic disease transmission systems involve sets of species interacting with each other and their environment. This complexity impedes development of disease monitoring and control programs that require reliable identification of spatial and biotic variables and mechanisms facilitating disease emergence. To overcome this difficulty, we propose a framework that simultaneously examines all species involved in disease emergence by integrating concepts and methods from population genetics, landscape ecology, and spatial statistics. Multi-taxa integrated landscape genetics (MTILG) can reveal how interspecific interactions and landscape variables influence disease emergence patterns. We test the potential of our MTILG-based framework by modelling the emergence of a disease system across multiple species dispersal, interspecific interaction, and landscape scenarios. Our simulations showed that both interspecific-dependent dispersal patterns and landscape characteristics significantly influenced disease spread. Using our framework, we were able to detect statistically similar inter-population genetic differences and highly correlated spatial genetic patterns that imply species-dependent dispersal. Additionally, species that were assigned coupled-dispersal patterns were affected to the same degree by similar landscape variables. This study underlines the importance of an integrated approach to investigating emergence of disease systems. MTILG is a robust approach for such studies and can identify potential avenues for targeted disease management strategies.

  10. Genetic Variability and Microdistribution of Triatoma infestans Genotypes and Trypanosoma cruzi Clones in Arequipa Region (Peru

    Directory of Open Access Journals (Sweden)

    Brenière Simone F

    1997-01-01

    Full Text Available The genetic variability of Triatoma infestans and Trypanosoma cruzi populations was studied by isoenzyme analysis in two distinct areas of Arequipa province (Peru; one, Santa Rita de Siguas, being an endemic area for Chagas' disease, the second, Arequipa, recently infected. Analysis of T. infestans genetic variability indicates, (i temporal stability of genotypes found in Santa Rita de Siguas, (ii high genetic differences between Arequipa and Santa Rita de Siguas populations suggesting minor contact between them, (iii multiple origin of the T. infestans population in Arequipa, and (iv poor dispersal capacity of T. infestans: the panmictic unit could be reduce to a house. Parasite isoenzyme analysis was performed in 29 Peruvian stocks of T. cruzi, mainly isolated from bugs taken in a single locality, Santa Rita de Siguas. The results show, (i a high genetic polymorphism, (ii nine different multilocus genotypes were detected and clustered in two different clades, (iii most of the parasite isolates pertained to one of the clade and were genetically similar to those analyzed 12 years before. This sample allowed the study of the mating system of T. cruzi in strict sympatic conditions and gave more strength to the hypothesis of the clonal structure of T. cruzi populations

  11. Genetic variability and microdistribution of Triatoma infestans genotypes and Trypanosoma cruzi clones in Arequipa region (Peru).

    Science.gov (United States)

    Brenière, S F; Lopez, J; Vargas, F; Barnabé, C

    1997-01-01

    The genetic variability of Triatoma infestans and Trypanosoma cruzi populations was studied by isoenzyme analysis in two distinct areas of Arequipa province (Peru); one, Santa Rita de Siguas, being an endemic area for Chagas' disease, the second, Arequipa, recently infected. Analysis of T. infestans genetic variability indicates, (i) temporal stability of genotypes found in Santa Rita de Siguas, (ii) high genetic differences between Arequipa and Santa Rita de Siguas populations suggesting minor contact between them, (iii) multiple origin of the T. infestans population in Arequipa, and (iv) poor dispersal capacity of T. infestans: the panmictic unit could be reduce to a house. Parasite isoenzyme analysis was performed in 29 Peruvian stocks of T. cruzi, mainly isolated from bugs taken in a single locality, Santa Rita de Siguas. The results show, (i) a high genetic polymorphism, (ii) nine different multilocus genotypes were detected and clustered in two different clades, (iii) most of the parasite isolates pertained to one of the clade and were genetically similar to those analyzed 12 years before. This sample allowed the study of the mating system of T. cruzi in strict sympathic conditions and gave more strength to the hypothesis of the clonal structure of T. cruzi populations.

  12. Comparison of external genetic of Wareng and Kampung Chicken, observed from introgression rate and genetic variability

    Directory of Open Access Journals (Sweden)

    T Sartika

    2008-12-01

    Full Text Available Wareng and Kampung chicken are Indonesian native chicken that have good potential to be dual purpose chicken. Information on these chickens has not hast’n widely published so that their genetic potential is unknown. The purpose of this research is to collect basic data of the external genetic characteristic from Wareng and Kampung chickens consisting feather color, feather pattern, feather feature, feather shine, shank color and comb shape; to identify rate of introgression imported breed (Rhode Island Red, White Leghorn and Barred Plymouth Rock, the purity and genetic variability of Wareng and Kampung chickens. This study was carried out at the Research Institute for Animal Production, Ciawi, Bogor. Materials used were 361 of Wareng chickens (313 females, 48 males and 439 of Kampung chickens (352 females, 87 males. Data were analyzed using formulas to identify gene frequency, rate of introgression of purity native gene frequency and the genetic variability. The result showed that the control of gene constitution on external characteristic of Wareng chicken was I_ E_ bb S_ Id_ pp and ii e+ _bb ss idid pp on Kampung chicken. Wareng chicken own constitution of gene the same as with White Leghorn (II EE SS BB IdId pp. Wareng Chicken is not containing frequency of original gene of Indonesian local chicken (Kampung. The level of influence value (rate of introgression from Europe and American chicken for Wareng chicken was of equal to 84% and 25% to Kampung chicken. So that the purity for Wareng chicken was 16% and 75% was for Kampung chicken. The variability genetic of Kampung chickens (39% higher than Wareng chicken (16%.

  13. Microsatellite variability reveals high genetic diversity and low genetic differentiation in a critical giant panda population

    Institute of Scientific and Technical Information of China (English)

    Jiandong YANG; Zhihe ZHANG; Fujun SHEN; Xuyu YANG; Liang ZHANG; Limin CHEN; Wenping ZHANG; Qing ZHU; Rong HOU

    2011-01-01

    Understanding present patterns of genetic diversity is critical in order to design effective conservation and management strategies for endangered species.Tangjiahe Nature Reserve (NR) is one of the most important national reserves for giant pandas Ailuropoda melanoleuca in China.Previous studies have shown that giant pandas in Tangjiahe NR may be threatened by population decline and fragmentation.Here we used 10 microsatellite DNA markers to assess the genetic variability in the Tangjiahe population.The results indicate a low level of genetic differentiation between the Hongshihe and Motianling subpopulations in the reserve.Assignment tests using the Bayesian clustering method in STRUCTURE identified one genetic cluster from 42 individuals of the two subpopulations.All individuals from the same subpopulation were assigned to one cluster.This indicates high gene flow between subpopulations.F statistic analyses revealed a low Fls-value of 0.024 in the total population and implies a randomly mating population in Tangjiahe NR.Additionally,our data show a high level of genetic diversity for the Tangjiahe population.Mean allele number (A),Allelic richness (AR) and mean expected heterozygosity (HE) for the Tangiiahe population was 5.9,5.173 and 0.703,respectively.This wild giant panda population can be restored through concerted effort [Current Zoology 57 (6):717-724,2011].

  14. Microsatellite variability reveals high genetic diversity and low genetic differentiation in a critical giant panda population

    Directory of Open Access Journals (Sweden)

    Jiandong YANG, Zhihe ZHANG, Fujun SHEN, Xuyu YANG, Liang ZHANG, Limin CHEN, Wenping ZHANG, Qing ZHU, Rong HOU

    2011-12-01

    Full Text Available Understanding present patterns of genetic diversity is critical in order to design effective conservation and management strategies for endangered species. Tangjiahe Nature Reserve (NR is one of the most important national reserves for giant pandas Ailuropoda melanoleuca in China. Previous studies have shown that giant pandas in Tangjiahe NR may be threatened by population decline and fragmentation. Here we used 10 microsatellite DNA markers to assess the genetic variability in the Tangjiahe population. The results indicate a low level of genetic differentiation between the Hongshihe and Motianling subpopulations in the reserve. Assignment tests using the Bayesian clustering method in STRUCTURE identified one genetic cluster from 42 individuals of the two subpopulations. All individuals from the same subpopulation were assigned to one cluster. This indicates high gene flow between subpopulations. F statistic analyses revealed a low FIS-value of 0.024 in the total population and implies a randomly mating population in Tangjiahe NR. Additionally, our data show a high level of genetic diversity for the Tangjiahe population. Mean allele number (A, Allelic richness (AR and mean expected heterozygosity (HE for the Tangjiahe population was 5.9, 5.173 and 0.703, respectively. This wild giant panda population can be restored through concerted effort [Current Zoology 57 (6: 717–724, 2011].

  15. Adenoviral targeting using genetically incorporated camelid single variable domains.

    Science.gov (United States)

    Kaliberov, Sergey A; Kaliberova, Lyudmila N; Buggio, Maurizio; Tremblay, Jacqueline M; Shoemaker, Charles B; Curiel, David T

    2014-08-01

    The unique ability of human adenovirus serotype 5 (Ad5) to accomplish efficient transduction has allowed the use of Ad5-based vectors for a range of gene therapy applications. Several strategies have been developed to alter tropism of Ad vectors to achieve a cell-specific gene delivery by using fiber modifications via genetic incorporation of targeting motifs. In this study, we have explored the utility of novel anti-human carcinoembryonic antigen (hCEA) single variable domains derived from heavy chain (VHH) camelid family of antibodies to achieve targeted gene transfer. To obtain anti-CEA VHHs, we produced a VHH-display library from peripheral blood lymphocytes RNA of alpacas at the peak of immune response to the hCEA antigen (Ag). We genetically incorporated an anti-hCEA VHH into a de-knobbed Ad5 fiber-fibritin chimera and demonstrated selective targeting to the cognate epitope expressed on the membrane surface of target cells. We report that the anti-hCEA VHH used in this study retains Ag recognition functionality and provides specificity for gene transfer of capsid-modified Ad5 vectors. These studies clearly demonstrated the feasibility of retargeting of Ad5-based gene transfer using VHHs.

  16. Clinical Characteristics and Genetic Variability of Human Rhinovirus in Mexico

    Directory of Open Access Journals (Sweden)

    Hilda Montero

    2012-01-01

    Full Text Available Human rhinovirus (HRV is a leading cause of acute respiratory infection (ARI in young children and infants worldwide and has a high impact on morbidity and mortality in this population. Initially, HRV was classified into two species: HRV-A and HRV-B. Recently, a species called HRV-C and possibly another species, HRV-D, were identified. In Mexico, there is little information about the role of HRV as a cause of ARI, and the presence and importance of species such as HRV-C are not known. The aim of this study was to determine the clinical characteristics and genetic variability of HRV in Mexican children. Genetic characterization was carried out by phylogenetic analysis of the 5′-nontranslated region (5′-NTR of the HRV genome. The results show that the newly identified HRV-C is circulating in Mexican children more frequently than HRV-B but not as frequently as HRV-A, which was the most frequent species. Most of the cases of the three species of HRV were in children under 2 years of age, and all species were associated with very mild and moderate ARI.

  17. Detection of Genetically Modified Food: Has Your Food Been Genetically Modified?

    Science.gov (United States)

    Brandner, Diana L.

    2002-01-01

    Explains the benefits and risks of genetically-modified foods and describes methods for genetically modifying food. Presents a laboratory experiment using a polymerase chain reaction (PCR) test to detect foreign DNA in genetically-modified food. (Contains 18 references.) (YDS)

  18. Detection of Genetically Modified Food: Has Your Food Been Genetically Modified?

    Science.gov (United States)

    Brandner, Diana L.

    2002-01-01

    Explains the benefits and risks of genetically-modified foods and describes methods for genetically modifying food. Presents a laboratory experiment using a polymerase chain reaction (PCR) test to detect foreign DNA in genetically-modified food. (Contains 18 references.) (YDS)

  19. Increasing genetic variability in black oats using gamma irradiation.

    Science.gov (United States)

    Silveira, G; Moliterno, E; Ribeiro, G; Costa, P M A; Woyann, L G; Tessmann, E W; Oliveira, A C; Cruz, C D

    2014-12-04

    The black oat (Avena strigosa Schreb) is commonly used for forage, soil cover, and green manure. Despite its importance, little improvement has been made to this species, leading to high levels of genotypic disuniformity within commercial cultivars. The objective of this study was to evaluate the efficiency of different doses of gamma rays [(60)Co] applied to black oat seeds on the increase of genetic variability of agronomic traits. We applied doses of 0, 10, 50, 100, and 200 Gy to the genotype ALPHA 94087 through exposure to [(60)Co]. Two experiments were conducted in the winter of 2008. The first aimed to test forage trait measurements such as plant height, dry matter yield, number of surviving tillers, and seedling stand. The second test assessed seed traits, such as yield and dormancy levels. Gamma irradiation seems not to increase seed yield in black oats, but it was effective in generating variability for the other traits. Tiller number and plant height are important selection traits to increase dry matter yield. Selection in advanced generations of mutant populations can increase the probability of identifying superior genotypes.

  20. Genetic variability and correlation studies in sunflower (Helianthus annuus L.

    Directory of Open Access Journals (Sweden)

    Sheshaiah and Shankergoud I.

    2015-06-01

    Full Text Available The present study was conducted in order to investigate genetic variability and to understand the relationship and contribution of characters towards total dry matter and root length. The investigation was carried out at Main Agricultural Research Station, UAS, Raichur during Rabi 2012-13, 32 genotypes were evaluated in RBD fashion under root structures. At flowering stage all morphological and root characters were scored. The total dry matter content was assessed after drying the root, stem, leaf, petiole and flower of the plant at 70 0C in an oven.. High GCV coupled with high PCV recorded for most of the characters except stem girth, SPAD reading and number of leaves, indicating more variability for these traits and are less influenced by the environment. High heritability coupled with high GAM reported for all the traits under study suggested for the greater effectiveness for selection and improvement expected for these traits in future generations. The total dry matter and root length had very highly significant positive association with plant height, root volume, fresh root weight, dry root weight, fresh stem weight, dry stem weight, fresh leaf weight and dry leaf weight indicating the importance of root characters in determining the moisture stress tolerance and putforthing the total dry matter content of the plant.

  1. Genetic variability of Echinococcus granulosus based on the mitochondrial 16S ribosomal RNA gene.

    Science.gov (United States)

    Wang, Ning; Wang, Jiahai; Hu, Dandan; Zhong, Xiuqin; Jiang, Zhongrong; Yang, Aiguo; Deng, Shijin; Guo, Li; Tsering, Dawa; Wang, Shuxian; Gu, Xiaobin; Peng, Xuerong; Yang, Guangyou

    2015-06-01

    Echinococcus granulosus is the etiological agent of cystic echinococcosis, a major zoonotic disease of both humans and animals. In this study, we assessed genetic variability and genetic structure of E. granulosus in the Tibet plateau, using the complete mitochondrial 16 S ribosomal RNA gene for the first time. We collected and sequenced 62 isolates of E. granulosus from 3 populations in the Tibet plateau. A BLAST analysis indicated that 61 isolates belonged to E. granulosus sensu stricto (genotypes G1-G3), while one isolate belonged to E. canadensis (genotype G6). We detected 16 haplotypes with a haplotype network revealing a star-like expansion, with the most common haplotype occupying the center of the network. Haplotype diversity and nucleotide diversity were low, while negative values were observed for Tajima's D and Fu's Fs. AMOVA results and Fst values revealed that the three geographic populations were not genetically differentiated. Our results suggest that a population bottleneck or population expansion has occurred in the past, and that this explains the low genetic variability of E. granulosus in the Tibet Plateau.

  2. Genetic variability and homozygosity in a F4 castor bean population by microsatellite markers

    Directory of Open Access Journals (Sweden)

    Edna Lobo Machado

    2016-01-01

    Full Text Available ABSTRACT The objectives of this study were to identify the genetic variability and estimate the level of homozygosity in a castor bean F4 population using microsatellite markers (SSR. To this end, it was performed the genotyping of the population through 53 pairs of SSR primers. Allele frequencies were estimated by number of alleles per locus, expected heterozygosity (He, observed heterozygosity (Ho and polymorphic information content (PIC. An array of genetic dissimilarity was generated by Nei and Li index, and hierarchical cluster analysis was performed using the Unweighted Pair-Group Method Averages (UPGMA method. Polymorphism was detected in a total of eight loci (15.09% of the 53 evaluated, with the presence of two alleles per locus. Allele frequencies varied between 0.71 and 0.53, and the PIC, between 0.32 and 0.37. The average observed heterozygosity Ho (0.30 was lower than the expected heterozygosity He (0.47. Five dissimilar groups were formed, showing that there is genetic variability among the evaluated genotypes. The highest genetic dissimilarity was 0.708 and the lowest, 0.00. The percentages of homozygous genotypes varied from 25 to 75%. These results show that controlled selfing in castor bean raises the level of homozygosity, important for the breeding program.

  3. [Environmental and genetic variables related with alterations in language acquisition in early childhood].

    Science.gov (United States)

    Moriano-Gutierrez, A; Colomer-Revuelta, J; Sanjuan, J; Carot-Sierra, J M

    2017-01-01

    A great deal of research has addressed problems in the correct acquisition of language, but with few overall conclusions. The reasons for this lie in the individual variability, the existence of different measures for assessing language and the fact that a complex network of genetic and environmental factors are involved in its development. To review the environmental and genetic variables that have been studied to date, in order to gain a better under-standing of the causes of specific language impairment and create new evidence that can help in the development of screening systems for the early detection of these disorders. The environmental variables related with poorer early child language development include male gender, low level of education of the mother, familial history of problems with language or psychiatric problems, perinatal problems and health problems in early childhood. Bilingualism seems to be a protective factor. Temperament and language are related. Within the genetic factors there are several specific genes associated with language, two of which have a greater influence on its physiological acquisition: FOXP2 and CNTNAP2. The other genes that are most related with specific language disorders are ATP2C2, CMIP, ROBO2, ZNF277 and NOP9. The key to comprehending the development of specific language disorders lies in reaching an understanding of the true role played by genes in the ontogenesis, in the regulation of the different developmental processes, and how this role is modulated by the environment.

  4. GARD: a genetic algorithm for recombination detection

    National Research Council Canada - National Science Library

    Kosakovsky Pond, Sergei L; Posada, David; Gravenor, Michael B; Woelk, Christopher H; Frost, Simon D W

    2006-01-01

    .... We developed a likelihood-based model selection procedure that uses a genetic algorithm to search multiple sequence alignments for evidence of recombination breakpoints and identify putative recombinant sequences...

  5. Quantifying the lag time to detect barriers in landscape genetics

    Science.gov (United States)

    E. L. Landguth; S. A Cushman; M. K. Schwartz; K. S. McKelvey; M. Murphy; G. Luikart

    2010-01-01

    Understanding how spatial genetic patterns respond to landscape change is crucial for advancing the emerging field of landscape genetics. We quantified the number of generations for new landscape barrier signatures to become detectable and for old signatures to disappear after barrier removal. We used spatially explicit, individualbased simulations to examine the...

  6. Tomato second cycle hybrids as a source of genetic variability for fruit quality traits

    Directory of Open Access Journals (Sweden)

    Pereira da Costa JH

    2016-11-01

    Full Text Available The objective of this study was to investigate the phenotypic and molecular variability in a F2 generation derived from a SCH (Second Cycle Hybrid in order to detect QTLs for some fruit traits of tomato. Genome coverage at different levels was achieved by three types of molecular markers (polypeptides, sequence-related amplified polymorphism-SRAP and amplified restriction fragment polymorphism - AFLP. Different degrees of polymorphism were detected by SRAP and AFLP at the DNA structure level and also by polypeptides at the DNA expression level. The first two markers, associated with phenotypic variation, detected QTLs involved in important agronomic traits such as fruit shelf life, soluble solids content, pH, and titratable acidity. New gene blocks originated by recombination during the first cycle of crossing were detected. This study confirmed that the observed phenotypic differences represent a new gene rearrangement and that these new gene blocks are responsible for the presence of the genetic variability detected for these traits.

  7. Genetic Variability of Apolipoprotein E in Different Populations from Venezuela

    Directory of Open Access Journals (Sweden)

    M. T. Fernández-Mestre

    2005-01-01

    Full Text Available The genetic variation at the Apolipoprotein E locus (APOE is an important determinant of plasma lipids and has been implicated in various human pathological conditions. The objective of the present study was to estimate the distribution of APOE alleles in five Venezuelan communities: two Amerindian tribes (Bari and Yucpa, one Negroid population from Curiepe, one Caucasoid population from Colonia Tovar and the mestizo urban population living in Caracas. The APOE*3 allele was the most common allele in all populations studied. However, a significant increase in the APOE*2 allele frequency in the Mestizo (18.96% and Negroid (16.25% populations was found. Similar to results reported in other Native American populations we have found that the APOE*2 allele is completely absent in the Bari and Yucpa Amerindians. Frequencies found in the Colonia Tovar population are in agreement with those reported in the population of Germany, indicating a high degree of relatedness. The results support the notion that the distribution of the APOE alleles shows ethnic variability.

  8. Reproductive strategies and genetic variability in tropical freshwater fish

    Directory of Open Access Journals (Sweden)

    Maria Dolores Peres Lassala

    2007-01-01

    Full Text Available We estimated the genetic variability of nine fish species from the Brazilian upper Paraná River floodplain (Astyanax altiparanae, Hoplias malabaricus, Leporinus lacustris, Loricariichthys platymetopon, Parauchenipterus galeatus, Pimelodus maculatus, Rhaphiodon vulpinus, Roeboides paranensis and Serrasalmus marginatus based on data for 36 putative allozyme loci obtained using corn starch gel electrophoresis of 13 enzymatic systems: aspartate aminotransferase (EC 2.6.1.1, acid phosphatase (EC 3.1.3.2, esterase (EC 3.1.1.1, glycerol-3-phosphate dehydrogenase (EC 1.1.1.8, glucose-6-phosphate dehydrogenase (EC 1.1.1.49, glucose-6-phosphate isomerase (EC 5.3.1.9, Iditol dehydrogenase (EC 1.1.1.14, isocitrate dehydrogenase - NADP+ (EC 1.1.1.42, L-lactate dehydrogenase (EC 1.1.1.27, malate dehydrogenase (EC 1.1.1.37, malate dehydrogenase-NADP+ (EC 1.1.1.40, phosphoglucomutase (EC 5.4.2.2 and superoxide dismutase, (EC 1.15.1.1. The mean expected heterozygosity varied from zero to 0.147. When data from the literature for 75 species of tropical fish were added to the nine species of this study, the heterozygosity values differed significantly among the groups of different reproductive strategies. The highest mean heterozygosity was for the non-migratory without parental care, followed by the long-distance migratory, and the lowest mean was for the non-migratory with parental care or internal fecundation.

  9. Variability and Multiwavelength Detected AGN in the GOODS Fields

    CERN Document Server

    Sarajedini, Vicki L; Klesman, Alison J; Laird, Elise S; Gonzalez, Pablo G Perez; Mozena, Mark

    2011-01-01

    We identify 85 variable galaxies in the GOODS North and South fields using 5 epochs of HST ACS V-band (F606W) images spanning 6 months. The variables are identified through significant flux changes in the galaxy's nucleus and represent ~2% of the survey galaxies. With the aim of studying the active galaxy population in the GOODS fields, we compare the variability-selected sample with X-ray and mid-IR AGN candidates. Forty-nine percent of the variables are associated with X-ray sources identified in the 2Ms Chandra surveys. Twenty-four percent of X-ray sources likely to be AGN are optical variables and this percentage increases with decreasing hardness ratio of the X-ray emission. Stacking of the non-X-ray detected variables reveals marginally significant soft X-ray emission. Forty-eight percent of mid-IR power-law sources are optical variables, all but one of which are also X-ray detected. Thus, about half of the optical variables are associated with either X-ray or mid-IR power-law emission. The slope of the...

  10. Improved Genetic Algorithm Application in Textile Defect Detection

    Institute of Scientific and Technical Information of China (English)

    GENG Zhao-feng; Li Bei-bei; ZHAO Zhi-hong

    2007-01-01

    Based on an efficient improved genetic algorithm,a pattern recognition approach is represented for textile defects inspection. An image process is developed to automatically detect the drawbacks on textile caused by three circumstances: break, dual, and jump of yams. By statistic method, some texture feature values of the image with defects points can be achieved. Therefore, the textile defects are classified properly. The advanced process of the defect image is done. Image segmentation is realized by an improved genetic algorithm to detect the defects. This method can be used to automatically classify and detect textile defects. According to different users' requirements, ifferent types of textile material can be detected.

  11. Epigenetic variability in the genetically uniform forest tree species Pinus pinea L.

    Science.gov (United States)

    Sáez-Laguna, Enrique; Guevara, María-Ángeles; Díaz, Luis-Manuel; Sánchez-Gómez, David; Collada, Carmen; Aranda, Ismael; Cervera, María-Teresa

    2014-01-01

    There is an increasing interest in understanding the role of epigenetic variability in forest species and how it may contribute to their rapid adaptation to changing environments. In this study we have conducted a genome-wide analysis of cytosine methylation pattern in Pinus pinea, a species characterized by very low levels of genetic variation and a remarkable degree of phenotypic plasticity. DNA methylation profiles of different vegetatively propagated trees from representative natural Spanish populations of P. pinea were analyzed with the Methylation Sensitive Amplified Polymorphism (MSAP) technique. A high degree of cytosine methylation was detected (64.36% of all scored DNA fragments). Furthermore, high levels of epigenetic variation were observed among the studied individuals. This high epigenetic variation found in P. pinea contrasted with the lack of genetic variation based on Amplified Fragment Length Polymorphism (AFLP) data. In this manner, variable epigenetic markers clearly discriminate individuals and differentiates two well represented populations while the lack of genetic variation revealed with the AFLP markers fail to differentiate at both, individual or population levels. In addition, the use of different replicated trees allowed identifying common polymorphic methylation sensitive MSAP markers among replicates of a given propagated tree. This set of MSAPs allowed discrimination of the 70% of the analyzed trees.

  12. Edge detection of range images using genetic neural networks

    Institute of Scientific and Technical Information of China (English)

    FAN Jian-ying; DU Ying; ZHOU Yang; WANG Yang

    2009-01-01

    Due to the complexity and asymmetrical illumination, the images of object are difficult to be effectively segmented by some routine method. In this paper, a kind of edge detection method based on image features and genetic algorithms neural network for range images was proposed. Fully considering the essential difference between an edge point and a noise point, some characteristic parameters were extracted from range maps as the input nodes of the network in the algorithm. Firstly, a genetic neural network was designed and implemented. The neural network is trained by genetic algorithm, and then genetic neural network algorithm is combined with the virtue of global optimization of genetic algorithm and the virtue of parallel computation of neural network, so that this algorithm is of good global property. The experimental results show that this method can get much faster and more accurate detection results than the classical differential algorithm, and has better anti-noise performance.

  13. Genetic variability analysis of Byrsonima crassifolia germplasm collected in Pará State using ISSR markers.

    Science.gov (United States)

    Rodrigues, S M; Moura, E F; Ramos, G K S; Oliveira, M S P

    2016-10-17

    Native of the Amazon, the nanche (Byrsonima crassifolia) is a fruit cultivated by family farmers and used in cooking; as such, it represents an opportunity for regional agribusiness. The Embrapa Eastern Amazon set up an active germplasm bank (BAG) consisting of 22 accessions sampled in 11 municipalities of Pará State. Due to its economic potential, there is an interest to advance the genetic breeding program of this species. The aim of this study was to characterize the BAG nanche collection using inter-simple sequence repeat (ISSR) markers. Accessions were genotyped using 23 pre-selected ISSR primers resulting in 109 amplified polymorphic and 51 monomorphic bands. With eight polymorphic bands each, the most polymorphic primers were UBC 809 and UBC 848. An unweighted pair-group method with arithmetic average cluster analysis based on Jaccard's coefficient indicated that the individuals clustered into two distinct groups. Accessions Igarapé Açu-2 and Augusto Corrêa-Pl 1 were most similar. The genetic dissimilarity values ranged from 0.10 to 0.59. We conclude that the ISSR markers were efficient in detecting polymorphisms in the nanche accessions, and that it is possible to infer the genetic variability among accessions of the collection. This demonstrate the importance of using molecular markers in poorly studied species and the advantages that this information can bring to the genetic improvement of such species.

  14. Small target detection using quantum genetic morphological filter

    Science.gov (United States)

    Deng, Lizhen; Zhu, Hu; Wei, Yantao; Lu, Guanmin; Wei, Yu

    2015-12-01

    Small target detection plays a crucial role in infrared warning and tracking systems. A background suppression method using morphological filter based on quantum genetic algorithm (QGMF) is presented to detect small targets in infrared image. Structure element of morphological filter is encoded and the best structure element is selected using quantum genetic algorithm. The optimized structure element is used for background suppression to detect small target. Experimental results demonstrate that QGMF has good performance in clutter suppression, and obtains higher signal-to-clutter ratio gain (SCRG) and background suppression factor (BSF) than the one using the fixed structure element with the same size.

  15. Periodic Optical Variability of Radio Detected Ultracool Dwarfs

    CERN Document Server

    Harding, Leon K; Boyle, Richard P; Golden, Aaron; Singh, Navtej; Sheehan, Brendan; Zavala, Robert T; Butler, Ray F

    2013-01-01

    A fraction of very low mass stars and brown dwarfs are known to be radio active, in some cases producing periodic pulses. Extensive studies of two such objects have also revealed optical periodic variability and the nature of this variability remains unclear. Here we report on multi-epoch optical photometric monitoring of six radio detected dwarfs, spanning the $\\sim$M8 - L3.5 spectral range, conducted to investigate the ubiquity of periodic optical variability in radio detected ultracool dwarfs. This survey is the most sensitive ground-based study carried out to date in search of periodic optical variability from late-type dwarfs, where we obtained 250 hours of monitoring, delivering photometric precision as low as $\\sim$0.15%. Five of the six targets exhibit clear periodicity, in all cases likely associated with the rotation period of the dwarf, with a marginal detection found for the sixth. Our data points to a likely association between radio and optical periodic variability in late-M/early-L dwarfs, alth...

  16. Variability of microchip capillary electrophoresis with conductivity detection.

    Science.gov (United States)

    Tantra, Ratna; Robinson, Kenneth; Sikora, Aneta

    2014-02-01

    Microfluidic CE with conductivity detection platforms could have an impact on the future development of smaller, faster and portable devices. However, for the purpose of reliable identification and quantification, there is a need to understand the degree of irreproducibility associated with the analytical technique. In this study, a protocol was developed to remove baseline drift problems sometimes observed in such devices. The protocol, which consisted of pre-conditioning steps prior to analysis, was used to further assess measurement variability from 24 individual microchips fabricated from six separate batches of glass substrate. Results show acceptable RSD percentage for retention time measurements but large variability in their corresponding peak areas (with some microchips having variability of ∼50%). Sources of variability were not related to substrate batch but possibly to a number of factors such as applied voltage fluctuations or variations in microchannel quality, for example surface roughness that will subsequently affect microchannel dimensions.

  17. Making genetic biodiversity measurable : a review of statistical multivariate methods to study variability at gene level

    OpenAIRE

    2011-01-01

    Measures of agro-ecosystems genetic variability are essential to sustain scientific-based actions and policies tending to protect the ecosystem services they provide. To build the genetic variability datum it is necessary to deal with a large number and different types of variables. Molecular marker data is highly dimensional by nature, and frequently additional types of information are obtained, as morphological and physiological traits. This way, gene...

  18. Periodic optical variability of radio-detected ultracool dwarfs

    Energy Technology Data Exchange (ETDEWEB)

    Harding, L. K.; Golden, A.; Singh, Navtej; Sheehan, B.; Butler, R. F. [Centre for Astronomy, National University of Ireland, Galway, University Road, Galway (Ireland); Hallinan, G. [Cahill Center for Astrophysics, California Institute of Technology, 1200 East California Boulevard, MC 249-17, Pasadena, CA 91125 (United States); Boyle, R. P. [Vatican Observatory Research Group, Steward Observatory, University of Arizona, Tucson, AZ 85721 (United States); Zavala, R. T., E-mail: lkh@astro.caltech.edu [United States Naval Observatory, Flagstaff Station, Flagstaff, AZ 86001 (United States)

    2013-12-20

    A fraction of very low mass stars and brown dwarfs are known to be radio active, in some cases producing periodic pulses. Extensive studies of two such objects have also revealed optical periodic variability, and the nature of this variability remains unclear. Here, we report on multi-epoch optical photometric monitoring of six radio-detected dwarfs, spanning the ∼M8-L3.5 spectral range, conducted to investigate the ubiquity of periodic optical variability in radio-detected ultracool dwarfs. This survey is the most sensitive ground-based study carried out to date in search of periodic optical variability from late-type dwarfs, where we obtained 250 hr of monitoring, delivering photometric precision as low as ∼0.15%. Five of the six targets exhibit clear periodicity, in all cases likely associated with the rotation period of the dwarf, with a marginal detection found for the sixth. Our data points to a likely association between radio and optical periodic variability in late-M/early-L dwarfs, although the underlying physical cause of this correlation remains unclear. In one case, we have multiple epochs of monitoring of the archetype of pulsing radio dwarfs, the M9 TVLM 513–46546, spanning a period of 5 yr, which is sufficiently stable in phase to allow us to establish a period of 1.95958 ± 0.00005 hr. This phase stability may be associated with a large-scale stable magnetic field, further strengthening the correlation between radio activity and periodic optical variability. Finally, we find a tentative spin-orbit alignment of one component of the very low mass binary, LP 349–25.

  19. Detection of genetically modified organisms by electrochemiluminescence PCR method.

    Science.gov (United States)

    Liu, Jinfeng; Xing, Da; Shen, Xingyan; Zhu, Debin

    2004-10-15

    With the development of biotechnology, more and more genetically modified organisms (GMOs) have entered commercial market. Because of the safety concerns, detection and characterization of GMOs have attracted much attention recently. In this study, electrochemiluminescence polymerase chain reaction (ECL-PCR) combined with hybridization technique was applied to detect the GMOs in genetically modified (GM) soybeans and papayas for the first time. Whether the soybeans and the papayas contain GM components was discriminated by detecting the Cauliflower mosaic virus 35S (CaMV35S) promoter. The experiment results show that the detection limit for CaMV35S promoter is 100 fmol, and the GM components can be clearly identified in GM soybeans and papayas. The technique may provide a new means in GMOs detection due to its simplicity and high efficiency.

  20. Genetic analysis of Phytophthora infestans populations in the Nordic European countries reveals high genetic variability

    DEFF Research Database (Denmark)

    Brurberg, May Bente; Elameen, Abdelhameed; Le, Ving Hong

    2011-01-01

    Late blight, caused by the oomycete Phytophthora infestans, is the most important disease of potato (Solanum tuberosum). The pathogen is highly adaptable and to get an overview of the genetic variation in the Nordic countries, Denmark, Finland, Norway and Sweden we have analyzed 200 isolates from...... different fields using nine simple-sequence repeat (SSR) markers. Forty-nine alleles were detected among the nine SSR loci and isolates from all four Nordic countries shared the most common alleles across the loci. In total 169 multilocus genotypes (based on seven loci) were identified among 191 isolates....... The genotypic diversities, quantified by a normalized Shannon’s diversity index (Hs), were 0.95 for the four Nordic countries. The low FST value of 0.04 indicates that the majority of variation is found within the four Nordic countries. The large number of genotypes and the frequency distribution of mating...

  1. Method of detecting genetic translocations identified with chromosomal abnormalities

    Energy Technology Data Exchange (ETDEWEB)

    Gray, Joe W. (Livermore, CA); Pinkel, Daniel (Walnut Creek, CA); Tkachuk, Douglas (Livermore, CA)

    2001-01-01

    Methods and compositions for staining based upon nucleic acid sequence that employ nucleic acid probes are provided. Said methods produce staining patterns that can be tailored for specific cytogenetic analyses. Said probes are appropriate for in situ hybridization and stain both interphase and metaphase chromosomal material with reliable signals. The nucleic acid probes are typically of a complexity greater than 50 kb, the complexity depending upon the cytogenetic application. Methods and reagents are provided for the detection of genetic rearrangements. Probes and test kits are provided for use in detecting genetic rearrangements, particularly for use in tumor cytogenetics, in the detection of disease related loci, specifically cancer, such as chronic myelogenous leukemia (CML) and for biological dosimetry. Methods and reagents are described for cytogenetic research, for the differentiation of cytogenetically similar but genetically different diseases, and for many prognostic and diagnostic applications.

  2. Incorporating privileged genetic information for fundus image based glaucoma detection.

    Science.gov (United States)

    Duan, Lixin; Xu, Yanwu; Li, Wen; Chen, Lin; Wing, Damon Wing Kee; Wong, Tien Yin; Liu, Jiang

    2014-01-01

    Visual features extracted from retinal fundus images have been increasingly used for glaucoma detection, as those images are generally easy to acquire. In recent years, genetic researchers have found that some single nucleic polymorphisms (SNPs) play important roles in the manifestation of glaucoma and also show superiority over fundus images for glaucoma detection. In this work, we propose to use the SNPs to form the so-called privileged information and deal with a practical problem where both fundus images and privileged genetic information exist for the training subjects, while the test objects only have fundus images. To solve this problem, we present an effective approach based on the learning using privileged information (LUPI) paradigm to train a predictive model for the image visual features. Extensive experiments demonstrate the usefulness of our approach in incorporating genetic information for fundus image based glaucoma detection.

  3. Chromosome-specific staining to detect genetic rearrangements

    Energy Technology Data Exchange (ETDEWEB)

    Gray, Joe W.; Pinkel, Daniel; Tkachuk, Douglas; Westbrook, Carol

    2013-04-09

    Methods and compositions for staining based upon nucleic acid sequence that employ nucleic acid probes are provided. Said methods produce staining patterns that can be tailored for specific cytogenetic analyzes. Said probes are appropriate for in situ hybridization and stain both interphase and metaphase chromosomal material with reliable signals. The nucleic acid probes are typically of a complexity greater than 50 kb, the complexity depending upon the cytogenetic application. Methods and reagents are provided for the detection of genetic rearrangements. Probes and test kits are provided for use in detecting genetic rearrangements, particularly for use in tumor cytogenetics, in the detection of disease related loci, specifically cancer, such as chronic myelogenous leukemia (CML) and for biological dosimetry. Methods and reagents are described for cytogenetic research, for the differentiation of cytogenetically similar but genetically different diseases, and for many prognostic and diagnostic applications.

  4. Method of detecting genetic deletions identified with chromosomal abnormalities

    Energy Technology Data Exchange (ETDEWEB)

    Gray, Joe W; Pinkel, Daniel; Tkachuk, Douglas

    2013-11-26

    Methods and compositions for staining based upon nucleic acid sequence that employ nucleic acid probes are provided. Said methods produce staining patterns that can be tailored for specific cytogenetic analyzes. Said probes are appropriate for in situ hybridization and stain both interphase and metaphase chromosomal material with reliable signals. The nucleic acids probes are typically of a complexity greater tha 50 kb, the complexity depending upon the cytogenetic application. Methods and reagents are provided for the detection of genetic rearrangements. Probes and test kits are provided for use in detecting genetic rearrangements, particlularly for use in tumor cytogenetics, in the detection of disease related loci, specifically cancer, such as chronic myelogenous leukemia (CML) and for biological dosimetry. Methods and reagents are described for cytogenetic research, for the differentiation of cytogenetically similar ut genetically different diseases, and for many prognostic and diagnostic applications.

  5. Method of detecting genetic deletions identified with chromosomal abnormalities

    Science.gov (United States)

    Gray, Joe W; Pinkel, Daniel; Tkachuk, Douglas

    2013-11-26

    Methods and compositions for staining based upon nucleic acid sequence that employ nucleic acid probes are provided. Said methods produce staining patterns that can be tailored for specific cytogenetic analyzes. Said probes are appropriate for in situ hybridization and stain both interphase and metaphase chromosomal material with reliable signals. The nucleic acids probes are typically of a complexity greater tha 50 kb, the complexity depending upon the cytogenetic application. Methods and reagents are provided for the detection of genetic rearrangements. Probes and test kits are provided for use in detecting genetic rearrangements, particlularly for use in tumor cytogenetics, in the detection of disease related loci, specifically cancer, such as chronic myelogenous leukemia (CML) and for biological dosimetry. Methods and reagents are described for cytogenetic research, for the differentiation of cytogenetically similar ut genetically different diseases, and for many prognostic and diagnostic applications.

  6. Chromosome-specific staining to detect genetic rearrangements

    Science.gov (United States)

    Gray, Joe W.; Pinkel, Daniel; Tkachuk, Douglas; Westbrook, Carol

    2013-04-09

    Methods and compositions for staining based upon nucleic acid sequence that employ nucleic acid probes are provided. Said methods produce staining patterns that can be tailored for specific cytogenetic analyzes. Said probes are appropriate for in situ hybridization and stain both interphase and metaphase chromosomal material with reliable signals. The nucleic acid probes are typically of a complexity greater than 50 kb, the complexity depending upon the cytogenetic application. Methods and reagents are provided for the detection of genetic rearrangements. Probes and test kits are provided for use in detecting genetic rearrangements, particularly for use in tumor cytogenetics, in the detection of disease related loci, specifically cancer, such as chronic myelogenous leukemia (CML) and for biological dosimetry. Methods and reagents are described for cytogenetic research, for the differentiation of cytogenetically similar but genetically different diseases, and for many prognostic and diagnostic applications.

  7. NOTE - Genetic variability among cassava accessions based on SSR markers

    Directory of Open Access Journals (Sweden)

    Márcia de Nazaré Oliveira Ribeiro

    2011-01-01

    Full Text Available The aim of this study was to characterize and estimate the genetic similarity among 93 cassava accessions. The DNAamplification was performed with 14 microsatellite primers. The amplification products were separated by a polyacrylamide gelelectrophoresis, showing a polymorphism formation, through which the accessions were discriminated against. The genetic similarityamong accessions of cassava was estimated by the Dice coefficient. Cluster analysis was carried out using the UPGMA method. Thepolymorphic primers amplified a total of 26 alleles with 2-4 alleles per loci. The genetic similarity ranged from 0.16 to 0.96. Theaverage values for observed and expected heterozygosity were 0.18 and 0.46, respectively. Twenty genetic similarity clusters weredetermined, demonstrating diversity among accessions, suggesting the possibility of heterotic hybrid generation.

  8. Genetic variability in the endophytic fungus Guignardia citricarpa isolated from citrus plants

    Directory of Open Access Journals (Sweden)

    Chirlei Glienke-Blanco

    2002-01-01

    Full Text Available During some phases of of their life-cycle endophytic fungi colonize plants asymptomatically being found most frequently inside the aerial part of plant tissues. After surface disinfection of apparently healthy leaves from three varieties of mandarin orange and one tangor, and after incubation on appropriate culture medium, 407 fungal isolates were obtained, giving a total infection frequency of 81%. No fungal growth was observed from disinfected seeds, indicating that fungi are probably not transmitted via seeds. Of the fungal isolates, 27% belonged to the genus Guignardia, with 12 isolates being identified as Guignardia citricarpa Kiely, which is described as a citrus pathogen. The isolates were variable in respect to the presence of sexual structures and growth rates. Most of the isolates produces mature asci, supporting the hypothesis that they are nonpathogenic endophytes, which recently were identified as G. mangiferae. High intraspecific genetic variability (an average similarity coefficient of 0.6 was detected using random amplified polymorphic DNA (RAPD markers generated by seven different primers. The highest similarity coefficient (0.9 was between isolates P15 and M86 and the smallest (0.22 between isolates P15 and C145. These results did not allow us to establish an association between genetic similarity of the fungal isolates and the citrus varieties from which they were obtained.

  9. Rapid detection of genetic modification for GMO monitoring in agriculture

    Directory of Open Access Journals (Sweden)

    Petrović Sofija

    2015-01-01

    Full Text Available Transgenic technology has expanded the ways of new genetic variability creation. Genetically modified organisms (GMOs are organisms which total genome is altered in a way that could not happen in nature. GM crops recorded a steady increase in its share in agricultural production. However, for the most part, GMO in agriculture has been limited to two cultivars - soy and corn, and the two genetic modifications, the total herbicide resistance and pest of the Lepidoptera genus. In order to monitor cultivation and trade of GMOs, tests of different precision are used, qualitatively and/or quantitatively determining the presence of genetic modification. Tests for the rapid determination of the presence of GM are suitable, since they can be implemented quickly and accurately, in terms of declared sensitivity, outside or in the laboratory. The example of the use of rapid tests demonstrates their value in use for rapid and efficient monitoring.

  10. Genetic loci associated with heart rate variability and their effects on cardiac disease risk

    Science.gov (United States)

    Nolte, Ilja M.; Munoz, M. Loretto; Tragante, Vinicius; Amare, Azmeraw T.; Jansen, Rick; Vaez, Ahmad; von der Heyde, Benedikt; Avery, Christy L.; Bis, Joshua C.; Dierckx, Bram; van Dongen, Jenny; Gogarten, Stephanie M.; Goyette, Philippe; Hernesniemi, Jussi; Huikari, Ville; Hwang, Shih-Jen; Jaju, Deepali; Kerr, Kathleen F.; Kluttig, Alexander; Krijthe, Bouwe P.; Kumar, Jitender; van der Laan, Sander W.; Lyytikäinen, Leo-Pekka; Maihofer, Adam X.; Minassian, Arpi; van der Most, Peter J.; Müller-Nurasyid, Martina; Nivard, Michel; Salvi, Erika; Stewart, James D.; Thayer, Julian F.; Verweij, Niek; Wong, Andrew; Zabaneh, Delilah; Zafarmand, Mohammad H.; Abdellaoui, Abdel; Albarwani, Sulayma; Albert, Christine; Alonso, Alvaro; Ashar, Foram; Auvinen, Juha; Axelsson, Tomas; Baker, Dewleen G.; de Bakker, Paul I. W.; Barcella, Matteo; Bayoumi, Riad; Bieringa, Rob J.; Boomsma, Dorret; Boucher, Gabrielle; Britton, Annie R.; Christophersen, Ingrid; Dietrich, Andrea; Ehret, George B.; Ellinor, Patrick T.; Eskola, Markku; Felix, Janine F.; Floras, John S.; Franco, Oscar H.; Friberg, Peter; Gademan, Maaike G. J.; Geyer, Mark A.; Giedraitis, Vilmantas; Hartman, Catharina A.; Hemerich, Daiane; Hofman, Albert; Hottenga, Jouke-Jan; Huikuri, Heikki; Hutri-Kähönen, Nina; Jouven, Xavier; Junttila, Juhani; Juonala, Markus; Kiviniemi, Antti M.; Kors, Jan A.; Kumari, Meena; Kuznetsova, Tatiana; Laurie, Cathy C.; Lefrandt, Joop D.; Li, Yong; Li, Yun; Liao, Duanping; Limacher, Marian C.; Lin, Henry J.; Lindgren, Cecilia M.; Lubitz, Steven A.; Mahajan, Anubha; McKnight, Barbara; zu Schwabedissen, Henriette Meyer; Milaneschi, Yuri; Mononen, Nina; Morris, Andrew P.; Nalls, Mike A.; Navis, Gerjan; Neijts, Melanie; Nikus, Kjell; North, Kari E.; O'Connor, Daniel T.; Ormel, Johan; Perz, Siegfried; Peters, Annette; Psaty, Bruce M.; Raitakari, Olli T.; Risbrough, Victoria B.; Sinner, Moritz F.; Siscovick, David; Smit, Johannes H.; Smith, Nicholas L.; Soliman, Elsayed Z.; Sotoodehnia, Nona; Staessen, Jan A.; Stein, Phyllis K.; Stilp, Adrienne M.; Stolarz-Skrzypek, Katarzyna; Strauch, Konstantin; Sundström, Johan; Swenne, Cees A.; Syvänen, Ann-Christine; Tardif, Jean-Claude; Taylor, Kent D.; Teumer, Alexander; Thornton, Timothy A.; Tinker, Lesley E.; Uitterlinden, André G.; van Setten, Jessica; Voss, Andreas; Waldenberger, Melanie; Wilhelmsen, Kirk C.; Willemsen, Gonneke; Wong, Quenna; Zhang, Zhu-Ming; Zonderman, Alan B.; Cusi, Daniele; Evans, Michele K.; Greiser, Halina K.; van der Harst, Pim; Hassan, Mohammad; Ingelsson, Erik; Järvelin, Marjo-Riitta; Kääb, Stefan; Kähönen, Mika; Kivimaki, Mika; Kooperberg, Charles; Kuh, Diana; Lehtimäki, Terho; Lind, Lars; Nievergelt, Caroline M.; O'Donnell, Chris J.; Oldehinkel, Albertine J.; Penninx, Brenda; Reiner, Alexander P.; Riese, Harriëtte; van Roon, Arie M.; Rioux, John D.; Rotter, Jerome I.; Sofer, Tamar; Stricker, Bruno H.; Tiemeier, Henning; Vrijkotte, Tanja G. M.; Asselbergs, Folkert W.; Brundel, Bianca J. J. M.; Heckbert, Susan R.; Whitsel, Eric A.; den Hoed, Marcel; Snieder, Harold; de Geus, Eco J. C.

    2017-01-01

    Reduced cardiac vagal control reflected in low heart rate variability (HRV) is associated with greater risks for cardiac morbidity and mortality. In two-stage meta-analyses of genome-wide association studies for three HRV traits in up to 53,174 individuals of European ancestry, we detect 17 genome-wide significant SNPs in eight loci. HRV SNPs tag non-synonymous SNPs (in NDUFA11 and KIAA1755), expression quantitative trait loci (eQTLs) (influencing GNG11, RGS6 and NEO1), or are located in genes preferentially expressed in the sinoatrial node (GNG11, RGS6 and HCN4). Genetic risk scores account for 0.9 to 2.6% of the HRV variance. Significant genetic correlation is found for HRV with heart rate (−0.74heart rhythm regulation, with a key role for genetic variants (GNG11, RGS6) that influence G-protein heterotrimer action in GIRK-channel induced pacemaker membrane hyperpolarization. PMID:28613276

  11. Economic Statistical Design of Variable Sampling Interval X¯$\\overline X $ Control Chart Based on Surrogate Variable Using Genetic Algorithms

    Directory of Open Access Journals (Sweden)

    Lee Tae-Hoon

    2016-12-01

    Full Text Available In many cases, a X¯$\\overline X $ control chart based on a performance variable is used in industrial fields. Typically, the control chart monitors the measurements of a performance variable itself. However, if the performance variable is too costly or impossible to measure, and a less expensive surrogate variable is available, the process may be more efficiently controlled using surrogate variables. In this paper, we present a model for the economic statistical design of a VSI (Variable Sampling Interval X¯$\\overline X $ control chart using a surrogate variable that is linearly correlated with the performance variable. We derive the total average profit model from an economic viewpoint and apply the model to a Very High Temperature Reactor (VHTR nuclear fuel measurement system and derive the optimal result using genetic algorithms. Compared with the control chart based on a performance variable, the proposed model gives a larger expected net income per unit of time in the long-run if the correlation between the performance variable and the surrogate variable is relatively high. The proposed model was confined to the sample mean control chart under the assumption that a single assignable cause occurs according to the Poisson process. However, the model may also be extended to other types of control charts using a single or multiple assignable cause assumptions such as VSS (Variable Sample Size X¯$\\overline X $ control chart, EWMA, CUSUM charts and so on.

  12. Genetic variability and relationships for populations of Cerastoderma edule and of the C. Glaucum complex

    Science.gov (United States)

    Hummel, H.; Wolowicz, M.; Bogaards, R. H.

    Genetic variability and relationships of populations of the cockles Cerastoderma edule and of the C. glaucum complex in Europe were determined by means of isoenzyme electrophoresis. Distinct isoenzyme markers allowed a clear distinction between these two taxa. C edule showed a higher genetic intra-population variability than the other cockle species. The imbalance of the genotypes within popuulation and the inter-population differentiation of the C. glaucum complex are stronger than in C. edule. The genetic variability is related to the different habitats of the species, the members of the C. glaucum complex living in more isolated areas and having more limited gene flow.

  13. First evidence of genetic intraspecific variability and occurrence of Entamoeba gingivalis in HIV(+)/AIDS.

    Science.gov (United States)

    Cembranelli, Sibeli B S; Souto, Fernanda O; Ferreira-Paim, Kennio; Richinho, Túlio T; Nunes, Poliana L; Nascentes, Gabriel A N; Ferreira, Thatiana B; Correia, Dalmo; Lages-Silva, Eliane

    2013-01-01

    Entamoeba gingivalis is considered an oral commensal but demonstrates a pathogenic potential associated with periodontal disease in immunocompromised individuals. Therefore, this study evaluated the occurrence, opportunistic conditions, and intraspecific genetic variability of E. gingivalis in HIV(+)/AIDS patients. Entamoeba gingivalis was studied using fresh examination (FE), culture, and PCR from bacterial plaque samples collected from 82 HIV(+)/AIDS patients. Genetic characterization of the lower ribosomal subunit of region 18S (18S-SSU rRNA) was conducted in 9 positive samples using low-stringency single specific primer PCR (LSSP-PCR) and sequencing analysis. Entamoeba gingivalis was detected in 63.4% (52/82) of the samples. No association was detected between the presence of E. gingivalis and the CD4(+) lymphocyte count (≤200 cells/mm(3) (p = 0.912) or viral load (p = 0.429). The LSSP-PCR results helped group E. gingivalis populations into 2 polymorphic groups (68.3% similarity): group I, associated with 63.6% (7/11) of the samples, and group II, associated with 36.4% (4/11) of the samples, which shared 74% and 83.7% similarity and association with C and E isolates from HIV(-) individuals, respectively. Sequencing of 4 samples demonstrated 99% identity with the reference strain ATCC 30927 and also showed 2 divergent clusters, similar to those detected by LSSP-PCR. Opportunistic behavior of E. gingivalis was not detected, which may be related to the use of highly active antiretroviral therapy by all HIV(+)/AIDS patients. The high occurrence of E. gingivalis in these patients can be influenced by multifactorial components not directly related to the CD4(+) lymphocyte counts, such as cholesterol and the oral microbiota host, which could mask the potential opportunistic ability of E. gingivalis. The identification of the 18S SSU-rRNA polymorphism by LSSP-PCR and sequencing analysis provides the first evidence of genetic variability in E. gingivalis

  14. Gearbox Deterioration Detection under Steady State, Variable Load, and Variable Speed Conditions

    Institute of Scientific and Technical Information of China (English)

    SHAO Yimin; CHRIS K Mechcfske; OU Jiafu; HU Yumei

    2009-01-01

    Multiple dominant gear meshing frequencies are present in the vibration signals collected from gearboxes and the conventional spiky features that represent initial gear fault conditions are usually difficult to detect. In order to solve this problem, we propose a new gearbox deterioration detection technique based on autoregressive modeling and hypothesis testing in this paper. A stationary autoregressive model was built by using a normal vibration signal from each shaft. The established autoregressive model was then applied to process fault signals from each shaft of a two-stage gearbox. What this paper investigated is a combined technique which unites a time-varying autoregressive model and a two sample Kolmogorov-Smirnov goodness-of-fit test, to detect the deterioration of gearing system with simultaneously variable shaft speed and variable load. The time-varying autoregressive model residuals representing both healthy and faulty gear conditions were compared with the original healthy time-synchronons average signals. Compared with the traditional kurtosis statistic, this technique for gearbox deterioration detection has shown significant advantages in highlighting the presence of incipient gear fault in all different speed shafts involved in the meshing motion under variable conditions.

  15. Genetic variability of fatty acids in bovine milk

    Directory of Open Access Journals (Sweden)

    Soyeurt H.

    2008-01-01

    Full Text Available Fatty acids composition of bovine milk influences the technological properties of butterfat and also presents some potential benefits for human health. Impact of feeding on fat composition is well described in the literature; less information is available about the impact of genetics. Based on few studies, essentially conducted to isolate some feeding effect, the breed seemed to influence the fatty acids composition. The variation in the activity of δ-9 desaturase, key enzyme in the production of monounsaturated fatty acids and conjugated linoleic acids in milk, could explain these differences. Very few studies have been focussing on the estimation of genetic parameters of fatty acids composition. However, the moderate heritability estimates observed by these studies for the major fatty acids could suggest a potential genetic effect.

  16. Sylvatic plague reduces genetic variability in black-tailed prairie dogs.

    Science.gov (United States)

    Trudeau, Kristie M; Britten, Hugh B; Restani, Marco

    2004-04-01

    Small, isolated populations are vulnerable to loss of genetic diversity through in-breeding and genetic drift. Sylvatic plague due to infection by the bacterium Yersinia pestis caused an epizootic in the early 1990s resullting in declines and extirpations of many black-tailed prairie dog (Cynomys ludovicianus) colonies in north-central Montana, USA. Plague-induced population bottlenecks may contribute to significant reductions in genetic variability. In contrast, gene flow maintains genetic variability within colonies. We investigated the impacts of the plague epizootic and distance to nearest colony on levels of genetic variability in six prairie dog colonies sampled between June 1999 and July 2001 using 24 variable randomly amplified polymorphic DNA (RAPD) markers. Number of effective alleles per locus (n(e)) and gene diversity (h) were significantly decreased in the three colonies affected by plague that were recovering from the resulting bottlenecks compared with the three colonies that did not experience plague. Genetic variability was not significantly affected by geographic distance between colonies. The majority of variance in gene fieqnencies was found within prairie clog colonies. Conservation of genetic variability in black-tailed prairie dogs will require the preservation of both large and small colony complexes and the gene flow amonog them.

  17. Determination of genetic variability of traditional varieties of Brazilian rice using microsatellite markers

    Directory of Open Access Journals (Sweden)

    Claudio Brondani

    2006-01-01

    Full Text Available The rice (Oryza sativa breeding program of the Rice and Bean research center of the Brazilian agricultural company Empresa Brasileira de Pesquisa Agropecuária (Embrapa is well established and provides new cultivars every year to attend the demand for improved high yielding varieties with tolerance to biotic and abiotic stresses. However, the elite genitors used to compose new populations for selection are closely related, contributing to the yield plateau reached in the last 20 years. To overcome this limit, it is necessary to broaden the genetic basis of the cultivars using diverse germplasm such as wild relatives or traditional varieties, with the latter being more practical because they are more easily crossed with elite germplasm to accelerate the recovery of modern plant types in the breeding lines. The objective of our study was to characterize the allelic diversity of 192 traditional varieties of Brazilian rice using 12 simple sequence repeat (SSR or microsatellite markers. The germplasm was divided into 39 groups by common name similarity. A total of 176 alleles were detected, 30 of which (from 23 accessions were exclusive. The number of alleles per marker ranged from 6 to 22, with an average of 14.6 alleles per locus. We identified 16 accessions as a mixture of pure lines or heterozygous plants. Dendrogram analysis identified six clusters of identical accessions with different common names and just one cluster with identical accessions with the same common name, indicating that SSR markers are fundamental to determining the genetic relationship between landraces. A subset of 24 landraces, representatives of the 13 similarity groups plus the 11 accessions not grouped, was the most variable set of genotypes analyzed. These accessions can be used as genitors to increase the genetic variability available to rice breeding programs.

  18. Genetic variables of various manifestations of osteochondrosis and their correlations between and within joints in Dutch warmblood horses

    NARCIS (Netherlands)

    Grevenhof, van E.M.; Schurink, A.; Ducro, B.J.; Weeren, van P.R.; Tartwijk, van J.M.F.M.

    2009-01-01

    Osteochondrosis (OC) is an important orthopedic developmental disorder in many horse populations. A review of the literature revealed widely variable heritability estimates for the disorder. We estimated the genetic variables (heritabilities and genetic correlations) of various manifestations of OC.

  19. Multivariate Outlier Detection in Genetic Evaluation in Nordic Jersey Cattle

    DEFF Research Database (Denmark)

    Gao, Hongding; Madsen, Per; Pösö, Jukka

    A procedure was developed for detection of multivariate outliers based on an approximation for Mahanalobis Distance (MD) and was implemented in the Nordic Jersey population. Evaluations are carried out by Nordic Cattle Genetic Evaluation (NAV), who uses a 9 trait model for milk, protein and fat...

  20. Lightning Mapping Array flash detection performance with variable receiver thresholds

    Science.gov (United States)

    Chmielewski, Vanna C.; Bruning, Eric C.

    2016-07-01

    This study characterizes Lightning Mapping Array performance for networks that participated in the Deep Convective Clouds and Chemistry field program using new Monte Carlo and curvature matrix model simulations. These open-source simulation tools are readily adapted to real-time operations or detailed studies of performance. Each simulation accounted for receiver threshold and location, as well as a reference distribution of source powers and flash sizes based on thunderstorm observations and the mechanics of station triggering. Source and flash detection efficiency were combined with solution bias and variability to predict flash area distortion at long ranges. Location errors and detection efficiency were highly dependent on the station configuration and thresholds, especially at longer ranges, such that performance varied more than expected across different networks and with azimuth within networks. Error characteristics matched prior studies, which led to an increase in flash distortion with range. Predicted flash detection efficiency exceeded 95% within 100 km of all networks.

  1. Variable threshold method for ECG R-peak detection.

    Science.gov (United States)

    Kew, Hsein-Ping; Jeong, Do-Un

    2011-10-01

    In this paper, a wearable belt-type ECG electrode worn around the chest by measuring the real-time ECG is produced in order to minimize the inconvenient in wearing. ECG signal is detected using a potential instrument system. The measured ECG signal is transmits via an ultra low power consumption wireless data communications unit to personal computer using Zigbee-compatible wireless sensor node. ECG signals carry a lot of clinical information for a cardiologist especially the R-peak detection in ECG. R-peak detection generally uses the threshold value which is fixed. There will be errors in peak detection when the baseline changes due to motion artifacts and signal size changes. Preprocessing process which includes differentiation process and Hilbert transform is used as signal preprocessing algorithm. Thereafter, variable threshold method is used to detect the R-peak which is more accurate and efficient than fixed threshold value method. R-peak detection using MIT-BIH databases and Long Term Real-Time ECG is performed in this research in order to evaluate the performance analysis.

  2. Genetic variability in Sudanese Acacia senegal (L.) assessed by ...

    African Journals Online (AJOL)

    TUOYO

    2010-07-26

    Jul 26, 2010 ... Gum Arabic producing agroforestry tree species in. Sudan. A. senegal .... Algadamblia 4, simmer 2, Simmer 1 and Nabg as sisters,. (Alphil 1, alphil 2 as .... RAPD markers could be used for differentiating Acacia senegal genotypes ... the result of genetic stability due to long overlapping generations, and a ...

  3. Genetics Home Reference: familial focal epilepsy with variable foci

    Science.gov (United States)

    ... Med Genet. 2016 Aug;53(8):503-10. doi: 10.1136/jmedgenet-2016-103883. Review. Citation on PubMed Baulac S, Ishida S, Marsan E, Miquel C, Biraben A, Nguyen DK, Nordli D, Cossette P, ... 2015 Apr;77(4):675-83. doi: 10.1002/ana.24368. Epub 2015 Mar 13. ...

  4. Genetic Variability in Barley (Hordeum vulgare l.) Landraces from ...

    African Journals Online (AJOL)

    The phenotypic frequencies of morphological characters (qualitative ... of genetic variation among segregating progeny for pure line cultivar development ...... provided discrimination between landraces according to their origin because the .... categories of descriptors evolving along different evolutionary lines (Asfaw, 1989b ...

  5. Genetic Variability in Soybean (Glycine max L.) for Low Soil ...

    African Journals Online (AJOL)

    Abush Tesfaye

    The application of inorganic P fertilizers is one of the possibilities for addressing the problem of low P ..... (2011), traits combining such high H2 and genetic advance are predominantly controlled ..... Genstat Release 11.1 (PC/Windows). Wang ...

  6. Bayesian methods for meta-analysis of causal relationships estimated using genetic instrumental variables

    DEFF Research Database (Denmark)

    2010-01-01

    Genetic markers can be used as instrumental variables, in an analogous way to randomization in a clinical trial, to estimate the causal relationship between a phenotype and an outcome variable. Our purpose is to extend the existing methods for such Mendelian randomization studies to the context...... of multiple genetic markers measured in multiple studies, based on the analysis of individual participant data. First, for a single genetic marker in one study, we show that the usual ratio of coefficients approach can be reformulated as a regression with heterogeneous error in the explanatory variable....... This can be implemented using a Bayesian approach, which is next extended to include multiple genetic markers. We then propose a hierarchical model for undertaking a meta-analysis of multiple studies, in which it is not necessary that the same genetic markers are measured in each study. This provides...

  7. Genetic variability of Dactylopius opuntiae (Hemiptera, Dactylopiidae) on forage cactus in northeast Brazil.

    Science.gov (United States)

    Silva, D M P; do E S Mergulhão, A C; de Medeiros, L V; Figueiredo, M V B; Burity, H A

    2013-10-30

    The carmine cochineal Dactylopius opuntiae is a key pest in productive fields of forage cactus in Pernambuco, Brazil. Species identification by means of molecular markers assists in understanding the genetic profile, underpins morphological characterization, and supports the monitoring of populations in integrated management programs designed to control this pest. We evaluated the genetic variability of natural populations of D. opuntiae. Genetic variability was analyzed with ISSR and RAPD primers in 24 populations from 12 municipalities of Pernambuco State in Brazil. Morphological characterization confirmed that D. opuntiae was the only cochineal species present in all samples. Nine ISSR primers and six RAPD produced a total of 62 and 58 polymorphic fragments, respectively. Both types of markers showed an average genetic similarity of 80% regardless of the geographic origin of samples. The low genetic variability demonstrates a high degree of relatedness among these D. opuntiae populations.

  8. Safety assessment and detection methods of genetically modified organisms.

    Science.gov (United States)

    Xu, Rong; Zheng, Zhe; Jiao, Guanglian

    2014-01-01

    Genetically modified organisms (GMOs), are gaining importance in agriculture as well as the production of food and feed. Along with the development of GMOs, health and food safety concerns have been raised. These concerns for these new GMOs make it necessary to set up strict system on food safety assessment of GMOs. The food safety assessment of GMOs, current development status of safety and precise transgenic technologies and GMOs detection have been discussed in this review. The recent patents about GMOs and their detection methods are also reviewed. This review can provide elementary introduction on how to assess and detect GMOs.

  9. Genetic variability in the mitochondrial DNA of the Danish Pine marten

    DEFF Research Database (Denmark)

    Pertoldi, Cino; Muñoz, Joaquin; Madsen, Aksel Bo;

    2008-01-01

    Here we study genetic differentiation and changes over time in genetic variability in the rare pine marten Martes martes. Samples from three isolated geographic regions: Jutland and Sealand (Denmark) and southern Scania (southernmost Sweden), were genotyped by sequencing the hypervariable domain ...

  10. Genetic Instrumental Variable (GIV) Regression: Explaining Socioeconomic and Health Outcomes in Non-Experimental Data

    NARCIS (Netherlands)

    T.A. DiPrete (Thomas); C. Burik (Casper); Ph.D. Koellinger (Philipp)

    2017-01-01

    textabstractWe introduce Genetic Instrumental Variables (GIV) regression – a method to estimate causal effects in non-experimental data with many possible applications in the social sciences and epidemiology. In non-experimental data, genetic correlation between the outcome and the exposure of

  11. Microbialite genetic diversity and composition relate to environmental variables.

    Science.gov (United States)

    Centeno, Carla M; Legendre, Pierre; Beltrán, Yislem; Alcántara-Hernández, Rocío J; Lidström, Ulrika E; Ashby, Matthew N; Falcón, Luisa I

    2012-12-01

    Microbialites have played an important role in the early history of life on Earth. Their fossilized forms represent the oldest evidence of life on our planet dating back to 3500 Ma. Extant microbialites have been suggested to be highly productive and diverse communities with an evident role in the cycling of major elements, and in contributing to carbonate precipitation. Although their ecological and evolutionary importance has been recognized, the study of their genetic diversity is yet scanty. The main goal of this study was to analyse microbial genetic diversity of microbialites living in different types of environments throughout Mexico, including desert ponds, coastal lagoons and a crater-lake. We followed a pyrosequencing approach of hypervariable regions of the 16S rRNA gene. Results showed that microbialite communities were very diverse (H' = 6-7) and showed geographic variation in composition, as well as an environmental effect related to pH and conductivity, which together explained 33% of the genetic variation. All microbialites had similar proportions of major bacterial and archaeal phyla. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  12. Genetic components of litter size variability in sheep

    Directory of Open Access Journals (Sweden)

    Chevalet Claude

    2001-05-01

    Full Text Available Abstract Classical selection for increasing prolificacy in sheep leads to a concomitant increase in its variability, even though the objective of the breeder is to maximise the frequency of an intermediate litter size rather than the frequency of high litter sizes. For instance, in the Lacaune sheep breed raised in semi-intensive conditions, ewes lambing twins represent the economic optimum. Data for this breed, obtained from the national recording scheme, were analysed. Variance components were estimated in an infinitesimal model involving genes controlling the mean level as well as its environmental variability. Large heritability was found for the mean prolificacy, but a high potential for increasing the percentage of twins at lambing while reducing the environmental variability of prolificacy is also suspected. Quantification of the response to such a canalising selection was achieved.

  13. Genetic components of litter size variability in sheep

    Science.gov (United States)

    SanCristobal-Gaudy, Magali; Bodin, Loys; Elsen, Jean-Michel; Chevalet, Claude

    2001-01-01

    Classical selection for increasing prolificacy in sheep leads to a concomitant increase in its variability, even though the objective of the breeder is to maximise the frequency of an intermediate litter size rather than the frequency of high litter sizes. For instance, in the Lacaune sheep breed raised in semi-intensive conditions, ewes lambing twins represent the economic optimum. Data for this breed, obtained from the national recording scheme, were analysed. Variance components were estimated in an infinitesimal model involving genes controlling the mean level as well as its environmental variability. Large heritability was found for the mean prolificacy, but a high potential for increasing the percentage of twins at lambing while reducing the environmental variability of prolificacy is also suspected. Quantification of the response to such a canalising selection was achieved. PMID:11403747

  14. Genetics and early detection in idiopathic pulmonary fibrosis.

    Science.gov (United States)

    Putman, Rachel K; Rosas, Ivan O; Hunninghake, Gary M

    2014-04-01

    Genetic studies hold promise in helping to identify patients with early idiopathic pulmonary fibrosis (IPF). Recent studies using chest computed tomograms (CTs) in smokers and in the general population have demonstrated that imaging abnormalities suggestive of an early stage of pulmonary fibrosis are not uncommon and are associated with respiratory symptoms, physical examination abnormalities, and physiologic decrements expected, but less severe than those noted in patients with IPF. Similarly, recent genetic studies have demonstrated strong and replicable associations between a common promoter polymorphism in the mucin 5B gene (MUC5B) and both IPF and the presence of abnormal imaging findings in the general population. Despite these findings, it is important to note that the definition of early-stage IPF remains unclear, limited data exist to definitively connect abnormal imaging findings to IPF, and genetic studies assessing early-stage pulmonary fibrosis remain in their infancy. In this perspective we provide updated information on interstitial lung abnormalities and their connection to IPF. We summarize information on the genetics of pulmonary fibrosis by focusing on the recent genetic findings of MUC5B. Finally, we discuss the implications of these findings and suggest a roadmap for the use of genetics in the detection of early IPF.

  15. Comparison of gSSR and EST-SSR markers for analyzing genetic variability among tomato cultivars (Solanum lycopersicum L.).

    Science.gov (United States)

    Zhou, R; Wu, Z; Jiang, F L; Liang, M

    2015-10-27

    In order to study genetic variability and develop better strategies for the utilization of 48 tomato cultivars from America, China, the Netherlands, and Portugal, genomic simple sequence repeat (gSSR) and EST-derived SSR (EST-SSR) markers were applied. In all, 15 of 82 gSSR and 18 of 115 EST-SSR markers showed polymorphic loci. There were 995 and 2072 clear fragments amplified by polymorphic gSSR and EST-SSR markers, respectively. The total and average number of alleles detected by EST-SSRs (75, 4.2) was more than gSSRs (54, 3.6) as a result of some multi-locus EST-SSRs. A lower polymorphism information content value was found in gSSRs (0.529) compared to EST-SSRs (0.620). Similarity coefficient matrixes of the 48 tomato cultivars were established based on the gSSRs and EST-SSRs, and UPGMA dendrograms were constructed from the gSSRs and EST-SSRs similarity coefficient matrixes. A high similarity was observed between the gSSRs and EST-SSRs dendrograms. Genetic variability of four tomato populations from different countries showed that the observed number of alleles and Nei's genetic diversity were highest in the American population, and the effective number of alleles was highest in the Dutch population. The estimated genetic structure showed some tomato cultivars from different countries shared a common genetic background, which might be related to gene flow. It was inferred that both gSSR and EST-SSR markers were effective to assess genetic variability of tomato cultivars, and the combination of both markers could be more effective for genetic diversity analysis in tomato.

  16. Genetic variation in the vulnerable and endemic Monkey Puzzle tree, detected using RAPDs.

    Science.gov (United States)

    Bekessy, Sarah A; Allnutt, T R; Premoli, A C; Lara, A; Ennos, R A; Burgman, M A; Cortes, M; Newton, A C

    2002-04-01

    Araucaria araucana (Monkey Puzzle), a southern South American tree species of exceptional cultural and economic importance, is of conservation concern owing to extensive historical clearance and current human pressures. Random amplified polymorphic DNA (RAPD) markers were used to characterise genetic heterogeneity within and among 13 populations of this species from throughout its natural range. Extensive genetic variability was detected and partitioned by analysis of molecular variance, with the majority of variation existing within populations (87.2%), but significant differentiation was recorded among populations (12.8%). Estimates of Shannon's genetic diversity and percent polymorphism were relatively high for all populations and provide no evidence for a major reduction in genetic diversity from historical events, such as glaciation. All pairwise genetic distance values derived from analysis of molecular variance (Phi(ST)) were significant when individual pairs of populations were compared. Although populations are geographically divided into Chilean Coastal, Chilean Andes and Argentinean regions, this grouping explained only 1.77% of the total variation. Within Andean groups there was evidence of a trend of genetic distance with increasing latitude, and clustering of populations across the Andes, suggesting postglacial migration routes from multiple refugia. Implications of these results for the conservation and use of the genetic resource of this species are discussed.

  17. Genetic variability of Verbascum populations from metal polluted and unpolluted sites

    Directory of Open Access Journals (Sweden)

    Danilović Gordana

    2015-01-01

    Full Text Available Mullein (Verbascum plants have extensive distribution and can grow in variable environmental conditions. Seed was collected from mullein plants grown at 4 locations, two metals contaminated and two metal uncontaminated areas. Genetic variability of progeny was examined. Populations collected from unpolluted areas were genetically more similar than those collected from polluted areas as revealed by RAPD and SSR markers and UPGMA analysis. The results indicate that there is genetic differentiation between examined populations and therefore they represent suitable material for further investigation of plant adaptation mechanisms to increased metal content. [Projekat Ministarstva nauke Republike Srbije, br. III43010

  18. Current perspectives on genetically modified crops and detection methods.

    Science.gov (United States)

    Kamle, Madhu; Kumar, Pradeep; Patra, Jayanta Kumar; Bajpai, Vivek K

    2017-07-01

    Genetically modified (GM) crops are the fastest adopted commodities in the agribiotech industry. This market penetration should provide a sustainable basis for ensuring food supply for growing global populations. The successful completion of two decades of commercial GM crop production (1996-2015) is underscored by the increasing rate of adoption of genetic engineering technology by farmers worldwide. With the advent of introduction of multiple traits stacked together in GM crops for combined herbicide tolerance, insect resistance, drought tolerance or disease resistance, the requirement of reliable and sensitive detection methods for tracing and labeling genetically modified organisms in the food/feed chain has become increasingly important. In addition, several countries have established threshold levels for GM content which trigger legally binding labeling schemes. The labeling of GM crops is mandatory in many countries (such as China, EU, Russia, Australia, New Zealand, Brazil, Israel, Saudi Arabia, Korea, Chile, Philippines, Indonesia, Thailand), whereas in Canada, Hong Kong, USA, South Africa, and Argentina voluntary labeling schemes operate. The rapid adoption of GM crops has increased controversies, and mitigating these issues pertaining to the implementation of effective regulatory measures for the detection of GM crops is essential. DNA-based detection methods have been successfully employed, while the whole genome sequencing using next-generation sequencing (NGS) technologies provides an advanced means for detecting genetically modified organisms and foods/feeds in GM crops. This review article describes the current status of GM crop commercialization and discusses the benefits and shortcomings of common and advanced detection systems for GMs in foods and animal feeds.

  19. Bayesian methods for meta-analysis of causal relationships estimated using genetic instrumental variables

    DEFF Research Database (Denmark)

    Burgess, Stephen; Thompson, Simon G; Andrews, G

    2010-01-01

    Genetic markers can be used as instrumental variables, in an analogous way to randomization in a clinical trial, to estimate the causal relationship between a phenotype and an outcome variable. Our purpose is to extend the existing methods for such Mendelian randomization studies to the context o...

  20. Identifying genetic variants for heart rate variability in the acetylcholine pathway

    NARCIS (Netherlands)

    Riese, Harriëtte; Muñoz Venegas, Loretto; Hartman, Catharina A; Ding, Xiuhua; Su, Shaoyong; Oldehinkel, Albertine J; van Roon, Arie M; van der Most, Peter J; Lefrandt, Joop; Gansevoort, Ronald; van der Harst, Pim; Verweij, Niek; Licht, Carmilla M M; Boomsma, Dorret I; Hottenga, Jouke-Jan; Willemsen, Gonneke; Penninx, Brenda W J H; Nolte, Ilja M; de Geus, Eco J C; Wang, Xiaoling; Snieder, Harold

    2014-01-01

    Heart rate variability is an important risk factor for cardiovascular disease and all-causemortality. The acetylcholine pathway plays a key role in explaining heart rate variability in humans. We assessed whether 443 genotyped and imputed common genetic variants in eight key genes (CHAT, SLC18A3,

  1. Genetic variability in captive populations of the stingless bee Tetragonisca angustula.

    Science.gov (United States)

    Santiago, Leandro R; Francisco, Flávio O; Jaffé, Rodolfo; Arias, Maria C

    2016-08-01

    Low genetic variability has normally been considered a consequence of animal husbandry and a major contributing factor to declining bee populations. Here, we performed a molecular analysis of captive and wild populations of the stingless bee Tetragonisca angustula, one of the most commonly kept species across South America. Microsatellite analyses showed similar genetic variability between wild and captive populations However, captive populations showed lower mitochondrial genetic variability. Male-mediated gene flow, transport and division of nests are suggested as the most probable explanations for the observed patterns of genetic structure. We conclude that increasing the number of colonies kept through nest divisions does not negatively affect nuclear genetic variability, which seems to be maintained by small-scale male dispersal and human-mediated nest transport. However, the transport of nests from distant localities should be practiced with caution given the high genetic differentiation observed between samples from western and eastern areas. The high genetic structure verified is the result of a long-term evolutionary process, and bees from distant localities may represent unique evolutionary lineages.

  2. GENETIC VARIABILITY AND CORRELATION STUDIES IN BRINJAL (SOLANUM MELONGENA L.)

    OpenAIRE

    Bhukya Ravi Nayak; P. K. Nagre

    2013-01-01

    The present investigation was conducted at Department of Horticulture, Horticulture Garden, Dr. PDKV, Akola (M.S.), during kharif 2012-13. The experimental material comprised of 20 genotypes along with one check of brinjal and the experimental was laid out in randomized block design with three replications. Variability studies revealed that highly significant differences were recorded among the varieties for all characters. Correlation and path analysis revealed that fruit length, diameter, w...

  3. Variables Affecting Secondary School Students' Willingness to Eat Genetically Modified Food Crops

    Science.gov (United States)

    Maes, Jasmien; Bourgonjon, Jeroen; Gheysen, Godelieve; Valcke, Martin

    2017-04-01

    A large-scale cross-sectional study (N = 4002) was set up to determine Flemish secondary school students' willingness to eat genetically modified food (WTE) and to link students' WTE to previously identified key variables from research on the acceptance of genetic modification (GM). These variables include subjective and objective knowledge about genetics and biotechnology, perceived risks and benefits of GM food crops, trust in information from different sources about GM, and food neophobia. Differences between WTE-related variables based on students' grade level, educational track, and gender were analyzed. The students displayed a rather indecisive position toward GM food and scored weakly on a genetics and biotechnology knowledge test. WTE correlated most strongly with perceived benefits and subjective and objective knowledge. The results have clear implications for education, as they reiterate the need to strengthen students' scientific knowledge base and to introduce a GM-related debate at a much earlier stage in their school career.

  4. Detection of sequence variability of the collagen type IIalpha 1 3' variable number of tandem repeat.

    Science.gov (United States)

    van Meurs, J B; Arp, P P; Fang, Y; Slagboom, P E; Meulenbelt, I; van Leeuwen, J P; Pols, H A; Uitterlinden, A G

    2000-11-01

    The variable number of tandem repeat (VNTR) 3' of the collagen type II (COL2A1) gene has been shown to be highly variable with a complex molecular structure. In a previous pilot experiment we observed discordance between methods to genotype this informative marker. To further investigate the extent and molecular nature of this discordance, we genotyped a random sample of 207 Caucasian individuals with two genotyping methods and sequenced new alleles. We compared single-strand (SS) analysis, which is based on detection of size differences between the different alleles, and heteroduplex analysis (HA), which is sensitive to both size and sequence differences. Overall, 26% of discordance between the two methods was detected. Approximately two thirds of this discordance was caused by subdivision of SS-alleles 13R1 and 14R2 into HA-alleles 4A + 4B and 3B + 3C, respectively. Sequence analysis of the COL2A1 VNTR alleles 4B and 3C showed that these alleles differed in sequence, but not in size, from already described SS-alleles, which explains why they escape detection by SS. The 4B allele is a frequent allele in the population (14%) and is, therefore, important to distinguish in association studies. We conclude that HA is a reliable method when the described optimized electrophoretic conditions are used. HA is a sensitive genotyping method to document allelic diversity at this locus, which can distinguish more alleles compared to the SS method.

  5. Assessing genetic variability in two ancient chicken breeds of Padova area

    Directory of Open Access Journals (Sweden)

    Martino Cassandro

    2010-01-01

    Full Text Available Genetic diversity in two ancient indigenous chicken breeds of the Veneto region was assessed using Amplified Fragment Length Polymorphism (AFLP markers. A total of 63 individuals were analysed using three selected AFLP primer combinations that produced 66 clear polymorphisms. The breeds analyzed were the Padovana and the Polverara (two ancient breeds and a reference broiler line. The expected heterozygosity (Het did not differ significantly among breeds. The variability at AFLP loci was largely maintained across breeds, as indicated by the coefficient of genetic differentiation (Gst value. The lowest genetic distance is found between the Padovana and Polverara breeds suggesting that they could be genetically close.

  6. An Adaptive Immune Genetic Algorithm for Edge Detection

    Science.gov (United States)

    Li, Ying; Bai, Bendu; Zhang, Yanning

    An adaptive immune genetic algorithm (AIGA) based on cost minimization technique method for edge detection is proposed. The proposed AIGA recommends the use of adaptive probabilities of crossover, mutation and immune operation, and a geometric annealing schedule in immune operator to realize the twin goals of maintaining diversity in the population and sustaining the fast convergence rate in solving the complex problems such as edge detection. Furthermore, AIGA can effectively exploit some prior knowledge and information of the local edge structure in the edge image to make vaccines, which results in much better local search ability of AIGA than that of the canonical genetic algorithm. Experimental results on gray-scale images show the proposed algorithm perform well in terms of quality of the final edge image, rate of convergence and robustness to noise.

  7. Epidemiology and genetic variability of HHV-8/KSHV in Pygmy and Bantu populations in Cameroon.

    Directory of Open Access Journals (Sweden)

    Edouard Betsem

    2014-05-01

    Full Text Available BACKGROUND: Kaposi's sarcoma associated herpesvirus (KSHV/HHV-8 is the causal agent of all forms of Kaposi sarcoma. Molecular epidemiology of the variable K1 region identified five major subtypes exhibiting a clear geographical clustering. The present study is designed to gain new insights into the KSHV epidemiology and genetic diversity in Cameroon. METHODOLOGY/PRINCIPAL FINDINGS: Bantu and Pygmy populations from remote rural villages were studied. Antibodies directed against latent nuclear antigens (LANA were detected by indirect immunofluorescence using BC3 cells. Peripheral blood cell DNAs were subjected to a nested PCR amplifying a 737 bp K1 gene fragment. Consensus sequences were phylogenetically analyzed. We studied 2,063 persons (967 females, 1,096 males, mean age 39 years, either Bantus (1,276 or Pygmies (787. The Bantu group was older (42 versus 35 years: P<10(-4. KSHV anti-LANA seroprevalence was of 37.2% (768/2063, with a significant increase with age (P<10(-4 but no difference according to sex. Seroprevalence, as well as the anti-LANA antibodies titres, were higher in Bantus (43.2% than in Pygmies (27.6% (P<10(-4, independently of age. We generated 29 K1 sequences, comprising 24 Bantus and five Pygmies. These sequences belonged to A5 (24 cases or B (five cases subtypes. They exhibited neither geographical nor ethnic aggregation. A5 strains showed a wide genetic diversity while the B strains were more homogenous and belonged to the B1 subgroup. CONCLUSION: These data demonstrate high KSHV seroprevalence in the two major populations living in Southern and Eastern Cameroon with presence of mostly genetically diverse A5 but also B K1 subtypes.

  8. Genetic variability in the Florida manatee (Trichechus manatus)

    Science.gov (United States)

    McClenaghan, Leroy R.; O'Shea, Thomas J.

    1988-01-01

    Tissue was obtained from 59 manatee (Trichechus manatus) carcasses salvaged from 20 counties in Florida. Allozyme phenotypes at 24 structural loci were determined by gel electrophoresis. Averages for the proportion of polymorphic loci and mean heterozygosity were 0.300 (range, 0.167-0.417) and 0.050 (range, 0.028-0.063), respectively. These estimates are equivalent to or higher than those generally reported for other species of marine mammals and do not support the hypothesis that body size and heterozygosity in mammals are related inversely. Among-region gene diversity accounted for only 4% of the total diversity. High rates of gene flow probably account for genetic homogeneity across regions. An F-statistic analysis revealed a general tendency toward excess homozygosity within regions. Management efforts to prevent future reductions in population size that would erode existing genic diversity should continue.

  9. Influence from genetic variability on opioid use for cancer pain: a European genetic association study of 2294 cancer pain patients

    DEFF Research Database (Denmark)

    Klepstad, P; Fladvad, T; Skorpen, F;

    2011-01-01

    Cancer pain patients need variable opioid doses. Preclinical and clinical studies suggest that opioid efficacy is related to genetic variability. However, the studies have small samples, findings are not replicated, and several candidate genes have not been studied. Therefore, a study of genetic...... variability with opioid doses in a large population using a confirmatory validation population was warranted. We recruited 2294 adult European patients using a World Health Organization (WHO) step III opioid and analyzed single nucleotide polymorphisms (SNPs) in genes with a putative influence on opioid...... mechanisms. The patients' mean age was 62.5 years, and the average pain intensity was 3.5. The patients' primary opioids were morphine (n=830), oxycodone (n=446), fentanyl (n=699), or other opioids (n=234). Pain intensity, time on opioids, age, gender, performance status, and bone or CNS metastases predicted...

  10. Genetic variability of Triatoma flavida and Triatoma bruneri (Hemiptera: Reduviidae by RAPD-PCR technique

    Directory of Open Access Journals (Sweden)

    Jorge Fraga

    2011-02-01

    Full Text Available The Triatominae (Hemiptera:Reduviidae contains the principal and potential Chagas disease vectors present in Mexico, Central America and South America. Triatoma flavida and T. bruneri are Cuban species. These species are closely related according to morphology and were considered synonyms until 1981, when they were separated on the grounds of external characters of the body and the morphology of male genitalia. The present study seeks to analyze genetic polymorphism of T. flavida and T. bruneri populations using RAPD techniques, and to assess the genetic relationship between these species. Ten random primers were used to evaluate the genetic variability among species using RAPD-PCR. The genetic flow among them was calculated. The dendrogram based on calculated Jaccard distances showed two clearly distinguishable clusters which coincided with the studied species. Within each species, moderate genetic differentiation (Fst 0.05-0.15 and migration rates (N > 1 were found among populations, that reveal gene flow and genetic homogeneity. Between species, the Fst value showed a high genetic differentiation and the migration rate was insufficient to maintain genetic homogeneity, and confirmed the absence of gene flow between them. Our results confirm the genetic variability among T. flavida and T. bruneri species.

  11. Genetic variability of Triatoma flavida and Triatoma bruneri (Hemiptera: Reduviidae) by RAPD-PCR technique.

    Science.gov (United States)

    Fraga, Jorge; Rodriguez, Jinnay; Fuentes, Omar; Hernández, Yenin; Castex, Mayda; Gonzalez, Raul; Fernández-Calienes, Aymé

    2011-01-01

    The Triatominae (Hemiptera:Reduviidae) contains the principal and potential Chagas disease vectors present in Mexico, Central America and South America. Triatoma flavida and T. bruneri are Cuban species. These species are closely related according to morphology and were considered synonyms until 1981, when they were separated on the grounds of external characters of the body and the morphology of male genitalia. The present study seeks to analyze genetic polymorphism of T. flavida and T. bruneri populations using RAPD techniques, and to assess the genetic relationship between these species. Ten random primers were used to evaluate the genetic variability among species using RAPD-PCR. The genetic flow among them was calculated. The dendrogram based on calculated Jaccard distances showed two clearly distinguishable clusters which coincided with the studied species. Within each species, moderate genetic differentiation (Fst 0.05-0.15) and migration rates (N > 1) were found among populations, that reveal gene flow and genetic homogeneity. Between species, the Fst value showed a high genetic differentiation and the migration rate was insufficient to maintain genetic homogeneity, and confirmed the absence of gene flow between them. Our results confirm the genetic variability among T. flavida and T. bruneri species.

  12. Effects of HBV Genetic Variability on RNAi Strategies

    Directory of Open Access Journals (Sweden)

    Nattanan Panjaworayan

    2011-01-01

    Full Text Available RNAi strategies present promising antiviral strategies against HBV. RNAi strategies require base pairing between short RNAi effectors and targets in the HBV pregenome or other RNAs. Natural variation in HBV genotypes, quasispecies variation, or mutations selected by the RNAi strategy could potentially make these strategies less effective. However, current and proposed antiviral strategies against HBV are being, or could be, designed to avoid this. This would involve simultaneous targeting of multiple regions of the genome, or regions in which variation or mutation is not tolerated. RNAi strategies against single genotypes or against variable regions of the genome would need to have significant other advantages to be part of robust therapies.

  13. Genetic diversity and variability in two Italian autochthonous donkey genetic types assessed by microsatellite markers

    Directory of Open Access Journals (Sweden)

    Donato Matassino

    2014-01-01

    Full Text Available Since 13rd century, Italian domestic autochthonous donkey population has been characterised by Mediterranean grey mousy cruciate ancestral phenotype, currently typical of Amiata donkey (AD genetic type. This phenotype persisted up to the 16th century when a marked introduction of Hispanic and French big sized and dark bay or darkish coloured sires occurred. In the context of a safeguard programme of Latial Equide resources, the aim of this research was to evaluate the genetic diversity and similarity between the AD breed and an autochthonous donkey population native from Lazio, the Viterbese donkey (VD, using molecular markers. A total of 135 animals (50 AD and 85 VD were genetically characterised by using 16 short tandem repeat markers. A high genetic differentiation between populations (FST=0.158; P<0.01 and a low betweenbreeds genetic similarity (0.233±0.085 were observed. Correspondence analysis, the result of STRUCTURE software analysis and analysis of molecular variance would seem to indicate genetically different entities as well. It would be desirable to increase the number of comparison with other breeds to better understand the origin of VD. Moreover, results obtained in this study suggest that the loss of genetic variation observed in VD could mainly derive from unnoticed sub-population structuring (Wahlund effect, rather than to other factors such as inbreeding, null alleles or selection influence.

  14. Genetic variation in variability: phenotypic variability of fledging weight and its evolution in a songbird population

    NARCIS (Netherlands)

    Mulder, H.A.; Gienapp, P; Visser, ME

    2016-01-01

    Variation in traits is essential for natural selection to operate and genetic and environmental effects can contribute to this phenotypic variation. From domesticated populations, we know that families can differ in their level of within-family variance, which leads to the intriguing situation that

  15. Genetic variation in variability : phenotypic variability of fledging weight and its evolution in a songbird population

    NARCIS (Netherlands)

    Mulder, Han A.; Gienapp, P; Visser, Marcel

    2016-01-01

    Variation in traits is essential for natural selection to operate and genetic and environmental effects can contribute to this phenotypic variation. From domesticated populations we know that families can differ in their level of within-family variance, which leads to the intriguing situation that w

  16. Sleep apnea detection using time-delayed heart rate variability.

    Science.gov (United States)

    Nano, Marina-Marinela; Xi Long; Werth, Jan; Aarts, Ronald M; Heusdens, Richard

    2015-01-01

    Sleep apnea is a sleep disorder distinguished by repetitive absence of breathing. Compared with the traditional expensive and cumbersome methods, sleep apnea diagnosis or screening with physiological information that can be easily acquired is needed. This paper describes algorithms using heart rate variability (HRV) to automatically detect sleep apneas as long as it can be easily acquired with unobtrusive sensors. Because the changes in cardiac activity are usually hysteretic than the presence of apneas with a few minutes, we propose to use the delayed HRV features to identify the episodes with sleep apneic events. This is expected to help improve the apnea detection performance. Experiments were conducted with a data set of 23 sleep apnea patients using support vector machine (SVM) classifiers and cross validations. Results show that using eleven HRV features with a time delay of 1.5 minutes rather than the features without time delay for SA detection, the overall accuracy increased from 74.9% to 76.2% and the Cohen's Kappa coefficient increased from 0.49 to 0.52. Further, an accuracy of 94.5% and a Kappa of 0.89 were achieved when applying subject-specific classifiers.

  17. Genetic variability and population structure of endangered Panax ginseng in the Russian Primorye

    Directory of Open Access Journals (Sweden)

    Muzarok Tamara I

    2010-06-01

    Full Text Available Abstract Background The natural habitat of wild P. ginseng is currently found only in the Russian Primorye and the populations are extremely exhausted and require restoration. Analysis of the genetic diversity and population structure of an endangered species is a prerequisite for conservation. The present study aims to investigate the patterns and levels of genetic polymorphism and population structures of wild P. ginseng with the AFLP method to (1 estimate the level of genetic diversity in the P. ginseng populations in the Russian Primorsky Krai, (2 calculate the distribution of variability within a population and among populations and (3 examine the genetic relationship between the populations. Methods Genetic variability and population structure of ten P. ginseng populations were investigated with Amplified Fragment Length Polymorphism (AFLP markers. The genetic relationships among P. ginseng plants and populations were delineated. Results The mean genetic variability within populations was high. The mean level of polymorphisms was 55.68% at the population level and 99.65% at the species level. The Shannon's index ranged between 0.1602 and 0.3222 with an average of 0.2626 at the population level and 0.3967 at the species level. The analysis of molecular variances (AMOVA showed a significant population structure in P. ginseng. The partition of genetic diversity with AMOVA suggested that the majority of the genetic variation (64.5% was within populations of P. ginseng. The inter-population variability was approximately 36% of the total variability. The genetic relationships among P. ginseng plants and populations were reconstructed by Minimum Spanning tree (MS-tree on the basis of Euclidean distances with ARLEQUIN and NTSYS, respectively. The MS-trees suggest that the southern Uss, Part and Nad populations may have promoted P. ginseng distribution throughout the Russian Primorye. Conclusion The P. ginseng populations in the Russian Primorye

  18. Genetic variability of Taenia saginata inferred from mitochondrial DNA sequences.

    Science.gov (United States)

    Rostami, Sima; Salavati, Reza; Beech, Robin N; Babaei, Zahra; Sharbatkhori, Mitra; Harandi, Majid Fasihi

    2015-04-01

    Taenia saginata is an important tapeworm, infecting humans in many parts of the world. The present study was undertaken to identify inter- and intraspecific variation of T. saginata isolated from cattle in different parts of Iran using two mitochondrial CO1 and 12S rRNA genes. Up to 105 bovine specimens of T. saginata were collected from 20 slaughterhouses in three provinces of Iran. DNA were extracted from the metacestode Cysticercus bovis. After PCR amplification, sequencing of CO1 and 12S rRNA genes were carried out and two phylogenetic analyses of the sequence data were generated by Bayesian inference on CO1 and 12S rRNA sequences. Sequence analyses of CO1 and 12S rRNA genes showed 11 and 29 representative profiles respectively. The level of pairwise nucleotide variation between individual haplotypes of CO1 gene was 0.3-2.4% while the overall nucleotide variation among all 11 haplotypes was 4.6%. For 12S rRNA sequence data, level of pairwise nucleotide variation was 0.2-2.5% and the overall nucleotide variation was determined as 5.8% among 29 haplotypes of 12S rRNA gene. Considerable genetic diversity was found in both mitochondrial genes particularly in 12S rRNA gene.

  19. Genetic variation in variability: Phenotypic variability of fledging weight and its evolution in a songbird population.

    Science.gov (United States)

    Mulder, Han A; Gienapp, Philip; Visser, Marcel E

    2016-09-01

    Variation in traits is essential for natural selection to operate and genetic and environmental effects can contribute to this phenotypic variation. From domesticated populations, we know that families can differ in their level of within-family variance, which leads to the intriguing situation that within-family variance can be heritable. For offspring traits, such as birth weight, this implies that within-family variance in traits can vary among families and can thus be shaped by natural selection. Empirical evidence for this in wild populations is however lacking. We investigated whether within-family variance in fledging weight is heritable in a wild great tit (Parus major) population and whether these differences are associated with fitness. We found significant evidence for genetic variance in within-family variance. The genetic coefficient of variation (GCV) was 0.18 and 0.25, when considering fledging weight a parental or offspring trait, respectively. We found a significant quadratic relationship between within-family variance and fitness: families with low or high within-family variance had lower fitness than families with intermediate within-family variance. Our results show that within-family variance can respond to selection and provides evidence for stabilizing selection on within-family variance. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

  20. Genetic variability testing of neurodevelopmental genes in schizophrenic patients.

    Science.gov (United States)

    Terzić, Tea; Kastelic, Matej; Dolžan, Vita; Plesničar, Blanka Kores

    2015-05-01

    This study investigated the associations between single nucleotide polymorphisms in the neurodevelopmental Disrupted In Schizophrenia 1 (DISC1 ), neuregulin 1 (NRG1), brain-derived neurotrophic factor (BDNF) and NOTCH4 genes and the clinical symptoms and the occurrence of treatment-resistant schizophrenia in the Slovenian population. We included 138 schizophrenia patients, divided into treatment-responsive and treatment-resistant group and 94 healthy blood donors. All subjects were genotyped for eight polymorphisms (DISC1 rs6675281, DISC1 rs821616, NRG1 rs3735781, NRG1 rs3735782, NRG1 rs10503929, NRG1 rs3924999, BDNF rs6265, NOTCH rs367398) and investigated for associations with clinical variables. NOTCH4 rs367398 AA/AG was significantly associated with worse Positive and Negative Syndrome Scale (PANSS) and Clinical Global Impression (CGI) score. NOTCH4 rs367398 was not statistically significantly associated with the occurrence of treatment-resistant schizophrenia after the correction for multiple testing. Our data indicate that NOTCH4 polymorphism can influence clinical symptoms in Slovenian patients with schizophrenia.

  1. Disentangling the effects of genetic, prenatal and parenting influences on children’s cortisol variability

    OpenAIRE

    MARCEAU, KRISTINE; Ram, Nilam; Neiderhiser, Jenae M.; Laurent, Heidemarie K.; Daniel S Shaw; Fisher, Phil; Natsuaki, Misaki N.; Leve, Leslie D.

    2013-01-01

    Developmental plasticity models hypothesize the role of genetic and prenatal environmental influences on the development of the hypothalamic–pituitary–adrenal (HPA) axis and highlight that genes and the prenatal environment may moderate early postnatal environmental influences on HPA functioning. This article examines the interplay of genetic, prenatal and parenting influences across the first 4.5 years of life on a novel index of children’s cortisol variability. Repeated measures data were o...

  2. Genetic variability of lactoferrin content estimated by mid-infrared spectrometry in bovine milk

    OpenAIRE

    Soyeurt, Hélène; Colinet, Frédéric; Arnould, Valérie; Dardenne, Pierre; Bertozzi, Carlo; Renaville, Robert; Portetelle, Daniel; Gengler, Nicolas

    2007-01-01

    The effects of lactoferrin (LF) on the immune system have already been shown by many studies. Unfortunately, the current methods used to measure LF levels in milk do not permit the study of the genetic variability of lactoferrin or the performance of routine genetic evaluations. The first aim of this research was to derive a calibration equation permitting the prediction of LF in milk by mid-infrared spectrometry (MIR). The calibration with partial least squares on 69 ...

  3. Hybrid model based on Genetic Algorithms and SVM applied to variable selection within fruit juice classification.

    Science.gov (United States)

    Fernandez-Lozano, C; Canto, C; Gestal, M; Andrade-Garda, J M; Rabuñal, J R; Dorado, J; Pazos, A

    2013-01-01

    Given the background of the use of Neural Networks in problems of apple juice classification, this paper aim at implementing a newly developed method in the field of machine learning: the Support Vector Machines (SVM). Therefore, a hybrid model that combines genetic algorithms and support vector machines is suggested in such a way that, when using SVM as a fitness function of the Genetic Algorithm (GA), the most representative variables for a specific classification problem can be selected.

  4. Do clones degenerate over time? Explaining the genetic variability of asexuals through population genetic models

    Directory of Open Access Journals (Sweden)

    Drozd Pavel

    2011-03-01

    Full Text Available Abstract Background Quest for understanding the nature of mechanisms governing the life span of clonal organisms lasts for several decades. Phylogenetic evidence for recent origins of most clones is usually interpreted as proof that clones suffer from gradual age-dependent fitness decay (e.g. Muller's ratchet. However, we have shown that a neutral drift can also qualitatively explain the observed distribution of clonal ages. This finding was followed by several attempts to distinguish the effects of neutral and non-neutral processes. Most recently, Neiman et al. 2009 (Ann N Y Acad Sci.:1168:185-200. reviewed the distribution of asexual lineage ages estimated from a diverse array of taxa and concluded that neutral processes alone may not explain the observed data. Moreover, the authors inferred that similar types of mechanisms determine maximum asexual lineage ages in all asexual taxa. In this paper we review recent methods for distinguishing the effects of neutral and non-neutral processes and point at methodological problems related with them. Results and Discussion We found that contemporary analyses based on phylogenetic data are inadequate to provide any clear-cut answer about the nature and generality of processes affecting evolution of clones. As an alternative approach, we demonstrate that sequence variability in asexual populations is suitable to detect age-dependent selection against clonal lineages. We found that asexual taxa with relatively old clonal lineages are characterised by progressively stronger deviations from neutrality. Conclusions Our results demonstrate that some type of age-dependent selection against clones is generally operational in asexual animals, which cover a wide taxonomic range spanning from flatworms to vertebrates. However, we also found a notable difference between the data distribution predicted by available models of sequence evolution and those observed in empirical data. These findings point at the

  5. Genetic variability of histamine receptors in patients with Parkinson's disease

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    Martínez Carmen

    2008-03-01

    Full Text Available Abstract Background Changes in the density and expression of histamine receptors (HRH have been detected in Parkinson's disease (PD patients, and HRH antagonists bring about improvements in motor and other symptoms, thus suggesting that HRH play a role in the clinical response of PD patients. This study is aimed to analyse polymorphic variations of HRH in patients with PD. Methods Leukocytary DNA from 195 PD patients and a control group of 231 unrelated healthy individuals was studied for the nonsynonymous HRH1Leu449Ser and the promoter HRH2G-1018A polymorphisms by using amplification-restriction analyses. Results The HRH1Leu449Ser amino acid substitution was identified in two women with late-onset PD whereas it was not observed among healthy subjects. The HRH2G-1018A polymorphism was observed with allele frequencies = 3.59 (95% CI = 1.74–5.44 and 5.0 (95% CI = 3.00–6.96 for patients with PD and healthy controls, respectively. These frequencies were independent of gender and age of onset of the disease. Multiple comparison analyses revealed that differences were not statistically significant. Conclusion These results indicate that the polymorphisms analyzed are not a major risk factor for PD, although the HRH1Leu449Ser amino acid substitution might be related to PD.

  6. Perspectives on genetically modified crops and food detection

    Directory of Open Access Journals (Sweden)

    Chih-Hui Lin

    2016-01-01

    Full Text Available Genetically modified (GM crops are a major product of the global food industry. From 1996 to 2014, 357 GM crops were approved and the global value of the GM crop market reached 35% of the global commercial seed market in 2014. However, the rapid growth of the GM crop-based industry has also created controversies in many regions, including the European Union, Egypt, and Taiwan. The effective detection and regulation of GM crops/foods are necessary to reduce the impact of these controversies. In this review, the status of GM crops and the technology for their detection are discussed. As the primary gap in GM crop regulation exists in the application of detection technology to field regulation, efforts should be made to develop an integrated, standardized, and high-throughput GM crop detection system. We propose the development of an integrated GM crop detection system, to be used in combination with a standardized international database, a decision support system, high-throughput DNA analysis, and automated sample processing. By integrating these technologies, we hope that the proposed GM crop detection system will provide a method to facilitate comprehensive GM crop regulation.

  7. Electrochemiluminescence-PCR detection of genetically modified organisms

    Science.gov (United States)

    Liu, Jinfeng; Xing, Da; Shen, Xingyan; Zhu, Debin

    2005-01-01

    The detection methods for genetically modified (GM) components in foods have been developed recently. But many of them are complicated and time-consuming; some of them need to use the carcinogenic substance, and can"t avoid false-positive results. In this study, an electrochemiluminescence polymerase chain reaction (ECL-PCR) method for detection GM tobaccos is proposed. The Cauliflower mosaic virus 35S (CaMV35S) promoter was amplified by PCR, Then hybridized with a Ru(bpy)32+ (TBR)-labeled and a biotinylated probe. The hybridization products were captured onto streptavidin-coated paramagnetic beads, and detected by measuring the electrochemiluminescence (ECL) signal of the TBR label. Whether the tobaccos contain GM components was discriminated by detecting the ECL signal of CaMV35S promoter. The experiment results show that the detection limit for CaMV35S promoter is 100 fmol, and the GM components can be clearly identified in GM tobaccos. The ECL-PCR method provide a new means in GMOs detection due to its safety, simplicity and high efficiency.

  8. Influence from genetic variability on opioid use for cancer pain: a European genetic association study of 2294 cancer pain patients

    DEFF Research Database (Denmark)

    Klepstad, P; Fladvad, T; Skorpen, F;

    2011-01-01

    Cancer pain patients need variable opioid doses. Preclinical and clinical studies suggest that opioid efficacy is related to genetic variability. However, the studies have small samples, findings are not replicated, and several candidate genes have not been studied. Therefore, a study of genetic...... mechanisms. The patients' mean age was 62.5 years, and the average pain intensity was 3.5. The patients' primary opioids were morphine (n=830), oxycodone (n=446), fentanyl (n=699), or other opioids (n=234). Pain intensity, time on opioids, age, gender, performance status, and bone or CNS metastases predicted......C, HTR3D, HTR3E, HTR1, or CNR1 showed significant associations with opioid dose in both the development and the validation analyzes. These findings do not support the use of pharmacogenetic analyses for the assessed SNPs to guide opioid treatment. The study also demonstrates the importance...

  9. Disentangling the effects of genetic, prenatal and parenting influences on children's cortisol variability.

    Science.gov (United States)

    Marceau, Kristine; Ram, Nilam; Neiderhiser, Jenae M; Laurent, Heidemarie K; Shaw, Daniel S; Fisher, Phil; Natsuaki, Misaki N; Leve, Leslie D

    2013-11-01

    Developmental plasticity models hypothesize the role of genetic and prenatal environmental influences on the development of the hypothalamic-pituitary-adrenal (HPA) axis and highlight that genes and the prenatal environment may moderate early postnatal environmental influences on HPA functioning. This article examines the interplay of genetic, prenatal and parenting influences across the first 4.5 years of life on a novel index of children's cortisol variability. Repeated measures data were obtained from 134 adoption-linked families, adopted children and both their adoptive parents and birth mothers, who participated in a longitudinal, prospective US domestic adoption study. Genetic and prenatal influences moderated associations between inconsistency in overreactive parenting from child age 9 months to 4.5 years and children's cortisol variability at 4.5 years differently for mothers and fathers. Among children whose birth mothers had high morning cortisol, adoptive fathers' inconsistent overreactive parenting predicted higher cortisol variability, whereas among children with low birth mother morning cortisol adoptive fathers' inconsistent overreactive parenting predicted lower cortisol variability. Among children who experienced high levels of prenatal risk, adoptive mothers' inconsistent overreactive parenting predicted lower cortisol variability and adoptive fathers' inconsistent overreactive parenting predicted higher cortisol variability, whereas among children who experienced low levels of prenatal risk there were no associations between inconsistent overreactive parenting and children's cortisol variability. Findings supported developmental plasticity models and uncovered novel developmental, gene × environment and prenatal × environment influences on children's cortisol functioning.

  10. Genetic variability of an endangered Bromeliaceae species (Pitcairnia albiflos) from the Brazilian Atlantic rainforest.

    Science.gov (United States)

    Domingues, R; Machado, M A; Forzza, R C; Melo, T D; Wohlres-Viana, S; Viccini, L F

    2011-10-13

    Pitcairnia albiflos is a Bromeliaceae species endemic to Brazil that has been included as data-deficient in the extinction risk list of Brazilian flora. We analyzed genetic variability in P. albiflos populations using RAPD markers to investigate population structure and reproductive mechanisms and also to evaluate the actual extinction risk level of this species. Leaves of 56 individuals of P. albiflos from three populations were collected: Urca Hill (UH, 20 individuals), Chacrinha State Park (CSP, 24 individuals) and Tijuca National Park (TNP, 12 individuals). The RAPD technique was effective in characterizing the genetic diversity in the P. albiflos populations since it was possible to differentiate the populations and to identify exclusive bands for at least two of them. Even if there is low genetic diversity among them (CSP-UH = 0.463; CSP-TNP = 0.440; UH-TNP = 0.524), the populations seem to be isolated according to the low genetic diversity observed within them (H(pop) CSP = 0.060; H(pop) UH = 0.042; H(pop) TNP = 0.130). This fact might be the result of clonal and self-reproduction predominance and also from environmental degradation around the collection areas. Consequently, it would be important to protect all populations both in situ and ex situ to prevent the decrease of genetic variability. The low genetic variability among individuals of the same population confirms the inclusion of this species as critically endangered in the risk list for Brazilian flora.

  11. Dynamics of genetic variability in Anastrepha fraterculus (Diptera: Tephritidae) during adaptation to laboratory rearing conditions.

    Science.gov (United States)

    Parreño, María A; Scannapieco, Alejandra C; Remis, María I; Juri, Marianela; Vera, María T; Segura, Diego F; Cladera, Jorge L; Lanzavecchia, Silvia B

    2014-01-01

    Anastrepha fraterculus is one of the most important fruit fly plagues in the American continent and only chemical control is applied in the field to diminish its population densities. A better understanding of the genetic variability during the introduction and adaptation of wild A. fraterculus populations to laboratory conditions is required for the development of stable and vigorous experimental colonies and mass-reared strains in support of successful Sterile Insect Technique (SIT) efforts. The present study aims to analyze the dynamics of changes in genetic variability during the first six generations under artificial rearing conditions in two populations: a) a wild population recently introduced to laboratory culture, named TW and, b) a long-established control line, named CL. Results showed a declining tendency of genetic variability in TW. In CL, the relatively high values of genetic variability appear to be maintained across generations and could denote an intrinsic capacity to avoid the loss of genetic diversity in time. The impact of evolutionary forces on this species during the adaptation process as well as the best approach to choose strategies to introduce experimental and mass-reared A. fraterculus strains for SIT programs are discussed.

  12. Use of the IRAP marker to study genetic variability in Pseudocercospora fijiensis populations.

    Science.gov (United States)

    de Queiroz, Casley Borges; Santana, Mateus Ferreira; da Silva, Gilvan Ferreira; Mizubuti, Eduardo Seiti Gomide; de Araújo, Elza Fernandes; de Queiroz, Marisa Vieira

    2014-03-01

    Pseudocercospora fijiensis is the etiological agent of black Sigatoka, which is currently considered as one of the most destructive banana diseases in all locations where it occurs. It is estimated that a large portion of the P. fijiensis genome consists of transposable elements, which allows researchers to use transposon-based molecular markers in the analysis of genetic variability in populations of this pathogen. In this context, the inter-retrotransposon-amplified polymorphism (IRAP) was used to study the genetic variability in P. fijiensis populations from different hosts and different geographical origins in Brazil. A total of 22 loci were amplified and 77.3 % showed a polymorphism. Cluster analysis revealed two major groups in Brazil. The observed genetic diversity (H E) was 0.22, and through molecular analysis of variance, it was determined that the greatest genetic variability occurs within populations. The discriminant analysis of principal components revealed no structuring related to the geographical origin of culture of the host. The IRAP-based marker system is a suitable tool for the study of genetic variability in P. fijiensis.

  13. Improved Genetic Algorithm with Two-Level Approximation for Truss Optimization by Using Discrete Shape Variables

    Directory of Open Access Journals (Sweden)

    Shen-yan Chen

    2015-01-01

    Full Text Available This paper presents an Improved Genetic Algorithm with Two-Level Approximation (IGATA to minimize truss weight by simultaneously optimizing size, shape, and topology variables. On the basis of a previously presented truss sizing/topology optimization method based on two-level approximation and genetic algorithm (GA, a new method for adding shape variables is presented, in which the nodal positions are corresponding to a set of coordinate lists. A uniform optimization model including size/shape/topology variables is established. First, a first-level approximate problem is constructed to transform the original implicit problem to an explicit problem. To solve this explicit problem which involves size/shape/topology variables, GA is used to optimize individuals which include discrete topology variables and shape variables. When calculating the fitness value of each member in the current generation, a second-level approximation method is used to optimize the continuous size variables. With the introduction of shape variables, the original optimization algorithm was improved in individual coding strategy as well as GA execution techniques. Meanwhile, the update strategy of the first-level approximation problem was also improved. The results of numerical examples show that the proposed method is effective in dealing with the three kinds of design variables simultaneously, and the required computational cost for structural analysis is quite small.

  14. Genetic variability in mitochondrial and nuclear genes of Larus dominicanus (Charadriiformes, Laridae from the Brazilian coast

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    Gisele Pires de Mendonça Dantas

    2012-01-01

    Full Text Available Several phylogeographic studies of seabirds have documented low genetic diversity that has been attributed to bottleneck events or individual capacity for dispersal. Few studies have been done in seabirds on the Brazilian coast and all have shown low genetic differentiation on a wide geographic scale. The Kelp Gull is a common species with a wide distribution in the Southern Hemisphere. In this study, we used mitochondrial and nuclear markers to examine the genetic variability of Kelp Gull populations on the Brazilian coast and compared this variability with that of sub-Antarctic island populations of this species. Kelp Gulls showed extremely low genetic variability for mitochondrial markers (cytb and ATPase and high diversity for a nuclear locus (intron 7 of the β-fibrinogen. The intraspecific evolutionary history of Kelp Gulls showed that the variability found in intron 7 of the β-fibrinogen gene was compatible with the variability expected under neutral evolution but suggested an increase in population size during the last 10,000 years. However, none of the markers revealed evidence of a bottleneck population. These findings indicate that the recent origin of Kelp Gulls is the main explanation for their nuclear diversity, although selective pressure on the mtDNA of this species cannot be discarded.

  15. Genetic variability in mitochondrial and nuclear genes of Larus dominicanus (Charadriiformes, Laridae) from the Brazilian coast

    Science.gov (United States)

    de Mendonça Dantas, Gisele Pires; Meyer, Diogo; Godinho, Raquel; Ferrand, Nuno; Morgante, João Stenghel

    2012-01-01

    Several phylogeographic studies of seabirds have documented low genetic diversity that has been attributed to bottleneck events or individual capacity for dispersal. Few studies have been done in seabirds on the Brazilian coast and all have shown low genetic differentiation on a wide geographic scale. The Kelp Gull is a common species with a wide distribution in the Southern Hemisphere. In this study, we used mitochondrial and nuclear markers to examine the genetic variability of Kelp Gull populations on the Brazilian coast and compared this variability with that of sub-Antarctic island populations of this species. Kelp Gulls showed extremely low genetic variability for mitochondrial markers (cytb and ATPase) and high diversity for a nuclear locus (intron 7 of the β-fibrinogen). The intraspecific evolutionary history of Kelp Gulls showed that the variability found in intron 7 of the β-fibrinogen gene was compatible with the variability expected under neutral evolution but suggested an increase in population size during the last 10,000 years. However, none of the markers revealed evidence of a bottleneck population. These findings indicate that the recent origin of Kelp Gulls is the main explanation for their nuclear diversity, although selective pressure on the mtDNA of this species cannot be discarded. PMID:23271950

  16. Exploring the genetic variability in water use efficiency: Evaluation of inter and intra cultivar genetic diversity in grapevines.

    Science.gov (United States)

    Tortosa, Ignacio; Escalona, José Mariano; Bota, Josefina; Tomás, Magdalena; Hernández, Esther; Escudero, Enrique García; Medrano, Hipólito

    2016-10-01

    Genetic improvement of crop Water Use Efficiency (WUE) is a general goal because the increasing water scarcity and the trend to a more sustainable agriculture. For grapevines, this subject is relevant and need an urgent response because their wide distribution in semi-arid areas. New cultivars are difficult to introduce in viticulture due to the narrow dependency of consumer appreciation often linked to a certain particular wine taste. Clones of reputed cultivars would presumably be more accepted but little is known on the intra-cultivar genetic variability of the WUE. The present work compares, on the basis of two field assays, the variability of intrinsic water use efficiency (WUEi) in a large collection of cultivars in contrast with a collection of clones of Tempranillo cultivar. The results show that clonal variability of WUEi was around 80% of the inter-cultivar, thus providing a first assessment on the opportunity for clonal selection by WUE. Plotting the WUEi data against stem water potential or stomatal conductance it was possible to identify cultivars and clones out of the confidence intervals of this linear regression thus with significantly higher and lower WUEi values. The present results contribute to open the expectative for a genetic improvement of grapevine WUE. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  17. Molecular genetic variability, population structure and mating system in tropical forages

    Directory of Open Access Journals (Sweden)

    Melissa Garcia

    2013-09-01

    Full Text Available Microsatellite (SSR markers were developed for the following tropical forage species, using accessions available from the plant genetic resources (PGR collections held by EMBRAPA (Brazilian Agricultural Research Corporation: Brachiaria brizantha, B. humidicola, Panicum maximum, Paspalum spp., Stylosanthes capitata, S. guianensis, S. macrocephala, Calopogonium mucunoides and Centrosema spp. The markers were used to analyze population structure and genetic diversity, evolution and origin of the genetic variability in the center of origin, mating systems and genetic resources in EMBRAPA’s germplasm bank. The results shed light on the amount of genetic variation within and between populations, revealed the need in some cases for further plant collection to adequately represent the species in PGR collections, allowed us to assemble core collections (subsets of the total collections that should contain most of the available diversity and (in the case of the legumes showed the need to avoid unwanted outcrossing when regenerating conserved material. The data will allow plant breeders to better select accessions for hybrid production, discriminate between genotypes and use marker-assisted selection in breeding programs. Our results will also underpin the construction of genetic maps, mapping of genes of agronomic interest and numerous other studies on genetic variability, population structure, gene flow and reproductive systems for the tropical forage species studied in this work.

  18. Estimates of genetic variability and association studies in quantitative plant traits of Eruca spp. landraces

    Directory of Open Access Journals (Sweden)

    Bozokalfa Kadri Mehmet

    2010-01-01

    Full Text Available Despite the increasing of economical importance of rocket plant limited information is available on genetic variability for the agronomic traits among Eruca spp. Hence, heritability and association studies of plant properties are necessities for a successful further rocket breeding programme. The objective of this study was to examine phenotypic and genotypic variability, broad sense heritability, genetic advance, genotypic and phenotypic correlation and mean for agronomic traits of rocket plant. The magnitude of phenotypic coefficient of variation values for all the traits were higher than the corresponding values and broad sense heritability estimates exceeded 65% for all traits. Phenotypic coefficients of variability (PCV ranged from 7.60 to 34.34% and genotypic coefficients of variability (GCV ranged between 5.58% for petiole thickness and 34.30% for plant weight. The results stated that plant weight, siliqua width, seed per siliqua and seed weight could be useful character for improved Eruca spp. breeding programme.

  19. Multivariate Outlier Detection in Genetic Evaluation in Nordic Jersey Cattle

    DEFF Research Database (Denmark)

    Gao, Hongding; Madsen, Per; Pösö, Jukka

    A procedure was developed for detection of multivariate outliers based on an approximation for Mahanalobis Distance (MD) and was implemented in the Nordic Jersey population. Evaluations are carried out by Nordic Cattle Genetic Evaluation (NAV), who uses a 9 trait model for milk, protein and fat...... means and co-variance matrix for the actual PY, lactation and DIM. Accuracy of EBV’s is improved for animals having extreme outlier record(s) deleted compared to EBV’s based on data not filtered for MD....

  20. Detecting structural breaks in time series via genetic algorithms

    DEFF Research Database (Denmark)

    Doerr, Benjamin; Fischer, Paul; Hilbert, Astrid

    2016-01-01

    Detecting structural breaks is an essential task for the statistical analysis of time series, for example, for fitting parametric models to it. In short, structural breaks are points in time at which the behaviour of the time series substantially changes. Typically, no solid background knowledge...... and mutation operations for this problem, we conduct extensive experiments to determine good choices for the parameters and operators of the genetic algorithm. One surprising observation is that use of uniform and one-point crossover together gave significantly better results than using either crossover...

  1. Molecular variability and genetic structure of Chrysodeixis includens (Lepidoptera: Noctuidae), an important soybean defoliator in Brazil.

    Science.gov (United States)

    Palma, Janine; Maebe, Kevin; Guedes, Jerson Vanderlei Carús; Smagghe, Guy

    2015-01-01

    This study provides the first genetic characterization of the soybean looper, Chrysodeixis includens (Walker, 1857), an important defoliating pest species of soybean crops in Brazil. Population genetic variability and the genetic structure of C. includens populations were evaluated by using ISSR markers with samples from the major soybean producing regions in Brazil in the growing seasons 2011/2012. Seven different primers were applied for population characterization of the molecular variability and genetic structure of 8 soybean looper populations from 8 states of Brazil. The seven ISSR loci generated 247 bands in 246 individuals of C. includens sampled. The expected heterozygosity (HE) in the populations varied between 0.093 and 0.106, while the overall HE was 0.099, indicating low genetic diversity. The analysis of molecular variance indicated that 98% of the variability was expressed among individuals within populations (FST = 0.021, p = 0.001). The low level of polymorphism over all populations, the high levels of gene flow, and the low genetic structure are indicatives of the exchange of genetic information between the different sampled regions. Population structuring suggests the presence of two major groups which do not correlate with their geographic sampling location in Brazil. These results may indicate recent recolonization of C. includens in Brazil or migration patterns following source-sink dynamics. Furthermore, the presence of two groups within C. includens suggests that a study on development of resistance or any other genetic-based trait needs to be evaluated on both groups, and pest management in soybean fields should be aware that differences may come to the control strategies they use.

  2. Molecular variability and genetic structure of Chrysodeixis includens (Lepidoptera: Noctuidae, an important soybean defoliator in Brazil.

    Directory of Open Access Journals (Sweden)

    Janine Palma

    Full Text Available This study provides the first genetic characterization of the soybean looper, Chrysodeixis includens (Walker, 1857, an important defoliating pest species of soybean crops in Brazil. Population genetic variability and the genetic structure of C. includens populations were evaluated by using ISSR markers with samples from the major soybean producing regions in Brazil in the growing seasons 2011/2012. Seven different primers were applied for population characterization of the molecular variability and genetic structure of 8 soybean looper populations from 8 states of Brazil. The seven ISSR loci generated 247 bands in 246 individuals of C. includens sampled. The expected heterozygosity (HE in the populations varied between 0.093 and 0.106, while the overall HE was 0.099, indicating low genetic diversity. The analysis of molecular variance indicated that 98% of the variability was expressed among individuals within populations (FST = 0.021, p = 0.001. The low level of polymorphism over all populations, the high levels of gene flow, and the low genetic structure are indicatives of the exchange of genetic information between the different sampled regions. Population structuring suggests the presence of two major groups which do not correlate with their geographic sampling location in Brazil. These results may indicate recent recolonization of C. includens in Brazil or migration patterns following source-sink dynamics. Furthermore, the presence of two groups within C. includens suggests that a study on development of resistance or any other genetic-based trait needs to be evaluated on both groups, and pest management in soybean fields should be aware that differences may come to the control strategies they use.

  3. Vibration-Based Damage Detection in Beams by Cooperative Coevolutionary Genetic Algorithm

    Directory of Open Access Journals (Sweden)

    Kittipong Boonlong

    2014-03-01

    Full Text Available Vibration-based damage detection, a nondestructive method, is based on the fact that vibration characteristics such as natural frequencies and mode shapes of structures are changed when the damage happens. This paper presents cooperative coevolutionary genetic algorithm (CCGA, which is capable for an optimization problem with a large number of decision variables, as the optimizer for the vibration-based damage detection in beams. In the CCGA, a minimized objective function is a numerical indicator of differences between vibration characteristics of the actual damage and those of the anticipated damage. The damage detection in a uniform cross-section cantilever beam, a uniform strength cantilever beam, and a uniform cross-section simply supported beam is used as the test problems. Random noise in the vibration characteristics is also considered in the damage detection. In the simulation analysis, the CCGA provides the superior solutions to those that use standard genetic algorithms presented in previous works, although it uses less numbers of the generated solutions in solution search. The simulation results reveal that the CCGA can efficiently identify the occurred damage in beams for all test problems including the damage detection in a beam with a large number of divided elements such as 300 elements.

  4. Pollen genetic markers for detection of mutagens in the environment

    Energy Technology Data Exchange (ETDEWEB)

    Nilan, R.A.; Rosichan, J.L.; Arenaz, P.; Hodgdon, A.L.; Kleinhofs, A.

    1980-01-01

    To utilize and exploit pollen for in situ mutagen monitoring, screening and toxicology, the range of genetic traits in pollen must be identified and analyzed. To be useful for the development of mutagen detection systems proteins should be: (1) activity stainable or immunologically identifiable in the pollen, (2) the products of one to three loci; and (3) gametophytic and nuclear in origin. Several proteins, including alcohol dehydrogenase in maize, which meet these criteria are discussed. The waxy locus in barley and maize which controls starch deposition for pollen screening and mutant detection. Thirty waxy mutant lines, induced by sodium azide and gamma-rays are characterized for spontaneous and induced reversion frequencies, allelism, karyotype, amylose content, and UDPglucose glucosyltransferase (waxy gene product) activity. Twelve mutant alleles are being mapped by recombinant frequencies.

  5. Emergence and genetic variability of Anaplasma species in small ruminants and ticks from Central Europe.

    Science.gov (United States)

    Derdáková, Markéta; Stefančíková, Astéria; Spitalská, Eva; Tarageľová, Veronika; Košťálová, Tatiana; Hrkľová, Gabriela; Kybicová, Kateřina; Schánilec, Pavel; Majláthová, Viktória; Várady, Marián; Peťko, Branislav

    2011-12-15

    Anaplasmoses are common tick-borne zoonotic bacterial diseases of livestock and free-living ungulates from the genus Anaplasma that are recently emerging in Central Europe. The main aim of this study was to analyze the prevalence and genetic variability of Anaplasma phagocytophilum and Anaplasma ovis in small ruminants and questing ticks from six different sites in Slovakia and the Czech Republic using the PCR of the msp4 gene followed by the sequence analysis. At two farms from southeastern Slovakia, 66.1% small ruminants were infected with A. ovis in contrast to one positive animal from both sites in northern Slovakia. It was represented by two different genotypes. A. phagocytophilum was present in all tested flocks with the infection prevalence ranging from 0.9% to 5.7%. None of the tested questing ticks carried A. ovis. A. phagocytophilum was detected in 1.1% and 7.8% of questing Ixodes ricinus ticks collected around the farms located in southeastern and northern Slovakia, respectively. A. phagocytophilum revealed higher intraspecific diversity than A. ovis. Copyright © 2011 Elsevier B.V. All rights reserved.

  6. A novel genetic programming approach for epileptic seizure detection.

    Science.gov (United States)

    Bhardwaj, Arpit; Tiwari, Aruna; Krishna, Ramesh; Varma, Vishaal

    2016-02-01

    The human brain is a delicate mix of neurons (brain cells), electrical impulses and chemicals, known as neurotransmitters. Any damage has the potential to disrupt the workings of the brain and cause seizures. These epileptic seizures are the manifestations of epilepsy. The electroencephalograph (EEG) signals register average neuronal activity from the cerebral cortex and label changes in activity over large areas. A detailed analysis of these electroencephalograph (EEG) signals provides valuable insights into the mechanisms instigating epileptic disorders. Moreover, the detection of interictal spikes and epileptic seizures in an EEG signal plays an important role in the diagnosis of epilepsy. Automatic seizure detection methods are required, as these epileptic seizures are volatile and unpredictable. This paper deals with an automated detection of epileptic seizures in EEG signals using empirical mode decomposition (EMD) for feature extraction and proposes a novel genetic programming (GP) approach for classifying the EEG signals. Improvements in the standard GP approach are made using a Constructive Genetic Programming (CGP) in which constructive crossover and constructive subtree mutation operators are introduced. A hill climbing search is integrated in crossover and mutation operators to remove the destructive nature of these operators. A new concept of selecting the Globally Prime offspring is also presented to select the best fitness offspring generated during crossover. To decrease the time complexity of GP, a new dynamic fitness value computation (DFVC) is employed to increase the computational speed. We conducted five different sets of experiments to evaluate the performance of the proposed model in the classification of different mixtures of normal, interictal and ictal signals, and the accuracies achieved are outstandingly high. The experimental results are compared with the existing methods on same datasets, and these results affirm the potential use of

  7. Genetic variability in common wheat germplasm based on coefficients of parentage

    Directory of Open Access Journals (Sweden)

    Fernanda Bered

    2002-01-01

    Full Text Available The characterization of genetic variability and an estimate of the genetic relationship among varieties are essential to any breeding program, because artificial crosses among less similar parents allow a larger segregation and the combination of different favorable alleles. Genetic variability can be evaluated in different ways, including the Coefficient of Parentage (COP, which estimates the probability of two alleles in two different individuals being identical by descent. In this study, we evaluated the degree of genetic relationship among 53 wheat genotypes, and identified the ancestor genotypes which contributed the most to the current wheat germplasm, as a prediction of the width of the genetic base of this cereal. The results revealed a mean COP of 0.07 and the formation of 22 similarity groups. The ancestor genotypes Ciano 67 and Mentana were those which contributed the most to the current wheat germplasm. According to the COP analyses, the genetic base of wheat rests on a small number of ancestral genotypes.

  8. Exome Sequence Analysis Suggests that Genetic Burden Contributes to Phenotypic Variability and Complex Neuropathy

    Directory of Open Access Journals (Sweden)

    Claudia Gonzaga-Jauregui

    2015-08-01

    Full Text Available Charcot-Marie-Tooth (CMT disease is a clinically and genetically heterogeneous distal symmetric polyneuropathy. Whole-exome sequencing (WES of 40 individuals from 37 unrelated families with CMT-like peripheral neuropathy refractory to molecular diagnosis identified apparent causal mutations in ∼45% (17/37 of families. Three candidate disease genes are proposed, supported by a combination of genetic and in vivo studies. Aggregate analysis of mutation data revealed a significantly increased number of rare variants across 58 neuropathy-associated genes in subjects versus controls, confirmed in a second ethnically discrete neuropathy cohort, suggesting that mutation burden potentially contributes to phenotypic variability. Neuropathy genes shown to have highly penetrant Mendelizing variants (HPMVs and implicated by burden in families were shown to interact genetically in a zebrafish assay exacerbating the phenotype established by the suppression of single genes. Our findings suggest that the combinatorial effect of rare variants contributes to disease burden and variable expressivity.

  9. Genetic variability in wild genotypes of Passiflora cincinnata based on RAPD markers.

    Science.gov (United States)

    Cerqueira-Silva, C B M; Conceição, L D H C S; Santos, E S L; Cardoso-Silva, C B; Pereira, A S; Oliveira, A C; Corrêa, R X

    2010-12-21

    The genetic diversity and characteristics of commercial interest of Passiflora species make it useful to characterize wild germplasm, because of their potential use for fruit, ornamental and medicinal purposes. We evaluated genetic diversity, using RAPD markers, of 32 genotypes of Passiflora cincinnata collected from the wild in the region of Vitória da Conquista, Bahia, Brazil. Thirteen primers generated 95 polymorphic markers and only one monomorphic marker. The mean genetic distance between the genotypes estimated by the complement of the Dice index was 0.51 (ranging from 0.20-0.85), and genotype grouping based on the UPGMA algorithm showed wide variability among the genotypes. This type of information contributes to identification and conservation of the biodiversity of this species and for the identification of pairs of divergent individuals for maximum exploitation of existing variability.

  10. Genetic variability in progenies of Eucalyptus dunnii Maiden for resistance to Puccinia psidii

    Directory of Open Access Journals (Sweden)

    Cleber da Silva Pinto

    2014-10-01

    Full Text Available This study investigated the genetic variability in progenies of Eucalyptus dunnii Maiden for resistance against rust (Puccinia psidii. Field experiments were installed in two regions with different soil-climatic conditions. Open-pollinated progenies were established in a randomized complete block design. Sixty and 48 progenies were evaluated under field conditions at two sites, respectively, with six replications and eight trees per plot. In another experiment in a controlled environment, 53 progenies were evaluated in randomized blocks with six replications and nine plants per plot. The following traits were evaluated: plant height, severity of pest attack and the most susceptible stage to the leaf disease. The genetic variability for rust resistance in the E. dunnii population under study was high, with a genetic coefficient of variation of 36.07%; 7% of the evaluated progenies were rust-resistant. It indicates a high potential for selection and breeding of the species.

  11. Exome sequence analysis suggests genetic burden contributes to phenotypic variability and complex neuropathy

    Science.gov (United States)

    Gonzaga-Jauregui, Claudia; Harel, Tamar; Gambin, Tomasz; Kousi, Maria; Griffin, Laurie B.; Francescatto, Ludmila; Ozes, Burcak; Karaca, Ender; Jhangiani, Shalini; Bainbridge, Matthew N.; Lawson, Kim S.; Pehlivan, Davut; Okamoto, Yuji; Withers, Marjorie; Mancias, Pedro; Slavotinek, Anne; Reitnauer, Pamela J; Goksungur, Meryem T.; Shy, Michael; Crawford, Thomas O.; Koenig, Michel; Willer, Jason; Flores, Brittany N.; Pediaditrakis, Igor; Us, Onder; Wiszniewski, Wojciech; Parman, Yesim; Antonellis, Anthony; Muzny, Donna M.; Katsanis, Nicholas; Battaloglu, Esra; Boerwinkle, Eric; Gibbs, Richard A.; Lupski, James R.

    2015-01-01

    Charcot-Marie-Tooth (CMT) disease is a clinically and genetically heterogeneous distal symmetric polyneuropathy. Whole-exome sequencing (WES) of 40 individuals from 37 unrelated families with CMT-like peripheral neuropathy refractory to molecular diagnosis identified apparent causal mutations in ~45% (17/37) of families. Three candidate disease genes are proposed, supported by a combination of genetic and in vivo studies. Aggregate analysis of mutation data revealed a significantly increased number of rare variants across 58 neuropathy associated genes in subjects versus controls; confirmed in a second ethnically discrete neuropathy cohort, suggesting mutation burden potentially contributes to phenotypic variability. Neuropathy genes shown to have highly penetrant Mendelizing variants (HMPVs) and implicated by burden in families were shown to interact genetically in a zebrafish assay exacerbating the phenotype established by the suppression of single genes. Our findings suggest that the combinatorial effect of rare variants contributes to disease burden and variable expressivity. PMID:26257172

  12. Occurrence and genetic variability of Phlebotomus papatasi in an urban area of southern Italy

    Directory of Open Access Journals (Sweden)

    Dantas-Torres Filipe

    2010-08-01

    Full Text Available Abstract Background A phlebotomine sand fly was noticed in the second floor of an old building in a highly urbanized area of southern Italy. A short-term entomological survey was carried out in the subsequent weeks to this event, allowing the collection of additional phlebotomine sand flies that were later identified as Phlebotomus papatasi. We assessed the genetic variability among P. papatasi sequences obtained in this study and those available from Italy using a mitochondrial DNA (mtDNA fragment (from cytochrome b gene to NADH1 and the internal transcribed spacer 2 (ITS2 as genetic markers. Results From 9 June to 19 July, eight males and seven females (two blood-fed of P. papatasi were collected in the old town of Bari (southern Italy. The insects were found near the bed and in the bathroom and potential blood sources (e.g., pigeons and dogs for them were common in the neighbourhood. Again, five females of P. papatasi collected in Valenzano, another urban area in the province of Bari, were also identified and included in the genetic study. The mtDNA sequences (945 bp obtained from Bari and Valenzano were identical except for a single transition (T ↔ C at the 793 nucleotide residue. Pairwise comparison of the last 440 bp of the mtDNA fragment analyzed herein with other sequences of P. papatasi from Italy revealed a nucleotide variation ranging from 0.2 to 1.3%. Three ITS2 sequence types were detected within specimens collected in Valenzano, one of them identical to that from Bari. Pairwise comparison of ITS2 sequences of P. papatasi from Italy revealed a nucleotide variation up to 1.8%. Conclusions This study reports the occurrence of P. papatasi in an urban area of southern Italy and shows a low nucleotide difference among ITS2 and mtDNA sequences of this species available from Italy. The presence of P. papatasi in urban areas might represent a risk for human health, particularly for the potential transmission of sandfly fever viruses.

  13. Genetic variability of the whitefly Bemisia tabaci and its secondary endosymbionts in the Arabian Peninsula

    KAUST Repository

    Ragab, Alaa I.

    2013-05-01

    the Q biotype. All endosymbionts were detected, with Hamiltonella as the most predominant. Several instances of co-infection by two or more endosymbionts were observed. Samples from the geographically isolated and mountainous region of Fayfa demonstrated higher genetic variability compared to the other locations, leading to the possible identification of a new haplotype, as well as the first time identification of the A biotype in the region.

  14. Genetically engineered microorganisms for the detection of explosives' residues

    Directory of Open Access Journals (Sweden)

    Benjamin eShemer

    2015-10-01

    Full Text Available The manufacture and use of explosives throughout the past century has resulted in the extensive pollution of soils and groundwater, and the widespread interment of landmines imposes a major humanitarian risk and prevents civil development of large areas. As most current landmine detection technologies require actual presence at the surveyed areas, thus posing a significant risk to personnel, diverse research efforts are aimed at the development of remote detection solutions. One possible means proposed to fulfill this objective is the use of microbial bioreporters: genetically engineered microorganisms tailored to generate an optical signal in the presence of explosives’ vapors. The use of such sensor bacteria will allow to pinpoint the locations of explosive devices in a minefield. While no study has yet resulted in a commercially operational system, significant progress has been made in the design and construction of explosives-sensing bacterial strains. In this article we review the attempts to construct microbial bioreporters for the detection of explosives, and analyze the steps that need to be undertaken for this strategy to be applicable for landmine detection.

  15. Genetically engineered microorganisms for the detection of explosives’ residues

    Science.gov (United States)

    Shemer, Benjamin; Palevsky, Noa; Yagur-Kroll, Sharon; Belkin, Shimshon

    2015-01-01

    The manufacture and use of explosives throughout the past century has resulted in the extensive pollution of soils and groundwater, and the widespread interment of landmines imposes a major humanitarian risk and prevents civil development of large areas. As most current landmine detection technologies require actual presence at the surveyed areas, thus posing a significant risk to personnel, diverse research efforts are aimed at the development of remote detection solutions. One possible means proposed to fulfill this objective is the use of microbial bioreporters: genetically engineered microorganisms “tailored” to generate an optical signal in the presence of explosives’ vapors. The use of such sensor bacteria will allow to pinpoint the locations of explosive devices in a minefield. While no study has yet resulted in a commercially operational system, significant progress has been made in the design and construction of explosives-sensing bacterial strains. In this article we review the attempts to construct microbial bioreporters for the detection of explosives, and analyze the steps that need to be undertaken for this strategy to be applicable for landmine detection. PMID:26579085

  16. Improved Genetic Algorithm Optimization for Forward Vehicle Detection Problems

    Directory of Open Access Journals (Sweden)

    Longhui Gang

    2015-07-01

    Full Text Available Automated forward vehicle detection is an integral component of many advanced driver-assistance systems. The method based on multi-visual information fusion, with its exclusive advantages, has become one of the important topics in this research field. During the whole detection process, there are two key points that should to be resolved. One is to find the robust features for identification and the other is to apply an efficient algorithm for training the model designed with multi-information. This paper presents an adaptive SVM (Support Vector Machine model to detect vehicle with range estimation using an on-board camera. Due to the extrinsic factors such as shadows and illumination, we pay more attention to enhancing the system with several robust features extracted from a real driving environment. Then, with the introduction of an improved genetic algorithm, the features are fused efficiently by the proposed SVM model. In order to apply the model in the forward collision warning system, longitudinal distance information is provided simultaneously. The proposed method is successfully implemented on a test car and evaluation experimental results show reliability in terms of both the detection rate and potential effectiveness in a real-driving environment.

  17. Genetic Control of the Variable Innate Immune Response to Asymptomatic Bacteriuria

    Science.gov (United States)

    Hernández, Jenny Grönberg; Sundén, Fredrik; Connolly, John; Svanborg, Catharina; Wullt, Björn

    2011-01-01

    The severity of urinary tract infection (UTI) reflects the quality and magnitude of the host response. While strong local and systemic innate immune activation occurs in patients with acute pyelonephritis, the response to asymptomatic bacteriuria (ABU) is low. The immune response repertoire in ABU has not been characterized, due to the inherent problem to distinguish bacterial differences from host-determined variation. In this study, we investigated the host response to ABU and genetic variants affecting innate immune signaling and UTI susceptibility. Patients were subjected to therapeutic urinary tract inoculation with E. coli 83972 to ensure that they were exposed to the same E. coli strain. The innate immune response repertoire was characterized in urine samples, collected from each patient before and after inoculation with bacteria or PBS, if during the placebo arm of the study. Long-term E. coli 83972 ABU was established in 23 participants, who were followed for up to twelve months and the innate immune response was quantified in 233 urine samples. Neutrophil numbers increased in all but two patients and in an extended urine cytokine/chemokine analysis (31 proteins), the chemoattractants IL-8 and GRO-α, RANTES, Eotaxin-1 and MCP-1, the T cell chemoattractant and antibacterial peptide IP-10, inflammatory regulators IL-1-α and sIL-1RA and the T lymphocyte/dendritic cell product sIL-2Rα were detected and variably increased, compared to sterile samples. IL-6, which is associated with symptomatic UTI, remained low and numerous specific immune mediators were not detected. The patients were also genotyped for UTI-associated IRF3 and TLR4 promoter polymorphisms. Patients with ABU associated TLR4 polymorphisms had low neutrophil numbers, IL-6, IP-10, MCP-1 and sIL-2Rα concentrations. Patients with the ABU-associated IRF3 genotype had lower neutrophils, IL-6 and MCP-1 responses than the remaining group. The results suggest that the host-specific, low immune

  18. Genetic control of the variable innate immune response to asymptomatic bacteriuria.

    Directory of Open Access Journals (Sweden)

    Jenny Grönberg-Hernández

    Full Text Available The severity of urinary tract infection (UTI reflects the quality and magnitude of the host response. While strong local and systemic innate immune activation occurs in patients with acute pyelonephritis, the response to asymptomatic bacteriuria (ABU is low. The immune response repertoire in ABU has not been characterized, due to the inherent problem to distinguish bacterial differences from host-determined variation. In this study, we investigated the host response to ABU and genetic variants affecting innate immune signaling and UTI susceptibility. Patients were subjected to therapeutic urinary tract inoculation with E. coli 83972 to ensure that they were exposed to the same E. coli strain. The innate immune response repertoire was characterized in urine samples, collected from each patient before and after inoculation with bacteria or PBS, if during the placebo arm of the study. Long-term E. coli 83972 ABU was established in 23 participants, who were followed for up to twelve months and the innate immune response was quantified in 233 urine samples. Neutrophil numbers increased in all but two patients and in an extended urine cytokine/chemokine analysis (31 proteins, the chemoattractants IL-8 and GRO-α, RANTES, Eotaxin-1 and MCP-1, the T cell chemoattractant and antibacterial peptide IP-10, inflammatory regulators IL-1-α and sIL-1RA and the T lymphocyte/dendritic cell product sIL-2Rα were detected and variably increased, compared to sterile samples. IL-6, which is associated with symptomatic UTI, remained low and numerous specific immune mediators were not detected. The patients were also genotyped for UTI-associated IRF3 and TLR4 promoter polymorphisms. Patients with ABU associated TLR4 polymorphisms had low neutrophil numbers, IL-6, IP-10, MCP-1 and sIL-2Rα concentrations. Patients with the ABU-associated IRF3 genotype had lower neutrophils, IL-6 and MCP-1 responses than the remaining group. The results suggest that the host

  19. Genetic basis and detection of unintended effects in genetically modified crop plants.

    Science.gov (United States)

    Ladics, Gregory S; Bartholomaeus, Andrew; Bregitzer, Phil; Doerrer, Nancy G; Gray, Alan; Holzhauser, Thomas; Jordan, Mark; Keese, Paul; Kok, Esther; Macdonald, Phil; Parrott, Wayne; Privalle, Laura; Raybould, Alan; Rhee, Seung Yon; Rice, Elena; Romeis, Jörg; Vaughn, Justin; Wal, Jean-Michel; Glenn, Kevin

    2015-08-01

    In January 2014, an international meeting sponsored by the International Life Sciences Institute/Health and Environmental Sciences Institute and the Canadian Food Inspection Agency titled "Genetic Basis of Unintended Effects in Modified Plants" was held in Ottawa, Canada, bringing together over 75 scientists from academia, government, and the agro-biotech industry. The objectives of the meeting were to explore current knowledge and identify areas requiring further study on unintended effects in plants and to discuss how this information can inform and improve genetically modified (GM) crop risk assessments. The meeting featured presentations on the molecular basis of plant genome variability in general, unintended changes at the molecular and phenotypic levels, and the development and use of hypothesis-driven evaluations of unintended effects in assessing conventional and GM crops. The development and role of emerging "omics" technologies in the assessment of unintended effects was also discussed. Several themes recurred in a number of talks; for example, a common observation was that no system for genetic modification, including conventional methods of plant breeding, is without unintended effects. Another common observation was that "unintended" does not necessarily mean "harmful". This paper summarizes key points from the information presented at the meeting to provide readers with current viewpoints on these topics.

  20. Genetic variability and evolutionary dynamics of viruses of the family Closteroviridae

    Directory of Open Access Journals (Sweden)

    Luis eRubio

    2013-06-01

    Full Text Available RNA viruses have a great potential for genetic variation, rapid evolution and adaptation. Characterization of the genetic variation of viral populations provides relevant information on the processes involved in virus evolution and epidemiology and it is crucial for designing reliable diagnostic tools and developing efficient and durable disease control strategies. Here we performed an updated analysis of sequences available in Genbank and reviewed present knowledge on the genetic variability and evolutionary processes of viruses of the family Closteroviridae. Several factors have shaped the genetic structure and diversity of closteroviruses. I A strong negative selection seems to be responsible for the high genetic stability in space and time for some viruses. II Long distance migration, probably by human transport of infected propagative plant material, have caused that genetically similar virus isolates are found in distant geographical regions. III Recombination between divergent sequence variants have generated new genotypes and plays an important role for the evolution of some viruses of the family Closteroviridae. IV Interaction between virus strains or between different viruses in mixed infections may alter accumulation of certain strains. V Host change or virus transmission by insect vectors induced changes in the viral population structure due to positive selection of sequence variants with higher fitness for host-virus or vector-virus interaction (adaptation or by genetic drift due to random selection of sequence variants during the population bottleneck associated to the transmission process.

  1. Relative contributions of neutral and non-neutral genetic differentiation to inform conservation of steelhead trout across highly variable landscapes

    Science.gov (United States)

    Matala, Andrew P; Ackerman, Michael W; Campbell, Matthew R; Narum, Shawn R

    2014-01-01

    Mounting evidence of climatic effects on riverine environments and adaptive responses of fishes have elicited growing conservation concerns. Measures to rectify population declines include assessment of local extinction risk, population ecology, viability, and genetic differentiation. While conservation planning has been largely informed by neutral genetic structure, there has been a dearth of critical information regarding the role of non-neutral or functional genetic variation. We evaluated genetic variation among steelhead trout of the Columbia River Basin, which supports diverse populations distributed among dynamic landscapes. We categorized 188 SNP loci as either putatively neutral or candidates for divergent selection (non-neutral) using a multitest association approach. Neutral variation distinguished lineages and defined broad-scale population structure consistent with previous studies, but fine-scale resolution was also detected at levels not previously observed. Within distinct coastal and inland lineages, we identified nine and 22 candidate loci commonly associated with precipitation or temperature variables and putatively under divergent selection. Observed patterns of non-neutral variation suggest overall climate is likely to shape local adaptation (e.g., potential rapid evolution) of steelhead trout in the Columbia River region. Broad geographic patterns of neutral and non-neutral variation demonstrated here can be used to accommodate priorities for regional management and inform long-term conservation of this species. PMID:25067950

  2. Intra and inter populational genetic variability in Maytenus ilicifolia Mart. ex Reiss. 1861, through RAPD markers

    Directory of Open Access Journals (Sweden)

    AJ. Mossi

    Full Text Available Maytenus ilicifolia is a medicinal plant largely used in the South Brazilian folk medicine. The aim of this study was to quantify the intra and inter populational genetic variability in three populations of M. ilicifolia, focusing on the genetic conservation of this species, which has been threatened by anthropic action. RAPD (Random Amplified Polymorphic DNA markers were used to analyze 30 plants of each of the three populations collected in the Alto Uruguai Gaúcho region. Fourteen selected primers generated a total of 158 bands, 71.5% of which were polymorphic. The comparison of Jaccard’s distances showed that the intra populational variation was higher than the inter populational variability, and cluster analysis allowed the separation of the three populations. Just 7.6% of the bands were specific of at least two populations. Data indicate that the analyzed M. ilicifolia populations represent a single genetic pool, and therefore any of the population thoroughly can represent the overall genetic variability of the species in the sampled region.

  3. Genetic variability in Bracco Italiano dog breed assessed by pedigree data

    Directory of Open Access Journals (Sweden)

    Francesca Cecchi

    2013-07-01

    Full Text Available The Bracco Italiano is one of the oldest pointing dog breed, used for hunting ever since the Renaissance time. The complete electronic record of the breed was downloaded from the ENCI database [whole population (WP = 24,613 animals registered since 1970 to 2011] with the aim to estimate genetic variability in Bracco Italiano dog breed using pedigree records. Up to 97% of the individuals had registered parents and 86% registered grand-fathers. Average generation interval was 4.68±0.545 for stallions and 4.08±0.321 year for dams. Reference population (RP was defined as the population of interest that include living reproductive animals approaching the last three generations and include 9006 dogs of which 34% were inbreds. The number of ancestors was 564 in WP and 188 in RP, while the effective number of ancestors was 46 and 34 respectively. To explain 50% of the genetic variability, a total of 18 and 9 ancestors enough, respectively in the WP and RP. The average inbreeding coefficient in the RP resulted 6.7% while the average increase in inbreeding was estimated to be 1.29% (Ne=38.86. Nevertheless a regular monitoring of genetic variability of the population is important and must be adopted, in order to avoid the danger of an excessive increase of inbreeding in the future, which would result in significant inbreeding depression and in significant loss of genetic variation.

  4. Loss of genetic variability induced by Agroecosystems: Chrysoperla externa (Hagen) (Neuroptera: Chrysopidae) as a case study.

    Science.gov (United States)

    Morales, A C; Lavagnini, T C; Freitas, S

    2013-02-01

    Four species of green lacewings occur in Brazil, of which Chrysoperla externa (Hagen) (Neuroptera: Chrysopidae) exhibits the widest geographical distribution. Chrysoperla externa is a predatory insect that is potentially useful as a biological control agent of agricultural pests. Studies on the genetic diversity of lacewing populations are essential to reduce the environmental and economic harm that may be caused by organisms with a low ability to adapt to the adverse and/or different environmental conditions to which they are exposed. We used the cytochrome oxidase I mitochondrial gene as a molecular marker to investigate the genetic diversity of green lacewing species collected from native and agroecosystem environments. Populations derived from native areas showed higher rates of genetic variability compared to populations from agroecosystems. Demographic changes in the form of population expansion were observed in agroecosystems, whereas populations in the native environment appeared stable over time. A statistical analysis showed significant genetic structure between each of the sampled groups, combined with its complete absence within each group, corroborating each group's identity. We infer that the loss of variability exhibited by populations from the agroecosystems is the result of genetic drift by means of the founder effect, a similar effect that has been observed in other introduced populations. Agroecosystems might therefore function as exotic areas for green lacewings, even when these areas are within the normal range of the species.

  5. Detection and traceability of genetically modified organisms in the food production chain

    NARCIS (Netherlands)

    Miraglia, M.; Berdal, K.G.; Brera, C.; Corbisier, P.; Holst - Jensen, A.; Kok, E.J.; Marvin, H.J.P.; Schimmel, H.; Rentsch, J.; Rie, van J.P.P.F.; Zagon, J.

    2004-01-01

    Both labelling and traceability of genetically modified organisms are current issues that are considered in trade and regulation. Currently, labelling of genetically modified foods containing detectable transgenic material is required by EU legislation. A proposed package of legislation would extend

  6. Detection and traceability of genetically modified organisms in the food production chain

    NARCIS (Netherlands)

    Miraglia, M.; Berdal, K.G.; Brera, C.; Corbisier, P.; Holst - Jensen, A.; Kok, E.J.; Marvin, H.J.P.; Schimmel, H.; Rentsch, J.; Rie, van J.P.P.F.; Zagon, J.

    2004-01-01

    Both labelling and traceability of genetically modified organisms are current issues that are considered in trade and regulation. Currently, labelling of genetically modified foods containing detectable transgenic material is required by EU legislation. A proposed package of legislation would extend

  7. Degree of intraspecific genetic divergence and variability in three Sciaenid species

    Digital Repository Service at National Institute of Oceanography (India)

    Menezes, M.R.; Taniguchi, N.; Seki, S.

    stream_size 31514 stream_content_type text/plain stream_name Jap_J_Ichthyol_37_39.pdf.txt stream_source_info Jap_J_Ichthyol_37_39.pdf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 Japan.,." Journal...(Cultural Fisheries, Faculty of Agriculture, Kocbi University, Nankoku 7&3, Japan Abstrllct Genetic variations in Nibea mitsukurii, N. albijfora and Pennahia argentara from different localities were assayed electrophoretically. The genetic variability in N. mirsukurii...

  8. [Application of characteristic NIR variables selection in portable detection of soluble solids content of apple by near infrared spectroscopy].

    Science.gov (United States)

    Fan, Shu-Xiang; Huang, Wen-Qian; Li, Jiang-Bo; Guo, Zhi-Ming; Zhaq, Chun-Jiang

    2014-10-01

    In order to detect the soluble solids content(SSC)of apple conveniently and rapidly, a ring fiber probe and a portable spectrometer were applied to obtain the spectroscopy of apple. Different wavelength variable selection methods, including unin- formative variable elimination (UVE), competitive adaptive reweighted sampling (CARS) and genetic algorithm (GA) were pro- posed to select effective wavelength variables of the NIR spectroscopy of the SSC in apple based on PLS. The back interval LS- SVM (BiLS-SVM) and GA were used to select effective wavelength variables based on LS-SVM. Selected wavelength variables and full wavelength range were set as input variables of PLS model and LS-SVM model, respectively. The results indicated that PLS model built using GA-CARS on 50 characteristic variables selected from full-spectrum which had 1512 wavelengths achieved the optimal performance. The correlation coefficient (Rp) and root mean square error of prediction (RMSEP) for prediction sets were 0.962, 0.403°Brix respectively for SSC. The proposed method of GA-CARS could effectively simplify the portable detection model of SSC in apple based on near infrared spectroscopy and enhance the predictive precision. The study can provide a reference for the development of portable apple soluble solids content spectrometer.

  9. Atrial fibrillation detection by heart rate variability in Poincare plot

    Directory of Open Access Journals (Sweden)

    Jeon Moongu

    2009-12-01

    Full Text Available Abstract Background Atrial fibrillation (AFib is one of the prominent causes of stroke, and its risk increases with age. We need to detect AFib correctly as early as possible to avoid medical disaster because it is likely to proceed into a more serious form in short time. If we can make a portable AFib monitoring system, it will be helpful to many old people because we cannot predict when a patient will have a spasm of AFib. Methods We analyzed heart beat variability from inter-beat intervals obtained by a wavelet-based detector. We made a Poincare plot using the inter-beat intervals. By analyzing the plot, we extracted three feature measures characterizing AFib and non-AFib: the number of clusters, mean stepping increment of inter-beat intervals, and dispersion of the points around a diagonal line in the plot. We divided distribution of the number of clusters into two and calculated mean value of the lower part by k-means clustering method. We classified data whose number of clusters is more than one and less than this mean value as non-AFib data. In the other case, we tried to discriminate AFib from non-AFib using support vector machine with the other feature measures: the mean stepping increment and dispersion of the points in the Poincare plot. Results We found that Poincare plot from non-AFib data showed some pattern, while the plot from AFib data showed irregularly irregular shape. In case of non-AFib data, the definite pattern in the plot manifested itself with some limited number of clusters or closely packed one cluster. In case of AFib data, the number of clusters in the plot was one or too many. We evaluated the accuracy using leave-one-out cross-validation. Mean sensitivity and mean specificity were 91.4% and 92.9% respectively. Conclusions Because pulse beats of ventricles are less likely to be influenced by baseline wandering and noise, we used the inter-beat intervals to diagnose AFib. We visually displayed regularity of the inter

  10. Cardio Vascular Detection with Neuro Computing and Genetic Algorithm

    Directory of Open Access Journals (Sweden)

    T. John Peter

    2014-09-01

    Full Text Available For human the most fundamental requirement is having a healthy life, which is being difficult to maintain day to day as we are getting more progress in technological era. Among the possible reasons of unnatural death, heart disease based causes are showing very significant part. The diagnosis of heart diseases is a vital and intricate job. The recognition of heart disease from diverse features or signs is a multi-layered problem that is highly sensitive with respect diagnostic tests and establishing the relationship with multiple parameters is very difficult. In result decision is not free from false assumptions and is frequently accompanied by impulsive effects. This encourages developing a more reliable and cost effective knowledge based algorithmic approach to detect the heart disease. From engineering point of view, solution for detecting the presence of heart diseases is developed with the concept of artificial intelligence in data mining in this study. Feed forward architecture of neural network technology is taken as platform of computation to generate the intelligence in association with well established field of genetic algorithm (GA. A comparative performance has presented between both learning concepts with various different size of architecture.

  11. Bearing Fault Detection Using Artificial Neural Networks and Genetic Algorithm

    Directory of Open Access Journals (Sweden)

    Samanta B

    2004-01-01

    Full Text Available A study is presented to compare the performance of bearing fault detection using three types of artificial neural networks (ANNs, namely, multilayer perceptron (MLP, radial basis function (RBF network, and probabilistic neural network (PNN. The time domain vibration signals of a rotating machine with normal and defective bearings are processed for feature extraction. The extracted features from original and preprocessed signals are used as inputs to all three ANN classifiers: MLP, RBF, and PNN for two-class (normal or fault recognition. The characteristic parameters like number of nodes in the hidden layer of MLP and the width of RBF, in case of RBF and PNN along with the selection of input features, are optimized using genetic algorithms (GA. For each trial, the ANNs are trained with a subset of the experimental data for known machine conditions. The ANNs are tested using the remaining set of data. The procedure is illustrated using the experimental vibration data of a rotating machine with and without bearing faults. The results show the relative effectiveness of three classifiers in detection of the bearing condition.

  12. Establishing a diagnostic system for detecting Ralstonia solanacearum and genetic differentiation using RAPD molecular markers

    Directory of Open Access Journals (Sweden)

    Edisson Chavarro Mesa

    2007-02-01

    Full Text Available A polymerase chain reaction-based diagnostic test (PCR has been developed for amplifying a región and obtaining a 292 bp product by using specific 16S rDNA primers for the rapid and precise identification of the causative agent (Ralstonia solanacearum of bacterial withering of potato in asymptomatic tubers. The bacteria was isolated from potato tubers and banana fruit using culturing techniques and immunological and molecular ELISA-NCM and PCR tests, respectively. PCR detected the presence of R. solanacearum on asymptomatic tubers by contrast with ELISA-NCM which did not detect this pathogen. Analysing random amplified polymorphic DNA (RAPD led to differentiating and grouping R. solanacearum by geographical región and bacterial strain, suggesting that differences exist amongst existing collections according to their place of origin, presenting high genetic variability. The results showed that PCR is a sensitive and specific test for detecting R. solanacearum and can therefore be implemented as a method for controlling this pathogen in seed production and certification programmes in áreas free of the disease. The pathogen has been shown to be genetically heterogeneous according to the samples' geographical área thereby hampering control in áreas of Colombia experiencing phytosanitary problems with R. solanacearum in potato crops Key words: bacterial withered, moko, PCR-16S rADN, ELISA-NCM, PCR-RAPD.

  13. Genetic variability and population structure of the mushroom Pleurotus eryngii var. tuoliensis.

    Directory of Open Access Journals (Sweden)

    Mengran Zhao

    Full Text Available The genetic diversity of 123 wild strains of Pleurotus eryngii var. tuoliensis, which were collected from nine geographical locations in Yumin, Tuoli, and Qinghe counties in the Xinjiang Autonomous Region of China, was analysed using two molecular marker systems (inter-simple sequence repeat and start codon targeted. At the variety level, the percentage of polymorphic loci and Nei's gene diversity index for P. eryngii var. tuoliensis was 96.32% and 0.238, respectively. At the population level, Nei's gene diversity index ranged from 0.149 to 0.218 with an average of 0.186, and Shannon's information index ranged from 0.213 to 0.339 with an average of 0.284. These results revealed the abundant genetic variability in the wild resources of P. eryngii var. tuoliensis. Nei's gene diversity analysis indicated that the genetic variance was mainly found within individual geographical populations, and the analysis of molecular variance revealed low but significant genetic differentiation among local and regional populations. The limited gene flow (Nm = 1.794 was inferred as a major reason for the extent of genetic differentiation of P. eryngii var. tuoliensis. The results of Mantel tests showed that the genetic distance among geographical populations of P. eryngii var. tuoliensis was positively correlated with the geographical distance and the longitudinal distances (rGo = 0.789 and rLn = 0.873, respectively, which indicates that geographical isolation is an important factor for the observed genetic differentiation. Nine geographical populations of P. eryngii var. tuoliensis were divided into three groups according to their geographical origins, which revealed that the genetic diversity was closely related to the geographical distribution of this wild fungus.

  14. Genetic Variability Overrides the Impact of Parental Cell Type and Determines iPSC Differentiation Potential

    Directory of Open Access Journals (Sweden)

    Aija Kyttälä

    2016-02-01

    Full Text Available Reports on the retention of somatic cell memory in induced pluripotent stem cells (iPSCs have complicated the selection of the optimal cell type for the generation of iPSC biobanks. To address this issue we compared transcriptomic, epigenetic, and differentiation propensities of genetically matched human iPSCs derived from fibroblasts and blood, two tissues of the most practical relevance for biobanking. Our results show that iPSC lines derived from the same donor are highly similar to each other. However, genetic variation imparts a donor-specific expression and methylation profile in reprogrammed cells that leads to variable functional capacities of iPSC lines. Our results suggest that integration-free, bona fide iPSC lines from fibroblasts and blood can be combined in repositories to form biobanks. Due to the impact of genetic variation on iPSC differentiation, biobanks should contain cells from large numbers of donors.

  15. Genetic variability of two populations of Pseudoplatystoma reticulatum from the Upper Paraguay River Basin

    Directory of Open Access Journals (Sweden)

    Marcia Matos de Abreu

    2009-01-01

    Full Text Available Catfishes of the genus Pseudoplatystoma are very important species due to both their high commercial value and their ecological role as voracious predators. They undertake lengthy migratory movements during their life-cycle, this including reproductive migration which occurs from October to December in the rainy season. In the present study, seven microsatellite loci were analyzed to access genetic variability in two samples of P. reticulatum from the Upper Paraguay Basin. The loci were highly polymorphic (mean = 7.28. According to all analysis, the two samples of P. reticulatum revealed pronounced genetic differentiation. Fst value was 0.2290, Rst value 0.1067 and AMOVA 22.90% (Fst and 10.67% (Rst, all being highly significant (p < 0.001. The division of the fishes into two groups was confirmed by microsatellite multi-locus Bayesian assignment testing. The results obtained present evidence of genetic structuring in a P. reticulatum population.

  16. Genetic Polymorphism of Aedes albopictus Population Inferred From ND5 Gene Variabilities In Subang Jaya, Malaysia.

    Science.gov (United States)

    Adilah-Amrannudin, Nurul; Hamsidi, Mayamin; Ismail, Nurul-Ain; Ismail, Rodziah; Dom, Nazri Che; Ahmad, Abu Hassan; Mastuki, Mohd Fahmi; Basri, Tengku Shahrul Anuar Tengku Ahmad; Khalid, Adira; Muslim, Mohammad; Daud, Nurul Amalina Ahmad; Camalxaman, Siti Nazrina

    2016-12-01

    This study was performed to establish the genetic variability of Aedes albopictus within Subang Jaya, Selangor, Malaysia, by using the nicotinamide adenine dinucleotide dehydrogenase 5 subunit (ND5) mitochondrial DNA (mtDNA) marker. A total of 90 samples were collected from 9 localities within an area of the Subang Jaya Municipality. Genetic variability was determined through the amplification and sequencing of a fragment of the ND5 gene. Eight distinct mtDNA haplotypes were identified. The evolutionary relationship of the local haplotypes alongside 28 reference strains was used to construct a phylogram, the analysis of which revealed low genetic differentiation in terms of both nucleotide and haplotype diversity. Bayesian method was used to infer the phylogenetic tree, revealing a unique relationship between local isolates. The study corroborates the reliability of ND5 to identify distinct lineages for polymorphism-based studies and supplements the existing body of knowledge regarding its genetic diversity. This in turn could potentially aid existing vector control strategies to help mitigate the risk and spread of the dengue virus.

  17. Genetic and environmental influences on blood pressure variability: a study in twins.

    Science.gov (United States)

    Xu, Xiaojing; Ding, Xiuhua; Zhang, Xinyan; Su, Shaoyong; Treiber, Frank A; Vlietinck, Robert; Fagard, Robert; Derom, Catherine; Gielen, Marij; Loos, Ruth J F; Snieder, Harold; Wang, Xiaoling

    2013-04-01

    Blood pressure variability (BPV) and its reduction in response to antihypertensive treatment are predictors of clinical outcomes; however, little is known about its heritability. In this study, we examined the relative influence of genetic and environmental sources of variance of BPV and the extent to which it may depend on race or sex in young twins. Twins were enrolled from two studies. One study included 703 white twins (308 pairs and 87 singletons) aged 18-34 years, whereas another study included 242 white twins (108 pairs and 26 singletons) and 188 black twins (79 pairs and 30 singletons) aged 12-30 years. BPV was calculated from 24-h ambulatory blood pressure recording. Twin modeling showed similar results in the separate analysis in both twin studies and in the meta-analysis. Familial aggregation was identified for SBP variability (SBPV) and DBP variability (DBPV) with genetic factors and common environmental factors together accounting for 18-40% and 23-31% of the total variance of SBPV and DBPV, respectively. Unique environmental factors were the largest contributor explaining up to 82-77% of the total variance of SBPV and DBPV. No sex or race difference in BPV variance components was observed. The results remained the same after adjustment for 24-h blood pressure levels. The variance in BPV is predominantly determined by unique environment in youth and young adults, although familial aggregation due to additive genetic and/or common environment influences was also identified explaining about 25% of the variance in BPV.

  18. Genetic variability of rice recurrent selection populations as affected by male sterility or manual recombination

    Directory of Open Access Journals (Sweden)

    Letícia da Silveira Pinheiro

    2012-06-01

    Full Text Available The objective of this work was to determine the effect of male sterility or manual recombination on genetic variability of rice recurrent selection populations. The populations CNA-IRAT 4, with a gene for male sterility, and CNA 12, which was manually recombined, were evaluated. Genetic variability among selection cycles was estimated using14 simple sequence repeat (SSR markers. A total of 926 plants were analyzed, including ten genitors and 180 individuals from each of the evaluated cycles (1, 2 and 5 of the population CNA-IRAT 4, and 16 genitors and 180 individuals from each of the cycles (1 and 2 of CNA 12. The analysis allowed the identification of alleles not present among the genitors for both populations, in all cycles, especially for the CNA-IRAT 4 population. These alleles resulted from unwanted fertilization with genotypes that were not originally part of the populations. The parameters of Wright's F-statistic (F IS and F IT indicated that the manual recombination expands the genetic variability of the CNA 12 population, whereas male sterility reduces the one of CNA-IRAT 4.

  19. Prevalence and Genetic Variability in Capsid L1 Gene of Rare Human Papillomaviruses (HPV Found in Cervical Lesions of Women from North-East Brazil

    Directory of Open Access Journals (Sweden)

    Ana Pavla Almeida Diniz Gurgel

    2013-01-01

    Full Text Available The aim of this study was to examine the prevalence and genetic variability of the capsid L1 gene of rare HPV genotypes that were found in the cervical lesions of women from North-East Brazil. A total number of 263 patients were included in this study. HPV detection was performed using PCR followed by direct sequencing of MY09/11, as well as type-specific PCR to detect the Alpha-9 species. Epitope prediction was performed to determine whether or not the genetic variants are inserted in B-cell and T-cell epitopes. The prevalence of rare HPV types in cervical lesions was found to be 9.47%. The rare HPV genotypes that were detected were HPV-53, 54, 56, 61, 62, 66, 70, and 81. The genetic variability in the L1 gene of rare HPV types involved thirty nucleotide changes, eight of which were detected for the first time in this study. Moreover, some of these variants are embedded in B-cell or T-cell epitope regions. The results of this research suggest that rare HPV types might be involved in cervical lesions and some of these variants can be found in B-cell and T-cell epitopes. Data on the prevalence and variability of rare HPV types will assist in clarifying the role of these viruses in carcinogenesis.

  20. Reliability of genetic bottleneck tests for detecting recent population declines

    NARCIS (Netherlands)

    Peery, M. Zachariah; Kirby, Rebecca; Reid, Brendan N.; Stoelting, Ricka; Doucet-Beer, Elena; Robinson, Stacie; Vasquez-Carrillo, Catalina; Pauli, Jonathan N.; Palsboll, Per J.

    2012-01-01

    The identification of population bottlenecks is critical in conservation because populations that have experienced significant reductions in abundance are subject to a variety of genetic and demographic processes that can hasten extinction. Genetic bottleneck tests constitute an appealing and popula

  1. Genetic variability of Amorphophallus muelleri Blume in Java based on Random Amplified Polymorphic DNA

    Directory of Open Access Journals (Sweden)

    DIYAH MARTANTI

    2008-10-01

    Full Text Available Amorphophallus muelleri Blume (Araceae is valued for its glucomanan content for use in food industry (healthy diet food, paper industry, pharmacy and cosmetics. The species is triploid (2n=3x=39 and the seed is developed apomictically. The present research is aimed to identify genetic variability of six population of A. muelleri from Java (consisted of 50 accessions using random amplified polymorphic DNA (RAPD. The six populations of the species are: East Java: (1 Silo-Jember, (2 Saradan-Madiun, (3 IPB (cultivated, from Saradan-Madiun, (4 Panti-Jember, (5 Probolinggo; and Central Java: (6 Cilacap. The results showed that five RAPD primers generated 42 scorable bands of which 29 (69.05% were polymorphic. Size of the bands varied from 300bp to 1.5kbp. The 50 accessions of A. muelleri were divided into two main clusters, some of them were grouped based on their populations, and some others were not. The range of individual genetic dissimilarity was from 0.02 to 0.36. The results showed that among six populations investigated, Saradan population showed the highest levels of genetic variation with mean values of na = 1.500+ 0.5061, ne = 1.3174 + 0.3841, PLP = 50% and He = 0, 0.1832+0.2054, whereas Silo-Jember population showed the lowest levels of genetic variation with mean values na = 1.2619+ 0.4450, ne = 1.1890 + 0.3507, PLP = 26.19% and He = 0.1048+0.1887. Efforts to conserve, domesticate, cultivate and improve genetically should be based on the genetic properties of each population and individual within population, especially Saradan population which has the highest levels of genetic variation, need more attention for its conservation.

  2. Identifying genetic variants for heart rate variability in the acetylcholine pathway.

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    Harriëtte Riese

    Full Text Available Heart rate variability is an important risk factor for cardiovascular disease and all-cause mortality. The acetylcholine pathway plays a key role in explaining heart rate variability in humans. We assessed whether 443 genotyped and imputed common genetic variants in eight key genes (CHAT, SLC18A3, SLC5A7, CHRNB4, CHRNA3, CHRNA, CHRM2 and ACHE of the acetylcholine pathway were associated with variation in an established measure of heart rate variability reflecting parasympathetic control of the heart rhythm, the root mean square of successive differences (RMSSD of normal RR intervals. The association was studied in a two stage design in individuals of European descent. First, analyses were performed in a discovery sample of four cohorts (n = 3429, discovery stage. Second, findings were replicated in three independent cohorts (n = 3311, replication stage, and finally the two stages were combined in a meta-analysis (n = 6740. RMSSD data were obtained under resting conditions. After correction for multiple testing, none of the SNPs showed an association with RMSSD. In conclusion, no common genetic variants for heart rate variability were identified in the largest and most comprehensive candidate gene study on the acetylcholine pathway to date. Future gene finding efforts for RMSSD may want to focus on hypothesis free approaches such as the genome-wide association study.

  3. Identifying Genetic Variants for Heart Rate Variability in the Acetylcholine Pathway

    Science.gov (United States)

    Riese, Harriëtte; Muñoz, Loretto M.; Hartman, Catharina A.; Ding, Xiuhua; Su, Shaoyong; Oldehinkel, Albertine J.; van Roon, Arie M.; van der Most, Peter J.; Lefrandt, Joop; Gansevoort, Ron T.; van der Harst, Pim; Verweij, Niek; Licht, Carmilla M. M.; Boomsma, Dorret I.; Hottenga, Jouke-Jan; Willemsen, Gonneke; Penninx, Brenda W. J. H.; Nolte, Ilja M.; de Geus, Eco J. C.; Wang, Xiaoling; Snieder, Harold

    2014-01-01

    Heart rate variability is an important risk factor for cardiovascular disease and all-cause mortality. The acetylcholine pathway plays a key role in explaining heart rate variability in humans. We assessed whether 443 genotyped and imputed common genetic variants in eight key genes (CHAT, SLC18A3, SLC5A7, CHRNB4, CHRNA3, CHRNA, CHRM2 and ACHE) of the acetylcholine pathway were associated with variation in an established measure of heart rate variability reflecting parasympathetic control of the heart rhythm, the root mean square of successive differences (RMSSD) of normal RR intervals. The association was studied in a two stage design in individuals of European descent. First, analyses were performed in a discovery sample of four cohorts (n = 3429, discovery stage). Second, findings were replicated in three independent cohorts (n = 3311, replication stage), and finally the two stages were combined in a meta-analysis (n = 6740). RMSSD data were obtained under resting conditions. After correction for multiple testing, none of the SNPs showed an association with RMSSD. In conclusion, no common genetic variants for heart rate variability were identified in the largest and most comprehensive candidate gene study on the acetylcholine pathway to date. Future gene finding efforts for RMSSD may want to focus on hypothesis free approaches such as the genome-wide association study. PMID:25384021

  4. Genetic variability and relationship between MT-1 elephant grass and closely related cultivars assessed by SRAP markers

    Indian Academy of Sciences (India)

    Xin-Ming Xie; Feng Zhou; Xiang-Qian Zhang; Ju-Ming Zhang

    2009-12-01

    Genetic variability and relationships among elephant grass cultivars were estimated by the SRAP (sequence-related amplified polymorphism) assay. A total of 60 individuals collected from five cultivars in China were analysed. Sixty-two selected primer combinations generated 1395 bands, with an average of 22.5 per primer combination. The average value of percentage of polymorphic bands (PPB) was 72.8% at species level. The PPB was from 15.2% to 75%, with an average of 39.6% at cultivar level. $H_{POP}$, within-cultivar Shannon’s index was 1.738 at cultivar level; at species level, the Shannon’s index $(H_{SP})$ was 3.880. An assessment of diversity between cultivars $[(H_{SP} −H_{POP})/H_{SP}]$ indicated that most of the diversity (55.2%) was detected among cultivars, and only 44.8% was within cultivars in total genetic variation. According to UPGMA dendrogram, the five cultivars were clustered into three main groups. One group included MT-1 and Mott with a bootstrap support of 100%, another consisted of Huanan and N51 with a bootstrap support of 81%, and last one was only Guimu-1. The results indicate that the MT-1 and Mott have a closest genetic relationship; Huanan and N51 possess a relatively close relationship, and Guimu-1 is the most distinct from the other four cultivars.

  5. Unintended effects and their detection in genetically modified crops.

    Science.gov (United States)

    Cellini, F; Chesson, A; Colquhoun, I; Constable, A; Davies, H V; Engel, K H; Gatehouse, A M R; Kärenlampi, S; Kok, E J; Leguay, J-J; Lehesranta, S; Noteborn, H P J M; Pedersen, J; Smith, M

    2004-07-01

    The commercialisation of GM crops in Europe is practically non-existent at the present time. The European Commission has instigated changes to the regulatory process to address the concerns of consumers and member states and to pave the way for removing the current moratorium. With regard to the safety of GM crops and products, the current risk assessment process pays particular attention to potential adverse effects on human and animal health and the environment. This document deals with the concept of unintended effects in GM crops and products, i.e. effects that go beyond that of the original modification and that might impact primarily on health. The document first deals with the potential for unintended effects caused by the processes of transgene insertion (DNA rearrangements) and makes comparisons with genetic recombination events and DNA rearrangements in traditional breeding. The document then focuses on the potential value of evolving "profiling" or "omics" technologies as non-targeted, unbiased approaches, to detect unintended effects. These technologies include metabolomics (parallel analysis of a range of primary and secondary metabolites), proteomics (analysis of polypeptide complement) and transcriptomics (parallel analysis of gene expression). The technologies are described, together with their current limitations. Importantly, the significance of unintended effects on consumer health are discussed and conclusions and recommendations presented on the various approaches outlined.

  6. Genetically modified cotton in India and detection strategies.

    Science.gov (United States)

    Randhawa, Gurinder Jit; Chhabra, Rashmi

    2013-01-01

    India is one of the largest cotton-growing countries. Cotton is a fiber crop with varied applications from making tiny threads to fashionable clothing in the textile sector. In the near future, cotton crop will gain popularity as a multipurpose crop in India. The commercialization of Bt cotton in 2002 and consequently the fast adoption of Bt cotton hybrids by cotton farmers have enhanced the cotton production in India. Presently, genetically modified (GM) cotton has occupied 21.0 million hectares (mha) that comprise 14% of the global area under GM cultivation. In the coming years, improved cotton hybrids, with stacked and multiple gene events for improved fiber quality, insect resistance, drought tolerance, and herbicide tolerance, would further significantly improve the cotton production in India. With the dramatic increase in commercialization of GM crops, there is an urgent need to develop cost-effective and robust GM detection methods for effective risk assessment and management, post release monitoring, and to solve the legal disputes. DNA-based GM diagnostics are most robust assays due to their high sensitivity, specificity, and stability of DNA molecule.

  7. Genetic variability of Echinococcus granulosus from the Tibetan plateau inferred by mitochondrial DNA sequences.

    Science.gov (United States)

    Yan, Ning; Nie, Hua-Ming; Jiang, Zhong-Rong; Yang, Ai-Guo; Deng, Shi-Jin; Guo, Li; Yu, Hua; Yan, Yu-Bao; Tsering, Dawa; Kong, Wei-Shu; Wang, Ning; Wang, Jia-Hai; Xie, Yue; Fu, Yan; Yang, De-Ying; Wang, Shu-Xian; Gu, Xiao-Bin; Peng, Xue-Rong; Yang, Guang-You

    2013-09-01

    To analyse genetic variability and population structure, 84 isolates of Echinococcus granulosus (Cestoda: Taeniidae) collected from various host species at different sites of the Tibetan plateau in China were sequenced for the whole mitochondrial nad1 (894 bp) and atp6 (513 bp) genes. The vast majority were classified as G1 genotype (n=82), and two samples from human patients in Sichuan province were identified as G3 genotype. Based on the concatenated sequences of nad1+atp6, 28 different haplotypes (NA1-NA28) were identified. A parsimonious network of the concatenated sequence haplotypes showed star-like features in the overall population, with NA1 as the major haplotype in the population networks. By AMOVA it was shown that variation of E. granulosus within the overall population was the main pattern of the total genetic variability. Neutrality indexes of the concatenated sequence (nad1+atp6) were computed by Tajima's D and Fu's Fs tests and showed high negative values for E. granulosus, indicating significant deviations from neutrality. FST and Nm values suggested that the populations were not genetically differentiated.

  8. Genetic variability and heritability in cultivated okra [Abel moschus esculentus (L.) Moench

    Energy Technology Data Exchange (ETDEWEB)

    Nwangburuka, C. C.; Denton, O. A.; Khinde, O. B.; Ojo, D. K.; Popoola, A. R.

    2012-11-01

    Twenty-nine okra accessions from different agro-ecological regions in Nigeria were grown during the rainy and dry seasons, between 2006 and 2007 at Abeokuta (derived savanah) and Ilishan (rainforest) and assessed to determine their genetic variability, heritability and genetic advance from eight yield related characters. The experiment was laid out in a Randomized Complete Block Design with five replications. There was high genotypic coefficient of variability, % broad-sense heritability and genetic advance in traits such as plant height (26.2, 90.7, 51.5), fresh pod length (23.9, 98.5, 48.8), fresh pod width (23.9, 98.5, 48.8), mature pod length (28.6, 98.5, 52.3), branching per plant (29.3, 82.3, 54.8) and pod weight per plant (33.9, 90.0, 63.3), suggesting the effect of additive genes and reliability of selection based on phenotype of these traits for crop improvement. The positive and significant phenotypic and genotypic correlation between plant height at maturity, fresh pod width, seeds per pod and pods per plant, branches per plant with seed weight per plant and pod weight per plant, suggests that selection on the basis of the phenotype of these characters will lead to high seed and pod yield in okra. (Author) 26 refs.

  9. Optimization of cocoa butter analog synthesis variables using neural networks and genetic algorithm.

    Science.gov (United States)

    Shekarchizadeh, Hajar; Tikani, Reza; Kadivar, Mahdi

    2014-09-01

    Cocoa butter analog was prepared from camel hump fat and tristearin by enzymatic interesterification in supercritical carbon dioxide (SC-CO2) using immobilized Thermomyces lanuginosus lipase (Lipozyme TL IM) as a biocatalyst. Optimal process conditions were determined using neural networks and genetic algorithm optimization. Response surfaces methodology was used to design the experiments to collect data for the neural network modelling. A general regression neural network model was developed to predict the response of triacylglycerol (TAG) distribution of cocoa butter analog from the process pressure, temperature, tristearin/camel hump fat ratio, water content, and incubation time. A genetic algorithm was used to search for a combination of the process variables for production of most similar cocoa butter analog to the corresponding cocoa butter. The combinations of the process variables during genetic algorithm optimization were evaluated using the neural network model. The pressure of 10 MPa; temperature of 40 °C; SSS/CHF ratio of 0.6:1; water content of 13 % (w/w); and incubation time of 4.5 h were found to be the optimum conditions to achieve the most similar cocoa butter analog to the corresponding cocoa butter.

  10. Genetic variability in maned wolf based on heterologous short-tandem repeat markers from domestic dog.

    Science.gov (United States)

    Salim, D C; Akimoto, A A; Carvalho, C B; Oliveira, S F; Grisolia, C K; Moreira, J R; Klautau-Guimarães, M N

    2007-06-20

    The maned wolf (Chrysocyon brachyurus) is the largest South American canid. Habitat loss and fragmentation, due to agricultural expansion and predatory hunting, are the main threats to this species. It is included in the official list of threatened wildlife species in Brazil, and is also protected by IUCN and CITES. Highly variable genetic markers such as microsatellites have the potential to resolve genetic relationships at all levels of the population structure (among individuals, demes or metapopulations) and also to identify the evolutionary unit for strategies for the conservation of the species. Tests were carried out to verify whether a class of highly polymorphic tetranucleotide repeats described for the domestic dog effectively amplifies DNA in the maned wolf. All five loci studied were amplified; however, one of these, was shown to be monomorphic in 69 maned wolf samples. The average allele number and estimated heterozygosity per polymorphic locus were 4.3 and 67%, respectively. The genetic variability found for this species, which is considered threatened with extinction, showed similar results when compared to studies of other canids.

  11. Genetic variability of garlic accessions as revealed by agro-morphological traits evaluated under different environments.

    Science.gov (United States)

    Hoogerheide, E S S; Azevedo Filho, J A; Vencovsky, R; Zucchi, M I; Zago, B W; Pinheiro, J B

    2017-05-31

    The cultivated garlic (Allium sativum L.) displays a wide phenotypic diversity, which is derived from natural mutations and phenotypic plasticity, due to dependence on soil type, moisture, latitude, altitude and cultural practices, leading to a large number of cultivars. This study aimed to evaluate the genetic variability shown by 63 garlic accessions belonging to Instituto Agronômico de Campinas and the Escola Superior de Agricultura "Luiz de Queiroz" germplasm collections. We evaluated ten quantitative characters in experimental trials conducted under two localities of the State of São Paulo: Monte Alegre do Sul and Piracicaba, during the agricultural year of 2007, in a randomized blocks design with five replications. The Mahalanobis distance was used to measure genetic dissimilarities. The UPGMA method and Tocher's method were used as clustering procedures. Results indicated significant variation among accessions (P < 0.01) for all evaluated characters, except for the percentage of secondary bulb growth in MAS, indicating the existence of genetic variation for bulb production, and germplasm evaluation considering different environments is more reliable for the characterization of the genotypic variability among garlic accessions, since it diminishes the environmental effects in the clustering of genotypes.

  12. Comparative performance of selected variability detection techniques in photometric time series data

    CERN Document Server

    Sokolovsky, K V; Karampelas, A; Antipin, S V; Bellas-Velidis, I; Benni, P; Bonanos, A Z; Burdanov, A Y; Derlopa, S; Hatzidimitriou, D; Khokhryakova, A D; Kolesnikova, D M; Korotkiy, S A; Lapukhin, E G; Moretti, M I; Popov, A A; Pouliasis, E; Samus, N N; Spetsieri, Z; Veselkov, S A; Volkov, K V; Yang, M; Zubareva, A M

    2016-01-01

    Photometric measurements are prone to systematic errors presenting a challenge to low-amplitude variability detection. In search for a general-purpose variability detection technique able to recover a broad range of variability types including currently unknown ones, we test 18 statistical characteristics quantifying scatter and/or correlation between brightness measurements. We compare their performance in identifying variable objects in seven time-series datasets obtained with telescopes ranging in size from a telephoto lens to 1m-class and probing variability on timescales from minutes to decades. The test datasets together include lightcurves of 127539 objects, among them 1251 variable stars of various types and represent a range of observing conditions often found in ground-based variability surveys. The real data are complemented by simulations. We propose a combination of two indices that together recover a broad range of variability types from photometric data characterized by a wide variety of sampli...

  13. Genetic variability of the neogregarine Apicystis bombi, an etiological agent of an emergent bumblebee disease.

    Directory of Open Access Journals (Sweden)

    Jafar Maharramov

    Full Text Available The worldwide spread of diseases is considered a major threat to biodiversity and a possible driver of the decline of pollinator populations, particularly when novel species or strains of parasites emerge. Previous studies have suggested that populations of introduced European honeybee (Apis mellifera and bumblebee species (Bombus terrestris and Bombus ruderatus in Argentina share the neogregarine parasite Apicystis bombi with the native bumblebee (Bombus dahlbomii. In this study we investigated whether A. bombi is acting as an emergent parasite in the non-native populations. Specifically, we asked whether A. bombi, recently identified in Argentina, was introduced by European, non-native bees. Using ITS1 and ITS2 to assess the parasite's intraspecific genetic variation in bees from Argentina and Europe, we found a largely unstructured parasite population, with only 15% of the genetic variation being explained by geographic location. The most abundant haplotype in Argentina (found in all 9 specimens of non-native species was identical to the most abundant haplotype in Europe (found in 6 out of 8 specimens. Similarly, there was no evidence of structuring by host species, with this factor explaining only 17% of the genetic variation. Interestingly, parasites in native Bombus ephippiatus from Mexico were genetically distant from the Argentine and European samples, suggesting that sufficient variability does exist in the ITS region to identify continent-level genetic structure in the parasite. Thus, the data suggest that A. bombi from Argentina and Europe share a common, relatively recent origin. Although our data did not provide information on the direction of transfer, the absence of genetic structure across space and host species suggests that A. bombi may be acting as an emergent infectious disease across bee taxa and continents.

  14. Structure and Genetic Variability of the Oceanic Whitetip Shark, Carcharhinus longimanus, Determined Using Mitochondrial DNA

    Science.gov (United States)

    Camargo, Sâmia M.; Coelho, Rui; Chapman, Demian; Howey-Jordan, Lucy; Brooks, Edward J.; Fernando, Daniel; Mendes, Natalia J.; Hazin, Fabio H. V.; Oliveira, Claudio; Santos, Miguel N.; Foresti, Fausto; Mendonça, Fernando F.

    2016-01-01

    Information regarding population structure and genetic connectivity is an important contribution when establishing conservation strategies to manage threatened species. The oceanic whitetip shark, Carcharhinus longimanus, is a highly migratory, large-bodied, pelagic shark listed by the IUCN (International Union for Conservation of Nature) Red List as "vulnerable" throughout its range and “critically endangered” in the western north Atlantic. In 2014, the species was protected globally under Appendix II of CITES (Convention on International Trade in Endangered Species), limiting and regulating trade. This study used partial sequences of mitochondrial DNA (mtDNA) control region to determine the population genetic structure of oceanic whitetip sharks across the Atlantic and Indian Oceans. 724 base pairs were obtained from 215 individuals that identifed nine polymorphic sites and defined 12 distinct haplotypes. Total nucleotide diversity (π) was 0.0013 and haplotype diversity (h) was 0.5953. The Analysis of Molecular Variance (AMOVA) evidenced moderate levels of population structure (ɸST = 0.1039) with restricted gene flow between the western and eastern Atlantic Ocean, and a strong relationship between the latter region and the Indian Ocean. Even though the oceanic whitetip is a highly migratory animal the results presented here show that their genetic variability is slightly below average of other pelagic sharks. Additionally, this study recommends that at least two populations in the Atlantic Ocean should be considered distinct (eastern and western Atlantic) and conservation efforts should be focused in areas with the greatest genetic diversity by environmental managers. PMID:27187497

  15. Structure and Genetic Variability of the Oceanic Whitetip Shark, Carcharhinus longimanus, Determined Using Mitochondrial DNA.

    Science.gov (United States)

    Camargo, Sâmia M; Coelho, Rui; Chapman, Demian; Howey-Jordan, Lucy; Brooks, Edward J; Fernando, Daniel; Mendes, Natalia J; Hazin, Fabio H V; Oliveira, Claudio; Santos, Miguel N; Foresti, Fausto; Mendonça, Fernando F

    2016-01-01

    Information regarding population structure and genetic connectivity is an important contribution when establishing conservation strategies to manage threatened species. The oceanic whitetip shark, Carcharhinus longimanus, is a highly migratory, large-bodied, pelagic shark listed by the IUCN (International Union for Conservation of Nature) Red List as "vulnerable" throughout its range and "critically endangered" in the western north Atlantic. In 2014, the species was protected globally under Appendix II of CITES (Convention on International Trade in Endangered Species), limiting and regulating trade. This study used partial sequences of mitochondrial DNA (mtDNA) control region to determine the population genetic structure of oceanic whitetip sharks across the Atlantic and Indian Oceans. 724 base pairs were obtained from 215 individuals that identifed nine polymorphic sites and defined 12 distinct haplotypes. Total nucleotide diversity (π) was 0.0013 and haplotype diversity (h) was 0.5953. The Analysis of Molecular Variance (AMOVA) evidenced moderate levels of population structure (ɸST = 0.1039) with restricted gene flow between the western and eastern Atlantic Ocean, and a strong relationship between the latter region and the Indian Ocean. Even though the oceanic whitetip is a highly migratory animal the results presented here show that their genetic variability is slightly below average of other pelagic sharks. Additionally, this study recommends that at least two populations in the Atlantic Ocean should be considered distinct (eastern and western Atlantic) and conservation efforts should be focused in areas with the greatest genetic diversity by environmental managers.

  16. Assessment of genetic variability of fish personality traits using rainbow trout isogenic lines.

    Science.gov (United States)

    Millot, Sandie; Péan, Samuel; Labbé, Laurent; Kerneis, Thierry; Quillet, Edwige; Dupont-Nivet, Mathilde; Bégout, Marie-Laure

    2014-07-01

    The study of inter-individual variability of personality in fish is a growing field of interest but the genetic basis of this complex trait is still poorly investigated due to the difficulty in controlling fish genetic origin and life history. When available, isogenic lines that allow performing independent tests on different individuals having identical genotype constitute a very relevant experimental material to disentangle the genetic and environmental components of behavioural individuality. We took advantage of heterozygous isogenic lines to investigate the personality in rainbow trout through the analysis of their reactions to different experimental situations. To this end, seven to ten rainbow trout isogenic lines were screened for their spatial exploratory behaviour, their flight response toward a stressor and their risk taking behaviour. Results showed that some lines seemed less sensitive to new events or environmental changes and could be defined as low responsive, while others were very sensitive and defined as high responsive. The use of isogenic lines highlighted the importance of genetic factors, in combination with life history, in the expression of personality in domesticated fish.

  17. Genetic variability and identification of the intermediate snail hosts of Schistosoma mansoni

    Directory of Open Access Journals (Sweden)

    Teofânia HDA Vidigal

    1998-01-01

    Full Text Available Studies based on shell or reproductive organ morphology and genetic considerations suggest extensive intraspecific variation in Biomphalaria snails. The high variability at the morphological and genetic levels, as well as the small size of some specimens and similarities between species complicate the correct identification of these snails. Here we review our work using methods based on polymerase chain reaction (PCR amplification for analysis of genetic variation and identification of Biomphalaria snails from Brazil, Argentina, Uruguay and Paraguay. Arbitrarily primed-PCR revealed that the genome of B. glabrata exihibits a remarkable degree of intraespecific polymorphism. Low stringency-PCR using primers for 18S rRNA permited the identification of B. glabrata, B. tenagophila and B. occidentalis. The study of individuals obtained from geographically distinct populations exhibits significant intraspecific DNA polymorphism, however specimens from the same species, exhibit some species specific LSPs. We also showed that PCR-restriction fragment of length polymorphism of the internal transcribed spacer region of Biomphalaria rDNA, using DdeI permits the differentiation of the three intermediate hosts of Schistosoma mansoni. The molecular biological techniques used in our studies are very useful for the generation of new knowledge concerning the systematics and population genetics of Biomphalaria snails.

  18. Structure and Genetic Variability of the Oceanic Whitetip Shark, Carcharhinus longimanus, Determined Using Mitochondrial DNA.

    Directory of Open Access Journals (Sweden)

    Sâmia M Camargo

    Full Text Available Information regarding population structure and genetic connectivity is an important contribution when establishing conservation strategies to manage threatened species. The oceanic whitetip shark, Carcharhinus longimanus, is a highly migratory, large-bodied, pelagic shark listed by the IUCN (International Union for Conservation of Nature Red List as "vulnerable" throughout its range and "critically endangered" in the western north Atlantic. In 2014, the species was protected globally under Appendix II of CITES (Convention on International Trade in Endangered Species, limiting and regulating trade. This study used partial sequences of mitochondrial DNA (mtDNA control region to determine the population genetic structure of oceanic whitetip sharks across the Atlantic and Indian Oceans. 724 base pairs were obtained from 215 individuals that identifed nine polymorphic sites and defined 12 distinct haplotypes. Total nucleotide diversity (π was 0.0013 and haplotype diversity (h was 0.5953. The Analysis of Molecular Variance (AMOVA evidenced moderate levels of population structure (ɸST = 0.1039 with restricted gene flow between the western and eastern Atlantic Ocean, and a strong relationship between the latter region and the Indian Ocean. Even though the oceanic whitetip is a highly migratory animal the results presented here show that their genetic variability is slightly below average of other pelagic sharks. Additionally, this study recommends that at least two populations in the Atlantic Ocean should be considered distinct (eastern and western Atlantic and conservation efforts should be focused in areas with the greatest genetic diversity by environmental managers.

  19. A genetic algorithm for variable selection in logistic regression analysis of radiotherapy treatment outcomes.

    Science.gov (United States)

    Gayou, Olivier; Das, Shiva K; Zhou, Su-Min; Marks, Lawrence B; Parda, David S; Miften, Moyed

    2008-12-01

    A given outcome of radiotherapy treatment can be modeled by analyzing its correlation with a combination of dosimetric, physiological, biological, and clinical factors, through a logistic regression fit of a large patient population. The quality of the fit is measured by the combination of the predictive power of this particular set of factors and the statistical significance of the individual factors in the model. We developed a genetic algorithm (GA), in which a small sample of all the possible combinations of variables are fitted to the patient data. New models are derived from the best models, through crossover and mutation operations, and are in turn fitted. The process is repeated until the sample converges to the combination of factors that best predicts the outcome. The GA was tested on a data set that investigated the incidence of lung injury in NSCLC patients treated with 3DCRT. The GA identified a model with two variables as the best predictor of radiation pneumonitis: the V30 (p=0.048) and the ongoing use of tobacco at the time of referral (p=0.074). This two-variable model was confirmed as the best model by analyzing all possible combinations of factors. In conclusion, genetic algorithms provide a reliable and fast way to select significant factors in logistic regression analysis of large clinical studies.

  20. The TAOS Project Stellar Variability II. Detection of 15 Variable Stars

    Energy Technology Data Exchange (ETDEWEB)

    Mondal, S; Lin, C C; Zhang, Z W; Alcock, C; Axelrod, T; Bianco, F B; Byun, Y I; Coehlo, N K; Cook, K H; Dave, R; Kim, D W; King, S K; Lee, T; Lehner, M J; Lin, H C; Marshall, S L; Protopapas, P; Rice, J A; Schwamb, M E; Wang, J H; Wang, S Y; Wen, C Y

    2010-01-28

    The Taiwanese-American Occultation Survey (TAOS) project has collected more than a billion photometric measurements since 2005 January. These sky survey data - covering timescales from a fraction of a second to a few hundred days - are a useful source to study stellar variability. A total of 167 star fields, mostly along the ecliptic plane, have been selected for photometric monitoring with the TAOS telescopes. This paper presents our initial analysis of a search for periodic variable stars from the time-series TAOS data on one particular TAOS field, No. 151 (RA = 17{sup h} 30{sup m} 6.67{sup s}, Dec = 27 degrees, 17 minutes, 30 seconds, J2000), which had been observed over 47 epochs in 2005. A total of 81 candidate variables are identified in the 3 square degree field, with magnitudes in the range 8 < R < 16. On the basis of the periodicity and shape of the lightcurves, 32 variables, 18 of which were previously unknown, are classified as RR Lyrae, Cepheid, {delta} Scuti, SX Phonencis, semi-regular and eclipsing binaries.

  1. Genetic variability of bottle gourd Lagenaria siceraria (Mol. Standley and its morphological characterization by multivariate analysis

    Directory of Open Access Journals (Sweden)

    Mladenović Emina

    2012-01-01

    Full Text Available A wide range of bottle gourd Lagenaria siceraria (Mol. Standley germplasm was collected from different parts of the world. Genetic resource preservation and determination of genetic variability was carried out as a foundation for future breeding work. The germplasm diversity collected in Serbia is a result of its adaptation to diverse ecological conditions and farmers’ selection in accordance with their preference and ethnobotanical utilization. The broad intraspecific variation of the plant, fruit and seed morphology is a direct result of the research carried out. Principal component analysis (PCA of L. siceraria with 13 quantitative traits showed continuous variation among accessions, primarily due to fruit and seed size and shape. The evident reduction in trait variation is a direct result of the preference for ornamental use that favored certain shapes and sizes of the fruit, which has not significantly changed over the centuries.

  2. Intraspecific genetic variability in a population of Moroccan Leishmania infantum revealed by PCR-RFLP of kDNA minicircles.

    Science.gov (United States)

    El Hamouchi, Adil; Ejghal, Rajaa; Hida, Moustapha; Lemrani, Meryem

    2017-05-01

    In Morocco, Leishmania infantum is the main etiologic agent of human and canine visceral leishmaniasis (VL). This species has been proven to be an opportunistic agent in HIV+ patients and is also responsible of sporadic cutaneous leishmaniasis (CL).This work aims to evaluate the genetic variability of Moroccan L. infantum strains based on PCR-RFLP analysis of the kinetoplastid DNA (kDNA) minicircles. A total of 75 DNA samples extracted from positive Giemsa-stained smears (n=32) and from L. infantum cultures (n=43) was studied. The samples have been taken from VL patients infected (n=7) or not (n=56) by HIV, patients with CL (n=2) and finally from infected dogs (n=10). An hypervariable region of kDNA was amplified using the primers MC1 and MC2; the PCR products were digested separately by a panel of nine restriction enzymes. The presence or absence of restriction fragments was scored in a binary matrix and the SplitsTree4 software was used for the construction of a Neighbor-Net network. Moroccan L. infantum population showed an important level of variability with the identification of 6 genotypes. For each genotype a PCR product was sequenced, confirming the presence of all the expected restriction sites. The predominant profile was the genotype B. A new genotype, named Q was detected for the first time, whereas the four other genotypes (G, K, N and O) were reported sporadically in the Mediterranean basin. The Neighbor-Net network segregates our L. infantum population into 3 clusters: Cluster I includes genotype B, cluster II grouping the genotypes O, Q and G and finally the cluster III contains the genotype N. The kDNA-PCR-RFLP assay is suitable for use directly on biological samples; it reveals an important degree of genetic variability among L. infantum strains even those belonging to the same zymodeme what is of great epidemiological interest.

  3. Genetic variability of lactoferrin content estimated by mid-infrared spectrometry in bovine milk.

    Science.gov (United States)

    Soyeurt, H; Colinet, F G; Arnould, V M-R; Dardenne, P; Bertozzi, C; Renaville, R; Portetelle, D; Gengler, N

    2007-09-01

    The effects of lactoferrin (LF) on the immune system have already been shown by many studies. Unfortunately, the current methods used to measure LF levels in milk do not permit the study of the genetic variability of lactoferrin or the performance of routine genetic evaluations. The first aim of this research was to derive a calibration equation permitting the prediction of LF in milk by mid-infrared spectrometry (MIR). The calibration with partial least squares on 69 samples showed a ratio of standard error of cross-validation to standard deviation equal to 1.98. Based on this value, the calibration equation was used to establish an LF indicator trait (predicted LF; pLF) on a large number of milk samples (n = 7,690). A subsequent study of its variability was conducted, which confirmed that stage of lactation and lactation number influence the overall pLF level. Small differences in mean pLF among 7 dairy breeds were also observed. The pLF content of Jersey milk was significantly higher than that in Holstein milk. Therefore, the choice of breed could change the expected LF level. Heritability estimated for pLF was 19.7%. The genetic and phenotypic correlations between somatic cell score and pLF were 0.04 and 0.26, respectively. As somatic cell score increases in presence of mastitis, this observation seems to indicate that pLF, or a function of observed pLF, compared with expected LF might have potential as an indicator of mastitis. The negative genetic correlation (-0.36) between milk yield and pLF could indicate an undesirable effect of selection for high milk production on the overall LF level.

  4. Influence of immunoprotection on genetic variability of cysteine proteinases from Haemonchus contortus adult worms.

    Science.gov (United States)

    Martín, S; Molina, J M; Hernández, Y I; Ferrer, O; Muñoz, Ma C; López, A; Ortega, L; Ruiz, A

    2015-11-01

    The limitations associated with the use of anthelmintic drugs in the control of gastrotintestinal nematodosis, such as the emergence of anthelmintic resistance, have stimulated the study of the immunological control of many parasites. In the case of Haemonchus contortus, several vaccination trials using native and recombinant antigens have been conducted. A group of antigens with demonstrated immunoprotective value are cathepsin B - like proteolytic enzymes of the cysteine proteinase type. These enzymes, which have been observed in both excretory-secretory products and somatic extracts of H. contortus, may vary among different geographic isolates and on strains isolated from different hosts, or even from the same host, as has been demonstrated in some comparative studies of genetic variability. In the present study, we evaluated the genetic variability of the worms that fully developed their endogenous cycle in immunised sheep and goat in order to identify the alleles of most immunoprotective value. To address these objectives, groups of sheep and goats were immunised with PBS soluble fractions enriched for cysteine proteinases from adult worms of H. contortus from either a strain of H. contortus isolated from goats of Gran Canaria Island (SP) or a strain isolated from sheep of North America (NA). The results confirmed the immunoprophylactic value of this type of enzyme against haemonchosis in both sheep and goats in association with increased levels of specific IgG. The genetic analysis demonstrated that the immunisation had a genetic selection on proteinase-encoding genes. In all the immunised animals, allelic frequencies were statistically different from those observed in non-immunised control animals in the four analysed genes. The reduction in the allelic frequencies suggests that parasites expressing these proteases are selectively targeted by the vaccine, and hence they should be considered in any subunit vaccine approach to control haemonchosis in small

  5. Insecticide resistance and genetic variability in natural populations of Aedes (Stegomyia aegypti (Diptera: Culicidae from Colombia

    Directory of Open Access Journals (Sweden)

    Oscar A. Aguirre-Obando

    2015-02-01

    Full Text Available Mosquito control prevails as the most efficient method to protect humans from the dengue virus, despite recent efforts to find a vaccine for this disease. We evaluated insecticide resistance and genetic variability in natural populations of Aedes aegypti (Linnaeus, 1762 from Colombia. This is the first Colombian study examining kdr mutations and population structure. Bioassays with larvae of three mosquito populations (Armenia, Calarcá and Montenegro were performed according to the World Health Organization (WHO guidelines, using Temephos. For the analysis of the Val1016Ile mutation and genetic diversity, we sampled recently-emerged adults from four mosquito populations (Armenia, Calarcá, Montenegro and Barcelona. Following the WHO protocol, bioassays implemented with larvae showed resistance to Temephos in mosquito populations from Armenia (77% ± 2 and Calarcá (62% ± 14, and an incipient altered susceptibility at Montenegro (88% ± 8. The RR95 of mosquito populations ranged from 3.7 (Montenegro to 6.0 (Calarca. The Val1016Ile mutation analysis of 107 genotyped samples indicates that 94% of the specimens were homozygous for the wild allele (1016Val and 6% were heterozygous (Val1016Ile. The 1016Ile allele was not found in Barcelona. Genetic variability analysis found three mitochondrial lineages with low genetic diversity and gene flow. In comparison with haplotypes from the American continent, those from this study suggest connections with Mexican and North American populations. These results confirm that a continuous monitoring and managing program of A. aegypti resistance in the state of Quindío is required.

  6. Comparative performance of selected variability detection techniques in photometric time series data

    Science.gov (United States)

    Sokolovsky, K. V.; Gavras, P.; Karampelas, A.; Antipin, S. V.; Bellas-Velidis, I.; Benni, P.; Bonanos, A. Z.; Burdanov, A. Y.; Derlopa, S.; Hatzidimitriou, D.; Khokhryakova, A. D.; Kolesnikova, D. M.; Korotkiy, S. A.; Lapukhin, E. G.; Moretti, M. I.; Popov, A. A.; Pouliasis, E.; Samus, N. N.; Spetsieri, Z.; Veselkov, S. A.; Volkov, K. V.; Yang, M.; Zubareva, A. M.

    2017-01-01

    Photometric measurements are prone to systematic errors presenting a challenge to low-amplitude variability detection. In search for a general-purpose variability detection technique able to recover a broad range of variability types including currently unknown ones, we test 18 statistical characteristics quantifying scatter and/or correlation between brightness measurements. We compare their performance in identifying variable objects in seven time series data sets obtained with telescopes ranging in size from a telephoto lens to 1 m-class and probing variability on time-scales from minutes to decades. The test data sets together include light curves of 127 539 objects, among them 1251 variable stars of various types and represent a range of observing conditions often found in ground-based variability surveys. The real data are complemented by simulations. We propose a combination of two indices that together recover a broad range of variability types from photometric data characterized by a wide variety of sampling patterns, photometric accuracies and percentages of outlier measurements. The first index is the interquartile range (IQR) of magnitude measurements, sensitive to variability irrespective of a time-scale and resistant to outliers. It can be complemented by the ratio of the light-curve variance to the mean square successive difference, 1/η, which is efficient in detecting variability on time-scales longer than the typical time interval between observations. Variable objects have larger 1/η and/or IQR values than non-variable objects of similar brightness. Another approach to variability detection is to combine many variability indices using principal component analysis. We present 124 previously unknown variable stars found in the test data.

  7. Comparative performance of selected variability detection techniques in photometric time series data

    Science.gov (United States)

    Sokolovsky, K. V.; Gavras, P.; Karampelas, A.; Antipin, S. V.; Bellas-Velidis, I.; Benni, P.; Bonanos, A. Z.; Burdanov, A. Y.; Derlopa, S.; Hatzidimitriou, D.; Khokhryakova, A. D.; Kolesnikova, D. M.; Korotkiy, S. A.; Lapukhin, E. G.; Moretti, M. I.; Popov, A. A.; Pouliasis, E.; Samus, N. N.; Spetsieri, Z.; Veselkov, S. A.; Volkov, K. V.; Yang, M.; Zubareva, A. M.

    2016-09-01

    Photometric measurements are prone to systematic errors presenting a challenge to low-amplitude variability detection. In search for a general-purpose variability detection technique able to recover a broad range of variability types including currently unknown ones, we test 18 statistical characteristics quantifying scatter and/or correlation between brightness measurements. We compare their performance in identifying variable objects in seven time-series datasets obtained with telescopes ranging in size from a telephoto lens to 1 m-class and probing variability on timescales from minutes to decades. The test datasets together include lightcurves of 127539 objects, among them 1251 variable stars of various types and represent a range of observing conditions often found in ground-based variability surveys. The real data are complemented by simulations. We propose a combination of two indices that together recover a broad range of variability types from photometric data characterized by a wide variety of sampling patterns, photometric accuracies, and percentages of outlier measurements. The first index is the interquartile range (IQR) of magnitude measurements, sensitive to variability irrespective of a timescale and resistant to outliers. It can be complemented by the ratio of the lightcurve variance to the mean square successive difference, 1/η, which is efficient in detecting variability on timescales longer than the typical time interval between observations. Variable objects have larger 1/η and/or IQR values than non-variable objects of similar brightness. Another approach to variability detection is to combine many variability indices using principal component analysis. We present 124 previously unknown variable stars found in the test data.

  8. Evaluating Genetic Variability of Sorghum Mutant Lines Tolerant to Acid Soil

    Directory of Open Access Journals (Sweden)

    W. Puspitasari

    2012-12-01

    Full Text Available High rainfall in some parts in Indonesia causes soil become acidic. The main constraint of acid soil is phosphor (P deficiency and aluminum (Al toxicity which decrease plant productivity. To overcome this problem, it is important to develop a crop variety tolerant to such conditions. Sorghum is probably one of the potential crops to meet that objective. Sorghum has been reported to have wide adaptability to various agro-ecology and can be used as food and animal feed. Unfortunately, sorghum is not Indonesian origin so its genetic variability is still low. From previous breeding works with induced mutation, some promising mutant lines have been developed. These mutant lines were included in the experiment carried out in Tenjo with soil condition was classified as acid soil with pH 4.8 and exchangeable-Al content 2.43 me/100 g. The objectives of this experiment were to study the magnitude of genetic variability of agronomy and grain quality characters in sorghum in order to facilitate the breeding improvement of the species. Plant materials used in this study were ten genotypes, including 6 mutant lines and 4 control varieties. The randomized block design with three replications was used in the experiment. The genetic variabilities of agronomic and grain quality characters existed among genotypes, such as plant height, number of leaves, stalk diameter, biomass weight, panicle length, grain yield per plant, 100 seed weight and tannin content in the grain. The broad sense heritabilities of agronomic characters were estimated ranging from medium to high. Grain yield showed significantly positive correlation with agronomic characters observed, but it was negatively correlated with protein content

  9. Evaluating Genetic Variability of Sorghum Mutant Lines Tolerant to Acid Soil

    Directory of Open Access Journals (Sweden)

    W. Puspitasari

    2012-08-01

    Full Text Available High rainfall in some parts in Indonesia causes soil become acidic. The main constraint of acid soil is phosphor (P deficiency and aluminum (Al toxicity which decrease plant productivity. To overcome this problem, it is important to develop a crop variety tolerant to such conditions. Sorghum is probably one of the potential crops to meet that objective. Sorghum has been reported to have wide adaptability to various agro-ecology and can be used as food and animal feed. Unfortunately, sorghum is not Indonesian origin so its genetic variability is still low. From previous breeding works with induced mutation, some promising mutant lines have been developed. These mutant lines were included in the experiment carried out in Tenjo with soil condition was classified as acid soil with pH 4.8 and exchangeable-Al content 2.43 me/100 g. The objectives of this experiment were to study the magnitude of genetic variability of agronomy and grain quality characters in sorghum in order to facilitate the breeding improvement of the species. Plant materials used in this study were ten genotypes, including 6 mutant lines and 4 control varieties. The randomized block design with three replications was used in the experiment. The genetic variabilities of agronomic and grain quality characters existed among genotypes, such as plant height, number of leaves, stalk diameter, biomass weight, panicle length, grain yield per plant, 100 seed weight and tannin content in the grain. The broad sense heritabilities of agronomic characters were estimated ranging from medium to high. Grain yield showed significantly positive correlation with agronomic characters observed, but it was negatively correlated with protein content

  10. Heirloom tomato cultivars and local populations as sources of genetic variability for breeding

    Directory of Open Access Journals (Sweden)

    Glogovac Svetlana

    2010-01-01

    Full Text Available Five local tomato populations and fourteen heirloom cultivars were analyzed in this study. The analyzed genotypes represent a part of tomato collection of Institute of Field and Vegetable Crops in Novi Sad. The following fruit and plant traits were analyzed: growth type, fruit color, fruit shape index, fruit weight, number of locules and dry matter content. Cluster analysis was performed so as to group the analyzed genotypes by homology and divergence. The aim of this article was to determine the importance of heirloom cultivars and local populations as sources of genetic variability in tomato breeding process.

  11. [Phenotypic variability in a family with genetically verified familial hemiplegic migraine type 2].

    Science.gov (United States)

    Hogaard, Nina; Klit, Henriette; Vogel, Ida; Thelle, Thomas

    2015-01-26

    After playing handball, a 13-year-old girl developed a comatose condition during 7-10 days with hemiparesis and aphasia. From age three to nine she was treated for partial epilepsy. She never had symptoms of migraine. Her father had childhood epilepsy and at the age of 40 and 44 he experienced two attacks with prolonged coma, fever, seizures, hemiparesis and aphasia. His mother had symptoms of severe hemiplegic migraine. Father and daughter were genetically tested and an earlier described mutation in ATP1A2 gene was found. These cases illustrate the phenotypic variability in familial hemiplegic migraine type 2.

  12. A Novel Sliding Mode Variable Structure Controller Based on a Genetic Algorithm

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    A novel control method has been proposed by using the genetic algorithm ( GA ) for nonlinear and complex plants. The proposed control strategy is based on a variable structure control, it overcomes the defects of other adaptive methods such as strong dependence to the system. A GA is used to learn to optimally select integral coefficient C. Simulation results verified the effectiveness of the controller. For position control of Direct Current (DC) motor in practice, this method has good performance and strong robustness, and both dynamic and steady performances were improved.

  13. Prevalence and detection of psychosocial problems in cancer genetic counseling

    NARCIS (Netherlands)

    Eijzenga, W.; Bleiker, E.M.A.; Hahn, D.E.E.; van der Kolk, L.E.; Sidharta, G.N.; Aaronson, N.K.

    2015-01-01

    Only a minority of individuals who undergo cancer genetic counseling experience heightened levels of psychological distress, but many more experience a range of cancer genetic-specific psychosocial problems. The aim of this study was to estimate the prevalence of such psychosocial problems, and to i

  14. Microsatellite DNA typing for assessment of genetic variability in Marwari breed of Indian goat

    Directory of Open Access Journals (Sweden)

    Anoop Singh Yadav

    2015-07-01

    Full Text Available Aim: To estimate existing within-breed genetic variability in Marwari goats under field conditions and the generated data that can be used to determine genetic relationships with other breed of goats. Materials and Methods: A total of 146 blood samples of goats of Marwari breed were randomly collected from genetically unrelated animals from different villages of Bikaner Districts of Rajasthan, India. Genomic DNA was extracted from whole blood using proteinase K-digestion followed by standard phenol–chloroform extraction procedure at room temperature and confirmed through horizontal electrophoresis on 0.8% agarose gel containing ethidium bromide. Fifteen caprine microsatellite markers were used to estimate genetic variability among the goats of Marwari breed in terms of allelic and genotype frequencies, heterozygosities and polymorphism information content (PIC value. Results: A total of 74 alleles were contributed by Marwari goat across all 15 microsatellite loci. The number of alleles per locus varied from two (ILSTS-087 to 9 (ILSTS-058 alleles, with a mean of 4.93 whereas the effective number of allele varied from 1.35 (ILSTS-005 to 3.129 (ILSTS011 with a mean of 2.36. The effective number of allele is lesser than observed number at all the loci. Allelic sizes ranged from 125 bp (ILSTS-028 and ILSTS-033 to 650 bp (ILSTS-011 and ILSTS-019. The expected heterozygosity ranged from 0.240 (locus ILSTS-005 to 0.681 (locus ILSTS-011, with an average value of 0.544. The observed heterozygosity (Ho ranged from 0.1428 (locus ILSTS-087 to 0.9285 (locus ILSTS-034, with an average value of 0.5485 indicates substantial and very good number of heterozygotes, in the population. The highest PIC value (1.1886 was observed at ILSTS-044 locus and least (0.0768 at ILSTS-065 locus for Marwari goat. Conclusion: Microsatellite analysis revealed a high level of polymorphism across studied microsatellite markers and informativeness of the markers for genetic

  15. [Cercospora kikuchii isolated from Province of Santa Fe (Argentina): genetic variability and cercosporin production].

    Science.gov (United States)

    González, Ana María; Turino, Ludmila; Latorre Rapela, María Gabriela; Lurá, María Cristina

    2008-12-31

    The aims of the present study were to analyze the genetic variability of Cercospora kikuchii isolates and the in vitro cercosporin production, of these isolates obtained from soybean at the central-northern region of Santa Fe province (Argentina). Also the relationship between RAPD profiles and toxin production was also assessed. The strain C. kikuchii NBRC 6711 and 13 soybean isolates with symptoms of leaf blight were tested. Cercosporin production was analyzed by growing the fungus on Potato Dextrose Agar, extracting the toxin in alkaline medium and determining its concentration by spectrophotometry. The population of C. kikuchii studied showed variability, both genotypically, nine different groups were encountered, and have the ability to produce cercosporin. No relationship was found between toxin production and the RAPD profiles.

  16. Grizzly Bear Noninvasive Genetic Tagging Surveys: Estimating the Magnitude of Missed Detections.

    Science.gov (United States)

    Fisher, Jason T; Heim, Nicole; Code, Sandra; Paczkowski, John

    2016-01-01

    Sound wildlife conservation decisions require sound information, and scientists increasingly rely on remotely collected data over large spatial scales, such as noninvasive genetic tagging (NGT). Grizzly bears (Ursus arctos), for example, are difficult to study at population scales except with noninvasive data, and NGT via hair trapping informs management over much of grizzly bears' range. Considerable statistical effort has gone into estimating sources of heterogeneity, but detection error-arising when a visiting bear fails to leave a hair sample-has not been independently estimated. We used camera traps to survey grizzly bear occurrence at fixed hair traps and multi-method hierarchical occupancy models to estimate the probability that a visiting bear actually leaves a hair sample with viable DNA. We surveyed grizzly bears via hair trapping and camera trapping for 8 monthly surveys at 50 (2012) and 76 (2013) sites in the Rocky Mountains of Alberta, Canada. We used multi-method occupancy models to estimate site occupancy, probability of detection, and conditional occupancy at a hair trap. We tested the prediction that detection error in NGT studies could be induced by temporal variability within season, leading to underestimation of occupancy. NGT via hair trapping consistently underestimated grizzly bear occupancy at a site when compared to camera trapping. At best occupancy was underestimated by 50%; at worst, by 95%. Probability of false absence was reduced through successive surveys, but this mainly accounts for error imparted by movement among repeated surveys, not necessarily missed detections by extant bears. The implications of missed detections and biased occupancy estimates for density estimation-which form the crux of management plans-require consideration. We suggest hair-trap NGT studies should estimate and correct detection error using independent survey methods such as cameras, to ensure the reliability of the data upon which species management and

  17. Detection of Periodic Variability in Simulated QSO Light Curves

    CERN Document Server

    Westman, David B; Ivezic, Zeljko

    2010-01-01

    Periodic light curve behavior predicted for some binary black hole systems might be detected in large samples, such as the multi-million quasar sample expected from the Large Synoptic Survey Telescope (LSST). We investigate the false-alarm probability for the discovery of a periodic signal in light curves simulated using damped random walk (DRW) model. This model provides a good description of observed light curves, and does not include periodic behavior. We used the Lomb-Scargle periodogram to search for a periodic signal in a million simulated light curves that properly sample the DRW parameter space, and the LSST cadence space. We find that even a very conservative threshold for the false-alarm probability still yields thousands of "good" binary black hole candidates. We conclude that the future claims for binary black holes based on Lomb-Scargle analysis of LSST light curves will have to be interpreted with caution.

  18. Detecting the harmonics of oscillations with time-variable frequencies

    Science.gov (United States)

    Sheppard, L. W.; Stefanovska, A.; McClintock, P. V. E.

    2011-01-01

    A method is introduced for the spectral analysis of complex noisy signals containing several frequency components. It enables components that are independent to be distinguished from the harmonics of nonsinusoidal oscillatory processes of lower frequency. The method is based on mutual information and surrogate testing combined with the wavelet transform, and it is applicable to relatively short time series containing frequencies that are time variable. Where the fundamental frequency and harmonics of a process can be identified, the characteristic shape of the corresponding oscillation can be determined, enabling adaptive filtering to remove other components and nonoscillatory noise from the signal. Thus the total bandwidth of the signal can be correctly partitioned and the power associated with each component then can be quantified more accurately. The method is first demonstrated on numerical examples. It is then used to identify the higher harmonics of oscillations in human skin blood flow, both spontaneous and associated with periodic iontophoresis of a vasodilatory agent. The method should be equally relevant to all situations where signals of comparable complexity are encountered, including applications in astrophysics, engineering, and electrical circuits, as well as in other areas of physiology and biology.

  19. Phenotypic effects of genetic variability in human clock genes on circadian and sleep parameters

    Indian Academy of Sciences (India)

    Malcolm Von Schantz

    2008-12-01

    Circadian rhythms and sleep are two separate but intimately related processes. Circadian rhythms are generated through the precisely controlled, cyclic expression of a number of genes designated clock genes. Genetic variability in these genes has been associated with a number of phenotypic differences in circadian as well as sleep parameters, both in mouse models and in humans. Diurnal preferences as determined by the selfreported Horne–Östberg (HÖ) questionnaire, has been associated with polymorphisms in the human genes CLOCK, PER1, PER2 and PER3. Circadian rhythm-related sleep disorders have also been associated with mutations and polymorphisms in clock genes, with the advanced type cosegrating in an autosomal dominant inheritance pattern with mutations in the genes PER2 and CSNK1D, and the delayed type associating without discernible Mendelian inheritance with polymorphisms in CLOCK and PER3. Several mouse models of clock gene null alleles have been demonstrated to have affected sleep homeostasis. Recent findings have shown that the variable number tandem polymorphism in PER3, previously linked to diurnal preference, has profound effects on sleep homeostasis and cognitive performance following sleep loss, confirming the close association between the processes of circadian rhythms and sleep at the genetic level.

  20. Characterization of Fusarium verticillioides strains isolated from maize in Italy: fumonisin production, pathogenicity and genetic variability.

    Science.gov (United States)

    Covarelli, Lorenzo; Stifano, Simonetta; Beccari, Giovanni; Raggi, Lorenzo; Lattanzio, Veronica Maria Teresa; Albertini, Emidio

    2012-08-01

    Fusarium verticillioides (teleomorph Gibberella moniliformis) is the main fungal agent of ear and kernel rot of maize (Zea mays L.) worldwide, including Italy. F.verticillioides is a highly toxigenic species since it is able to produce the carcinogenic mycotoxins fumonisins. In this study, 25 F. verticillioides strains, isolated from maize in different regions of Italy were analyzed for their ability to produce fumonisins, their pathogenicity and their genetic variability. A further referenced strain of G. moniliformis isolated from maize in USA was also used as outgroup. The fumonisins B₁, B₂, and B₃ were analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Pathogenicity tests were carried out by symptom observation and determination of growth parameters after inoculation of maize seeds, seedlings and wounded detached leaves. Total genomic DNA was used for Amplified Fragment Length Polymorphism (AFLP) analysis. About 20% of the analyzed strains were unable to produce fumonisins in in vitro experiments on inoculated maize flour, while, among fumonisin producers, a great variability was observed, with values ranging from 1 to 115 mg kg⁻¹. The different analyzed strains showed a wide range of pathogenicity in terms of effect on seed germination, seedling development and of symptoms produced on detached leaves, which were not correlated with the different in vitro fumonisin production. AFLP analysis indicated the presence of genetic diversity not only between the Italian strains and the American reference but also among the Italian isolates. Copyright © 2012 Elsevier Ltd. All rights reserved.

  1. The link between genetic variation and variability in vaccine responses: systematic review and meta-analyses.

    Science.gov (United States)

    Posteraro, Brunella; Pastorino, Roberta; Di Giannantonio, Paolo; Ianuale, Carolina; Amore, Rosarita; Ricciardi, Walter; Boccia, Stefania

    2014-03-26

    Although immune response to vaccines can be influenced by several parameters, human genetic variations are thought to strongly influence the variability in vaccine responsiveness. Systematic reviews and meta-analyses are needed to clarify the genetic contribution to this variability, which may affect the efficacy of existing vaccines. We performed a systematic literature search to identify all studies describing the associations of allelic variants or single nucleotide polymorphisms in immune response genes with vaccine responses until July 2013. The studies fulfilling inclusion criteria were meta-analyzed. Thirteen studies (11,686 subjects) evaluated the associations of human leukocyte antigen (HLA) and other immunity gene variations with the responses to single vaccines, including MMR-II (measles and rubella virus), HepB (hepatitis virus), influenza virus, and MenC (serogroup C meningococcus) vaccines. Seven HLA genetic variants were included in the meta-analyses. The pooled ORs showed that DRB1*07 (2.46 [95% CI=1.60-3.77]; P for heterogeneity=0.117; I(2)=49.1%), DQA1*02:01 (2.21 [95% CI=1.22-4.00]; P for heterogeneity=0.995; I(2)=0.0%), DQB1*02:01 (2.03 [95% CI=1.35-3.07]; P for heterogeneity=0.449; I(2)=0.0%), and DQB1*03:03 (3.31 [95% CI=1.12-9.78]; P for heterogeneity=0.188; I(2)=42.4%) were associated with a significant decrease of antibody responses to MMR-II, HepB, and influenza vaccines. The pooled ORs showed that DRB1*13 (0.52 [95% CI=0.32-0.84]; P for heterogeneity=0.001; I(2)=85.1%) and DRB1*13:01 (0.19 [95% CI=0.06-0.58]; P for heterogeneity=0.367; I(2)=0.0%) were associated with a significant increase of antibody responses to the above vaccines. While our findings reinforce the concept that individuals with a particular HLA allelic composition are more likely to respond efficiently to vaccines, future studies should be encouraged to further elucidate the link between genetic variation and variability of the human immune response to vaccines

  2. Genetic Variability of Macrophomina phaseolina Isolates from Dry Beans in Turkey

    Directory of Open Access Journals (Sweden)

    Serkan Yeşil

    2016-04-01

    Full Text Available Charcoal rot is a soil and seed borne, economically important fungal disease on dry bean in Turkey. Twenty bean isolates of M. phaseolina collected from different locations in Turkey during 2008 and 2012 years were studied for genetic variability using random amplified polymorphic DNA (RAPD assay, chlorate sensitivity on medium supplemented with 120mM of potassium, phenotype of colony, and pathogenicity. Isolates were identified as M. phaseolina based on morhological features and PCR assays using species-specific primers (MPKF1and MPKR1. Isolates of M. phaseolina were analysed for their aggressiveness on the susceptible bean cv. Akman 98, by soil inoculation method. Isolates exhibiting a dense chlorate phenotype were chlorate-resistant, while those possessing feathery and restricted chlorate phenotypes were chlorate-sensitive. More than half of the isolates (55% were resistant to chlorate and produced dense phenotype, while 35% isolates showed feathery and two isolates (10% showed restricted growth. DNA from 20 isolates was subjected to genetic diversity analysis by the RAPD method using 14 randomly chosen 10-base random primers, and low genetic diversity (33.3% was observed among the tested isolates.

  3. Genetic variability among 18 cultivars of cooking bananas and plantains by RAPD and ISSR markers

    Directory of Open Access Journals (Sweden)

    YUYU SURYASARI POERBA

    2010-07-01

    Full Text Available Poerba YS, Ahmad F (2010 Genetic variability among 18 cultivars of cooking bananas and plantains by RAPD and ISSR markers. Biodiversitas 11: 118-123. This study was done to assess the molecular diversity of 36 accessions (18 cultivars of the plantain and cooking bananas (Musa acuminata x M. balbisiana, AAB, ABB subgroups based on Random amplified polymorphic DNA (RAPD and and Inter Simple Sequence Repeats (ISSR markers and to determine genetic relationships in the bananas. RAPD and ISSR fingerprinting of these banana varieties was carried out by five primers of RAPDs and two primers of ISSRs. RAPD primers produced 63 amplified fragments varying from 250 to 2500 bp in size. 96.82% of the amplification bands were polymorphic. ISSR primers produced 26 amplified fragments varying from 350 bp to 2000 bp in size. The results showed that 92.86% of the amplification bands were polymorphic. The range of genetic distance of 18 cultivars was from 0.06-0.67.

  4. Genetic variability in Colombian Creole cattle populations estimated by pedigree information.

    Science.gov (United States)

    Martínez, R A; García, D; Gallego, J L; Onofre, G; Pérez, J; Cañón, J

    2008-03-01

    The genetic structure of 4 Colombian Creole cattle breeds, namely, Costeño con Cuernos, Blanco Orejinegro (BON), Romosinuano (ROMO), and Sanmartinero (SM), was studied with an analysis of the available pedigree data. The comparison between the effective number of founders (f(e)) and the effective number of ancestors (f(a)) revealed a decrease in the genetic variation that was rather important for the ROMO and San Martinero breeds, which had the lowest f(a)/f(e) ratios (0.34 and 0.53, respectively). All breeds showed similar values for the number of equivalent generations traced, ranging from 3.1 in BON to 4.8 in ROMO. These 2 populations also had the lowest and the highest population sizes, respectively. The lowest average inbreeding coefficient considering the whole pedigree was obtained by BON (0.18%), whereas the highest was attained by ROMO (1.22%). Finally, the percentage of individuals with an inbreeding level greater than 6.25% in the reference population was high, indicating that the existing conservation management strategies could be improved to successfully maintain the genetic variability of these populations.

  5. Genetic variability for iron and zinc content in common bean lines and interaction with water availability.

    Science.gov (United States)

    Pereira, H S; Del Peloso, M J; Bassinello, P Z; Guimarães, C M; Melo, L C; Faria, L C

    2014-08-28

    The common bean is an important source of iron and zinc in humans. Increases in the contents of these minerals can combat mineral deficiencies, but these contents are influenced by environmental conditions. Thus, the objectives of this study were to investigate the interaction between common bean lines and water availability on iron and zinc contents (CFe and CZn, respectively), identify superior lines with stable CFe and CZn, and test for a genetic relationship between CFe and CZn. Six crop trials were performed using a randomized block design with three replications. The trials were performed during the winter sowing period for three different combinations of year and site in Brazil. For each combination, 53 lines were evaluated across two parallel trials; one trial was irrigated according to the crop requirements, and the other trial operated under a water deficit. Interaction was detected between lines and environments, and between lines and water availability for CFe and CZn. However, some lines exhibited high CFe and CZn in both conditions. Lines G 6492 and G 6490 exhibited high mean values, stability, and adaptability for both minerals. Other lines exhibited high CFe (Xamego) or CZn (Bambuí and Iapar 65). A moderate genetic correlation (0.62) between CFe and CZn was detected. Water availability during the common bean cycle had an effect on CFe and CZn; however, lines with high CFe and CZn in different conditions of water availability and environment were detected.

  6. Genetic and Pathogenic Variability of Fusarium oxysporum f. sp. cepae Isolated from Onion and Welsh Onion in Japan.

    Science.gov (United States)

    Sasaki, Kazunori; Nakahara, Katsuya; Tanaka, Shuhei; Shigyo, Masayoshi; Ito, Shin-ichi

    2015-04-01

    Fusarium oxysporum f. sp. cepae causes Fusarium basal rot in onion (common onion) and Fusarium wilt in Welsh onion. Although these diseases have been detected in various areas in Japan, knowledge about the genetic and pathogenic variability of F. oxysporum f. sp. cepae is very limited. In this study, F. oxysporum f. sp. cepae was isolated from onion and Welsh onion grown in 12 locations in Japan, and a total of 55 F. oxysporum f. sp. cepae isolates (27 from onion and 28 from Welsh onion) were characterized based on their rDNA intergenic spacer (IGS) and translation elongation factor-1α (EF-1α) nucleotide sequences, vegetative compatibility groups (VCGs), and the presence of the SIX (secreted in xylem) homologs. Phylogenetic analysis of IGS sequences showed that these isolates were grouped into eight clades (A to H), and 20 onion isolates belonging to clade H were monophyletic and assigned to the same VCG. All the IGS-clade H isolates possessed homologs of SIX3, SIX5, and SIX7. The SIX3 homolog was located on a 4 Mb-sized chromosome in the IGS-clade H isolates. Pathogenicity tests using onion seedlings showed that all the isolates with high virulence were in the IGS-clade H. These results suggest that F. oxysporum f. sp. cepae isolates belonging to the IGS-clade H are genetically and pathogenically different from those belonging to the other IGS clades.

  7. Genetic and virulence variability among Erwinia tracheiphila strains recovered from different cucurbit hosts.

    Science.gov (United States)

    Rojas, E Saalau; Dixon, P M; Batzer, J C; Gleason, M L

    2013-09-01

    The causal agent of cucurbit bacterial wilt, Erwinia tracheiphila, has a wide host range in the family Cucurbitaceae, including economically important crops such as muskmelon (Cucumis melo), cucumber (C. sativus), and squash (Cucurbita spp.). Genetic variability of 69 E. tracheiphila strains was investigated by repetitive-element polymerase chain reaction (rep-PCR) using BOXA1R and ERIC1-2 primers. Fingerprint profiles revealed significant variability associated with crop host; strains isolated from Cucumis spp. were clearly distinguishable from Cucurbita spp.-isolated strains regardless of geographic origin. Twelve E. tracheiphila strains isolated from muskmelon, cucumber, or summer squash were inoculated onto muskmelon and summer squash seedlings, followed by incubation in a growth chamber. Wilt symptoms were assessed over 3 weeks, strains were reisolated, and rep-PCR profiles were compared with the inoculated strains. Wilting occurred significantly faster when seedlings were inoculated with strains that originated from the same crop host genus (P<0.001). In the first run of the experiment, cucumber and muskmelon strains caused wilting on muskmelon seedlings at a median of 7.8 and 5.6 days after inoculation (dai), respectively. Summer squash seedlings wilted 18.0, 15.7, and 5.7 dai when inoculated with muskmelon-, cucumber-, and squash-origin strains, respectively. In a second run of the experiment, cucumber and muskmelon strains caused wilting on muskmelon at 7.0 and 6.9 dai, respectively, whereas summer squash seedlings wilted at 23.6, 29.0 and 9.0 dai when inoculated with muskmelon-, cucumber-, and squash-origin strains, respectively. Our results provide the first evidence of genetic diversity within E. tracheiphila and suggest that strain specificity is associated with plant host. This advance is a first step toward understanding the genetic and population structure of E. tracheiphila.

  8. Detecting and estimating continuous-variable entanglement by local orthogonal observables.

    Science.gov (United States)

    Zhang, Chengjie; Yu, Sixia; Chen, Qing; Oh, C H

    2013-11-01

    Entanglement detection and estimation are fundamental problems in quantum information science. Compared with discrete-variable states, for which lots of efficient entanglement detection criteria and lower bounds of entanglement measures have been proposed, the continuous-variable entanglement is much less understood. Here we shall present a family of entanglement witnesses based on continuous-variable local orthogonal observables (CVLOOs) to detect and estimate entanglement of Gaussian and non-Gaussian states, especially for bound entangled states. By choosing an optimal set of CVLOOs, our entanglement witness is equivalent to the realignment criterion and can be used to detect bound entanglement of a class of 2+2 mode Gaussian states. Via our entanglement witness, lower bounds of two typical entanglement measures for arbitrary two-mode continuous-variable states are provided.

  9. Foot-and-Mouth Disease Virus Serotype O Phylodynamics: Genetic Variability Associated with Epidemiological Factors in Pakistan

    DEFF Research Database (Denmark)

    Brito, B. P.; Perez, A. M.; Jamal, S. M.;

    2013-01-01

    One of the most challenging aspects of foot-and-mouth disease (FMD) control is the high genetic variability of the FMD virus (FMDV). In endemic settings such as the Indian subcontinent, this variability has resulted in the emergence of pandemic strains that have spread widely and caused devastati...... into Europe (Bulgaria) and Africa (Libya)....

  10. Climate variables explain neutral and adaptive variation within salmonid metapopulations: the importance of replication in landscape genetics.

    Science.gov (United States)

    Hand, Brian K; Muhlfeld, Clint C; Wade, Alisa A; Kovach, Ryan P; Whited, Diane C; Narum, Shawn R; Matala, Andrew P; Ackerman, Michael W; Garner, Brittany A; Kimball, John S; Stanford, Jack A; Luikart, Gordon

    2016-02-01

    Understanding how environmental variation influences population genetic structure is important for conservation management because it can reveal how human stressors influence population connectivity, genetic diversity and persistence. We used riverscape genetics modelling to assess whether climatic and habitat variables were related to neutral and adaptive patterns of genetic differentiation (population-specific and pairwise FST ) within five metapopulations (79 populations, 4583 individuals) of steelhead trout (Oncorhynchus mykiss) in the Columbia River Basin, USA. Using 151 putatively neutral and 29 candidate adaptive SNP loci, we found that climate-related variables (winter precipitation, summer maximum temperature, winter highest 5% flow events and summer mean flow) best explained neutral and adaptive patterns of genetic differentiation within metapopulations, suggesting that climatic variation likely influences both demography (neutral variation) and local adaptation (adaptive variation). However, we did not observe consistent relationships between climate variables and FST across all metapopulations, underscoring the need for replication when extrapolating results from one scale to another (e.g. basin-wide to the metapopulation scale). Sensitivity analysis (leave-one-population-out) revealed consistent relationships between climate variables and FST within three metapopulations; however, these patterns were not consistent in two metapopulations likely due to small sample sizes (N = 10). These results provide correlative evidence that climatic variation has shaped the genetic structure of steelhead populations and highlight the need for replication and sensitivity analyses in land and riverscape genetics.

  11. Climate variables explain neutral and adaptive variation within salmonid metapopulations: The importance of replication in landscape genetics

    Science.gov (United States)

    Hand, Brian K; Muhlfeld, Clint C.; Wade, Alisa A.; Kovach, Ryan; Whited, Diane C.; Narum, Shawn R.; Matala, Andrew P; Ackerman, Michael W.; Garner, B. A.; Kimball, John S; Stanford, Jack A.; Luikart, Gordon

    2016-01-01

    Understanding how environmental variation influences population genetic structure is important for conservation management because it can reveal how human stressors influence population connectivity, genetic diversity and persistence. We used riverscape genetics modelling to assess whether climatic and habitat variables were related to neutral and adaptive patterns of genetic differentiation (population-specific and pairwise FST) within five metapopulations (79 populations, 4583 individuals) of steelhead trout (Oncorhynchus mykiss) in the Columbia River Basin, USA. Using 151 putatively neutral and 29 candidate adaptive SNP loci, we found that climate-related variables (winter precipitation, summer maximum temperature, winter highest 5% flow events and summer mean flow) best explained neutral and adaptive patterns of genetic differentiation within metapopulations, suggesting that climatic variation likely influences both demography (neutral variation) and local adaptation (adaptive variation). However, we did not observe consistent relationships between climate variables and FST across all metapopulations, underscoring the need for replication when extrapolating results from one scale to another (e.g. basin-wide to the metapopulation scale). Sensitivity analysis (leave-one-population-out) revealed consistent relationships between climate variables and FST within three metapopulations; however, these patterns were not consistent in two metapopulations likely due to small sample sizes (N = 10). These results provide correlative evidence that climatic variation has shaped the genetic structure of steelhead populations and highlight the need for replication and sensitivity analyses in land and riverscape genetics.

  12. Chicken meat quality: genetic variability and relationship with growth and muscle characteristics

    Directory of Open Access Journals (Sweden)

    Santé-Lhoutellier Véronique

    2008-08-01

    Full Text Available Abstract Background The qualitative properties of the meat are of major importance for poultry breeding, since meat is now widely consumed as cuts or as processed products. The aim of this study was to evaluate the genetic parameters of several breast meat quality traits and their genetic relationships with muscle characteristics in a heavy commercial line of broilers. Results Significant levels of heritability (averaging 0.3 were obtained for breast meat quality traits such as pH at 15 min post-slaughter, ultimate pH (pHu, color assessed by lightness L*, redness a* and yellowness b*, drip loss, thawing-cooking loss and shear-force. The rate of decrease in pH early post-mortem and the final pH of the meat were shown to be key factors of chicken meat quality. In particular, a decrease in the final pH led to paler, more exudative and tougher breast meat. The level of glycogen stored in breast muscle estimated by the Glycolytic Potential (GP at slaughter time was shown to be highly heritable (h2 0.43. There was a very strong negative genetic correlation (rg with ultimate meat pH (rg -0.97, suggesting a common genetic control for GP and pHu. While breast muscle weight was genetically positively correlated with fiber size (rg 0.76, it was negatively correlated with the level of glycogen stored in the muscle (rg -0.58, and as a consequence it was positively correlated with the final pH of the meat (rg 0.84. Conclusion This genetic study confirmed that selection should be useful to improve meat characteristics of meat-type chickens without impairing profitability because no genetic conflict was detected between meat quality and meat quantity. Moreover, the results suggested relevant selection criteria such as ultimate pH, which is strongly related to color, water-holding capacity and texture of the meat in this heavy chicken line.

  13. Genetic variability among the wild boars (Sus scrofa scrofa, crossbred animals and pigs using microsatellite markers (STRs

    Directory of Open Access Journals (Sweden)

    Paula Viana Correa da Silva

    2011-04-01

    Full Text Available The aim of this work was to study the genetic variability among the wild boars, crossbred animals and pigs using microsatellite markers. Five genetic groups were studied. The fragments of three microsatellites developed for Sus scrofa domestica - IGF1, ACTG2 and TNFB - were amplified through PCR technique to evaluate the expected intra populacion variability (He and observed (Ho heterozygosity, and endogamy coefficient (F IS within each population and inter population variability F IS , testing relationship among five genetic groups to establish the genetic distance among them. The high level of observed heterozygosity values varied between 0.537 and 0.7871. Generally, F IS was low, suggesting that the endogamy did not exist between the tested animals.

  14. Network-based group variable selection for detecting expression quantitative trait loci (eQTL

    Directory of Open Access Journals (Sweden)

    Zhang Xuegong

    2011-06-01

    Full Text Available Abstract Background Analysis of expression quantitative trait loci (eQTL aims to identify the genetic loci associated with the expression level of genes. Penalized regression with a proper penalty is suitable for the high-dimensional biological data. Its performance should be enhanced when we incorporate biological knowledge of gene expression network and linkage disequilibrium (LD structure between loci in high-noise background. Results We propose a network-based group variable selection (NGVS method for QTL detection. Our method simultaneously maps highly correlated expression traits sharing the same biological function to marker sets formed by LD. By grouping markers, complex joint activity of multiple SNPs can be considered and the dimensionality of eQTL problem is reduced dramatically. In order to demonstrate the power and flexibility of our method, we used it to analyze two simulations and a mouse obesity and diabetes dataset. We considered the gene co-expression network, grouped markers into marker sets and treated the additive and dominant effect of each locus as a group: as a consequence, we were able to replicate results previously obtained on the mouse linkage dataset. Furthermore, we observed several possible sex-dependent loci and interactions of multiple SNPs. Conclusions The proposed NGVS method is appropriate for problems with high-dimensional data and high-noise background. On eQTL problem it outperforms the classical Lasso method, which does not consider biological knowledge. Introduction of proper gene expression and loci correlation information makes detecting causal markers more accurate. With reasonable model settings, NGVS can lead to novel biological findings.

  15. Variability in seed traits and genetic divergence in a clonal seed orchard of Dalbergia sissoo Roxb.

    Institute of Scientific and Technical Information of China (English)

    Ombir singh; Altaf Hussain Soft

    2012-01-01

    The variations in seed and pod traits,genetic superiority and genetic divergence were evaluated for a Clonal Seed Orchard (CSO) of Dalbergia sissoo Roxb.at Bithmera,India consisting of 20 clones from different agro-climatic conditions of four northern states (Uttar Pradesh,Uttarakhand,Haryana and Rajasthan).The seeds and pods of various clones in the orchard exhibited significant variability in size,weight and other characters.Significant positive correlations were observed between seed length and seed width (p<0.05),seed length and seed thickness (p<0.01),seed length and seed weight (p<0.0l),seed thickness and seed weight (p<0.01),seed length and germination value (p<0.05).The genetic parameters for seed and pod traits also showed a wide range of variations in the orchard.Heritability values were found to be over 50 vpereent for most of the seed and pod traits.Seed weight,seed length and seed thickness showed high heritability values coupled with maximum genetic gain for these characters.Ward's minimum variance dendrogram of clones of D.sissoo showed three distinct clusters; cluster 1 was the largest with 12 better clones whereas cluster 2 and 3 consisting of seven moderate clones and one poor clone,respectively.Mean cluster values showed sufficient variation among the clusters for seed weight,germination value and seed length.The possible hybridization between best clones of cluster 1 to the disease resistant clone of cluster 2 (resistant against deadly Gandoderma lucidum root rot disease of D.sissoo) is also suggested for further breeding programmes of the species.The deployment of clone 194 (better performed and disease resistant) is also recommended in future plantation programmes of D.sissoo in northern India.

  16. [Genetic variability of juniper tall (Juniperus excelsa Bieb.) in the northern and southern limits of the natural distribution].

    Science.gov (United States)

    Korshikov, I I; Nikolaeva, A V

    2013-01-01

    Genetic structure, subdivision and differentiation of six populations of juniper tall (Juniperus excelsa Bieb.) of the Crimean Mountains and of one population in Lebanon were investigated using 18 polymorphic allozyme loci as genetic markers. The high level of genetic variability of J. excelsa was established in the northern and the southern limits of its natural habitat. The mean values of the main indicators of genetic polymorphism were: P99 = 1,000, A = 3,167, H(E) = 0,370, H(o) = 0,405. Subdivision and differentiation of populations were low (F(ST) = 0,032, D(N) = 0,026) indicating similarity of their gene pools.

  17. Genetic variability among natural populations of Zaprionus indianus (Drosophilidae) in the States of São Paulo and Minas Gerais, Brazil.

    Science.gov (United States)

    Braganholi, D; Bélo, M; Bertoni, B W; Fachin, A L; Beleboni, R O; Zingaretti, S M

    2010-01-01

    Random amplified polymorphic DNA (RAPD) was used to detect polymorphisms among Zaprionus indianus fly populations collected from six municipalities in the States of São Paulo and Minas Gerais, Brazil. This species is an important, recently introduced fruit fly pest of figs and other fruit. Among 21 primers, 16 produced 73 reproducible polymorphic fragments; primer AM-9 produced the greatest number of polymorphic bands (nine), with 52% genetic variability among populations. Genetic divergence analysis of the Z. indianus populations demonstrated two major groups, named Western and Eastern groups. There was greater gene flow within than between groups. The correlation coefficient for genetic and geographic distances (Mantel test) was significant, demonstrating isolation by distance.

  18. Genetic variability and individual assignment of Chinese indigenous sheep populations (Ovis aries) using microsatellites.

    Science.gov (United States)

    Niu, L L; Li, H B; Ma, Y H; Du, L X

    2012-02-01

    The purpose of this study was to assess the genetic characteristics of six breeds of Chinese local sheep using 19 microsatellite loci and to effectively validate statistical methods for individual assignment based on informative microsatellites. All the six breeds deviated from Hardy-Weinberg equilibrium expectations, while the majority of markers complied. The polymorphism information content (PIC) of overall loci for the six populations ranged from 0.283 (SRCRSP5) to 0.852 (OarVH72). Tibetan sheep were the most diverse population with the highest mean allelic richness (6.895), while Ujmuqin (UQ) harboured the lowest allelic richness (6.000). The F-statistics for the six populations were F(IS)  = -0.172, F(IT)  = -0.082 and F(ST)  = 0.077, respectively. Furthermore, the pair-wise F(IS) revealed a moderate genetic differentiation among populations (P individual assignment will ensure a powerful detection of individual origin, with accuracy up to 91.87%, when the likelihood-based method is used. Overall, these findings shed light onto the genetic characteristics of Chinese indigenous sheep and offer a set of microsatellite loci that is simple, economic and highly informative for individual assignment of Chinese sheep.

  19. The Detection of Genetically Modified Organisms: An Overview

    Science.gov (United States)

    Ovesná, Jaroslava; Demnerová, Kateřina; Pouchová, Vladimíra

    Genetically modified organisms (GMOs) are those whose genetic material has been altered by the insertion of a new gene or by the deletion of an existing one(s). Modern biotechnology, in particular, the rise of genetic engineering, has supported the development of GMOs suitable for research purposes and practical applications (Gepts, 2002; Novoselova,Meuwissen, & Huirne, 2007; Sakakibara & Saito, 2006). For over 20 years GM bacteria and other GM organisms have been used in laboratories for the study of gene functions (Maliga & Small, 2007; Ratledge & Kristiansen, 2006). Agricultural plants were the first GMOs to be released into the environment and placed on the market. Farmers around the world use GMsoybeans, GMcorn and GM cotton that are herbicide tolerant, or insect resistant, or combine several traits that reduce the costs associated with crop production (Corinne, Fernandez-Cornejo, & Goodhue, 2004).

  20. Components of genetic variability and heritability of grain yield of silage maize

    Directory of Open Access Journals (Sweden)

    Sečanski Mile D.

    2004-01-01

    Full Text Available The aim of the present study was to evaluate the following parameters for the grain yield of silage maize: variability of inbred lines and their diallel hybrids, superior-parent heterosis and components of genetic variability and heritability on the basis of the diallel set. The two-year four-replicate trial was set up according to the randomized complete-block design at Zemun Polje. It was determined that a genotype, year and their interaction significantly affected variability of this trait. The highest. i.e. the lowest grain yield, on the average for both investigation years. was recorded in the silage maize inbred lines ZPLB402 and ZPLB405. respectively. The analysis of components of genetic variance for grain yield shows that the additive component (D was lower than the dominant (H1 and H2 genetic variance, while a positive component F and the frequency of dominant (u and recessive (v genes for this observed trait point to prevalence of dominant genes over recessive ones. Furthermore. this is confirmed by the ratio of dominant to recessive genes in parental genotypes for grain yield (Kd/Kr> 1 that is greater than unity in both years of investigation. The estimated value of the average degree of dominance (H1/D1/2 exceeds unity, pointing out to superdominance in inheritance of this trait in both years of investigation. Results of Vr/Vr regression analysis indicate superdominance in inheritance of grain yield. Moreover. a registered presence of non-allelic interaction points out to the need to study effects of epistasis, as it can have a greater significance in certain hybrids. A greater value of dominant than additive variance resulted in high values of broad-sense heritability for grain yield in both investigation years (98.71%, i.e. 97.19% in 1997, i.e. 1998, respectively. and low values of narrow-sense heritability (11.9% in 1997 and 12.2% in 1998.

  1. A Domain-Independent Window Approach to Multiclass Object Detection Using Genetic Programming

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    Mengjie Zhang

    2003-07-01

    Full Text Available This paper describes a domain-independent approach to the use of genetic programming for object detection problems in which the locations of small objects of multiple classes in large images must be found. The evolved program is scanned over the large images to locate the objects of interest. The paper develops three terminal sets based on domain-independent pixel statistics and considers two different function sets. The fitness function is based on the detection rate and the false alarm rate. We have tested the method on three object detection problems of increasing difficulty. This work not only extends genetic programming to multiclass-object detection problems, but also shows how to use a single evolved genetic program for both object classification and localisation. The object classification map developed in this approach can be used as a general classification strategy in genetic programming for multiple-class classification problems.

  2. Comparison of genetic detection efficiency of different markers ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-06-03

    Jun 3, 2009 ... in phenotypic differences (Parra et al., 2003; Brutsaert et al., 2005) ... tion of neutral genetic variation among popula-tions, and ... relationship among breeds and exploring the evolution .... was not only related with their origin, but also related with ... National High Technology Research and Development.

  3. Structural chromosomal anomalies detected by prenatal genetic diagnosis: our experience.

    Science.gov (United States)

    Farcaş, Simona; Crişan, C D; Andreescu, Nicoleta; Stoian, Monica; Motoc, A G M

    2013-01-01

    The prenatal diagnosis is currently widely spread and facilitates the acquiring of important genetic information about the fetus by a rate extremely accelerate and considered without precedent. In this paper, we like to present our experience concerning the genetic diagnosis and counseling offered for pregnancies in which a structural chromosomal aberration was found. The study group is formed by 528 prenatal samples of amniotic fluid and chorionic villi, received by our laboratory from 2006 through October 2012 for cytogenetic diagnosis. The appropriate genetic investigation was selected based on the indications for prenatal diagnosis. The cases with structural chromosomal anomalies and polymorphic variants were analyzed as regard to the maternal age, gestational age, referral indications and type of chromosomal anomaly found. A total number of 21 structural chromosomal anomalies and polymorphic variants were identified in the study group. Out of 21 structural chromosomal anomalies and polymorphic variants, six deletions and microdeletions, four situations with abnormal long "p" arm of acrocentric chromosomes, two duplications, two reciprocal translocations, two inversions, two additions, one Robertsonian translocation associating trisomy 13, one 9q heteromorphism and one complex chromosome rearrangement were noticed. To the best of our knowledge, this is the first Romanian study in which the diagnostic strategies and the management of the prenatal cases with structural rearrangements are presented. The data provided about the diagnosis strategy and the management of the prenatal cases with structural chromosomal anomalies represents a useful tool in genetic counseling of pregnancies diagnosed with rare structural chromosomal anomalies.

  4. Detected microsatellite polymorphisms in genetically altered inbred mouse strains.

    Science.gov (United States)

    Du, Xiaoyan; Cui, Jing; Wang, Chao; Huo, Xueyun; Lu, Jing; Li, Yichen; Chen, Zhenwen

    2013-08-01

    Microsatellites are 50-200 repetitive DNA sequences composed of 1- to 6-base-pair-long reiterative motifs within the genome. They are vulnerable to DNA modifications, such as recombination and/or integration, and are recognized as "sentinel" DNA. Our previous report indicated that the genotypes of the microsatellite loci could change from mono- to poly-morphisms (CMP) in gene knockout (KO) mice, implying that genetic modification induces microsatellite mutation. However, it is still unclear whether the random insertion of DNA fragments into mice genomes produced via transgene (Tg) or N-ethyl-N-nitrosourea (ENU) would also result in microsatellite mutations or microsatellite loci genotypes changes. This study was designed to find possible clues to answer this question. In brief, 198 microsatellite loci that were distributed among almost all of the chromosomes (except for the Y) were examined through polymerase chain reaction to screen possible CMPs in six Tg strains. First, for each strain, the microsatellite sequences of all loci were compared between Tg and the corresponding background strain to exclude genetic interference. Simultaneously, to exclude spontaneous mutation-related CMPs that might exist in the examined six strains, mice from five spontaneously mutated inbred strains were used as the negative controls. Additionally, the sequences of all loci in these spontaneous mutated mice were compared to corresponding genetic background controls. The results showed that 40 of the 198 (20.2%) loci were identified as having CMPs in the examined Tg mice strains. The CMP genotypes were either homozygous or heterozygous compared to the background controls. Next, we applied the 40 CMP positive loci in ENU-mutated mice and their corresponding background controls. After that, a general comparison of CMPs that exist among Tg, ENU-treated and KO mouse strains was performed. The results indicated that four (D11mit258, D13mit3, D14mit102 and DXmit172) of the 40 (10%) CMP

  5. SOUR CHERRY (Prunus cerasus L. GENETIC VARIABILITY AND PHOTOSYNTHETIC EFFICIENCY DURING DROUGHT

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    Marija Viljevac

    2012-12-01

    Full Text Available Sour cherry is an important fruit in Croatian orchards. Cultivar Oblačinska is predominant in existing orchards with noted intracultivar phenotypic heterogeneity. In this study, the genetic variability of 22 genotypes of cvs. Oblačinska, Maraska and Cigančica, as well as standard cvs. Kelleris 14, Kelleris 16, Kereška, Rexelle and Heimann conserved were investigated. Two types of molecular markers were used: microsatellite markers (SSR in order to identify intercultivar, and AFLP in order to identify intracultivar variabilities. A set of 12 SSR markers revealed small genetic distance between cvs. Maraska and Oblačinska while cv. Cigančica is affined to cv. Oblačinska. Furthermore, cvs. Oblačinska, Cigančica and Maraska were characterized compared to standard ones. AFLP markers didn`t confirm significant intracultivar variability of cv. Oblačinska although the variability has been approved at the morphological, chemical and pomological level. Significant corelation between SSR and AFLP markers was found. Identification of sour cherry cultivars tolerant to drought will enable the sustainability of fruit production with respect to the climate change in the future. For this purpose, the tolerance of seven sour cherry genotypes (cvs. Kelleris 16, Maraska, Cigančica and Oblačinska represented by 4 genotypes: OS, 18, D6 and BOR to drought conditions was tested in order to isolate genotypes with the desired properties. In the greenhouse experiment, cherry plants were exposed to drought stress. The leaf relative water content, OJIP test parameters which specify efficiency of the photosynthetic system based on measurements of chlorophyll a fluorescence, and concentrations of photo-synthetic pigments during the experiment were measured as markers of drought tolerance. Photosynthetic performance index (PIABS comprises three key events in the reaction centre of photosystem II affecting the photosynthetic activity: the absorption of energy

  6. Detecting multiple outliers in linear functional relationship model for circular variables using clustering technique

    Science.gov (United States)

    Mokhtar, Nurkhairany Amyra; Zubairi, Yong Zulina; Hussin, Abdul Ghapor

    2017-05-01

    Outlier detection has been used extensively in data analysis to detect anomalous observation in data and has important application in fraud detection and robust analysis. In this paper, we propose a method in detecting multiple outliers for circular variables in linear functional relationship model. Using the residual values of the Caires and Wyatt model, we applied the hierarchical clustering procedure. With the use of tree diagram, we illustrate the graphical approach of the detection of outlier. A simulation study is done to verify the accuracy of the proposed method. Also, an illustration to a real data set is given to show its practical applicability.

  7. Genetic variability in environmental isolates of Legionella pneumophila from Comunidad Valenciana (Spain).

    Science.gov (United States)

    Coscollá, Mireia; Gosalbes, María José; Catalán, Vicente; González-Candelas, Fernando

    2006-06-01

    Legionella pneumophila is associated to recurrent outbreaks in several Comunidad Valenciana (Spain) localities, especially in Alcoi, where social and climatic conditions seem to provide an excellent environment for bacterial growth. We have analysed the nucleotide sequences of three loci from 25 environmental isolates from Alcoi and nearby locations sampled over 3 years. The analysis of these isolates has revealed a substantial level of genetic variation, with consistent patterns of variability across loci, and comparable to that found in a large, European-wide sampling of clinical isolates. Among the tree loci studied, fliC showed the highest level of nucleotide diversity. The analysis of isolates sampled in different years revealed a clear differentiation, with samples from 2001 being significantly distinct from those obtained in 2002 and 2003. Furthermore, although linkage disequilibrium measures indicate a clonal nature for population structure in this sample, the presence of some recombination events cannot be ruled out.

  8. MORPHOLOGICAL TRAITS AS TOOL TO VERIFY GENETIC VARIABILITY OF INTERSPECIFIC DRAGON FRUIT HYBRIDS

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    ADRIANA DE CASTRO CORREIA DA SILVA

    Full Text Available ABSTRACT With recent cultivation in Brazil, the dragon fruit still have lacks related to the selection of promising materials and there are not yet commercial varieties in the country. Therefore, manual pollination cross were held in 2010, between plants of H. undatus x H. polyrhizus and H. undatus x H. setaceus. Aiming evaluate the genetic diversity of the progenies for future use in breeding program, based on cladodes characteristics, six characters were assessed: length and diameter of stem, distance between areoles, arch height, number and size of spines/areole. From the Euclidean distance matrix analysis was constructed a dendrogram by the UPGMA method. There was great variability among hybrids, and eight of them have shown promise for use in breeding program.

  9. Copy number variants and genetic traits: closer to the resolution of phenotypic to genotypic variability.

    Science.gov (United States)

    Beckmann, Jacques S; Estivill, Xavier; Antonarakis, Stylianos E

    2007-08-01

    A considerable and unanticipated plasticity of the human genome, manifested as inter-individual copy number variation, has been discovered. These structural changes constitute a major source of inter-individual genetic variation that could explain variable penetrance of inherited (Mendelian and polygenic) diseases and variation in the phenotypic expression of aneuploidies and sporadic traits, and might represent a major factor in the aetiology of complex, multifactorial traits. For these reasons, an effort should be made to discover all common and rare copy number variants (CNVs) in the human population. This will also enable systematic exploration of both SNPs and CNVs in association studies to identify the genomic contributors to the common disorders and complex traits.

  10. α-synuclein genetic variability: A biomarker for dementia in Parkinson disease.

    Science.gov (United States)

    Guella, Ilaria; Evans, Daniel M; Szu-Tu, Chelsea; Nosova, Ekaterina; Bortnick, Stephanie F; Goldman, Jennifer G; Dalrymple-Alford, John C; Geurtsen, Gert J; Litvan, Irene; Ross, Owen A; Middleton, Lefkos T; Parkkinen, Laura; Farrer, Matthew J

    2016-06-01

    The relationship between Parkinson disease (PD), PD with dementia (PDD), and dementia with Lewy bodies (DLB) has long been debated. Although PD is primarily considered a motor disorder, cognitive impairment is often present at diagnosis, and only ∼20% of patients remain cognitively intact in the long term. Alpha-synuclein (SNCA) was first implicated in the pathogenesis of the disease when point mutations and locus multiplications were identified in familial parkinsonism with dementia. In worldwide populations, SNCA genetic variability remains the most reproducible risk factor for idiopathic PD. However, few investigators have looked at SNCA variability in terms of cognitive outcomes. We have used targeted high-throughput sequencing to characterize the 135kb SNCA locus in a large multinational cohort of patients with PD, PDD, and DLB and healthy controls. An analysis of 43 tagging single nucleotide polymorphisms across the SNCA locus shows 2 distinct association profiles for symptoms of parkinsonism and/or dementia, respectively, toward the 3' or the 5' of the SNCA gene. In addition, we define a specific haplotype in intron 4 that is directly associated with PDD. The PDD risk haplotype has been interrogated at single nucleotide resolution and is uniquely tagged by an expanded TTTCn repeat. Our data show that PD, PDD, and DLB, rather than a disease continuum, have distinct genetic etiologies albeit within one genomic locus. Such results may serve as prognostic biomarkers to these disorders, to inform physicians and patients, and to assist in the design and stratification of clinical trials aimed at disease modification. Ann Neurol 2016;79:991-999. © 2016 American Neurological Association.

  11. Variability, heritability and genetic association in vegetable amaranth (Amaranthus tricolor L.)

    Energy Technology Data Exchange (ETDEWEB)

    Sarker, U.; Islam, Md T.; Rabbani, Md G.; Oba, S.

    2015-07-01

    Forty three vegetable amaranth (Amaranthus tricolor L.) genotypes selected from different eco-geographic regions of Bangladesh were evaluated during 3 years (2012-2014) for genetic variability, heritability and genetic association among mineral elements and quality and agronomic traits in randomized complete block design (RCBD) with five replications. The analysis showed that vegetable amaranth is a rich source of K, Ca, Mg, proteins and dietary fibre with average values among the 43 genotypes (1.014%, 2.476%, 2.984, 1.258% and 7.81%, respectively). Six genotypes (VA13, VA14, VA16, VA18, VA26, VA27) showed a biological yield >2000 g/m2 and high mineral, protein and dietary fibre contents; eleven genotypes had high amount of minerals, protein and dietary fibre with above average biological yield; nine genotypes had below average biological yield but were rich in minerals, protein and dietary fibre. Biological yield exhibited a strong positive correlation with leaf area, shoot weight, shoot/root weight and stem base diameter. Insignificant genotypic correlation was observed among mineral, quality and agronomic traits, except K vs. Mg, protein vs. dietary fibre and stem base diameter vs. Ca. Some of these genotypes can be used for improvement of vegetable amaranth regarding mineral, protein and dietary fibre content without compromising yield loss. (Author)

  12. Prioritizing individual genetic variants after kernel machine testing using variable selection.

    Science.gov (United States)

    He, Qianchuan; Cai, Tianxi; Liu, Yang; Zhao, Ni; Harmon, Quaker E; Almli, Lynn M; Binder, Elisabeth B; Engel, Stephanie M; Ressler, Kerry J; Conneely, Karen N; Lin, Xihong; Wu, Michael C

    2016-12-01

    Kernel machine learning methods, such as the SNP-set kernel association test (SKAT), have been widely used to test associations between traits and genetic polymorphisms. In contrast to traditional single-SNP analysis methods, these methods are designed to examine the joint effect of a set of related SNPs (such as a group of SNPs within a gene or a pathway) and are able to identify sets of SNPs that are associated with the trait of interest. However, as with many multi-SNP testing approaches, kernel machine testing can draw conclusion only at the SNP-set level, and does not directly inform on which one(s) of the identified SNP set is actually driving the associations. A recently proposed procedure, KerNel Iterative Feature Extraction (KNIFE), provides a general framework for incorporating variable selection into kernel machine methods. In this article, we focus on quantitative traits and relatively common SNPs, and adapt the KNIFE procedure to genetic association studies and propose an approach to identify driver SNPs after the application of SKAT to gene set analysis. Our approach accommodates several kernels that are widely used in SNP analysis, such as the linear kernel and the Identity by State (IBS) kernel. The proposed approach provides practically useful utilities to prioritize SNPs, and fills the gap between SNP set analysis and biological functional studies. Both simulation studies and real data application are used to demonstrate the proposed approach.

  13. Basil (Ocimum basilicum Genetic Variability and Viral Disease Assessment in Nigeria

    Directory of Open Access Journals (Sweden)

    O.D. Ojo

    2012-01-01

    Full Text Available The study aims at assessing Basil’s genetic phenotypic variability and viral disease incidence in Nigeria for sustainable pathological interventions. Basil (Ocimum basilicum is important for it’s medicinal and nutritive value. It is highly adaptable as a potential crop in the tropics and could therefore enhance the food security of sub Saharan Africa nations. Germplasm seed evaluation and characterization was therefore carried out from the nationwide National Horticultural Research Institute (NIHORT seed collection survey to expand NIHORT basil genetic base. The field layout was completely randomized design with five replications. The treatments were: O. basilicum, O. gratissimum and the local basil. Treatments were randomly allocated per replication. There were significant phenotypic differences in the O. basilicum variety. These differences were observed in the plant coloration ranging from deep to light purple coloration of stem, leaf, leaf vein and petiole. Our observations also revealed for the first time significant tolerance to Venial Mottle Mosaic Virus (VMMV in the purple colored compared to the green O. basilicum in the early stages of growth till 50% anthesis. This is the first report of this observation in the African continent. Tolerance to VMMV symptoms increased significantly (LSD 5% with purplish coloration. We concluded that inducement of purplish coloration in Basil through breeding might improve tolerance to VMMV and thereby increase market value of Basil with sustainable pathological interventions.

  14. Variability, heritability and genetic association in vegetable amaranth (Amaranthus tricolorL.

    Directory of Open Access Journals (Sweden)

    Umakanta Sarker

    2015-06-01

    Full Text Available Forty three vegetable amaranth (Amaranthus tricolor L. genotypes selected from different eco-geographic regions of Bangladesh were evaluated during 3 years (2012-2014 for genetic variability, heritability and genetic association among mineral elements and quality and agronomic traits in randomized complete block design (RCBD with five replications. The analysis showed that vegetable amaranth is a rich source of K, Ca, Mg, proteins and dietary fibre with average values among the 43 genotypes (1.014%, 2.476%, 2.984, 1.258% and 7.81%, respectively. Six genotypes (VA13, VA14, VA16, VA18, VA26, VA27 showed a biological yield >2000 g/m2 and high mineral, protein and dietary fibre contents; eleven genotypes had high amount of minerals, protein and dietary fibre with above average biological yield; nine genotypes had below average biological yield but were rich in minerals, protein and dietary fibre. Biological yield exhibited a strong positive correlation with leaf area, shoot weight, shoot/root weight and stem base diameter. Insignificant genotypic correlation was observed among mineral, quality and agronomic traits, except K vs. Mg, protein vs. dietary fibre and stem base diameter vs. Ca. Some of these genotypes can be used for improvement of vegetable amaranth regarding mineral, protein and dietary fibre content without compromising yield loss.

  15. A colony of dog guides: analysis of the genetic variability assessed by pedigree data

    Directory of Open Access Journals (Sweden)

    Roberta Ciampolini

    2010-01-01

    Full Text Available The study presents the analysis of the genetic variability in a colony of dog guides. Three breeds, Labrador (L, Golden Retriever (GR, and German Shepherd (GS, were evaluated. Pedigrees data on 370 L, 260 GR, and 85 GS dogs bred for guide by the National Guide Dog School (SNCG of Scandicci (Florence, Italy were used. Data were available beginning from 1994. The average coefficient of coancestry and the mean F were 0.8% and 0.45% in GR, 0.7% and 0.38% in L, 1.0% and 0.49% in GS, respectively. The rate of increase in inbreeding was lower in L population (0.17 than in GR population (0.54, while in GS only the dogs with 5 e 7 traced generations resulted inbred. The results of this research point out that the genetic management of the dogs seems to be carefully and rationally monitored. Nevertheless, the population that may require a greater attention seems to be the GR, where a higher increase of the coefficient of inbreeding per generation is observed; therefore, the importation of germplasm from other working dogs is desirable in order to avoid in future an excessive increase of the inbreeding that could lead to adverse consequences for dogs health and fertility.

  16. Variability of yield traits and disease resistance in winter triticale genetic resources accessions

    Directory of Open Access Journals (Sweden)

    Wanda Kociuba

    2014-07-01

    Full Text Available A systematic gathering of winter triticale accessions was started in Poland in 1982 by the Institute of Genetics, Breeding and Seed Science at the Agricultural University in Lublin (at present its name is: Institute of Genetics, Breeding and Plant Biotechnology at the University of Life Sciences in Lublin. First, breeding lines obtained in local breeding stations were gathered. Next, accessions were imported from the following world gene banks: Beltsville, Gatersleben, and VIR. Interesting hybrid materials obtained in research centers were also included in the collection. Now, the collection includes 2349 accessions (1329 of winter triticale and 1020 of spring triticale. The evaluation is conducted in a 4-year cycle of field experiments using the same methods. The gathered accessions represent a large range of variability of both morphological and commercial traits. The large differentiation of accessions especially concerns traits such as: plant height, number and weight of grains per spi- ke, protein content in grain, field resistance to powdery mildew, brown rust and leaf and spike diseases.

  17. GENETIC VARIABILITY OF CULTURED PLANT TISSUES UNDER NORMAL CONDITIONS AND UNDER STRESS

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    Dolgikh Yu.I.

    2012-08-01

    Full Text Available The genetic variability induced by in vitro conditions known as somaclonal variation is of practical interest due to its potential uses in plant breeding but, on the other hand, if clonal propagation or transformation is main goal, it becomes an unwelcome phenomenon. Thus, it is important to know frequency, the genomic distribution, the mechanisms and factors influencing somaclonal variation. We studied variability of PCR-based DNA markers of cultured tissues and regenerated plants of maize and bread wheat. The original A188 line of maize and the somaclones obtained were tested using 38 RAPD and 10 ISSR primers. None of the A188 plants showed variation in the RAPD and ISSR spectra for any of the primers used. However, the PCR spectra obtained from the somaclones demonstrated some variations, i.e., 22 RAPD primers and 6 ISSR primers differentiated at least one somaclonal variant from the progenitor line. Six SCAR markers were developed based on several RAPD and ISSR fragments. The inheritance of these SCAR markers was verified in the selfing progeny of each somaclone in the R1–R4 generations and in the hybrids, with A188 as the parental line in the F1 and F2 generations. These markers were sequenced and bioinformatic searches were performed to understand the molecular events that may underlie the variability observed in the somaclones. All changes were found in noncoding sequences and were induced by different molecular events, such as the insertion of long terminal repeat transposon, precise miniature inverted repeat transposable element (MITE excision, microdeletion, recombination, and a change in the pool of mitochondrial DNA. In two groups of independently produced somaclones, the same features (morphological, molecular were variable, which confirms the theory of ‘hot spots’ occurring in the genome. The presence of the same molecular markers in the somaclones and in different non-somaclonal maize variants suggests that in some cases

  18. Pedigree analysis of the Turkish Arab horse population: structure, inbreeding and genetic variability.

    Science.gov (United States)

    Duru, S

    2017-09-01

    The aim of this study was to evaluate genetic variability in the Turkish Arab horse population using pedigree information. This study is the first detailed pedigree analysis of the breed in Turkey. Pedigree data were collected from the National Studbook. The pedigree data for 23 668 horses, born between 1904 and 2014, were used in the analysis. From this data set, a reference population (RP) of 14 838 animals symbolising the last generation was defined. Demographic parameters, the inbreeding level (F), the average relatedness (AR), the effective population size (N e), the effective number of founders (f e), the effective number of ancestors (f a) and the number of founder genome equivalents (f g) were calculated for the population. The average generation interval for the RP was 12.2±4.6 years, whereas the calculated pedigree completeness levels were 98.2%, 96.6% and 95.0% for the first, second and third known generations. The mean equivalent generations (t), the average complete generations and the mean maximum generations for the RP were 7.8, 5.4 and 12.2, respectively, whereas the mean F and AR were 4.6% and 9.5% for the RP. The rate of inbred animals was 94.2% for the RP, whereas the number of founders, the number of ancestors and the f e, f a and f g were 342, 223, 40, 22 and 9.6 for the RP. The large differences observed between f e, and the number of founders demonstrates that genetic diversity decreased between the founder and the RP. Contribution of the 14 most influential founder to the RP was 50.0%, whereas just eight ancestral horses can account for 50% of the genetic variability. N e estimated via an individual increase in inbreeding per generation ( $$ \\hskip3pt{\\bar{\\hskip-2ptN}_{{\\rm e}} } $$ ), and paired increase in coancestry $$\\left(\\! \\hskip3pt{\\bar{\\hskip-2ptN}_{{ eC}} } \\right)$$ , were 74.4±3.9 and 73.5±0.58, respectively. The inbreeding increases with the pedigree knowledge. In addition, the decrease in inbreeding in last years

  19. Genetic variability in three Italian beef cattle breeds derived from pedigree information

    Directory of Open Access Journals (Sweden)

    Francesco Filippini

    2010-01-01

    Full Text Available The aim of the present work was to estimate genetic variability in Chianina (CH, Marchigiana (MC and Romagnola (RO breeds using pedigree information. Different approaches based on probability of identity-by-descent (effective population size through an increase in inbreeding Ne or probability of gene origin (total number of founders f, effective number of founders fe, ancestors fa and founder genomes fg were used. Reference populations were defined using female animals born between 1996 and 2000 where both parents are known. Generation intervals were 5.35, 4.93 and 5.15 years for CH, MC and RO, respectively. The total number of founders were 7092, 11947, 3928, for CH, MC and RO, respectively. Complete generation equivalent showed the relative high quality of pedigree information: 5.66 for CH, 4.54 for MC and 4.95 for RO. For CH, MC and RO, respectively, a fe value of 152.1, 70.9 and 89.8, a fa value of 73.6, 48.0 and 59.5 and a fg value of 39.5, 25.0 and 38.5, were calculated. When inbreeding was used effective population sizes were 138, 122 and 124 for CH, MC and RO, respectively. Parameters derived from the probabilities of gene origin were variable among the investigated breeds and the results for MC demonstrate the need to pay specific attention to breeding strategies.

  20. Genetic variability of Brazilian populations of Lymnaea columella (Gastropoda: Lymnaeidae), an intermediate host of Fasciola hepatica (Trematoda: Digenea).

    Science.gov (United States)

    Cardoso, Paula Cristina Marques; Caldeira, Roberta Lima; Lovato, Maria Bernadete; Coelho, Paulo Marcos Zech; Berne, Maria Elisabeth Aires; Müller, Gertrud; Carvalho, Omar dos Santos

    2006-03-01

    In Brazil, Lymnaea columella is the most important intermediate host of Fasciola hepatica, the etiological agent of fasciolosis, which is a parasitic disease of veterinarian and human importance. Random amplified polymorphic DNA (RAPD) was used to investigate the genetic variability within and among nine Brazilian populations of L. columella comprising 205 individuals. A number of four primers were used for analysis of molecular variance (AMOVA). Out of 83 RAPD markers, 63 (76%) were polymorphic and revealed 119 unique RAPD profiles. The levels of genetic variability found in the populations were low and most of the genetic variation was interpopulational (81.6%) when compared to intrapopulational variability (18.4%). These results are in accordance with the dynamics and distribution of the populations analyzed.

  1. Breast cancer genetic risk profile is differentially associated with interval and screen-detected breast cancers.

    Science.gov (United States)

    Li, J; Holm, J; Bergh, J; Eriksson, M; Darabi, H; Lindström, L S; Törnberg, S; Hall, P; Czene, K

    2015-03-01

    Polygenic risk profiles computed from multiple common susceptibility alleles for breast cancer have been shown to identify women at different levels of breast cancer risk. We evaluated whether this genetic risk stratification can also be applied to discriminate between screen-detected and interval cancers, which are usually associated with clinicopathological and survival differences. A 77 single-nucleotide polymorphism polygenic risk score (PRS) was constructed for breast cancer overall and by estrogen receptor (ER) status. PRS was inspected as a continuous (per standard deviation increment) variable in a case-only design. Modification of the PRS by mammographic density was evaluated by fitting an additional interaction term. PRS weighted by breast cancer overall estimates was found to be differentially associated with 1865 screen-detected and 782 interval cancers in the LIBRO-1 study {age-adjusted odds ratio (OR)perSD [95% confidence interval (CI)] 0.91 [0.83-0.99], P = 0.023}. The association was found to be more significant for PRS weighted by ER-positive breast cancer estimates [ORperSD = 0.90 (0.82-0.98), P = 0.011]. This result was corroborated by two independent studies [combined ORperSD = 0.87 (0.76-1.00), P = 0.058] with no evidence of heterogeneity. When enriched for 'true' interval cancers among nondense breasts, the difference in the association with PRS in screen-detected and interval cancers became more pronounced [ORperSD = 0.74 (0.62-0.89), P = 0.001], with a significant interaction effect between PRS and mammographic density (Pinteraction = 0.017). To our knowledge, this is the first report looking into the genetic differences between screen-detected and interval cancers. It is an affirmation that the two types of breast cancer may have unique underlying biology. © The Author 2014. Published by Oxford University Press on behalf of the European Society for Medical Oncology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  2. Genetic variability of Passiflora spp. from commercial fields in the Federal District, Brazil Variabilidade genética de Passiflora spp. em plantios comerciais do Distrito Federal, Brasil

    Directory of Open Access Journals (Sweden)

    Ana Paula Gomes de Castro

    2011-06-01

    Full Text Available This study aimed to characterize the genetic variability in commercial accessions of passion fruit from the Federal District, Brazil, by RAPD markers. Genetic analyses were done with leaf samples of 30 accessions. DNA samples were amplified by RAPD technique, and respective markers converted into a binary matrix, from which the genetic distances between the accessions were estimated. Clustering analyis based on genetic distances allowed to detect a wide range of genetic variabillity among the accessions of sour passion fruit, and to separate them from the two sweet passion fruit. The graphical positioning of 'BRS Ouro Vermelho' confirms its potential to improve the genetic variability of commercial varieties of sour passion fruit. Dispersal of genetic distances among commercial accessions of sour passion fruit supports evidence for different genetic origins of the materials planted in the Federal District. The verified genetic variability indicates the potential success of future breeding programs for this region.Este estudo teve como objetivo caracterizar a variabilidade genética de acessos de maracujá comerciais no Distrito Federal por meio de marcadores RAPD. Análises genéticas foram feitas com amostras foliares de 30 acessos. As amostras de DNA foram amplificadas pela técnica de RAPD e os respectivos marcadores convertidos em uma matriz binária, a partir da qual as distâncias genéticas entre os acessos foram estimadas. Análises de agrupamento baseadas em distâncias genéticas permitiram detectar uma ampla gama de variabilidade genética entre os acessos de maracujazeiro-azedo, bem como para separá-los dos dois de maracujazeiro-doce. O posicionamento gráfico de 'BRS Ouro Vermelho' confirma a sua importante contribuição para aumentar a variabilidade genética das atuais variedades comerciais de maracujazeiro-azedo. A dispersão das distâncias genéticas entre os acessos comerciais de maracujazeiro-azedo suportam as evid

  3. Genetic characterization of Toxoplasma gondii isolates from Portugal, Austria, and Israel reveals higher genetic variability within the type II lineage

    Science.gov (United States)

    This study compared genetic diversity of Toxoplasma gondii isolates from Portugal, Austria and Israel. For this, we genotyped 90 T. gondii isolates (16 from Portugal, 67 from Austria and 7 from Israel) using 10 nested PCR-restriction length polymorphism (RFLP) genetic markers and 15 microsatellite (...

  4. Induced genetic variability and correlation studies for yield and its component traits in Groundnut (Arachis hypogaea L.

    Directory of Open Access Journals (Sweden)

    Channayya P. Hiremath , H. L. Nadaf and Keerthi,C.M

    2011-03-01

    Full Text Available Groundnut is one of the principal economic oilseed crops of the world, which has been exposed extensively to mutagenictreatments for induction of genetic variability. In the present experiment, estimates of genetic variability, heritability and geneticadvance were assessed for 12 different quantitative traits in the mutants derived from two Spanish Bunch groundnut cultivars, viz.TPG-41 and GPBD-4 with chemical and physical mutagenic agents. Wide genetic variations were observed for most of thequantitative traits studied as evidenced by higher mean, range, PCV and GCV values. Further genetic improvement throughselection for yield improvement should rely on number of primary branches per plant, 100-kernel weight, SMK% and shellingper cent as these mutants recorded higher genetic variability, heritability and genetic advance for these quantitative traits. Podyield was positively and significantly associated with number of primary branches, pod weight per plant, 100-kernel weight,sound matured per cent kernel and oil yield. These results clearly indicate that idirect selection for yield in groundnut is possiblethrough simultaneous improvement of these yield components

  5. The assessment of genetic variability and taxonomic affi nity of local pummelo accessions from Yogyakarta, Indonesia based on RAPD

    Directory of Open Access Journals (Sweden)

    Ratna Susandarini

    2016-02-01

    Full Text Available Pummelo (Citrus maxima is one of three biotypes considered as true species within the genus Citrus.A major issue of pummelo taxonomy in Indonesia is the high number of cultivars showing variability inphenotypic characters but of unknown genetic diversity. In this study, the assessment of genetic variabilityand taxonomic affi nity of local accessions of C. maxima from Yogyakarta was examined based on RAPDfi ngerprinting. The availability of universal primers and technical simplicity makes RAPD as a molecular toolof choice for the assessment of genetic variability at various taxonomic levels. In this study, 13 accessions of C.maxima collected from Yogyakarta were observed for their genetic variability. An additional three registeredcultivars were included for comparative purpose. Two decamer primers used for the amplifi cation of DNAproduced 222 bands with 174 of them were polymorphic. The data was subjected to cluster analysis to observethe grouping of accessions and taxonomic affi nity. Results indicated high genetic variability among accessions.The dendrogram constructed using UPGMA method based on simple matching coeffi cient showed twomain clusters were which was in line to morphological characters. The grouping of accessions showed cleardifferentiation between accessions bearing white and those with reddish fruit fl esh, and thus demonstratestaxonomic value of this study in recognizing important agronomic character for this tropical fruit crop.

  6. Genetic structure and molecular variability of Cucumber mosaic virus isolates in the United States.

    Directory of Open Access Journals (Sweden)

    Shahideh Nouri

    Full Text Available Cucumber mosaic virus (CMV has a worldwide distribution and the widest host range of any known plant virus. From 2000 to 2012, epidemics of CMV severely affected the production of snap bean (Phaseulos vulgaris L. in the Midwest and Northeastern United States. Virus diversity leading to emergence of new strains is often considered a significant factor in virus epidemics. In addition to epidemics, new disease phenotypes arising from genetic exchanges or mutation can compromise effectiveness of plant disease management strategies. Here, we captured a snapshot of genetic variation of 32 CMV isolates collected from different regions of the U.S including new field as well as historic isolates. Nucleotide diversity (π was low for U.S. CMV isolates. Sequence and phylogenetic analyses revealed that CMV subgroup I is predominant in the US and further showed that the CMV population is a mixture of subgroups IA and IB. Furthermore, phylogenetic analysis suggests likely reassortment between subgroups IA and IB within five CMV isolates. Based on phylogenetic and computational analysis, recombination between subgroups I and II as well as IA and IB in RNA 3 was detected. This is the first report of recombination between CMV subgroups I and II. Neutrality tests illustrated that negative selection was the major force operating upon the CMV genome, although some positively selected sites were detected for all encoded proteins. Together, these data suggest that different regions of the CMV genome are under different evolutionary constraints. These results also delineate composition of the CMV population in the US, and further suggest that recombination and reassortment among strain subgroups does occur but at a low frequency, and point towards CMV genomic regions that differ in types of selection pressure.

  7. ADM-CLE approach for detecting slow variables in continuous time Markov chains and dynamic data

    CERN Document Server

    Cucuringu, Mihai

    2015-01-01

    A method for detecting intrinsic slow variables in high-dimensional stochastic chemical reaction networks is developed and analyzed. It combines anisotropic diffusion maps (ADM) with approximations based on the chemical Langevin equation (CLE). The resulting approach, called ADM-CLE, has the potential of being more efficient than the ADM method for a large class of chemical reaction systems, because it replaces the computationally most expensive step of ADM (running local short bursts of simulations) by using an approximation based on the CLE. The ADM-CLE approach can be used to estimate the stationary distribution of the detected slow variable, without any a-priori knowledge of it. If the conditional distribution of the fast variables can be obtained analytically, then the resulting ADM-CLE approach does not make any use of Monte Carlo simulations to estimate the distributions of both slow and fast variables.

  8. Detection of Low-Amplitude Photometric Variability of Magnetic White Dwarfs

    Science.gov (United States)

    Valeev, A. F.; Antonyuk, K. A.; Pit, N. V.; Moskvitin, A. S.; Grauzhanina, A. O.; Gadelshin, D. R.; Kolesnikov, S. V.; Burlakova, T. E.; Galazutdinov, G. A.; Gutaev, A. G.; Zhuchkov, R. Ya.; Ikhsanova, A. I.; Joshi, A.; Pandey, J. C.; Zhuzhulina, E. A.; Valyavin, G. G.

    2017-06-01

    We present the results of the ongoing photometric survey of magnetic white dwarfs. Variability of fluxes from WD 0009+501, GD 229, GRW+70°8247, and GD 56 has been detected. The detected variability of GD 356 is specially discussed. In case of GRW+70°8247 the V-band photometric variability amplitude is about 0fm04, the most probable period is from days to several tens of days. The degenerate GD 229 demonstrates the amplitude of the flux variation of about 0fm05 with a period between 10 and 20 days. In both cases the variability is most likely associated with rotation of these stars. These findings contradict with an idea on the existence of a special class of strong-magnetic very slowly rotating white dwarfs, the periods of which are estimated to have tens or even hundreds of years.

  9. Mt. Suhora M dwarf survey - Detection of eight short-period variable stars

    CERN Document Server

    Machado, L Fox; Winiarski, M; Krzesiński, J; Dróżdz, M

    2011-01-01

    The Mt. Suhora M\\,dwarf survey searching for pulsations in low mass main sequence stars has acquired CCD photometry of 46 M\\,dwarf stars during the first year of the project (Baran et al 2011). As a by-product of this search hundreds field stars have been checked for variability. This paper presents our initial result of a search for periodic variables in field stars observed in the course of the survey. On the basis of the periodicity and the shape of the light curves, eight new variables has been detected, among which five are $\\delta$ Scuti stars and three likely RR Lyrae stars. Although variation in one of the stars has been previously detected, it was classified incorrectly. To support our classification, in August 2010, we performed spectroscopic observations to derive spectral types and luminosity classes for all eight variable stars.

  10. Genetic algorithm for flood detection and evacuation route planning

    Science.gov (United States)

    Gomes, Rahul; Straub, Jeremy

    2017-05-01

    A genetic-type algorithm is presented that uses satellite geospatial data to determine the most probable path to safety for individuals in a disaster area, where a traditional routing system cannot be used. The algorithm uses geological features and disaster information to determine the shortest safe path. It predicts how a flood can change a landform over time and uses this data to predict alternate routes. It also predicts safe routes in rural locations where GPS/map-based routing data is unavailable or inaccurate. Reflectance and a supervised classification algorithm are used and the output is compared with RFPI and PCR-GLOBWB data.

  11. Genetic basis and detection of unintended effects in genetically modified crop plants

    NARCIS (Netherlands)

    Ladics, G.S.; Bartholomaeus, A.; Bregitzer, P.; Doerrer, N.G.; Gray, A.; Holzhauzer, T.; Jordan, M.; Keese, P.; Kok, E.J.; Macdonald, P.; Parrott, W.; Privalle, L.; Raybould, A.; Rhee, S.Y.; Rice, E.; Romeis, J.; Vaughn, J.; Wal, J.M.; Glenn, K.

    2015-01-01

    In January 2014, an international meeting sponsored by the International Life Sciences Institute/Health and Environmental Sciences Institute and the Canadian Food Inspection Agency titled “Genetic Basis of Unintended Effects in Modified Plants” was held in Ottawa, Canada, bringing together over 75 s

  12. Geographic patterns of (genetic, morphologic, linguistic) variation: how barriers can be detected by using Monmonier's algorithm.

    Science.gov (United States)

    Manni, Franz; Guérard, Etienne; Heyer, Evelyne

    2004-04-01

    When sampling locations are known, the association between genetic and geographic distances can be tested by spatial autocorrelation or regression methods. These tests give some clues to the possible shape of the genetic landscape. Nevertheless, correlation analyses fail when attempting to identify where genetic barriers exist, namely, the areas where a given variable shows an abrupt rate of change. To this end, a computational geometry approach is more suitable because it provides the locations and the directions of barriers and because it can show where geographic patterns of two or more variables are similar. In this frame we have implemented Monmonier's (1973) maximum difference algorithm in a new software package to identify genetic barriers. To provide a more realistic representation of the barriers in a genetic landscape, we implemented in the software a significance test by means of bootstrap matrices analysis. As a result, the noise associated with genetic markers can be visualized on a geographic map and the areas where genetic barriers are more robust can be identified. Moreover, this multiple matrices approach can visualize the patterns of variation associated with different markers in the same overall picture. This improved Monmonier's method is highly reliable and can be applied to nongenetic data whenever sampling locations and a distance matrix between corresponding data are available.

  13. Behavior Genetics and the Within-Person Variability of Daily Interpersonal Styles: The Heritability of Flux, Spin and Pulse

    OpenAIRE

    Markey, Patrick M.; Racine, Sarah E.; Markey, Charlotte N; Hopwood, Christopher J.; Keel, Pamela K.; Burt, S. Alexandra; Neale, Michael C.; Sisk, Cheryl L.; Boker, Steven M.; Kelly L. Klump

    2014-01-01

    A classical twin study was used to estimate the magnitude of genetic and environmental influences on four measurements of within-person variability: dominance flux, warmth flux, spin and pulse. Flux refers to the variability of an individual’s interpersonal dominance and warmth. Spin measures changes in the tone of interpersonal styles and pulse measures changes in the intensity of interpersonal styles. Daily reports of interpersonal styles were collected from 494 same-sex female twins (142 m...

  14. Variabilidade genética em biotipos de leiteiro de Londrina/PR Genetic variability among Euphorbia heterophylla

    Directory of Open Access Journals (Sweden)

    Maria José V. de Vasconcelos

    2000-08-01

    Full Text Available Euphorbia heterophylla, também conhecida como amendoim-bravo ou leiteira, é considerada planta invasora importante em mais de 56 países, inclusive no Brasil, tendo acarretado perdas de até 33 % na cultura da soja. Fenotipicamente, é uma espécie de características variáveis, especialmente em relação ao formato do limbo foliar. Esta variabilidade fenotípica tem sido utilizada para diferenciar e classificar as plantas, sugerindo a vários autores que a leiteira seria, de fato, constituída por diferentes espécies. Para estudar a variabilidade genética a nível de DNA entre plantas de Euphorbia heterophylla, que apresentam folhas morfologicamente diferentes, foram analisadas dez plantas diferentes coletadas em campos de soja, em Londrina/PR. As plantas foram transplantadas para casa-devegetação e o DNA das folhas foi extraído para análise pela técnica de RAPD. Vinte seis diferentes "primers", de dez nucleotídeos de sequência aleatória, geraram total de 102 bandas de DNA, sendo 38 delas polimórficas. A distância genética entre os indivíduos foi calculada em função da presença e da ausência das bandas, variando de 1 a 39% entre plantas. A análise de agrupamento dividiu as plantas em dois grupos, considerando limite de distância relativa de 22%. Os grupos gerados separaram nitidamente as plantas quanto ao formato do limbo foliar (estreito ou arredondado e quanto á ramificação (densa ou normal.Euphorbia heterophylla is an important weed affecting the performance of annual and perennial crops. It is native from tropical and subtropical regions in the American continent, and has been detected at high densities in 20 different countries worldwide, and at low densities in other 40 countries. In Brazil, it has been inclued among the ten most important weeds affecting different crops, causing yield losses up to 33% in soybean fields. Phenotypically, this species is extremely variable, especially in relation to leaf shape and

  15. Detection and traceability of genetically modified organisms in the food production chain.

    Science.gov (United States)

    Miraglia, M; Berdal, K G; Brera, C; Corbisier, P; Holst-Jensen, A; Kok, E J; Marvin, H J P; Schimmel, H; Rentsch, J; van Rie, J P P F; Zagon, J

    2004-07-01

    Both labelling and traceability of genetically modified organisms are current issues that are considered in trade and regulation. Currently, labelling of genetically modified foods containing detectable transgenic material is required by EU legislation. A proposed package of legislation would extend this labelling to foods without any traces of transgenics. These new legislations would also impose labelling and a traceability system based on documentation throughout the food and feed manufacture system. The regulatory issues of risk analysis and labelling are currently harmonised by Codex Alimentarius. The implementation and maintenance of the regulations necessitates sampling protocols and analytical methodologies that allow for accurate determination of the content of genetically modified organisms within a food and feed sample. Current methodologies for the analysis of genetically modified organisms are focused on either one of two targets, the transgenic DNA inserted- or the novel protein(s) expressed- in a genetically modified product. For most DNA-based detection methods, the polymerase chain reaction is employed. Items that need consideration in the use of DNA-based detection methods include the specificity, sensitivity, matrix effects, internal reference DNA, availability of external reference materials, hemizygosity versus homozygosity, extrachromosomal DNA, and international harmonisation. For most protein-based methods, enzyme-linked immunosorbent assays with antibodies binding the novel protein are employed. Consideration should be given to the selection of the antigen bound by the antibody, accuracy, validation, and matrix effects. Currently, validation of detection methods for analysis of genetically modified organisms is taking place. In addition, new methodologies are developed, including the use of microarrays, mass spectrometry, and surface plasmon resonance. Challenges for GMO detection include the detection of transgenic material in materials

  16. An Enhancement of the Replacement Steady State Genetic Algorithm for Intrusion Detection

    Directory of Open Access Journals (Sweden)

    Reyadh Naoum

    2014-06-01

    Full Text Available In these days, Internet and computer systems face many intrusions, thus for this purpose we need to build a detection or prevention security system. Intrusion Detection System (IDS is a system used to detect attacks, Steady State Genetic Algorithm (SSGA is applied to support IDS by supplying the rule pool with additional data, these data can be used in testing phase to detect the attacks. The main goal of this research is to enhance Replacement steady state genetic algorithm to detect intrusions. This enhancement has been achieved by comparing replacement methods. This research proved that the Triple Tournament Replacement is better than Binary Tournament Replacement to increase Detection Rate and there are no effects on False Positive Rate. In this research represent the results of DR equal 100% for three types of attack (DoS, Probe and R2T, and 53% for U2R.

  17. Data from: Genetic variation in variability: phenotypic variability of fledging weight and its evolution in a songbird population

    NARCIS (Netherlands)

    Mulder, H.A.; Gienapp, P.; Visser, M.E.

    2016-01-01

    Variation in traits is essential for natural selection to operate and genetic and environmental effects can contribute to this phenotypic variation. From domesticated populations, we know that families can differ in their level of within-family variance, which leads to the intriguing situation that

  18. Prenetal Detection of Oral Clefts : Diagnostic, Genetic and Ethical Aspects

    NARCIS (Netherlands)

    Maarse, W.

    2015-01-01

    Since the introduction of routine prenatal screening with ultrasound in the Netherlands in 2007, parents are confronted with the diagnosis of oral cleft (OC) already during pregnancy. This imposed a new dimension in cleft care in the Netherlands. As a consequence to increasing prenatal detection rat

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

    Science.gov (United States)

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

    2014-07-03

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

  20. Genetic rearrangements of variable di-residue (RVD)-containing repeat arrays in a baculoviral TALEN system.

    Science.gov (United States)

    Lau, Cia-Hin; Zhu, Haibao; Tay, Johan Chin-Kang; Li, Zhendong; Tay, Felix Chang; Chen, Can; Tan, Wee-Kiat; Du, Shouhui; Sia, Vic-Ki; Phang, Rui-Zhe; Tang, Shin-Yi; Yang, Chiyun; Chi, Zhixia; Liang, Chieh-Ching; Ning, Er; Wang, Shu

    2014-01-01

    Virus-derived gene transfer vectors have been successfully employed to express the transcription activator-like effector nucleases (TALENs) in mammalian cells. Since the DNA-binding domains of TALENs consist of the variable di-residue (RVD)-containing tandem repeat modules and virus genome with repeated sequences is susceptible to genetic recombination, we investigated several factors that might affect TALEN cleavage efficiency of baculoviral vectors. Using a TALEN system designed to target the AAVS1 locus, we observed increased sequence instability of the TALE repeat arrays when a higher multiplicity of infection (MOI) of recombinant viruses was used to produce the baculoviral vectors. We also detected more deleterious mutations in the TALE DNA-binding domains when both left and right TALEN arms were placed into a single expression cassette as compared to the viruses containing one arm only. The DNA sequence changes in the domains included deletion, addition, substitution, and DNA strand exchange between the left and right TALEN arms. Based on these observations, we have developed a protocol using a low MOI to produce baculoviral vectors expressing TALEN left and right arms separately. Cotransduction of the viruses produced by this optimal protocol provided an improved TALEN cleavage efficiency and enabled effective site-specific transgene integration in human cells.

  1. Worldwide genetic variability of the Duffy binding protein: insights into Plasmodium vivax vaccine development.

    Directory of Open Access Journals (Sweden)

    Taís Nóbrega de Sousa

    Full Text Available The dependence of Plasmodium vivax on invasion mediated by Duffy binding protein (DBP makes this protein a prime candidate for development of a vaccine. However, the development of a DBP-based vaccine might be hampered by the high variability of the protein ligand (DBP(II, known to bias the immune response toward a specific DBP variant. Here, the hypothesis being investigated is that the analysis of the worldwide DBP(II sequences will allow us to determine the minimum number of haplotypes (MNH to be included in a DBP-based vaccine of broad coverage. For that, all DBP(II sequences available were compiled and MNH was based on the most frequent nonsynonymous single nucleotide polymorphisms, the majority mapped on B and T cell epitopes. A preliminary analysis of DBP(II genetic diversity from eight malaria-endemic countries estimated that a number between two to six DBP haplotypes (17 in total would target at least 50% of parasite population circulating in each endemic region. Aiming to avoid region-specific haplotypes, we next analyzed the MNH that broadly cover worldwide parasite population. The results demonstrated that seven haplotypes would be required to cover around 60% of DBP(II sequences available. Trying to validate these selected haplotypes per country, we found that five out of the eight countries will be covered by the MNH (67% of parasite populations, range 48-84%. In addition, to identify related subgroups of DBP(II sequences we used a Bayesian clustering algorithm. The algorithm grouped all DBP(II sequences in six populations that were independent of geographic origin, with ancestral populations present in different proportions in each country. In conclusion, in this first attempt to undertake a global analysis about DBP(II variability, the results suggest that the development of DBP-based vaccine should consider multi-haplotype strategies; otherwise a putative P. vivax vaccine may not target some parasite populations.

  2. The effects of selective breeding against scrapie susceptibility on the genetic variability of the Latxa Black-Faced sheep breed

    Directory of Open Access Journals (Sweden)

    Legarra Andrés

    2006-09-01

    Full Text Available Abstract Breeding sheep populations for scrapie resistance could result in a loss of genetic variability. In this study, the effect on genetic variability of selection for increasing the ARR allele frequency was estimated in the Latxa breed. Two sources of information were used, pedigree and genetic polymorphisms (fifteen microsatellites. The results based on the genealogical information were conditioned by a low pedigree completeness level that revealed the interest of also using the information provided by the molecular markers. The overall results suggest that no great negative effect on genetic variability can be expected in the short time in the population analysed by selection of only ARR/ARR males. The estimated average relationship of ARR/ARR males with reproductive females was similar to that of all available males whatever its genotype: 0.010 vs. 0.012 for a genealogical relationship and 0.257 vs. 0.296 for molecular coancestry, respectively. However, selection of only ARR/ARR males implied important losses in founder animals (87 percent and low frequency alleles (30 percent in the ram population. The evaluation of mild selection strategies against scrapie susceptibility based on the use of some ARR heterozygous males was difficult because the genetic relationships estimated among animals differed when pedigree or molecular information was used, and the use of more molecular markers should be evaluated.

  3. Genetic characterization of feline bocavirus detected in cats in Japan.

    Science.gov (United States)

    Takano, Tomomi; Takadate, Yoshihiro; Doki, Tomoyoshi; Hohdatsu, Tsutomu

    2016-10-01

    Feline bocavirus (FBoV) has been classified into three genotypes (FBoV1-FBoV3). FBoVs are mainly detected in feces. In the present study, we collected rectal swabs from cats in Japan and examined the samples for the presence of FBoV. The FBoV infection rate was 9.9 % in 101 cats. No significant association was observed between FBoV infection and clinical symptoms. Based on the full-length NS1 protein, the three strains of FBoVs detected in the present study shared high homologies with the genotype 2 FBoV POR1 strain. This is the first study to report FBoV in Japan.

  4. Sensitivity of Climate Change Detection and Attribution to the Characterization of Internal Climate Variability

    KAUST Repository

    Imbers, Jara

    2014-05-01

    The Intergovernmental Panel on Climate Change\\'s (IPCC) "very likely" statement that anthropogenic emissions are affecting climate is based on a statistical detection and attribution methodology that strongly depends on the characterization of internal climate variability. In this paper, the authors test the robustness of this statement in the case of global mean surface air temperature, under different representations of such variability. The contributions of the different natural and anthropogenic forcings to the global mean surface air temperature response are computed using a box diffusion model. Representations of internal climate variability are explored using simple stochastic models that nevertheless span a representative range of plausible temporal autocorrelation structures, including the short-memory first-order autoregressive [AR(1)] process and the long-memory fractionally differencing process. The authors find that, independently of the representation chosen, the greenhouse gas signal remains statistically significant under the detection model employed in this paper. The results support the robustness of the IPCC detection and attribution statement for global mean temperature change under different characterizations of internal variability, but they also suggest that a wider variety of robustness tests, other than simple comparisons of residual variance, should be performed when dealing with other climate variables and/or different spatial scales. © 2014 American Meteorological Society.

  5. A genetic algorithm-based approach to flexible flow-line scheduling with variable lot sizes.

    Science.gov (United States)

    Lee, I; Sikora, R; Shaw, M J

    1997-01-01

    Genetic algorithms (GAs) have been used widely for such combinatorial optimization problems as the traveling salesman problem (TSP), the quadratic assignment problem (QAP), and job shop scheduling. In all of these problems there is usually a well defined representation which GA's use to solve the problem. We present a novel approach for solving two related problems-lot sizing and sequencing-concurrently using GAs. The essence of our approach lies in the concept of using a unified representation for the information about both the lot sizes and the sequence and enabling GAs to evolve the chromosome by replacing primitive genes with good building blocks. In addition, a simulated annealing procedure is incorporated to further improve the performance. We evaluate the performance of applying the above approach to flexible flow line scheduling with variable lot sizes for an actual manufacturing facility, comparing it to such alternative approaches as pair wise exchange improvement, tabu search, and simulated annealing procedures. The results show the efficacy of this approach for flexible flow line scheduling.

  6. Evolving Neural Network Using Variable String Genetic Algorithm for Color Infrared Aerial Image Classification

    Institute of Scientific and Technical Information of China (English)

    FU Xiaoyang; P E R Dale; ZHANG Shuqing

    2008-01-01

    Coastal wetlands are characterized by complex patterns both in their geomorphic and ecological features.Besides field observations,it is necessary to analyze the land cover of wetlands through the color infrared (CIR) aerial photography or remote sensing image.In this paper,we designed an evolving neural network classifier using variable string genetic algorithm (VGA) for the land cover classification of CIR aerial image.With the VGA,the classifier that we designed is able to evolve automatically the appropriate number of hidden nodes for modeling the neural network topology optimally and to find a near-optimal set of connection weights globally.Then,with backpropagation algorithm (BP),it can find the best connection weights.The VGA-BP classifier,which is derived from hybrid algorithms mentioned above,is demonstrated on CIR images classification effectively.Compared with standard classifiers,such as Bayes maximum-likelihood classifier,VGA classifier and BP-MLP (multi-layer perception) classifier,it has shown that the VGA-BP classifier can have better performance on highly resolution land cover classification.

  7. Genetic variability and limited clonality of Mycoplasma hyorhinis in pig herds.

    Science.gov (United States)

    Trüeb, Bettina; Catelli, Elena; Luehrs, Adrian; Nathues, Heiko; Kuhnert, Peter

    2016-08-15

    Mycoplasma hyorhinis is a common inhabitant of the upper respiratory tract and tonsils of pigs. Its role as a possible pathogen remains controversial. In order to gain more insight into the epidemiology and population structure of M. hyorhinis we genetically characterized 60 isolates by multi locus sequence typing (MLST). The M. hyorhinis strains originated from Swiss and German pig herds with knowledge on the clinical background. The MLST scheme of Tocqueville et al. (J. Clin. Microbiol. 2014) was optimized, primers for the six MLST gene fragments were newly designed to allow amplification and sequencing with a single protocol. A total of 27 ST were observed with the 60 strains, 26 of those were previously unknown types. Generally identical genotypes were observed within a farm but they differed between farms. The identical genotype was also observed in three different Swiss farms. On the other hand different genotypes within a farm were found with three German farms. The Swiss isolates formed a distinct cluster but otherwise there was no geographical nor a clinical association with specific clusters observed. Data shows a high variability of M. hyorhinis comparable to what is observed for Mycoplasma hyopneumoniae. Similar to this pathogen the population structure of M. hyorhinis also shows some limited clonality with predominant genotypes within an animal and a single farm but different ones between farms. The comparable population structure of M. hyopneumoniae and M. hyorhinis could indicate a similar evolution of the two species in the common pig host.

  8. Genetic variability and social structure of colonies in Acromyrmex heyeri and A. striatus (Hymenoptera: Formicidae

    Directory of Open Access Journals (Sweden)

    E. DIEHI

    Full Text Available The breeding structure of both colony and population of social insects can be examined by genetic analysis. Colonies of the leaf-cutting ants Acromyrmex heyeri and A. striatus (Myrmicinae, Attini were thus analyzed for isoenzyme systems MDH, a-GPDH, and AMY to describe genotype variability and social structure. A total of five loci were investigated (three for amylase and one for each other system. Ninety-seven colonies of A. heyeri and 103 of A. striatus were sampled in different localities in Southern Brazil (State of Rio Grande do Sul. The genotypes found show the occurrence of monogyny and polygyny associated or not with polyandry, which indicates that the social organization is colony-specific. The polygyny and polyandry observed are likely to be responsible for the great genotypic diversity of the colonies. The average inbreeding coefficient per colony was higher in A. striatus than in A. heyeri, which may reflect the different patterns of production of sexual individuals and nuptial flight of those two species.

  9. A Variable Interval Rescheduling Strategy for Dynamic Flexible Job Shop Scheduling Problem by Improved Genetic Algorithm

    Directory of Open Access Journals (Sweden)

    Lei Wang

    2017-01-01

    Full Text Available In real-world manufacturing systems, production scheduling systems are often implemented under random or dynamic events like machine failure, unexpected processing times, stochastic arrival of the urgent orders, cancellation of the orders, and so on. These dynamic events will lead the initial scheduling scheme to be nonoptimal and/or infeasible. Hence, appropriate dynamic rescheduling approaches are needed to overcome the dynamic events. In this paper, we propose a dynamic rescheduling method based on variable interval rescheduling strategy (VIRS to deal with the dynamic flexible job shop scheduling problem considering machine failure, urgent job arrival, and job damage as disruptions. On the other hand, an improved genetic algorithm (GA is proposed for minimizing makespan. In our improved GA, a mix of random initialization population by combining initialization machine and initialization operation with random initialization is designed for generating high-quality initial population. In addition, the elitist strategy (ES and improved population diversity strategy (IPDS are used to avoid falling into the local optimal solution. Experimental results for static and several dynamic events in the FJSP show that our method is feasible and effective.

  10. Influence of sex and genetic variability on expression of X-linked genes in human monocytes.

    Science.gov (United States)

    Castagné, Raphaële; Zeller, Tanja; Rotival, Maxime; Szymczak, Silke; Truong, Vinh; Schillert, Arne; Trégouët, David-Alexandre; Münzel, Thomas; Ziegler, Andreas; Cambien, François; Blankenberg, Stefan; Tiret, Laurence

    2011-11-01

    In humans, the fraction of X-linked genes with higher expression in females has been estimated to be 5% from microarray studies, a proportion lower than the 25% of genes thought to escape X inactivation. We analyzed 715 X-linked transcripts in circulating monocytes from 1,467 subjects and found an excess of female-biased transcripts on the X compared to autosomes (9.4% vs 5.5%, pgenes not previously known to escape inactivation, the most significant one was EFHC2 whose 20% of variability was explained by sex. We also investigated cis expression quantitative trait loci (eQTLs) by analyzing 15,703 X-linked SNPs. The frequency and magnitude of X-linked cis eQTLs were quite similar in males and females. Few genes exhibited a stronger genetic effect in females than in males (ARSD, DCX, POLA1 and ITM2A). These genes would deserve further investigation since they may contribute to sex pathophysiological differences.

  11. Multi-Conditional Latent Variable Model for Joint Facial Action Unit Detection

    NARCIS (Netherlands)

    Eleftheriadis, Stefanos; Rudovic, Ognjen; Pantic, Maja

    2015-01-01

    We propose a novel multi-conditional latent variable model for simultaneous facial feature fusion and detection of facial action units. In our approach we exploit the structure-discovery capabilities of generative models such as Gaussian processes, and the discriminative power of classifiers such as

  12. Change detection in variable speed limits: failed to look or looked but failed to see?

    NARCIS (Netherlands)

    Harms, Ilse M.; Brookhuis, Karel A.

    2012-01-01

    Variable speed limits (VSL) are used to adjust real-time driver speed to the circumstances of the road condition. Based on theoretical research it has been proposed that change blindness - the failure to detect, identify and localise changes - might play a role in the effectiveness of VSL in terms o

  13. The Detection and Interpretation of Interaction Effects between Continuous Variables in Multiple Regression.

    Science.gov (United States)

    Jaccard, James; And Others

    1990-01-01

    Issues in the detection and interpretation of interaction effects between quantitative variables in multiple regression analysis are discussed. Recent discussions associated with problems of multicollinearity are reviewed in the context of the conditional nature of multiple regression with product terms. (TJH)

  14. Genetic Variability of Stolbur Phytoplasma in Hyalesthes obsoletus (Hemiptera: Cixiidae) and its Main Host Plants in Vineyard Agroecosystems.

    Science.gov (United States)

    Landi, Lucia; Riolo, Paola; Murolo, Sergio; Romanazzi, Gianfranco; Nardi, Sandro; Isidoro, Nunzio

    2015-08-01

    Bois noir is an economically important grapevine yellows that is induced by 'Candidatus Phytoplasma solani' and principally vectored by the planthopper Hyalesthes obsoletus Signoret (Hemiptera: Cixiidae). This study explores the 'Ca. P. solani' genetic variability associated to the nettle-H. obsoletus and bindweed-H. obsoletus systems in vineyard agroecosystems of the central-eastern Italy. Molecular characterization of 'Ca. P. solani' isolates was carried out using polymerase chain reaction/restriction fragment length polymorphism to investigate the nonribosomal vmp1 gene. Seven phytoplasma vmp-types were detected among the host plants- and insect-associated field-collected samples. The vmp1 gene showed the highest polymorphism in the bindweed-H. obsoletus system, according to restriction fragment length polymorphism analysis, which is in agreement with nucleotide sequence analysis. Five vmp-types were associated with H. obsoletus from bindweed, of which one was solely restricted to planthoppers, with one genotype also in planthoppers from nettle. Type V12 was the most prevalent in both planthoppers and bindweed. H. obsoletus from nettle harbored three vmp-types, of which V3 was predominant. V3 was the only type detected for nettle. Our data demonstrate that planthoppers might have acquired some 'Ca. P. solani' profiles from other plant hosts before landing on nettle or bindweed. Overall, the different vmp1 gene rearrangements observed in these two plant hosts-H. obsoletus systems might represent different adaptations of the pathogen to the two host plants. Molecular information about the complex of vmp-types provides useful data for better understanding of Bois noir epidemiology in vineyard agroecosystem. © The Authors 2015. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  15. The study of micro crack detection in dissimilar metal weld using a variable ultrasound infrared thermography

    Energy Technology Data Exchange (ETDEWEB)

    Park, Jeong Hak; Choi, Man Yong; Kwon, Koo Ahn [Dept. of Research and Development, Korea Research Institute of Smart Material and Structures System Association, Daejeon (Korea, Republic of); Park, Hee Sang [Center of Safety Measurements, Korea Research Institute of Standards and Science, Daejeon (Korea, Republic of)

    2015-06-15

    As a nondestructive inspection technology currently in use, infrared thermography has gradually expanded its application range to industry. The method detects only defect areas by grafting ultrasound on a technique of detecting infrared energy emitted from all objects with absolute temperature of 0 K and converting this energy into thermography for inspection. Ultrasound infrared thermography has merits including the ability to inspect a wide area in a short time without contacting the target object. This study investigated the applicability of the technique for defect detection using variable ultrasound excitation inspection methods on samples of Terfenol-D, a magnetostrictive material with a tunable natural resonant frequency.

  16. EVALUATION OF GENETIC VARIABILITY OF FRESHWATER PRAWN COLLECTED FROM MAKASSAR-SULAWESI, PANGKALANBUNKALIMANTAN, JAMBI-SUMATRA, SUKABUMI-JAVA, AND GIMacro USING mtDNA CO-I MARKERS

    Directory of Open Access Journals (Sweden)

    Estu Nugroho

    2009-06-01

    Full Text Available The objective of this research is to evaluate the genetic variability of freshwater prawn, Macrobrachium rosenbergii. The genetic variability of freshwater prawn collected from Makassar-Sulawesi, Pangkalanbun-Kalimantan, Jambi-Sumatra, Sukabumi-Java, and GIMacro strain was examined using polymorphism of the mitochondria DNA (mtDNA markers. Twelve composite haplotypes were detected following digestion of CO1 sequences with four endonucleases: Hae III, Rsa I, Mbo I, and Taq I. The average haplotype diversity was 0.217. Significant genetic difference was observed among freshwater prawn populations, especially among Makassar-Sulawesi population and others. Makassar-Sulawesi strain has future prospect for genetic resources in breeding program.

  17. Tracing fecal pollution sources in karst groundwater by Bacteroidales genetic biomarkers, bacterial indicators, and environmental variables.

    Science.gov (United States)

    Zhang, Ya; Kelly, Walton R; Panno, Samuel V; Liu, Wen-Tso

    2014-08-15

    Fecal contamination in Midwestern karst regions was evaluated by simultaneously measuring traditional bacterial indicators (coliforms and Escherichia coli), Bacteroidales-based biomarkers, and environmental variables. Water samples from springs and wells were collected from karst regions in Illinois (IL), Wisconsin (WI), Kentucky (KY), and Missouri (MO). Quantitative PCR (Q-PCR) with seven primer sets targeting different members of Bacteroidales was used to determine the origin of fecal contamination (i.e., from human waste, livestock waste, or both). Most samples were contaminated by both human and animal waste, with a few samples showing pollution solely by one or the other. Spring water tended to have higher levels of contamination than well water, and higher concentrations of fecal biomarkers were detected in urban springs compared to rural spring systems. However, there were discrepancies on contamination profile determined by Bacteroidales-based biomarkers and by traditional bacterial indicators. Among all the environmental parameters examined, E. coli, sulfate, total dissolved solids (TDS), and silicon were significantly correlated (pgroundwater systems in Midwestern regions, and the inclusion of traditional bacterial indicators, environmental variables, and Bacteroidales-based MST is an effective approach for identifying fecal contamination in karst regions. Copyright © 2014 Elsevier B.V. All rights reserved.

  18. Detection of Babesia bigemina in cattle of different genetic groups and in Rhipicephalus (Boophilus) microplus tick.

    Science.gov (United States)

    Oliveira, M C S; Oliveira-Sequeira, T C G; Regitano, L C A; Alencar, M M; Néo, T A; Silva, A M; Oliveira, H N

    2008-08-17

    Babesia bigemina infections were investigated in four genetic groups of beef cattle and in Rhipicephalus (Boophilus) microplus engorged female ticks. Blood samples and engorged female ticks were collected from 15 cows and 15 calves from each of the following genetic groups: Nelore, Angus x Nelore, Canchim x Nelore, and Simmental x Nelore. Microscopic examination of blood smears and tick hemolymph revealed that merozoites of B. bigemina (6/60) as well as kinetes of Babesia spp. (9/549) were only detected in samples (blood and ticks, respectively) originated from calves. PCR-based methods using primers for specific detection of B. bigemina revealed 100% infection in both calves and cows, regardless the genetic group. Tick infection was detected by nested-PCR amplifications showing that the frequency of B. bigemina was higher (P0.05).

  19. Effect of genetic homogeneity on behavioural variability in an object recognition test in cloned Göttingen minipigs

    DEFF Research Database (Denmark)

    Søndergaard, Lene Vammen; Herskin, Mette S.; Ladewig, Jan;

    2012-01-01

    The number of animals used in research should be limited as much as possible. Among cloned animals, genetic variation is minimal and to the extent that behaviour is genetically determined inter-individual variability is expected to be higher among naturally bred animals. However, the cloning...... in these behavioural variables in cloned minipigs is less than in naturally bred control subjects and therefore does not directly support the hypothesis that cloning may be used to replicate animals in order to reduce group size in experimentation animals....... were subjected to a behavioural test of memory, the spontaneous object recognition test, from an early age. At ages 1 and 2 years no evidence of memory decline was found, yet the data showed striking behavioural variability among the cloned groups. The aim of the present study was to investigate...

  20. A unifying study of phenotypic and molecular genetic variability in natural populations of Anadenanthera colubrina var. cebil from Yungas and Paranaense biogeographic provinces in Argentina

    Indian Academy of Sciences (India)

    María Victoria García; Kathleen Prinz; María Eugenia Barrandeguy; Marcos Miretti; Reiner Finkeldey

    2014-04-01

    Anadenanthera colubrina var. cebil is a discontinuously distributed native tree species in South American subtropical forests. Thirteen quantitative traits and eight nuclear microsatellite loci were examined in individuals from two biogeographic provinces of Argentina to determine the number and composition of genetically distinguishable groups of individuals and explore possible spatial patterns of the phenotypic and genetic variability. Means of reproductive traits were higher in the Yungas than in the Paranaense biogeographic province, whereas five out of eight nonreproductive quantitative traits showed higher mean values in the latter. Variance coefficients were moderate, and there were significant differences between and within provinces. Three clusters were defined based on spatial model for cluster membership for quantitative traits. One cluster grouped the individuals from the Paranaense biogeographic province whereas the individuals from the Yungas biogeographic province grouped regarding its population of origin. Parameters of molecular genetic variability showed higher values in the Yungas than in the Paranaense biogeographic province. Observed heterozygosity was lower than expected heterozygosity in both biogeographic provinces, indicating an excess of homozygosity. The homozygosity test by Watterson and the exact test by Slatkin suggested diversifying selection for locus Ac41.1. Bayesian clustering spatial model for microsatellites loci data were performed for both all loci and for all loci excluding locus Ac41.1. In both analyses two clusters were inferred. Analysis of molecular variance revealed similar results for all genotypes and for all genotypes defined excluding locus Ac41.1. Most of the total variance is attributable to genetic variation within clusters. The presence of homogeneous clusters was detected for both the phenotypic and molecular genetic variability. Two Bayesian clustering analyses were performed according to molecular genetic data

  1. Genetic variability and fumonisin production by Fusarium proliferatum isolated from durum wheat grains in Argentina.

    Science.gov (United States)

    Palacios, S A; Susca, A; Haidukowski, M; Stea, G; Cendoya, E; Ramírez, M L; Chulze, S N; Farnochi, M C; Moretti, A; Torres, A M

    2015-05-18

    Fusarium proliferatum is a member of the Fusarium fujikuroi species complex (FFSC) involved in the maize ear rot together with Fusarium verticillioides, which is a very closely related species. Recently, different studies have detected natural fumonisin contamination in wheat kernels and most of them have shown that the main species isolated was F. proliferatum. Fusarium strains obtained from freshly harvested durum wheat samples (2008 to 2011 harvest seasons) from Argentina were characterized through a phylogenetic analysis based on translation elongation factor-1 alpha (EF-1α) and calmodulin (CaM) genes, determination of mating type alleles, and evaluation of fumonisin production capability. The strains were identified as F. proliferatum (72%), F. verticillioides (24%) and other Fusarium species. The ratio of mating type alleles (MAT-1 and MAT-2) obtained for both main populations suggests possible occurrence of sexual reproduction in the wheat fields, although this seems more frequent in F. proliferatum. Phylogenetic analysis revealed greater nucleotide variability in F. proliferatum strains than in F. verticillioides, however this was not related to origin, host or harvest year. The fumonisin-producing ability was detected in 92% of the strains isolated from durum wheat grains. These results indicate that F. proliferatum and F. verticillioides, among the fumonisin producing species, frequently contaminate durum wheat grains in Argentina, presenting a high risk for human and animal health. Copyright © 2015 Elsevier B.V. All rights reserved.

  2. A Genetic Algorithm and Fuzzy Logic Approach for Video Shot Boundary Detection

    Directory of Open Access Journals (Sweden)

    Dalton Meitei Thounaojam

    2016-01-01

    Full Text Available This paper proposed a shot boundary detection approach using Genetic Algorithm and Fuzzy Logic. In this, the membership functions of the fuzzy system are calculated using Genetic Algorithm by taking preobserved actual values for shot boundaries. The classification of the types of shot transitions is done by the fuzzy system. Experimental results show that the accuracy of the shot boundary detection increases with the increase in iterations or generations of the GA optimization process. The proposed system is compared to latest techniques and yields better result in terms of F1score parameter.

  3. A Genetic Algorithm and Fuzzy Logic Approach for Video Shot Boundary Detection.

    Science.gov (United States)

    Thounaojam, Dalton Meitei; Khelchandra, Thongam; Manglem Singh, Kh; Roy, Sudipta

    2016-01-01

    This paper proposed a shot boundary detection approach using Genetic Algorithm and Fuzzy Logic. In this, the membership functions of the fuzzy system are calculated using Genetic Algorithm by taking preobserved actual values for shot boundaries. The classification of the types of shot transitions is done by the fuzzy system. Experimental results show that the accuracy of the shot boundary detection increases with the increase in iterations or generations of the GA optimization process. The proposed system is compared to latest techniques and yields better result in terms of F1score parameter.

  4. Detection of genetically modified soybean in crude soybean oil.

    Science.gov (United States)

    Nikolić, Zorica; Vasiljević, Ivana; Zdjelar, Gordana; Ðorđević, Vuk; Ignjatov, Maja; Jovičić, Dušica; Milošević, Dragana

    2014-02-15

    In order to detect presence and quantity of Roundup Ready (RR) soybean in crude oil extracted from soybean seed with a different percentage of GMO seed two extraction methods were used, CTAB and DNeasy Plant Mini Kit. The amplifications of lectin gene, used to check the presence of soybean DNA, were not achieved in all CTAB extracts of DNA, while commercial kit gave satisfactory results. Comparing actual and estimated GMO content between two extraction methods, root mean square deviation for kit is 0.208 and for CTAB is 2.127, clearly demonstrated superiority of kit over CTAB extraction. The results of quantification evidently showed that if the oil samples originate from soybean seed with varying percentage of RR, it is possible to monitor the GMO content at the first stage of processing crude oil.

  5. In situ detection of horizontal transfer of mobile genetic elements

    DEFF Research Database (Denmark)

    Haagensen, Janus Anders Juul; Hansen, Susse Kirkelund; Johansen, Tove;

    2002-01-01

    Plasmid transfer was investigated in microbial populations associated with different types of surfaces. The general strategy behind these investigations was to label the transferable plasmid with a gene encoding a fluorescent protein in order to make it a transfer reporter. This was achieved...... promoters (transfer reporters) it was thus possible to detect transfer events in situ and correlate these with either the location of donor and recipient cells or with the growth activity of the cells. In some cases, expression of unstable Gfp from a growth-controlled promoter, rrnB from Escherichia coli...... by fusing the reporter gene with a lac promoter expression cassette and combining this with a donor cell-associated lacI repressor cassette. After construction of a range of strains and plasmids with combinations of genes expressing fluorescent proteins from constitutive (cell tagging) or regulated...

  6. Analysis of genetic variability in three species of Pimelodidae (Ostariophysi - Siluriformes

    Directory of Open Access Journals (Sweden)

    Fernanda S. de Almeida

    1998-12-01

    Full Text Available Genetic variability of three Pimelodidae species, Pimelodus maculatus, Iheringichthys labrosus, and Pinirampus pirinampu, collected at one site in the Tibagi River, was comparatively analyzed using protein data for six systems which code 15 loci in liver, muscle, and heart. The proportion of polymorphic loci ( for P. maculatus, I. labrosus, and P. pirinampu was 13.33, 20, and 6.67%, respectively, and mean heterozigosity was 6, 8.3, and 4.3%. The genetic identity value (I was 0.32 between P. maculatus and I. labrosus, 0.37 between P. maculatus and P. pirinampu, and 0.58 between I. labrosus and P. pirinampu. This value suggests that these two latter species are congeneric. However, morphological characteristics place these species in distinct genera.A variabilidade genética de 3 espécies da família Pimelodidae, Pimelodus maculatus, Iheringichthys labrosus e Pinirampus pirinampu, coletadas em um ponto do rio Tibagi, foi analisada comparativamente utilizando dados protéicos de 6 sistemas que codificam 15 locos em fígado, músculo e coração. A proporção de locos polimórficos ( para P. maculatus, I. labrosus e P. pirinampu foi de 13,33, 20 e 6,67%, respectivamente, e a heterozigosidade média foi de 6, 8,3 e 4,3%. A identidade genética (I foi de 0,32 entre P. maculatus e I. labrosus, 0,37 entre P. maculatus e P. pirinampu e 0,58 entre I. labrosus e P. pirinampu. O valor de I (0,58 encontrado entre I. labrosus e P. pirinampu sugere que estas são espécies congenéricas. No entanto, as características morfológicas colocam estas espécies em gêneros distintos. Os resultados obtidos nesse estudo podem ser úteis para um melhor conhecimento de espécies de Pimelodidae. Elas também reforçam a necessidade da preservação do rio Tibagi (Paraná - Brasil através de uma análise cuidadosa no caso de construção de hidroelétricas.

  7. Detecting network intrusions by data mining and variable-length sequence pattern matching

    Institute of Scientific and Technical Information of China (English)

    Tian Xinguang; Duan Miyi; Sun Chunlai; Liu Xin

    2009-01-01

    Anomaly detection has been an active research topic in the field of network intrusion detection for many years. A novel method is presented for anomaly detection based on system calls into the kernels of Unix or Linux systems. The method uses the data mining technique to model the normal behavior of a privileged program and uses a variable-length pattern matching algorithm to perform the comparison of the current behavior and historic normal behavior, which is more suitable for this problem than the fixed-length pattern matching algorithm proposed by Forrest et al. At the detection stage, the particularity of the audit data is taken into account, and two alternative schemes could be used to distinguish between normalities and intrusions. The method gives attention to both computational efficiency and detection accuracy and is especially applicable for on-line detection. The performance of the method is evaluated using the typical testing data set, and the results show that it is significantly better than the anomaly detection method based on hidden Markov models proposed by Yan et al. and the method based on fixed-length patterns proposed by Forrest and Hofmeyr. The novel method has been applied to practical hosted-based intrusion detection systems and achieved high detection performance.

  8. Deltamethrin flea-control preserves genetic variability of black-tailed prairie dogs during a plague outbreak

    Science.gov (United States)

    Jones, P.H.; Biggins, D.E.; Eads, D.A.; Eads, S.L.; Britten, H.B.

    2012-01-01

    Genetic variability and structure of nine black-tailed prairie dog (BTPD, Cynomys ludovicianus) colonies were estimated with 15 unlinked microsatellite markers. A plague epizootic occurred between the first and second years of sampling and our study colonies were nearly extirpated with the exception of three colonies in which prairie dog burrows were previously dusted with an insecticide, deltamethrin, used to control fleas (vectors of the causative agent of plague, Yersinia pestis). This situation provided context to compare genetic variability and structure among dusted and non-dusted colonies pre-epizootic, and among the three dusted colonies pre- and post-epizootic. We found no statistical difference in population genetic structures between dusted and non-dusted colonies pre-epizootic. On dusted colonies, gene flow and recent migration rates increased from the first (pre-epizootic) year to the second (post-epizootic) year which suggested dusted colonies were acting as refugia for prairie dogs from surrounding colonies impacted by plague. Indeed, in the dusted colonies, estimated densities of adult prairie dogs (including dispersers), but not juveniles (non-dispersers), increased from the first year to the second year. In addition to preserving BTPDs and many species that depend on them, protecting colonies with deltamethrin or a plague vaccine could be an effective method to preserve genetic variability of prairie dogs. ?? 2011 Springer Science+Business Media B.V.

  9. Effects of atmospheric water vapor on detection performance of a linear variable filter based instrument

    Science.gov (United States)

    Shen, Sylvia S.; Miller, David P.; Lewis, Paul E.

    2010-08-01

    Linear variable filter design and fabrication for LWIR is now commercially available for use in the development of airborne reconnaissance or surveillance systems. The linear variable filter is attached directly to the cold shield of the focal plane array. The resulting compact spectrometer assemblies are completely contained in the Dewar system. This approach eliminates many of the wavelength calibration problems associated with current prism and grating systems and also facilitates the cost effective design and fabrication of aerial sensing systems for specific applications. An optimal 32 band linear-variablefilter- based system for detecting and discriminating a set of 11 chemicals representing a high probability of occurrence during a typical emergency response chemical incident was determined in a companion paper entitled "Linear Variable Filter Optimization for Emergency Response Chemical Detection and Discrimination". This paper addresses the effects of atmospheric water vapor on the performance of this optimal 32 band linear-variable-filter-based system. This paper also determines at what increased concentration levels above the optimal system design goal of 30 ppm-m can detection and discrimination of these 11 chemicals be achieved in realistic but imperfect atmospheric water vapor removal scenarios.

  10. Genetic variability of a population of Aedes aegypti from Paraná, Brazil, using the mitochondrial ND4 gene

    Directory of Open Access Journals (Sweden)

    Adriana L. Twerdochlib

    2012-06-01

    Full Text Available Genetic variability of a population of Aedes aegypti from Paraná, Brazil, using the mitochondrial ND4 gene. To analyze the genetic variability of populations of Aedes aegypti, 156 samples were collected from 10 municipalities in the state of Paraná, Brazil. A 311 base pairs (bp region of the NADH dehydrogenase subunit 4 (ND4 mitochondrial gene was examined. An analysis of this fragment identified eight distinct haplotypes. The mean genetic diversity was high (h = 0.702; p = 0.01556. AMOVA analysis indicated that most of the variation (67% occurred within populations and the F ST value (0.32996 was highly significant. F ST values were significant in most comparisons among cities. The isolation by distance was not significant (r = -0.1216 and p = 0, 7550, indicating that genetic distance is not related to geographic distance. Neighbor-joining analysis showed two genetically distinct groups within Paraná. The DNA polymorphism and AMOVA data indicate a decreased gene flow in populations from Paraná, which can result in increased vectorial competence.

  11. Genetic variability of wild cherry (Prunus avium L.) seed stands in Slovenia as revealed by nuclear microsatellite loci.

    Science.gov (United States)

    Jarni, Kristjan; De Cuyper, Bart; Brus, Robert

    2012-01-01

    Microsatellite markers were used to describe the genetic variability of four seed stands of wild cherry (Prunus avium L.). One hundred and thirty one individuals were genotyped at ten nuclear microsatellite loci. Total genetic diversity was high (H(E) = 0.704), while differences between stands were small but significant (F(ST) = 0.053, G'(ST) = 0.234). There was a significant amount of clonal reproduction in one stand, with only 11 genotypes identified among 36 trees. One stand showed a significant excess (F(IS) = -0.044) of heterozygosity, and one showed a deficit (F(IS) = 0.044). Our results demonstrate the importance of taking into account the biological and genetic characteristics of species in forest management, especially when determining a new seed stand. The small genetic differences found between seed stands indicate that a large number of stands are not required. However, they should be carefully selected and should possess adequate genetic variability to ensure low relatedness between seed trees.

  12. Genetic variability of wild cherry (Prunus avium L. seed stands in Slovenia as revealed by nuclear microsatellite loci.

    Directory of Open Access Journals (Sweden)

    Kristjan Jarni

    Full Text Available Microsatellite markers were used to describe the genetic variability of four seed stands of wild cherry (Prunus avium L.. One hundred and thirty one individuals were genotyped at ten nuclear microsatellite loci. Total genetic diversity was high (H(E = 0.704, while differences between stands were small but significant (F(ST = 0.053, G'(ST = 0.234. There was a significant amount of clonal reproduction in one stand, with only 11 genotypes identified among 36 trees. One stand showed a significant excess (F(IS = -0.044 of heterozygosity, and one showed a deficit (F(IS = 0.044. Our results demonstrate the importance of taking into account the biological and genetic characteristics of species in forest management, especially when determining a new seed stand. The small genetic differences found between seed stands indicate that a large number of stands are not required. However, they should be carefully selected and should possess adequate genetic variability to ensure low relatedness between seed trees.

  13. Detection and Genetic Characterization of Rabies Virus from Human Patients

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Saliva and blood were collected from two patients who had not received post exposure prophylaxis in the cities of Wenzhou and Xinning respectively. Both patients were confirmed as positive for rabies by detection of rabies virus specific nucleoprotein antibodies in the sera by Western Blot. However, rabies virus specific RNA was only identified in the saliva collected from the patient in Wenzhou. Furthermore, the isolate Zhejiang Wz0 (H) was obtained by inoculating one-day-old suckling mice. Both nucleoprotein (N) and glycoprotein (G) genes from the isolate were amplified by RT-PCR and sequenced. Phylogenetic analysis indicated that the isolate belonged to classic rabies virus, and shared a higher homology with the street viruses from dogs in the main endemic areas in China and the street virus from dogs in Indonesia than with other known strains. Further comparison of the deduced amino acid sequences between the isolate and the vaccine strains used in China showed that the virus had a higher level of homology with the vaccine strain CTN than with the other vaccine strains (3aG, PV, PM and ERA). In particular, amino acid residues substitutions located in antigenic site Ⅲ in the G protein, which could react with the neutralizing antibodies, were observed. These results suggested that the virus belonged to the classic rabies virus, and both N and G genes diverged from the current vaccine strains used in China at either the nucleotide or the amino acid level.

  14. Design of a DNA chip for detection of unknown genetically modified organisms (GMOs).

    Science.gov (United States)

    Nesvold, Håvard; Kristoffersen, Anja Bråthen; Holst-Jensen, Arne; Berdal, Knut G

    2005-05-01

    Unknown genetically modified organisms (GMOs) have not undergone a risk evaluation, and hence might pose a danger to health and environment. There are, today, no methods for detecting unknown GMOs. In this paper we propose a novel method intended as a first step in an approach for detecting unknown genetically modified (GM) material in a single plant. A model is designed where biological and combinatorial reduction rules are applied to a set of DNA chip probes containing all possible sequences of uniform length n, creating probes capable of detecting unknown GMOs. The model is theoretically tested for Arabidopsis thaliana Columbia, and the probabilities for detecting inserts and receiving false positives are assessed for various parameters for this organism. From a theoretical standpoint, the model looks very promising but should be tested further in the laboratory. The model and algorithms will be available upon request to the corresponding author.

  15. Detection of Fast Radio Variability of Radio Objects with Continuous Optical Spectra

    Science.gov (United States)

    Pustilnik, S. A.

    The results of the search for rapid variability (T > 1 day) in centimeter range using RATAN-600 in 14 radio objects with contiuous optical spectra are given. In 9 of them, namely 0109+224, 0139-097, 0300+471, 0306+102, 0754+100, 0818-128, 0823-223, 1034-293 and 1538+149 the rapid variability is detected at the wavelengths either 3.9 or 8.2 cm with the confidence probability > 0.98. The conclusion is reached on the close correlation of the presence of the rapid radiovariability and the relative power of non-thermal optical continuum.

  16. Detection of Genetic Diversity in Synthetic Hexaploid Wheats Using Microsatellite Markers

    Institute of Scientific and Technical Information of China (English)

    CHEN Guo-yue; LI Li-hui

    2007-01-01

    Ninety-five synthetic hexaploid wheats(2n=6x=42,AABBDD)were analyzed using 45 microsatellite markers to investigate the potential genetic diversity in wheat breeding programs.A total of 326 alleles were detected by these microsatellite primer pairs,with an average of 6.65 alleles per locus.The polymorphic information content(PIC),Simpson index(SI),and genetic similarity(GS)coefficient showed that the D genome is of the highest genetic diversity among the A,B,and D genomes in the synthetic hexaploid wheats.The results also indicated that the synthetic hexaploid wheat is an efficient way to enrich wheat genetic backgrounds,especially to use the genetic variations of the D genome from Aegilops squarrosa for wheat improvement.The UPGMA dendogram,based on a similarity matrix by a simple matching coefficient algorithm,delineated the above accessions into 5 major clusters and was in accordance with the available pedigree information.The results demonstrated the utility of microsatellite markers in detecting DNA polymorphism and estimating genetic diversity.

  17. Butyrylcholinesterase genetic variability in Guarani Amerindians from the Brazilian state of Mato Grosso do Sul

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    Lupe Furtado

    2006-01-01

    Full Text Available Human butyrylcholinesterase (BChE; EC 3.1.1.8 is a polymorphic enzyme coded by the BCHE gene (3q26.1-q26.2 while the CHE2 gene (2q33-q35 determines a still not characterized substance that forms a complex with BChE (C5, being the CHE2 C5+ and CHE2 C5- phenotypes detected in electrophoresis. The present study investigated BCHE and CHE2 variability and the BChE activity of Brazilian Guarani Amerindians from the Kaiowá and Ñandeva sub-groups living in several indigenous territories in the Brazilian state of Mato Grosso do Sul. The frequency of the BCHE exon 2 D70G (A allele was 0.60% ± 0.35% while that of the BCHE exon 2 G390V (F-2 allele, never before screened in Amerindians, was 8.82% ± 1.35%. This is the first time that the BCHE gene exon 4 A539T (K allele has been surveyed in Brazilian Amerindians where it was found at a frequency of 3.69% ± 0.85%, similar to that found in Chilean Mapuche Amerindians. The BCHE gene variability seen in this survey differs from that of non-isolated populations in respect to both A539T and G390V allele frequency. The CHE2 C5+ phenotype frequency was 14.40% ± 2.22% and falls within the range of that found for other Brazilian Amerindian samples.

  18. GENETIC VARIABILITY OF POLYMESODA EROSA POPULATION IN THE SEGARA ANAKAN CILACAP

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    AGUS NURYANTO

    2010-01-01

    Full Text Available Mud clams, Polymesoda erosa, in the Segara Anakan Cilacap are highly exploited by the local communities for daily consumption. This is presumed causing population decline and potentially causing loss of genetic diversity. Genetic diversity level within population can be obtained by population genetic study using molecular marker such as randomly amplified polymorphic DNA (RAPD. Here we amplified RAPD marker using ten arbitrary primers to assess genetic diversity of P. erosa population in the Segara Anakan Cilacap to provide genetic data for its sustainable use. The results proved that the use of RAPD marker has high polymorphisms. The mud clam population also showed a high level of heterozygosity and genetic diversity. This has important implication for the management plan towards sustainable use of P. erosa in the Segara Anakan Cilacap.

  19. Chinese Xibe population genetic composition according to linkage groups of X-chromosomal STRs: population genetic variability and interpopulation comparisons.

    Science.gov (United States)

    Meng, Hao-Tian; Shen, Chun-Mei; Zhang, Yu-Dang; Dong, Qian; Guo, Yu-Xin; Yang, Guang; Yan, Jiang-Wei; Liu, Yao-Shun; Mei, Ting; Shi, Jian-Feng; Zhu, Bo-Feng

    2017-09-01

    The Xibe population is one of China's officially recognised populations and is now distributed separately from west to east in the northern part of China. X-chromosomal short tandem repeats have a special inheritance pattern, and could be used as complements in forensic application, especially for complex or deficiency cases. This study obtained the allelic and haplotypic frequencies of 19 X-STR loci in the Xibe population from Xinjiang Uygur Autonomous Region, China, and studied the genetic differentiations between the Xibe and other populations. The combined power of discrimination in females and males and mean exclusion chances in deficiency cases, normal trios and duo cases was at least 0.999 999 994. In the haplotypic study, the Xibe population showed a more similar pattern of haplotype distribution with Asian populations than populations from other continents, while allelic study also indicated a closer relationship between the Xibe and Asian populations. The 19 X-STR loci would be useful in forensic application in the studied population. The Xibe population showed a closer genetic relationship with Asian populations in the study, and more population data would be necessary for more detailed genetic relationship studies.

  20. Adaptive genetic variability and differentiation of Croatian and Austrian Quercus robur L. populations at a drought prone field trial

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    Saša Bogdan

    2017-07-01

    Full Text Available Provenance trials, where populations of different geographical origin are tested in a common environment (common garden test, are a tool suited to allow the study of intraspecific adaptive genetic variation. Research of pedunculate oak (Quercus robur L. adaptive genetic variability through analyses of populations in common garden tests has a long tradition. However, pedunculated oak populations originating south-eastern from the Alps have been scarcely studied in this way. This study addresses the adaptive genetic variability and differentiation of pedunculate oak populations originating from Austria and Croatia in a provenance/progeny field trial. Studied plants were six years old and were growing at the trial for three years. After two years of unusually low precipitations height and survival were analysed. The total mean height of all plants in the trial was 137.8 cm and ranged from 123.0 cm to 151.8 cm. The overall mean survival rate was rather high (0.85. Mean population survival ranged from 0.64 to 0.94. Individual narrow-sense heritabilities (hi2, family mean heritabilities (hf2, the coefficients of additive genetic variation (CVA and quantitative genetic differentiation coefficients (QST were calculated. A multivariate regression tree (MRT analysis was used to determine the pattern of genetic differentiation of the populations. Individual heritabilities for height ranged between 0.00 and 0.39. Family mean heritabilities for height were rather low in most populations as well (<0.5. Family mean heritabilities for survival were higher than for height (ranging between 0.00 and 0.77. Calculated QST coefficients (0.25 for height and 0.14 for survival indicated between-population genetic differentiation. The populations were separated into two clusters by MRT analysis regarding a climatic variable, namely Hargreaves’ reference evapotranspiration. Populations originating from comparatively more humid habitats were grouped in the first

  1. Nonequilibrium Conditions Explain Spatial Variability in Genetic Structuring of Little Penguin (Eudyptula minor).

    Science.gov (United States)

    Burridge, Christopher P; Peucker, Amanda J; Valautham, Sureen K; Styan, Craig A; Dann, Peter

    2015-01-01

    Factors responsible for spatial structuring of population genetic variation are varied, and in many instances there may be no obvious explanations for genetic structuring observed, or those invoked may reflect spurious correlations. A study of little penguins (Eudyptula minor) in southeast Australia documented low spatial structuring of genetic variation with the exception of colonies at the western limit of sampling, and this distinction was attributed to an intervening oceanographic feature (Bonney Upwelling), differences in breeding phenology, or sea level change. Here, we conducted sampling across the entire Australian range, employing additional markers (12 microsatellites and mitochondrial DNA, 697 individuals, 17 colonies). The zone of elevated genetic structuring previously observed actually represents the eastern half of a genetic cline, within which structuring exists over much shorter spatial scales than elsewhere. Colonies separated by as little as 27 km in the zone are genetically distinguishable, while outside the zone, homogeneity cannot be rejected at scales of up to 1400 km. Given a lack of additional physical or environmental barriers to gene flow, the zone of elevated genetic structuring may reflect secondary contact of lineages (with or without selection against interbreeding), or recent colonization and expansion from this region. This study highlights the importance of sampling scale to reveal the cause of genetic structuring. © The American Genetic Association 2015.

  2. Genetic variability among populations of the sand fly Lutzomyia (Lutzomyia) longipalpis (Diptera: Psychodidae) from Central America.

    Science.gov (United States)

    Mutebi, J P; Rowton, E; Herrero, M V; Ponce, C; Belli, A; Valle, S; Lanzaro, G C

    1998-03-01

    Eleven Central American populations of Lutzomyia longipalpis (Lutz & Neiva) were analyzed for genetic variation at 16 enzyme loci. The aim was to study the genetic structure among populations within this region and to identify demes that may represent different sibling species. Genotypic frequencies within populations agreed with Hardy-Weinberg expectations, indicating that there were no sympatric sibling species among these 11 populations. Levels of genetic distance between pairs of populations were very low (migration rates among populations (Nm) were low (3.7), indicating that gene flow was restricted. These data explained observed genetic substructuring when all genotypes were pooled.

  3. Detecting Genetic Isolation in Human Populations: A Study of European Language Minorities

    Science.gov (United States)

    Capocasa, Marco; Battaggia, Cinzia; Anagnostou, Paolo; Montinaro, Francesco; Boschi, Ilaria; Ferri, Gianmarco; Alù, Milena; Coia, Valentina; Crivellaro, Federica; Bisol, Giovanni Destro

    2013-01-01

    The identification of isolation signatures is fundamental to better understand the genetic structure of human populations and to test the relations between cultural factors and genetic variation. However, with current approaches, it is not possible to distinguish between the consequences of long-term isolation and the effects of reduced sample size, selection and differential gene flow. To overcome these limitations, we have integrated the analysis of classical genetic diversity measures with a Bayesian method to estimate gene flow and have carried out simulations based on the coalescent. Combining these approaches, we first tested whether the relatively short history of cultural and geographical isolation of four “linguistic islands” of the Eastern Alps (Lessinia, Sauris, Sappada and Timau) had left detectable signatures in their genetic structure. We then compared our findings to previous studies of European population isolates. Finally, we explored the importance of demographic and cultural factors in shaping genetic diversity among the groups under study. A combination of small initial effective size and continued genetic isolation from surrounding populations seems to provide a coherent explanation for the diversity observed among Sauris, Sappada and Timau, which was found to be substantially greater than in other groups of European isolated populations. Simulations of micro-evolutionary scenarios indicate that ethnicity might have been important in increasing genetic diversity among these culturally related and spatially close populations. PMID:23418562

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

    Science.gov (United States)

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

  5. Fault detection and accommodation via neural network and variable structure control

    Institute of Scientific and Technical Information of China (English)

    Hao YANG; Bin JIANG

    2007-01-01

    This paper proposes a novel idea that classifies faults into two different kinds: serious faults and small faults,and treats them with different strategies respectively. A kind of artificial neural network (ANN) is proposed for detecting serious faults, and variable structure (VS) model-following control is constructed for accommodating small faults. The proposed framework takes both advantages of qualitative way and quantitative way of fault detection and accommodation.Moreover, the uncertainty case is investigated and the VS controller is modified. Simulation results of a remotely piloted aircraft with control actuator failures illustrate the performance of the developed algorithm.

  6. Variables Affecting Probability of Detection in Bolt Hole Eddy Current Inspection

    Science.gov (United States)

    Lemire, H.; Krause, T. W.; Bunn, M.; Butcher, D. J.

    2009-03-01

    Physical variables affecting probability of detection (POD) in a bolt-hole eddy current inspection were examined. The POD study involved simulated bolt holes in 7075-T6 aluminum coupons representative of wing areas on CC-130 and CP-140 aircraft. The data were obtained from 24 inspectors who inspected 468 coupons, containing a subset of coupons with 45 electric discharge machined notches and 72 laboratory grown fatigue cracks located at the inner surface corner of the bi-layer structures. A comparison of physical features of cracks and notches in light of skin depth effects and probe geometry was used to identify length rather than depth as the significant variable producing signal variation. Probability of detection based on length produced similar results for the two discontinuity types, except at lengths less than 0.4 mm, where POD for cracks was found to be higher than that of notches.

  7. Detection of land surface memory by correlations between thickness of colluvial deposits and morphometric variables

    Science.gov (United States)

    Mitusov, A. V.; Dreibrodt, S.; Mitusova, O. E.; Khamnueva, S. V.; Bork, H.-R.

    2013-06-01

    Some morphometric variables store information about past land surfaces longer than others. This property of morphometric variables is recognised as land surface memory. Slope deposits, soils, and vegetation also have this memory. In this study, a memory effect was quantitatively detected by Spearman correlations between thickness of colluvium and morphometric variables of the modern land surface. During long-term sedimentation, the sign of horizontal curvature (kh) may be inverted from minus to plus, suggesting that locations with positive kh values are not accumulation zones. However, the thickness of colluvial deposits at such locations in our study area indicates sediment accumulation. The sign of minimal curvature (kmin) tends to be more stable and remains negative. This difference provides the stronger correlation of colluvial layer thickness with kmin than with kh. The strongest correlation was found for total thickness of the colluvial deposits of the Neolithic and Iron Age with kmin (- 0.84); the correlation with kh was weaker (- 0.71).

  8. DAMPE detection of variable GeV gamma-ray emission from blazar CTA 102

    Science.gov (United States)

    Xu, Zun-Lei; Caragiulo, Micaela; Chang, Jin; Duan, Kai-Kai; Fan, Yi-Zhong; Gargano, Fabio; Lei, Shi-Jun; Li, Xiang; Liang, Yun-Feng; Mazziotta, M. Nicola; Shen, Zhao-Qiang; Su, Meng; Tykhonov, Andrii; Yuan, Qiang; Zimmer, Stephan; Dampe Collaboration; Li, Bin; Zhao, Hai-Bin; Cneost Group

    2016-12-01

    The DArk Matter Particle Explorer (DAMPE), has detected variable gamma-ray emission from a source positionally coincident with the flat spectrum radio quasar CTA 102 (also known as 4C +11.69) with redshift of z=1.037 (Schmidt 1965, ApJ, 141, 1295) and coordinates (J2000.0, from VLBI) of R.A.: 338.151704 deg, Dec.: 11.730807 deg (Johnston et al. 1995, AJ, 110, 880).

  9. Analysis of Genetic Variability among thirty accessions of Andean Lupin (Lupinus mutabilis Sweet using ISSR molecular markers

    Directory of Open Access Journals (Sweden)

    Michelle C. Chirinos-Arias

    2015-03-01

    Full Text Available In order to make the genetic variability analysis among thirty accessions of andean lupine (L. mutabilis Sweet belonging to Agrarian Innovation National Institute (INIA Seed Bank. DNA was extracted from 300 plants and we made bulks. We standardized amplification protocol of Inter Simple Sequence Repeat (ISSR primers, we chose the most polymorphic primers to run in acrylamide gel. We found 255 ISSR loci with 8 primers. It was found high genetic variability of the samples under study by ISSR markers. Also observed relatively high polymorphism for autogamous species such as andean lupine. Finally phenograms showed a relationship with the geographical location, possibly due to in situ gene flow due to the exchange or sale of seeds in markets near the collection area.

  10. Behavior Genetics and the Within-Person Variability of Daily Interpersonal Styles: The Heritability of Flux, Spin and Pulse.

    Science.gov (United States)

    Markey, Patrick M; Racine, Sarah E; Markey, Charlotte N; Hopwood, Christopher J; Keel, Pamela K; Burt, S Alexandra; Neale, Michael C; Sisk, Cheryl L; Boker, Steven M; Klump, Kelly L

    2014-04-01

    A classical twin study was used to estimate the magnitude of genetic and environmental influences on four measurements of within-person variability: dominance flux, warmth flux, spin and pulse. Flux refers to the variability of an individual's interpersonal dominance and warmth. Spin measures changes in the tone of interpersonal styles and pulse measures changes in the intensity of interpersonal styles. Daily reports of interpersonal styles were collected from 494 same-sex female twins (142 monozygotic pairs and 105 dizygotic pairs) over 45 days. For dominance flux, warmth flux, and spin, genetic effects accounted for a larger proportion of variance (37%, 24%, and 30%, respectively) than shared environmental effects (14%, 13%, 0%, respectively), with the remaining variance due to the non-shared environment (62%, 50%, 70% respectively). Pulse appeared to be primarily influenced by the non-shared environment, although conclusions about the contribution of familial influences were difficult to draw from this study.

  11. Genetic variability of an unusual apomictic triploid cactus--Haageocereus tenuis Ritter--from the Coast of Central Peru.

    Science.gov (United States)

    Arakaki, Mónica; Speranza, Pablo; Soltis, Pamela S; Soltis, Douglas E

    2013-01-01

    Haageocereus tenuis is a prostrate cactus restricted to a small area of 2 km(2) near the city of Lima, Peru. The species is triploid and propagates mainly through stem fragmentation. In addition, propagation via agamospermy is documented and adventitious embryony is also inferred as a mechanism. Although seedling recruitment has not been observed in nature, we have shown that asexually produced seeds are viable. About 45 adult individuals, plus 9 individuals obtained from seeds, were sampled and 5 microsatellite markers were used to assess genetic variability. Microsatellite analysis confirms that individuals from the only existing population are genetically identical and that the population likely represents a single clone. The absence of mutations in any individual, even in highly variable microsatellite loci, may indicate that the species is also of recent origin. Other prostrate species of Haageocereus are suspected to be occasional apomicts. This phenomenon has significant implications for the evolutionary biology and ecology of Haageocereus and other clonal Cactaceae.

  12. Genetics

    Science.gov (United States)

    ... Inheritance; Heterozygous; Inheritance patterns; Heredity and disease; Heritable; Genetic markers ... The chromosomes are made up of strands of genetic information called DNA. Each chromosome contains sections of ...

  13. [Macrogeographic genetic variability in the gastropod mollusk Littorina sitkana from the northwest Pacific].

    Science.gov (United States)

    Zaslavskaya, N I; Pudovkin, A I

    2005-03-01

    Variation at four highly polymorphic allozyme loci (inorganic pyrophosphatase, peptidase, and two esterase loci) was examined in 25 settlements of the marine snail Littorina sitkana (Mollusca, Gastropoda). The sampling localities covered a wide part of the species range: from the Peter the Great Bay (the Sea of Japan) at the southwest to the Mednyi Island (Commander Islands) at the northeast. Like other littorines lacking the pelagic stage, L. sitkana was characterized by significant genetic differentiation (G(ST) for the pooled sample was 0.310). Cluster analysis and nonmetric multidimensional scaling conducted on a matrix of pairwise genetic distances between all of the settlements studied revealed four genetically different groups: southern Primorye, northern Prymorye, Sakhalin, and Kuril-Commanders. The population-genetic structure of the L. sitkana settlements is close to that described by the isolation-by-distance and stepping-stone models: the geographic and the genetic distances between the most settlements examined are distinctly correlated.

  14. GENOTYPIC VARIABILITY, HERITABILITY AND GENETIC ADVANCE IN ETHIOPIAN MUSTARD (BRASSICA CARINATA A.BRAUN. GENOTYPES AT NORTHWESTERN ETHIOPIA

    Directory of Open Access Journals (Sweden)

    Tesfaye W. Mekonnen

    2015-07-01

    Full Text Available The assessment of genetic variability is fundamental for the purpose of to identify the most important traits in Ethiopian mustard breeding program. The objective of the study was to estimate variability, heritability and genetic advance on thirty six morphological characters of Ethiopian mustard (Brassica carinata genotypes were evaluated Adet Agricultural Research Center, Ethiopia. The experiment was laid out in simple lattice design. ANOVA of the experiment showed highly significant (p<0.01 for Day of maturity, grain filling period, number of pod per plot, secondary branches  per plant, harvest index, seed yield per plot, seed yield per hectare and oil content. Significant differences (p<0.01 were noted for day of flowering, plant height, primary branch per plant, biomass per plot, oil yield per plot. High phenotypic coefficient of variation (PCV was recorded for days to flowering, grain filling period, plant height, secondary branches per plant, harvest index, oil yield per plot, seed yield per plot and hectare. The magnitudes of PCV and genotypic coefficient of variation (GCV were high for grain filling period, plant height and secondary branches per plant. Heritability estimates were high for days to maturity, grain-filling period, days to flowering, plant height, biomass per plot, secondary branches per plant, primary branches per plant, oil content and oil yield per plot. High heritability was coupled with high genetic advance as percent of mean for plant height, grain filling period, secondary branches per plant were recorded. The study showed that there are variation in the extent of genetic variability, heritability and genetic advance in traits under study which can facilitate selection for further improvement of important traits of Ethiopian mustard.

  15. Patterns of Genetic Variability in Island Populations of the Cane Toad (Rhinella marina) from the Mouth of the Amazon

    Science.gov (United States)

    Bessa-Silva, Adam Rick; Vallinoto, Marcelo; Sodré, Davidson; da Cunha, Divino Bruno; Hadad, Dante; Asp, Nils Edvin; Sampaio, Iracilda; Schneider, Horacio; Sequeira, Fernando

    2016-01-01

    The Amazonian coast has several unique geological characteristics resulting from the interaction between drainage pattern of the Amazon River and the Atlantic Ocean. It is one of the most extensive and sedimentologically dynamic regions of the world, with a large number of continental islands mostly formed less than 10,000 years ago. The natural distribution of the cane toad (Rhinella marina), one of the world’s most successful invasive species, in this complex Amazonian system provides an intriguing model for the investigation of the effects of isolation or the combined effects of isolation and habitat dynamic changes on patterns of genetic variability and population differentiation. We used nine fast-evolving microsatellite loci to contrast patterns of genetic variability in six coastal (three mainlands and three islands) populations of the cane toad near the mouth of the Amazon River. Results from Bayesian multilocus clustering approach and Discriminant Analyses of Principal Component were congruent in showing that each island population was genetically differentiated from the mainland populations. All FST values obtained from all pairwise comparisons were significant, ranging from 0.048 to 0.186. Estimates of both recent and historical gene flow were not significantly different from zero across all population pairs, except the two mainland populations inhabiting continuous habitats. Patterns of population differentiation, with a high level of population substructure and absence/restricted gene flow, suggested that island populations of R. marina are likely isolated since the Holocene sea-level rise. However, considering the similar levels of genetic variability found in both island and mainland populations, it is reliable to assume that they were also isolated for longer periods. Given the genetic uniqueness of each cane toad population, together with the high natural vulnerability of the coastal regions and intense human pressures, we suggest that these

  16. Population structure and genetic variability in the Murrah dairy breed of water buffalo in Brazil accessed via pedigree analysis.

    Science.gov (United States)

    Malhado, Carlos Henrique Mendes; Malhado, Ana Claudia Mendes; Carneiro, Paulo Luiz Souza; Ramos, Alcides Amorim; Ambrosini, Diego Pagung; Pala, Akin

    2012-12-01

    The objective of this study was to use pedigree analysis to evaluate the population structure and genetic variability in the Murrah dairy breed of water buffalo (Bubalus bubalis) in Brazil. Pedigree analysis was performed on 5,061 animals born between 1972 and 2002. The effective number of founders (fe) was 60, representing 6.32 % of the potential number of founders. The effective number of ancestors (fa) was 36 and the genetic contribution of the 17 most influent ancestors explained 50 % of the genetic variability in the population. The ratio fe/fa (effective number of founders/effective number of ancestors), which expresses the effect of population bottlenecks, was 1.66. Completeness level for the whole pedigree was 76.8, 49.2, 27.7, and 12.8 % for, respectively, the first, second, third, and fourth known parental generations. The average inbreeding values for the whole analyzed pedigree and for inbreed animals were, respectively, 1.28 and 7.64 %. The average relatedness coefficient between individuals of the population was estimated to be 2.05 %-the highest individual coefficient was 10.31 %. The actual inbreeding and average relatedness coefficient are probably higher than estimated due to low levels of pedigree completeness. Moreover, the inbreeding coefficient increased with the addition of each generation to the pedigree, indicating that incomplete pedigrees tend to underestimate the level of inbreeding. Introduction of new sires with the lowest possible average relatedness coefficient and the use of appropriate mating strategies are recommended to keep inbreeding at acceptable levels and increase the genetic variability in this economically important species, which has relatively low numbers compared to other commercial cattle breeds. The inclusion of additional parameters, such as effective number of founders, effective number of ancestors, and fe/fa ratio, provides better resolution as compared to the inclusion of inbreeding coefficient and may help

  17. The Murmur of the Sleeping Black Hole: Detection of Nuclear Ultraviolet Variability in LINER Galaxies

    CERN Document Server

    Maoz, D; Falcke, H; Wilson, A S; Maoz, Dan; Nagar, Neil M.; Falcke, Heino; Wilson, Andrew S.

    2005-01-01

    LINER nuclei, which are present in many nearby galactic bulges, may be the manifestation of low-rate or low-radiative-efficiency accretion onto supermassive central black holes. However, it has been unclear whether the compact UV nuclear sources present in many LINERs are clusters of massive stars, rather than being directly related to the accretion process. We have used HST to monitor the UV variability of a sample of 17 galaxies with LINER nuclei and compact nuclear UV sources. Fifteen of the 17 galaxies were observed more than once, with two to five epochs per galaxy, spanning up to a year. We detect significant variability in most of the sample, with peak-to-peak amplitudes from a few percent to 50%. In most cases, correlated variations are seen in two independent bands (F250W and F330W). Comparison to previous UV measurements indicates, for many objects, long-term variations by factors of a few over decade timescales. Variability is detected in LINERs with and without detected compact radio cores, in LIN...

  18. Epigenetic-genetic chromosome dosage approach for fetal trisomy 21 detection using an autosomal genetic reference marker.

    Directory of Open Access Journals (Sweden)

    Yu K Tong

    Full Text Available BACKGROUND: The putative promoter of the holocarboxylase synthetase (HLCS gene on chromosome 21 is hypermethylated in placental tissues and could be detected as a fetal-specific DNA marker in maternal plasma. Detection of fetal trisomy 21 (T21 has been demonstrated by an epigenetic-genetic chromosome dosage approach where the amount of hypermethylated HLCS in maternal plasma is normalized using a fetal genetic marker on the Y chromosome as a chromosome dosage reference marker. We explore if this method can be applied on both male and female fetuses with the use of a paternally-inherited fetal single nucleotide polymorphism (SNP allele on a reference chromosome for chromosome dosage normalization. METHODOLOGY: We quantified hypermethylated HLCS molecules using methylation-sensitive restriction endonuclease digestion followed by real-time or digital PCR analyses. For chromosome dosage analysis, we compared the amount of digestion-resistant HLCS to that of a SNP allele (rs6636, a C/G SNP that the fetus has inherited from the father but absent in the pregnant mother. PRINCIPAL FINDINGS: Using a fetal-specific SNP allele on a reference chromosome, we analyzed 20 euploid and nine T21 placental tissue samples. All samples with the fetal-specific C allele were correctly classified. One sample from each of the euploid and T21 groups were misclassified when the fetal-specific G allele was used as the reference marker. We then analyzed 33 euploid and 14 T21 maternal plasma samples. All but one sample from each of the euploid and T21 groups were correctly classified using the fetal-specific C allele, while correct classification was achieved for all samples using the fetal-specific G allele as the reference marker. CONCLUSIONS: As a proof-of-concept study, we have demonstrated that the epigenetic-genetic chromosome dosage approach can be applied to the prenatal diagnosis of trisomy 21 for both male and female fetuses.

  19. Genetic variability studies for yield and its component traits in RIL population of blackgram (Vigna mungo (L. Hepper

    Directory of Open Access Journals (Sweden)

    Sowmini.K and Jayamani. P

    2013-03-01

    Full Text Available Blackgram or Urdbean, being a fourth important pulse crop in India has low genetic variability, low harvest index and nosignificant improvement in its productivity till date. An inter sub specific mapping population was developed by crossingVBN(Bg 5 x Vigna mungo var. silvestris 22/10 by single seed decent method. The genetic variability parameters werestudied in a RIL (Recombinant Inbred Line population consisting of 193 lines and their parents. The higher estimates ofPCV were observed for all the traits when compared with GCV. However, GCV was found to be high for the traits singleplant yield, number of clusters per plant and number of pods per plant. High heritability per cent was observed for days tomaturity, number of seeds per pod and hundred seed weight. High genetic advance as per cent of mean was observed forplant height, number of clusters per plant, number of pods per plant, single plant yield and hundred seed weight. Highheritability coupled with high genetic advance as per cent of mean was observed for hundred seed weight. Transgressivesegregants were observed for all the traits. These could be used further for yield testing apart from utilizing it as prebreeding material. The mapping population could be used for mapping of genes for important traits.

  20. Genetic variability of the pattern of night melatonin blood levels in relation to coat changes development in rabbits.

    Science.gov (United States)

    Allain, Daniel; Malpaux, Benoit; Puechal, François; Thébault, René Gérard; De Rochambeau, Hubert; Chemineau, Philippe

    2004-01-01

    To assess the genetic variability in both the nocturnal increase pattern of melatonin concentration and photoresponsiveness in coat changes, an experiment on 422 Rex rabbits (from 23 males) raised under a constant light programme from birth was performed. The animals were sampled at 12 weeks of age, according to 4 periods over a year. Blood samples were taken 7 times during the dark phase and up to 1 h after the lighting began. Maturity of the fur was assessed at pelting. Heritability estimates of blood melatonin concentration (0.42, 0.17 and 0.11 at mid-night, 13 and 15 h after lights-out respectively) and strong genetic correlations between fur maturity and melatonin levels at the end of the dark phase (-0.64) indicates that (i) the variability of the nocturnal pattern of melatonin levels is under genetic control and (ii) the duration of the nocturnal melatonin increase is a genetic component of photoresponsiveness in coat changes.

  1. Genetic variability of the pattern of night melatonin blood levels in relation to coat changes development in rabbits

    Directory of Open Access Journals (Sweden)

    Chemineau Philippe

    2004-03-01

    Full Text Available Abstract To assess the genetic variability in both the nocturnal increase pattern of melatonin concentration and photoresponsiveness in coat changes, an experiment on 422 Rex rabbits (from 23 males raised under a constant light programme from birth was performed. The animals were sampled at 12 weeks of age, according to 4 periods over a year. Blood samples were taken 7 times during the dark phase and up to 1 h after the lighting began. Maturity of the fur was assessed at pelting. Heritability estimates of blood melatonin concentration (0.42, 0.17 and 0.11 at mid-night, 13 and 15 h after lights-out respectively and strong genetic correlations between fur maturity and melatonin levels at the end of the dark phase (-0.64 indicates that (i the variability of the nocturnal pattern of melatonin levels is under genetic control and (ii the duration of the nocturnal melatonin increase is a genetic component of photoresponsiveness in coat changes.

  2. Detection of Genetically Modified Maize in Processed Foods Sold Commercially in Iran by Qualitative PCR

    Science.gov (United States)

    Rabiei, Maryam; Mehdizadeh, Mehrangiz; Rastegar, Hossein; Vahidi, Hossein; Alebouyeh, Mahmoud

    2013-01-01

    Detection of genetically modified organisms (GMOs) in food is an important issue for all the subjects involved in food control and customer’s right. Due to the increasing number of GMOs imported to Iran during the past few years, it has become necessary to screen the products in order to determine the identity of the consumed daily foodstuffs. In this study, following the extraction of genomic DNA from processed foods sold commercially in Iran, qualitative PCR was performed to detect genetically modified maize. The recombinant DNA target sequences were detected with primers highly specific for each investigated transgene such as CaMV35s gene, Bt-11, MON810 and Bt-176 separately. Based on the gel electrophoresis results, Bt- 11 and MON810 events were detected in some maize samples, while, in none of them Bt- 176 modified gene was detected. For the first time, the results demonstrate the presence of genetically modified maize in Iranian food products, reinforcing the need for the development of labeling system and valid quantitative methods in routine analyses. PMID:24250568

  3. Comparison of Bayesian clustering and edge detection methods for inferring boundaries in landscape genetics

    Science.gov (United States)

    Safner, T.; Miller, M.P.; McRae, B.H.; Fortin, M.-J.; Manel, S.

    2011-01-01

    Recently, techniques available for identifying clusters of individuals or boundaries between clusters using genetic data from natural populations have expanded rapidly. Consequently, there is a need to evaluate these different techniques. We used spatially-explicit simulation models to compare three spatial Bayesian clustering programs and two edge detection methods. Spatially-structured populations were simulated where a continuous population was subdivided by barriers. We evaluated the ability of each method to correctly identify boundary locations while varying: (i) time after divergence, (ii) strength of isolation by distance, (iii) level of genetic diversity, and (iv) amount of gene flow across barriers. To further evaluate the methods' effectiveness to detect genetic clusters in natural populations, we used previously published data on North American pumas and a European shrub. Our results show that with simulated and empirical data, the Bayesian spatial clustering algorithms outperformed direct edge detection methods. All methods incorrectly detected boundaries in the presence of strong patterns of isolation by distance. Based on this finding, we support the application of Bayesian spatial clustering algorithms for boundary detection in empirical datasets, with necessary tests for the influence of isolation by distance. ?? 2011 by the authors; licensee MDPI, Basel, Switzerland.

  4. Simultaneous Detection of Genetically Modified Organisms in a Mixture by Multiplex PCR-Chip Capillary Electrophoresis.

    Science.gov (United States)

    Patwardhan, Supriya; Dasari, Srikanth; Bhagavatula, Krishna; Mueller, Steffen; Deepak, Saligrama Adavigowda; Ghosh, Sudip; Basak, Sanjay

    2015-01-01

    An efficient PCR-based method to trace genetically modified food and feed products is in demand due to regulatory requirements and contaminant issues in India. However, post-PCR detection with conventional methods has limited sensitivity in amplicon separation that is crucial in multiplexing. The study aimed to develop a sensitive post-PCR detection method by using PCR-chip capillary electrophoresis (PCR-CCE) to detect and identify specific genetically modified organisms in their genomic DNA mixture by targeting event-specific nucleotide sequences. Using the PCR-CCE approach, novel multiplex methods were developed to detect MON531 cotton, EH 92-527-1 potato, Bt176 maize, GT73 canola, or GA21 maize simultaneously when their genomic DNAs in mixtures were amplified using their primer mixture. The repeatability RSD (RSDr) of the peak migration time was 0.06 and 3.88% for the MON531 and Bt176, respectively. The RSD (RSDR) of the Cry1Ac peak ranged from 0.12 to 0.40% in multiplex methods. The method was sensitive in resolving amplicon of size difference up to 4 bp. The PCR-CCE method is suitable to detect multiple genetically modified events in a composite DNA sample by tagging their event specific sequences.

  5. High genetic variability in endophytic fungi from the genus Diaporthe isolated from common bean (Phaseolus vulgaris L.) in Brazil.

    Science.gov (United States)

    Dos Santos, T T; de Souza Leite, T; de Queiroz, C B; de Araújo, E F; Pereira, O L; de Queiroz, M V

    2016-02-01

    The goals of the present study were to identify, to analyse the phylogenetic relations and to evaluate the genetic variability in Diaporthe endophytic isolates from common bean. Diaporthe sp., D. infecunda and D. phaseolorum strains were identified using multilocus phylogeny (rDNA ITS region; EF1-α, β-tubulin, and calmodulin genes). IRAP (Inter-Retrotransposon Amplified Polymorphism) and REMAP (Retrotransposon-Microsatellite Amplified Polymorphism) molecular markers reveal the existence of high genetic variability, especially among D. infecunda isolates. It was concluded that the multilocus phylogenetic approach was more effective than individual analysis of ITS sequences, in identifying the isolates to species level, and that IRAP and REMAP markers can be used for studying the genetic variability in the genus Diaporthe particularly at the intraspecific level. The combined use of molecular tools such as multilocus phylogenetic approach and molecular markers, as performed in this study, is the best way to distinguish endophytic strains of Diaporthe isolated from common bean (Phaseolus vulgaris L.). © 2015 The Society for Applied Microbiology.

  6. Differential detection of genetic Loci underlying stem and root lignin content in Populus.

    Directory of Open Access Journals (Sweden)

    Tongming Yin

    Full Text Available In this study, we established a comprehensive genetic map with a large number of progeny from a three-generation hybrid Populus intercross, and phenotyped the lignin content, S/G ratio and 28 cell wall subcomponents both in stems and roots for the mapping individuals. Phenotypic analysis revealed that lignin content and syringyl-to-guaiacyl (S/G ratio using pyrolysis molecular beam mass spectroscopy (pyMBMS varied among mapping individuals. Phenotypic analysis revealed that stem lignin content is significantly higher than that in root and the quantified traits can be classified into four distinct groups, with strong correlations observed among components within organs. Altogether, 179 coordinating QTLs were detected, and they were co-localized into 49 genetic loci, 27 of which appear to be pleiotropic. Many of the detected genetic loci were detected differentially in stem and root. This is the first report of separate genetic loci controlling cell wall phenotypes above and below ground. These results suggest that it may be possible to modify lignin content and composition via breed and/or engineer as a means of simultaneously improving Populus for cellulosic ethanol production and carbon sequestration.

  7. Efficient detection of citrus fruits in the tree canopy under variable illumination conditions

    Science.gov (United States)

    Lu, Jun; Sang, Nong

    2013-10-01

    This paper focuses on the detection of citrus fruits in the tree canopy under variable illumination and different degree occlusion. We applied a novel segmentation method to detect the visible parts of fruits by fusing the segmentation results of chromatic aberration map, normalized RGB model, and illumination map. This fusion method can detect the highlights, shadows and diffuse zones of fruit targets. The 3-D surface topography of the visible parts of fruits were recovered by the classical algorithm of shade from shading, the fruit targets were recovered by sphere fitting using these point cloud data, and the valid ones were chosen out by validity check. The results showed that the occlusion zones of targets were effectively recovered under various light conditions integrally using the proposed method.

  8. An information-gain approach to detecting three-way epistatic interactions in genetic association studies

    DEFF Research Database (Denmark)

    Hu, Ting; Chen, Yuanzhu; Kiralis, Jeff W;

    2013-01-01

    Background Epistasis has been historically used to describe the phenomenon that the effect of a given gene on a phenotype can be dependent on one or more other genes, and is an essential element for understanding the association between genetic and phenotypic variations. Quantifying epistasis....... In the tuberculosis data, we found a statistically significant pure three-way epistatic interaction effect that was stronger than any lower-order associations. Conclusion Our study provides a methodological basis for detecting and characterizing high-order gene-gene interactions in genetic association studies....

  9. Graph-based and statistical approaches for detecting spectrally variable target materials

    Science.gov (United States)

    Ziemann, Amanda K.; Theiler, James

    2016-05-01

    In discriminating target materials from background clutter in hyperspectral imagery, one must contend with variability in both. Most algorithms focus on the clutter variability, but for some materials there is considerable variability in the spectral signatures of the target. This is especially the case for solid target materials, whose signatures depend on morphological properties (particle size, packing density, etc.) that are rarely known a priori. In this paper, we investigate detection algorithms that explicitly take into account the diversity of signatures for a given target. In particular, we investigate variable target detectors when applied to new representations of the hyperspectral data: a manifold learning based approach, and a residual based approach. The graph theory and manifold learning based approach incorporates multiple spectral signatures of the target material of interest; this is built upon previous work that used a single target spectrum. In this approach, we first build an adaptive nearest neighbors (ANN) graph on the data and target spectra, and use a biased locally linear embedding (LLE) transformation to perform nonlinear dimensionality reduction. This biased transformation results in a lower-dimensional representation of the data that better separates the targets from the background. The residual approach uses an annulus based computation to represent each pixel after an estimate of the local background is removed, which suppresses local backgrounds and emphasizes the target-containing pixels. We will show detection results in the original spectral space, the dimensionality-reduced space, and the residual space, all using subspace detectors: ranked spectral angle mapper (rSAM), subspace adaptive matched filter (ssAMF), and subspace adaptive cosine/coherence estimator (ssACE). Results of this exploratory study will be shown on a ground-truthed hyperspectral image with variable target spectra and both full and mixed pixel targets.

  10. Genetic variability and structure of jaguar (Panthera onca) in Mexican zoos.

    Science.gov (United States)

    Rueda-Zozaya, Pilar; Mendoza-Martínez, Germán D; Martínez-Gómez, Daniel; Monroy-Vilchis, Octavio; Godoy, José Antonio; Sunny, Armando; Palomares, Francisco; Chávez, Cuauhtémoc; Herrera-Haro, José

    2016-02-01

    Genealogical records of animals (studbook) are created to avoid reproduction between closely related individuals, which could cause inbreeding, particularly for such endangered species as the Panthera onca (Linnaeus, 1758). Jaguar is the largest felid in the Americas and is considered an important ecological key species. In Mexico, wild jaguar populations have been significantly reduced in recent decades, and population decline typically accompany decreases in genetic variation. There is no current census of captive jaguars in Mexico, and zoos do not follow a standardized protocol in breeding programs based on genetic studies. Here, we emphasise the importance of maintaining an adequate level of genetic variation and propose the implementation of standardised studbooks for jaguars in Mexico, mainly to avoid inbreeding. In addition, achieving the aims of studbook registration would provide a population genetic characterisation that could serve as a basis for ex situ conservation programmes.

  11. Characterization of Genetic Variability and Population Structure of the Tick Amblyomma aureolatum (Acari: Ixodidae).

    Science.gov (United States)

    Ogrzewalska, Maria; Schwarcz, Kaiser; Bajay, Miklos M; Bajay, Stephanie K; Pinheiro, José B; Zucchi, Maria I; Pinter, Adriano; Labruna, Marcelo B

    2016-07-01

    The hard tick Amblyomma aureolatum (Pallas) is a vector of the bacterium Rickettsia rickettsii, the etiologic agent of Brazilian spotted fever (BSF) in parts of Brazil. Despite its wide distribution in southeastern South America and its public health importance, there is no information about genetic variation of this species that might help to understand the epidemiology of BSF. Using data from eight microsatellite markers and ticks from six localities, we used a population genetics approach to test the hypothesis that tick populations from areas with the presence of R. rickettsii are genetically different from ticks from areas without R. rickettsii Contrary to expectations, we found low genetic structure between studied regions. Thus, the presence of R. rickettsii in the specific area is more likely correlated with ecological and the environmental conditions or due to unknown gene coding regions of A. aureolatum genome that would be related to R. rickettsii infection resistance.

  12. Genetic variability and population structure of Plasmodium falciparum parasite populations from different malaria ecological regions of Kenya.

    Science.gov (United States)

    Ingasia, Luicer A; Cheruiyot, Jelagat; Okoth, Sheila Akinyi; Andagalu, Ben; Kamau, Edwin

    2016-04-01

    Transmission intensity, movement of human and vector hosts, biogeographical features, and malaria control measures are some of the important factors that determine Plasmodium falciparum parasite genetic variability and population structure. Kenya has different malaria ecologies which might require different disease intervention methods. Refined parasite population genetic studies are critical for informing malaria control and elimination strategies. This study describes the genetic diversity and population structure of P. falciparum parasites from the different malaria ecological zones in Kenya. Twelve multi-locus microsatellite (MS) loci previously described were genotyped in 225 P. falciparum isolates collected between 2012 and 2013 from five sites; three in lowland endemic regions (Kisumu, Kombewa, and Malindi) and two in highland, epidemic regions (Kisii and Kericho). Parasites from the lowland endemic and highland epidemic regions of western Kenya had high genetic diversity compared to coastal lowland endemic region of Kenya [Malindi]. The Kenyan parasites had a mean genetic differentiation index (FST) of 0.072 (p=0.011). The multi-locus genetic analysis of the 12 MS revealed all the parasites had unique haplotypes. Significant linkage disequilibrium (LD) was observed in all the five parasite populations. Kisumu had the most significant index of association values (0.16; pmalaria has been on the decline. The presence of significant LD suggests that there is occurrence of inbreeding in the parasite population. Parasite populations from Kisii showed the strongest evidence for epidemic population structure whereas the rest of the regions showed panmixia. Defining the genetic diversity of the parasites in different ecological regions of Kenya after introduction of the artemether-lumefantrine is important in refining the spread of drug resistant strains and malaria transmission for more effective control and eventual elimination of malaria in Kenya. Copyright

  13. Cryptosporidium,Giardia, Cryptococcus, Pneumocystis genetic variability: cryptic biological species or clonal near-clades?

    OpenAIRE

    2014-01-01

    An abundant literature dealing with the population genetics and taxonomy of Giardia duodenalis, Cryptosporidium spp., Pneumocystis spp., and Cryptococcus spp., pathogens of high medical and veterinary relevance, has been produced in recent years. We have analyzed these data in the light of new population genetic concepts dealing with predominant clonal evolution (PCE) recently proposed by us. In spite of the considerable phylogenetic diversity that exists among these pathogens, we have found ...

  14. An electrochemiluminescence non-PCR method for the detection of genetically modified organisms

    Science.gov (United States)

    Liu, Jinfeng; Xing, Da; Zhu, Debin

    2006-09-01

    An electrochemiluminescence non-PCR method has been developed for the detection of genetically modified organisms (GMOs) in crops. Genomic DNA of GMOs was digested with two restriction endonucleases (FOK I and BsrD I), and hybridized with three Ru(bpy) 3 2+ (TBR)-labeled and one biotinylated probes. The hybridization products were captured onto streptavidin-coated paramagnetic beads, and detected by measuring the electrochemiluminescence (ECL) signal of the TBR label. Whether the tobaccos contain GM components was discriminated by detecting the ECL signal of CaMV35S promoter. The experiment results show that the detection limit for CaMV35S promoter is 100 fmol, and the GM components can be clearly identified in GM tobaccos. The ECL non-PCR method will provide a new means in GMOs detection due to its safety, simplicity and high efficiency.

  15. Statistical power to detect genetic (covariance of complex traits using SNP data in unrelated samples.

    Directory of Open Access Journals (Sweden)

    Peter M Visscher

    2014-04-01

    Full Text Available We have recently developed analysis methods (GREML to estimate the genetic variance of a complex trait/disease and the genetic correlation between two complex traits/diseases using genome-wide single nucleotide polymorphism (SNP data in unrelated individuals. Here we use analytical derivations and simulations to quantify the sampling variance of the estimate of the proportion of phenotypic variance captured by all SNPs for quantitative traits and case-control studies. We also derive the approximate sampling variance of the estimate of a genetic correlation in a bivariate analysis, when two complex traits are either measured on the same or different individuals. We show that the sampling variance is inversely proportional to the number of pairwise contrasts in the analysis and to the variance in SNP-derived genetic relationships. For bivariate analysis, the sampling variance of the genetic correlation additionally depends on the harmonic mean of the proportion of variance explained by the SNPs for the two traits and the genetic correlation between the traits, and depends on the phenotypic correlation when the traits are measured on the same individuals. We provide an online tool for calculating the power of detecting genetic (covariation using genome-wide SNP data. The new theory and online tool will be helpful to plan experimental designs to estimate the missing heritability that has not yet been fully revealed through genome-wide association studies, and to estimate the genetic overlap between complex traits (diseases in particular when the traits (diseases are not measured on the same samples.

  16. The genetic variability of the Podolica cattle breed from the Gargano area. Preliminary results

    Directory of Open Access Journals (Sweden)

    Dario Cianci

    2010-01-01

    Full Text Available The Podolica cattle breed is autochthonous of Southern Italy and denoted by its particular rusticity. This study presents the preliminary results of the genetic characterization of the Podolica breed using DNA STR markers. A total of 20 microsatellite loci were analysed in 79 individuals reared in the Gargano area. Number of polymorphisms, allele fre- quencies, deviations from Hardy-Weinberg proportions, linkage disequilibrium between loci and genetic similarities between animals were calculated. The results showed a high deficiency of heterozygotes, the observed mean of het- erozygosis being 0.449, whereas the expected mean was 0.766. Many markers showed also deviations from the Hardy- Weinberg proportions and significant linkage disequilibrium between loci. However the genetic similarity within the pop- ulation was low (0.281 and the average number of alleles per locus was high (10, representing a high genetic vari- ability. In order to explain these results, a stratification of the breed in sub-populations with a high interior genetic homo- geneity but markedly differentiated one from each other could be hypothesized; this situation probably derived from non- random mating within each herd (consanguinity and from the lack of exchange of genetic material between the herds. A further study is needed on a wider sample and extending the analysis to FAO-ISAG microsatellite panel in order to con- firm this hypothesis. This could eventually provide the information necessary for the correct management of the repro- ductive schemes and for genomic traceability of meat production.

  17. Genetic variability of Appaloosa horses: a study of a closed breeding population from Argentina

    Directory of Open Access Journals (Sweden)

    Claudia Malena CORBI-BOTTO,Sebastian Andres SADABA,Elina Ines FRANCISCO,Paula Belen KALEMKERIAN,Juan Pedro LIRON,Egle Etel VILLEGAS-CASTAGNASSO,Guillermo GIOVAMBATTISTA,Pilar PERAL-GARCIA,Silvina DIAZ

    2014-09-01

    Full Text Available The genetic diversity and structure of 72 Appaloosa horses belonging to a closed breeding population from an ecological reserve in Buenos Aires, Argentina, was investigated using eight microsatellite markers from the International Society for Animal Genetics panel. Our data showed that this Appaloosa horse population had an elevated degree of genetic diversity (He= 0.746 and did not present a significant increase of homozygous individuals (FIS~0. However, the short tandem repeats, AHT5, ASB2, HTG10 and VHL20, were not in Hardy–Weinberg equilibrium (P-value<0.05. Genetic relationships between this population and other well known horse breeds showed that Appaloosa horses from Argentina could have had their origin in the horses of the Nez Perce's people in Idaho while other Appaloosa horses may have had influences from Andalusian and Lusitano breeds. This closed breeding population conserves an important degree of Appaloosa genetic diversity and notwithstanding its particular breeding characteristics, represents a valuable genetic resource for conservation.

  18. Evaluation of genetic variability in micropropagated propagules of ornamental pineapple [Ananas comosus var. bracteatus (Lindley) Coppens and Leal] using RAPD markers.

    Science.gov (United States)

    Santos, M D M; Buso, G C S; Torres, A C

    2008-10-21

    The objective of the present study was to evaluate the genetic variability in micropropagated plantlets of ornamental pineapple, after the fourth period of subculture. The basal culture medium consisted of MS salts, vitamins, 3% sucrose, liquid formulation, supplemented with 6-benzylaminopurine (BAP) at concentrations of 0.125, 0.25, 0.5, 1.0, and 2.0 mg/L. The addition of BAP influenced the occurrence of genetic variation revealed using random amplified polymorphic DNA (RAPD) markers. Of a total of 520 primers tested, 44 were selected and amplified; 402 monomorphic bands (97.2%) and 18 polymorphic bands (2.8%) resulted among regenerated plantlets. The polymorphic fragments were produced by 12 primers (OPA-01, OPA-20, OPB-01, OPB-19, OPC-19, OPF-13, OPL-17, OPM-13, OPP-16, OPT-07, OPV-19, and OPX-03). Among the primers that identified polymorphism, OPA-01, OPA-20, OPB-19, OPC-19, OPL-17, OPP-16, and OPX-3 each showed, one polymorphic band and OPF-13 amplified a maximum of three bands. In this study, the RAPD technique was effective in showing the occurrence of somaclonal variations that occur during the micropropagation process of ornamental pineapple cultivation in BAP-supplemented medium, and it is possible to detect the presence of genetic variation in early stages of plant development.

  19. APPLICATION OF GENETIC DEAFNESS GENE CHIP FOR DETECTION OF GENE MUTATION OF DEAFNESS IN PREGNANT WOMEN

    Institute of Scientific and Technical Information of China (English)

    CHANG Liang; ZHONG Su; ZHAO Nan; LIU Ping; ZHAO Yangyu; QIAO Jie

    2014-01-01

    Objective The study is to identify the carrier rate of common deafness mutation in Chinese pregnant women via detecting deafness gene mutations with gene chip. Methods The pregnant women in obstetric clinic without hearing impairment and hearing disorders family history were selected. The informed consent was signed. Peripheral blood was taken to extract genom-ic DNA. Application of genetic deafness gene chip for detecting 9 mutational hot spot of the most common 4 Chinese deafness genes, namely GJB2 (35delG,176del16bp, 235delC, 299delAT), GJB3 (C538T) ,SLC26A4 ( IVS72A>G, A2168G) and mito-chondrial DNA 12S rRNA (A1555G, C1494T) . Further genetic testing were provided to the spouses and newborns of the screened carriers. Results Peripheral blood of 430 pregnant women were detected,detection of deafness gene mutation carri-ers in 24 cases(4.2%), including 13 cases of the GJB2 heterozygous mutation, 3 cases of SLC26A4 heterozygous mutation, 1 cases of GJB3 heterozygous mutation, and 1 case of mitochondrial 12S rRNA mutation. 18 spouses and 17 newborns took fur-ther genetic tests, and 6 newborns inherited the mutation from their mother. Conclusion The common deafness genes muta-tion has a high carrier rate in pregnant women group,235delC and IVS7-2A>G heterozygous mutations are common.

  20. Molecular detection and genetic diversity of Babesia gibsoni in dogs in Bangladesh.

    Science.gov (United States)

    Terao, Masashi; Akter, Shirin; Yasin, Md Golam; Nakao, Ryo; Kato, Hirotomo; Alam, Mohammad Zahangir; Katakura, Ken

    2015-04-01

    Babesia gibsoni is a tick-borne hemoprotozoan parasite of dogs that often causes fever and hemolytic illness. Detection of B. gibsoni has been predominantly reported in Asian countries, including Japan, Korea, Taiwan, Malaysia, Bangladesh and India. The present study shows the first molecular characterization of B. gibsoni detected from dogs in Bangladesh. Blood samples were collected on FTA® Elute cards from 50 stray dogs in Mymensingh District in Bangladesh. DNA eluted from the cards was subjected to nested PCR for the 18S rRNA gene of Babesia species. Approximately 800bp PCR products were detected in 15 of 50 dogs (30%). Based on restriction fragment length polymorphism (RFLP) and direct sequencing of the PCR products, all parasite isolates were identified as B. gibsoni. Furthermore, the BgTRAP (B. gibsoni thrombospondin-related adhesive protein) gene fragments were detected in 13 of 15 18S rRNA gene PCR positive blood samples. Phylogenetic analysis of the BgTRAP gene revealed that B. gibsoni parasites in Bangladesh formed a cluster, which was genetically different from other Asian B. gibsoni isolates. In addition, tandem repeat analysis of the BgTRAP gene clearly showed considerable genetic variation among Bangladeshi isolates. These results suggested that B. gibsoni parasites in a different genetic clade are endemic in dogs in Bangladesh. Further studies are required to elucidate the origin, distribution, vector and pathogenesis of B. gibsoni parasites circulating in dogs in Bangladesh.

  1. The value of small habitat islands for the conservation of genetic variability in a steppe grass species

    Science.gov (United States)

    Wódkiewicz, Maciej; Dembicz, Iwona; Moysiyenko, Ivan I.

    2016-10-01

    The habitat loss and fragmentation due to agricultural land-conversion affected the steppe throughout its range. In Ukraine, 95% of steppe was destroyed in the last two centuries. Remaining populations are confined to few refuges, like nature reserves, loess ravines, and kurgans (small burial mounds), the latter being often subject to destruction by archeological excavations. Stipa capillata L. is a typical grass species of Eurasian steppes and extrazonal dry grasslands, that was previously used as a model species in studies on steppe ecology. The aim of our research was to assess genetic diversity of S. capillata populations within different types of steppe refuges (loess ravines, biosphere reserve, kurgan) and to evaluate the value of the latter group for the preservation of genetic diversity in the study species. We assessed genetic diversity of 266 individuals from 15 populations (nine from kurgans, three from loess ravines and three from Askania-Nova Biosphere Reserve) with eight Universal Rice Primers (URPs). Studied populations showed high intra-population variability (I: 0.262-0.419, PPB: 52.08-82.64%). Populations from kurgans showed higher genetic differentiation (ΦST = 0.247) than those from loess ravines (ΦST = 0.120) and the biosphere reserve (ΦST = 0.142). Although the diversity metrics were to a small extent lower for populations from kurgans than from larger refugia we conclude that all studied populations of the species still preserve high genetic variability and are valuable for protection. To what extent this pattern holds true under continuous fragmentation in the future must be carefully monitored.

  2. Deriving estimates of individual variability in genetic potentials of performance traits for 3 dairy breeds, using a model of lifetime nutrient partitioning

    DEFF Research Database (Denmark)

    Phuong, H N; Martin, O; de Boer, I J M;

    2015-01-01

    , body reserve usage, and growth for different genotypes of cow. Moreover, it can be used to separate genetic variability in performance between individual cows from environmental noise. The model enables simulation of the effects of a genetic selection strategy on lifetime efficiency of individual cows......, which has a main advantage of including the rearing costs, and thus, can be used to explore the impact of future selection on animal performance and efficiency.......This study explored the ability of an existing lifetime nutrient partitioning model for simulating individual variability in genetic potentials of dairy cows. Generally, the model assumes a universal trajectory of dynamic partitioning of priority between life functions and genetic scaling...

  3. Defect occurrence, detection, location and characterization; essential variables of the LBB concept application to primary piping

    Energy Technology Data Exchange (ETDEWEB)

    Crutzen, S.; Koble, T.D.; Lemaitre, P. [and others

    1997-04-01

    Applications of the Leak Before Break (LBB) concept involve the knowledge of flaw presence and characteristics. In Service Inspection is given the responsibility of detecting flaws of a determined importance to locate them precisely and to classify them in broad families. Often LBB concepts application imply the knowledge of flaw characteristics such as through wall depth; length at the inner diameter (ID) or outer diameter (OD) surface; orientation or tilt and skew angles; branching; surface roughness; opening or width; crack tip aspect. Besides detection and characterization, LBB evaluations consider important the fact that a crack could be in the weld material or in the base material or in the heat affected zone. Cracks in tee junctions, in homogenous simple welds and in elbows are not considered in the same way. Essential variables of a flaw or defect are illustrated, and examples of flaws found in primary piping as reported by plant operators or service vendors are given. If such flaw variables are important in the applications of LBB concepts, essential is then the knowledge of the performance achievable by NDE techniques, during an ISI, in detecting such flaws, in locating them and in correctly evaluating their characteristics.

  4. A study of soil moisture variability for landmine detection by the neutron technique

    Directory of Open Access Journals (Sweden)

    Avdić Senada

    2007-01-01

    Full Text Available This paper is focused on the space and temporal variability of soil moisture experimental data acquired at a few locations near landmine fields in the Tuzla Canton, as well as on the quantification of the statistical nature of soil moisture data on a small spatial scale. Measurements of soil water content at the surface were performed by an electro-magnetic sensor over 1 25, and 100 m2 grids, at intervals of 0.2, 0.5, and 1 m, respectively. The sampling of soil moisture at different spatial resolutions and over different grid sizes has been investigated in order to achieve the quantification of the statistical nature of soil moisture distribution. The statistical characterization of spatial variability was performed through variogram and correlogram analysis of measurement results. The temporal variability of the said samples was examined over a two-season period. For both sampling periods, the spatial correlation length is about 1 to 2 m, respectively, or less. Thus, sampling should be done on a larger spatial scale, in order to capture the variability of the investigated areas. Since the characteristics of many landmine sensors depend on soil moisture, the results of this study could form a useful data base for multisensor landmine detection systems with a promising performance.

  5. Linear variable filter optimization for emergency response chemical detection and discrimination

    Science.gov (United States)

    Shen, Sylvia S.; Lewis, Paul E.

    2010-08-01

    Linear variable filter design and fabrication for LWIR is now commercially available for use in the development of remote sensing systems. The linear variable filter is attached directly to the cold shield of the focal plane array. The resulting compact spectrometer assemblies are completely contained in the Dewar system. This approach eliminates many of the wavelength calibration problems associated with current prism and grating systems and also facilitates the cost effective design and fabrication of aerial sensing systems for specific applications. This paper describes a study that was conducted with the following three objectives: 1) Determine if a multi-channel linear-variable-filter-based line scanner system can be used to discriminate a set of chemical vapors that represent a high probability of occurrence during a typical emergency response chemical incident; 2) Determine which multi-channel linear variable filter design is optimal; and 3) Determine the acceptable instrument noise equivalent spectral radiance for this application. A companion paper describes a separate study that was conducted to determine the concentration levels at which detection and discrimination can be achieved for the various chemicals based on the optimal filter design under various degrees of imperfect atmospheric correction.

  6. Duplex microfluidic SERS detection of pathogen antigens with nanoyeast single-chain variable fragments.

    Science.gov (United States)

    Wang, Yuling; Rauf, Sakandar; Grewal, Yadveer S; Spadafora, Lauren J; Shiddiky, Muhammad J A; Cangelosi, Gerard A; Schlücker, Sebastian; Trau, Matt

    2014-10-07

    Quantitative and accurate detection of multiple biomarkers would allow for the rapid diagnosis and treatment of diseases induced by pathogens. Monoclonal antibodies are standard affinity reagents applied for biomarkers detection; however, their production is expensive and labor-intensive. Herein, we report on newly developed nanoyeast single-chain variable fragments (NYscFv) as an attractive alternative to monoclonal antibodies, which offers the unique advantage of a cost-effective production, stability in solution, and target-specificity. By combination of surface-enhanced Raman scattering (SERS) microspectroscopy using glass-coated, highly purified SERS nanoparticle clusters as labels, with a microfluidic device comprising multiple channels, a robust platform for the sensitive duplex detection of pathogen antigens has been developed. Highly sensitive detection for individual Entamoeba histolytica antigen EHI_115350 (limit of detection = 1 pg/mL, corresponding to 58.8 fM) and EHI_182030 (10 pg/mL, corresponding 453 fM) with high specificity has been achieved, employing the newly developed corresponding NYscFv as probe in combination with SERS microspectroscopy at a single laser excitation wavelength. Our first report on SERS-based immunoassays using the novel NYscFv affinity reagent demonstrates the flexibility of NYscFv fragments as viable alternatives to monoclonal antibodies in a range of bioassay platforms and paves the way for further applications.

  7. Compact Radio Sources in Orion: New Detections, Time Variability, and Objects in OMC-1S

    CERN Document Server

    Zapata, L A; Kurtz, S E; O'Dell, C R; Zapata, Luis A.; Rodriguez, Luis F.; Kurtz, Stanley E.

    2004-01-01

    We present the analysis of four 3.6 cm radio continuum archival observations of Orion obtained using the Very Large Array in its A-configuration, with $0\\rlap.{''}3$ angular resolution. The observations were made during the period 1994-1997. In a region of $4' \\times 4'$, we detect a total of 77 compact radio sources. Of the total of detected sources, 54 are detected in one or more of the individual observations and 36 of these show time variability (by more than 30%) between the observed epochs. A deep image made from averaging all data shows an additional 23 faint sources, in the range of 0.1 to 0.3 mJy. Of the total of 77 sources, 39 are new centimeter detections. However, only 9 of the 77 sources do not have a previously reported counterpart at near-infrared, optical, or X-ray wavelengths. In particular, we detect three faint sources in the OMC-1S region that may be related to the sources that power the multiple outflows that emanate from this part of the Orion nebula. %We discuss the nature of these sour...

  8. SNP interaction detection with Random Forests in high-dimensional genetic data

    Directory of Open Access Journals (Sweden)

    Winham Stacey J

    2012-07-01

    Full Text Available Abstract Background Identifying variants associated with complex human traits in high-dimensional data is a central goal of genome-wide association studies. However, complicated etiologies such as gene-gene interactions are ignored by the univariate analysis usually applied in these studies. Random Forests (RF are a popular data-mining technique that can accommodate a large number of predictor variables and allow for complex models with interactions. RF analysis produces measures of variable importance that can be used to rank the predictor variables. Thus, single nucleotide polymorphism (SNP analysis using RFs is gaining popularity as a potential filter approach that considers interactions in high-dimensional data. However, the impact of data dimensionality on the power of RF to identify interactions has not been thoroughly explored. We investigate the ability of rankings from variable importance measures to detect gene-gene interaction effects and their potential effectiveness as filters compared to p-values from univariate logistic regression, particularly as the data becomes increasingly high-dimensional. Results RF effectively identifies interactions in low dimensional data. As the total number of predictor variables increases, probability of detection declines more rapidly for interacting SNPs than for non-interacting SNPs, indicating that in high-dimensional data the RF variable importance measures are capturing marginal effects rather than capturing the effects of interactions. Conclusions While RF remains a promising data-mining technique that extends univariate methods to condition on multiple variables simultaneously, RF variable importance measures fail to detect interaction effects in high-dimensional data in the absence of a strong marginal component, and therefore may not be useful as a filter technique that allows for interaction effects in genome-wide data.

  9. Genetic variability and population structure of Salvia lachnostachys: implications for breeding and conservation programs.

    Science.gov (United States)

    Erbano, Marianna; Schühli, Guilherme Schnell E; Santos, Élide Pereira Dos

    2015-04-08

    The genetic diversity and population structure of Salvia lachnostachys Benth were assessed. Inter Simple Sequence Repeat (ISSR) molecular markers were used to investigate the restricted distribution of S. lachnostachys in Parana State, Brazil. Leaves of 73 individuals representing three populations were collected. DNA was extracted and submitted to PCR-ISSR amplification with nine tested primers. Genetic diversity parameters were evaluated. Our analysis indicated 95.6% polymorphic loci (stress value 0.02) with a 0.79 average Simpson's index. The Nei-Li distance dendrogram and principal component analysis largely recovered the geographical origin of each sample. Four major clusters were recognized representing each collected population. Nei's gene diversity and Shannon's information index were 0.25 and 0.40 respectively. As is typical for outcrossing herbs, the majority of genetic variation occurred at the population level (81.76%). A high gene flow (Nm = 2.48) was observed with a correspondingly low fixation index. These values were generally similar to previous studies on congeneric species. The results of principal coordinate analysis (PCA) and of arithmetic average (UPGMA) were consistent and all three populations appear distinct as in STRUCTURE analysis. In addition, this analysis indicated a majority intrapopulation genetic variation. Despite the human pressure on natural populations our study found high levels of genetic diversity for S. lachnostachys. This was the first molecular assessment for this endemic species with medicinal proprieties and the results can guide for subsequent bioprospection, breeding programs or conservation actions.

  10. Genetic variability of the common Snook Centropomus undecimalis (Perciformes: Centropomidae) in connected marine and riverine environments.

    Science.gov (United States)

    Hernández-Vidal, Ulises; Lesher-Gordillo, Julia; Contreras-Sánchez, Wilfrido M; Chiappa-Carrara, Xavier

    2014-06-01

    The Common Snook, Centropomus undecimalis, inhabits riverine and marine areas of Southern Gulf of Mexico, where it is subject to intense use and exploitation. It has been reported that the genetic identification of fish stocks constitutes a valuable tool for wild population management; nevertheless, there is no available information on the genetic identification on fish stocks of this species in the region. The aim of this study was to determine the genetic relationship between C. undecimalis captured in marine and freshwater environments of the Gulf of Mexico and the San Pedro River. For this, muscle tissue samples of 79 specimens were obtained from areas located more than 300km apart. The genotype of each individual was determined using seven microsatellite primer pairs. Five primers amplified efficiently presenting between six and 28 alleles per locus. High levels of heterozygosis were observed in samples from both environments. Deviation from HWE due to an excess of heterozygotes was observed. The values of genetic difference indicate an absence of population structure (F(ST) = 0.0075 and R(ST) = (0.016, p = 0.051) and similarity in the allele frequencies, defined by Nei's index (0.805). Data showed the existence of a high gene flow due to the number of migrants (Nm = 18.7). Our results suggest that individuals living in these environments belong to the same genetic population. We suggest the development of management and protection plans for this fish species population in the wild.

  11. Genetic variability of the Bracco Italiano dog breed based on microsatellite polimorphysm

    Directory of Open Access Journals (Sweden)

    Silvano Presciuttini

    2011-10-01

    Full Text Available The Bracco Italiano is one of the oldest breeds of Italian pointing dogs, used for hunting ever since Renaissance times. After the Second World War it was included among the breeds officially recorded by the ENCI (the Italian Cynological Club, and since 1970 more than 23,000 animals have been registered; there are currently approximately 750 births per year. In this paper, we present the breed characterization of the population at the molecular level using 21 STR markers from the panels recommended for the 2006, 2008 and 2010 ISAG canine comparison test. Number of alleles, allele frequencies, deviations from Hardy-Weinberg proportions, linkage disequilibrium among loci, genetic similarity, genetic distances and molecular co-ancestry-based parameters were calculated. The number of alleles ranged from 3 to 9 (mean 6.43 whereas the expected heterozygosity ranged from 0.44 to 0.81 (mean 0.64. There was a high genetic similarity within the whole population (0.455 showing the great homogeneity of the sampled animals, as confirmed also by the small kinship distance (0.336, by the high values of the self molecular coancestry (0.703 and of the inbreeding coefficient (0.406. These results suggest the need for a careful genetic management of the population in order to avoid the risk of an excessive increase in the inbreeding level which would result in significant inbreeding depression and in significant loss of genetic variation.

  12. Evaluation of terrestrial microcosms for detection, fate, and survival analysis of genetically engineered microorganisms and their recombinant genetic material

    Energy Technology Data Exchange (ETDEWEB)

    Fredrickson, J.K.; Seidler, R.J.

    1989-02-01

    The research included in this document represents the current scientific information available regarding the applicability of terrestrial microcosms and related methodologies for evaluating detection methods and the fate and survival of microorganisms in the environment. The three terrestrial microcosms described in this document were used to evaluate the survival and fate of recombinant bacteria in soils and in association with plant surfaces and insects and their transport through soil with percolating water and root systems, and to test new methods and procedures to improve detection and enumeration of bacteria in soil. Simple (potting soil composed of peat mix and perlite, lacking environmental control and monitoring) and complex microcosms (agricultural soil with partial control and monitoring of environmental conditions) were demonstrated to be useful tools for preliminary assessments of microbial viability in terrestrial ecosystems. These studies evaluated the survival patterns of Enterobacter cloacae (pBR322) in soil and on plant surfaces and the ingestion of this same microorganism by cutworms and survival in the foregut and frass. The Versacore microcosm design was used to monitor the fate and competitiveness of genetically engineered bacteria in soil. Both selective media and gene probes were used successfully to follow the fate of two recombinant Pseudomonas sp. introduced into Versacore microcosms. Intact soil-core microcosms were employed to evaluate the fate and transport of genetically altered Azospirillum sp. and Pseudomonas sp. in soil and the plant rhizosphere. The usefulness of these various microcosms as a tool for risk assessment is underscored by the ease in obtaining soil from a proposed field release site to evaluate subsequent GEM fate and survival.

  13. Measuring local genetic variability in populations of codling moth (Lepidoptera: Tortricidae) across an unmanaged and commercial orchard interface.

    Science.gov (United States)

    Fuentes-Contreras, Eduardo; Basoalto, Esteban; Franck, Pierre; Lavandero, Blas; Knight, Alan L; Ramírez, Claudio C

    2014-04-01

    The genetic structure of adult codling moth, Cydia pomonella (L.), populations was characterized both inside a managed apple, Malus domestica Borkdhausen, orchard and in surrounding unmanaged hosts and nonhost trees in central Chile during 2006-2007. Adult males were collected using an array of sex pheromone-baited traps. Five microsatellite genetic markers were used to study the population genetic structure across both spatial (1-100 ha) and temporal (generations within a season) gradients. Analysis of molecular variance (AMOVA) found a significant, but weak, association in both the spatial and temporal genetic structures. Discriminant analysis also found significant differentiation between the first and second generation for traps located either inside or outside the managed orchard. The Bayesian assignment test detected three genetic clusters during each of the two generations, which corresponded to different areas within the unmanaged and managed apple orchard interface. The lack of a strong spatial structure at a local scale was hypothesized to be because of active adult movement between the managed and unmanaged hosts and the asymmetry in the insecticide selection pressure inside and outside the managed habitats. These data highlight the importance of developing area-wide management programs that incorporate management tactics effective at the landscape level for successful codling moth control.

  14. Microsatellite variation reveals high levels of genetic variability and population structure in the gorgonian coral Pseudopterogorgia elisabethae across the Bahamas.

    Science.gov (United States)

    Gutierrez-Rodriguez, Carla; Lasker, Howard R

    2004-08-01

    The primary mechanism of gene flow in marine sessile invertebrates is larval dispersal. In Pseudopterogorgia elisabethae, a commercially important Caribbean gorgonian coral, a proportion of the larvae drop to the substratum within close proximity to the maternal colony, and most matings occur between individuals in close proximity to each other. Such limited dispersal of reproductive propagules suggests that gene flow is limited in this gorgonian. In this study, we characterized the population genetic structure of P. elisabethae across the Bahamas using six microsatellite loci. P. elisabethae was collected from 18 sites across the Bahamas. Significant deviations from Hardy-Weinberg equilibrium due to deficits of heterozygotes within populations were detected for all 18 populations in at least one of the six screened loci. Levels of genetic structure among populations of P. elisabethae were high and significant. A distance analysis placed populations within three groups, one formed by populations located within Exuma Sound, a semi-isolated basin, another consisting of populations located outside the basin and a third group comprising two populations from San Salvador Island. The patterns of genetic variation found in this study are concordant with the life-history traits of the species and in part with the geography of the Bahamas. Conservation and management plans developed for P. elisabethae should considered the high degree of genetic structure observed among populations of the species, as well as the high genetic diversity found in the San Salvador and the Exuma Sound populations. Copyright 2004 Blackwell Publishing Ltd

  15. Detection vs. selection: integration of genetic, epigenetic and environmental cues in fluctuating environments.

    Science.gov (United States)

    McNamara, John M; Dall, Sasha R X; Hammerstein, Peter; Leimar, Olof

    2016-10-01

    There are many inputs during development that influence an organism's fit to current or upcoming environments. These include genetic effects, transgenerational epigenetic influences, environmental cues and developmental noise, which are rarely investigated in the same formal framework. We study an analytically tractable evolutionary model, in which cues are integrated to determine mature phenotypes in fluctuating environments. Environmental cues received during development and by the mother as an adult act as detection-based (individually observed) cues. The mother's phenotype and a quantitative genetic effect act as selection-based cues (they correlate with environmental states after selection). We specify when such cues are complementary and tend to be used together, and when using the most informative cue will predominate. Thus, we extend recent analyses of the evolutionary implications of subsets of these effects by providing a general diagnosis of the conditions under which detection and selection-based influences on development are likely to evolve and coexist.

  16. Genetic variability and resistance of cultivars of cowpea [Vigna unguiculata (L.) Walp] to cowpea weevil (Callosobruchus maculatus Fabr.).

    Science.gov (United States)

    Vila Nova, M X; Leite, N G A; Houllou, L M; Medeiros, L V; Lira Neto, A C; Hsie, B S; Borges-Paluch, L R; Santos, B S; Araujo, C S F; Rocha, A A; Costa, A F

    2014-03-31

    The cowpea weevil (Callosobruchus maculatus Fabr.) is the most destructive pest of the cowpea bean; it reduces seed quality. To control this pest, resistance testing combined with genetic analysis using molecular markers has been widely applied in research. Among the markers that show reliable results, the inter-simple sequence repeats (ISSRs) (microsatellites) are noteworthy. This study was performed to evaluate the resistance of 27 cultivars of cowpea bean to cowpea weevil. We tested the resistance related to the genetic variability of these cultivars using ISSR markers. To analyze the resistance of cultivars to weevil, a completely randomized test design with 4 replicates and 27 treatments was adopted. Five pairs of the insect were placed in 30 grains per replicate. Analysis of variance showed that the number of eggs and emerged insects were significantly different in the treatments, and the means were compared by statistical tests. The analysis of the large genetic variability in all cultivars resulted in the formation of different groups. The test of resistance showed that the cultivar Inhuma was the most sensitive to both number of eggs and number of emerged adults, while the TE96-290-12-G and MNC99-537-F4 (BRS Tumucumaque) cultivars were the least sensitive to the number of eggs and the number of emerged insects, respectively.

  17. Estimating breast tomosynthesis performance in detection tasks with variable-background phantoms

    Science.gov (United States)

    Young, Stefano; Park, Subok; Anderson, S. Kyle; Badano, Aldo; Myers, Kyle J.; Bakic, Predrag

    2009-02-01

    Digital breast tomosynthesis (DBT) shows potential for improving breast cancer detection. However, this technique has not yet been fully characterized with consideration of the various uncertainties in the imaging chain and optimized with respect to system acquisition parameters. To obtain maximum diagnostic information in DBT, system optimization needs to be performed across a range of patients and acquisition parameters to quantify their impact on tumor detection performance. In addition, a balance must be achieved between x-ray dose and image quality to minimize risk to the patient while maximizing the system's detection performance. To date, researchers have applied a task-based approach to the optimization of DBT with use of mathematical observers for tasks in the signal-known-exactly background-known-exactly (SKE/BKE) and signal-known-exactly background-known statistically (SKE/BKS) paradigms1-3. However, previous observer models provided insufficient treatment of the spatial correlations between multi-angle DBT projections, so we incorporated this correlation information into the modeling methodology. We developed a computational approach that includes three-dimensional variable background phantoms for incorporating background variability, accurate ray-tracing and Poisson distributions for generating noise-free and noisy projections of the phantoms, and a channelized-Hotelling observer4 (CHO) for estimating performance in DBT. We demonstrated our method for a DBT acquisition geometry and calculated the performance of the CHO with Laguerre-Gauss channels as a function of the angular span of the system. Preliminary results indicate that the implementation of a CHO model that incorporates correlations between multi-angle projections gives different performance predictions than a CHO model that ignores multi-angle correlations. With improvement of the observer design, we anticipate more accurate investigations into the impact of multi-angle correlations and

  18. Genetic variability of woolly aphid (Adelges laricis Vall.) resistance in European larch (Larix decidua Mill.)

    Energy Technology Data Exchange (ETDEWEB)

    Blada, I. [Forest Research Inst., Bucharest (Romania)

    1995-12-31

    One hundred and eleven clones of European larch were exposed to the woolly aphid and then outplanted in three locations using a randomized complete block design. At ages 11 and 19 years resistance was measured on 102 clones at 2 locations. Highly significant genetic differences were observed among the clones at both locations and at both ages. Highly significant clone x location, clone x location x age interactions were also observed. Differences between the most resistant and most susceptible clones was 483%. Sufficient genetic variation for a breeding program was present. Broad-sense heritability estimates for Adelges resistance varied by location. Significant age to age, location to location and age to location phenotypic correlation for resistance were found. Larch resistance seems to be under polygenic control. A substantial genetic gain could be achieved by selecting the best clones and using vegetative propagation, including somaclonal embryogenesis, for multiplication. 23 refs, 2 figs, 8 tabs

  19. Study of genetic variability in Vitis vinifera L. germplasm by high-throughput Vitis18kSNP array: the case of Georgian genetic resources.

    Science.gov (United States)

    De Lorenzis, Gabriella; Chipashvili, Ramaz; Failla, Osvaldo; Maghradze, David

    2015-06-23

    Georgia, in the Caucasian region, is considered the first domestication centre of grapevine. This country is characterized by high morphological variability of cultivated (Vitis vinifera L. subsp. sativa (DC.) Hegi) and wild (Vitis vinifera L. subsp. sylvestris (Gmel.) Hegi) compartments. The main objective of this study was to investigate the level of genetic diversity obtained by the novel custom Vitis18kSNP array, in order to analyse 71 grapevine accessions representative of wild and cultivated Georgian germplasms. The number of loci successfully amplified was 15,317 out of 18,775 SNP and 79 % of loci resulted polymorphic. Sixty-eight unique profiles were identified, 42 for the sativa and 26 for the sylvestris compartment. Cluster analysis highlighted two main groups, one for cultivars and another for wild individuals, while a genetic structure according to accession taxonomic status and cultivar geographical origin was revealed by multivariate analysis, differentiating clearly the genotypes into 3 main groups, two groups including cultivars and one for wild individuals, even though a considerable overlapping area was observed. Pattern of genetic diversity structure presented an additional proof that grapevine domestication events took place in the Caucasian region contributing to the crop evolution. Our results demonstrated a moderate differentiation between sativa and sylvestris compartments, even though a connection between several samples of both subspecies may be assumed for the occurrence of cross hybridization events among native wild populations and the cultivated accessions. Nevertheless, first degree relationships have not been discovered between wild and cultivated individuals.

  20. Genetic variability of pain perception and treatment--clinical pharmacological implications.

    Science.gov (United States)

    Lötsch, Jörn

    2011-06-01

    Evidence of a genetic control of pain has led to efforts to exploit genotyping information from pain patients for the development of analgesics and for the selection of pharmacological approaches to pain. Research on translating the genetic bases of familial insensitivity to pain has contributed to the discovery of crucial molecular pathways of pain and to the identification of new analgesic targets (e.g., the Na(v)1.7 sodium channel, neurotrophic tyrosine kinase receptors, nerve growth factor). Moreover, human genetic variants leading to enhanced or reduced function of specific molecular pathways are employed as substitutes for the lack of modulator molecules usable in humans, enabling nociceptive or anti-nociceptive pathways in humans to be studied before drug development. Translational approaches have also been used to verify the importance of experimentally discovered pain pathways in humans, such as GTP cyclohydrolase 1 and the potassium channel K(v)9.1. In addition to these uses of genetics as a research tool, an individualized pharmacological therapy based on the patient's genotype has been attempted. In terms of analgesics in clinical use, such an approach is at the present time only marginally available. For future analgesic targeting, for example, Na(v)1.7 or TRPA1, the genotype may be the target of a selective cure for syndromes caused by increased-function mutations in the coding genes. The consideration of human genetics in drug studies may accelerate analgesic drug development while reducing cost because the clinical success may be partly anticipated by including information of functional genetic variants that mimic the action of future analgesics. These developments show that genotyping information obtained from studies on pain patients plays a role in the clinical pharmacology of pain.

  1. Genetic variability of attachment (G and Fusion (F protein genes of human metapneumovirus strains circulating during 2006-2009 in Kolkata, Eastern India

    Directory of Open Access Journals (Sweden)

    Chawla-Sarkar Mamta

    2011-02-01

    Full Text Available Abstract Background Human metapneumovirus (hMPV is associated with the acute respiratory tract infection (ARTI in all the age groups. However, there is limited information on prevalence and genetic diversity of human metapneumovirus (hMPV strains circulating in India. Objective To study prevalence and genomic diversity of hMPV strains among ARTI patients reporting in outpatient departments of hospitals in Kolkata, Eastern India. Methods Nasal and/or throat swabs from 2309 patients during January 2006 to December 2009, were screened for the presence of hMPV by RT-PCR of nucleocapsid (N gene. The G and F genes of representative hMPV positive samples were sequenced. Results 118 of 2309 (5.11% clinical samples were positive for hMPV. The majority (≈80% of the positive cases were detected during July−November all through the study period. Genetic analysis revealed that 77% strains belong to A2 subgroup whereas rest clustered in B1 subgroup. G sequences showed higher diversity at the nucleotide and amino acid level. In contrast, less than 10% variation was observed in F gene of representative strains of all four years. Sequence analysis also revealed changes in the position of stop codon in G protein, which resulted in variable length (217-231 aa polypeptides. Conclusion The study suggests that approximately 5% of ARTI in the region were caused by hMPV. This is the first report on the genetic variability of G and F gene of hMPV strains from India which clearly shows that the G protein of hMPV is continuously evolving. Though the study partially fulfills lacunae of information, further studies from other regions are necessary for better understanding of prevalence, epidemiology and virus evolution in Indian subcontinent.

  2. Detection and genetic characterization of a novel parvovirus distantly related to human bufavirus in domestic pigs.

    Science.gov (United States)

    Hargitai, Renáta; Pankovics, Péter; Kertész, Attila Mihály; Bíró, Hunor; Boros, Ákos; Phan, Tung Gia; Delwart, Eric; Reuter, Gábor

    2016-04-01

    In this study, a novel parvovirus (strain swine/Zsana3/2013/HUN, KT965075) was detected in domestic pigs and genetically characterized by viral metagenomics and PCR methods. The novel parvovirus was distantly related to the human bufaviruses and was detected in 19 (90.5 %) of the 21 and five (33.3 %) of the 15 faecal samples collected from animals with and without cases of posterior paraplegia of unknown etiology from five affected farms and one control farm in Hungary, respectively. Swine/Zsana3/2013/HUN is highly prevalent in domestic pigs and potentially represents a novel parvovirus species in the subfamily Parvovirinae.

  3. Fast detection of genetic information by an optimized PCR in an interchangeable chip.

    KAUST Repository

    Wu, Jinbo

    2012-02-01

    In this paper, we report the construction of a polymerase chain reaction (PCR) device for fast amplification and detection of DNA. This device consists of an interchangeable PCR chamber, a temperature control component as well as an optical detection system. The DNA amplification happens on an interchangeable chip with the volumes as low as 1.25 μl, while the heating and cooling rate was as fast as 12.7°C/second ensuring that the total time needed of only 25 min to complete the 35 cycle PCR amplification. An optimized PCR with two-temperature approach for denaturing and annealing (Td and Ta) of DNA was also formulated with the PCR chip, with which the amplification of male-specific sex determining region Y (SRY) gene marker by utilizing raw saliva was successfully achieved and the genetic identification was in-situ detected right after PCR by the optical detection system.

  4. Apparatus, System and Method for Fast Detection of Genetic Information by PCR in an Interchangeable Chip

    KAUST Repository

    Wen, Weijia

    2011-03-03

    A polymerase chain reaction (PCR) device for fast amplification and detection of DNA includes an interchangeable PCR chamber, a temperature control component, and an optical detection system. The DNA amplification is performed on an interchangeable chip with volumes as small as 1.25 µl, while the heating and cooling rate may be as fast as 12.7 °C/second ensuring that the total time needed of only 25 minutes to complete the 35 cycle PCR amplification. The PCR may be performed according to a two-temperature approach for denaturing and annealing (Td and Ta) of DNA with the PCR chip, with which the amplification of male-specific SRY gene marker by utilizing raw saliva may be achieved. The genetic identification may be in-situ detected after PCR by the optical detection system.

  5. Automated detection of lung nodules in CT images using shape-based genetic algorithm.

    Science.gov (United States)

    Dehmeshki, Jamshid; Ye, Xujiong; Lin, Xinyu; Valdivieso, Manlio; Amin, Hamdan

    2007-09-01

    A shape-based genetic algorithm template-matching (GATM) method is proposed for the detection of nodules with spherical elements. A spherical-oriented convolution-based filtering scheme is used as a pre-processing step for enhancement. To define the fitness function for GATM, a 3D geometric shape feature is calculated at each voxel and then combined into a global nodule intensity distribution. Lung nodule phantom images are used as reference images for template matching. The proposed method has been validated on a clinical dataset of 70 thoracic CT scans (involving 16,800 CT slices) that contains 178 nodules as a gold standard. A total of 160 nodules were correctly detected by the proposed method and resulted in a detection rate of about 90%, with the number of false positives at approximately 14.6/scan (0.06/slice). The high-detection performance of the method suggested promising potential for clinical applications.

  6. Role of genetic detection in peritoneal washes with gastric carcinoma: The past, present and future

    Institute of Scientific and Technical Information of China (English)

    Hyun-Dong Chae

    2016-01-01

    The most frequent cause of treatment failure following surgery for gastric cancer is peritoneal dissemination, mainly caused by the seeding of free cancer cells from the primary gastric cancer, which is the most common type of spread. Unfortunately, there is no standard modality of intraperitoneal free cancer cells detection to predict peritoneal metastasis until now. We reviewed English literature in Pub Med was done using the Me SH terms for gastric cancer, peritoneal wash, and reverse transcriptase polymerase chain reaction. All the articles were reviewed and core information was tabulated for reference. After a comprehensive review of all articles, the data was evaluated by clinical implication and predictive value of each marker for peritoneal recurrence. There are still many limitations to overcome before the genetic diagnosis for free cancer cells detection can be considered as routine assay. To make it a reliable diagnostic tool for detecting free cancer cells, the process and method of genetic detection with peritoneal washes should be standardized, and the development of simple diagnostic devices and easily available kits are necessary. Herein, we reviewed the past, present and future perspectives of the peritoneal lavage for the detection of intraperitoneal free cancer cells in patients with gastric cancer.

  7. Model studies on the detectability of genetically modified feeds in milk.

    Science.gov (United States)

    Poms, R E; Hochsteiner, W; Luger, K; Glössl, J; Foissy, H

    2003-02-01

    Detecting the use of genetically modified feeds in milk has become important, because the voluntary labeling of milk and dairy products as "GMO free" or as "organically grown" prohibits the employment of genetically modified organisms (GMOs). The aim of this work was to investigate whether a DNA transfer from foodstuffs like soya and maize was analytically detectable in cow's milk after digestion and transportation via the bloodstream of dairy cows and, thus, whether milk could report for the employment of transgene feeds. Blood, milk, urine, and feces of dairy cows were examined, and foreign DNA was detected by polymerase chain reaction by specifically amplifying a 226-bp fragment of the maize invertase gene and a 118-bp fragment of the soya lectin gene. An intravenous application of purified plant DNA showed a fast elimination of marker DNA in blood or its reduction below the detection limit. With feeding experiments, it could be demonstrated that a specific DNA transfer from feeds into milk was not detectable. Therefore, foreign DNA in milk cannot serve as an indicator for the employment of transgene feeds unless milk is directly contaminated with feed components or airborne feed particles.

  8. Automatic Mexico Gulf Oil Spill Detection from Radarsat-2 SAR Satellite Data Using Genetic Algorithm

    Science.gov (United States)

    Marghany, Maged

    2016-10-01

    In this work, a genetic algorithm is exploited for automatic detection of oil spills of small and large size. The route is achieved using arrays of RADARSAT-2 SAR ScanSAR Narrow single beam data obtained in the Gulf of Mexico. The study shows that genetic algorithm has automatically segmented the dark spot patches related to small and large oil spill pixels. This conclusion is confirmed by the receiveroperating characteristic (ROC) curve and ground data which have been documented. The ROC curve indicates that the existence of oil slick footprints can be identified with the area under the curve between the ROC curve and the no-discrimination line of 90%, which is greater than that of other surrounding environmental features. The small oil spill sizes represented 30% of the discriminated oil spill pixels in ROC curve. In conclusion, the genetic algorithm can be used as a tool for the automatic detection of oil spills of either small or large size and the ScanSAR Narrow single beam mode serves as an excellent sensor for oil spill patterns detection and surveying in the Gulf of Mexico.

  9. Molecular Detection of Bladder Cancer by Fluorescence Microsatellite Analysis and an Automated Genetic Analyzing System

    Directory of Open Access Journals (Sweden)

    Sarel Halachmi

    2007-01-01

    Full Text Available To investigate the ability of an automated fluorescent analyzing system to detect microsatellite alterations, in patients with bladder cancer. We investigated 11 with pathology proven bladder Transitional Cell Carcinoma (TCC for microsatellite alterations in blood, urine, and tumor biopsies. DNA was prepared by standard methods from blood, urine and resected tumor specimens, and was used for microsatellite analysis. After the primers were fluorescent labeled, amplification of the DNA was performed with PCR. The PCR products were placed into the automated genetic analyser (ABI Prism 310, Perkin Elmer, USA and were subjected to fluorescent scanning with argon ion laser beams. The fluorescent signal intensity measured by the genetic analyzer measured the product size in terms of base pairs. We found loss of heterozygocity (LOH or microsatellite alterations (a loss or gain of nucleotides, which alter the original normal locus size in all the patients by using fluorescent microsatellite analysis and an automated analyzing system. In each case the genetic changes found in urine samples were identical to those found in the resected tumor sample. The studies demonstrated the ability to detect bladder tumor non-invasively by fluorescent microsatellite analysis of urine samples. Our study supports the worldwide trend for the search of non-invasive methods to detect bladder cancer. We have overcome major obstacles that prevented the clinical use of an experimental system. With our new tested system microsatellite analysis can be done cheaper, faster, easier and with higher scientific accuracy.

  10. Automatic Mexico Gulf Oil Spill Detection from Radarsat-2 SAR Satellite Data Using Genetic Algorithm

    Directory of Open Access Journals (Sweden)

    Marghany Maged

    2016-10-01

    Full Text Available In this work, a genetic algorithm is exploited for automatic detection of oil spills of small and large size. The route is achieved using arrays of RADARSAT-2 SAR ScanSAR Narrow single beam data obtained in the Gulf of Mexico. The study shows that genetic algorithm has automatically segmented the dark spot patches related to small and large oil spill pixels. This conclusion is confirmed by the receiver-operating characteristic (ROC curve and ground data which have been documented. The ROC curve indicates that the existence of oil slick footprints can be identified with the area under the curve between the ROC curve and the no-discrimination line of 90%, which is greater than that of other surrounding environmental features. The small oil spill sizes represented 30% of the discriminated oil spill pixels in ROC curve. In conclusion, the genetic algorithm can be used as a tool for the automatic detection of oil spills of either small or large size and the ScanSAR Narrow single beam mode serves as an excellent sensor for oil spill patterns detection and surveying in the Gulf of Mexico.

  11. Porous silicon biosensor for detection of variable domain of heavy-chain of HCAb antibody

    Institute of Scientific and Technical Information of China (English)

    ZHANG Hong-yan; Lü Xiao-yi; JIA Zhen-hong; LI Jiang-wei; ZHANG Fu-chun

    2012-01-01

    In this paper,we produce porous silicon (PSi) by electrochemical etching,and it is the first time to evaluate the performance of label-free porous silicon biosensor for detection of variable domain of heavy chain of heavy-chain antibody (VHH).The binding of hen egg white lysozyme (HEWL) and VHH causes a red shift in the reflection spectrum of the biosensor.The red shift is proportional to the VHH concentration in the range from 14 μg · ml-1 to 30μg·ml-1 with a detection limit of 0.648 ng ·ml-1.The research is useful for the development of label-free biosensor applied in the rapid and sensitive determination of small molecules.

  12. Exploring the role of genetic variability and lifestyle in oxidative stress response for healthy aging and longevity.

    Science.gov (United States)

    Dato, Serena; Crocco, Paolina; D'Aquila, Patrizia; de Rango, Francesco; Bellizzi, Dina; Rose, Giuseppina; Passarino, Giuseppe

    2013-08-08

    Oxidative stress is both the cause and consequence of impaired functional homeostasis characterizing human aging. The worsening efficiency of stress response with age represents a health risk and leads to the onset and accrual of major age-related diseases. In contrast, centenarians seem to have evolved conservative stress response mechanisms, probably derived from a combination of a diet rich in natural antioxidants, an active lifestyle and a favorable genetic background, particularly rich in genetic variants able to counteract the stress overload at the level of both nuclear and mitochondrial DNA. The integration of these factors could allow centenarians to maintain moderate levels of free radicals that exert beneficial signaling and modulator effects on cellular metabolism. Considering the hot debate on the efficacy of antioxidant supplementation in promoting healthy aging, in this review we gathered the existing information regarding genetic variability and lifestyle factors which potentially modulate the stress response at old age. Evidence reported here suggests that the integration of lifestyle factors (moderate physical activity and healthy nutrition) and genetic background could shift the balance in favor of the antioxidant cellular machinery by activating appropriate defense mechanisms in response to exceeding external and internal stress levels, and thus possibly achieving the prospect of living a longer life.

  13. Effects of reconstruction filter and input parameter variability on object detectability in CT imaging

    Science.gov (United States)

    Boedeker, Kirsten L.

    The purpose of this work is to investigate and quantify the effects of technical parameter variability and reconstruction algorithm on image quality and object detectability. To accomplish this, metrics of both noise and signal to noise ratio (SNR) are explored and then applied in object detection tasks using a computer aided diagnosis (CAD) system. The noise power spectrum (NPS) is investigated as a noise metric in that it describes both the magnitude of noise and the spatial characteristics of noise that are introduced by the reconstruction algorithm. The NPS was found to be much more robust than the conventional standard deviation metric. The noise equivalent quanta (NEQ) is also studied as a tool for comparing effects of acquisition parameters (esp. mAs) on noise and, as NEQ is not influenced by reconstruction filter or other post-processing, its utility for comparison across different techniques and manufacturers is demonstrated. The Ideal Bayesian Observer (IBO) and Non-Prewhitening Matched Filter (NPWMF) are investigated as SNR metrics under a variety of acquisition and reconstruction conditions. The signal and noise processes of image formation were studied individually, which allowed for analysis of their separate effects on the overall SNR. The SNR metrics were found to characterize the influence of reconstruction filter and technical parameter variability with high sensitivity. To correlate the above SNR metrics with detection, signal images were combined with noise images and passed to a CAD system. A simulated lung nodule detection task was performed on a series of objects of increasing contrast. The average minimum contrast detected and corresponding IBO and NPWMF SNR values were recorded over 100 trials for each reconstruction filter and technical parameter condition studied. Among the trends discovered, it was found that detectability scales with SNR as mAs is varied. Furthermore, the CAD system appears to under-perform when sharp algorithms are

  14. Hybrids of a Genetically Engineered Antibody and a Carbon Nanotube Transistor for Detection of Prostate Cancer Biomarkers

    CERN Document Server

    Lerner, Mitchell B; Pazina, Tatiana; Dailey, Jennifer; Goldsmith, Brett R; Robinson, Matthew K; Johnson, A T Charlie

    2013-01-01

    We developed a novel detection method for osteopontin (OPN), a new biomarker for prostate cancer, by attaching a genetically engineered single chain variable fragment (scFv) protein with high binding affinity for OPN to a carbon nanotube field-effect transistor (NTFET). Chemical functionalization using diazonium salts is used to covalently attach scFv to NT-FETs, as confirmed by atomic force microscopy, while preserving the activity of the biological binding site for OPN. Electron transport measurements indicate that functionalized NT-FET may be used to detect the binding of OPN to the complementary scFv protein. A concentration-dependent increase in the source-drain current is observed in the regime of clinical significance, with a detection limit of approximately 30 fM. The scFv-NT hybrid devices exhibit selectivity for OPN over other control proteins. These devices respond to the presence of OPN in a background of concentrated bovine serum albumin, without loss of signal. Based on these observations, the d...

  15. Contribution of VPS35 genetic variability to LBD in the Flanders-Belgian population

    NARCIS (Netherlands)

    Verstraeten, Aline; Wauters, Eline; Crosiers, David; Meeus, Bram; Corsmit, Ellen; Elinck, Ellen; Mattheijssens, Maria; Peeters, Karin; Cras, Patrick; Pickut, Barbara; Vandenberghe, Rik; Engelborghs, Sebastiaan; De Deyn, Peter Paul; Van Broeckhoven, Christine; Theuns, Jessie

    2012-01-01

    VPS35 was recently identified as a novel autosomal dominant gene for Parkinson disease. In this study, we aimed to determine the contribution of simple and complex VPS35 variations to the genetic etiology of the spectrum of Lewy body disorders (LBD) in a Flanders-Belgian patient cohort (n = 677). We

  16. Correlations among Jamaican 12th-Graders' Five Variables and Performance in Genetics

    Science.gov (United States)

    Bloomfield, Deen-Paul; Soyibo, Kola

    2008-01-01

    This study was aimed at finding out if the level of performance of selected Jamaican Grade 12 students on an achievement test on the concept of genetics was satisfactory; if there were statistically significant differences in their performance on the concept linked to their gender, self-esteem, cognitive abilities in biology, school-type and…

  17. Molecular variability and genetic relationship among Brazilian strains of the sugarcane smut fungus.

    Science.gov (United States)

    Benevenuto, Juliana; Longatto, Daniel P; Reis, Gislaine V; Mielnichuk, Natalia; Palhares, Alessandra C; Carvalho, Giselle; Saito, Suzane; Quecine, Maria C; Sanguino, Alvaro; Vieira, Maria Lucia C; Camargo, Luis Eduardo A; Creste, Silvana; Monteiro-Vitorello, Claudia B

    2016-12-01

    Sporisorium scitamineum is the fungus that causes sugarcane smut disease. Despite of the importance of sugarcane for Brazilian agribusiness and the persistence of the pathogen in most cropping areas, genetic variation studies are still missing for Brazilian isolates. In this study, sets of isolates were analyzed using two molecular markers (AFLP and telRFLP) and ITS sequencing. Twenty-two whips were collected from symptomatic plants in cultivated sugarcane fields of Brazil. A total of 41 haploid strains of compatible mating types were selected from individual teliospores and used for molecular genetic analyses. telRFLP and ITS analyses were expanded to six Argentine isolates, where the sugarcane smut was first recorded in America. Genetic relationship among strains suggests the human-mediated dispersal of S. scitamineum within the Brazilian territory and between the two neighboring countries. Two genetically distinct groups were defined by the combined analysis of AFLP and telRFLP. The opposite mating-type strains derived from single teliospores were clustered together into these main groups, but had not always identical haplotypes. telRFLP markers analyzed over two generations of selfing and controlled outcrossing confirmed the potential for emergence of new variants and occurrence of recombination, which are relevant events for evolution of virulence and environmental adaptation.

  18. Proteomic studies related to genetic determinants of variability in protein concentrations

    NARCIS (Netherlands)

    Horvatovich, Peter; Franke, Lude; Bischoff, Rainer

    2014-01-01

    Genetic variation has multiple effects on the proteome. It may influence the expression level of proteins, modify their sequences through single nucleotide polymorphisms, the occurrence of allelic variants, or alternative splicing (ASP) events. This perspective paper summarizes the major effects of

  19. Mean Platelet Volume and Arterial Stiffness – Clinical Relationship and Common Genetic Variability

    Science.gov (United States)

    Panova-Noeva, Marina; Arnold, Natalie; Hermanns, M. Iris; Prochaska, Jürgen H.; Schulz, Andreas; Spronk, Henri M.; Binder, Harald; Pfeiffer, Norbert; Beutel, Manfred; Blankenberg, Stefan; Zeller, Tanja; Lotz, Johannes; Münzel, Thomas; Lackner, Karl J.; ten Cate, Hugo; Wild, Philipp S.

    2017-01-01

    Vessel wall stiffening is an important clinical parameter, but it is unknown whether platelets, key elements in the pathogenesis of arterial thrombosis, are associated with arterial stiffness. The present studies sought to determine whether mean platelet volume (MPV), a potential marker of platelet activation, is linked to vascular elasticity as assessed by the augmentation index (AIx), in 15,010 individuals from the population-based Gutenberg Health Study. Multivariable analysis showed that MPV in both males (β 0.776; 95thCI [0.250;1.16]; p = 0.0024) and females (β 0.881[0.328;1.43]; p = 0.0018) is strongly associated with AIx. Individuals with MPV and AIx above the sex-specific medians had worse survival. Association analysis between MPV-related genetic variants and arterial stiffness identified four genetic variants in males and one in females related with AIx. Cox regression analysis for mortality identified one of these joint genetic variants close to ring finger protein 145 gene (RNF145, rs10076782) linked with increased mortality (hazard ratio 2.02; 95thCI [1.35;3.02]; p = 0.00061). Thus, these population-based data demonstrate a close relation between platelet volume as a potential marker of platelet activation and arterial stiffness in both sexes. Further research is warranted to further elucidate the mechanisms underlying larger platelets‘ role in arterial stiffening including the role of shared common genetics. PMID:28059166

  20. [Genetic variability and phylogenetic analysis of 39 short tandem repeat loci in Beijing Han population].

    Science.gov (United States)

    Xiuyan, Ruan; Weini, Wang; Yaran, Yang; Bingbing, Xie; Jing, Chen; Yacheng, Liu; Jiangwei, Yan

    2015-07-01

    In this study, we studied the genetic polymorphisms of short tandem repeat (STR) loci from 13 CODIS and 26 non-CODIS system in Beijing Han population for the first time, and established a database of 39 STR loci whose forensic parameters were further evaluated. Our results demonstrated no significant deviation from the Hardy-Weinberg equilibrium of 39 STR loci and no pairwise linkage disequilibrium between them. The power of discriminations, expected heterozygosity, polymorphic information content, and power of exclusion of 39 STR loci ranged from 0.7740-0.9818, 0.6000-0.9350, 0.5317-0.9047 and 0.2909-0.8673. The cumulated discrimination power and cumulative probability of exclusion were 0.999999999999999999999999999999999999999964971 and 0.999999999973878, respectively. Moreover, the genetic distance was calculated based on allele frequency and phylogenetic tree was built using STR loci data from Beijing Han and other 11 Chinese ethnic groups.This study provides important basic data for Chinese forensic DNA database and population genetics database, and has important significance in carrying out forensic individual identification, paternity testing, and population genetic study.

  1. Genetic variability in spotted seatrout (Cynoscion nebulosus), determined with microsatellite DNA markers

    Science.gov (United States)

    Ward, R.; Bowers, K.; Hensley, R.; Mobley, B.; Belouski, E.

    2007-01-01

    Variation in the allele frequencies of five microsatellite loci was surveyed in 1256 individual spotted seatrout (Cynoscion nebulosus) obtained from 12 bays and estuaries from Laguna Madre, Texas, to Charlotte Harbor, Florida, to St. John's River on the Florida Atlantic Coast. Texas and Louisiana collection sites were resampled each year for two to four years (1998-2001). Genetic differentiation was observed. Spotted seatrout from Florida waters were strongly differentiated from spotted seatrout collected in Louisiana and Texas. The greatest genetic discontinuity was observed between Tampa Bay and Charlotte Harbor, and Charlotte Harbor seatrout were most similar to Atlantic Coast spotted seatrout. Texas and Louisiana samples were not strongly structured within the northwestern Gulf of Mexico and there was little evidence of temporal differentiation within bays. These findings are contrary to those of earlier analyses with allozymes and mitochondrial DNA (mtDNA) where evidence of spatial differentiation was found for spotted seatrout resident on the Texas coast. The differences in genetic structure observed among these markers may reflect differences in response to selective pressure, or may be due to differences in underlying genetic processes.

  2. Variability in anthocyanin content among Abutilon theophrasti, and Urena lobata genetic resources .

    Science.gov (United States)

    Plants contain bioactive phytochemicals and nutraceuticals to be utilized in the pharmaceutical and nutraceutical markets. Sixty-two accessions of Abutilon theophrasti, Basella alba, and Urena lobata are conserved at the USDA, ARS, Plant Genetic Resources Conservation Unit, Griffin, GA. Anthocyanins...

  3. Genetic variability in apomictic mangosteen (Garcinia mangostana and its close relatives (Garcinia spp. based on ISSR markers

    Directory of Open Access Journals (Sweden)

    SOBIR

    2011-04-01

    Full Text Available Sobir, Poerwanto R, Santosa E, Sinaga S, Mansyah E (2011 Genetic variability in apomictic mangosteen (Garcinia mangostana and its close relatives (Garcinia spp. based on ISSR markers. Biodiversitas 12: 59-63. In order to reveal phylogenetic relationship of mangosteen and several close relatives (Garcinia spp., we employed seven ISSR dinucleotide primer systems on eleven close relatives of mangosteen and 28 mangosteen accessions from four islands in Indonesia (Sumatra, Java, Kalimantan and Lombok. ISSR analysis successfully amplified 43 bands on average 6.1 fragments for each primer system, and these all fragments were polymorphic. Seven close relatives of mangosteen were separated with mangosteen accessions at 0.22 level of dissimilarity, while other four including G. malaccensis, were clustered with mangosteen accessions, this results supported proposal that G. malaccensis was allopolyploid derivative of mangosteen. Clustering pattern among mangosteen accessions, however, not represented their origin, indicated that distribution of the accessions was not linked to their genetic properties.

  4. Genetic variability of Herpailurus yagouaroundi, Puma concolor and Panthera onca (Mammalia, Felidae studied using Felis catus microsatellites

    Directory of Open Access Journals (Sweden)

    Vanessa Roma Moreno

    2006-01-01

    Full Text Available We used four microsatellite loci (Fca08, Fca45, Fca77 and Fca96 from the domestic cat, Felis catus, to investigate genetic variability in specimens of Herpailurus yagouaroundi (jaguarundi, otter cat, eyra, Puma concolor (cougar, mountain lion, puma and Panthera onca (jaguar held in various Brazilian zoos. Samples of DNA from the cats were PCR amplified and then sequenced before being analyzed using the CERVUS program. Our results show a mean polymorphic information content (PIC of 0.83 for H. yagouaroundi, 0.66 for P. concolor and 0.69 for P. onca and a mean of 10.3 alleles for the Fca08 locus, 5.3 for Fca 45, 9 for Fca 77 and 14 for Fca 96. These results indicate a relatively high level of genetic diversity for the specimens studied.

  5. Blastocystis Isolates from Patients with Irritable Bowel Syndrome and from Asymptomatic Carriers Exhibit Similar Parasitological Loads, but Significantly Different Generation Times and Genetic Variability across Multiple Subtypes.

    Science.gov (United States)

    Vargas-Sanchez, Gie-Bele; Romero-Valdovinos, Mirza; Ramirez-Guerrero, Celedonio; Vargas-Hernandez, Ines; Ramirez-Miranda, Maria Elena; Martinez-Ocaña, Joel; Valadez, Alicia; Ximenez, Cecilia; Lopez-Escamilla, Eduardo; Hernandez-Campos, Maria Elena; Villalobos, Guiehdani; Martinez-Hernandez, Fernando; Maravilla, Pablo

    2015-01-01

    Blastocystis spp is a common intestinal parasite of humans and animals that has been associated to the etiology of irritable bowel syndrome (IBS); however, some studies have not found this association. Furthermore, many biological features of Blastocystis are little known. The objective of present study was to assess the generation times of Blastocystis cultures, from IBS patients and from asymptomatic carriers. A total of 100 isolates were obtained from 50 IBS patients and from 50 asymptomatic carriers. Up to 50 mg of feces from each participant were cultured in Barret's and in Pavlova's media during 48 h. Initial and final parasitological load were measured by microscopy and by quantitative PCR. Amplicons were purified, sequenced and submitted to GenBank; sequences were analysed for genetic diversity and a Bayesian inference allowed identifying genetic subtypes (ST). Generation times for Blastocystis isolates in both media, based on microscopic measures and molecular assays, were calculated. The clinical symptoms of IBS patients and distribution of Blastocystis ST 1, 2 and 3 in both groups was comparable to previous reports. Interestingly, the group of cases showed scarce mean nucleotide diversity (π) as compared to the control group (0.011±0.016 and 0.118±0.177, respectively), whilst high gene flow and small genetic differentiation indexes between different ST were found. Besides, Tajima's D test showed negative values for ST1-ST3. No statistical differences regarding parasitological load between cases and controls in both media, as searched by microscopy and by qPCR, were detected except that parasites grew faster in Barret's than in Pavlova's medium. Interestingly, slow growth of isolates recovered from cases in comparison to those of controls was observed (pBlastocystis might be easily affected by intestinal environmental changes due to IBS probably because virulent strains with slow growth may be selected, reducing their genetic variability.

  6. Blastocystis Isolates from Patients with Irritable Bowel Syndrome and from Asymptomatic Carriers Exhibit Similar Parasitological Loads, but Significantly Different Generation Times and Genetic Variability across Multiple Subtypes.

    Directory of Open Access Journals (Sweden)

    Gie-Bele Vargas-Sanchez

    Full Text Available Blastocystis spp is a common intestinal parasite of humans and animals that has been associated to the etiology of irritable bowel syndrome (IBS; however, some studies have not found this association. Furthermore, many biological features of Blastocystis are little known. The objective of present study was to assess the generation times of Blastocystis cultures, from IBS patients and from asymptomatic carriers. A total of 100 isolates were obtained from 50 IBS patients and from 50 asymptomatic carriers. Up to 50 mg of feces from each participant were cultured in Barret's and in Pavlova's media during 48 h. Initial and final parasitological load were measured by microscopy and by quantitative PCR. Amplicons were purified, sequenced and submitted to GenBank; sequences were analysed for genetic diversity and a Bayesian inference allowed identifying genetic subtypes (ST. Generation times for Blastocystis isolates in both media, based on microscopic measures and molecular assays, were calculated. The clinical symptoms of IBS patients and distribution of Blastocystis ST 1, 2 and 3 in both groups was comparable to previous reports. Interestingly, the group of cases showed scarce mean nucleotide diversity (π as compared to the control group (0.011±0.016 and 0.118±0.177, respectively, whilst high gene flow and small genetic differentiation indexes between different ST were found. Besides, Tajima's D test showed negative values for ST1-ST3. No statistical differences regarding parasitological load between cases and controls in both media, as searched by microscopy and by qPCR, were detected except that parasites grew faster in Barret's than in Pavlova's medium. Interestingly, slow growth of isolates recovered from cases in comparison to those of controls was observed (p<0.05. We propose that generation times of Blastocystis might be easily affected by intestinal environmental changes due to IBS probably because virulent strains with slow growth may be

  7. Genetic Variability and Population Structure of Salvia lachnostachys: Implications for Breeding and Conservation Programs

    Directory of Open Access Journals (Sweden)

    Marianna Erbano

    2015-04-01

    Full Text Available The genetic diversity and population structure of Salvia lachnostachys Benth were assessed. Inter Simple Sequence Repeat (ISSR molecular markers were used to investigate the restricted distribution of S. lachnostachys in Parana State, Brazil. Leaves of 73 individuals representing three populations were collected. DNA was extracted and submitted to PCR-ISSR amplification with nine tested primers. Genetic diversity parameters were evaluated. Our analysis indicated 95.6% polymorphic loci (stress value 0.02 with a 0.79 average Simpson’s index. The Nei-Li distance dendrogram and principal component analysis largely recovered the geographical origin of each sample. Four major clusters were recognized representing each collected population. Nei’s gene diversity and Shannon’s information index were 0.25 and 0.40 respectively. As is typical for outcrossing herbs, the majority of genetic variation occurred at the population level (81.76%. A high gene flow (Nm = 2.48 was observed with a correspondingly low fixation index. These values were generally similar to previous studies on congeneric species. The results of principal coordinate analysis (PCA and of arithmetic average (UPGMA were consistent and all three populations appear distinct as in STRUCTURE analysis. In addition, this analysis indicated a majority intrapopulation genetic variation. Despite the human pressure on natural populations our study found high levels of genetic diversity for S. lachnostachys. This was the first molecular assessment for this endemic species with medicinal proprieties and the results can guide for subsequent bioprospection, breeding programs or conservation actions.

  8. MODEL-ASSISTED ESTIMATION OF THE GENETIC VARIABILITY IN PHYSIOLOGICAL PARAMETERS RELATED TO TOMATO FRUIT GROWTH UNDER CONTRASTED WATER CONDITIONS

    Directory of Open Access Journals (Sweden)

    Dario Constantinescu

    2016-12-01

    Full Text Available Drought stress is a major abiotic stres threatening plant and crop productivity. In case of fleshy fruits, understanding Drought stress is a major abiotic stress threatening plant and crop productivity. In case of fleshy fruits, understanding mechanisms governing water and carbon accumulations and identifying genes, QTLs and phenotypes, that will enable trade-offs between fruit growth and quality under Water Deficit (WD condition is a crucial challenge for breeders and growers. In the present work, 117 recombinant inbred lines of a population of Solanum lycopersicum were phenotyped under control and WD conditions. Plant water status, fruit growth and composition were measured and data were used to calibrate a process-based model describing water and carbon fluxes in a growing fruit as a function of plant and environment. Eight genotype-dependent model parameters were estimated using a multiobjective evolutionary algorithm in order to minimize the prediction errors of fruit dry and fresh mass throughout fruit development. WD increased the fruit dry matter content (up to 85 % and decreased its fresh weight (up to 60 %, big fruit size genotypes being the most sensitive. The mean normalized root mean squared errors of the predictions ranged between 16-18 % in the population. Variability in model genotypic parameters allowed us to explore diverse genetic strategies in response to WD. An interesting group of genotypes could be discriminated in which i the low loss of fresh mass under WD was associated with high active uptake of sugars and low value of the maximum cell wall extensibility, and ii the high dry matter content in control treatment (C was associated with a slow decrease of mass flow. Using 501 SNP markers genotyped across the genome, a QTL analysis of model parameters allowed to detect three main QTLs related to xylem and phloem conductivities, on chromosomes 2, 4 and 8. The model was then applied to design ideotypes with high dry matter

  9. Intra-individual Variability in Prodromal Huntington Disease and Its Relationship to Genetic Burden.

    Science.gov (United States)

    Musso, Mandi; Westervelt, Holly James; Long, Jeffrey D; Morgan, Erin; Woods, Steven Paul; Smith, Megan M; Lu, Wenjing; Paulsen, Jane S

    2015-01-01

    The current study sought to examine the utility of intra-individual variability (IIV) in distinguishing participants with prodromal Huntington disease (HD) from nongene-expanded controls. IIV across 15 neuropsychological tasks and within-task IIV using a self-paced timing task were compared as a single measure of processing speed (Symbol Digit Modalities Test [SDMT]) in 693 gene-expanded and 191 nongene-expanded participants from the PREDICT-HD study. After adjusting for depressive symptoms and motor functioning, individuals estimated to be closest to HD diagnosis displayed higher levels of across- and within-task variability when compared to controls and those prodromal HD participants far from disease onset (F ICV(3,877)=11.25; p<.0001; F PacedTiming(3,877)=22.89; p<.0001). When prodromal HD participants closest to HD diagnosis were compared to controls, Cohen's d effect sizes were larger in magnitude for the within-task variability measure, paced timing (-1.01), and the SDMT (-0.79) and paced tapping coefficient of variation (CV) (-0.79) compared to the measures of across-task variability [CV (0.55); intra-individual standard deviation (0.26)]. Across-task variability may be a sensitive marker of cognitive decline in individuals with prodromal HD approaching disease onset. However, individual neuropsychological tasks, including a measure of within-task variability, produced larger effect sizes than an index of across-task IIV in this sample.

  10. Variability, heritability and genetic advance in some agronomic and forage quality characters of spring triticale in western Canada.

    Science.gov (United States)

    Aljarrah, Mazen; Oatway, Lori; Albers, Susan; Bergen, Colin

    2014-01-01

    The aim of this study was to estimate variability, broad sense heritability, and genetic advance for dry matter yield (DMY), days to anthesis (ANTH), plant height (HT), in-vitro fiber digestibility-30h (IVFD), lignin (LIGN), starch (STAR %), crude protein content (CP %), acid detergent fiber (ADF) and neutral detergent fiber (NDF) in spring triticale genotypes. Eighteen genotypes were tested at the Field Crop Development Centre (FCDC) in Lacombe, Alberta in 2010-2011 and 2011-2012 growing season. The experimental design was randomized complete block design with 3 replicates. Combined analysis of variance was carried out using SAS Enterprise 4.2 statistical package. Heritability was estimated following the variance component method. Simple correlation coefficients were determined among all traits using two years average data. The genotype mean squares were significant (P ≤ 0.05) for DMY, ANTH, HT, IFVD, ADF, NDF, STAR %, LIGN, and CP %. The effect of year was also highly significant on all studied traits. The phenotypic coefficient of variation was higher than the genetic coefficient of variation for all traits, indicating high influence of the environment on these traits. The significant genetic variability and the high heritability combined with high genetic advance of HT, STAR% and ADF in triticale genotypes suggested that selection could be successfully practiced for those traits. Correlation analysis showed significant and positive correlation of DMY with ANTH and HT, indicating that late and tall genotypes are more suitable as a forage type and they tend to produce more biomass yield. However, DMY did not show any significant correlation with the digestibility. IVFD and STAR % were negatively correlated with LIGN. In general, these results indicated that breeding for low lignin and high starch content will improve the digestibility in triticale genotypes. The preliminary results of this study were promising. Further research must include more diverse

  11. Genetic variables of various manifestations of osteochondrosis and their correlations between and within joints in Dutch warmblood horses.

    Science.gov (United States)

    van Grevenhof, E M; Schurink, A; Ducro, B J; van Weeren, P R; van Tartwijk, J M F M; Bijma, P; van Arendonk, J A M

    2009-06-01

    Osteochondrosis (OC) is an important orthopedic developmental disorder in many horse populations. A review of the literature revealed widely variable heritability estimates for the disorder. We estimated the genetic variables (heritabilities and genetic correlations) of various manifestations of OC. Femoropatellar, tarsocrural, and metacarpophalangeal and metatarsophalangeal joints of 811 randomly selected yearlings from the Royal Warmblood Studbook of The Netherlands, descending from 32 representative stallions, were scored for OC at 28 predilection sites. At each site, OC was scored in 5 categories, distinguishing between flattened bone contours and fragments. At the animal level, the overall heritability of OC was 0.23, the heritability of flattened bone contours was 0.08, and the heritability of fragments was 0.22. At the joint level, heritability was greatest in the tarsocrural joints, intermediate in the metacarpophalangeal and metatarsophalangeal joints, and least in the femoropatellar joints. The heritability estimates for the contralateral joint homologs were very similar. The genetic correlation between the tarsocrural and femoropatellar joint was strong, whereas correlations between the metacarpophalangeal and metatarsophalangeal and other joints were moderate. The genetic correlation between flattened bone contours and fragments at the animal level was 0.80. Scoring OC on a 5-point categorical scale resulted in greater heritability on the observed scale than when analyzing OC as a binary trait. Our results suggest that selection against OC could best be performed by taking into account the OC status of all 4 joints, the femoropatellar, the tarsocrural, and the metacarpophalangeal and metatarsophalangeal joints, and discerning between flattened bone contours and fragments.

  12. Genetic variability of sexual size dimorphism in a natural population of Drosophila melanogaster: an isofemale-line approach

    Indian Academy of Sciences (India)

    Jean R. David; Patricia Gibert; Sandrine Mignon-Grasteau; Hélène Legout; Georges Pétavy; Catherine Beaumont; Brigitte Moreteau

    2003-12-01

    Most animal species exhibit sexual size dimorphism (SSD). SSD is a trait difficult to quantify for genetical purposes since it must be simultaneously measured on two kinds of individuals, and it is generally expressed either as a difference or as a ratio between sexes. Here we ask two related questions: What is the best way to describe SSD, and is it possible to conveniently demonstrate its genetic variability in a natural population? We show that a simple experimental design, the isofemale-line technique (full-sib families), may provide an estimate of genetic variability, using the coefficient of intraclass correlation. We consider two SSD indices, the female–male difference and the female/male ratio. For two size-related traits, wing and thorax length, we found that both SSD indices were normally distributed. Within each family, the variability of SSD was estimated by considering individual values in one sex (the female) with respect to the mean value in the other sex (the male). In a homogeneous sample of 30 lines of Drosophila melanogaster, both indices provided similar intraclass correlations, on average 0.21, significantly greater than zero but lower than those for the traits themselves: 0.50 and 0.36 for wing and thorax length respectively. Wing and thorax length were strongly positively correlated within each sex. SSD indices of wing and thorax length were also positively correlated, but to a lesser degree than for the traits themselves. For comparative evolutionary studies, the ratio between sexes seems a better index of SSD since it avoids scaling effects among populations or species, permits comparisons between different traits, and has an unambiguous biological significance. In the case of D. melanogaster grown at 25°C, the average female/male ratios are very similar for the wing (1.16) and the thorax (1.15), and indicate that, on average, these size traits are 15–16% longer in females.

  13. Assessing the intra-species genetic variability in the clonal pathogen Campylobacter fetus: CRISPRs are highly polymorphic DNA markers.

    Science.gov (United States)

    Calleros, Lucía; Betancor, Laura; Iraola, Gregorio; Méndez, Alejandra; Morsella, Claudia; Paolicchi, Fernando; Silveyra, Silvia; Velilla, Alejandra; Pérez, Ruben

    2017-01-01

    Campylobacter fetus is a Gram-negative, microaerophilic bacterium that infects animals and humans. The subspecies Campylobacter fetus subsp. fetus (Cff) affects a broad range of vertebrate hosts and induces abortion in cows and sheep. Campylobacter fetus subsp. venerealis (Cfv) is restricted to cattle and causes the endemic disease bovine genital campylobacteriosis, which triggers reproductive problems and is responsible for major economic losses. Campylobacter fetus subsp. testudinum (Cft) has been isolated mostly from apparently healthy reptiles belonging to different species but also from ill snakes and humans. Genotypic differentiation of Cff and Cfv is difficult, and epidemiological information is scarce because there are few methods to study the genetic diversity of the strains. We analyze the efficacy of MLST, ribosomal sequences (23S gene and internal spacer region), and CRISPRs to assess the genetic variability of C. fetus in bovine and human isolates. Sequences retrieved from complete genomes were included in the analysis for comparative purposes. MLST and ribosomal sequences had scarce or null variability, while the CRISPR-cas system structure and the sequence of CRISPR1 locus showed remarkable diversity. None of the sequences here analyzed provided evidence of a genetic differentiation of Cff and Cfv in bovine isolates. Comparison of bovine and human isolates with Cft strains showed a striking divergence. Inter-host differences raise the possibility of determining the original host of human infections using CRISPR sequences. CRISPRs are the most variable sequences analyzed in C. fetus so far, and constitute excellent representatives of a dynamic fraction of the genome. CRISPR typing is a promising tool to characterize isolates and to track the source and transmission route of C. fetus infections.

  14. Variabilidad gen��tica de los caballos criollos del Uruguay Genetic variability of uruguayan creole horse

    Directory of Open Access Journals (Sweden)

    L. KELLY

    2002-01-01

    Full Text Available El caballo Criollo del Uruguay (CCU corresponde al biotipo de caballo de trabajo americano, adaptado y criado en vastas zonas ganaderas. El objetivo de este trabajo es estudiar su variabilidad genética y establecer la diferenciación entre las subpoblaciones que componen la muestra con el fin de analizar la variabilidad entre las mismas. El estudio se realiza mediante 16 marcadores genéticos (7 grupos sanguíneos y 9 polimorfismos bioquímicos, analizándose 145 CCU pertenecientes a 4 Departamentos del país. Los sistemas electroforéticos analizados dentro de las 4 subpoblaciones (A, B, C, D se encontraron en equilibrio génico. La variabilidad genética racial se estimó mediante el Índice de Heterocigosidad media esperada (IH para los 16 marcadores genéticos (MG, el número total de variantes y el índice de consanguinidad (f. Los resultados fueron: 0.424, 62 y 0,049 respectivamente. La variabilidad de cada una de las subpoblaciones se evaluó mediante el índice F de fijación de Wright (F y el IH. Todas las subpoblaciones presentaron F negativo, siendo la de menor variabilidad la B (IH= 0.265. Se calculó la distancia genética de Nei entre las 4 subpoblaciones. Esta fue en orden creciente con respecto a la A: C (0.007, D (0.014 y B (0.058. Se realizó un análisis de "cluster" mediante el método de UPGMA, obteniéndose un dendograma en el que se agrupan las subpoblaciones A, C y D. Se puede concluir que el CCU tiene una variabilidad genética de intermedia a alta, conservando el polimorfismos de las razas ancestrales. En cuanto a la variabilidad intrapoblacional se comprueba la presencia de una línea (B dentro de la razaThe Uruguayan Creole Horse corresponds to the biotype of American horse for work, adapted and bred in vast cattle areas. The objective of this work is to study its genetic variability and to establish the differentiation among farms included in the sample with the purpose of analyzing the variability among them. The

  15. Trend Change Detection in NDVI Time Series: Effects of Inter-Annual Variability and Methodology

    Science.gov (United States)

    Forkel, Matthias; Carvalhais, Nuno; Verbesselt, Jan; Mahecha, Miguel D.; Neigh, Christopher S.R.; Reichstein, Markus

    2013-01-01

    Changing trends in ecosystem productivity can be quantified using satellite observations of Normalized Difference Vegetation Index (NDVI). However, the estimation of trends from NDVI time series differs substantially depending on analyzed satellite dataset, the corresponding spatiotemporal resolution, and the applied statistical method. Here we compare the performance of a wide range of trend estimation methods and demonstrate that performance decreases with increasing inter-annual variability in the NDVI time series. Trend slope estimates based on annual aggregated time series or based on a seasonal-trend model show better performances than methods that remove the seasonal cycle of the time series. A breakpoint detection analysis reveals that an overestimation of breakpoints in NDVI trends can result in wrong or even opposite trend estimates. Based on our results, we give practical recommendations for the application of trend methods on long-term NDVI time series. Particularly, we apply and compare different methods on NDVI time series in Alaska, where both greening and browning trends have been previously observed. Here, the multi-method uncertainty of NDVI trends is quantified through the application of the different trend estimation methods. Our results indicate that greening NDVI trends in Alaska are more spatially and temporally prevalent than browning trends. We also show that detected breakpoints in NDVI trends tend to coincide with large fires. Overall, our analyses demonstrate that seasonal trend methods need to be improved against inter-annual variability to quantify changing trends in ecosystem productivity with higher accuracy.

  16. Detection of anthrax toxin genetic sequences by the solid phase oligo-probes

    Directory of Open Access Journals (Sweden)

    K C Addanki

    2011-01-01

    Full Text Available Purpose: There is an urgent need to detect a rapid field-based test to detect anthrax. We have developed a rapid, highly sensitive DNA-based method to detect the anthrax toxin lethal factor gene located in pXO1, which is necessary for the pathogenicity of Bacillus anthracis. Materials and Methods: We have adopted the enzyme-linked immunosorbent assay (ELISA so that instead of capturing antibodies we capture the DNA of the target sequence by a rapid oligo-based hybridization and then detect the captured DNA with another oligoprobe that binds to a different motif of the captured DNA sequences at a dissimilar location. We chose anthrax lethal factor endopeptidase sequences located in pXO1 and used complementary oligoprobe, conjugated with biotin, to detect the captured anthrax specific sequence by the streptavidin-peroxidase-based colorimetric assay. Result: Our system can detect picomoles (pMoles of anthrax (approximately 33 spores of anthrax and is >1000 times more sensitive than the current ELISA, which has a detection range of 0.1 to 1.0 ng/mL. False positive results can be minimized when various parameters and the colour development steps are optimized. Conclusion: Our results suggest that this assay can be adapted for the rapid detection of minuscule amounts of the anthrax spores that are aerosolized in the case of a bioterrorism attack. This detection system does not require polymerase chain reaction (PCR step and can be more specific than the antibody method. This method can also detect genetically engineered anthrax. Since, the antibody method is so specific to the protein epitope that bioengineered versions of anthrax may not be detected.

  17. Ultraspectral sounder data compression using error-detecting reversible variable-length coding

    Science.gov (United States)

    Huang, Bormin; Ahuja, Alok; Huang, Hung-Lung; Schmit, Timothy J.; Heymann, Roger W.

    2005-08-01

    Nonreversible variable-length codes (e.g. Huffman coding, Golomb-Rice coding, and arithmetic coding) have been used in source coding to achieve efficient compression. However, a single bit error during noisy transmission can cause many codewords to be misinterpreted by the decoder. In recent years, increasing attention has been given to the design of reversible variable-length codes (RVLCs) for better data transmission in error-prone environments. RVLCs allow instantaneous decoding in both directions, which affords better detection of bit errors due to synchronization losses over a noisy channel. RVLCs have been adopted in emerging video coding standards--H.263+ and MPEG-4--to enhance their error-resilience capabilities. Given the large volume of three-dimensional data that will be generated by future space-borne ultraspectral sounders (e.g. IASI, CrIS, and HES), the use of error-robust data compression techniques will be beneficial to satellite data transmission. In this paper, we investigate a reversible variable-length code for ultraspectral sounder data compression, and present its numerical experiments on error propagation for the ultraspectral sounder data. The results show that the RVLC performs significantly better error containment than JPEG2000 Part 2.

  18. A Monitoring Campaign for Luhman 16AB. I. Detection of Resolved Near-Infrared Spectroscopic Variability

    CERN Document Server

    Burgasser, Adam J; Faherty, Jacqueline K; Radigan, Jacqueline; J., Amaury H M; Plavchan, Peter; Street, Rachel; Jehin, E; Delrez, L; Opitom, C

    2014-01-01

    [abbreviated] We report resolved near-infrared spectroscopic monitoring of the nearby L dwarf/T dwarf binary WISE J104915.57-531906.1AB (Luhman 16AB), as part of a broader campaign to characterize the spectral energy distribution and temporal variability of this system. A continuous 45-minute sequence of low-resolution IRTF/SpeX data spanning 0.8-2.4 micron were obtained, concurrent with combined-light optical photometry with ESO/TRAPPIST. Our spectral observations confirm the flux reversal of this binary, and we detect a wavelength-dependent decline in the relative spectral fluxes of the two components coincident with a decline in the combined-light optical brightness of the system over the course of the observation. These data are successfully modeled as a combination of brightness and color variability in the T0.5 Luhman 16B, consistent cloud variations; and no significant variability in L7.5 Luhman 16A. We estimate a peak-to-peak amplitude of 13.5% at 1.25 micron over the full lightcurve. Using a two-spot...

  19. Mid-infrared prediction of milk titratable acidity and its genetic variability in first-parity cows

    OpenAIRE

    Colinet, Frédéric; Vanlierde, Amélie; Vanden Bossche, sandrine; Sindic, Marianne; Dehareng, Frédéric; Sinnaeve, Georges; Vandenplas, Jérémie; Soyeurt, Hélène; Bastin, Catherine; Gengler, Nicolas

    2012-01-01

    Coagulation of milkhas a direct effect on cheese yield. Among several parameters, titratable acidity of milk (TA) influences all the phases of milk coagulation. In order to study the genetic variability of this trait on a large scale, mid-infrared (MIR) chemometric methods were used to predict TA. A total of 507 milk samples collected in the Walloon Region of Belgium from individual cows were analyzed using a MIR spectrometer. TA was recorded as Dornic degree. An equation to predict TA from m...

  20. The power to detect recent fragmentation events using genetic differentiation methods.

    Directory of Open Access Journals (Sweden)

    Michael W Lloyd

    Full Text Available Habitat loss and fragmentation are imminent threats to biological diversity worldwide and thus are fundamental issues in conservation biology. Increased isolation alone has been implicated as a driver of negative impacts in populations associated with fragmented landscapes. Genetic monitoring and the use of measures of genetic divergence have been proposed as means to detect changes in landscape connectivity. Our goal was to evaluate the sensitivity of Wright's F st, Hedrick' G'st , Sherwin's MI, and Jost's D to recent fragmentation events across a range of population sizes and sampling regimes. We constructed an individual-based model, which used a factorial design to compare effects of varying population size, presence or absence of overlapping generations, and presence or absence of population sub-structuring. Increases in population size, overlapping generations, and population sub-structuring each reduced F st, G'st , MI, and D. The signal of fragmentation was detected within two generations for all metrics. However, the magnitude of the change in each was small in all cases, and when N e was >100 individuals it was extremely small. Multi-generational sampling and population estimates are required to differentiate the signal of background divergence from changes in Fst , G'st , MI, and D associated with fragmentation. Finally, the window during which rapid change in Fst , G'st , MI, and D between generations occurs can be small, and if missed would lead to inconclusive results. For these reasons, use of F st, G'st , MI, or D for detecting and monitoring changes in connectivity is likely to prove difficult in real-world scenarios. We advocate use of genetic monitoring only in conjunction with estimates of actual movement among patches such that one could compare current movement with the genetic signature of past movement to determine there has been a change.

  1. JRC GMO-Matrix: a web application to support Genetically Modified Organisms detection strategies.

    Science.gov (United States)

    Angers-Loustau, Alexandre; Petrillo, Mauro; Bonfini, Laura; Gatto, Francesco; Rosa, Sabrina; Patak, Alexandre; Kreysa, Joachim

    2014-12-30

    The polymerase chain reaction (PCR) is the current state of the art technique for DNA-based detection of Genetically Modified Organisms (GMOs). A typical control strategy starts by analyzing a sample for the presence of target sequences (GM-elements) known to be present in many GMOs. Positive findings from this "screening" are then confirmed with GM (event) specific test methods. A reliable knowledge of which GMOs are detected by combinations of GM-detection methods is thus crucial to minimize the verification efforts. In this article, we describe a novel platform that links the information of two unique databases built and maintained by the European Union Reference Laboratory for Genetically Modified Food and Feed (EU-RL GMFF) at the Joint Research Centre (JRC) of the European Commission, one containing the sequence information of known GM-events and the other validated PCR-based detection and identification methods. The new platform compiles in silico determinations of the detection of a wide range of GMOs by the available detection methods using existing scripts that simulate PCR amplification and, when present, probe binding. The correctness of the information has been verified by comparing the in silico conclusions to experimental results for a subset of forty-nine GM events and six methods. The JRC GMO-Matrix is unique for its reliance on DNA sequence data and its flexibility in integrating novel GMOs and new detection methods. Users can mine the database using a set of web interfaces that thus provide a valuable support to GMO control laboratories in planning and evaluating their GMO screening strategies. The platform is accessible at http://gmo-crl.jrc.ec.europa.eu/jrcgmomatrix/ .

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

    NARCIS (Netherlands)

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

    2014-01-01

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

  3. Frequency modulated weak signal detection based on stochastic resonance and genetic algorithm

    Institute of Scientific and Technical Information of China (English)

    XING; Hongyan; LU; Chunxia; ZHANG; Qiang

    2016-01-01

    Stochastic resonance system is subject to the restriction of small frequency parameter in weak signal detection,in order to solve this problem,a frequency modulated weak signal detection method based on stochastic resonance and genetic algorithm is presented in this paper. The frequency limit of stochastic resonance is eliminated by introducing carrier signal,which is multiplied with the measured signal to be injected in the stochastic resonance system,meanwhile,using genetic algorithm to optimize the carrier signal frequency,which determine the generated difference-frequency signal in the lowfrequency range,so as to achieve the stochastic resonance weak signal detection. Results showthat the proposed method is feasible and effective,which can significantly improve the output SNR of stochastic resonance,in addition,the system has the better self-adaptability,according to the operation result and output phenomenon,the unknown frequency of the signal to be measured can be obtained,so as to realize the weak signal detection of arbitrary frequency.

  4. Endpoint Visual Detection of Three Genetically Modified Rice Events by Loop-Mediated Isothermal Amplification

    Directory of Open Access Journals (Sweden)

    Qing Zhu

    2012-11-01

    Full Text Available Genetically modified (GM rice KMD1, TT51-1, and KF6 are three of the most well known transgenic Bt rice lines in China. A rapid and sensitive molecular assay for risk assessment of GM rice is needed. Polymerase chain reaction (PCR, currently the most common method for detecting genetically modified organisms, requires temperature cycling and relatively complex procedures. Here we developed a visual and rapid loop-mediated isothermal amplification (LAMP method to amplify three GM rice event-specific junction sequences. Target DNA was amplified and visualized by two indicators (SYBR green or hydroxy naphthol blue [HNB] within 60 min at an isothermal temperature of 63 °C. Different kinds of plants were selected to ensure the specificity of detection and the results of the non-target samples were negative, indicating that the primer sets for the three GM rice varieties had good levels of specificity. The sensitivity of LAMP, with detection limits at low concentration levels (0.01%–0.005% GM, was 10- to 100-fold greater than that of conventional PCR. Additionally, the LAMP assay coupled with an indicator (SYBR green or HNB facilitated analysis. These findings revealed that the rapid detection method was suitable as a simple field-based test to determine the status of GM crops.

  5. Genetic variability of glutathione S-transferase enzymes in human populations: functional inter-ethnic differences in detoxification systems.

    Science.gov (United States)

    Polimanti, Renato; Carboni, Cinzia; Baesso, Ilenia; Piacentini, Sara; Iorio, Andrea; De Stefano, Gian Franco; Fuciarelli, Maria

    2013-01-01

    Glutathione S-Transferase enzymes (GSTs) constitute the principal Phase II superfamily which plays a key role in cellular detoxification and in other biological processes. Studies of GSTs have revealed that genetic polymorphisms are present in these enzymes and that some of these are Loss-of-Function (LoF) variants, which affect enzymatic functions and are related to different aspects of human health. The aim of this study was to analyze functional genetic differences in GST enzymes among human populations. Attention was focused on LoF polymorphisms of GSTA1, GSTM1, GSTO1, GSTO2, GSTP1 and GSTT1 genes. These LoF variants were analyzed in 668 individuals belonging to six human groups with different ethnic backgrounds: Amhara and Oromo from Ethiopia; Colorado and Cayapa Amerindians and African Ecuadorians from Ecuador; and one sample from central Italy. The HapMap database was used to compare our data with reference populations and to analyze the haplotype and Linkage Disequilibrium diversity in different ethnic groups. Our results highlighted that ethnicity strongly affects the genetic variability of GST enzymes. In particular, GST haplotypes/variants with functional impact showed significant differences in human populations, according to their ethnic background. These data underline that human populations have different structures in detoxification genes, suggesting that these ethnic differences influence disease risk or response to drugs and therefore have implications for genetic association studies involving GST enzymes. In conclusion, our investigation provides data about the distribution of important LoF variants in GST genes in human populations. This information may be useful for designing and interpreting genetic association studies.

  6. Shared language, diverging genetic histories: high-resolution analysis of Y-chromosome variability in Calabrian and Sicilian Arbereshe.

    Science.gov (United States)

    Sarno, Stefania; Tofanelli, Sergio; De Fanti, Sara; Quagliariello, Andrea; Bortolini, Eugenio; Ferri, Gianmarco; Anagnostou, Paolo; Brisighelli, Francesca; Capelli, Cristian; Tagarelli, Giuseppe; Sineo, Luca; Luiselli, Donata; Boattini, Alessio; Pettener, Davide

    2016-04-01

    The relationship between genetic and linguistic diversification in human populations has been often explored to interpret some specific issues in human history. The Albanian-speaking minorities of Sicily and Southern Italy (Arbereshe) constitute an important portion of the ethnolinguistic variability of Italy. Their linguistic isolation from neighboring Italian populations and their documented migration history, make such minorities particularly effective for investigating the interplay between cultural, geographic and historical factors. Nevertheless, the extent of Arbereshe genetic relationships with the Balkan homeland and the Italian recipient populations has been only partially investigated. In the present study we address the genetic history of Arbereshe people by combining highly resolved analyses of Y-chromosome lineages and extensive computer simulations. A large set of slow- and fast-evolving molecular markers was typed in different Arbereshe communities from Sicily and Southern Italy (Calabria), as well as in both the putative Balkan source and Italian sink populations. Our results revealed that the considered Arbereshe groups, despite speaking closely related languages and sharing common cultural features, actually experienced diverging genetic histories. The estimated proportions of genetic admixture confirm the tight relationship of Calabrian Arbereshe with modern Albanian populations, in accordance with linguistic hypotheses. On the other hand, population stratification and/or an increased permeability of linguistic and geographic barriers may be hypothesized for Sicilian groups, to account for their partial similarity with Greek populations and their higher levels of local admixture. These processes ultimately resulted in the differential acquisition or preservation of specific paternal lineages by the present-day Arbereshe communities.

  7. Genetic Variability of the Essential Oil Content of Melissa officinalis1.

    Science.gov (United States)

    Adzet, T; Ponz, R; Wolf, E; Schulte, E

    1992-12-01

    The essential oil content of various populations of MELISSA OFFICINALIS L. (Lamiaceae), cultivated under Mediterranean climatic conditions (Ebro-Delta, Spain) has been investigated during five years of selection and improvement of the genetic plant material. Starting with an essential oil content of 0.2-0.3%, a content of more than 0.5% was obtained as a result of genetic improvement. A weak negative correlation between the content of essential oil and phenotypical growth parameters such as the number of branches per plant and height was observed. No correlation between biomass production per plant and essential oil content could be found. By the method of hybridization, M. OFFICINALIS synthetics with a high yield of biomass and essential oil content were selected.

  8. Genetics of glioblastoma: a window into its imaging and histopathologic variability.

    Science.gov (United States)

    Belden, Clifford J; Valdes, Pablo A; Ran, Cong; Pastel, David A; Harris, Brent T; Fadul, Camilo E; Israel, Mark A; Paulsen, Keith; Roberts, David W

    2011-10-01

    Glioblastoma is a highly malignant brain tumor that relentlessly defies therapy. Efforts over the past decade have begun to tease out the biochemical details that lead to its aggressive behavior and poor prognosis. There is hope that this new understanding will lead to improved treatment strategies for patients with glioblastoma, in the form of targeted, molecularly based therapies that are individualized to specific changes in individual tumors. However, these new therapies have the potential to fundamentally alter the biologic behavior of glioblastoma and, as a result, its imaging appearance. Knowledge about common genetic alterations and the resultant cellular and tissue changes (ie, induced angiogenesis and abnormal cell survival, proliferation, and invasion) in glioblastomas is important as a basis for understanding imaging findings before treatment. It is equally critical that radiologists understand which genetic pathway is targeted by each specific therapeutic agent or class of agents in order to accurately interpret changes in the imaging appearances of treated tumors.

  9. Hierarchical spatial structure of genetically variable nucleopolyhedroviruses infecting cyclic populations of western tent caterpillars.

    Science.gov (United States)

    Cooper, Dawn; Cory, Jenny S; Myers, Judith H

    2003-04-01

    The cyclic population dynamics of western tent caterpillars, Malacosoma californicum pluviale, are associated with epizootics of a nucleopolyhedrovirus, McplNPV. Given the dynamic fluctuations in host abundance and levels of viral infection, host resistance and virus virulence might be expected to change during different phases of the cycle. As a first step in determining if McplNPV virulence and population structure change with host density, we used restriction fragment length polymorphism (RFLP) analysis to examine the genetic diversity of McplNPV infecting western tent caterpillar populations at different spatial scales. Thirteen dominant genetic variants were identified in 39 virus isolates (individual larvae) collected from field populations during one year of low host density, and another distinct variant was discovered among nine additional isolates in two subsequent years of declining host density. The distribution of these genetic variants was not random and indicated that the McplNPV population was structured at several spatial levels. A high proportion of the variation could be explained by family grouping, which suggested that isolates collected within a family were more likely to be the same than isolates compared among populations. Additionally, virus variants from within populations (sites) were more likely to be the same than isolates collected from tent caterpillar populations on different islands. This may indicate that there is limited mixing of virus among tent caterpillar families and populations when host population density is low. Thus there is potential for the virus to become locally adapted to western tent caterpillar populations in different sites. However, no dominant genotype was observed at any site. Whether and how selection acts on the genetically diverse nucleopolyhedrovirus populations as host density changes will be investigated over the next cycle of tent caterpillar populations.

  10. Common genetic variability in ESR1 and EGF in relation to endometrial cancer risk and survival

    OpenAIRE

    Einarsdóttir, K; Darabi, H; Czene, K.; Li, Y; Low, Y.L.; Y. Q. Li; Bonnard, C.; Wedrén, S.; Liu, E. T.; Hall, P; Liu, J; Humphreys, K.

    2009-01-01

    We investigated common genetic variation in the entire ESR1 and EGF genes in relation to endometrial cancer risk, myometrial invasion and endometrial cancer survival. We genotyped a dense set of single-nucleotide polymorphisms (SNPs) in both genes and selected haplotype tagging SNPs (tagSNPs). The tagSNPs were genotyped in 713 Swedish endometrial cancer cases and 1567 population controls and the results incorporated into logistic regression and Cox proportional hazards models. We found five a...

  11. Optimization of cocoa butter analog synthesis variables using neural networks and genetic algorithm

    OpenAIRE

    Shekarchizadeh, Hajar; Tikani, Reza; Kadivar, Mahdi

    2012-01-01

    Cocoa butter analog was prepared from camel hump fat and tristearin by enzymatic interesterification in supercritical carbon dioxide (SC-CO2) using immobilized Thermomyces lanuginosus lipase (Lipozyme TL IM) as a biocatalyst. Optimal process conditions were determined using neural networks and genetic algorithm optimization. Response surfaces methodology was used to design the experiments to collect data for the neural network modelling. A general regression neural network model was developed...

  12. Genetic variability and nitrogenase activity of cyanobacterial communities associated with tropical seagrass meadows (western Indian Ocean)

    OpenAIRE

    Hamisi, Mariam

    2010-01-01

    Tropical seagrass ecosystems are highly productive and important for sustaining marine life and associated coastal societies. In this study, the diversity and role of nitrogen-fixing cyanobacteria associated with five common seagrass genera in coastal regions of the western Indian Ocean (WIO; Tanzania) were examined, as well as the impact of anthropogenic activities. Cyanobacteria were characterized morphologically and genetically (16S rRNA and nifH gene phylogeny), as were diel variations in...

  13. Extremely low genetic variability within and among locations of the greenfish holothurian Stichopus chloronotus Brandt, 1835 in Okinawa, Japan

    Directory of Open Access Journals (Sweden)

    Taha Soliman

    2016-09-01

    Full Text Available The greenfish sea cucumber Stichopus chloronotus is an economically and ecologically important sea cucumber species throughout its range. This species is widely distributed, inhabiting coral reefs of the Indo-Pacific Ocean. Our study evaluated population genetic structure and levels of genetic diversity in southern Japan. A total of 180 individuals were collected from eight locations from Okinawa and Okinoerabu Islands and sequenced using mitochondrial 16S ribosomal DNA (16S and nuclear histone H3 (H3 gene. Only three 16S haplotypes were detected (518 bp with haplotype diversity ranging from 0 to 0.56 and nucleotide diversity from 0 to 0.1%. H3 showed no variation among the studied locations. It is plausible that such results could be due to a shift to asexual reproduction. Additionally, the presence of the species on the east coast of Okinawa could only be detected in one location and all individuals consisted of a single haplotype. Genetic differences between the east and west coasts of Okinawa have been noticed in other coral reef organisms, and attributed to either ecological or biogeographical historical differences between the coasts due to differing levels of isolation during Pleistocene ice ages. Results from the present study should inform management and conservation policies of S. chloronotus in southern Japan.

  14. Extremely low genetic variability within and among locations of the greenfish holothurian Stichopus chloronotus Brandt, 1835 in Okinawa, Japan

    Science.gov (United States)

    Takama, Okuto; Fernandez-Silva, Iria; Reimer, James D.

    2016-01-01

    The greenfish sea cucumber Stichopus chloronotus is an economically and ecologically important sea cucumber species throughout its range. This species is widely distributed, inhabiting coral reefs of the Indo-Pacific Ocean. Our study evaluated population genetic structure and levels of genetic diversity in southern Japan. A total of 180 individuals were collected from eight locations from Okinawa and Okinoerabu Islands and sequenced using mitochondrial 16S ribosomal DNA (16S) and nuclear histone H3 (H3) gene. Only three 16S haplotypes were detected (518 bp) with haplotype diversity ranging from 0 to 0.56 and nucleotide diversity from 0 to 0.1%. H3 showed no variation among the studied locations. It is plausible that such results could be due to a shift to asexual reproduction. Additionally, the presence of the species on the east coast of Okinawa could only be detected in one location and all individuals consisted of a single haplotype. Genetic differences between the east and west coasts of Okinawa have been noticed in other coral reef organisms, and attributed to either ecological or biogeographical historical differences between the coasts due to differing levels of isolation during Pleistocene ice ages. Results from the present study should inform management and conservation policies of S. chloronotus in southern Japan. PMID:27703841

  15. High genetic variability of HIV-1 in female sex workers from Argentina

    Directory of Open Access Journals (Sweden)

    Carr Jean K

    2007-08-01

    Full Text Available Abstract Background A cross-sectional study on 625 Female Sex Workers (FSWs was conducted between 2000 and 2002 in 6 cities in Argentina. This study describes the genetic diversity and the resistance profile of the HIV-infected subjects. Results Seventeen samples from HIV positive FSWs were genotyped by env HMA, showing the presence of 9 subtype F, 6 subtype B and 2 subtype C. Sequence analysis of the protease/RT region on 16 of these showed that 10 were BF recombinants, three were subtype B, two were subtype C, and one sample presented a dual infection with subtype B and a BF recombinant. Full-length genomes of five of the protease/RT BF recombinants were also sequenced, showing that three of them were CRF12_BF. One FSW had a dual HIV-1 infection with subtype B and a BF recombinant. The B sections of the BF recombinant clustered closely with the pure B sequence isolated from the same patient. Major resistance mutations to antiretroviral drugs were found in 3 of 16 (18.8% strains. Conclusion The genetic diversity of HIV strains among FSWs in Argentina was extensive; about three-quarters of the samples were infected with diverse BF recombinants, near twenty percent had primary ART resistance and one sample presented a dual infection. Heterosexual transmission of genetically diverse, drug resistant strains among FSWs and their clients represents an important and underestimated threat, in Argentina.

  16. Cryptosporidium,Giardia, Cryptococcus, Pneumocystis genetic variability: cryptic biological species or clonal near-clades?

    Directory of Open Access Journals (Sweden)

    Michel Tibayrenc

    2014-04-01

    Full Text Available An abundant literature dealing with the population genetics and taxonomy of Giardia duodenalis, Cryptosporidium spp., Pneumocystis spp., and Cryptococcus spp., pathogens of high medical and veterinary relevance, has been produced in recent years. We have analyzed these data in the light of new population genetic concepts dealing with predominant clonal evolution (PCE recently proposed by us. In spite of the considerable phylogenetic diversity that exists among these pathogens, we have found striking similarities among them. The two main PCE features described by us, namely highly significant linkage disequilibrium and near-clading (stable phylogenetic clustering clouded by occasional recombination, are clearly observed in Cryptococcus and Giardia, and more limited indication of them is also present in Cryptosporidium and Pneumocystis. Moreover, in several cases, these features still obtain when the near-clades that subdivide the species are analyzed separately ("Russian doll pattern". Lastly, several sets of data undermine the notion that certain microbes form clonal lineages simply owing to a lack of opportunity to outcross due to low transmission rates leading to lack of multiclonal infections ("starving sex hypothesis". We propose that the divergent taxonomic and population genetic inferences advanced by various authors about these pathogens may not correspond to true evolutionary differences and could be, rather, the reflection of idiosyncratic practices among compartmentalized scientific communities. The PCE model provides an opportunity to revise the taxonomy and applied research dealing with these pathogens and others, such as viruses, bacteria, parasitic protozoa, and fungi.

  17. Genetic variability and selection for laticiferous system characters in Hevea brasiliensis

    Directory of Open Access Journals (Sweden)

    Paulo de Souza Gonçalves

    2005-09-01

    Full Text Available Six laticiferous system characters were investigated in 22 three-year-old, half-sib rubber tree [Hevea brasiliensis (Willd. ex Adr. de Juss. Muell.-Arg.] progenies, evaluated at three sites (Votuporanga, Pindorama and Jaú, all in the São Paulo State, Brazil. The traits examined were: average rubber yield (Pp, average bark thickness (Bt, number of latex vessel rings (Lv, average distance between consecutive latex vessel rings (Dc, density of latex vessels per 5 mm per ring averaged over all rings (Dd and the diameter of the latex vessels (Di. The joint analysis showed that site effect and progeny x sites interaction were significant for all traits, except Lv. Estimates of individual heritabilities across the three sites were high for Bt; moderate for Lv, Pp and Dc; low for Dd and very low for Di. Genetic correlations in the joint analysis showed high positive correlations between Pp and the other traits. Selecting the best five progenies would result in genetic gains of 24.91% for Pp while selecting best two plants within a progeny would result in a Pp genetic gain of 30.98%.

  18. Cryptosporidium,Giardia, Cryptococcus, Pneumocystis genetic variability: cryptic biological species or clonal near-clades?

    Science.gov (United States)

    Tibayrenc, Michel; Ayala, Francisco J

    2014-04-01

    An abundant literature dealing with the population genetics and taxonomy of Giardia duodenalis, Cryptosporidium spp., Pneumocystis spp., and Cryptococcus spp., pathogens of high medical and veterinary relevance, has been produced in recent years. We have analyzed these data in the light of new population genetic concepts dealing with predominant clonal evolution (PCE) recently proposed by us. In spite of the considerable phylogenetic diversity that exists among these pathogens, we have found striking similarities among them. The two main PCE features described by us, namely highly significant linkage disequilibrium and near-clading (stable phylogenetic clustering clouded by occasional recombination), are clearly observed in Cryptococcus and Giardia, and more limited indication of them is also present in Cryptosporidium and Pneumocystis. Moreover, in several cases, these features still obtain when the near-clades that subdivide the species are analyzed separately ("Russian doll pattern"). Lastly, several sets of data undermine the notion that certain microbes form clonal lineages simply owing to a lack of opportunity to outcross due to low transmission rates leading to lack of multiclonal infections ("starving sex hypothesis"). We propose that the divergent taxonomic and population genetic inferences advanced by various authors about these pathogens may not correspond to true evolutionary differences and could be, rather, the reflection of idiosyncratic practices among compartmentalized scientific communities. The PCE model provides an opportunity to revise the taxonomy and applied research dealing with these pathogens and others, such as viruses, bacteria, parasitic protozoa, and fungi.

  19. Geographic, genetic and life-history variability in a sex-changing fish

    Directory of Open Access Journals (Sweden)

    Chiara Benvenuto

    2015-11-01

    Full Text Available Sequential hermaphroditism, commonly referred to as sex change or sex reversal, is a striking phenomenon in mating-system evolution and the most remarkable example of sexual plasticity. Among vertebrates, it is specific to teleosts. Some fish species reproduce initially as females and then change into males (protogynous hermaphrodites or vice versa (protandrous hermaphrodites. The white sea bream, Diplodus sargus, exhibits a high degree of sexual plasticity: populations have been reported to be gonochoristic, protandrous or digynic (with primary females, derived from intersexual juveniles, and secondary females, derived from males. We analysed populations collected from eight different locations across the species distribution range (between the Mediterranean and the North-Eastern Atlantic. These populations are characterized by different degrees of connectivity, spatial demographics and life histories. Using individual-based analyses, we linked the genetic structure of each specimen with environmental heterogeneity, life-history traits and reproductive modes. Our aim is to gather a better understanding of the variation in reproductive life-history strategies in this sexually plastic species. Diplodus sargus is a valuable candidate organism to investigate sequential hermaphroditism and it also has a commercial value. The application of population genetics tools against the background of life-history theory can bring valuable insights for the management of marine resources. The geographical patterns of sex change (and of age- and size-at-sex change linked with population genetics can be pivotal for both theoretical investigations and conservation and management plans in marine areas.

  20. Multi-objective optimization in systematic conservation planning and the representation of genetic variability among populations.

    Science.gov (United States)

    Schlottfeldt, S; Walter, M E M T; Carvalho, A C P L F; Soares, T N; Telles, M P C; Loyola, R D; Diniz-Filho, J A F

    2015-06-18

    Biodiversity crises have led scientists to develop strategies for achieving conservation goals. The underlying principle of these strategies lies in systematic conservation planning (SCP), in which there are at least 2 conflicting objectives, making it a good candidate for multi-objective optimization. Although SCP is typically applied at the species level (or hierarchically higher), it can be used at lower hierarchical levels, such as using alleles as basic units for analysis, for conservation genetics. Here, we propose a method of SCP using a multi-objective approach. We used non-dominated sorting genetic algorithm II in order to identify the smallest set of local populations of Dipteryx alata (baru) (a Brazilian Cerrado species) for conservation, representing the known genetic diversity and using allele frequency information associated with heterozygosity and Hardy-Weinberg equilibrium. We worked in 3 variations for the problem. First, we reproduced a previous experiment, but using a multi-objective approach. We found that the smallest set of populations needed to represent all alleles under study was 7, corroborating the results of the previous study, but with more distinct solutions. In the 2nd and 3rd variations, we performed simultaneous optimization of 4 and 5 objectives, respectively. We found similar but refined results for 7 populations, and a larger portfolio considering intra-specific diversity and persistence with populations ranging from 8-22. This is the first study to apply multi-objective algorithms to an SCP problem using alleles at the population level as basic units for analysis.

  1. Neuronal detection thresholds during vestibular compensation: contributions of response variability and sensory substitution.

    Science.gov (United States)

    Jamali, Mohsen; Mitchell, Diana E; Dale, Alexis; Carriot, Jerome; Sadeghi, Soroush G; Cullen, Kathleen E

    2014-04-01

    The vestibular system is responsible for processing self-motion, allowing normal subjects to discriminate the direction of rotational movements as slow as 1-2 deg s(-1). After unilateral vestibular injury patients' direction-discrimination thresholds worsen to ∼20 deg s(-1), and despite some improvement thresholds remain substantially elevated following compensation. To date, however, the underlying neural mechanisms of this recovery have not been addressed. Here, we recorded from first-order central neurons in the macaque monkey that provide vestibular information to higher brain areas for self-motion perception. Immediately following unilateral labyrinthectomy, neuronal detection thresholds increased by more than two-fold (from 14 to 30 deg s(-1)). While thresholds showed slight improvement by week 3 (25 deg s(-1)), they never recovered to control values - a trend mirroring the time course of perceptual thresholds in patients. We further discovered that changes in neuronal response variability paralleled changes in sensitivity for vestibular stimulation during compensation, thereby causing detection thresholds to remain elevated over time. However, we found that in a subset of neurons, the emergence of neck proprioceptive responses combined with residual vestibular modulation during head-on-body motion led to better neuronal detection thresholds. Taken together, our results emphasize that increases in response variability to vestibular inputs ultimately constrain neural thresholds and provide evidence that sensory substitution with extravestibular (i.e. proprioceptive) inputs at the first central stage of vestibular processing is a neural substrate for improvements in self-motion perception following vestibular loss. Thus, our results provide a neural correlate for the patient benefits provided by rehabilitative strategies that take advantage of the convergence of these multisensory cues.

  2. The variability of nonmigrating tides detected from TIMED/SABER observations

    Science.gov (United States)

    Li, Xing; Liu, Libo; Ning, Baiqi; Ren, Zhipeng; Wan, Weixing

    2016-07-01

    This work deals with the variability of the nonmigrating tides detected from the observation of the SABER instrument on board the TIMED satellite during the 11 year solar period from 2002 to 2012. The longitudinal wave number spectra with 1 day resolution were first estimated from the temperature data measured at the MLT altitudes (70-110 km) and at the lower midlatitudes and low latitudes (between ±±45°°). Then we used the wave number 4 component to obtain the nonmigrating tides in which the dominant component DE3 was further analyzed in detail. We found that the properties of the spatial distribution and large time scale variation of the DE3 component are similar to those of the previous works, which used the interpolated data with 2 month resolution. These properties are that the DE3 component occurs mainly at the low latitudes within ±30° and at the altitudes from 90 to 110 km; the tidal amplitude is larger during boreal summer and early autumn, smaller in spring and almost tends to disappear in winter; the component is slightly stronger during the eastward wind QBO phase than the westward phase. Practically, the higher-resolution data were used to reveal the day-to-day variability of the DE3 component. It is found that (1) the variability occurs mainly at the altitudes from 100 to 110 km with a peak at 106 km; (2) it is strong at the low latitudes and peaks around the equator, as well, slightly stronger in the Southern Hemisphere than in northern one; (3) it is considerably larger around solstitial months than equinoctial months; and (4) it would not experience an obvious interannual variation. The day-to-day variability of the DE3 component may be explained by the variance of the absolute amplitudes and the contribution of the wave phases, and the later seems to play more important role.

  3. Nonlinear detection of paleoclimate-variability transitions possibly related to human evolution.

    Science.gov (United States)

    Donges, Jonathan F; Donner, Reik V; Trauth, Martin H; Marwan, Norbert; Schellnhuber, Hans-Joachim; Kurths, Jürgen

    2011-12-20

    Potential paleoclimatic driving mechanisms acting on human evolution present an open problem of cross-disciplinary scientific interest. The analysis of paleoclimate archives encoding the environmental variability in East Africa during the past 5 Ma has triggered an ongoing debate about possible candidate processes and evolutionary mechanisms. In this work, we apply a nonlinear statistical technique, recurrence network analysis, to three distinct marine records of terrigenous dust flux. Our method enables us to identify three epochs with transitions between qualitatively different types of environmental variability in North and East Africa during the (i) Middle Pliocene (3.35-3.15 Ma B.P.), (ii) Early Pleistocene (2.25-1.6 Ma B.P.), and (iii) Middle Pleistocene (1.1-0.7 Ma B.P.). A deeper examination of these transition periods reveals potential climatic drivers, including (i) large-scale changes in ocean currents due to a spatial shift of the Indonesian throughflow in combination with an intensification of Northern Hemisphere glaciation, (ii) a global reorganization of the atmospheric Walker circulation induced in the tropical Pacific and Indian Ocean, and (iii) shifts in the dominating temporal variability pattern of glacial activity during the Middle Pleistocene, respectively. A reexamination of the available fossil record demonstrates statistically significant coincidences between the detected transition periods and major steps in hominin evolution. This result suggests that the observed shifts between more regular and more erratic environmental variability may have acted as a trigger for rapid change in the development of humankind in Africa.

  4. A monitoring campaign for Luhman 16AB. I. Detection of resolved near-infrared spectroscopic variability

    Energy Technology Data Exchange (ETDEWEB)

    Burgasser, Adam J. [Center for Astrophysics and Space Science, University of California San Diego, La Jolla, CA 92093 (United States); Gillon, Michaël; Jehin, E.; Delrez, L.; Opitom, C. [Institute of Astrophysics and Géophysique, Université of Liège, allée du 6 Août 17, B-4000 Liège (Belgium); Faherty, Jacqueline K. [Department of Terrestrial Magnetism, Carnegie Institution of Washington, 5241 Broad Branch Road NW, Washington, DC 20015 (United States); Radigan, Jacqueline [Space Telescope Science Institute, 3700 San Martin Drive, Baltimore, MD 21218 (United States); Triaud, Amaury H. M. J. [Massachusetts Institute of Technology, Kavli Institute for Astrophysics and Space Research, 77 Massachusetts Avenue, Cambridge, MA 02139 (United States); Plavchan, Peter [NASA Exoplanet Science Institute, California Institute of Technology, M/C 100-22, 770 South Wilson Avenue, Pasadena, CA 91125 (United States); Street, Rachel, E-mail: aburgasser@ucsd.edu [LCOGT, 6740 Cortona Drive, Suite 102, Goleta, CA 93117 (United States)

    2014-04-10

    We report resolved near-infrared spectroscopic monitoring of the nearby L dwarf/T dwarf binary WISE J104915.57–531906.1AB (Luhman 16AB), as part of a broader campaign to characterize the spectral energy distribution and temporal variability of this system. A continuous 45 minute sequence of low-resolution IRTF/SpeX data spanning 0.8-2.4 μm were obtained, concurrent with combined-light optical photometry with ESO/TRAPPIST. Our spectral observations confirm the flux reversal of this binary, and we detect a wavelength-dependent decline in the relative spectral fluxes of the two components coincident with a decline in the combined-light optical brightness of the system over the course of the observation. These data are successfully modeled as a combination of achromatic (brightness) and chromatic (color) variability in the T0.5 Luhman 16B, consistent with variations in overall cloud opacity; and no significant variability was found in L7.5 Luhman 16A, consistent with recent resolved photometric monitoring. We estimate a peak-to-peak amplitude of 13.5% at 1.25 μm over the full light curve. Using a simple two-spot brightness temperature model for Luhman 16B, we infer an average cold covering fraction of ≈30%-55%, varying by 15%-30% over a rotation period assuming a ≈200-400 K difference between hot and cold regions. We interpret these variations as changes in the covering fraction of a high cloud deck and corresponding 'holes' which expose deeper, hotter cloud layers, although other physical interpretations are possible. A Rhines scale interpretation for the size of the variable features explains an apparent correlation between period and amplitude for Luhman 16B and the variable T dwarfs SIMP 0136+0933 and 2MASS J2139+0220, and predicts relatively fast winds (1-3 km s{sup –1}) for Luhman 16B consistent with light curve evolution on an advective time scale (1-3 rotation periods). The strong variability observed in this flux reversal brown dwarf pair

  5. A Monitoring Campaign for Luhman 16AB. I. Detection of Resolved Near-infrared Spectroscopic Variability

    Science.gov (United States)

    Burgasser, Adam J.; Gillon, Michaël; Faherty, Jacqueline K.; Radigan, Jacqueline; Triaud, Amaury H. M. J.; Plavchan, Peter; Street, Rachel; Jehin, E.; Delrez, L.; Opitom, C.

    2014-04-01

    We report resolved near-infrared spectroscopic monitoring of the nearby L dwarf/T dwarf binary WISE J104915.57-531906.1AB (Luhman 16AB), as part of a broader campaign to characterize the spectral energy distribution and temporal variability of this system. A continuous 45 minute sequence of low-resolution IRTF/SpeX data spanning 0.8-2.4 μm were obtained, concurrent with combined-light optical photometry with ESO/TRAPPIST. Our spectral observations confirm the flux reversal of this binary, and we detect a wavelength-dependent decline in the relative spectral fluxes of the two components coincident with a decline in the combined-light optical brightness of the system over the course of the observation. These data are successfully modeled as a combination of achromatic (brightness) and chromatic (color) variability in the T0.5 Luhman 16B, consistent with variations in overall cloud opacity; and no significant variability was found in L7.5 Luhman 16A, consistent with recent resolved photometric monitoring. We estimate a peak-to-peak amplitude of 13.5% at 1.25 μm over the full light curve. Using a simple two-spot brightness temperature model for Luhman 16B, we infer an average cold covering fraction of ≈30%-55%, varying by 15%-30% over a rotation period assuming a ≈200-400 K difference between hot and cold regions. We interpret these variations as changes in the covering fraction of a high cloud deck and corresponding "holes" which expose deeper, hotter cloud layers, although other physical interpretations are possible. A Rhines scale interpretation for the size of the variable features explains an apparent correlation between period and amplitude for Luhman 16B and the variable T dwarfs SIMP 0136+0933 and 2MASS J2139+0220, and predicts relatively fast winds (1-3 km s-1) for Luhman 16B consistent with light curve evolution on an advective time scale (1-3 rotation periods). The strong variability observed in this flux reversal brown dwarf pair supports the model of

  6. Genetic variation detected by RAPD markers in natural populations of babassu palm (Attalea speciosa Mart.).

    Science.gov (United States)

    Santos, M F; Damasceno-Silva, K J; Carvalhaes, M A; Lima, P S C

    2015-06-10

    The purpose of this study was to analyze the effects of management on the genetic structure of natural populations of Attalea speciosa in the State of Piauí, Brazil, using random-amplified polymorphic DNA (RAPD) markers. Three babassu populations under different management systems were selected. Polymerase chain reactions were performed for 20 RAPD primers. A total of 146 bands were generated, 141 of which were polymorphic (96.58%), with a variation of 4 and 12 loci and an average of 7 bands per primer. A dendrogram revealed a clear separation between the three populations (0.57). Data reliability and node consistency were verified by bootstrap values and the cophenetic correlation coefficient (88.15%). Coefficients of similarity between pairs of genotypes ranged from 0.26 to 0.86, with a mean of 0.57. Nei's genetic diversity index (HE) value of the population sampled in Teresina was 0.212, of Esperantina it was 0.195, and of José de Freitas it was 0.207. After the HE was decomposed, the complete diversity was found to be 0.3213. Genetic differentiation between populations was 0.362, and the estimation of gene flow between populations was low (0.879). Analysis of molecular variance revealed that 59.52% of the variation was contained within populations, and 40.48% was between populations. RAPD markers were effective for genetic diversity analysis within and between natural babassu populations, and exhibited a high level of polymorphism. Genetic diversity was the highest within populations; variability was lower in the managed populations than in the undisturbed populations.

  7. Improved Variable Star Search in Large Photometric Data Sets -- New Variables in CoRoT Field LRa02 Detected ba BEST II

    CERN Document Server

    Fruth, T; Cabrera, J; Chini, R; Csizmadia, Sz; Eigmüller, P; Erikson, A; Kirste, S; Lemke, R; Murphy, M; Pasternacki, T; Rauer, H; Titz-Weider, R; 10.1088/0004-6256/143/6/140

    2012-01-01

    The CoRoT field LRa02 has been observed with the Berlin Exoplanet Search Telescope II (BEST II) during the southern summer 2007/2008. A first analysis of stellar variability led to the publication of 345 newly discovered variable stars. Now, a deeper analysis of this data set was used to optimize the variability search procedure. Several methods and parameters have been tested in order to improve the selection process compared to the widely used J index for variability ranking. This paper describes an empirical approach to treat systematic trends in photometric data based upon the analysis of variance statistics that can significantly decrease the rate of false detections. Finally, the process of reanalysis and method improvement has virtually doubled the number of variable stars compared to the first analysis by Kabath et al. A supplementary catalog of 272 previously unknown periodic variables plus 52 stars with suspected variability is presented. Improved ephemerides are given for 19 known variables in the ...

  8. Genetic characterization, species differentiation and detection of Fasciola spp. by molecular approaches

    Directory of Open Access Journals (Sweden)

    Li Hai-Long

    2011-06-01

    Full Text Available Abstract Liver flukes belonging to the genus Fasciola are among the causes of foodborne diseases of parasitic etiology. These parasites cause significant public health problems and substantial economic losses to the livestock industry. Therefore, it is important to definitively characterize the Fasciola species. Current phenotypic techniques fail to reflect the full extent of the diversity of Fasciola spp. In this respect, the use of molecular techniques to identify and differentiate Fasciola spp. offer considerable advantages. The advent of a variety of molecular genetic techniques also provides a powerful method to elucidate many aspects of Fasciola biology, epidemiology, and genetics. However, the discriminatory power of these molecular methods varies, as does the speed and ease of performance and cost. There is a need for the development of new methods to identify the mechanisms underpinning the origin and maintenance of genetic variation within and among Fasciola populations. The increasing application of the current and new methods will yield a much improved understanding of Fasciola epidemiology and evolution as well as more effective means of parasite control. Herein, we provide an overview of the molecular techniques that are being used for the genetic characterization, detection and genotyping of Fasciola spp..

  9. Detecting a hierarchical genetic population structure via Multi-InDel markers on the X chromosome

    Science.gov (United States)

    Fan, Guang Yao; Ye, Yi; Hou, Yi Ping

    2016-01-01

    Detecting population structure and estimating individual biogeographical ancestry are very important in population genetics studies, biomedical research and forensics. Single-nucleotide polymorphism (SNP) has long been considered to be a primary ancestry-informative marker (AIM), but it is constrained by complex and time-consuming genotyping protocols. Following up on our previous study, we propose that a multi-insertion-deletion polymorphism (Multi-InDel) with multiple haplotypes can be useful in ancestry inference and hierarchical genetic population structures. A validation study for the X chromosome Multi-InDel marker (X-Multi-InDel) as a novel AIM was conducted. Genetic polymorphisms and genetic distances among three Chinese populations and 14 worldwide populations obtained from the 1000 Genomes database were analyzed. A Bayesian clustering method (STRUCTURE) was used to discern the continental origins of Europe, East Asia, and Africa. A minimal panel of ten X-Multi-InDels was verified to be sufficient to distinguish human ancestries from three major continental regions with nearly the same efficiency of the earlier panel with 21 insertion-deletion AIMs. Along with the development of more X-Multi-InDels, an approach using this novel marker has the potential for broad applicability as a cost-effective tool toward more accurate determinations of individual biogeographical ancestry and population stratification. PMID:27535707

  10. Detecting novel genetic mutations in Chinese Usher syndrome families using next-generation sequencing technology.

    Science.gov (United States)

    Qu, Ling-Hui; Jin, Xin; Xu, Hai-Wei; Li, Shi-Ying; Yin, Zheng-Qin

    2015-02-01

    Usher syndrome (USH) is the most common cause of combined blindness and deafness inherited in an autosomal recessive mode. Molecular diagnosis is of great significance in revealing the molecular pathogenesis and aiding the clinical diagnosis of this disease. However, molecular diagnosis remains a challenge due to high phenotypic and genetic heterogeneity in USH. This study explored an approach for detecting disease-causing genetic mutations in candidate genes in five index cases from unrelated USH families based on targeted next-generation sequencing (NGS) technology. Through systematic data analysis using an established bioinformatics pipeline and segregation analysis, 10 pathogenic mutations in the USH disease genes were identified in the five USH families. Six of these mutations were novel: c.4398G > A and EX38-49del in MYO7A, c.988_989delAT in USH1C, c.15104_15105delCA and c.6875_6876insG in USH2A. All novel variations segregated with the disease phenotypes in their respective families and were absent from ethnically matched control individuals. This study expanded the mutation spectrum of USH and revealed the genotype-phenotype relationships of the novel USH mutations in Chinese patients. Moreover, this study proved that targeted NGS is an accurate and effective method for detecting genetic mutations related to USH. The identification of pathogenic mutations is of great significance for elucidating the underlying pathophysiology of USH.

  11. Whole genome sequence analysis of unidentified genetically modified papaya for development of a specific detection method.

    Science.gov (United States)

    Nakamura, Kosuke; Kondo, Kazunari; Akiyama, Hiroshi; Ishigaki, Takumi; Noguchi, Akio; Katsumata, Hiroshi; Takasaki, Kazuto; Futo, Satoshi; Sakata, Kozue; Fukuda, Nozomi; Mano, Junichi; Kitta, Kazumi; Tanaka, Hidenori; Akashi, Ryo; Nishimaki-Mogami, Tomoko

    2016-08-15

    Identification of transgenic sequences in an unknown genetically modified (GM) papaya (Carica papaya L.) by whole genome sequence analysis was demonstrated. Whole genome sequence data were generated for a GM-positive fresh papaya fruit commodity detected in monitoring using real-time polymerase chain reaction (PCR). The sequences obtained were mapped against an open database for papaya genome sequence. Transgenic construct- and event-specific sequences were identified as a GM papaya developed to resist infection from a Papaya ringspot virus. Based on the transgenic sequences, a specific real-time PCR detection method for GM papaya applicable to various food commodities was developed. Whole genome sequence analysis enabled identifying unknown transgenic construct- and event-specific sequences in GM papaya and development of a reliable method for detecting them in papaya food commodities.

  12. Detection rates of geckos in visual surveys: Turning confounding variables into useful knowledge

    Science.gov (United States)

    Lardner, Bjorn; Rodda, Gordon H.; Yackel Adams, Amy A.; Savidge, Julie A.; Reed, Robert N.

    2016-01-01

    Transect surveys without some means of estimating detection probabilities generate population size indices prone to bias because survey conditions differ in time and space. Knowing what causes such bias can help guide the collection of relevant survey covariates, correct the survey data, anticipate situations where bias might be unacceptably large, and elucidate the ecology of target species. We used negative binomial regression to evaluate confounding variables for gecko (primarily Hemidactylus frenatus and Lepidodactylus lugubris) counts on 220-m-long transects surveyed at night, primarily for snakes, on 9,475 occasions. Searchers differed in gecko detection rates by up to a factor of six. The worst and best headlamps differed by a factor of at least two. Strong winds had a negative effect potentially as large as those of searchers or headlamps. More geckos were seen during wet weather conditions, but the effect size was small. Compared with a detection nadir during waxing gibbous (nearly full) moons above the horizon, we saw 28% more geckos during waning crescent moons below the horizon. A sine function suggested that we saw 24% more geckos at the end of the wet season than at the end of the dry season. Fluctuations on a longer timescale also were verified. Disturbingly, corrected data exhibited strong short-term fluctuations that covariates apparently failed to capture. Although some biases can be addressed with measured covariates, others will be difficult to eliminate as a significant source of error in longterm monitoring programs.

  13. Technology for Fissionable Materials Detection by Use of 100 MeV Variable Linac

    CERN Document Server

    Karasyov, Sergey P; Dovbnja, Anatoliy N; Eran, L; Kiryukhin, Nikolay M; Melnik, Yu M; Ran'iuk, Yu; Shlyakhov, Il'ya N; Trubnikov, Sergiy V

    2005-01-01

    A new concept for a two-step facility to increase the accuracy/reliability of detecting heavily shielded fissionable materials (FM) in marine containers is presented. The facility will detect FM in two steps. An existing dual-view; dual-energy X-ray scanner, which is based on 7 MeV electron accelerator, will select the suspicious places inside container. The linac with variable energy (up to 100 MeV) will be used for the second step. The technology will detect fissionable nuclei by gamma induced fission reactions and delayed neutron registration. A little-known Ukrainian experimental data obtained in Chernobil' clean-up program will be presented to ground proposed concept. The theoretical calculations of neutron fluxes scale these results to marine container size. Modified GEANT code for electron/gamma penetration and authors' own software for neutron yield/penetration are used for these calculations. Available facilities (X-ray scanners; linac; detectors), which will be used for concept proof, are described....

  14. Time-Frequency Analysis of Heart Rate Variability for Neonatal Seizure Detection

    Science.gov (United States)

    Malarvili, M. B.; Mesbah, Mostefa; Boashash, Boualem

    2007-12-01

    There are a number of automatic techniques available for detecting epileptic seizures using solely electroencephalogram (EEG), which has been the primary diagnosis tool in newborns. The electrocardiogram (ECG) has been much neglected in automatic seizure detection. Changes in heart rate and ECG rhythm were previously linked to seizure in case of adult humans and animals. However, little is known about heart rate variability (HRV) changes in human neonate during seizure. In this paper, we assess the suitability of HRV as a tool for seizure detection in newborns. The features of HRV in the low-frequency band (LF: 0.03-0.07 Hz), mid-frequency band (MF: 0.07-0.15 Hz), and high-frequency band (HF: 0.15-0.6 Hz) have been obtained by means of the time-frequency distribution (TFD). Results of ongoing time-frequency (TF) research are presented. Based on our preliminary results, the first conditional moment of HRV which is the mean/central frequency in the LF band and the variance in the HF band can be used as a good feature to discriminate the newborn seizure from the nonseizure.

  15. Change detection from very high resolution satellite time series with variable off-nadir angle

    Science.gov (United States)

    Barazzetti, Luigi; Brumana, Raffaella; Cuca, Branka; Previtali, Mattia

    2015-06-01

    Very high resolution (VHR) satellite images have the potential for revealing changes occurred overtime with a superior level of detail. However, their use for metric purposes requires accurate geo-localization with ancillary DEMs and GCPs to achieve sub-pixel terrain correction, in order to obtain images useful for mapping applications. Change detection with a time series of VHS images is not a simple task because images acquired with different off-nadir angles have a lack of pixel-to-pixel image correspondence, even after accurate geo-correction. This paper presents a procedure for automatic change detection able to deal with variable off-nadir angles. The case study concerns the identification of damaged buildings from pre- and post-event images acquired on the historic center of L'Aquila (Italy), which was struck by an earthquake in April 2009. The developed procedure is a multi-step approach where (i) classes are assigned to both images via object-based classification, (ii) an initial alignment is provided with an automated tile-based rubber sheeting interpolation on the extracted layers, and (iii) change detection is carried out removing residual mis-registration issues resulting in elongated features close to building edges. The method is fully automated except for some thresholds that can be interactively set to improve the visualization of the damaged buildings. The experimental results proved that damages can be automatically found without additional information, such as digital surface models, SAR data, or thematic vector layers.

  16. Time-Frequency Analysis of Heart Rate Variability for Neonatal Seizure Detection

    Directory of Open Access Journals (Sweden)

    Boualem Boashash

    2007-01-01

    Full Text Available There are a number of automatic techniques available for detecting epileptic seizures using solely electroencephalogram (EEG, which has been the primary diagnosis tool in newborns. The electrocardiogram (ECG has been much neglected in automatic seizure detection. Changes in heart rate and ECG rhythm were previously linked to seizure in case of adult humans and animals. However, little is known about heart rate variability (HRV changes in human neonate during seizure. In this paper, we assess the suitability of HRV as a tool for seizure detection in newborns. The features of HRV in the low-frequency band (LF: 0.03–0.07 Hz, mid-frequency band (MF: 0.07–0.15 Hz, and high-frequency band (HF: 0.15–0.6 Hz have been obtained by means of the time-frequency distribution (TFD. Results of ongoing time-frequency (TF research are presented. Based on our preliminary results, the first conditional moment of HRV which is the mean/central frequency in the LF band and the variance in the HF band can be used as a good feature to discriminate the newborn seizure from the nonseizure.

  17. Detection of Causality between Process Variables Based on Industrial Alarm Data Using Transfer Entropy

    Directory of Open Access Journals (Sweden)

    Weijun Yu

    2015-08-01

    Full Text Available In modern industrial processes, it is easier and less expensive to configure alarms by software settings rather than by wiring, which causes the rapid growth of the number of alarms. Moreover, because there exist complex interactions, in particular the causal relationship among different parts in the process, a fault may propagate along propagation pathways once an abnormal situation occurs, which brings great difficulty to operators to identify its root cause immediately and to take proper actions correctly. Therefore, causality detection becomes a very important problem in the context of multivariate alarm analysis and design. Transfer entropy has become an effective and widely-used method to detect causality between different continuous process variables in both linear and nonlinear situations in recent years. However, such conventional methods to detect causality based on transfer entropy are computationally costly. Alternatively, using binary alarm series can be more computational-friendly and more direct because alarm data analysis is straightforward for alarm management in practice. The methodology and implementation issues are discussed in this paper. Illustrated by several case studies, including both numerical cases and simulated industrial cases, the proposed method is demonstrated to be suitable for industrial situations contaminated by noise.

  18. New trends in bioanalytical tools for the detection of genetically modified organisms: an update.

    Science.gov (United States)

    Michelini, Elisa; Simoni, Patrizia; Cevenini, Luca; Mezzanotte, Laura; Roda, Aldo

    2008-10-01

    Despite the controversies surrounding genetically modified organisms (GMOs), the production of GM crops is increasing, especially in developing countries. Thanks to new technologies involving genetic engineering and unprecedented access to genomic resources, the next decade will certainly see exponential growth in GMO production. Indeed, EU regulations based on the precautionary principle require any food containing more than 0.9% GM content to be labeled as such. The implementation of these regulations necessitates sampling protocols, the availability of certified reference materials and analytical methodologies that allow the accurate determination of the content of GMOs. In order to qualify for the validation process, a method should fulfil some criteria, defined as "acceptance criteria" by the European Network of GMO Laboratories (ENGL). Several methods have recently been developed for GMO detection and quantitation, mostly based on polymerase chain reaction (PCR) technology. PCR (including its different formats, e.g., double competitive PCR and real-time PCR) remains the technique of choice, thanks to its ability to detect even small amounts of transgenes in raw materials and processed foods. Other approaches relying on DNA detection are based on quartz crystal microbalance piezoelectric biosensors, dry reagent dipstick-type sensors and surface plasmon resonance sensors. The application of visible/near-infrared (vis/NIR) spectroscopy or mass spectrometry combined with chemometrics techniques has also been envisaged as a powerful GMO detection tool. Furthermore, in order to cope with the multiplicity of GMOs released onto the market, the new challenge is the development of routine detection systems for the simultaneous detection of numerous GMOs, including unknown GMOs.

  19. Genetic influences on heart rate variability at rest and during stress

    NARCIS (Netherlands)

    Wang, Xiaoling; Ding, Xiuhua; Su, Shaoyong; Li, Zhibin; Riese, Harriette; Thayer, Julian F.; Treiber, Frank; Snieder, Harold

    2009-01-01

    We tested whether the heritability of heart rate variability (HRV) under stress is different from rest and its dependency on ethnicity or gender. HRV indexed by root mean square of successive differences (RMSSD) and high-frequency (HF) power was measured at rest and during 3 stressors in 427 Europea

  20. Unraveling the genetic expression of the highly variable immune receptors of a killer

    NARCIS (Netherlands)

    Vendelbosch, S.

    2015-01-01

    The Killer Immunoglobulin-like Receptors (KIRs) are a family of highly variable receptors which regulate cytotoxicity of Natural Killer (NK) cells and a subset of T-cells. The KIR genes, clustered on the genome in the KIR locus, are distributed unequally across the population due to variation in gen

  1. SNP detection and prediction of variability between chicken lines using genome resequencing of DNA pools

    Directory of Open Access Journals (Sweden)

    Carlborg Örjan

    2010-11-01

    Full Text Available Abstract Background Next-generation sequencing technologies are widely used for detection of millions of Single Nucleotide Polymorphisms (SNPs and also provide a means of assessing their variation. This information is useful for composing subsets of highly informative SNPs for region-specific or genome-wide analysis and to identify mutations regulating phenotypic differences within or between populations. In this study, we investigated the sensitivity of SNP detection and introduced the flanking SNPs value (FSV as a novel measure for predicting SNP-variability using ~5X genome resequencing with ABI SOLID and DNA pools from two chicken lines divergently selected for juvenile bodyweight. Results Genotyping with a 60 K SNP chip revealed polymorphisms within or between two divergently selected chicken lines for 31 363 SNPs, 48% of which were also detected using resequencing of DNA pools. SNP detection using resequencing was more powerful for positions with larger differences in allele frequency between the lines. About 50% of the SNPs with non-reference allele frequencies in the range 0.5-0.6 and 67% of those with frequencies > 0.9 could be detected. On average, ~3.7 SNPs/kb were detected by resequencing, with about 5% lower density on microchromosomes than on macrochromosomes. There was a positive correlation between the observed between-line SNP variation from the 60 K chip analysis and our proposed FSV score computed from the genome resequencing data. The strongest correlations on macrochromosomes and microchromosomes were observed when the FSV was calculated with total flanking regions of 62 kb (correlation 0.55 and 38 kb (correlation 0.45, respectively. Conclusions Genome resequencing with limited coverage (~5X using pooled DNA samples and three non-reference reads as a threshold for SNP detection, identified 50 - 67% of the 60 K SNPs with a non-reference allele frequency larger than 0.5. The SNP density was around 5% lower on the

  2. Genetic Variability and Phylogenetic Relationships within Trypanosoma cruzi I Isolated in Colombia Based on Miniexon Gene Sequences

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    Claudia Herrera

    2009-01-01

    Full Text Available Phylogenetic studies of Trypanosoma cruzi have identified the existence of two groups: T. cruzi I and T. cruzi II. There are aspects that still remain unknown about the genetic variability within the T. cruzi I group. Given its epidemiological importance, it is necessary to have a better understanding of T. cruzi transmission cycles. Our purpose was to corroborate the existence of haplotypes within the T. cruzi I group and to describe the genetic variability and phylogenetic relationships, based on single nucleotide polymorphisms (SNPs found in the miniexon gene intergenic region, for the isolates from di